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Matthew J. Gonzales, Eric Delwart, Soo-Yon Rhee, Rose Tsui, Andrew R. Zolopa, Jonathan Taylor, Robert W. Shafer, Lack of Detectable Human Immunodeficiency Virus Type 1 Superinfection during 1072 Person-Years of Observation, The Journal of Infectious Diseases, Volume 188, Issue 3, 1 August 2003, Pages 397–405, https://doi.org/10.1086/376534
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Abstract
We examined consecutive protease (PR) and reverse transcriptase (RT) sequences from human immunodeficiency virus (HIV) type 1-infected individuals, to distinguish changes resulting from sequence evolution due to possible superinfection. Between July 1997 and December 2001, ⩾2 PR and RT samples from 718 persons were sequenced at Stanford University Hospital. Thirty-seven persons had highly divergent sequence pairs characterized by a nucleotide distance of >4.5% in PR or >3.0% in RT. In 16 of 37 sequence pairs, divergence resulted from the loss of mutations during a treatment interruption or from the gain of mutations with reinstitution of treatment. tat and/or gag sequencing of HIV-1 from cryopreserved plasma samples could be performed on 15 of the 21 divergent isolate pairs from persons without a treatment interruption. The sequences of these genes, unaffected by selective drug pressure, were monophyletic. Although HIV-1 PR and RT genes from treated persons may become highly divergent, these changes usually are the result of sequence evolution, rather than superinfection.