HIV-1 pol gene diversity and molecular dating of subtype C from Sri Lanka

PloS One
Ajit PatilSwarali Kurle

Abstract

The first case of HIV infection in Sri Lanka was reported in 1987 and at the end of 2018 there were 3500 people living with HIV. There have been commendable efforts made towards the detection, treatment, and prevention of HIV in the country. Even though the genetic diversity of HIV has been shown to affect the parameters ranging from detection to vaccine development, there is no data available with respect to the molecular epidemiology of HIV-1 in Sri Lanka. In this report we have performed the ancillary analysis of pol gene region sequences (n = 85) obtained primarily for the purpose of HIV-1 drug resistance genotyping. Briefly, dried blood spot specimens (DBS) collected from HIV-1 infected individuals between December 2015 and August 2018 were subjected to pol gene amplification and sequencing. These pol gene sequences were used to interpret the drug resistance mutation profiles. Further, sequences were subjected to HIV-1 subtyping using REGA 3.0, COMET, jPHMM and, RIP online subtyping tools. Moreover, Bayesian phylogenetic analysis was employed to estimate the evolutionary history of HIV-1 subtype C in Sri Lanka. Our analysis revealed that the majority (51.8%) of pol gene sequences were subtype C. Other than subtype C, there...Continue Reading

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Methods Mentioned

BETA
genotyping
total
PCR
RIP

Software Mentioned

BEAGLE
ViroBLAST
HIV Drawing Tool
MEGA
Tracer
jModelTest
REGA
Tree Annotator
jPHMM
BLAST ( Basic Local Alignment Search Tool )

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