Universa Medicina (Apr 2014)
Subtypes and phylogenetic analysis of human immunodeficiency virus-1 in Jayapura
Abstract
BACKGROUND Human immunodeficiency virus (HIV), a retrovirus that infects the human immune system, is genetically differentiated into HIV-1 and HIV-2. HIV1 is classified into 3 groups: M,N and O. Group M is subdivided into 9 subtypes, namely: A, B, C, D, F, G, H, J and K. HIV subtype mapping would constitute a good reference base to study the epidemiology of HIV-1. HIV phylogenetic analysis is required to understand virus origin, geographical distribution and tracking parameters of the HIV transmission process in a sample area. The objective of this study was to determine HIV-1 subtype distribution and the relationship between HIV-1 subtypes with genBank HIV isolates based on envelope gene fragments. METHODS A cross-sectional study was conducted involving 36 subjects in Jayapura Regency between January and March 2013. Blood samples were taken and analyzed using reverse transcription polymerase chain reaction (RT-PCR) and nested PCR, and confirmed with sequencing. Phylogenetic analysis was performed along 400 bp of envelope gene fragment. The data were analyzed with Bioedit ver.7 and MEGA 5.1. software. RESULTS Two HIV-1 subtypes were found in Jayapura Regency. Subtype CRF01_AE was confirmed in 31 patients (86.1%) and subtype B in 5 patients (13.9%). Phylogenetic analysis showed phylogenetic relationships between CRF01_AE from Jayapura and subtypes from Singapore and Thailand, while subtype B from Jayapura was closely related to subtypes from United States and United Kingdom CONCLUSION The results of this study reflect the independent introduction of multiple HIV-1 strains into Papua, with the rapid spread of a single strain of HIV-1 (CRF01_AE) in the majority of infected patients tested.
