Evidence for a recombinant origin of HIV-1 Group M from genomic variation
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Summary
A dated-tip analysis of all near full-length HIV-1/M genome sequences that were published in the GenBank database demonstrates that a sliding window approach can accommodate early recombination events outside the established nomenclature of HIV/M subtypes, although it is difficult to incorporate the earliest available samples due to their limited genome coverage.
- Type
- article
- Published
- 2018-07-06
- Cited by
- 7
- References
- 50
- Access
- Open access
- OpenAlex
- https://openalex.org/W2950255151
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:59248687
Keywords
Genome, Biology, Breakpoint, Phylogenetic tree, GenBank
References
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- Estimating the Rate of Intersubtype Recombination in Early HIV-1 Group M Strains
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- The PANGEA-HIV Consortium: Phylogenetics and Networks for Generalised HIV Epidemics in Africa
- The origin and diversity of the HIV-1 pandemic.
- Timing the ancestor of the HIV-1 pandemic strains.
- FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments
- IDEPI: Rapid Prediction of HIV-1 Antibody Epitopes and Other Phenotypic Features from Sequence Data Using a Flexible Machine Learning Platform
- Genetic Characterization of Eight Full-Length HIV Type 1 Genomes from the Democratic Republic of Congo (DRC) Reveal a New Subsubtype, A5, in the A Radiation That Predominates in the Recombinant Structure of CRF26_A5U
- An Evolutionary Model-Based Algorithm for Accurate Phylogenetic Breakpoint Mapping and Subtype Prediction in HIV-1
- A Computer Program Designed to Screen Rapidly for HIV Type 1 Intersubtype Recombinant Sequences
- Identifying the Important HIV-1 Recombination Breakpoints
- Relaxed Phylogenetics and Dating with Confidence
- Declining transition/transversion ratios through time reveal limitations to the accuracy of nucleotide substitution models
- Purifying Selection Can Obscure the Ancient Age of Viral Lineages
- Within-host and between-host evolutionary rates across the HIV-1 genome
- The role of recombination in the emergence of a complex and dynamic HIV epidemic
Cited by
- Phylogenetic measures of indel rate variation among the HIV-1 group M subtypes
- Pervasive and non-random recombination in near full-length HIV genomes from Uganda
- TickSialoFam (TSFam): A Database That Helps to Classify Tick Salivary Proteins, a Review on Tick Salivary Protein Function and Evolution, With Considerations on the Tick Sialome Switching Phenomenon
- Current and historic HIV-1 molecular epidemiology in paediatric and adult population from Kinshasa in the Democratic Republic of Congo
- Genomic Epidemiology and Evolution of Scallion Mosaic Potyvirus From Asymptomatic Wild Japanese Garlic
- Revisiting the recombinant history of HIV-1 group M with dynamic network community detection
- Mutational Stability Profiling and Functional Analysis of Spike Protein in Indian Sars Cov-2 Delta Variants: an in Silico Analysis
- Revisiting the recombinant history of HIV-1 group M with dynamic network community detection
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