Genetic analysis of HIV-1 subtypes in recently infected-untreated and treatment experienced HIV patients from Panama
Y. Mendoza1, J. Castillo1, A.A. Martinez1, G. Arteaga1, I.L. de Rivera2, K.R. Page3, J.M. Pascale1, Gorgas, Panama
1Instituto Conmemorativo Gorgas de Estudios de la Salud, Genomica y Proteomica, Panama, Panama, 2Universidad Nacional Autonoma de Honduras, Tegucigalpa, Honduras, 3John Hopkins University- School of Medicine, Baltimore, United States
Background: Molecular epidemiology data for HIV genetic analysis in Central American countries is scarce. Genetic analysis of HIV subtypes provides information about patterns of genetic divergence that may have occurred during viral evolution, mechanisms of transmission, and help in vaccine design. In this study, HIV subtypes were analyzed in recently infected-untreated (UTP) and in treatment experienced patients (TEP).
Methods: Blood samples (n=113) from UTP (n=63) and TEP (n=50 ) patients were subjected to DNA extraction and PCR amplification of the HIV protease and reverse transcriptase genes. PCR amplicons were sequenced and aligned to reference subtypes sequences. A phylogenetic NJ tree were generated under the kimura-2-parameter model and confirmed with ME model using Mega. All sequences were individually analyzed for similarity with references by bootscanning using Rega HIV Subtyping (BioAfrica).
Results: Phylogenetic analysis from the 113 blood samples showed 110 isolates to be subtype B (33% of bootstrap confidence), 1 subtype CRF12BF (77%), 1 subtype G (87%) and 1 subtype CRF08BC (97%). Highly divergence was observed within B subtypes isolates. UTP and TEP sequences distributed among the 10 clades of B subtypes which implies co-existence of possibles resistance viral strains among UTP. Bootscanning similarity analyses showed B isolates recombination with subtypes D, F1 and G (40-76%) mostly observed in TEP, except by subtype BD presented in 8 UTP and 9 TEP. None of the BD-UTP subjects showed ARV resistance mutations, however, all BD-TEP patients had resistance associeted mutations.
Conclusions: HIV-1 subtypes from Panama are dominated by a genetically diverse clade B (97%) and new recombinants are reported. Further studies are guaranteed to confirm the establishment of BD and others recombinants in Panamanian HIV patients. Additionally, they will give information about how observed high viral genetic diversity could affect HIV patients monitoring tests, progression to AIDS, and transmission patterns.
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