• Skip to primary navigation
  • Skip to main content
  • Skip to footer
  • Biblioteca
  • Museu
  • Pessoal
    • Webmail
    • Área de Docentes
    • Área de Não-Docentes
  • Estudantes
    • Webmail
    • Moodle
    • NetP@
    • Escola Doutoral
    • Serviços Académicos
    • Trabalhar no IHMT
    • Programa Mentoria à Mesa – 1ª Edição

IHMT

Instituto de Higiene e Medicina Tropical

  • O Instituto
    • Missão
    • Mensagem do Diretor
    • Órgãos de governo
    • Docentes e investigadores
    • Portal de Denúncias UNL
  • Ensino
    • Mestrados
    • Doutoramentos
    • Cursos de Especialização
    • Formação transversal
    • Cursos de Curta Duração
    • Ensino à Distância
    • Apoio ao Desenvolvimento
    • Serviços académicos
    • NOVA Open Academy
    • Programa Mentoria à Mesa – 1ª Edição
  • Investigação
    • Centro GHTM
    • Unidades de Ensino e de Investigação (UEI)
      • Unidade de Clínica Tropical
      • Unidade de Microbiologia Médica
      • Unidade de Parasitologia Médica
      • Unidade de Saúde Pública Global
      • Serviço de Apoio à Ciência e Comunidade
    • Biobanco
    • BLOODless
    • Centro Colaborador OMS
    • Publicações
  • Serviços e gestão
    • Biblioteca
    • Sistema de Qualidade
    • Estatutos e regulamentos
    • Plano de Atividades
    • Relatório de Atividades
    • Relatório de Gestão
    • Contratos públicos
    • Recursos humanos
      • Concursos e bolsas
        • Concursos – Docentes e Investigadores
        • Concursos – Não Docentes e Não Investigadores
        • Bolsas de Investigação
      • Contratos
      • Avaliação de Desempenho
        • Ciclo Avaliativo
          • Biénio 2021-2022
          • Biénio 2023-2024
        • Conselho Coordenador de Avaliação
        • Comissão Paritária
      • Mobilidade
      • Listas Nominativas
  • Doenças Tropicais
    • Consulta do Viajante
    • Dossiês Informativos
    • Glossário
    • Museu
    • Vídeos
    • MosquitoWeb
  • Comunidade
    • Cooperação e Desenvolvimento
    • Formação
    • Parcerias
  • Contactos
  • Candidaturas
  • pt
    • pt
    • en
Home / Publicações / Comparative performance of the REGA subtyping tool version 2 versus version 1

Comparative performance of the REGA subtyping tool version 2 versus version 1

  • Autores: Abecasis AB, Camacho RJ, De Oliveira T, Imbrechts S, Libin P, Vandamme AM, Wang Y
  • Ano de Publicação: 2010
  • Journal: Infection Genetics and Evolution
  • Link: http://www.ncbi.nlm.nih.gov/pubmed/?term=Comparative+performance+of+the+REGA+subtyping+tool+version+2+versus+version+1

The REGA HIV-1 subtyping tool is a phylogenetic-based method for subtyping HIV-1 genomic sequences that was published in 2005. The subtyping tool combines phylogenetic approaches with recombination detection methods. Recently, version 2 was released (http://www.bioafrica.net/rega-genotype/html/index.html) as an improvement of version 1. Version 2 implements a Decision-Tree-based algorithm that was not implemented in version 1. We wanted to compare the two versions on a large sequence dataset to assess the improvements of version 2 and to verify whether features lost during updating the tool needed to be recovered. We analysed the results of the two versions in the genotyping of 4676 HIV-1 pol sequences. We compared those results to a manual approach, used in previous studies. Our results show that version 2 has an overall better sensitivity but especially for the detection of subtypes A, B, D, F, G and CRF14_BG and CRF06_CPX. For the other subtypes, no significant differences were observed in the sensitivity of versions 1 and 2. The overall increase in sensitivity was however accompanied by a decrease in the specificity for the detection of subtype B. This is the main limitation of version 2. However, while the number of false negatives decreased by 53 samples, the number of false positives increased only by 5 samples from version 1 to 2. The performance of the REGA HIV-1 subtyping tool was considerably improved from one version to the other. Our results are very valuable and allow us to make suggestions for further improvement of the tool for a version 3 release.

Comparative performance of the REGA subtyping tool version 2 versus version 1

  • Autores: Abecasis AB, Camacho RJ, De Oliveira T, Imbrechts S, Libin P, Vandamme AM, Wang Y
  • Ano de Publicação: 2010
  • Journal: Infection Genetics and Evolution
  • Link: http://www.ncbi.nlm.nih.gov/pubmed/?term=Comparative+performance+of+the+REGA+subtyping+tool+version+2+versus+version+1

The REGA HIV-1 subtyping tool is a phylogenetic-based method for subtyping HIV-1 genomic sequences that was published in 2005. The subtyping tool combines phylogenetic approaches with recombination detection methods. Recently, version 2 was released (http://www.bioafrica.net/rega-genotype/html/index.html) as an improvement of version 1. Version 2 implements a Decision-Tree-based algorithm that was not implemented in version 1. We wanted to compare the two versions on a large sequence dataset to assess the improvements of version 2 and to verify whether features lost during updating the tool needed to be recovered. We analysed the results of the two versions in the genotyping of 4676 HIV-1 pol sequences. We compared those results to a manual approach, used in previous studies. Our results show that version 2 has an overall better sensitivity but especially for the detection of subtypes A, B, D, F, G and CRF14_BG and CRF06_CPX. For the other subtypes, no significant differences were observed in the sensitivity of versions 1 and 2. The overall increase in sensitivity was however accompanied by a decrease in the specificity for the detection of subtype B. This is the main limitation of version 2. However, while the number of false negatives decreased by 53 samples, the number of false positives increased only by 5 samples from version 1 to 2. The performance of the REGA HIV-1 subtyping tool was considerably improved from one version to the other. Our results are very valuable and allow us to make suggestions for further improvement of the tool for a version 3 release.

Footer

INSTITUTO DE HIGIENE E
MEDICINA TROPICAL
UNIVERSIDADE NOVA DE LISBOA
Rua da Junqueira, 100 1349-008 Lisboa
T +351 213 652 600
geral@ihmt.unl.pt

Consulta do Viajante e Medicina Tropical
T +351 213 652 630
T +351 213 652 690
T +351 91 182 37 48
T +351 91 182 44 67
medicina.viagens@ihmt.unl.pt

  • Ensino
  • Investigação
  • Medicina Tropical
  • Cooperação
  • Portal de Denúncias UNL

NOVA University of Lisbon Logo

Siga-nos

  • Facebook
  • Instagram
  • LinkedIn
  • Twitter
  • YouTube

Receber a “newsletter”

© Copyright 2025 IHMT-UNL Todos os Direitos Reservados.
  • Universidade Nova de Lisboa
  • Fundação para a Ciência e a Tecnologia

    UIDB/04413/2020
    UIDP/04413/2020

We use cookies to ensure that we give you the best experience on our website. If you continue to use this site we will assume that you are happy with it.Ok