Automated subtyping of HIV-1 genetic sequences for clinical and surveillance purposes: Performance evaluation of the new REGA version 3 and seven other tools

Authors: Abecasis AB, Camacho RJ, De Oliveira T, Deforche K, Faria NR, Gomez-Lopez A, Imbrechts S, Libin P, Pineda-Peña AC, Vandamme AM
Journal: Infection Genetics and Evolution
Link: http://www.ncbi.nlm.nih.gov/pubmed/23660484

To investigate differences in pathogenesis, diagnosis and resistance pathways between HIV-1 subtypes, an accurate subtyping tool for large datasets is needed. We aimed to evaluate the performance of automated subtyping tools to classify the different subtypes and circulating recombinant forms using pol, the most sequenced region in clinical practice. We also present the upgraded version 3 of the Rega HIV subtyping tool (REGAv3).
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An integrated map of HIV genome-wide variation from a population perspective

Authors: Faria NR, Khouri R, Lemey P, Li G, Piampongsant S, Pineda-Peña AC, Theys K, Vandamme AM, Voet A
Publication Year: 2015
Journal: Retrovirology
Link: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4358901/

Background: The HIV pandemic is characterized by extensive genetic variability, which has challenged the development of HIV drugs and vaccines. Although HIV genomes have been classified into different types, groups, subtypes and recombinants, a comprehensive study that maps HIV genome-wide diversity at the population level is still lacking to date. This study aims to characterize […]
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The early spread and epidemic ignition of HIV-1 in human populations

Authors: Arinaminpathy N, Baele G, Bedford T, Faria NR, Lemey P, Peeters M, Pepin J, Posada D, Pybus OG, Rambaut A, Sousa JD, Suchard MA, Tatem AJ, Ward MJ
Publication Year: 2014
Journal: Science
Link: http://www.sciencemag.org/content/346/6205/56.abstract

Thirty years after the discovery of HIV-1, the early transmission, dissemination, and establishment of the virus in human populations remain unclear. Using statistical approaches applied to HIV-1 sequence data from central Africa, we show that from the 1920s Kinshasa (in what is now the Democratic Republic of Congo) was the focus of early transmission and the source of pre-1960 pandemic viruses elsewhere.
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Automated subtyping of HIV-1 genetic sequences for clinical and surveillance purposes: Performance evaluation of the new REGA version 3 and seven other tools

An integrated map of HIV genome-wide variation from a population perspective

The early spread and epidemic ignition of HIV-1 in human populations

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