2021
DOI: 10.1093/ve/veab055
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Phylogenetic analysis of HIV-1 shows frequent cross-country transmission and local population expansions

Abstract: Understanding of pandemics depends on characterization of pathogen collections from well-defined and demographically diverse cohorts. Since its emergence in Congo almost a century ago, HIV-1 has geographically spread and genetically diversified into distinct viral subtypes. Phylogenetic analysis can be used to reconstruct the ancestry of the virus to inform on the origin and distribution of subtypes. We sequenced two 3.6 kb amplicons of HIV-1 genomes from 3,197 participants in a clinical trial w… Show more

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Cited by 7 publications
(8 citation statements)
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“…The detailed subtyping description is available in other publications [22,25]. In short, the consensus sequences were used for subtyping using REGA version 3.0 [28] and the subtypes were confirmed by a manual inspection.…”
Section: Hiv Sequencing Alignment Variant Calling and Subtypingmentioning
confidence: 99%
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“…The detailed subtyping description is available in other publications [22,25]. In short, the consensus sequences were used for subtyping using REGA version 3.0 [28] and the subtypes were confirmed by a manual inspection.…”
Section: Hiv Sequencing Alignment Variant Calling and Subtypingmentioning
confidence: 99%
“…A total of 3,785 START clinical trial participants had HIV genomes sequenced [22,24,25]. After read alignment to the HXB2 reference genome, 1,135 genomes had 500 or less (out of 2,549) codon positions covered by �500 reads.…”
Section: Study Participants and Genome Sequencingmentioning
confidence: 99%
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“…Methods for sample preparation, amplification of viral RNA and NGS, identification of DRM by means of VirVarSeq, and determination of HIV subtype have been described elsewhere [25,26].…”
Section: Study Population and Sequencingmentioning
confidence: 99%
“…Sequence reads (FASTQ files) were analyzed with Vir-VarSeq version 20140929, which calls variants at the codon level [27]. From the output, we extracted amino acid frequencies in the pol gene from amino acid position 1-935 where positions 1-99 encode protease protein, positions 100-659 encode reverse transcriptase protein, and positions 660-935 partially encode integrase protein (our amplicon did not cover positions 936-947) [25].…”
Section: Study Population and Sequencingmentioning
confidence: 99%