Emergence of A/K related HIV-1 recombinant samples in an outskirt area of Rio de Janeiro, Brazil
M.G. Morgado1, A. Rodrigues-Pedro1, C.A. Velasco-de-Castro1, C. Gaido1, M. Santini2,3, B. Grinsztejn2, J.H. Pilotto2,3
1Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Laboratory of AIDS & Molecular Immunology, Rio de Janeiro, Brazil, 2Oswaldo Cruz Foundation - Evandro Chagas Clinical Research Institute (FIOCRUZ/RJ), Rio de Janeiro, Brazil, 3Hospital Geral de Nova Iguaçu, Nova Iguaçu, Brazil
Background: HIV is characterized by its rapid evolution due to mutations/deletions/insertions and recombination events, rapidly increasing its diversity worldwide. Globally, the predominant viral forms are subtypes A and C, followed by subtype B and the recombinants CRF01-AE and CRF02-AG. Subtype B is the most prevalent in Brazil, followed by subtype F and BF recombinants in most parts of the country, exception for the South where subtype C predominates. The aim of the present study is to describe the emergence and characterize the near full-length genomes of HIV-1 isolates showing A and K-like recombinant profiles.
Methods: Five unlinked HIV-1 recombinant samples were identified in three independent studies conducted with HIV seropositive individuals from an outskirt area of Rio de Janeiro, Brazil. Genotyping of gp120 C2-V3 (550bp) and gag-pol (HXB2 893-4104) were performed using a nested PCR protocol. Near full-length genome sequencing (around 8,500 pb) was possible for three of them. DNASTAR and MEGA 4 were used for edition, alignment and phylogenetic analysis (neighbor-joining). SIMPLOT was used to assess recombinant genomes.
Results: The 5 HIV-1 samples were first identified as having a subtype K fragment in the reverse transcriptase region. Additional phylogenetic analyses of the gag-pol regions (3,211bp) confirmed their relationship with subtype A and A1DHK and CRF09A1KU recombinant reference samples. Bootscan analyses showed that at least three of them (05BRRJVCT223, 08BRRJPG226 and BRRJPC3854) showed a gag-pol AUK profile, with very similar breakpoints, and a vif-vpu AGAK profile observed for the last two. Sample 08BRRJPC2818 presented A and K fragments in the gag-pol region with distinct breakpoints. Sample 07BRRJPG144 presented a BABKB gag-pol/Bnef profile. Exception for sample 08BRRJPC2818 (subtype G), all others have subtype A assigned for the env C2-V3 region.
Conclusions: The implications of these AK recombinant viruses, identified for the first time in Brazil, for the local epidemic profile should be addressed.
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