Affiliation: National Institutes of Health
- RT-SHIV subpopulation dynamics in infected macaques during anti-HIV therapyWei Shao
Advanced Biomedical Computing Center, SAIC Frederick, Inc, National Cancer Institute at Frederick, Frederick, MD, USA
Retrovirology 6:101. 2009..Bioinformatics tools were constructed to trace individual genomes from the beginning of infection to the end of the treatment...
- PAPNC, a novel method to calculate nucleotide diversity from large scale next generation sequencing dataWei Shao
Advanced Biomedical Computing Center, Leidos Biomedical Research, Inc, Frederick National Laboratory for Cancer Research, Frederick, MD, United States Electronic address
J Virol Methods 203:73-80. 2014..A Perl script implementing this method is available upon request. ..
- Analysis of 454 sequencing error rate, error sources, and artifact recombination for detection of Low-frequency drug resistance mutations in HIV-1 DNAWei Shao
Advanced Biomedical Computing Center, SAIC Frederick, Frederick National Laboratory for Cancer Research, PO Box B, Frederick, MD, USA
Retrovirology 10:18. 2013..We evaluated the performance of 454 sequencing for characterizing HIV populations with defined allele frequencies...
- Genetic diversity of simian immunodeficiency virus encoding HIV-1 reverse transcriptase persists in macaques despite antiretroviral therapyMary Kearney
HIV Drug Resistance Program, National Cancer Institute at Frederick, 1050 Boyles Street, Building 535, Room 109, Frederick, MD 21702 1201, USA
J Virol 85:1067-76. 2011....
- Ultrasensitive allele-specific PCR reveals rare preexisting drug-resistant variants and a large replicating virus population in macaques infected with a simian immunodeficiency virus containing human immunodeficiency virus reverse transcriptaseValerie F Boltz
HIV Drug Resistance Program, National Cancer Institute, Frederick, Maryland, USA
J Virol 86:12525-30. 2012..The rapid increase of 103N mutations from <0.001% to 20% of the viral population indicates that the replicating virus population size in RT-SHIV-infected macaques must be 10(6) or more infected cells per replication cycle...
- HIV populations are large and accumulate high genetic diversity in a nonlinear fashionFrank Maldarelli
HIV Drug Resistance Program, NCI Frederick, NIH, Frederick, Maryland, USA
J Virol 87:10313-23. 2013....
- Suppression of viremia and evolution of human immunodeficiency virus type 1 drug resistance in a macaque model for antiretroviral therapyZandrea Ambrose
HIV Drug Resistance Program, National Cancer Institute, Building 535, Room 123, Frederick, MD 21702, USA
J Virol 81:12145-55. 2007..By contrast, ART effectively suppressed RT-SHIV in 5/6 animals. These data indicate that suboptimal therapy facilitates HIV-1 drug resistance and suggest that this model can be used to investigate persisting viral reservoirs...
- Frequent polymorphism at drug resistance sites in HIV-1 protease and reverse transcriptaseMary Kearney
HIV Drug Resistance Program, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702 1201, USA
AIDS 22:497-501. 2008..Failure of antiretroviral therapy may result from the selection of pre-existing, drug-resistant HIV-1 variants, but the frequency and type of such variants have not been defined...
- Mutations in HIV-1 reverse transcriptase affect the errors made in a single cycle of viral replicationMichael E Abram
HIV Drug Resistance Program, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland, USA
J Virol 88:7589-601. 2014..This could, by implication, affect the generation of drug-resistant mutants and immunological-escape mutants in patients...
- Well-mixed plasma and tissue viral populations in RT-SHIV-infected macaques implies a lack of viral replication in the tissues during antiretroviral therapyMary F Kearney
HIV Dynamics and Replicaton Program, National Cancer Institute at Frederick, 1050 Boyles Street, Building 535, Room 109, Frederick, MD, 21702 1201, USA
Retrovirology 12:93. 2015..Two animals (6760 and 8232) were untreated and two animals (8030 and 8272) were treated with efavirenz, tenofovir, and emtricitabine for 20 weeks...
- Origin of Rebound Plasma HIV Includes Cells with Identical Proviruses That Are Transcriptionally Active before Stopping of Antiretroviral TherapyMary F Kearney
HIV Dynamics and Replication Program, National Cancer Institute, Frederick, Maryland, USA
J Virol 90:1369-76. 2015..These clonally expanding populations of HIV-infected cells may represent an important target for strategies aimed at achieving reservoir reduction and sustained virologic remission...
- Nature, position, and frequency of mutations made in a single cycle of HIV-1 replicationMichael E Abram
HIV Drug Resistance Program, National Cancer Institute at Frederick, Frederick, MD 21702 1201, USA
J Virol 84:9864-78. 2010..The pattern of hot spots seen in lacZalpha in vivo did not match any of the published data obtained when purified RT was used to copy lacZalpha in vitro...