Mapping HIV-1 Subtype C gp120Epitopes Using a Bioinformatic Approach

  • Dennis Maletich Junqueira
  • Rúbia Marília de Medeiros
  • Sabrina Esteves de Matos Almeida
  • Vanessa Rodrigues Paixão-Cortez
  • Paulo Michel Roehe
  • Fernando Rosado Spilki
Part of the Lecture Notes in Computer Science book series (LNCS, volume 5676)

Abstract

Human Immunodeficiency Type-1 subtype C (HIV-1C) is rapidly diverging among populations causing more than 48% of infections worldwide. HIV-1C gp120’s 128 sequences available at Genbank were aligned and submitted to phylogenetic analysis. Three major clusters were identified: 72 sequences aligned with a Brazilian 0072eference sequence; 44 sequences aligned with an Ethiopian sequence and 12 could be group along with Indian isolates. A search was made for conserved HIV-1C cytotoxic T lymphocyte (CTL) epitopes to A*0201, A*0301, A*1101 e B*07 human leukocyte antigen (HLA) alleles (using Epijen software). Five most conserved epitopes were recognized: QMHEDIISL, CTHGIKPVV, NLTNNVKTI, AITQACPKV, CTRPNNNTR. Our results showed a recognized evolutionary force of HIV-1 to escape from CTL responses mutating sites that can be negatively select by host’s immune system. The present study brings up a new approach to in silico epitope analysis taking into account geographical informations on virus diversity and host genetic background.

Keywords

HIV-1 subtype C bioinformatics epitope gp120 HLA 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2009

Authors and Affiliations

  • Dennis Maletich Junqueira
    • 1
  • Rúbia Marília de Medeiros
    • 1
  • Sabrina Esteves de Matos Almeida
    • 1
  • Vanessa Rodrigues Paixão-Cortez
    • 2
  • Paulo Michel Roehe
    • 3
  • Fernando Rosado Spilki
    • 4
  1. 1.Centro de Desenvolvimento Científico e Tecnológico (CDCT)Fundação Estadual de Produção e Pesquisa em Saúde (FEPPS)Porto Alegre/RSBrazil
  2. 2.Departamento de Genética, Instituto de BiociênciasUniversidade Federal do Rio Grande do SulPorto Alegre/RSBrazil
  3. 3.Virology Laboratory, Instituto de Pesquisas Veterinárias Desidério Finamor (CPVDF) – FEPAGRO Animal HealthBrazil
  4. 4.Instituto de Ciências da SaúdeCentro Universitário FEEVALENovo Hamburgo/RSBrazil

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