Genetic characterization of complex inter-recombinant HIV-1 strains circulating in Spain and reliability of distinct rapid subtyping tools

✍ Scribed by Africa Holguín; Eva Lospitao; Marisa López; Eva Ramírez de Arellano; María José Pena; Jorge del Romero; Cristina Martín; Vincent Soriano

• Publisher: John Wiley and Sons
• Year: 2008
• Tongue: English
• Weight: 186 KB
• Volume: 80
• Category: Article
• ISSN: 0146-6615
• DOI: 10.1002/jmv.21105

✦ Synopsis

Abstract

Genetic recombination and high rate of mutation increase HIV‐1 diversity, allowing viruses to escape more easily from the host immune response or antiretroviral drugs. The recombinant nature of full‐length HIV‐1 genomic sequences derived from viruses infecting five epidemiologically unlinked individuals carrying HIV‐1 non‐B variants was investigated. Overlapping PCR amplifications followed by direct sequencing of viral products derived from plasma and phylogenetic analyses were carried out. Four viral sequences clustered with CRF06_cpx and one with CRF02_AG. However, subtyping of separate genes within the same genome revealed that four were recombinant forms involving different subtypes and/or CRFs with distinct breakpoints. Two specimens included CRF02_AG and CRF06_cpx sequences with several fragments from other HIV‐1 clades along their genomes. Three rapid subtyping tools (Stanford, NCBI, and REGA) showed discrepant results when interpreting these viral sequences. This is the first description of CRF02_AG/CRF06_ cpx recombinants in Spain. The results highlight the tremendous heterogeneity of HIV‐1 recombinant strains currently in circulation. J. Med. Virol. 80:383–391, 2008. © 2008 Wiley‐Liss, Inc.