ArticlePloS one2011
Change of positive selection pressure on HIV-1 envelope gene inferred by early and recent samples.
Article in PloS one, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers, 1 of them a synthesis that pooled it.
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Who cites it
12 citing papers in PubMed, 1 synthesis or guideline pooled it, 40 citations in OpenAlex.
- The HIV Genomic Incidence Assay Meets False Recency Rate and Mean Duration of Recency Infection Performance Standards.Scientific reports · 2017Pooled it
- Cross-species transmission of an ancient endogenous retrovirus and convergent co-option of its envelope gene in two mammalian orders.PLoS genetics · 2022Article
- Comparative Transcriptomics Provides Insights into Reticulate and Adaptive Evolution of a Butterfly Radiation.Genome biology and evolution · 2019Article
- Many human RNA viruses show extraordinarily stringent selective constraints on protein evolution.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- HIV Progression Depends on Codon and Amino Acid Usage Profile of Envelope Protein and Associated Host-Genetic Influence.Frontiers in microbiology · 2017Article
- LMAP: Lightweight Multigene Analyses in PAML.BMC bioinformatics · 2016Article
- Article
- Characterization of red-capped mangabey tetherin: implication for the co-evolution of primates and their lentiviruses.Scientific reports · 2014Article
- Molecular evolutionary analysis of vertebrate transducins: a role for amino acid variation in photoreceptor deactivation.Journal of molecular evolution · 2013Article
- Captured retroviral envelope syncytin gene associated with the unique placental structure of higher ruminants.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Complex patterns of divergence among green-sensitive (RH2a) African cichlid opsins revealed by Clade model analyses.BMC evolutionary biology · 2012Article
- Ancestral capture of syncytin-Car1, a fusogenic endogenous retroviral envelope gene involved in placentation and conserved in Carnivora.Proceedings of the National Academy of Sciences of the United States of America · 2012Article
Corrections and comments
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Authors and funding
6 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
HIV-1 infection has been on the rise in Japan recently, and the main transmission route has changed from blood transmission in the 1980s to homo- and/or hetero-sexual transmission in the 2000s. The lack of early viral samples with clinical information made it difficult to investigate the possible virological changes over time. In this study, we sequenced 142 full-length env genes collected from 16 Japanese subjects infected with HIV-1 in the 1980s and in the 2000s. We examined the diversity change in sequences and potential adaptive evolution of the virus to the host population. We used a codon-based likelihood method under the branch-site and clade models to detect positive selection operating on the virus. The clade model was extended to account for different positive selection pressures in different viral populations. The result showed that the selection pressure was weaker in the 2000s than in the 1980s, indicating that it might have become easier for the HIV to infect a new host and to develop into AIDS now than 20 years ago and that the HIV may be becoming more virulent in the Japanese population. The study provides useful information on the surveillance of HIV infection and highlights the utility of the extended clade models in analysis of virus populations which may be under different selection pressures.
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