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Home / Archives for Faria NR

Faria NR

Phylogeographical footprint of colonial history in the global dispersal of human immunodeficiency virus type 2 group A.

  • Autores: Camacho RJ, de Sousa JD, Erasmus S, Faria NR, Goncalves MF, Goubau P, Hodges-Mameletzis I, Jallow S, Lemey P, Paolucci S, Pieniazek D, Rodés B, Ruelle J, Silva JC, Soriano V, Suchard MA, Taveira N, Treviño A, Vandamme AM, Xu L
  • Ano de Publicação: 2012
  • Journal: Journal of General Virology
  • Link: http://www.ncbi.nlm.nih.gov/pubmed/?term=Phylogeographical+footprint+of+colonial+history+in+the+global+dispersal+of+human+immunodeficiency+virus+type+2+group+A

Human immunodeficiency virus type 2 (HIV-2) emerged in West Africa and has spread further to countries that share socio-historical ties with this region. However, viral origins and dispersal patterns at a global scale remain poorly understood. Here, we adopt a Bayesian phylogeographic approach to investigate the spatial dynamics of HIV-2 group A (HIV-2A) using a collection of 320 partial pol and 248 partial env sequences sampled throughout 19 countries worldwide.
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Phylodynamics of the HIV-1 CRF02_AG clade in Cameroon.

  • Autores: Abecasis A, Bonfim I, Camacho RJ, Faria NR, Lemey P, Ndembi N, Sousa JD, Suchard MA, Vandamme AM
  • Ano de Publicação: 2012
  • Journal: Infection Genetics and Evolution
  • Link: http://www.ncbi.nlm.nih.gov/pubmed/?term=Phylodynamics+of+the+HIV-1+CRF02_AG+clade+in+Cameroon

Evolutionary analyses have revealed an origin of pandemic HIV-1 group M in the Congo River basin in the first part of the XX century, but the patterns of historical viral spread in or around its epicentre remain largely unexplored. Here, we combine epidemiologic and molecular sequence data to investigate the spatiotemporal patterns of the CRF02_AG clade.
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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

  • Autores: Abecasis AB, Camacho RJ, De Oliveira T, Deforche K, Faria NR, Gomez-Lopez A, Imbrechts S, Libin P, Pineda-Peña AC, Vandamme AM
  • Ano de Publicação: 2013
  • 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

  • Autores: Faria NR, Khouri R, Lemey P, Li G, Piampongsant S, Pineda-Pena A-C, Theys K, Vandamme A-M, Voet A
  • Ano de Publicação: 2015
  • Journal: Retrovirology
  • Link: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4358901/

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

  • Autores: 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
  • Ano de Publicação: 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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