pol gene diversity of five human immunodeficiency virus type 1 subtypes: evidence for naturally occurring mutations that contribute to drug resistance, limited recombination patterns, and common ancestry for subtypes B and D

Abstract

Naturally occurring mutations in the polymerase gene of human immunodeficiency virus type 1 (HIV-1) have important implications for therapy and the outcome of clinical studies. Using 42 virus isolates obtained from the UNAIDS sample collection, we analyzed the protease (99 amino acids [aa]) and the first 297 aa of reverse transcriptase (RT) coding regions. Based on the V3 sequence analysis, the collection includes subtype A (n ‫؍‬ 5), subtype B (n ‫؍‬ 12), subtype C (n ‫؍‬ 1), subtype D (n ‫؍‬ 11), and subtype E (n ‫؍‬ 13) viruses. Of the 42 protease genes, 37 contained naturally occurring mutations at positions in the gene that contribute to resistance to protease inhibitors (indinavir, saquinavir, ritonavir, and nelfinavir) in clade B isolates. The phenotypic effect of these substitutions in non-B isolates is unclear. The 5half RT coding region of the 42 isolates was found to be less variable, although 19 of the 42 RT sequences contained amino acid substitutions known to contribute to nucleoside and/or nonnucleoside drug resistance. Since the virus isolates were obtained in 1992, it is unlikely that the infected subjects received protease inhibitors, but we found evidence that one subject acquired a zidovudine (AZT)-resistant HIV-1 strain from a contact who had received AZT. Phylogenetic analysis identified five subtype pol clusters: A, B, C, D, and A. Comparison of env and pol sequences of the same viruses showed no more recombination events than were already identified on the basis of gag/env comparison (M. Cornelissen, G. Kampinga, F. Zorgdrager, J. Goudsmit, and the UNAIDS Network for HIV Isolation and Characterization, J. Virol. 70:8209-8212, 1996). In one of the known recombinants, a crossover site between subtypes A and C could be identified, and in another, a crossover site could not be identified due to lack of a reference subtype F pol sequence. We analyzed the ds/da ratio of gag, pol, and env sequences of 35 isolates, excluding the recombinants. Our analysis showed that gag and pol are subjected to purifying selection with an average ds/da ratio above 1, independent of the subtype and in contrast with V3 (ds/da Ϸ 1). Based on the low ds/da ratio of the intergroup analysis of A/E and B/D gag and pol sequences, we analyzed the evolutionary relation between subtypes B and D in more detail by constructing separate phylogenetic trees for synonymous and nonsynonymous substitutions. Our analysis suggests a common ancestry for subtypes B and D that is distinct from that of subtypes A and E.

Clinical relevance of viral dynamics and genotypes in hepatitis B virus

“…Mutations in these variants occur in the gene encoding the HIV-1 polymerase because of the lack of proof-reading ability of the viral reverse transcriptase. 14,15 A similar lack of proof-reading ability for the hepadnaviral polymerase has been reported. 16,17 It has been calculated that the annual hepadnaviral polymerase mutation rate of approximately 2 ¥ 10 -4 base substitutions per site is similar to that of the retroviral gag gene 18 but the nature of the overlapping reading frames of HBV may restrict the final number of viable viral mutants.…”

Performance of two commercially available sequence‐based HIV‐1 genotyping systems for the detection of drug resistance against HIV type 1 group M subtypes

“…Such laboratory-based research tests are reliant on polymerase chain reaction (PCR) amplification of HIV-1 template sequences and must therefore take account of HIV-1 sequence diversity to reduce or eliminate primertemplate mismatches. Thus, we assembled a panel of 35 HIV-1 isolates representing Group M env subtypes A-J (xpol subtypes A, B, C, D, and A 0 ) [Cornelissen et al, 1997], to assess the impact of genetic subtype on the ViroSeq (Version 2) Sequence-Based HIV-1 Genotyping System (Applied Biosystems), the TruGene HIV-1 Genotyping Kit (Visible Genetics), and seven DNA PCR protocols currently used in our laboratory for clinical applications.…”

Role of mathematical modeling on the optimal control of HIV‐1 pathogenesis

“…One is the expressive error‐prone nature of the viral reverse transcriptase, which lacks proofreading functions that result in nucleotide substitutions, deletions and insertions. A rate of 3.4 · 10 −5 misincorporation per replication cycle in vivo has been suggested 38, 77…”

“…The study of this multidisciplinary area, which is strongly characterized by its dynamic nature mainly because of new inputs related not only to drug chemotherapy research,60–61 new cellular and molecular immunology discoveries,62–74 but also to a better understanding of the pathogenic agent structure14, 75–82 and activity24, 25, 83–87 are continuously produced. Moreover, these must necessarily encompass the hard task of mathematical translation of biology into mathematics.…”