Stanford University HIV Drug Resistance Database - A curated public database designed to represent, store, and analyze the divergent forms of data underlying HIV drug resistance.

New Submissions

July 15, 2011
Transmitted drug resistance among newly HIV-1 diagnosed young individuals in Kampala.
Ndembi N, Hamers RL, Sigaloff KC, Lyagoba F, Magambo B, Nanteza B, Watera C, Kaleebu P, Rinke de Wit TF. Transmitted antiretroviral drug resistance among newly HIV-1 diagnosed young individuals in Kampala. AIDS, 2011

Drug resistance mutations among drug-naive patients in Morocco.
Annaz HE, Recordon-Pinson P, Baba N, Sedrati O, Mrani S, Fleury H. Presence of drug resistance mutations among drug-naive patients in Morocco. AIDS Res Hum Retrovirus, 2011

Early virological failure with the once-daily tenofovir/lamivudine/nevirapine.
Rey D, Hoen B, Chavanet P, Schmitt MP, Hoizey G, Meyer P, Peytavin G, Spire B, Allavena C, Diemer M, May T, Schmit JL, Duong M, Calvez V, Lang JM. High rate of early virological failure with the once-daily tenofovir/lamivudine/nevirapine combination in naive HIV-1-infected patients. J Antimicrob Chemother, 2009

Triple-nucleoside regimens versus efavirenz-containing regimens for the initial treatment of HIV-1 infection (ACTG A5095).
Gulick RM, Ribaudo HJ, Shikuma CM, Lustgarten S, Squires KE, Meyer WA 3rd, Acosta EP, Schackman BR, Pilcher CD, Murphy RL, Maher WE, Witt MD, Reichman RC, Snyder S, Klingman KL, Kuritzkes DR; AIDS Clinical Trials Group Study A5095 Team. Triple-nucleoside regimens versus efavirenz-containing regimens for the initial treatment of HIV-1 infection. N Engl J Med, 2004

Drug resistance among HIV-1-untreated patients in Guinea-Conakry and in Niger.
Charpentier C, Bellecave P, Cisse M, Mamadou S, Diakite M, Peytavin G, Tchiombiano S, Teisseire P, Pizarro L, Storto A, Brun-Vezinet F, Katlama C, Calvez V, Marcelin AG, Masquelier B, Descamps D. High prevalence of antiretroviral drug resistance among HIV-1-untreated patients in Guinea-Conakry and in Niger. Antivir Ther, 2011

Island Biogeography Reveals the Deep History of SIV.
Worobey M, Telfer P, Souquiere S, Hunter M, Coleman CA, Metzger MJ, Reed P, Makuwa M, Hearn G, Honarvar S, Roques P, Apetrei C, Kazanji M, Marx PA. Island Biogeography Reveals the Deep History of SIV Science, 2010


Identification of new CRF43_02G and CRF25_cpx in Saudi Arabia.
Yamaguchi J, Badreddine S, Swanson P, Bodelle P, Devare SG, Brennan CA. Identification of new CRF43_02G and CRF25_cpx in Saudi Arabia based on full genome sequence analysis of six HIV type 1 isolates. AIDS Res Hum Retrovirus, 2008

Identification of CRF44_BF in Chile.
Delgado E, Rios M, Fernandez J, Perez-Alvarez L, Najera R, Thomson MM. Identification of a new HIV type 1 BF intersubtype circulating recombinant form (CRF44_BF) in Chile. AIDS Res Hum Retrovirus , 2010

Angolan and Romanian HIV-1 subtype F1 isolates.
Guimaraes ML, Vicente AC, Otsuki K, da Silva RF, Francisco M, da Silva FG, Serrano D, Morgado MG, Bello G. Close phylogenetic relationship between Angolan and Romanian HIV-1 subtype F1 isolates. Retrovirology, 2009

Near full-length HIV sequences from Cyprus.
Kousiappa I, Van De Vijver DA, Kostrikis LG. Near full-length genetic analysis of HIV sequences derived from Cyprus: evidence of a highly polyphyletic and evolving infection. AIDS Res Hum Retrovirus, 2009

Identification of a CRF48_01B in Malaysia.
Li Y, Tee KK, Liao H, Hase S, Uenishi R, Li XJ, Tsuchiura T, Yang R, Govindasamy S, Yong YK, Tan HY, Pybus OG, Kamarulzaman A, Takebe Y. Identification of a novel second-generation circulating recombinant form (CRF48_01B) in Malaysia: a descendant of the previously identified CRF33_01B. JAIDS, 2010

Replication-competent molecular clone of HIV-1 CRF33_01B.
Tee KK, Kusagawa S, Li XJ, Onogi N, Isogai M, Hase S, Uenishi R, Liao H, Kamarulzaman A, Takebe Y. Isolation and characterization of a replication-competent molecular clone of an HIV-1 circulating recombinant form (CRF33_01B). PLoS One, 2009

Confirmation of putative HIV-1 group P in Cameroon.
Vallari A, Holzmayer V, Harris B, Yamaguchi J, Ngansop C, Makamche F, Mbanya D, Kaptué, Ndembi N, Gü L, Devare S, Brennan CA. Confirmation of putative HIV-1 group P in Cameroon. J Virol, 2011

Significant presence of CRF49_cpx in Gambia.
de Silva TI, Turner R, Hué, Trikha R, van Tienen C, Onyango C, Jaye A, Foley B, Whittle H, Rowland-Jones SL, Cotten M. HIV-1 subtype distribution in the Gambia and the significant presence of CRF49_cpx, a novel circulating recombinant form. AIDS Res Hum Retrovirus, 2011

HIV type 1 in Singapore and identification of novel CRF01_AE/B.
Ng OT, Munshaw S, Lamers SL, Chew KK, Lin L, Redd AD, Manucci J, Quinn TC, Ray SC, Chua A, Leo YS, Laeyendecker O. Molecular epidemiology of HIV type 1 in Singapore and identification of novel CRF01_AE/B recombinant forms. AIDS Res Hum Retrovirus , 2011

Prevalence of transmitted drug resistance in Tocantins, Brazil.
Carvalho BC, Cardoso LP, Damasceno S, de Araujo Stefani MM. Moderate prevalence of transmitted drug resistance and interiorization of HIV type 1 subtype C in the inland north state of Tocantins, Brazil. AIDS Res Hum Retrovirus, 2011

HIV-1 primary drug resistance prevalence in Cotonou, Benin.
Chamberland,A, Diabate,S, Sylla,M, Anagounou,SY, Geraldo,N, Zannou,DM, Labbe,AC, Worobey,M, Alary,M. HIV-1 primary drug resistance prevalence in Cotonou, Benin. Direct Genbank Submission, 2011

Transmitted drug resistance in therapy naive HIV-1 infected patients in Mwanza, Tanzania.
Kasang,C, Weissbrich,B, Scheller,C. High prevalence of transmitted drug resistance mutations in therapy naive HIV-1 infected patients in Mwanza, Lake Victoria zone, Tanzania. Direct Genbank Submission, 2010

Replication capacity on disease progression in recentsubtype C infections.
Wright JK, Novitsky V, Brockman MA, Brumme ZL, Brumme CJ, Carlson JM, Heckerman D, Wang B, Losina E, Leshwedi M, van der Stok M, Maphumulo L, Mkhwanazi N, Chonco F, Goulder PJ, Essex M, Walker BD, Ndung'u T. Influence of Gag-protease-mediated replication capacity on disease progression in individuals recently infected with HIV-1 subtype C. J Virol, 2011

Simian immunodeficiency virus (SIV) infecting a captive agile mangabey (Cercocebus agilis) is closely related to SIVrcm.
Ahuka-Mundeke S, Liegeois F, Ayouba A, Foupouapouognini Y, Nerrienet E, Delaporte E, Peeters M. Full-length genome sequence of a simian immunodeficiency virus (SIV) infecting a captive agile mangabey (Cercocebus agilis) is closely related to SIVrcm infecting wild red-capped mangabeys (Cercocebus torquatus) in Cameroon J Gen Virol, 2010

New simian immunodeficiency virus strain in a naturally infected Pan troglodytes troglodytes.
Etienne L, Nerrienet E, LeBreton M, Bibila GT, Foupouapouognigni Y, Rousset D, Nana A, Djoko CF, Tamoufe U, Aghokeng AF, Mpoudi-Ngole E, Delaporte E, Peeters M, Wolfe ND, Ayouba A. Characterization of a new simian immunodeficiency virus strain in a naturally infected Pan troglodytes troglodytes chimpanzee with AIDS related symptoms Retrovirology, 2011

Origin and epidemiological history of CRF14_BG. 
Bartolo I, Borrego P, Abecasis AB, McCutchan F, Taveira N. Origin and epidemiological history of CRF14_BG Direct Genbank Submission, 2010

HIV-1 molecular epidemiology in Cuba.
Perez L, Thomson MM, Bleda MJ, Aragones C, Gonzalez Z, Perez J, Sierra M, Casado G, Delgado E, Najera R. HIV Type 1 molecular epidemiology in cuba: high genetic diversity, frequent mosaicism, and recent expansion of BG intersubtype recombinant forms. AIDS Res Hum Retrovirus, 2006

Characterization of CRF27_cpx.
Vidal N, Frange P, Chaix ML, Mulanga C, Lepira F, Bazepeo SE, Goujard C, Meyer L, Rouzioux C, Delaporte E, Peeters M. Characterization of an old complex circulating recombinant form, CRF27_cpx, originating from the Democratic Republic of Congo (DRC) and circulating in France. AIDS Res Hum Retrovirus, 2008

Feb 22, 2011
Intermediate prevalence of HIV type 1 primary antiretroviral resistance in Ceara State, Northeast Brazil.
Arruda E, Simoes L, Sucupira C, Medeiros M, Arruda E, Diaz RS, Lima A.Intermediate prevalence of HIV type 1 primary antiretroviral resistance in Ceara State, Northeast Brazil.AIDS Research and Hum Retroviruses, 2011Feb;27(2)

Prevalence of genotypic resistance to antiretroviral drugs in treatment-naive youths infected with diverse HIV type 1 subtypes and recombinant forms in Dar es Salaam, Tanzania.
Mosha F, Urassa W, Aboud S, Lyamuya E, Sandstrom E, Bredell H, Williamson C.Prevalence of genotypic resistance to antiretroviral drugs in treatment-naive youths infected with diverse HIV type 1 subtypes and recombinant forms in Dar es Salaam, Tanzania.AIDS Research and Hum Retroviruses, 2010 Oct 18

Genotypic impact of prolonged detectable HIV type 1 RNA viral load after HAART failure in a CRF01_AE-infected cohort.
Zolfo M, Schapiro JM, Phan V, Koole O, Thai S, Vekemans M, Fransen K, Lynen L.Genotypic impact of prolonged detectable HIV type 1 RNA viral load after HAART failure in a CRF01_AE-infected cohort.AIDS Research and Hum Retroviruses, 2010

Low prevalence of transmitted drug resistance among newly diagnosed HIV-1 patients in Latvia.
Balode D, Westman M, Kolupajeva T, Rozentale B, Albert J.Low prevalence of transmitted drug resistance among newly diagnosed HIV-1 patients in Latvia.Journal of Medical Virology, 2010 Dec;82(12)

Frequency of primary resistance to antiretroviral drugs and genetic variability of HIV-1 among infected pregnant women recently diagnosed in Luanda-Angola.
Castelbranco EP, da Silva Souza E, Cavalcanti AM, Martins AN, de Alencar LC, Tanuri A.Frequency of primary resistance to antiretroviral drugs and genetic variability of HIV-1 among infected pregnant women recently diagnosed in Luanda-Angola. AIDS Research and Human Retroviruses, 2010 Dec;26(12)

Analysis of drug resistance in children receiving antiretroviral therapy for treatment of HIV-1 infection in Uganda
Towler WI, Barlow-Mosha L, Church JD, Bagenda D, Ajuna P, Mubiru M, Musoke P, Eshleman SH.Analysis of drug resistance in children receiving antiretroviral therapy for treatment of HIV-1 infection in Uganda. AIDS Research and Human Retroviruses,2010 May;26(5)

Emerging transmitted drug resistance in treatment-naive human immunodeficiency virus-1 CRF06_cpx-infected patients in Estonia.
Avi R, Huik K, Pauskar M, Ustina V, Karki T, Krispin T, Ainsalu K, Paap P,Schmidt J, Nikitina N, Lutsar I.Emerging transmitted drug resistance in treatment-naive human immunodeficiency virus-1 CRF06_cpx-infected patients in Estonia. Scandinavian Journal of Infectious Diseases, 2011 Feb;43(2)

Gag-protease-mediated replication capacity in HIV-1 subtype C chronic infection: associations with HLA type and clinical parameters.
Wright JK, Brumme ZL, Carlson JM, Heckerman D, Kadie CM, Brumme CJ, Wang B, Losina E, Miura T, Chonco F, van der Stok M, Mncube Z, Bishop K, Goulder PJ, Walker BD, Brockman MA, Ndung'u T.Gag-protease-mediated replication capacity in HIV-1 subtype C chronic infection: associations with HLA type and clinical parameters. Journal of Virology, 2010 Oct;84(20)

Sustained appearance of drug resistance-associated mutations in HIV-1 CRF01_AE protease and reverse transcriptase derived from protease inhibitor-naive Thai patients.
Jullaksorn D, Boonchawalit S, Uttiyoung J, Soonthornsata B, Yowang A, Krathong N, Chautrakul S, Ikuta K, Roobsoong A, Kanitvittaya S, Sawanpanyalert P, Kameoka M.Sustained appearance of drug resistance-associated mutations in HIV-1 CRF01_AE protease and reverse transcriptase derived from protease inhibitor-naive Thai patients. Scandinavian Journal of Infectious Diseases, 2010 Mar;41(2)

Nigerian HIV type 2 subtype A and B from heterotypic HIV type 1 and HIV type 2 or monotypic HIV type 2 infections.
Zeh C, Pieniazek D, Agwale SM, Robbins KE, Odama L, Sani-Gwarzo N, Gboun MS, Inyang US, Folks TM, Wambebe C, Kalish ML.Nigerian HIV type 2 subtype A and B from heterotypic HIV type 1 and HIV type 2 or monotypic HIV type 2 infections. AIDS Research and Human Retroviruses, 2005 Jan;21(1)

High HIV type 1 group M pol diversity and low rate of antiretroviral resistance mutations among the uniformed services in Kinshasa, DRC.
Djoko CF, Rimoin AW, Vidal N, Tamoufe U, Wolfe ND, Butel C, Lebreton M, Tshala FM, Kayembe PK, Muyembe JJ, Edidi-Basepeo S, Pike BL, Fair JN, Mbacham WF, Saylors KE, Mpoudi-Ngole E, Delaporte E, Grillo M, Peeters M.High HIV type 1 group M pol diversity and low rate of antiretroviral resistance mutations among the uniformed services in Kinshasa, DRC. AIDS Research and Human Retroviruses, 2010 Oct 18

HIV type 1 pol gene diversity and genotypic antiretroviral drug resistance mutations in Malabo, Equatorial Guinea.
Djoko CF, Wolfe ND, Vidal N, Tamoufe U, Montavon C, LeBreton M, Pike BL, Fair J, Mbacham WF, Benito A, Rimoin AW, Saylors K, Mpoudi-Ngole E, Grillo MP, Peeters M.HIV type 1 pol gene diversity and genotypic antiretroviral drug resistance mutations in Malabo, Equatorial Guinea. AIDS Research and Human Retroviruses, 2010Sep;26(9)

Full-length genome characterization of a novel simian immunodeficiency virus lineage (SIVolc) from olive Colobus (Procolobus verus) and new SIVwrcPbb strains from Western Red Colobus (Piliocolobus badius badius) from the Tai Forest in Ivory Coast.
Liegeois F, Lafay B, Formenty P, Locatelli S, Courgnaud V, Delaporte E, Peeters M.Full-length genome characterization of a novel simian immunodeficiency virus lineage (SIVolc) from olive Colobus (Procolobus verus) and new SIVwrcPbb strains from Western Red Colobus (Piliocolobus badius badius) from the Tai Forest in Ivory Coast. Journal of Virology, 2009 Jan;83(1)

Full molecular characterization of a simian immunodeficiency virus, SIVwrcpbt from Temminck's red colobus (Piliocolobus badius temminckii) from Abuko Nature Reserve, The Gambia.
Locatelli S, Lafay B, Liegeois F, Ting N, Delaporte E, Peeters M.Full molecular characterization of a simian immunodeficiency virus, SIVwrcpbt from Temminck's red colobus (Piliocolobus badius temminckii) from Abuko Nature Reserve, The Gambia. Virology, 2008 Jun 20;376(1)

Nov 10, 2010
NRTI and NNRTI-associated resistance mutations in AZT/3TC/ABC and AZT/3TC/NVP in Uganda: DART Virology Team
Ndembi N, Goodall RL, Dunn DT, McCormick A, Burke A, Lyagoba F, Munderi P, Katundu P, Kityo C, Robertson V, Yirrell DL, Walker AS, Gibb DM, Gilks CF, Kaleebu P, Pillay D. Viral rebound and emergence of drug resistance in the absence of viral load testing: a randomized comparison between zidovudine-lamivudine plus Nevirapine and zidovudine-lamivudine plus Abacavir. Journal of Infectious Disesases,2010 Jan 1;201(1):106-13

Emergence of HIV-1 drug resistance in subtype C isolates
Orrell C, Walensky RP, Losina E, Pitt J, Freedberg KA, Wood R. HIV type-1 clade C resistance genotypes in treatment-naive patients and after first virological failure in a large community antiretroviral therapy programme Antiviral Therapy,2009;14(4):523-31

HIV-1 PR and RT from newly diagnosed persons in British Columbia, Canada 2002 - 2005
Ragonnet-Cronin M, Ofner-Agostini M, Merks H, Pilon R, Rekart M, Archibald CP, Sandstrom PA, Brooks JI. Longitudinal phylogenetic surveillance identifies distinct patterns of cluster dynamics. Journal of Acquired Immune Deficiency Syndromes,2010 Sep 1;55(1):102-8

In vitro activity of S/GSK1349572 versus a range of INI-resistant HIV-1 isolates
Seki T, Kobayashi M, Wakasa-Morimoto C, Yoshinaga T, Sato A, Fujiwara T, Underwood M, Garvey EP, Johns BA. S/GSK1349572 is a potent next generation HIV integrase inhibitor and demonstrates a superior resistance profile substantiated with 60 integrase mutant molecular clones 17th CROI,17th CROI, February 16-19, 2010, San Francisco

NRTI and NNRTI-resistance mutations and risk of K65R in Nigerian HIV-1-infected persons in whom initial ARV therapy was unsuccessful
Hawkins CA, Chaplin B, Idoko J, Ekong E, Adewole I, Gashau W, Murphy RL, Kanki P, APIN Plus/Harvard PEPFAR Team. Clinical and genotypic findings in HIV-infected patients with the K65R mutation failing first-line antiretroviral therapy in Nigeria. Journal of Acquired Immune Deficiency Syndromes,2009 Oct 1;52(2):228-34

In vitro selection of INI-resistant viruses and their phenotypic characterization
Kobayashi M, Nakahara K, Seki T, Miki S, Kawauchi S, Suyama A, Wakasa-Morimoto C, Kodama M, Endoh T, Oosugi E, Matsushita Y, Murai H, Fujishita T, Yoshinaga T, Garvey E, Foster S, Underwood M, Johns B, Sato A, Fujiwara T. Selection of diverse and clinically relevant integrase inhibitor-resistant human immunodeficiency virus type 1 mutants. Antiviral Research,2008 Nov;80(2):213-22

In vitro selection of raltegravir-resistant viruses and their phenotypic characterization
Goethals O, Vos A, Van Ginderen M, Geluykens P, Smits V, Schols D, Hertogs K, Clayton R. Primary mutations selected in vitro with raltegravir confer large fold changes in susceptibility to first-generation integrase inhibitors, but minor fold changes to inhibitors with second-generation resistance profiles Virology,2010 Jul 5;402(2):338-46

Molecular characterization of INI drug resistance pathways
Fransen S, Gupta S, Danovich R, Hazuda D, Miller M, Witmer M, Petropoulos CJ, Huang W. Loss of raltegravir susceptibility by human immunodeficiency virus type 1 is conferred via multiple nonoverlapping genetic pathways. Journal of Virology,2009 Nov;83(22):11440-6

HIV-1 drug-resistance among ARV-treated persons in Mombasa, Kenya
Steegen K, Luchters S, Dauwe K, Reynaerts J, Mandaliya K, Jaoko W, Plum J, Temmerman M, Verhofstede C. Effectiveness of antiretroviral therapy and development of drug resistance in HIV-1 infected patients in Mombasa, Kenya Journal of Infectious Disesases,2009 Jun 16;6:12

HIV-1 RT sequences obtained before and after ARV and TB therapy in India
Rajesh L, Karunaianantham R, Narayanan PR, Swaminathan S. Antiretroviral drug-resistant mutations at baseline and at time of failure of antiretroviral therapy in HIV type 1-coinfected TB patients. AIDS Research and Human Retroviruses,2009 Nov;25(11):1179-85

Nelfinavir-resistance in HIV-1-infected Brazilian children
Machado ES, Lambert JS, Afonso AO, Cunha SM, Oliveira RH, Tanuri A, Sill AM, Costa AJ, Soares MA. Alternative, age- and viral load-related routes of nelfinavir resistance in human immunodeficiency virus type 1-infected children receiving highly active antiretroviral therapy Pediatr Infect Dis J,2004 Nov;23(11):1057-9

Phenotypic effects of RT K65R and K70E
Kagan RM, Lee TS, Ross L, Lloyd RM Jr, Lewinski MA, Potts SJ. Molecular basis of antagonism between K70E and K65R tenofovir-associated mutations in HIV-1 reverse transcriptase Antiviral Research,2007 Sep;75(3):210-8

HIV-1 IN diversity in Brazil
Passaes CB, Guimares ML, Fernandez SL, Lorete Rdos S, Teixeira SL, Fernandez JC, Morgado MG. Lack of primary mutations associated with integrase inhibitors among HIV-1 subtypes B, C, and F circulating in Brazil Journal of Acquired Immune Deficiency Syndromes,2009 May 1;51(1):7-12

Emergence of HIV-1 drug resistance during first-line therapy in Mumbai, India
Deshpande A, Jeannot AC, Schrive MH, Wittkop L, Pinson P, Fleury HJ. Analysis of RT sequences of subtype C HIV-type 1 isolates from indian patients at failure of a first-line treatment according to clinical and/or immunological WHO guidelines AIDS Research and Human Retroviruses,2010 Mar;26(3):343-50

Transmitted drug resistance in Sicily, Italy
Bonura F, Tramuto F, Vitale F, Perna AM, Viviano E, Romano N, Group for HIV-1 Antiretroviral Studies in Sicily. Transmission of drug-resistant HIV type 1 strains in HAART-naive patients: a 5-year retrospective study in Sicily, Italy. AIDS Research and Human Retroviruses,2010 Sep;26(9):961-5

Evolution of INI resistance.
Hatano H, Lampiris H, Fransen S, Gupta S, Huang W, Hoh R, Martin JN, Lalezari J, Bangsberg D, Petropoulos C, Deeks SG. Evolution of integrase resistance during failure of integrase inhibitor-based antiretroviral therapy Journal Acquired Immune Deficiency Syndromes,2010 Aug 1;54(4):389-93

Circulating subtype A viruses in Republic of Dagestan, Russian Federation
Vinogradova A, Gafurova E, Muoz-Nieto M, Rakhmanova A, Osmanov S, Thomson MM. Molecular epidemiology of HIV type 1 in the Republic of Dagestan, Russian Federation: virtually uniform circulation of subtype A, former Soviet Union variant, with predominance of the V77I(PR) subvariant AIDS Research and Human Retroviruses,2010 Apr;26(4):395-400

Transmitted drug resistance in Korea and China
Chin BS, Choi JY, Han Y, Kuang J, Li Y, Han SH, Choi H, Chae YT, Jin SJ, Baek JH, Lim YS, Kim CO, Song YG, Yong D, Li T, Kim JM. Comparison of genotypic resistance mutations in treatment-naive HIV type 1-infected patients in Korea and China. AIDS Research and Human Retroviruses,2010 Feb;26(2):217-21

Transmitted drug resistance in Vietnam
Phan TT, Ishizaki A, Phung DC, Bi X, Oka S, Ichimura H. Characterization of HIV type 1 genotypes and drug resistance mutations among drug-naive HIV type 1-infected patients in Northern Vietnam AIDS Research and Human Retroviruses,2010 Feb;26(2):233-5

Evolution of PI resistance mutations in PR and Gag in subtype G isolates
Knops E, Dumer M, Awerkiew S, Kartashev V, Schlter E, Kutsev S, Brakier-Gingras L, Kaiser R, Pfister H, Verheyen J. Evolution of protease inhibitor resistance in the gag and pol genes of HIV subtype G isolates The Journal of Antimicrobial Chemotherapy,2010 Jul;65(7):1472-6

Transmitted drug resistance in New York
Parker MM, Gordon D, Reilly A, Horowitz HW, Waters M, Bennett R, Hallack R, Smith J, Lamson D, Aydemir A, Dvali N, Agins BD, Drusano GL, Taylor J, Resistance Study Group. Prevalence of drug-resistant and nonsubtype B HIV strains in antiretroviral-naive, HIV-infected individuals in New York State AIDS Patient Care an,2007 Sep;21(9):644-52

HIV-1 CRF07_BC outbreak in Taiwan
Chang SY, Sheng WH, Lee CN, Sun HY, Kao CL, Chang SF, Liu WC, Yang JY, Wong WW, Hung CC, Chang SC. Molecular epidemiology of HIV type 1 subtypes in Taiwan: outbreak of HIV type 1 CRF07_BC infection in intravenous drug users. AIDS Research and Human Retroviruses,2006 Nov;22(11):1055-66

HIV-1 IN diversity in Thailand
Isarangkura-Na-Ayuthaya P, Kaewnoo W, Auwanit W, de Silva UC, Ikuta K, Sawanpanyalert P, Kameoka M. Appearance of drug resistance-associated mutations in human immunodeficiency virus type 1 CRF01_AE integrase derived from drug-naive Thai patients. AIDS Research and Human Retroviruses,2010 Sep 13. [Epub ahead of print]

Intersubypte HIV-1 BF recombinants in Argentina
Espinosa A, Vignoles M, Carrillo MG, Sheppard H, Donovan R, Peralta LM, Rossi D, Radulich G, Salomn H, Weissenbacher M. Intersubtype BF recombinants of HIV-1 in a population of injecting drug users in Argentina Journal of Acquired Immune Deficiency Syndromes,2004 May 1;36(1):630-6

PI mutations and PI cross-resistance
Rhee SY, Taylor J, Fessel WJ, Kaufman D, Towner W, Troia P, Ruane P, Hellinger J, Shirvani V, Zolopa A, Shafer RW. HIV-1 protease mutations and protease inhibitor cross resistance Antimicrobial Agents and Chemotherapy,2010 Oct;54(10):4253-61

INI genotype-phenotype correlations for S/GSK1265744
Nakahara K, Wakasa-Morimoto C, Kobayashi M, Miki S, Noshi T, Seki T, Kanamori-Koyama M, Kawauchi S, Suyama A, Fujishita T, Yoshinaga T, Garvey EP, Johns BA, Foster SA, Underwood MR, Sato A, Fujiwara T. Secondary mutations in viruses resistant to HIV-1 integrase inhibitors that restore viral infectivity and replication kinetics Antiviral Research,2009 Feb;81(2):141-6

IN susceptibility of INI-resistant isolates to S/GSK1265744
Underwood MR, St Clair M, Johns BA, Sato A, Fujiwara T, Spreen W. S/GSK1265744: A next generation integrase inhibitor (INI) with activity against raltegravir-resistant clinical isolates 18th IAC,18th International AIDS Conference, July 18-23, 2010 Vienna

In vitro susceptibility of IN isolates from patients receiving raltegravir
da Silva D, Van Wesenbeeck L, Breilh D, Reigadas S, Anies G, Van Baelen K, Morlat P, Neau D, Dupon M, Wittkop L, Fleury H, Masquelier B. HIV-1 resistance patterns to integrase inhibitors in antiretroviral-experienced patients with virological failure on raltegravir-containing regimens. The Journal of Antimicrobial Chemotherapy,010 Jun;65(6):1262-9

Drug-resistance mutations in ARV-nave persons from Lusaka, Zambia
Hamers RL, Siwale M, Wallis CL, Labib M, van Hasselt R, Stevens WS, Schuurman R, Wensing AM, Van Vugt M, Rinke de Wit TF; PharmAccess African Studies to Evaluate Resistance. HIV-1 drug resistance mutations are present in six percent of persons initiating antiretroviral therapy in Lusaka, Zambia. Journal of Acquired Immune Deficiency Syndromes,2010 Sep 1;55(1):95-101

Cross-resistance between nevirapine/efavirenz and etravirine in CRF01_AE isolates.
Manosuthi W, Butler DM, Chantratita W, Sukasem C, Richman DD, Smith DM. Patients infected with HIV type 1 subtype CRF01_AE and failing first-line nevirapine- and efavirenz-based regimens demonstrate considerable cross-resistance to etravirine. AIDS Research and Human Retroviruses,2010 Jun;26(6):609-11

HIV-1 polymerase diversity in HIV-1-infected treatment-nave persons in Cameroon
Soares EA, Makamche MF, Siqueira JD, Lumngwena E, Mbuagbaw J, Kaptue L, Asonganyi T, Seunez HN, Soares MA, Alemnji G. Molecular diversity and polymerase gene genotypes of HIV-1 among treatment-naive Cameroonian subjects with advanced disease. Journal of Clinical Virology,2010 Jul;48(3):173-9

A novel HIV-1 circularting recombinant form.
Gomez-Carrillo M, Quarleri JF, Rubio AE, Carobene MG, Dilernia D, Carr JK, Salomon H. Drug resistance testing provides evidence of the globalization of HIV type 1: a new circulating recombinant form. AIDS Research and Human Retroviruses,2004 Aug;20(8):885-8

Intra-subtype C recombinants in Ethiopia, India, and Souh Africa
Pollakis G, Abebe A, Kliphuis A, De Wit TF, Fisseha B, Tegbaru B, Tesfaye G, Negassa H, Mengistu Y, Fontanet AL, Cornelissen M, Goudsmit J.Recombination of HIV type 1C (C’/C”) in Ethiopia: possible link of EthHIV-1C' to subtype C sequences from the high-prevalence epidemics in India and Southern Africa. AIDS Research and Human Retroviruses,2003 Nov;19(11):999-1008

Baseline HIV-1 Drug Resistance in Malawi
Tymchuk CN. Baseline HIV resistance in Malawi GenBank submission,Genbank Submission

The PI-resistance mutation N88D facilitates co-occurrence of D30N and L90M
Mitsuya Y, Winters MA, Fessel WJ, Rhee SY, Hurley L, Horberg M, Schiffer CA, Zolopa AR, Shafer RW. N88D facilitates the co-occurrence of D30N and L90M and the development of multidrug resistance in HIV type 1 protease following nelfinavir treatment failure. AIDS Research and Human Retroviruses,2006 Dec;22(12):1300-5

Full-length genome HIV-1 sequencing of viruses from recently infected persons in Brazil
Sa-Filho D, Kallas EG, Sanabani S, Sabino E, Sucupira MC, Sanchez-Rosa AC, Tescarollo G, Tomiyama H, Bassichetto K, Janini LM, Diaz RS. Characterization of the full-length human immunodeficiency virus-1 genome from recently infected subjects in Brazil. AIDS Research and Human Retroviruses,2007 Sep;23(9):1087-94

CRF11-cpx in Central Africa
Montavon C, Vergne L, Bourgeois A, Mpoudi-Ngole E, Malonga-Mouellet G, Butel C, Toure-Kane C, Delaporte E, Peeters M. Identification of a new circulating recombinant form of HIV type 1, CRF11-cpx, involving subtypes A, G, J, and CRF01-AE, in Central Africa. AIDS Research and Human Retroviruses,2002 Feb 10;18(3):231-6

Distribution of HIV-1 subtypes in Uganda
Baker CA, Bousheri S, Ssewanyana I, Jones NG, K'aluoch O, Baliruno D, Ssali F, Huyen Cao. HIV subtypes distribution and implication for antiretroviral treatment in a ugandan population. Journal of International Association of Physicians in AIDS Care,2007 Dec;6(4):260-3

A dominant complex circulating recombinant form in Burkina Faso
Pieniazek D, Schaefer A, Mika J, Rose L, Heslop O, Rayfield M, Folks T, Kalish M. HIV-1 complex recombinant was the predominant strain in Burkina Faso by the mid-1980s 11th CROI,11th CROI, February 8-11, 2004, San Francisco

INI Resistance
Blanco JL, Varghese V, Rhee SY, Gatell JM, Shafer RW. HIV-1 integrase inhibitor resistance: new developments and their clinical implications Submitted,Submitted

HIV-1 PR and RT polymorphisms in CRF02-AG viruses from Saint-Etienne France
Lawrence P, Lutz MF, Saoudin H, Frsard A, Cazorla C, Fascia P, Pillet S, Pozzetto B, Lucht F, Bourlet T. Analysis of polymorphism in the protease and reverse transcriptase genes of HIV type 1 CRF02-AG subtypes from drug-naive patients from Saint-Etienne, France Journal of Acquired Immune Deficiency Syndromes,2006 Aug 1;42(4):396-404

Origin of the HIV-1 subtype A epidemic in former Soviet Union
Thomson MM, de Parga EV, Vinogradova A, Sierra M, Yakovlev A, Rakhmanova A, Delgado E, Casado G, Munoz M, Carmona R, Vega Y, Perez-Alvarez L, Contreras G, Medrano L, Osmanov S, Najera R. New insights into the origin of the HIV type 1 subtype A epidemic in former Soviet Union's countries derived from sequence analyses of preepidemically transmitted viruses. AIDS Research and Human Retroviruses,2007 Dec;23(12):1599-604

HIV-1 IN diversity in Venezuela
Rangel HR, Garzaro D, Fabbro R, Martinez N, Ossenkop J, Torres JR, Gutirrez CR, Pujol FH. Absence of primary integrase resistance mutations in HIV type 1-infected patients in Venezuela. AIDS Research and Human Retroviruses,2010 Aug;26(8):923-6

A novel subtype H isolate reported from London, UK
Holzmayer V, Aitken C, Skinner C, Ryall L, Devare SG, Hackett J Jr. Characterization of genetically diverse HIV type 1 from a London cohort: near full-length genomic analysis of a subtype H strain. AIDS Research and Human Retroviruses,2009 Jul;25(7):721-6

Recombinants with multiple parental strains in Cameroon
Carr JK, Wolfe ND, Torimiro JN, Tamoufe U, Mpoudi-Ngole E, Eyzaguirre L, Birx DL, McCutchan FE, Burke DS. HIV-1 recombinants with multiple parental strains in low-prevalence, remote regions of Cameroon: evolutionary relics? Retrovirology,2010 Apr 28;7:39

A novel circulating recombinant form CRF47_BF reported from Spain
Fernandez-Garcia A, Perez-Alvarez L, Cuevas MT, Delgado E, Munoz-Nieto M, Cilla G, Iribarren JA, Pinilla M, Ocampo A, Miralles C, Perez-Castro S, Gonzalez-Galeano M, de Castro RO, Trigo M, Garca V, Sanchez AM, Thomson MM. Identification of a new HIV type 1 circulating BF intersubtype recombinant form (CRF47_BF) in Spain. AIDS Research and Human Retroviruses,2010 Jul;26(7):827-32

IN and RT sequences of wild chimpanzees infected with SIVcpz
Keele BF, Jones JH, Terio KA, Estes JD, Rudicell RS, Wilson ML, Li Y, Learn GH, Beasley TM, Schumacher-Stankey J, Wroblewski E, Mosser A, Raphael J, Kamenya S, Lonsdorf EV, Travis DA, Mlengeya T, Kinsel MJ, Else JG, Silvestri G, Goodall J, Sharp PM, Shaw GM, Pusey AE, Hahn BH. Increased mortality and AIDS-like immunopathology in wild chimpanzees infected with SIVcpz. Nature,2009 Jul 23;460(7254):515-9

Complete genome sequences of CRF01_AE isolates in Guangxi, China
Li L, Liang S, Chen L, Liu W, Li H, Liu Y, Bao Z, Wang Z, Zhuang D, Liu S, Li J. Genetic characterization of 13 subtype CRF01_AE near full-length genomes in Guangxi, China. AIDS Research and Human Retroviruses,2010 Jun;26(6):699-704

Molecular epidemiology of HIV-1 in Northern Brazil
Machado LF, Ishak MO, Vallinoto AC, Lemos JA, Azevedo VN, Moreira MR, Souza MI, Fernandes LM, Souza LL, Ishak R. Molecular epidemiology of HIV type 1 in northern Brazil: identification of subtypes C and D and the introduction of CRF02_AG in the Amazon region of Brazil. AIDS Research and Human Retroviruses,2009 Oct;25(10):961-6

Subtype C infection among pregnant woman in Criciuma Brazil
Rodrigues R, Manenti S, Romao PR, de Paula Ferreira JL, Batista JP, Siqueira AF, de Macedo Brigido LF. Young pregnant women living with HIV/AIDS in Criciuma, Southern Brazil, are infected almost exclusively with HIV type 1 clade C. AIDS Research and Human Retroviruses,2010 Mar;26(3):351-7

Unique B/C recombinant forms from Southern Brazil
Passaes CP, Guimares ML, Bello G, Morgado MG. Near full-length genome characterization of HIV type 1 unique BC recombinant forms from Southern Brazil. AIDS Research and Human Retroviruses,2009 Dec;25(12):1339-44

Subtype F1 in Sao Paulo, Brazil.
Sanabani SS, Pastena ER, Kleine Neto W, Barreto CC, Ferrari KT, Kalmar EM, Ferreira S, Sabino EC. Near full-length genome analysis of low prevalent human immunodeficiency virus type 1 subclade F1 in Sao Paulo, Brazil. Virology Journal,2009 Jun 16;6:78

Isolation and characterization of a novel CRF33_01B recombinant in Indonesia.
Tee KK, Kusagawa S, Li XJ, Onogi N, Isogai M, Hase S, Uenishi R, Liao H, Kamarulzaman A, Takebe Y. Isolation and characterization of a replication-competent molecular clone of an HIV-1 circulating recombinant form (CRF33_01B). PLoS Medicine,2009 Aug 18;4(8):e6666

Two mosaic HIV-1 genomes related to CRF06_cpx and CRF18_cpx originating from DRC
Huang DD, Foley BT, Tolzmann CA, Ouma A, Bremer JW. Complex mosaic composition of near full-length genomes of two NED (NIH-ENVA-DOD) subtype panel HIV type 1 strains, BCF-Dioum and BCF-Kita, originating from the Democratic Republic of Congo (DRC) AIDS Research and Human Retroviruses,2009 Oct;25(10):1039-43

RT and PR mutations from heavily-treated individuals from Central Brazil
Cardoso LP, Stefani MM. High level of multidrug resistance mutations in HIV type 1 pol gene and resistance-associated mutations to enfuvirtide (T-20) among antiretroviral-experienced patients from central Brazil. AIDS Research and Human Retroviruses,2009 Oct;25(10):943-50

Phylogenetic analysis of HIV-1 subtype C isolates in South America
Jones LR, Dilernia DA, Manrique JM, Moretti F, Salomn H, Gomez-Carrillo M. In-depth analysis of the origins of HIV type 1 subtype C in South America. AIDS Research and Human Retroviruses,2009 Oct;25(10):951-9

HIV-1 subtype F isolates in St Petersburg, Russia
Fernandez-Garcia A, Cuevas MT, Vinogradova A, Rakhmanova A, Perez-Alvarez L, de Castro RO, Osmanov S, Thomson MM. Near full-length genome characterization of a newly identified HIV type 1 subtype F variant circulating in St. Petersburg, Russia. AIDS Research and Human Retroviruses,2009 Nov;25(11):1187-91

An HIV-1 group M / group O recombinant in West Africa
Vessiere A, Leoz M, Brodard V, Strady C, Lemee V, Depatureaux A, Simon F, Plantier JC. First evidence of a HIV-1 M/O recombinant form circulating outside Cameroon. AIDS,2010 Apr 24;24(7):1079-82

PR and Gag mutations in HIV-1 CRF01_AE in ARV-naive persons from Thailand
Jinnopat P, Isarangkura-na-ayuthaya P, Utachee P, Kitagawa Y, de Silva UC, Siripanyaphinyo U, Kameoka Y, Tokunaga K, Sawanpanyalert P, Ikuta K, Auwanit W, Kameoka M. Impact of amino acid variations in Gag and protease of HIV type 1 CRF01_AE strains on drug susceptibility of virus to protease inhibitors. Journal of Acquired Immune Deficiency Syndromes,2009 Nov 1;52(3):320-8

Drug resistance mutations in HIV-1 isolates from vertically infected children in Belo Horizonete, Brazil
Ferreira FG, Pinto JA, Kakehasi FM, Cleto S, Tupinambs U, Aleixo AW, Cardoso CS. Prevalence of primary drug resistance-associated mutations among HIV type 1 vertically Infected children in Belo Horizonte, Brazil. AIDS Research and Human Retroviruses,2010 Feb;26(2):229-32

HIV-1 IN diversity in South African persons
Fish MQ, Hewer R, Wallis CL, Venter WD, Stevens WS, Papathanasopoulos MA. Natural polymorphisms of integrase among HIV type 1-infected South African patients. AIDS Research and Human Retroviruses,2010 Apr;26(4):489-93

HIV-1 drug resistance among ARV-experienced patients in Iran
Hamkar R, Mohraz M, Lorestani S, Aghakhani A, Truong HH, McFarland W, Banifazl M, Eslamifar A, Foroughi M, Pakfetrat A, Ramezani A. Assessing subtype and drug-resistance-associated mutations among antiretroviral-treated HIV-infected patients AIDS,2010 Jul;24 Suppl 2:S85-91

A novel B/C recombinant form in Yunan, China
Li L, Chen L, Yang S, Liu Y, Li H, Bao Z, Wang Z, Zhuang D, Liu S, Li J. Near full-length genomic characterization of a novel HIV type 1 subtype B/C recombinant strain from Yunnan, China. AIDS Research and Human Retroviruses,2010 Jun;26(6):711-6

HIV-1 RT, PR, and IN diversity in a cohort of South African patients enrolled in the AIDS Vaccine Integrated Project
Papathanasopoulos MA, Vardas E, Wallis C, Glashoff R, Butt S, Poli G, Malnati M, Clerici M, Ensoli B. Characterization of HIV type 1 genetic diversity among South African participants enrolled in the AIDS Vaccine Integrated Project (AVIP) study. AIDS Research and Human Retroviruses,2010 Jun;26(6):705-9

A newly identified B/F1 recombinant in Sao Paulo, Brazil
Sanabani SS, Pastena ER, Neto WK, Martinez VP, Sabino EC. Characterization and frequency of a newly identified HIV-1 BF1 intersubtype circulating recombinant form in Sao Paulo, Brazil. Virology Journal,2010 Apr 16;7:74

Novel recombinant HIV-1 isolates in Afganistan
Sanders-Buell E, Bose M, Nasir A, Todd CS, Stanekzai MR, Tovanabutra S, Scott PT, Strathdee SA, Tjaden J, Michael NL, McCutchan FE. Distinct circulating recombinant HIV-1 strains among injecting drug users and sex workers in Afghanistan. AIDS Research and Human Retroviruses,2010 May;26(5):605-8

Four group N isolates in Cameroon
Vallari A, Bodelle P, Ngansop C, Makamche F, Ndembi N, Mbanya D, Kaptu L, Grtler LG, McArthur CP, Devare SG, Brennan CA. Four new HIV-1 group N isolates from Cameroon: Prevalence continues to be low. AIDS Research and Human Retroviruses,2010 Jan;26(1):109-15

A novel subtype J isolate in Cameroon
Yamaguchi J, Vallari A, Ngansop C, Makamche F, Ndembi N, Mbanya D, Kaptu L, Grtler LG, Devare SG, Brennan CA. Near full-length sequence of HIV type 1 subtype J strain 04CMU11421 from Cameroon. AIDS Research and Human Retroviruses,2010 Jun;26(6):693-7

Pol gene diversity in HIV-1-infected ARV-nave persons in Senegal
Diop-Ndiaye H, Toure-Kane C, Leye N, Ngom-Gueye NF, Montavon C, Peeters M, Mboup SAntiretroviral drug resistance mutations in antiretroviral-naive patients from Senegal. AIDS Research and Human Retroviruses,2010 Oct;26(10):1133-8

A novel recombinant form CRF22_01/A1 in Cameroon
Zhao J, Tang S, Ragupathy V, Carr JK, Wolfe ND, Awazi B, Hewlett I. Identification and genetic characterization of a novel CRF22_01A1 recombinant form of HIV type 1 in Cameroon AIDS Research and Human Retroviruses,2010 Sep;26(9):1033-45

HIV-1 genetic diversity among newly diagnosed HIV-1-infeced persons in Santos, Brazil
de Sa-Filho DJ, Ambar RF, Duarte NB, Matias RB, Candido V, Gagliani LH, Caseiro MM. HIV type 1 diversity from newly diagnosed patients in Santos metropolitan area/Brazil. AIDS Research and Human Retroviruses,2009 Sep;25(9):925-9

A cluster of infections with a novel HIV-1 B/F1 recombinant in Luxembourg
Struck D, Roman F, Lambert C, Masquelier C, Servais JY, Arendt V, Hemmer R, Staub T, Devaux C, Schmit JC. A new HIV-1 B/F1 unique recombinant form (URF) outbreak in Luxembourg: near full-length genome characterization and phylogenetic analysis GenBank submission,Genbank Submission

A novel circulating recombinant form CRF38_BF1 in Uruguay
Ruchansky D, Casado C, Russi JC, Arbiza JR, Lopez-Galindez C. Identification of a new HIV Type 1 circulating recombinant form (CRF38_BF1) in Uruguay AIDS Research and Human Retroviruses,2009 Mar;25(3):351-6

A novel subtype A1/C recombinant in Canada
Ntemgwa M, Toni TD, Brenner BG, Routy JP, Moisi D, Oliveira M, Wainberg MA. Near full-length genomic analysis of a novel subtype A1/C recombinant HIV type 1 isolate from Canada AIDS Research and Human Retroviruses,2008 Apr;24(4):655-9

A novel CRF01_AE/CRF07_BC recombinant in Jiangsu China
Guo H, Guo D, Wei JF, Yang H, Huan X, Tsui SK, Yang R, Zhang C. First detection of a novel HIV Type 1 CRF01_AE/07_BC recombinant among an epidemiologically linked cohort of IDUs in Jiangsu, China AIDS Research and Human Retroviruses,2009 Apr;25(4):463-7

HIV-1 CRF25_cpx in Cameroon
Luk KC, Holzmayer V, Ndembi N, Swanson P, Brennan CA, Ngansop C, Mbanya D, Kaptue L, Gurtler L, Devare SG, Hackett J. Near full-length genome characterization of an HIV type 1 CRF25_cpx strain from Cameroon AIDS Research and Human Retroviruses,2008 Oct;24(10):1309-14

HIV-1 B/C recombinants from India
Lakhashe S, Tripathy S, Paranjape R, Bhattacharya J. Characterization of B/C recombinants of near full-length HIV type 1 from northeastern India with mosaics identical to ARE195FL but with a different ancestral origin AIDS Research and Human Retroviruses,2008 Jan;24(1):92-9

A novel HIV-1 A/G recombinant from Southern Cameroon
Powell RL, Konings FA, Nanfack A, Burda S, Urbanski MM, Saa D, Nyambi PN. Quasispecies analysis of novel HIV-1 recombinants of subtypes A and G reveals no similarity to the mosaic structure of CRF02_AG Journal of Medical Virology,2007 Sep;79(9):1270-85

HIV-1 CRF33_01B in persons from Kuala Lumpur, Malaysia
Tee KK, Pybus OG, Parker J, Ng KP, Kamarulzaman A, Takebe Y. Estimating the date of origin of an HIV-1 circulating recombinant form. Virology,2009 Apr 25;387(1):229-34

IN diversity in ARV-nave individuals in Bangalore, India
Neogi U, Prarthana BS, Gupta S, D'souza G, De Costa A, Kuttiatt VS, Arumugam K, Shet ANaturally occurring polymorphisms and primary drug resistance profile among antiretroviral-naive individuals in Bangalore, India AIDS Research and Human Retroviruses,2010 Oct;26(10):1097-101

May 10, 2010
Drug resistance in recent infections in the ANRS12134 study
Ayouba A, Lien TT, Nouhin J, Vergne L, Aghokeng AF, Ngo-Giang-Huong N, Diop H, Kane CT, Valea, Rouet F, Joulia-Ekaza D, Toni TD, Nerrienet E, Ngole EM, Delaporte E, Costagliola D, Peeters M, Chaix ML. Low prevalence of HIV type 1 drug resistance mutations in untreated, recently infected patients from Burkina Faso, Cote d'Ivoire, Senegal, Thailand, and Vietnam: the ANRS 12134 study AIDS research and human retroviruses, 2009 Nov;25(11):1193-6

Emergence of raltegravir resistance mutations in the Aquitane Cohort
Wittkop L, Breilh D, Da Silva D, Duffau P, Mercie, Raymond I, Anies G, Fleury H, Saux MC, Dabis F, Fagard C, Thiebaut R, Masquelier B, Pellegrin I; ANRS CO3 Aquitaine Cohort. Virological and immunological response in HIV-1-infected patients with multiple treatment failures receiving raltegravir and optimized background therapy, ANRS CO3 Aquitaine Cohort Journal of Antimicrobials and Chemotherapy, 2009 Jun;63(6):1251-5. Epub 2009 Mar 31

Transmitted resistance in Japan
Gatanaga H, Ibe S, Matsuda M, Yoshida S, Asagi T, Kondo M, Sadamasu K, Tsukada H, Masakane A, Mori H, Takata N, Minami R, Tateyama M, Koike T, Itoh T, Imai M, Nagashima M, Gejyo F, Ueda M, Hamaguchi M, Kojima Y, Shirasaka T, Kimura A, Yamamoto M, Fujita J, Oka S, Sugiura W. Drug-resistant HIV-1 prevalence in patients newly diagnosed with HIV/AIDS in Japan Antiviral Research, 2007 Jul;75(1):75-82. Epub 2006 Dec 14

S/GSK1349572 resistance profile
Sato A, Kobayashi M, Yoshinaga T, Fujiwara T, Underwood M, Johns B, Foster S, Hazen R, Ferris R, Brown K, Spreen W, Garvey E. S/GSK1349572 Integrase Inhibitor Resistance Profile 12th Europen AIDS conference

Rilpivirine (TMC278) Resistance Profile
Azijn H, Tirry I, Vingerhoets J, de Bethune MP, Kraus G, Boven K, Jochmans D, Van Craenenbroeck E, Picchio G, Rimsky LT. TMC278, a Next-Generation NNRTI, Active Against Wild-Type and NNRTI-Resistant HIV-1 Antimicrobial Agents and Chemotherapy, 2010 Feb;54(2):718-27. Epub 2009 Nov 23

Drug resistance at ARV failure , South Africa
Wallis CL, Mellors JW, Venter WD, Sanne I, Stevens W. Varied HIV Drug Resistance Patterns Among Patients on Failing Antiretroviral Therapy in the South African National Roll-out Programme. Journal of Acquired Immune Deficiency Syndrome, 2010 Apr 1;53(4):480-4

Drug resistance surveillance in Venezuela
Castillo J, Comegna M, Quijada W, Jauvin V, Pinson P, Masquelier B, Fleury H, Castro E. Surveillance of HIV Type 1 Drug Resistance among Naive Patients from Venezuela AIDS research and human retroviruses, 2009 Dec;25(12):1329-33

Transmitted drug resistance in central Africa
Aghokeng AF, Vergne L, Mpoudi-Ngole E, Mbangue M, Deoudje N, Mokondji E, Nambei WS, Peyou-Ndi MM, Moka JJ, Delaporte E, Peeters M. Evaluation of transmitted HIV drug resistance among recently-infected antenatal clinic attendees in four Central African countries Antiviral Therapy, 2009;14(3):401-11

Non-B subtypes in Spain
Cuevas M, Fernandez-Garcia A, Sanchez-Garcia A, Gonzalez-Galeano M, Pinilla M, Sanchez-Martinez M, Garcia V, Perez-Alvarez L; Study group of HIV-1 newly diagnosed patients in Galicia, Spain. Incidence of non-B subtypes of HIV-1 in Galicia, Spain: high frequency and diversity of HIV-1 among men who have sex with men Euro Suveillance, 2009 Nov 26;14(47). pii: 19413

Emergence of raltegravir reistance mutations in Pavia Italy
Baldanti F, Paolucci S, Gulminetti R, Brandolini M, Barbarini G, Maserati R. Early emergence of raltegravir resistance mutations in patients receiving HAART salvage regimens Journal of Medical Virology, 2010 Jan;82(1):116-22

Association of protease mutations 76V, 46I and gag mutation 431V
Knops E, Kemper I, Schulter, Pfister H, Kaiser R, Verheyen J. The evolution of protease mutation 76V is associated with protease mutation 46I and gag mutation 431V AIDS, 2010 Mar 13;24(5):779-81

Prevalence of drug resistance in untreated individuals (Sout Africa)
Iweriebor,B.C., Mavhandu,L.C., Masebe,T.M., Nwobegahay,J., Rekosh,D., Hammarskjold,M.-L., Mphahlele,J.M., Pascal,P.O Molecular epidemiology of HIV in two highly endemic areas of north-eastern South Africa

CRF01_AE in Vietnam
Liao H, Tee KK, Hase S, Uenishi R, Li XJ, Kusagawa S, Thang PH, Hien NT, Pybus OG, Takebe Y. Phylodynamic analysis of the dissemination of HIV-1 CRF01_AE in Vietnam Virology, 2009 Aug 15;391(1):51-6. Epub 2009 Jun 21

Integrase variability in untreated individuals
Arruda LB, Fonseca LA, Duarte AJ, Casseb J. Genetic diversity on the integrase region of the pol gene among HIV type 1-infected patients naive for integrase inhibitors in Sao Paulo City, Brazil AIDS research and human retroviruses, 2010 Jan;26(1):105-7

Integrase variability in untreated individuals
Low A, Prada N, Topper M, Vaida F, Castor D, Mohri H, Hazuda D, Muesing M, Markowitz M. Natural polymorphisms of human immunodeficiency virus type 1 integrase and inherent susceptibilities to a panel of integrase inhibitors Antimicrobial Agents and Chemotherapy, 2009 Oct;53(10):4275-82. Epub 2009 Aug 3.

CRF-45_AKU recombinants (Central Africa)
Niama FR, Vidal N, Bazepeo SE, Mpoudi E, Toure-Kane C, Parra HJ, Delaporte E, Peeters M. CRF45_AKU, a circulating recombinant from Central Africa, is probably the common ancestor of HIV type 1 MAL and HIV type 1 NOGIL AIDS research and human retroviruses, 2009 Dec;25(12):1345-53

HIV-1 Group P
Plantier JC, Leoz M, Dickerson JE, De Oliveira F, Cordonnier F, Lemee, Damond F, Robertson DL, Simon F. A new human immunodeficiency virus derived from gorillas Nature Medicie, 2009 Aug;15(8):871-2. Epub 2009 Aug 2

HIV-1 in Kenya
Tovanabutra S, Sanders EJ, Graham SM, Mwangome M, Peshu N, McClelland RS, Muhaari A, Crossler J, Price MA, Gilmour J, Michael NL, McCutchan FM. Evaluation of HIV type 1 strains in men having sex with men and in female sex workers in Mombasa, Kenya AIDS research and human retroviruses, 2010 Feb;26(2):123-31

M41L transmission cluster in Sweden
Lindstrom, Ohlis A, Huigen M, Nijhuis M, Berglund T, Bratt G, Sandstrom, Albert J. HIV-1 transmission cluster with M41L 'singleton' mutation and decreased transmission of resistance in newly diagnosed Swedish homosexual men Antiviral Therapy, 2006;11(8):1031-9

HLA-associated immune escape pathways
Brumme ZL, John M, Carlson JM, Brumme CJ, Chan D, Brockman MA, Swenson LC, Tao I, Szeto S, Rosato P, Sela J, Kadie CM, Frahm N, Brander C, Haas DW, Riddler SA, Haubrich R, Walker BD, Harrigan PR, Heckerman D, Mallal S. HLA-associated immune escape pathways in HIV-1 subtype B Gag, Pol and Nef proteins PLoS One, 2009 Aug 19;4(8):e6687

Integrase polymorphism in Cambodia, Vietnam and Thailand
Nouhin,J, Donchai,T, Huynh Hoang,K.T, Ken,S, Kamkorn,J.Tran,T, Ayouba,A, Peeters,M, Chaix,M.L, Lien,T.X Natural polymorphisms of HIV-1 CRF01_AE integrase gene in ARV-naive individuals in Cambodia, Vietnam and Thailand: an ANRS AC12 resistance working group study

Non B Subtypes and Trnsmitted NNRTI Resistance (Spain)
Yebra G, de Mulder M, del Romero J, Rodriguez C, Holguin. HIV-1 non-B subtypes: High transmitted NNRTI-resistance in Spain and impaired genotypic resistance interpretation due to variability Antiviral Research,

Integrase variability in untreated individuals
Avi,R. and Lutsar,I Polymorphisms of HIV-1 CRF06_cpx integrases in Estonia

Resistance in untreated individuals (Zambia)
Gonzalez,S., Gondwe,C., Tully,D.C., Minhas,V., Shea,D., Kankasa,C.,Msoka,T. and Wood,C Anti-Retroviral Therapy Resistance Mutations Present in the HIV Type 1 Subtype C pol and env Regions from Therapy Naive Patients in Zambia

Resistance in untreated individuals (South Africa)
Nwobegahay J.M, Masebe T.M, Mavhandu L.G, Iweriebor B.C, Ndjeka N.O, Manhaeve C, Bessong,P.O Prevalence of drug resistance mutations among drug-naive HIV-1infected individuals in a treatment site in the Waterberg District of South Africa

Resistance in untreated individuals (South Africa)
Nwobegahay J.M, Masebe T.M, Mavhandu L.G, Iweriebor B.C, Ndjeka N.O, Manhaeve C, Bessong,P.O Baseline Genetic Resistance of HIV Infected Patients Entering Antiretroviral Treatment Program at Two Treatment Sites in Limpopo Province, South Africa

Resistance in untreated individuals (Mumbai, India)
Chaturbhuj D.N, Hingankar N.K, Garg R, Srikantiah P, Kabra S, Haldar P, Deshmukh P.S, Jadhav S.D, Thorat S.R, Datkar S.R, Mehta P, Ingole N, Mathur M, Ramachandran A, Bachani D, Rao S, Tripathy S.P, Paranjape R.S Human Immunodeficiency Virus Type 1 Transmitted Drug Resistance Threshold Surveillance among Newly HIV Type-1 diagnosed Drug Naive Clients attending Voluntary Counseling and Testing (VCT) sites in Mumbai, India

Fitness evolution
Weber J, Rangel HR, Chakraborty B, Marotta ML, Valdez H, Fransen K, Florence E, Connick E, Smith KY, Colebunders RL, Landay A, Kuritzkes DR, Lederman MM, Vanham G, Quinones-Mateu ME. Role of Baseline pol Genotype in HIV-1 Fitness Evolution Journal of Acquired Immune Deficiency Syndrome,

Resistance in untreated individuals (Sao Paulo, Brazil)
Gonsalez CR, Alcalde R, Nishiya A, Barreto CC, Silva FE, de Almeida A, Mendonca M, Ferreira F, Fernandes SS, Casseb J, Duarte AJ. Drug resistance among chronic HIV-1-infected patients naive for use of anti-retroviral therapy in Sao Paulo city Virus Research, 2007 Nov;129(2):87-90. Epub 2007 Aug 7

Resistance in untreated individuals (Chennai, India)
Iqbal HS, Solomon SS, Madhavan V, Solomon S, Balakrishnan P. Primary HIV-1 drug resistance and polymorphic patterns among injecting drug users (IDUs) in Chennai, Southern India Journal of the International Association of Physicians in AIDS Care, 2009 Sep-Oct;8(5):323-7. Epub 2009 Aug 31

Darunavir resistance
Saskova G, Kozisek M, Rezacova, Brynda J, Yashina T, Kagan RM, Konvalinka J. Molecular characterization of clinical isolates of human immunodeficiency virus resistant to the protease inhibitor darunavir Journal of Virology, 2009 Sep;83(17):8810-8. Epub 2009 Jun 17

Drug resistance in Cameroon
Burda ST, Viswanath R, Zhao J, Kinge T, Anyangwe C, Tinyami ET, Haldar B, Powell RL, Jarido V, Hewlett IK, Nyambi PN. HIV-1 reverse transcriptase drug-resistance mutations in chronically infected individuals receiving or naive to HAART in Cameroon Journal of Medical Virology, 2010 Feb;82(2):187-96

Y143 integrase mutations and Raltegravir
Delelis O, Thierry S, Subra F, Simon F, Malet I, Alloui C, Sayon S, Calvez V, Deprez E, Marcelin AG, Tchertanov L, Mouscadet JF. Impact of Y143 HIV-1 integrase mutations on resistance to raltegravir in vitro and in vivo Antimicrobial Agents and Chemotherapy, 2010 Jan;54(1):491-501. Epub 2009 Nov 9

Transmitted resistance in China
Zhang J, Kang D, Fu J, Sun X, Lin B, Bi Z, Nkengasong JN, Yang C. Surveillance of Transmitted HIV Type 1 Drug Resistance in Newly Diagnosed HIV Type 1-Infected Patients in Shandong Province, China AIDS research and human retroviruses, 2010 Jan;26(1):99-103

Prevalence of NNRTI Resistance
Maiga AI, Descamps D, Morand-Joubert L, Malet I, Derache A, Cisse M, Koita V, Akonde A, Diarra B, Wirden M, Tounkara A, Verlinden Y, Katlama C, Costagliola D, Masquelier B, Calvez V, Marcelin AG. Resistance-associated mutations to etravirine (TMC-125) in antiretroviral-naïve patients infected with non-B HIV-1 subtypes Antimicrobial Agents and Chemotherapy, 2010 Feb;54(2):728-33. Epub 2009 Dec 14

Transmission cluster with RT mutation T215D
Cuevas MT, Munoz-Nieto M, Thomson MM, Delgado E, Iribarren JA, Cilla G, Fernandez-Garcia A, Santamaria JM, Lezaun MJ, Jimenez L, Lopez-Soria LM, Sota M, Contreras G, Najera R, Perez-Alvarez L; Spanish Group of HIV-1 Antiretroviral Resistance Studies in the Basque Country. HIV-1 transmission cluster with T215D revertant mutation among newly diagnosed patients from the Basque Country, Spain Journal of Acquired Immune Deficiency Syndrome, 2009 May 1;51(1):99-103

Transmitted drug resistance in Europe
Vercauteren J, Wensing AM, van de Vijver DA, Albert J, Balotta C, Hamouda O, Kucherer C, Struck D, Schmit JC, Asjo Bruckova M, Camacho RJ, Clotet B, Coughlan S, Grossman Z, Horban A, Korn K, Kostrikis L, Nielsen C, Paraskevis D, Poljak M, Puchhammer-Stockl E, Riva C, Ruiz L, Salminen M, Schuurman R, Sonnerborg A, Stanekova D, Stanojevic M, Vandamme AM, Boucher CA. Transmission of Drug-Resistant HIV-1 Is Stabilizing in Europe Journal of Infectious Diseases, 2009 Nov 15;200(10):1503-8

Resistance in untreated individuals (San Diego, US)
Smith DM, May SJ, Tweeten S, Drumright L, Pacold ME, Kosakovsky Pond SL, Pesano RL, Lie YS, Richman DD, Frost SD, Woelk CH, Little SJ. A public health model for the molecular surveillance of HIV transmission in San Diego, California AIDS, 2009 Jan 14;23(2):225-32

Protease inhibitor resistance mutation L76V
Nijhuis M, Wensing AM, Bierman WF, de Jong D, Kagan R, Fun A, Jaspers CA, Schurink KA, van Agtmael MA, Boucher CA. Failure of treatment with first-line lopinavir boosted with ritonavir can be explained by novel resistance pathways with protease mutation 76V Journal of Infectious Diseases, 2009 Sep 1;200(5):698-709

December 15, 2009
Genotypes from North India
Arora SK, Gupta S, Toor JS, Singla A. Drug resistance-associated genotypic alterations in the pol gene of HIV type 1 isolates in ART-naive individuals in North India. AIDS Research and Human Retroviruses, 2008 Feb;24(2):125-30.

Treatment-naive Genotypes from Angola
Bartolo I, Rocha C, Bartolomeu J, Gama A, Fonseca M, Mendes A, Cristina F, Thamm S, Epalanga M, Silva PC, Taveira N. Antiretroviral drug resistance surveillance among treatment-naive human immunodeficiency virus type 1-infected individuals in Angola: evidence for low level of transmitted drug resistance. Antimicrobial Agents and Chemotherapy, 2009 Jul;53(7):3156-8. Epub 2009 May 11.

Genotypes from Mozambique
Bartolo I, Casanovas J, Bastos R, Rocha C, Abecasis AB, Folgosa E, Mondlane J, Manuel R, Taveira N. HIV-1 genetic diversity and transmitted drug resistance in health care settings in Maputo, Mozambique. Journal of Acquired Immune Deficiency Syndromes, 2009 Jul 1;51(3):323-31.

Genotypes from Mozambique - DREAM programme (sequences now available)
Bellocchi MC, Forbici F, Palombi L, Gori C, Coelho E, Svicher V, D'Arrigo R, Emberti-Gialloreti L, Ceffa S, Erba F, Marazzi MC, Silberstein FC, Perno CF. Subtype analysis and mutations to antiviral drugs in HIV-1-infected patients from Mozambique before initiation of antiretroviral therapy: results from the DREAM programme. Journal of Medical Virology, 2005 Aug;76(4):452-8.

Non-B US Genotypes
Brennan CA, Stramer SL, Holzmayer V, Yamaguchi J, Foster GA, Notari Iv EP, Schochetman G, Devare SG. Identification of human immunodeficiency virus type 1 non-B subtypes and antiretroviral drug-resistant strains in United States blood donors. Transfusion, 2009 Jan;49(1):125-33.

Transmission after acute/early HIV infection (sequences now available)
Brenner BG, Roger M, Routy JP, Moisi D, Ntemgwa M, Matte C, Baril JG, Thomas R, Rouleau D, Bruneau J, Leblanc R, Legault M, Tremblay C, Charest H, Wainberg MA. High rates of forward transmission events after acute/early HIV-1 infection. The Journal of Infectious Diseases, 2007 Apr 1;195(7):951-9.

Genotypes from Central West Brazil
Cardoso LP, Queiroz BB, de Araujo Stefani MM. HIV-1 pol phylogenetic diversity and antiretroviral resistance mutations in treatment naive patients from Central West Brazil. Journal of Clinical Virology, 2009 Aug 12 (Epub).

Genotypes from Treatment-naive Venezuela patients
Castillo J, Comegna M, Quijada W, Jauvin V, Pinson P, Masquelier B, Fleury H, Castro E. Surveillance of HIV Type 1 Drug Resistance among Naive Patients from Venezuela. AIDS Research and Human Retroviruses, 2009 Dec 2. [Epub ahead of print].

Trends of DRM in naive Taiwan patients
Chang SY, Chen MY, Lee CN, Sun HY, Ko W, Chang SF, Chang KL, Hsieh SM, Sheng WH, Liu WC, Wu CH, Kao CL, Hung CC, Chang SC. Trends of antiretroviral drug resistance in treatment-naive patients with human immunodeficiency virus type 1 infection in Taiwan. The Journal of Antimicrobial Chemotherapy, 2008 Mar;61(3):689-93.

NVP resistance in Uganda infants after SD NVP
Church JD, Omer SB, Guay LA, Huang W, Lidstrom J, Musoke P, Mmiro F, Jackson JB, Eshleman SH. Analysis of nevirapine (NVP) resistance in Ugandan infants who were HIV infected despite receiving single-Dose (SD) NVP versus SD NVP plus daily NVP up to 6 weeks of age to prevent HIV vertical transmission. The Journal of Infectious Diseases, 2008 Oct 1;198(7):1075-8.

Genotypes from Basque Country (Spain)
Cuevas MT, Munoz-Nieto M, Thomson MM, Delgado E, Iribarren JA, Cilla G, Fernandez-Garcia A, Santamaria JM, Lezaun MJ, Jimenez L, Lopez-Soria LM, Sota M, Contreras G, Najera R, Perez-Alvarez L. HIV-1 transmission cluster with T215D revertant mutation among newly diagnosed patients from the Basque Country, Spain. Journal of Acquired Immune Deficiency Syndromes, 2009 May 1;51(1):99-103.

Genotypes from Zimbabwe
Dalai SC, de Oliveira T, Harkins GW, Kassaye SG, Lint J, Manasa J, Johnston E, Katzenstein D. Evolution and molecular epidemiology of subtype C HIV-1 in Zimbabwe. AIDS, 2009 Sep 16.

Genotypes from Argentina (Buenos Aires)
Dilernia DA, Gomez AM, Lourtau L, Marone R, Losso MH, Salomon H, Gomez-Carrillo M. Drug-resistance surveillance among newly HIV-1 diagnosed individuals in Buenos Aires, Argentina. AIDS, 2007 Oct;23(10):1201-7.

Genotypes from Brazil patients with virological failure
Dumans AT, Barreto CC, Santos AF, Arruda M, Sousa TM, Machado ES, Sabino EC, Brindeiro RM, Tanuri A, Duarte AJ, Soares MA. Distinct resistance mutation and polymorphism acquisition in HIV-1 protease of subtypes B and F1 from children and adult patients under virological failure. Infection, Genetics and Evolution, 2009 Jan;9(1):62-70.

Genotypes with DRM from naive patients in Mexico (sequences now available)
Escoto-Delgadillo M, Vazquez-Valls E, Ramirez-Rodriguez M, Corona-Nakamura A, Amaya-Tapia G, Quintero-Perez N, Panduro-Cerda A, Torres-Mendoza BM. Drug-resistance mutations in antiretroviral-naive patients with established HIV-1 infection in Mexico. HIV Medicine, 2005 Nov;6(6):403-9.

Genotypes from Curitiba, Brazil
Ferreira JL, Thomaz M, Rodrigues R, Harrad D, Oliveira CM, Oliveira CA, Batista JP, Ito TS, Brigido LF. Molecular characterisation of newly identified HIV-1 infections in Curitiba, Brazil: preponderance of clade C among males with recent infections. Memorias do Instituto Oswaldo Cruz, 2008 Dec;103(8):800-8.

Integrase Mutations at 143, 148, 155 and Raltegravir
Fransen S, Gupta S, Frantzell A, Petropoulos C, Huang W. HIV-1 Mutations at Positions 143, 148, and 155 of Integrase Define Different Genetic Barriers to Raltegravir Resistance in vivo. 16th Conference on Retroviruses and Opportunistic Infections, 2009.

DRM in naive patients in Uganda and Rwanda
Galluzzo CM, Germinario EA, Bassani L, Mancini MG, Okong P, Vyankandondera J, Vella S, Giuliano M. Antiretroviral resistance mutations in untreated pregnant women with HIV infection in Uganda and Rwanda. AIDS Research and Human Retroviruses, 2007 Nov;23(11):1449-51.

DRM in naive patients in Sao Paulo, Brazil
Gonsalez CR, Alcalde R, Nishiya A, Barreto CC, Silva FE, de Almeida A, Mendonca M, Ferreira F, Fernandes SS, Casseb J, Duarte AJ. Drug resistance among chronic HIV-1-infected patients naive for use of anti-retroviral therapy in Sao Paulo city. Virus Research, 2007 Nov;129(2):87-90.

DRM in naive patients in Israel (sequences now available)
Grossman Z, Lorber M, Maayan S, Bar-Yacov N, Levy I, Averbuch D, Istomin V, Chowers M, Sthoeger Z, Ram D, Rudich H, Mileguir F, Pavel R, Almaliach R, Schlaeffer F, Kra-Oz Z, Mendelson E, Schapiro JM, Riesenberg K. Drug-resistant HIV infection among drug-naive patients in Israel. Clinical Infectious Disease, 2005 Jan 15;40(2):294-302.

Genotypes from the Canary Islands, Spain
Holguin A, Pena MJ, Troncoso F, Soriano V. Introduction of non-B subtypes among Spaniards newly diagnosed with HIV type 1 in the Canary Islands. AIDS Research and Human Retroviruses, 2007 Apr;23(4):498-502.

1st line treatment failure in Malawi
Hosseinipour MC, van Oosterhout JJ, Weigel R, Phiri S, Kamwendo D, Parkin N, Fiscus SA, Nelson JA, Eron JJ, Kumwenda J. The public health approach to identify antiretroviral therapy failure: high-level nucleoside reverse transcriptase inhibitor resistance among Malawians failing first-line antiretroviral therapy. AIDS, 2009 Jun 1;23(9):1127-34.

Genotypes from Cape Town, South Africa
Jacobs GB, Laten A, van Rensburg EJ, Bodem J, Weissbrich B, Rethwilm A, Preiser W, Engelbrecht S. Phylogenetic diversity and low level antiretroviral resistance mutations in HIV type 1 treatment-naive patients from Cape Town, South Africa. AIDS Research and Human Retroviruses, 2008 Jul;24(7):1009-12.

Genotypes from Canada: recent vs. established HIV infection
Jayaraman GC, Archibald CP, Kim J, Rekart ML, Singh AE, Harmen S, Wood M, Sandstrom P. A population-based approach to determine the prevalence of transmitted drug-resistant HIV among recent versus established HIV infections: results from the Canadian HIV strain and drug resistance surveillance program. Journal of Acquired Immune Deficiency Syndromes, 2006 May;42(1):86-90.

Genotypes from naive South India patients
Kandathil AJ, Kannangai R, Abraham OC, Rupali P, Pulimood SA, Verghese VP, Grant P, Pillay D, Sridharan G. The frequency of HIV-I drug resistance mutations among treatment-naive individuals at a tertiary care centre in south India. International Journal of STD & AIDS, 2009 Aug;20(8):522-6.

Genotypes from Singapore with acute and recent HIV infection
Lee CC, Sun YJ, Barkham T, Leo YS. Primary drug resistance and transmission analysis of HIV-1 in acute and recent drug-naive seroconverters in Singapore. HIV Medicine 2009 Jul;10(6):370-7.

DRM Genotypes from naive Greenland patients
Madsen TV, Lohse N, Jensen ES, Obel N, Ladefoged K, Gerstoft J, Petersen AB, Nielsen C, Jorgensen LB. High prevalence of drug-resistant human immunodeficiency virus type 1 in treatment-naive patients in Greenland. AIDS Research and Human Retroviruses, 2008 Aug;24(8):1073-7.

Genotypes from southern Spain
McConnell MJ, Docobo-Perez F, Mata RC, Fernandez-Cuenca F, Viciana P, Lopez-Cortes LF, Trastoy M, Pachon J, Perez-Romero P. Molecular epidemiology of HIV type 1 in newly diagnosed patients in southern Spain. AIDS Research and Human Retroviruses, 2008 Jun;24(6):881-7.

Genotypes from northeast Gabon
Mintsa-Ndong A, Caron M, Plantier JC, Makuwa M, Le Hello S, Courgnaud V, Roques P, Kazanji M. High HIV Type 1 prevalence and wide genetic diversity with dominance of recombinant strains but low level of antiretroviral drug-resistance mutations in untreated patients in northeast Gabon, Central Africa. AIDS Research and Human Retroviruses, Apr;25(4):411-8.

Genotypes from Hanoi, vietnam
Nguyen HT, Duc NB, Shrivastava R, Tran TH, Nguyen TA, Thang PH, McNicholl JM, Leelawiwat W, Chonwattana W, Sidibe K, Fujita M, Luu CM, Kakkar R, Bennett DE, Kaplan J, Cosimi L, Wolfe MI. HIV drug resistance threshold survey using specimens from voluntary counselling and testing sites in Hanoi, Vietnam. Antiviral Therapy, 2008;13 Suppl 2:115-21.

Treatment failure after Lopinavir/Ritonavir first-line treatment
Nijhuis M, Wensing AM, Bierman WF, de Jong D, Kagan R, Fun A, Jaspers CA, Schurink KA, van Agtmael MA, Boucher CA. Failure of treatment with first-line lopinavir boosted with ritonavir can be explained by novel resistance pathways with protease mutation 76V. The Journal of Infectious Diseases, 2009 Sep 1;200(5):698-709.

Genotypes from Malaga, Spain
Palacios R, Viciana I, Perez de Pedro I, de la Torre J, Ropero F, Fernandez S, Salgado F, Roldan J, de Dios Colmenero J, Marquez M, Santos J. Prevalence of primary resistance mutations in patients with newly diagnosed HIV infection in the province of Malaga (Spain). Enfermedades Infecciosas y Microbiologia Clinica, 2008 Mar;26(3):141-5.

Zidovudine and Tenofovir resistance
Park SS, Hong SK, Lee SG, Yoon JS, Yoo WC, Paik SY. In vitro selection and characterization of human immunodeficiency virus type 1 resistant to Zidovudine and tenofovir. Nucleosides, Nucleotides and Nucleic Acids, 2007;26(5):453-7.

Genotypes from Gauteng, South Africa
Pillay V, Ledwaba J, Hunt G, Rakgotho M, Singh B, Makubalo L, Bennett DE, Puren A, Morris L. Antiretroviral drug resistance surveillance among drug-naive HIV-1-infected individuals in Gauteng Province, South Africa in 2002 and 2004. Antiviral Therapy, 2008;13 Suppl 2:101-7.

Genotypes from Bulgaria
Salemi M, Goodenow MM, Montieri S, de Oliveira T, Santoro MM, Beshkov D, Alexiev I, Elenkov I, Elenkov I, Yakimova T, Varleva T, Rezza G, Ciccozzi M. The HIV type 1 epidemic in Bulgaria involves multiple subtypes and is sustained by continuous viral inflow from West and East European countries. AIDS Research and Human Retroviruses, 2008 Jun;24(6):771-9.

Genotypes from Gran Canaria, Spain
Sanchez Onoro M, Lopez MJ, Santana MA, Andes JM, Campelo FA. Primary antiretroviral drug resistance among patients diagnosed with HIV infection in Gran Canaria (Spain) between 2002 and 2005. Enfermedades Infecciosas y Microbiologia Clinica, 2007 Aug-Sep;25(7):437-40.

Genotypes from Thailand
Sirivichayakul S, Phanuphak P, Pankam T, O-Charoen R, Sutherland D, Ruxrungtham K. HIV drug resistance transmission threshold survey in Bangkok, Thailand. Antiviral Therapy, 2008;13 Suppl 2:109-13.

Genotyping naive patients with unknown infection period (sequences now available)
Smith D, Moini N, Pesano R, Cachay E, Aiem H, Lie Y, Richman D, Little S. Clinical utility of HIV standard genotyping among antiretroviral-naive individuals with unknown duration of infection. Clinical Infectious Disease, 2007 Feb 1;44(3):456-8.

HIV Surveillance in San Diego, US
Smith DM, May SJ, Tweeten S, Drumright L, Pacold ME, Kosakovsky Pond SL, Pesano RL, Lie YS, Richman DD, Frost SD, Woelk CH, Little SJ. A public health model for the molecular surveillance of HIV transmission in San Diego, California. AIDS 2009 Jan 14;23(2):225-32.

DRM in treated patients from Ouagadougou, Burkina Faso
Tebit DM, Sangare L, Makamste A, Yameogo S, Somlare H, Bado G, Kouldiaty BG, Sathiandee K, Tiba F, Sanou I, Ouedraogo-Traore R, Zoungrana L, Diallo I, Drabo JY, Krausslich HG. HIV Drug Resistance Pattern Among HAART-Exposed Patients With Suboptimal Virological Response in Ouagadougou, Burkina Faso. Journal of Acquired Immune Deficiency Syndromes, 2008 Sep 1;49(1):17-25.

RT M184V and K103N minority variants
Toni TA, Asahchop EL, Moisi D, Ntemgwa M, Oliveira M, Masquelier B, Brenner BG, Wainberg MA. Detection of human immunodeficiency virus (HIV) type 1 M184V and K103N minority variants in patients with primary HIV infection. Antimicrobial Agents and Chemotherapy, 2009 Apr;53(4):1670-2.

Combined Genotypic-Phenotypic recombinant virus assay
Van Baelen K, Rondelez E, Van Eygen V, Arien K, Clynhens M, Van den Zegel P, Winters B, Stuyver LJ. A combined genotypic and phenotypic human immunodeficiency virus type 1 recombinant virus assay for the reverse transcriptase and integrase genes. Journal of Virological Methods 2009 Nov;161(2):231-9. Epub 2009 Jun 25.

Genotypes from naive Rio de Janeiro, Brazil patients
Varella RB, Ferreira SB, de Castro MB, Zalis MG, Tavares MD. Human immunodeficiency virus type 1 protease and reverse transcriptase mutation patterns among treatment-naive patients in different stages of infection in Rio de Janeiro, Brazil. Journal of Medical Virology, 2007 Aug;79(8):1033-9.

SPREAD Programme in Europe
Vercauteren J, Wensing AM, van de Vijver DA, Albert J, Balotta C, Hamouda O, Kucherer C, Struck D, Schmit JC, Asjo B, Bruckova M, Camacho RJ, Clotet B, Coughlan S, Grossman Z, Horban A, Korn K, Kostrikis L, Nielsen C, Paraskevis D, Poljak M, Puchhammer-Stockl E, Riva C, Ruiz L, Salminen M, Schuurman R, Sonnerborg A, Stanekova D, Stanojevic M, Vandamme AM, Boucher CA. Transmission of Drug-Resistant HIV-1 Is Stabilizing in Europe. The Journal of Infectious Diseases, 2009 Nov 15;200(10):1503-8.

Genotypes from naive Togo patients
Yaotse DA, Nicole V, Roch NF, Mireille PD, Eric D, Martine P. Genetic characterization of HIV-1 strains in Togo reveals a high genetic complexity and genotypic drug-resistance mutations in ARV naive patients. Infection, Genetics and Evolution, 2009 Jul;9(4):646-52.

Recombinant From_BC Genotypes from patients in Guangdong, China
Yu G, Li Y, Li J, Diao L, Yan X, Lin P, He Q, Wang Y, Fu X, Yang F, Long Q, Lin P. Genetic Diversity and Drug Resistance of HIV Type 1 Circulating Recombinant Form_BC among Drug Users in Guangdong Province. AIDS Research and Human Retroviruses, 2009 Sep;25(9):869-75.

July 8, 2009
Predictive Value of Resistance Test Interpretation Algorithms
Rhee SY, Fessel WJ, Liu TF, Marlowe NM, Rowland CM, Rode RA, Vandamme AM, Van Laethem K, Brun-Vezinet F, Calvez V, Taylor J, Hurley L, Horberg M, Shafer RW. Predictive Value of HIV-1 Genotypic Resistance Test Interpretation Algorithms. The Journal of Infectious Diseases, 2009 Aug 1;200(3):453-463.

Genotypes from treatment-naive Thai patients
Auwanit W, Isarangkura-Na-Ayuthaya P, Kasornpikul D, Ikuta K, Sawanpanyalert P, Kameoka M. Detection of drug resistance-associated and background mutations in human immunodeficiency virus type 1 CRF01_AE protease and reverse transcriptase derived from drug treatment-naive patients residing in central Thailand. AIDS Research and Human Retroviruses, 2009 Jun;25(6):625-31.

Genotypes from treatment-naive Estonian patients
Avi R, Huik K, Sadam M, Karki T, Krispin T, Ainsalu K, Paap P, Schmidt J, Nikitina N, Lutsar I. Absence of genotypic drug resistance and presence of several naturally occurring polymorphisms of human immunodeficiency virus-1 CRF06_cpx in treatment-naive patients in Estonia. Journal of Medical Virology, 2009 Jun;81(6):953-8.

Integrase gene evolution in patients failing raltegravir treatment
Canducci F, Sampaolo M, Marinozzi MC, Boeri E, Spagnuolo V, Galli A, Castagna A, Lazzarin A, Clementi M, Gianotti N. Dynamic patterns of human immunodeficiency virus type 1 integrase gene evolution in patients failing raltegravir-based salvage therapies. AIDS, 2009 Feb 20;23(4):455-60.

Drug susceptibility in recently infected treatment-naive Ugandan patients
Eshleman SH, Laeyendecker O, Parkin N, Huang W, Chappey C, Paquet AC, Serwadda D, Reynolds SJ, Kiwanuka N, Quinn TC, Gray R, Wawer M. Antiretroviral drug susceptibility among drug-naive adults with recent HIV infection in Rakai, Uganda. AIDS, 2009 Apr 27;27(7):845-52.

Integrase genotype analysis using a prototype genotyping assay
Eshleman SH, Hudelson SE, Smith P, Hackett J, Holzmayer V, Swanson P, Devare SG, Marlowe N. Analysis of pol integrase sequences in diverse HIV type 1 strains using a prototype genotyping assay. AIDS Research and Human Retroviruses, 2009 Mar;25(3):343-5.

11-year HIV surveillance in Nagoya, Japan
Fujisaki S, Ibe S, Hattori J, Shigemi U, Fujisaki S, Shimizu K, Nakamura K, Yokomaku Y, Mamiya N, Utsumi M, Hamaguchi M, Kaneda T. An 11-Year Surveillance of HIV Type 1 Subtypes in Nagoya, Japan. AIDS Research and Human Retroviruses, 2009 Jan;25(1):15-21.

Resistance mutations in patients failing Raltegravir treatment
Garrido C, Anta L, Zahonero N, Sanchez-Hellin V, Imaz A, Garcia S, Cervero M, Gaspar J, Sarria C, Chocarro J, Barros C, Soriano V, de Mendoza C. Dynamics in the selection of resistance mutations in HIV patients failing Raltegravir and following its discountinuation. 7th European HIV Drug Resistance Workshop. 25-27 March 2009, Stockholm, Sweden, Abstract 44.

Near full-length genotypes from treatment-naive Japanese patients
Ibe S, Shigemi U, Sawaki K, Fujisaki S, Hattori J, Yokomaku Y, Mamiya N, Hamaguchi M, Kaneda T. Analysis of near full-length genomic sequences of drug-resistant HIV-1 spreading among therapy-naive individuals in Nagoya, Japan: amino acid mutations associated with viral replication activity. AIDS Research and Human Retroviruses, 2009 Aug;24(8):1121-5.

Genotypes from treatment-naive Vietnamese patients
Ishizaki A, Cuong NH, Thuc PV, Trung NV, Saijoh K, Kageyama S, Ishigaki K, Tanuma J, Oka S, Ichimura H. Profile of HIV type 1 infection and genotypic resistance mutations to antiretroviral drugs in treatment-naive HIV type 1-infected individuals in Hai Phong, Viet Nam. AIDS Research and Human Retroviruses, 2009 Feb;25(2):175-82.

Preclinical evaluation of GS-9160 (new Integrase inhibitor)
Jones GS, Yu F, Zeynalzadegan A, Hesselgesser J, Chen X, Chen J, Jin H, Kim CU, Wright M, Geleziunas R, Tsiang M. Preclinical evaluation of GS-9160, a novel inhibitor of human immunodeficiency virus type 1 integrase. Antimicrobial Agents and Chemotherapy, 2009 Mar;53(3):1194-203.

Envelope coreceptor tropism in ARV-treated subtype C patients
Kassaye S, Johnston E, McColgan B, Kantor R, Zijenah L, Katzenstein D. Envelope coreceptor tropism, drug resistance, and viral evolution among subtype C HIV-1-infected individuals receiving nonsuppressive antiretroviral therapy. Journal of Acquired Immune Deficiency Syndromes, 2009 Jan 1;50(1):9-18.

Drug resistance in treated Chad patients
Koyalta D, Charpentier C, Beassamda J, Rey E, Si-Mohamed A, Djemadji-Oudjeil N, Belec L. High frequency of antiretroviral drug resistance among HIV-infected adults receiving first-line highly active antiretroviral therapy in N'Djamena, Chad. Clinical Infectious Disease, 2009 Jul 1;49(1):155-9.

RT Mutation Q151L resistance to GS-9148, Tenofovir and Zidovudine
Kulkarni R, Margot NA, Myrick F, Svarovskaia J, Chen J, Lansdon E, Ray AS, Cihlar T, Swaminathan S, Miller MD, White KL. The HIV-1 RT Mutant Q151L Shows Decreased Replication Capacity, Selective High-Level Resistance to GS-9148 and Hypersusceptibility to Tenofovir and Zidovudine. 18th International HIV Drug Resisance Workshop, June 9-13 2009, Fort Meyers, Florida.

Genotypes from Chinese patients in rural Hubei province
Luo M, Liu H, Zhuang K, Liu L, Su B, Yang R, Tien P, Zhang L, Gui X, Chen Z. Prevalence of drug-resistant HIV-1 in rural areas of Hubei province in the People's Republic of China. Journal of Acquired Immune Deficiency Syndromes, 2009 Jan 1;50(1):1-8.

TMC278, a next-generation NNRTI
Rimsky LT, Azijn H, Tirry I, Vingerhoets J, Mersch R, Kraus G, de Bethune M-P, Picchio G. In-vitro resistance profile of TMC278, a next-generation NNRTI: evidence of a higher genetic barrier and a more robust resistance profile than first-generation NNRTIs. 18th International HIV Drug Resistance Workshop 2009, June 9-13 2009, Fort Meyers, Florida.

Evolution of raltegravir resistance during therapy
Sichtig N, Sierra S, Kaiser R, Daumer M, Reuter S, Schulter E, Altmann A, Fatkenheuer G, Dittmer U, Pfister H, Esser S. Evolution of raltegravir resistance during therapy. Antimicrobial Agents and Chemotherapy, 2009 Jul;64(1):25-32.

Predominance of Subtype A genotypes from Russian patients from St Petersburg
Thomson MM, Vinogradova A, Delgado E, Rakhmanova A, Yakovlev A, Cuevas MT, Munoz M, Pinilla M, Vega Y, Perez-Alvarez L, Osmanov S, Najera R. Molecular Epidemiology of HIV-1 in St Petersburg, Russia: Predominance of Subtype A, Former Soviet Union Variant, and Identification of Intrasubtype Subclusters. Journal of Acquired Immune Deficiency Syndromes, 2009 Apr 8.

HIV subtype and drug-resistance surveillance in Yunnan, China
Tu Y, Zheng Y, Jiang Y. Surveillance for human immunodeficiency virus-1 subtypes and drug resistance among volunteer blood donors in Yunnan, China.

Integrase polymorphisms and prior antiretroviral drug exposure
van Hal SJ, Herring B, Deris Z, Wang B, Saksena NK, Dwyer DE. HIV-1 integrase polymorphisms are associated with prior antiretroviral drug exposure. Retrovirology, 2009 Feb 9;6:12.

Genotypes from Cameroon patients
Yamaguchi J, Ndembi N, Ngansop C, Mbanya D, Kaptue L, Gurtler LG, Devare SG, Brennan CA HIV type 1 group M subtype G in Cameroon: five genome sequences. AIDS Research and Human Retroviruses, 2009 Apr;25(4):469-73.

March 18, 2009
Drug Resistant Mutations After WHO-Recommended Treatment
Gody JC, Charpentier C, Mbitikon O, Si-Mohamed A, LeGoff J, Gresenguet G, Belec L. High Prevalence of Antiretroviral Drug Resistance Mutations in HIV-1 Non-B Subtype Strains From African Children Receiving Antiretroviral Therapy Regimen According to the 2006 Revised WHO Recommendations Journal of Acquired Immune Deficiency Syndromes, 2008 Dec 15;49(5):566-9.

Genotypes from ARV-Experienced Thai Patients
Nukoolkarn S, Pongthapisith V, Panyim S, Leelamanit W. Sequence variability of the HIV type 1 protease gene in Thai patients experienced with antiretroviral therapy. AIDS Research and Human Retroviruses, 2004 Dec;20(12):1368-72.

Genotypes from South African Patients Failing ARV Treatment
Pillay V, Pillay C, Kantor R, Venter F, Levin L, Morris L. HIV type 1 subtype C drug resistance among pediatric and adult South African patients failing antiretroviral therapy AIDS Research and Human Retroviruses, 2008 Nov;24(11):1449-54

Etravirine Phenotypes from Patients Failing NNRTI Treatment
Poveda E, de Mendoza C, Pattery B, Gonzalez Mdel M, Villacian J, Soriano V Phenotypic impact of resistance mutations on etravirine susceptibility in HIV patients with prior failure to nonnucleoside analogues AIDS, 2008 Nov 12;22(17):2395-8

Genotypes from Cameroon
Brennan CA, Bodelle P, Coffey R, Devare SG, Golden A, Hackett J Jr, Harris B, Holzmayer V, Luk KC, Schochetman G, Swanson P, Yamaguchi J, Vallari A, Ndembi N, Ngansop C, Makamche F, Mbanya D, Gurtler LG, Zekeng L, Kaptue L. The Prevalence of Diverse HIV-1 Strains Was Stable in Cameroonian Blood Donors From 1996 to 2004 Journal of Acquired Immune Deficiency Syndromes 2008 Dec 1;49(4):432-9

Raltegravir susceptibility
Buzon MJ, Marfil S, Puertas MC, Garcia E, Clotet B, Ruiz L, Blanco J, Martinez-Picado J, Cabrera C. Raltegravir susceptibility and fitness progression of HIV type-1 integrase in patients on long-term antiretroviral therapy Antiviral Therapy, 2008;13(7):881-93

Genotypes from Cyprus
Kousiappa I, van de Vijver DA, Demetriades I, Kostrikis LG. Genetic analysis of HIV type 1 strains from newly infected untreated patients in Cyprus: high genetic diversity and low prevalence of drug resistance AIDS Research and Human Retroviruses, 2009 Jan;25(1):23-35

Genotypes from Tanzania
Nyombi BM, Kristiansen KI, Bjune G, Muller F, Holm-Hansen C. Diversity of human immunodeficiency virus type 1 subtypes in Kagera and Kilimanjaro regions, Tanzania AIDS Research and Human Retroviruses, 2008 Jun;24(6):761-9

Genotypes from Iran
Soheilli ZS, Ataiee Z, Tootian S, Zadsar M, Amini S, Abadi K, Jauvin V, Pinson P, Fleury HJ, Samiei S. Presence of HIV-1 CRF35_AD in Iran AIDS Research and Human Retroviruses, 2009 Jan;25(1):123-4

December 3, 2008
Genotypes from Gabon
Caron M, Makuwa M, Souquiere S, Descamps D, Brun-Vezinet F, Kazanji M. Human immunodeficiency virus type 1 seroprevalence and antiretroviral drug resistance-associated mutations in miners in Gabon, central Africa. AIDS Research and Human Retroviruses, 2008 Sep;24(9):1225-8.

Genotypes from Burkina Faso
Tebit DM, Ganame J, Sathiandee K, Nagabila Y, Coulibaly B, Krausslich HG. Diversity of HIV in rural Burkina Faso. Journal of Acquired Immune Deficiency Syndromes 2006 Oct 1;43(2):144-52.

Update of Etravirine DRMs from DUET-1 and DUET-2
Vingerhoets J, Peeters M, Azijn H, Tambuyzer L, Hoogstoel A, Nijs S, de Bethune MP, Picchio G. An update of the list of NNRTI mutations associated with decreased virologic response to etravirine (ETR): multivariate analyses on the pooled DUET-1 and DUET-2 clinical trial data. 17th International HIV Drug Resistance Workshop 2008

Comparison of different regimen types in treating ARV-naive patients
von Wyl V, Yerly S, Boni J, Burgisser P, Klimkait T, Battegay M, Furrer H, Telenti A, Hirschel B, Vernazza PL, Bernasconi E, Rickenbach M, Perrin L, Ledergerber B, Gunthard HF. Emergence of HIV-1 drug resistance in previously untreated patients initiating combination antiretroviral treatment: a comparison of different regimen types. Archives of Internal Medicine 2007 Sep 10;167(16):1782-90.

Darunavir/ritonavir virologic failures in Phase III TITAN trail
De Meyer S, Lathouwers E, Dierynck I, De Paepe E, Van Baelen B, Vangeneugden T, Spinosa-Guzman S, Picchio G, de Bethune MP Characterization of virologic failures on darunavir/ritonavir in the randomized, controlled, Phase III TITAN trial in treatment-experienced patients. 15th Conference on Retroviruses and Opportunistic Infections

Integrase mutations selected with Elvitegravir
Goethals O, Clayton R, Van Ginderen M, Vereycken I, Wagemans E, Geluykens P, Dockx K, Strijbos R, Smits V, Vos A, Meersseman G, Jochmans D, Vermeire K, Schols D, Hallenberger S, Hertogs K. Resistance mutations in HIV-1 integrase selected with Elvitegravir confer reduced susceptibility to a wide range of integrase inhibitors. Journal of Virology 2008 Nov;82(21):10366-74.

TMC278: strategic flexibility explains potency against DRMs
Das K, Bauman JD, Clark AD Jr, Frenkel YV, Lewi PJ, Shatkin AJ, Hughes SH, Arnold E. High-resolution structures of HIV-1 reverse transcriptase/TMC278 complexes: strategic flexibility explains potency against resistance mutations. Proceedings of the National Academy of Sciences of the United States of America 2008 Feb 5;105(5):1466-71.

Rare resistance profile of patient who failed regimen with tenofovir DF
Delaugerre C, Roudiere L, Peytavin G, Rouzioux C, Viard JP, Chaix ML. Selection of a rare resistance profile in an HIV-1-infected patient exhibiting a failure to an antiretroviral regimen including tenofovir DF. Journal of Clinical Virology 2005 Mar;32(3):241-4.

Differences in gag length in different subtypes
Holguin A, Alvarez A, Soriano V. Differences in the length of gag proteins among different HIV type 1 subtypes. AIDS Research and Human Retroviruses 2005 Oct;21(10):886-93.

Genotypes from southern China
Laeyendecker O, Zhang GW, Quinn TC, Garten R, Ray SC, Lai S, Liu W, Chen J, Yu XF. Molecular epidemiology of HIV-1 subtypes in southern China. Journal of Acquired Immune Deficiency Syndromes 2005 Mar 1;38(3):356-62.

Genotypes from western India
Lall M, Gupta RM, Sen S, Kapila K, Tripathy SP, Paranjape RS. Profile of primary resistance in HIV-1-infected treatment-naive individuals from Western India. AIDS Research and Human Retroviruses 2008 Jul;24(7):987-90.

NVP resistance mutations after single-dose NVP in women from Abidjan, Cote d'Ivoire
Toni TD, Masquelier B, Minga A, Anglaret X, Danel C, Coulibaly A, Chenal H, Dabis F, Salamon R, Fleury HJ. Characterization of nevirapine (NVP) resistance mutations and HIV type 1 subtype in women from Abidjan (Cote d'Ivoire) after NVP single-dose prophylaxis of HIV type 1 mother-to-child transmission. AIDS Research and Human Retroviruses 2005 Dec;21(12):1031-4.
September 16, 2008
Integrase L68V/I Associates with E92Q and Increases Resistance
Goodman DD, Hluhanich R, Waters J, Margot NA, Fransen S, Gupta S, Huang W, Parkin N, Borroto-Esoda K, Svarovskala ES, Miller MD, McColl DJ Integrase Inhibitor Resistance Involves Complex Interactions Among Primary and Secondary Resistance Mutations: A Novel Mutation L68V/I Associates with E92Q and Increases Resistance International HIV Drug Resistance Workshop, Sitges, Spain 2008.

Genotypes/Treatments from Mali and Burkina Faso Patients
Sylla M, Chamberland A, Boileau C, Traore HA, Ag-Aboubacrine S, Cisse M, Koala S, Drabo J, Diallo I, Niamba P, Tremblay-Sher D, Machouf N, Rashed S, Nickle DC, Nguyen VK, Tremblay CL; ATARAO Group. Characterization of drug resistance in antiretroviral-treated patients infected with HIV-1 CRF02_AG and AGK subtypes in Mali and Burkina Faso Antiviral Therapy, 2008;13(1):141-8.

Raltegravir Salvage Therapy Failure
Charpentier C, Karmochkine M, Laureillard D, Tisserand P, Belec L, Weiss L, Si-Mohamed A, Piketty C. Drug resistance profiles for the HIV integrase gene in patients failing raltegravir salvage therapy HIV Medicine, 2008 Jul 21.

Transmitted Drug Resistance in Women from Tazania
Somi GR, Kibuka T, Diallo K, Tuhuma T, Bennett DE, Yang C, Kagoma C, Lyamuya EF, Swai RO, Kassim S. Surveillance of transmitted HIV drug resistance among women attending antenatal clinics in Dar es Salaam, Tanzania Antiviral Therapy, 2008;13 Suppl 2:77-82.

Genotypes from Denmark
Andresen BS, Vinner L, Tang S, Bragstad K, Kronborg G, Gerstoft J, Corbet S, Fomsgaard A. Characterization of near full-length genomes of HIV type 1 strains in Denmark: basis for a universal therapeutic vaccine AIDS Research and Human Retroviruses, 2007 Nov;23(11):1442-8.

Evidence for positive epistasis in HIV-1
Bonhoeffer S, Chappey C, Parkin NT, Whitcomb JM, Petropoulos CJ. Evidence for positive epistasis in HIV-1 Science, 2004 Nov 26;306(5701):1547-50. Note: Sequences now available.

Genotypes from Brazilian Blood Donors (Significant Prevalence of B/F1 Recombinants)
Brennan CA, Brites C, Bodelle P, Golden A, Hackett J Jr, Holzmayer V, Swanson P, Vallari A, Yamaguchi J, Devare S, Pedroso C, Ramos A, Badaro R. HIV-1 strains identified in Brazilian blood donors: significant prevalence of B/F1 recombinants AIDS Research and Human Retroviruses, 2007 Nov;23(11):1434-41.

K65R Resistance to Tenofovir - Subtype C
Brenner BG, Oliveira M, Doualla-Bell F, Moisi DD, Ntemgwa M, Frankel F, Essex M, Wainberg MA. HIV-1 subtype C viruses rapidly develop K65R resistance to tenofovir in cell culture AIDS, 2006 Jun 12;20(9):F9-F13.

Evidence of Differential HLA Class I-Mediated Viral Evolution
Brumme ZL, Brumme CJ, Heckerman D, Korber BT, Daniels M, Carlson J, Kadie C, Bhattacharya T, Chui C, Szinger J, Mo T, Hogg RS, Montaner JS, Frahm N, Brander C, Walker BD, Harrigan PR. Evidence of differential HLA class I-mediated viral evolution in functional and accessory/regulatory genes of HIV-1 PLoS Pathogens, 2007 Jul;3(7):e94.

Genotypes from Newly Diagnosed Patients in Argentina, 2003-2005.
Dilernia DA, Gomez AM, Lourtau L, Marone R, Losso MH, Salomon H, Gomez-Carrillo M. HIV type 1 genetic diversity surveillance among newly diagnosed individuals from 2003 to 2005 in Buenos Aires, Argentina AIDS Research and Human Retroviruses, 2007 Oct;23(10):1201-7.

Complex Inter-Recombinant Genotypes from Spain
Holguin, Lospitao E, Lopez M, de Arellano ER, Pena MJ, del Romero J, Martin C, Soriano V. Genetic characterization of complex inter-recombinant HIV-1 strains circulating in Spain and reliability of distinct rapid subtyping tools Journal of Medical Virology, 2008 Mar;80(3):383-91.

Protease Genotypes from Vellore, India
Kandathil AJ, Kannangai R, Abraham OC, Sudarsanam TD, Pulimood SA, Sridharan G. Genotypic resistance profile of HIV-1 protease gene: A preliminary report from Vellore, south India Indian Journal of Medical Microbiology, 2008 Apr-Jun;26(2):151-4.

Genotypes from Nairobi, Kenya with High Proportion of Intersubtype Recombinants
Land AM, Ball TB, Luo M, Rutherford J, Sarna C, Wachihi C, Kimani J, Plummer FA. Full-length HIV type 1 proviral sequencing of 10 highly exposed women from Nairobi, Kenya reveals a high proportion of intersubtype recombinants AIDS Research and Human Retroviruses, 2008 Jun;24(6):865-72.

Persistence of Transmitted Drug Resistance
Little SJ, Frost SD, Wong JK, Smith DM, Pond SL, Ignacio CC, Parkin NT, Petropoulos CJ, Richman DD. Persistence of transmitted drug resistance among subjects with primary human immunodeficiency virus infection Journal of Virology, 2008 Jun;82(11):5510-8.

CRF01_AE Genotypes from Fujian, China.
Liu J, Yue J, Wu S, Yan Y. Polymorphisms and drug resistance analysis of HIV-1 CRF01_AE strains circulating in Fujian Province, China Archives of Virology, 2007;152(10):1799-805.

Protease Genotypes from PI-Naive Chinese Patients
Liu L, Lu HZ, Henry M, Tamalet C. Polymorphism and antiretroviral drug resistance patterns in the protease gene of HIV-1 subtypes infecting PI naive Chinese patients Unpublished

Evaluation of Dried Blood Spot for HIV Drug Resistance Testing
McNulty A, Jennings C, Bennett D, Fitzgibbon J, Bremer JW, Ussery M, Kalish ML, Heneine W, Garcia-Lerma JG. Evaluation of dried blood spots for human immunodeficiency virus type 1 drug resistance testing Journal of Clinical Microbiology, 2007 Feb;45(2):517-21.

Transmitted Drug Resistance in Entebbe, Uganda
Ndembi N, Lyagoba F, Nanteza B, Kushemererwa G, Serwanga J, Katongole-Mbidde E, Grosskurth H, Kaleebu P; Uganda HIV Drug Resistance Working Group. Transmitted Antiretroviral Drug Resistance Surveillance among Newly HIV Type 1-Diagnosed Women Attending an Antenatal Clinic in Entebbe, Uganda AIDS Research and Human Retroviruses, 2008 Jun;24(6):889-95.

Genotypes from Newly-Diagnosed Patients in Portugal
Palma AC, Araujo F, Duque V, Borges F, Paixao MT, Camacho R; Portuguese SPREAD Network. Molecular epidemiology and prevalence of drug resistance-associated mutations in newly diagnosed HIV-1 patients in Portugal Infection, Genetics and Evolution, 2007 Jun;7(3):391-8.

Subtype F Genotypes from Romania
Paraschiv S, Otelea D, Dinu M, Maxim D, Tinischi M. Polymorphisms and resistance mutations in the protease and reverse transcriptase genes of HIV-1 F subtype Romanian strains International Journal of Infectious Diseases, 2007 Mar;11(2):123-8.

Tipranavir/Darunavir Susceptibility
Poveda E, de Mendoza C, Parkin N, Choe S, Garcia-Gasco P, Corral A, Soriano V. Evidence for different susceptibility to tipranavir and darunavir in patients infected with distinct HIV-1 subtypes AIDS, 2008 Mar 12;22(5):611-6.

Phenotypes - Integrase Inhibitor L731,988 and L810,810
Van Baelen K, Clynhens M, Rondelez E, Van Eygen V, Van Den Zegel P, Vermeiren H, Vandenbroucke I, Stuyver LJ. Low Level of Baseline Resistance to Integrase Inhibitors L731,988 and L810,810 in Randomly Selected Subtype B and Non-B HIV-1 Strains International HIV Drug Resistance Workshop, Barbados 2007.
June 9, 2008
NVP Resistance Mutations in Treatment-naive Patients with Subtypes A, C, and D
Church JD, Hudelson SE, Guay LA, Chen S, Hoover DR, Parkin N, Fiscus SA, Mmiro F, Musoke P, Kumwenda N, Jackson JB, Taha TE, Eshleman SH. HIV type 1 variants with nevirapine resistance mutations are rarely detected in antiretroviral drug-naive African women with subtypes A, C, and D. AIDS Research and Human Retroviruses 2008 Jan;24(1):7-14.

Genotypes from Santos, Brazil
de Sa-Filho DJ, Da Silva Soares M, Candido V, Gagliani LH, Cavaliere E, Diaz RS, Caseiro MM. HIV Type 1 pol Gene Diversity and Antiretroviral Drug Resistance Mutations in Santos, Brazil AIDS Research and Human Retroviruses 2008 Mar;24(3):347-53.

Elvitegravir, Raltegravir and L870,810 Phenotypes
Hombrouck A, Voet A, Van Remoortel B, Desadeleer C, De Maeyer M, Debyser Z, Witvrouw M. Mutations in human immunodeficiency virus type 1 integrase confer resistance to the naphthyridine L-870,810 and cross-resistance to the clinical trial drug GS-9137 Antimicrobial Agents and Chemotherapy 2008 Jun;52(6):2069-78.

Genotypes from Nagoya, Japan, 1999-2006
Ibe S, Hattori J, Fujisaki S, Shigemi U, Fujisaki S, Shimizu K, Nakamura K, Kazumi T, Yokomaku Y, Mamiya N, Hamaguchi M, Kaneda T. Trend of drug-resistant HIV type 1 emergence among therapy-naive patients in Nagoya, Japan: an 8-year surveillance from 1999 to 2006 AIDS Research and Human Retroviruses 2008 Jan;24(1):7-14.

Genotypes from Patients who Failed Raltegravir Treatment
Malet I, Delelis O, Valantin MA, Montes B, Soulie C, Wirden M, Tchertanova L, Peytavin G, Reynes J, Mouscadet JF, Katlama C, Calvez V, Marcelin AG. Mutations Associated with Failure of Raltegravir Treatment affect integrase sensitivity to the inhibitor in vitro Antimicrobial Agents and Chemotherapy 2008 Apr;52(4):1351-8.

Genotypes from Patients from KwaZulu Natal, South Africa after First-Time ARV Treatment
Marconi VC, Sunpath H, Lu Z, Gordon M, Koranteng-Apeagyei K, Hampton J, Carpenter S, Giddy J, Ross D, Holst H, Losina E, Walker BD, Kuritzkes DR. Prevalence of HIV-1 drug resistance after failure of a first highly active antiretroviral therapy regimen in KwaZulu Natal, South Africa Clinical Infectious Disease 2008 May 15;46(10):1589-97.

Genotypes from the Southern Central African Republic
Punzi G, Saracino A, Brindicci G, Scarabaggio T, Lagioia A, Angarano G, Monno L. HIV infection and protease genetic diversity in a rural area of the Southern Central African Republic Journal of Medical Virology 2005 Dec;77(4):457-9.

Integrase Inhibitor Phenotypes
Ren C, May S, Miletti T, Bedard J. In vitro Cross-resistance Studies of Five Different Classes of Integrase Inhibitors in Recombinant HIV-1 Antiviral Therapy 2007 12:S3 (abstract no. 1).

The Discovery of Raltegravir
Rowley M. The Discovery of Raltegravir, an Integrase Inhibitor for the Treatment of HIV Infection Progress in Medicinal Chemistry 2008;46:1-28.

Genotypes from Newly Diagnosed Patients from Belgium, 2003-2006
Vercauteren J, Derdelinckx I, Sasse A, Bogaert M, Ceunen H, De Roo A, De Wit S, Deforche K, Echahidi F, Fransen K, Goffard JC, Goubau P, Goudeseune E, Yombi JC, Lacor P, Liesnard C, Moutschen M, Pierard D, Rens R, Schrooten Y, Vaira D, Van Den Heuvel A, Van Der Gucht B, Van Ranst M, Van Wijngaerden E, Vandercam B, Vekemans M, Verhofstede C, Clumeck N, Vandamme AM, Van Laethem K. Prevalence and Epidemiology of HIV Type 1 Drug Resistance among Newly Diagnosed Therapy-Naive Patients in Belgium from 2003 to 2006 AIDS Research and Human Retroviruses 2008 Mar;24(3):355-62.
March 12, 2008
Elvitegravir Genotype-Phenotypes
Shimura K, Kodama E, Sakagami Y, Matsuzaki Y, Watanabe W, Yamataka K, Watanabe Y, Ohata Y, Doi S, Sato M, Kano M, Ikeda S, Matsuoka M. Broad Anti-Retroviral Activity and Resistance Profile of a Novel Human Immunodeficiency Virus Integrase Inhibitor, Elvitegravir (JTK-303/GS-9137). Journal of Virology 2008 Jan;82(2):764-74.

Genotypes from ARV-Experienced Patients in Pune, India
Sen S, Tripathy SP, Patil AA, Chimanpure VM, Paranjape RS. High prevalence of human immunodeficiency virus type 1 drug resistance mutations in antiretroviral treatment-experienced patients from Pune, India. AIDS Research and Human Retroviruses 2007 Oct;23(10):1303-8.

Genotypes from ARV-Naive Patients from the former Soviet Union
Vazquez de Parga E, Rakhmanova A, Perez-Alvarez L, Vinogradova A, Delgado E, Thomson MM, Casado G, Sierra M, Munoz M, Carmona R, Vega Y, Contreras G, Medrano L, Osmanov S, Najera R. Analysis of drug resistance-associated mutations in treatment-naive individuals infected with different genetic forms of HIV-1 circulating in countries of the former Soviet Union. Journal of Medical Virology 2005 Nov;77(3):337-44. Note: Sequences are now in Genbank.

Genotypes from ARV-Naive Patients in Mali
Derache A, Traore O, Koita V, Sylla A, Tubiana R, Simon A, Canestri A, Carcelain G, Katlama C, Calvez V, Cisse M, Marcelin AG. Genetic diversity and drug resistance mutations in HIV type 1 from untreated patients in Bamako, Mali. Antiviral Therapy 2007;12(1):123-9.
Click this link for additional sequences

Genotypes from ARV-Treated and Naive patients in 2 Brazillian Cities
Eyer-Silva WA, Couto-Fernandez JC, Silva-de-Jesus C, Morgado, MG. Prevalence of HIV Type 1 Drug Resistance Mutations in Treatment-Naive and Experienced Patients from Resource-Limited Settings with Universal Access to Antiretroviral Therapy: a Survey in Two Small Brazilian Cities. Unpublished

Genotypes from Honduran Patients at the Beginning of a National ART Program
Lloyd B, O'Connell RJ, Michael NL, Aviles R, Palou E, Hernandez R, Cooley J, Jagodzinski LL. Prevalence of Resistance Mutations in HIV-1 Infected Hondurans at the Beginning of the National Antiretroviral Therapy Program. Unpublished

Prevalence of Primary Antiretroviral Resistance Trends in Korea
Bang JI, Song KH, Kim SH, Cho JH, Park WB, Park SW, Kim HB, Kim NJ, Oh MD, Choe KW. Prevalence of primary antiretroviral resistance: trends in Korea. AIDS Research and Human Retroviruses 2008 Jan;24(1):83-5.

Subtype C and CB Recombinants in Brazil
Brigido LF, Nunes CC, Oliveira CM, Knoll RK, Ferreira JL, Freitas CA, Alves MA, Dias C, Rodrigues R. HIV type 1 subtype C and CB Pol recombinants prevail at the cities with the highest AIDS prevalence rate in Brazil. AIDS Research and Human Retroviruses 2007 Dec;23(12):1579-86.

Genotype-phenotypes (Subtype A - NNRTI)
Eshleman SH, Jones D, Galovich J, Paxinos EE, Petropoulos CJ, Jackson JB, Parkin N. Phenotypic drug resistance patterns in subtype A HIV-1 clones with nonnucleoside reverse transcriptase resistance mutations. AIDS Research and Human Retroviruses 2006 Mar;22(3):289-93.

Genotype - Subtype D from South Africa
Jacobs G, Loxton A, Laten, A, Engelbrecht S. Complete genome sequencing of a non-syncytium-inducing HIV type 1 subtype D strain from Cape Town, South Africa. AIDS Research and Human Retroviruses 2007 Dec;23(12):1575-8.

Subtype C Genotypes from Southern Mozambique
Lahuerta M, Aparicio E, Bardaji A, Marco S, Sacarlal J, Mandomando I, Alonso P, Martinez MA, Menendez C, Naniche D. Rapid Spread and Genetic Diversification of HIV Type 1 Subtype C in a Rural Area of Southern Mozambique. AIDS Research and Human Retroviruses 2008 Feb;24(2):327-35..

Genotypes of Cambodian Patients after ART Prophylaxis Against HIV Perinatal Transmission
Ly N, Phoung V, Min DC, Srey C, Kruy LS, Koum K, Chhum V, Glaziou P, Fleury HJ, Reynes JM. Reverse transcriptase mutations in Cambodian CRF01_AE isolates after antiretroviral prophylaxis against HIV Type 1 perinatal transmission. AIDS Research and Human Retroviruses 2007 Dec;23(12):1563-8.

Genotypes of Children after Exposure to Single-Dose Nevirapine
Martinson NA, Morris L, Gray G, Moodley D, Pillay V, Cohen S, Dhlamini P, Puren A, Bhayroo S, Steyn J, McIntyre JA. Selection and persistence of viral resistance in HIV-infected children after exposure to single-dose nevirapine. Journal of Acquired Immune Deficiency Syndromes 2007 Feb 1;44(2):148-53.

Genotypes from Patients in Yaounde, Cameroon
Ndembi N, Abraha A, Pilch H, Ichimura H, Mbanya D, Kaptue L, Salata R, Arts EJ. Molecular Characterization of Human Immunodeficiency Virus Type 1 (HIV-1) and HIV-2 in Yaounde, Cameroon: Evidence of Major Drug Resistance Mutations in Newly Diagnosed Patients Infected with Subtypes Other than Subtype B. Journal of Clinical Microbiology 2008 Jan;46(1):177-84.

Genotypes of Infants whose Mothers Received Peripartum Nevirapine Prophylaxis in Jos, Nigeria
Ojesina AI, Mullins C, Imade G, Samuels J, Sankale JL, Pam S, Sagay S, Idoko J, Kanki PJ. Characterization of HIV type 1 reverse transcriptase mutations in infants infected by mothers who received peripartum nevirapine prophylaxis in Jos, Nigeria. AIDS Research and Human Retroviruses 2007 Dec;23(12):1587-92.

Genotype Diversity in the Seychelles
Razafindratsimandresy R, Hollanda J, Soares JL, Rousset D, Chetty AP, Reynes JM. HIV type 1 diversity in the Seychelles. AIDS Research and Human Retroviruses 2007 Jun;23(6):761-3.

Genotype Diversity in Shanghai, China
Zhong P, Pan Q, Ning Z, Xue Y, Gong J, Zhen X, Zhou L, Sheng F, Zhang W, Gai J, Cheng H, Yue Q, Xing H, Zhuang M, Lu W, Shao Y, Kang L. Genetic diversity and drug resistance of human immunodeficiency virus type 1 (HIV-1) strains circulating in Shanghai. AIDS Research and Human Retroviruses 2007 May 1;195(9):1283-93.
November 16, 2007


RT K70G+M184V Genotype with Tenofovir/Emtricitabine HAART
Bradshaw D, Malik S, Booth C, Van Houtte M, Pattery T, Waters A, Ainsworth J, Geretti AM. Characterization of a novel drug-resistance pattern associated with the mutations K70G and M184V in HIV-1 reverse transcriptase. Antimicrobial Agents and Chemotherapy 2007 Sep 17.

Elvitegravir (GS-9137) Genotype-Phenotypes
McColl DJ, Fransen S, Gupta S, Parkin N, Margot N, Chuck S, Cheng AK, Miller MD. Resistance and Cross-Resistance to First Generation Integrase Inhibitors: Insights from a Phase 2 Study of Elvitegravir (GS-9137). Antiviral Therapy 2007; 12:S11 (abstract no. 9).

RT 67N+70R+215Y Genotype in Subtype C Patients with ZDV/ddI HAART
Novitsky V, Wester CW, DeGruttola V, Bussmann H, Gaseitsiwe S, Thomas A, Moyo S, Musonda R, Van Widenfelt E, Marlink RG, Essex M. The reverse transcriptase 67N 70R 215Y genotype is the predominant TAM pathway associated with virologic failure among HIV type 1C-infected adults treated with ZDV/ddI-containing HAART in southern Africa. AIDS Research and Human Retroviruses 2007 Jul;23(7):868-78.

Genotypes from Drug-Naive Children in Southern India
Soundararajan L, Karunaianandham R, Jauvin V, Schrive MH, Ramachandran R, Narayanan PR, Fleury HJ, Swaminathan S. Characterization of HIV-1 isolates from antiretroviral drug-naive children in southern India. AIDS Research and Human Retroviruses 2007 Sep;23(9):1119-26.

Subtype G is a Circulating Recombinant Form
Abecasis AB, Lemey P, Vidal N, de Oliveira T, Peeters M, Camacho R, Shapiro B, Rambaut A, Vandamme AM. Recombination confounds the early evolutionary history of human immunodeficiency virus type 1: subtype G is a circulating recombinant form. Journal of Virology 2007 Aug;81(16):8543-51.

Genotypes from Wild Mustached Monkeys
Aghokeng AF, Bailes E, Loul S, Courgnaud V, Mpoudi-Ngolle E, Sharp PM, Delaporte E, Peeters M. Full-length sequence analysis of SIVmus in wild populations of mustached monkeys (Cercopithecus cephus) from Cameroon provides evidence for two co-circulating SIVmus lineages. Virology 2007 Apr 10;360(2):407-18.

Genotypes from Elite Suppressors
Blankson JN, Bailey JR, Thayil S, Yang HC, Lassen K, Lai J, Gandhi SK, Siliciano JD, Williams TM, Siliciano RF. Isolation and characterization of replication-competent human immunodeficiency virus type 1 from a subset of elite suppressors. Journal of Virology 2007 Mar;81(5):2508-18.

Genotypes from Kazakhstan
Eyzaguirre LM, Erasilova IB, Nadai Y, Saad MD, Kovtunenko NG, Gomatos PJ, Zeman VV, Botros BA, Sanchez JL, Birx DL, Earhart KC, Carr JK. Genetic characterization of HIV-1 strains circulating in Kazakhstan. Journal of Acquired Immune Deficiency Syndromes 2007 Sep 1;46(1):19-23.

Genotypes from Recently Infected IDU's in Western China
Liao L, Xing H, Li X, Ruan Y, Zhang Y, Qin G, Shao Y. Genotypic analysis of the protease and reverse transcriptase of HIV type 1 isolates from recently infected injecting drug users in western China. AIDS Research and Human Retroviruses 2007 Aug;23(8):1062-5.

CRF 13_cpx Genotypes from Cameroon
Luk KC, Holzmayer V, Yamaguchi J, Swanson P, Brennan CA, Ngansop C, Mbanya D, Gayum H, Djuidje MN, Ndembi N, Kamdem D, Kaptue L, Gurtler L, Devare SG, Hackett J. Near full-length genome characterization of three additional HIV type 1 CRF13_cpx strains from Cameroon. AIDS Research and Human Retroviruses 2007 Feb;23(2):297-302.

CRF 37_cpx Genotype from Cameroon
Powell RL, Zhao J, Konings FA, Tang S, Ewane L, Burda S, Urbanski MM, Saa DR, Hewlett I, Nyambi PN. Circulating recombinant form (CRF) 37_cpx: an old strain in Cameroon composed of diverse, genetically distant lineages of subtypes A and G. AIDS Research and Human Retroviruses 2007 Jul;23(7):923-33.

CRF 36_cpx Genotypes from Cameroon
Powell RL, Zhao J, Konings FA, Tang S, Nanfack A, Burda S, Urbanski MM, Saa DR, Hewlett I, Nyambi PN. Identification of a novel circulating recombinant form (CRF) 36_cpx in Cameroon that combines two CRFs (01_AE and 02_AG) with ancestral lineages of subtypes A and G. AIDS Research and Human Retroviruses 2007 Aug;23(8):1008-19.

Genotypes from Treatment-Naive Patients in Accra, Ghana
Sagoe KW, Dwidar M, Lartey M, Boamah I, Agyei AA, Hayford AA, Mingle JA, Arens MQ. Variability of the human immunodeficiency virus type 1 polymerase gene from treatment naive patients in Accra, Ghana. Journal of Clinical Virology 2007 Oct;40(2):163-7.

CRF 35_AD Genotypes in IDU's from Afghanistan
Sanders-Buell E, Saad MD, Abed AM, Bose M, Todd CS, Strathdee SA, Botros BA, Safi N, Earhart KC, Scott PT, Michael N, McCutchan FE. A nascent HIV type 1 epidemic among injecting drug users in Kabul, Afghanistan is dominated by complex AD recombinant strain, CRF35_AD. AIDS Research and Human Retroviruses 2007 Jun;23(6):834-9.

SIVcpz Genotypes From Fecal Consensus Sequences
Takehisa J, Kraus MH, Decker JM, Li Y, Keele BF, Bibollet-Ruche F, Zammit KP, Weng Z, Santiago ML, Kamenya S, Wilson ML, Pusey AE, Bailes E, Sharp PM, Shaw GM, Hahn BH. Generation of infectious molecular clones of simian immunodeficiency virus from fecal consensus sequences of wild chimpanzees. Journal of Virology 2007 Jul;81(14):7463-75.

Genotypes of Recently Infected Patients in Cote d'Ivoire
Toni T, Masquelier B, Minga A, Anglaret X, Danel C, Coulibaly A, Chenal H, Dabis F, Salamon R, Fleury HJ, Primo-CI ANRS 1220 Study Group. HIV-1 antiretroviral drug resistance in recently infected patients in Abidjan, Cote d'Ivoire: A 4-year survey, 2002-2006 AIDS Research and Human Retroviruses 2007 Sep;23(9):1155-60.

CRF 34_01B Genotypes from IDU's in Thailand
Tovanabutra S, Kijak GH, Beyrer C, Gammon-Richardson C, Sakkhachornphop S, Vongchak T, Jittiwutikarn J, Razak MH, Sanders-Buell E, Robb ML, Suriyanon V, Birx DL, Michael NL, Celentano DD, McCutchan FE. Identification of CRF34_01B, a second circulating recombinant form unrelated to and more complex than CRF15_01B, among injecting drug users in northern Thailand. AIDS Research and Human Retroviruses 2007 Jun;23(6):829-33.

CRF15_01B-like Genotype from Thailand
Warachit J, Iwabu Y, Li YG, Li GM, Isarangkura P, Ibrahim MS, Balachandra K, Tsuji S, Ikuta K. Aberrant life cycle of human immunodeficiency virus type 1 CRF15_01B-like clinical isolates from Thailand in human CD4+ T-cell lines. Microbes and Infection 2007 Apr;9(4):449-59.
July 25, 2007
Integrase genotypes
Lataillade M, Chiarella J, Kozal, MJ. Natural polymorphism of the HIV-1 integrase gene and mutations associated with integrase inhibitor resistance Antiviral Therapy 2007 12:563-570.

Genotype-treatment in Chile
Rios M, Delgado E, Perez-Alvarez L, Fernandez J, Galvez P, de Parga EV, Yung V, Thomson MM, Najera R Antiretroviral drug resistance and phylogenetic diversity of HIV-1 in Chile Journal of Medical Virology 2007.

RT & PR genotype-treatment in W. Africa
Seyler C, Adje-Toure C, Messou E, Dakoury-Dogbo N, Rouet F, Gabillard D, Nolan M, Toure S, Anglaret X. Impact of genotypic drug resistance mutations on clinical and immunological outcomes in HIV-infected adults on HAART in West Africa AIDS 2007.

ETV (TMC125) genotype-phenotype    View all ETV genotype-phenotype references
Vingerhoets J, Azijn H, Fransen E, De Baere I, Smeulders L, Jochmans D, Andries K, Pauwels R, de Bethune MP. TMC125 displays a high genetic barrier to the development of resistance: evidence from in vitro selection experiments Journal of Virology 2005.

ETV (TMC125) genotype-phenotype    View all ETV genotype-phenotype references
Andries K, Azijn H, Thielemans T, Ludovici D, Kukla M, Heeres J, Janssen P, De Corte B, Vingerhoets J, Pauwels R, de Bethune MP TMC125, a novel next-generation nonnucleoside reverse transcriptase inhibitor active against nonnucleoside reverse transcriptase inhibitor-resistant human immunodeficiency virus type 1 Antimicrobial Agents and Chemotherapy 2005.

Integrase genotypes in Saudi Arabia
Badreddine S, Smith K, Van Zyl H, Bodelle P, Yamaguchi J, Swanson P, Devare SG, Brennan CA Identification and Characterization of HIV Type 1 Subtypes Present in the Kingdom of Saudi Arabia: High Level of Genetic Diversity Found AIDS Research and Human Retroviruses 2007.

ETV (TMC125) genotype-phenotype    View all ETV genotype-phenotype references
Brillant JE, Klumpp K, Swallow S, Mirzadegan T, Cammack N, Heilek-Snyder G. In vitro Resistance Development for a second generation NNRTI: TMC125 XIII International HIV Drug Resistance Workshop, Tenerife 2004.

ETV (TMC125) genotype-phenotype    View all ETV genotype-phenotype references
Das K, Clark AD, Lewi PJ, Heeres J, De Jonge MR, Koymans LM, Vinkers HM, Daeyaert F, Ludovici DW, Kukla MJ, De Corte B, Kavash RW, Ho CY, Ye H, Lichtenstein MA, Andries K, Pauwels R, De Bethune MP, Boyer PL, Clark P, Hughes SH, Janssen PA, Arnold E. Roles of conformational and positional adaptability in structure-based design of TMC125-R165335 (etravirine) and related non-nucleoside reverse transcriptase inhibitors that are highly potent and effective against wild-type and drug-resistant HIV-1 variants Journal of Medicinal Chemistry 2004.

Primary infection genotypes
Eshleman SH, Husnik M, Hudelson S, Donnell D, Huang Y, Huang W, Hart S, Jackson B, Coates T, Chesney M, Koblin B. Antiretroviral drug resistance, HIV-1 tropism, and HIV-1 subtype among men who have sex with men with recent HIV-1 infection AIDS 2007.

R1206 genotype-phenotype
Guoping S, Yu L, Paul A, Hang J, Harris S, Hogg H, Dunn J, Yan JM, Chow E, Cammack N, Klumpp K, Heilek G In Vitro Selection and Characterization of Viruses Resistant to R1206, a Novel Nonnucleoside Reverse Transcriptase Inhibitor 16th International HIV Drug Resistance Workshop, Barbados 2007.

Genotypes in Liaoning, China.
Han X, Zhang M, Dai D, Wang Y, Zhang Z, Liu J, Geng W, Jiang Y, Takebe Y, Shang H Genotypic resistance mutations to antiretroviral drugs in treatment-naive HIV/AIDS patients living in Liaoning Province, China: baseline prevalence and subtype-specific difference AIDS Research and Human Retroviruses 2007.

Single-dose Nevirapine
Kurle SN, Gangakhedkar RR, Sen S, Hayatnagarkar SS, Tripathy SP, Paranjape RS Emergence of NNRTI Drug Resistance Mutations after Single-Dose Nevirapine Exposure in HIV Type 1 Subtype C-Infected Infants in India AIDS Research and Human Retroviruses 2007.

Genotype-treatment in Keyan children
Lwembe R, Ochieng W, Panikulam A, Mongoina CO, Palakudy T, Koizumi Y, Kageyama S, Yamamoto N, Shioda T, Musoke R, Owens M, Songok EM, Okoth FA, Ichimura H Anti-retroviral drug resistance-associated mutations among non-subtype B HIV-1-infected Kenyan children with treatment failure Journal of Medical Virology 2007.

BMS AI424089 Study (Atazanavir +/- Ritonavir)
McGrath D, Wirtz V, Yang R, Mathew M, Rightmire A, Schnittman S. Antiviral Efficacy and Emergent PI Substitutions in Treatment-Naive Subjects Receiving Atazanavir +/- Ritonavir-Based HAART in subtype B and Non-TYpe B HIV-1 Infection International HIV Drug Resistance Workshop, Barbados 2007.

PBMC genotyping
Vicenti I, Razzolini F, Saladini F, Romano L, Zazzi M Use of peripheral blood DNA for genotype antiretroviral resistance testing in drug-naive HIV-infected subjects Clinical Infectious Disease 2007.

ETV (TMC125) genotype-phenotype    View all ETV genotype-phenotype references
Vingerhoets J, De Baere I, Azijn H, Van den Bulcke T, McKenna P, Pattery T, Pauwels R, de Bethune MP Antiviral Activity of TMC125 against a Panel of Site-directed Mutants Encompassing Mutations Observed in vitro and in vivo 11th Conference on Retroviruses and Opportunistic Infections, San Francisco 2004.

ETV (TMC125) genotype-phenotype    View all ETV genotype-phenotype references
Vingerhoets J, Van Marck H, Veldeman J, Peeters M, McKenna P,de Bethune MP Antiviral Activity of TMC125, a Potent Next-Generation Non-Nucleoside Reverse Transcriptase Inhibitor (NNRTI), against >5000 Recombinant Clinical Isolates Exhibiting a Wide Range of NNRTI Resistance 12th International HIV Drug Resistance Workshop 2003.

IMPACT Study (Atazanavir)
Zolopa A, Towner W, Butcher D, Wang S, Maa JF, Seekins D Resistance Profile after Viral Rebound on Atazanavir-Containing Therapy: Focus on Protease Inhibitor Naive Subjects in the IMPACT Study (BMS AI424-128) International HIV Drug Resistance Workshop, Barbados 2007.