title: Genetic characterization of complex inter-recombinant HIV-1 strains circulating in Spain and reliability of distinct rapid subtyping tools.
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.
authors.affiliation: Department of Infectious Diseases, Hospital Carlos III, Madrid, Spain. aholguin.hciii@salud.madrid.org
authors.forename: Africa
authors.initials: A
authors.lastname: Holguín
authors.forename: Eva
authors.initials: E
authors.lastname: Lospitao
authors.forename: Marisa
authors.initials: M
authors.lastname: López
authors.forename: Eva Ramírez
authors.initials: ER
authors.lastname: de Arellano
authors.forename: María José
authors.initials: MJ
authors.lastname: Pena
authors.forename: Jorge
authors.initials: J
authors.lastname: del Romero
authors.forename: Cristina
authors.initials: C
authors.lastname: Martín
authors.forename: Vincent
authors.initials: V
authors.lastname: Soriano
mesh_terms: D000328:Adult; D019380:Anti-HIV Agents / Q000494:pharmacology / Q000627:therapeutic use*; D018791:CD4 Lymphocyte Count; D024882:Drug Resistance, Viral; D005260:Female; D014644:Genetic Variation; D016679:Genome, Viral; D005838:Genotype; D015658:HIV Infections / Q000188:drug therapy / Q000821:virology*; D015497:HIV-1 / Q000145:classification / Q000187:drug effects / Q000235:genetics*; D006801:Humans; D008297:Male; D009154:Mutation; D010802:Phylogeny; D016133:Polymerase Chain Reaction / Q000379:methods; D011995:Recombination, Genetic; D015203:Reproducibility of Results; D013030:Spain
chemical_list: D019380:Anti-HIV Agents