Molecular Characterization of a Highly Divergent HIV Type 1 Isolate Obtained Early in the AIDS Epidemic from the Democratic Republic of Congo

Gao, Feng; Trask, Stanley A.; Hui, Huxong; Мамаева, О. К.; Chen, Yalu; Theodore, Theodore S.; Foley, Brian; Korber, Bette T.; Shaw, George M.; Hahn, Beatrice H.

doi:10.1089/088922201316912826

Cited by 13 publications

(8 citation statements)

References 15 publications

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“…We also employed our method to investigate a highly divergent HIV-1 variant from the Democratic Republic of Congo (DRC) [ 50 , 51 ]. Although the DRC strain was positioned differently in phylogenetic trees of different genome regions (similar to subtype J in Figure 6b ), it did not cluster with any of the know subtypes and hence it was suggested as a candidate for a new subtype [ 50 ]. As reference strains, we included the sequence set for which no significant recombination could be detected (see above, including subtype A2, B, C, DUG114, H, and CRF02_AG).…”

Section: Resultsmentioning

confidence: 99%

“…This is illustrated by the highly divergent HIV-1 variant from the DRC. Although phylogenetic inhomogeneity was originally noted for this strain, the absence of strong bootstrap support for the different clustering deeper in the tree led to the suggestion that it could be a new subtype [ 50 ]. However, our test indicates that there is more phylogenetic inhomogeneity than expected by chance and thus classifies the DRC strain as a probable recombinant lineage.…”

Section: Discussionmentioning

confidence: 99%

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Identifying recombinants in human and primate immunodeficiency virus sequence alignments using quartet scanning

et al. 2009

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Background: Recombination has a profound impact on the evolution of viruses, but characterizing recombination patterns in molecular sequences remains a challenging endeavor. Despite its importance in molecular evolutionary studies, identifying the sequences that exhibit such patterns has received comparatively less attention in the recombination detection framework. Here, we extend a quartet-mapping based recombination detection method to enable identification of recombinant sequences without prior specifications of either query and reference sequences. Through simulations we evaluate different recombinant identification statistics and significance tests. We compare the quartet approach with triplet-based methods that employ additional heuristic tests to identify parental and recombinant sequences.

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Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Identifying recombinants in human and primate immunodeficiency virus sequence alignments using quartet scanning

et al. 2009

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“…However, this method is time consuming and labor intensive. Recently, we used the long-range PCR technique to obtain near-full-length HIV-1 genomes for the study of viral variation and evolution (9)(10)(11)(12). Only 191 bp of the HIV-1 genome is missing in the amplified PCR product.…”

Section: Resultsmentioning

confidence: 99%

Unselected Mutations in the Human Immunodeficiency Virus Type 1 Genome Are Mostly Nonsynonymous and Often Deleterious

Gao

Chen

Levy

et al. 2004

J Virol

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Mutation rates of human immunodeficiency virus type 1 (HIV-1) genomes have been estimated using purified reverse transcriptase or single-round infection system. Since small sequences were used as templates, the overall mutation rates could only be extrapolated and the biological significance of mutations is unknown. For direct estimation of HIV-1 mutation rates and understanding of the potential biological influences of mutations, we obtained 19 complete or nearly full-length proviral genomes from single-round-infected adherent cells of lymphocytes by using a lambda phage library method and a long-range PCR technique. Analysis of 160,000 bp of sequences showed that the overall mutation rate of HIV-1 genomes was 5.4 ؋ 10 ؊5 per base per replication cycle. On average, 1.1 mutations (range, 0 to 3) were generated in each viral genome during one infection cycle. Inspection of the mutations in the HIV-1 genome revealed that all site mutations within protein-coding regions were nonsynonymous mutations. Among all mutations, half were deleterious (premature stop codon and deletions) and would result in defective genomes. By applying the same system to an HIV-1 genome with a G262A mutation in the thumb region of the reverse transcriptase, a significant increase was observed in deletion and insertion mutation rates but no increase in the overall mutation rate in viral genomes was found.

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“…During the 20 th century, simian immunodeficiency viruses (SIV) from African primates were transmitted to humans on no fewer than 13 occasions [ 1 ]. One event, involving an SIV from chimpanzees, initiated the global human immunodeficiency virus type-1 (HIV-1) pandemic (group M) in the early 1900s [ 2 – 4 ]. Three additional HIV-1 groups are the result of independent cross-species transmission events of distinct SIVs from chimpanzees (group N) and gorillas (groups O and P) [ 5 – 7 ], while HIV type-2 (HIV-2) groups A-I arose from at least nine independent cross-species transmissions of SIVs from sooty mangabeys [ 8 – 10 ].…”

Section: Introductionmentioning

confidence: 99%

Phylogeny and History of the Lost SIV from Crab-Eating Macaques: SIVmfa

2016

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In the 20th century, thirteen distinct human immunodeficiency viruses emerged following independent cross-species transmission events involving simian immunodeficiency viruses (SIV) from African primates. In the late 1900s, pathogenic SIV strains also emerged in the United Sates among captive Asian macaque species following their unintentional infection with SIV from African sooty mangabeys (SIVsmm). Since their discovery in the 1980s, SIVs from rhesus macaques (SIVmac) and pig-tailed macaques (SIVmne) have become invaluable models for studying HIV pathogenesis, vaccine design and the emergence of viruses. SIV isolates from captive crab-eating macaques (SIVmfa) were initially described but lost prior to any detailed molecular and genetic characterization. In order to infer the origins of the lost SIVmfa lineage, we located archived material and colony records, recovered its genomic sequence by PCR, and assessed its phylogenetic relationship to other SIV strains. We conclude that SIVmfa is the product of two cross-species transmission events. The first was the established transmission of SIVsmm to rhesus macaques, which occurred at the California National Primate Research Center in the late 1960s and the virus later emerged as SIVmac. In a second event, SIVmac was transmitted to crab-eating macaques, likely at the Laboratory for Experimental Medicine and Surgery in Primates in the early 1970s, and it was later spread to the New England Primate Research Center colony in 1973 and eventually isolated in 1986. Our analysis suggests that SIVmac had already emerged by the early 1970s and had begun to diverge into distinct lineages. Furthermore, our findings suggest that pathogenic SIV strains may have been more widely distributed than previously appreciated, raising the possibility that additional isolates may await discovery.

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Molecular Characterization of a Highly Divergent HIV Type 1 Isolate Obtained Early in the AIDS Epidemic from the Democratic Republic of Congo

Cited by 13 publications

References 15 publications

Identifying recombinants in human and primate immunodeficiency virus sequence alignments using quartet scanning

Identifying recombinants in human and primate immunodeficiency virus sequence alignments using quartet scanning

Unselected Mutations in the Human Immunodeficiency Virus Type 1 Genome Are Mostly Nonsynonymous and Often Deleterious

Phylogeny and History of the Lost SIV from Crab-Eating Macaques: SIVmfa

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