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About the Authors:
John K. Bui
Affiliations Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America, Howard Hughes Medical Research Fellows Program, Howard Hughes Medical Institute, Bethesda, Maryland, United States of America
ORCID http://orcid.org/0000-0001-5905-2049
Michele D. Sobolewski
Affiliation: Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
Brandon F. Keele
Affiliation: AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research operated by Leidos Biomedical Research, Inc., Frederick, Maryland, United States of America
Jonathan Spindler
Affiliation: HIV Dynamics and Replication Program, National Cancer Institute, Frederick, Maryland, United States of America
Andrew Musick
Affiliation: HIV Dynamics and Replication Program, National Cancer Institute, Frederick, Maryland, United States of America
ORCID http://orcid.org/0000-0002-0470-9880
Ann Wiegand
Affiliation: HIV Dynamics and Replication Program, National Cancer Institute, Frederick, Maryland, United States of America
Brian T. Luke
Affiliation: Advanced Biomedical Computing Center, Frederick National Laboratory for Cancer Research operated by Leidos Biomedical Research, Inc., Frederick, Maryland, United States of America
ORCID http://orcid.org/0000-0002-2777-7376
Wei Shao
Affiliation: Advanced Biomedical Computing Center, Frederick National Laboratory for Cancer Research operated by Leidos Biomedical Research, Inc., Frederick, Maryland, United States of America
Stephen H. Hughes
Affiliation: HIV Dynamics and Replication Program, National Cancer Institute, Frederick, Maryland, United States of America
John M. Coffin
Affiliation: Department of Molecular Biology and Microbiology, Tufts University, Boston, Massachusetts, United States of America
Mary F. Kearney
Affiliation: HIV Dynamics and Replication Program, National Cancer Institute, Frederick, Maryland, United States of America
John W. Mellors
* E-mail: [email protected]
Affiliation: Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of AmericaAbstract
The major obstacle to curing HIV infection is the persistence of cells with intact proviruses that can produce replication-competent virus. This HIV reservoir is believed to exist primarily in CD4+ T-cells and is stable despite years of suppressive antiretroviral therapy. A potential mechanism for HIV persistence is clonal expansion of infected cells, but how often such clones carry replication-competent proviruses has been controversial. Here, we used single-genome sequencing to probe for identical HIV sequence matches among viruses recovered in different viral outgrowth cultures and between the sequences of outgrowth viruses and proviral or intracellular HIV...