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Items: 1 to 50 of 231

1.

Trends in Pretreatment HIV-1 Drug Resistance in Antiretroviral Therapy-naive Adults in South Africa, 2000-2016: A Pooled Sequence Analysis.

Chimukangara B, Lessells RJ, Rhee SY, Giandhari J, Kharsany ABM, Naidoo K, Lewis L, Cawood C, Khanyile D, Ayalew KA, Diallo K, Samuel R, Hunt G, Vandormael A, Stray-Pedersen B, Gordon M, Makadzange T, Kiepiela P, Ramjee G, Ledwaba J, Kalimashe M, Morris L, Parikh UM, Mellors JW, Shafer RW, Katzenstein D, Moodley P, Gupta RK, Pillay D, Abdool Karim SS, de Oliveira T.

EClinicalMedicine. 2019 Mar 18;9:26-34. doi: 10.1016/j.eclinm.2019.03.006. eCollection 2019 Mar.

2.

National and International Dimensions of Human Immunodeficiency Virus-1 Sequence Clusters in a Northern California Clinical Cohort.

Rhee SY, Magalis BR, Hurley L, Silverberg MJ, Marcus JL, Slome S, Kosakovsky Pond SL, Shafer RW.

Open Forum Infect Dis. 2019 Mar 14;6(4):ofz135. doi: 10.1093/ofid/ofz135. eCollection 2019 Apr.

3.

Multiplex Solid-Phase Melt Curve Analysis for the Point-of-Care Detection of HIV-1 Drug Resistance.

Clutter DS, Mazarei G, Sinha R, Manasa J, Nouhin J, LaPrade E, Bolouki S, Tzou PL, Hannita-Hui J, Sahoo MK, Kuimelis P, Kuimelis RG, Pinsky BA, Schoolnik GK, Hassibi A, Shafer RW.

J Mol Diagn. 2019 Jul;21(4):580-592. doi: 10.1016/j.jmoldx.2019.02.005. Epub 2019 Apr 23.

PMID:
31026601
4.

Curbing the rise of HIV drug resistance in low-income and middle-income countries: the role of dolutegravir-containing regimens.

Inzaule SC, Hamers RL, Doherty M, Shafer RW, Bertagnolio S, Rinke de Wit TF.

Lancet Infect Dis. 2019 Mar 19. pii: S1473-3099(18)30710-2. doi: 10.1016/S1473-3099(18)30710-2. [Epub ahead of print] Review.

PMID:
30902440
5.

Reply to Ambrosioni et al.

Günthard HF, Calvez V, Paredes R, Pillay D, Shafer RW, Wensing AM, Jacobsen DM, Richman DD.

Clin Infect Dis. 2019 May 17;68(11):1977-1978. doi: 10.1093/cid/ciy1022. No abstract available.

PMID:
30520997
6.

Moderate-to-High Levels of Pretreatment HIV Drug Resistance in KwaZulu-Natal Province, South Africa.

Chimukangara B, Kharsany ABM, Lessells RJ, Naidoo K, Rhee SY, Manasa J, Gräf T, Lewis L, Cawood C, Khanyile D, Diallo K, Ayalew KA, Shafer RW, Hunt G, Pillay D, Abdool SK, de Oliveira T.

AIDS Res Hum Retroviruses. 2019 Feb;35(2):129-138. doi: 10.1089/AID.2018.0202. Epub 2019 Jan 7.

PMID:
30430843
7.

The clinical implications of pretreatment drug resistance -- a moving target.

Shafer RW, Frenkel LM.

Clin Infect Dis. 2018 Oct 15. doi: 10.1093/cid/ciy895. [Epub ahead of print] No abstract available.

PMID:
30321316
8.

Baseline dasabuvir resistance in Hepatitis C virus from the genotypes 1, 2 and 3 and modeling of the NS5B-dasabuvir complex by the in silico approach.

Akaberi D, Bergfors A, Kjellin M, Kameli N, Lidemalm L, Kolli B, Shafer RW, Palanisamy N, Lennerstrand J.

Infect Ecol Epidemiol. 2018 Oct 5;8(1):1528117. doi: 10.1080/20008686.2018.1528117. eCollection 2018.

9.

Geographically-stratified HIV-1 group M pol subtype and circulating recombinant form sequences.

Rhee SY, Shafer RW.

Sci Data. 2018 Jul 31;5:180148. doi: 10.1038/sdata.2018.148.

10.

Human Immunodeficiency Virus Drug Resistance: 2018 Recommendations of the International Antiviral Society-USA Panel.

Günthard HF, Calvez V, Paredes R, Pillay D, Shafer RW, Wensing AM, Jacobsen DM, Richman DD.

Clin Infect Dis. 2019 Jan 7;68(2):177-187. doi: 10.1093/cid/ciy463.

11.

Selection analyses of paired HIV-1 gag and gp41 sequences obtained before and after antiretroviral therapy.

Tzou PL, Rhee SY, Pond SLK, Manasa J, Shafer RW.

Sci Data. 2018 Jul 24;5:180147. doi: 10.1038/sdata.2018.147.

12.

Trends in the Molecular Epidemiology and Genetic Mechanisms of Transmitted Human Immunodeficiency Virus Type 1 Drug Resistance in a Large US Clinic Population.

Rhee SY, Clutter D, Fessel WJ, Klein D, Slome S, Pinsky BA, Marcus JL, Hurley L, Silverberg MJ, Kosakovsky Pond SL, Shafer RW.

Clin Infect Dis. 2019 Jan 7;68(2):213-221. doi: 10.1093/cid/ciy453.

13.

Comparison of an In Vitro Diagnostic Next-Generation Sequencing Assay with Sanger Sequencing for HIV-1 Genotypic Resistance Testing.

Tzou PL, Ariyaratne P, Varghese V, Lee C, Rakhmanaliev E, Villy C, Yee M, Tan K, Michel G, Pinsky BA, Shafer RW.

J Clin Microbiol. 2018 May 25;56(6). pii: e00105-18. doi: 10.1128/JCM.00105-18. Print 2018 Jun.

14.

Diff-seq: A high throughput sequencing-based mismatch detection assay for DNA variant enrichment and discovery.

Aggeli D, Karas VO, Sinnott-Armstrong NA, Varghese V, Shafer RW, Greenleaf WJ, Sherlock G.

Nucleic Acids Res. 2018 Apr 20;46(7):e42. doi: 10.1093/nar/gky022.

15.

Human Immunodeficiency Virus Type 1 Drug Resistance Mutations Update.

Shafer RW.

J Infect Dis. 2017 Dec 1;216(suppl_9):S843-S846. doi: 10.1093/infdis/jix398.

16.

Evolution of gag and gp41 in Patients Receiving Ritonavir-Boosted Protease Inhibitors.

Manasa J, Varghese V, Pond SLK, Rhee SY, Tzou PL, Fessel WJ, Jang KS, White E, Rögnvaldsson T, Katzenstein DA, Shafer RW.

Sci Rep. 2017 Sep 14;7(1):11559. doi: 10.1038/s41598-017-11893-8.

17.

Prevalence of Drug-Resistant Minority Variants in Untreated HIV-1-Infected Individuals With and Those Without Transmitted Drug Resistance Detected by Sanger Sequencing.

Clutter DS, Zhou S, Varghese V, Rhee SY, Pinsky BA, Jeffrey Fessel W, Klein DB, Spielvogel E, Holmes SP, Hurley LB, Silverberg MJ, Swanstrom R, Shafer RW.

J Infect Dis. 2017 Aug 1;216(3):387-391. doi: 10.1093/infdis/jix338.

18.

Collaborative update of a rule-based expert system for HIV-1 genotypic resistance test interpretation.

Paredes R, Tzou PL, van Zyl G, Barrow G, Camacho R, Carmona S, Grant PM, Gupta RK, Hamers RL, Harrigan PR, Jordan MR, Kantor R, Katzenstein DA, Kuritzkes DR, Maldarelli F, Otelea D, Wallis CL, Schapiro JM, Shafer RW.

PLoS One. 2017 Jul 28;12(7):e0181357. doi: 10.1371/journal.pone.0181357. eCollection 2017.

19.

Mutational Correlates of Virological Failure in Individuals Receiving a WHO-Recommended Tenofovir-Containing First-Line Regimen: An International Collaboration.

Rhee SY, Varghese V, Holmes SP, Van Zyl GU, Steegen K, Boyd MA, Cooper DA, Nsanzimana S, Saravanan S, Charpentier C, de Oliveira T, Etiebet MA, Garcia F, Goedhals D, Gomes P, Günthard HF, Hamers RL, Hoffmann CJ, Hunt G, Jiamsakul A, Kaleebu P, Kanki P, Kantor R, Kerschberger B, Marconi VC, D'amour Ndahimana J, Ndembi N, Ngo-Giang-Huong N, Rokx C, Santoro MM, Schapiro JM, Schmidt D, Seu L, Sigaloff KCE, Sirivichayakul S, Skhosana L, Sunpath H, Tang M, Yang C, Carmona S, Gupta RK, Shafer RW.

EBioMedicine. 2017 Apr;18:225-235. doi: 10.1016/j.ebiom.2017.03.024. Epub 2017 Mar 19.

20.

NucAmino: a nucleotide to amino acid alignment optimized for virus gene sequences.

Tzou PL, Huang X, Shafer RW.

BMC Bioinformatics. 2017 Mar 1;18(1):138. doi: 10.1186/s12859-017-1555-6.

21.

2017 Update of the Drug Resistance Mutations in HIV-1.

Wensing AM, Calvez V, Günthard HF, Johnson VA, Paredes R, Pillay D, Shafer RW, Richman DD.

Top Antivir Med. 2017 Dec/Jan;24(4):132-133.

22.

Correction: More effective drugs lead to harder selective sweeps in the evolution of drug resistance in HIV-1.

Feder AF, Rhee SY, Holmes SP, Shafer RW, Petrov DA, Pennings PS.

Elife. 2017 Jan 19;6. pii: e24879. doi: 10.7554/eLife.24879. No abstract available.

23.

Occult HIV-1 drug resistance to thymidine analogues following failure of first-line tenofovir combined with a cytosine analogue and nevirapine or efavirenz in sub Saharan Africa: a retrospective multi-centre cohort study.

Gregson J, Kaleebu P, Marconi VC, van Vuuren C, Ndembi N, Hamers RL, Kanki P, Hoffmann CJ, Lockman S, Pillay D, de Oliveira T, Clumeck N, Hunt G, Kerschberger B, Shafer RW, Yang C, Raizes E, Kantor R, Gupta RK.

Lancet Infect Dis. 2017 Mar;17(3):296-304. doi: 10.1016/S1473-3099(16)30469-8. Epub 2016 Dec 1.

24.

HIV-1 drug resistance and resistance testing.

Clutter DS, Jordan MR, Bertagnolio S, Shafer RW.

Infect Genet Evol. 2016 Dec;46:292-307. doi: 10.1016/j.meegid.2016.08.031. Epub 2016 Aug 29. Review.

25.

Evaluation of the Aptima HIV-1 Quant Dx Assay Using Plasma and Dried Blood Spots.

Sahoo MK, Varghese V, White E, Winslow M, Katzenstein DA, Shafer RW, Pinsky BA.

J Clin Microbiol. 2016 Oct;54(10):2597-601. doi: 10.1128/JCM.01569-16. Epub 2016 Aug 17.

26.

Surveillance of HIV Transmitted Drug Resistance in Latin America and the Caribbean: A Systematic Review and Meta-Analysis.

Avila-Rios S, Sued O, Rhee SY, Shafer RW, Reyes-Teran G, Ravasi G.

PLoS One. 2016 Jun 29;11(6):e0158560. doi: 10.1371/journal.pone.0158560. eCollection 2016. Review.

27.

HIV-1 Protease, Reverse Transcriptase, and Integrase Variation.

Rhee SY, Sankaran K, Varghese V, Winters MA, Hurt CB, Eron JJ, Parkin N, Holmes SP, Holodniy M, Shafer RW.

J Virol. 2016 Jun 10;90(13):6058-6070. doi: 10.1128/JVI.00495-16. Print 2016 Jul 1.

28.

Q148N, a Novel Integrase Inhibitor Resistance Mutation Associated with Low-Level Reduction in Elvitegravir Susceptibility.

Varghese V, Pinsky BA, Smith DS, Klein D, Shafer RW.

AIDS Res Hum Retroviruses. 2016 Jul;32(7):702-4. doi: 10.1089/AID.2016.0038. Epub 2016 Apr 19.

29.

More effective drugs lead to harder selective sweeps in the evolution of drug resistance in HIV-1.

Feder AF, Rhee SY, Holmes SP, Shafer RW, Petrov DA, Pennings PS.

Elife. 2016 Feb 15;5. pii: e10670. doi: 10.7554/eLife.10670. Erratum in: Elife. 2017 Jan 19;6:.

30.

Genetic Variability of HIV-1 for Drug Resistance Assay Development.

Clutter DS, Rojas Sánchez P, Rhee SY, Shafer RW.

Viruses. 2016 Feb 11;8(2). pii: E48. doi: 10.3390/v8020048.

31.

Response to Therapy in Antiretroviral Therapy-Naive Patients With Isolated Nonnucleoside Reverse Transcriptase Inhibitor-Associated Transmitted Drug Resistance.

Clutter DS, Fessel WJ, Rhee SY, Hurley LB, Klein DB, Ioannidis JP, Silverberg MJ, Shafer RW.

J Acquir Immune Defic Syndr. 2016 Jun 1;72(2):171-6. doi: 10.1097/QAI.0000000000000942.

32.

HIV-1 Drug Resistance Mutations: Potential Applications for Point-of-Care Genotypic Resistance Testing.

Rhee SY, Jordan MR, Raizes E, Chua A, Parkin N, Kantor R, Van Zyl GU, Mukui I, Hosseinipour MC, Frenkel LM, Ndembi N, Hamers RL, Rinke de Wit TF, Wallis CL, Gupta RK, Fokam J, Zeh C, Schapiro JM, Carmona S, Katzenstein D, Tang M, Aghokeng AF, De Oliveira T, Wensing AM, Gallant JE, Wainberg MA, Richman DD, Fitzgibbon JE, Schito M, Bertagnolio S, Yang C, Shafer RW.

PLoS One. 2015 Dec 30;10(12):e0145772. doi: 10.1371/journal.pone.0145772. eCollection 2015.

33.

2015 Update of the Drug Resistance Mutations in HIV-1.

Wensing AM, Calvez V, Günthard HF, Johnson VA, Paredes R, Pillay D, Shafer RW, Richman DD.

Top Antivir Med. 2015 Oct-Nov;23(4):132-41.

34.

Modifying Antiretroviral Therapy in Virologically Suppressed HIV-1-Infected Patients.

Collins SE, Grant PM, Shafer RW.

Drugs. 2016 Jan;76(1):75-98. doi: 10.1007/s40265-015-0515-6. Review.

35.

Correction: Geographic and Temporal Trends in the Molecular Epidemiology and Genetic Mechanisms of Transmitted HIV-1 Drug Resistance: An Individual-Patient- and Sequence-Level Meta-Analysis.

Rhee SY, Blanco JL, Jordan MR, Taylor J, Lemey P, Varghese V, Hamers RL, Bertagnolio S, de Wit TF, Aghokeng AF, Albert J, Avi R, Avila-Rios S, Bessong PO, Brooks JI, Boucher CA, Brumme ZL, Busch MP, Bussmann H, Chaix ML, Chin BS, D'Aquin TT, De Gascun CF, Derache A, Descamps D, Deshpande AK, Djoko CF, Eshleman SH, Fleury H, Frange P, Fujisaki S, Harrigan PR, Hattori J, Holguin A, Hunt GM, Ichimura H, Kaleebu P, Katzenstein D, Kiertiburanakul S, Kim JH, Kim SS, Li Y, Lutsar I, Morris L, Ndembi N, Kee PN, Paranjape RS, Peeters M, Poljak M, Price MA, Ragonnet-Cronin ML, Reyes-Terán G, Rolland M, Sirivichayakul S, Smith DM, Soares MA, Soriano VV, Ssemwanga D, Stanojevic M, Stefani MA, Sugiura W, Sungkanuparph S, Tanuri A, Tee KK, Truong HM, van de Vijver DA, Vidal N, Yang C, Yang R, Yebra G, Ioannidis JP, Vandamme AM, Shafer RW.

PLoS Med. 2015 Jun 1;12(6):e1001845. doi: 10.1371/journal.pmed.1001845. eCollection 2015 Jun. No abstract available.

36.

Geographic and temporal trends in the molecular epidemiology and genetic mechanisms of transmitted HIV-1 drug resistance: an individual-patient- and sequence-level meta-analysis.

Rhee SY, Blanco JL, Jordan MR, Taylor J, Lemey P, Varghese V, Hamers RL, Bertagnolio S, Rinke de Wit TF, Aghokeng AF, Albert J, Avi R, Avila-Rios S, Bessong PO, Brooks JI, Boucher CA, Brumme ZL, Busch MP, Bussmann H, Chaix ML, Chin BS, D'Aquin TT, De Gascun CF, Derache A, Descamps D, Deshpande AK, Djoko CF, Eshleman SH, Fleury H, Frange P, Fujisaki S, Harrigan PR, Hattori J, Holguin A, Hunt GM, Ichimura H, Kaleebu P, Katzenstein D, Kiertiburanakul S, Kim JH, Kim SS, Li Y, Lutsar I, Morris L, Ndembi N, Ng KP, Paranjape RS, Peeters M, Poljak M, Price MA, Ragonnet-Cronin ML, Reyes-Terán G, Rolland M, Sirivichayakul S, Smith DM, Soares MA, Soriano VV, Ssemwanga D, Stanojevic M, Stefani MA, Sugiura W, Sungkanuparph S, Tanuri A, Tee KK, Truong HM, van de Vijver DA, Vidal N, Yang C, Yang R, Yebra G, Ioannidis JP, Vandamme AM, Shafer RW.

PLoS Med. 2015 Apr 7;12(4):e1001810. doi: 10.1371/journal.pmed.1001810. eCollection 2015 Apr. Erratum in: PLoS Med. 2015 Jun;12(6):e1001845.

37.

Lower prevalence of drug resistance mutations at first-line virological failure to first-line therapy with atripla vs. tenofovir + emtricitabine/lamivudine + efavirenz administered on a multiple tablet therapy.

Blanco JL, Montaner JS, Marconi VC, Santoro MM, Campos-Loza AE, Shafer RW, Miller MD, Paredes R, Harrigan R, Nguyen ML, Perno CF, Gonzalez-Hernandez LA, Gatell JM.

AIDS. 2014 Nov 13;28(17):2531-9. doi: 10.1097/QAD.0000000000000424.

PMID:
25574957
38.

Impact of drug resistance-associated amino acid changes in HIV-1 subtype C on susceptibility to newer nonnucleoside reverse transcriptase inhibitors.

Basson AE, Rhee SY, Parry CM, El-Khatib Z, Charalambous S, De Oliveira T, Pillay D, Hoffmann C, Katzenstein D, Shafer RW, Morris L.

Antimicrob Agents Chemother. 2015 Feb;59(2):960-71. doi: 10.1128/AAC.04215-14. Epub 2014 Nov 24.

39.

A uniquely prevalent nonnucleoside reverse transcriptase inhibitor resistance mutation in Russian subtype A HIV-1 viruses.

Kolomeets AN, Varghese V, Lemey P, Bobkova MR, Shafer RW.

AIDS. 2014 Nov 13;28(17):F1-8. doi: 10.1097/QAD.0000000000000485.

40.

Similar prevalence of low-abundance drug-resistant variants in treatment-naive patients with genotype 1a and 1b hepatitis C virus infections as determined by ultradeep pyrosequencing.

Margeridon-Thermet S, Le Pogam S, Li L, Liu TF, Shulman N, Shafer RW, Najera I.

PLoS One. 2014 Aug 20;9(8):e105569. doi: 10.1371/journal.pone.0105569. eCollection 2014.

41.

2014 Update of the drug resistance mutations in HIV-1.

Wensing AM, Calvez V, Günthard HF, Johnson VA, Paredes R, Pillay D, Shafer RW, Richman DD.

Top Antivir Med. 2014 Jun-Jul;22(3):642-50.

42.

Genome-wide association study of peripheral neuropathy with D-drug-containing regimens in AIDS Clinical Trials Group protocol 384.

Leger PD, Johnson DH, Robbins GK, Shafer RW, Clifford DB, Li J, McLaren PJ, Haas DW.

J Neurovirol. 2014 Jun;20(3):304-8. doi: 10.1007/s13365-014-0235-9. Epub 2014 Feb 20.

43.

HIV-1 transmission networks in a small world.

Pennings PS, Holmes SP, Shafer RW.

J Infect Dis. 2014 Jan 15;209(2):180-2. doi: 10.1093/infdis/jit525. Epub 2013 Oct 22. No abstract available.

44.

Site nurse-initiated adherence and symptom support telephone calls for HIV-positive individuals starting antiretroviral therapy, ACTG 5031: substudy of ACTG 384.

Robbins GK, Testa MA, Su M, Safren SA, Morse G, Lammert S, Shafer RW, Reynolds NR, Chesney MA.

HIV Clin Trials. 2013 Sep-Oct;14(5):235-53. doi: 10.1310/hct1405-235.

45.

Non-nucleoside reverse transcriptase inhibitor (NNRTI) cross-resistance: implications for preclinical evaluation of novel NNRTIs and clinical genotypic resistance testing.

Melikian GL, Rhee SY, Varghese V, Porter D, White K, Taylor J, Towner W, Troia P, Burack J, Dejesus E, Robbins GK, Razzeca K, Kagan R, Liu TF, Fessel WJ, Israelski D, Shafer RW.

J Antimicrob Chemother. 2014 Jan;69(1):12-20. doi: 10.1093/jac/dkt316. Epub 2013 Aug 9.

46.

Trends in Genotypic HIV-1 Antiretroviral Resistance between 2006 and 2012 in South African Patients Receiving First- and Second-Line Antiretroviral Treatment Regimens.

Van Zyl GU, Liu TF, Claassen M, Engelbrecht S, de Oliveira T, Preiser W, Wood NT, Travers S, Shafer RW.

PLoS One. 2013 Jun 26;8(6):e67188. doi: 10.1371/journal.pone.0067188. Print 2013.

47.

Prototypical Recombinant Multi-Protease-Inhibitor-Resistant Infectious Molecular Clones of Human Immunodeficiency Virus Type 1.

Varghese V, Mitsuya Y, Fessel WJ, Liu TF, Melikian GL, Katzenstein DA, Schiffer CA, Holmes SP, Shafer RW.

Antimicrob Agents Chemother. 2013 Sep;57(9):4290-4299. doi: 10.1128/AAC.00614-13. Epub 2013 Jun 24.

48.

Nucleoside reverse transcriptase inhibitor resistance mutations associated with first-line stavudine-containing antiretroviral therapy: programmatic implications for countries phasing out stavudine.

Tang MW, Rhee SY, Bertagnolio S, Ford N, Holmes S, Sigaloff KC, Hamers RL, de Wit TF, Fleury HJ, Kanki PJ, Ruxrungtham K, Hawkins CA, Wallis CL, Stevens W, van Zyl GU, Manosuthi W, Hosseinipour MC, Ngo-Giang-Huong N, Belec L, Peeters M, Aghokeng A, Bunupuradah T, Burda S, Cane P, Cappelli G, Charpentier C, Dagnra AY, Deshpande AK, El-Katib Z, Eshleman SH, Fokam J, Gody JC, Katzenstein D, Koyalta DD, Kumwenda JJ, Lallemant M, Lynen L, Marconi VC, Margot NA, Moussa S, Ndung'u T, Nyambi PN, Orrell C, Schapiro JM, Schuurman R, Sirivichayakul S, Smith D, Zolfo M, Jordan MR, Shafer RW.

J Infect Dis. 2013 Jun 15;207 Suppl 2:S70-7. doi: 10.1093/infdis/jit114.

49.

In vitro HIV-1 evolution in response to triple reverse transcriptase inhibitors & in silico phenotypic analysis.

Rath BA, Yousef KP, Katzenstein DK, Shafer RW, Schütte C, von Kleist M, Merigan TC.

PLoS One. 2013 Apr 17;8(4):e61102. doi: 10.1371/journal.pone.0061102. Print 2013.

50.

Update of the drug resistance mutations in HIV-1: March 2013.

Johnson VA, Calvez V, Gunthard HF, Paredes R, Pillay D, Shafer RW, Wensing AM, Richman DD.

Top Antivir Med. 2013 Feb-Mar;21(1):6-14. No abstract available. Erratum in: Top Antivir Med. 2013 Apr-May;21(2):46.

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