ArticleVirus evolution2019
Phylogenetic measures of indel rate variation among the HIV-1 group M subtypes.
Article in Virus evolution, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed, 17 citations in OpenAlex.
- Identification of Genes Associated with the Pan-Vibrios Resistance (PVR) Trait of Pacific White Shrimp (Biology · 2026Article
- Impact of Phylogenetic Method Choice on Indel Analyses in HIV-1 Subtype B.Genome biology and evolution · 2025Article
- Comparative Evaluation of Open-Source Bioinformatics Pipelines for Full-Length Viral Genome Assembly.Viruses · 2024Article
- Insertions and Deletions: Computational Methods, Evolutionary Dynamics, and Biological Applications.Molecular biology and evolution · 2024Review
- Please Mind the Gap: Indel-Aware Parsimony for Fast and Accurate Ancestral Sequence Reconstruction and Multiple Sequence Alignment Including Long Indels.Molecular biology and evolution · 2024Article
- New antiretroviral inhibitors and HIV-1 drug resistance: more focus on 90% HIV-1 isolates?FEMS microbiology reviews · 2023Review
- Increased Frequency of Indels in Hypervariable Regions of SARS-CoV-2 Proteins-A Possible Signature of Adaptive Selection.Frontiers in genetics · 2022Article
- Article
- On the stability of sequences inserted into viral genomes.Virus evolution · 2019Review
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The transmission fitness and pathogenesis of HIV-1 is disproportionately influenced by evolution in the five variable regions (V1-V5) of the surface envelope glycoprotein (gp120). Insertions and deletions (indels) are a significant source of evolutionary change in these regions. However, the rate and composition of indels has not yet been quantified through a large-scale comparative analysis of HIV-1 sequences. Here, we develop and report results from a phylogenetic method to estimate indel rates for the gp120 variable regions across five major subtypes and two circulating recombinant forms (CRFs) of HIV-1 group M. We processed over 26,000 published HIV-1 gp120 sequences, from which we extracted 6,605 sequences for phylogenetic analysis. We reconstructed time-scaled phylogenies by maximum likelihood and fit a binomial-Poisson model to the observed distribution of indels between closely related pairs of sequences in each tree (cherries). By focusing on cherries in each tree, we obtained phylogenetically independent indel reconstructions, and the shorter time scales in cherries reduced the bias due to purifying selection. Rate estimates ranged from
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