[Study on gag-pol region characteristics of HIV-1 strains epidemic in Liaoning province]

Abstract

Objective: To investigate the genetic subtypes and sequence characteristics of gag-pol region of HIV-1 epidemic in Liaoning province.

Methods: 99 whole blood samples of HIV-1 infected individuals of Liaoning province were collected. Provirus DNA was extracted from anti-coagulated peripheral whole blood, and then the sequences of gag-pol region were amplified through nested PCR and then sequenced. Genetic subtypes were identified by phylogenetic analysis, controlled with new version subtype reference sequences of HIV sequence database. The genetic distances of different coding regions were calculated by MEGA2.0 with Kimura 2-parameter model. The synonymous (Ks) and anonymous (Ka) as well as the ratio of Ks/Ka were analyzed by SNAP tool in HIV sequence database.

Results: There are many HIV-1subtypes epidemic in Liaoning province. We found five subtype: A, Thai B, B, C and G, five CRFs: CRF01, CRF03, CRF06, CRF07, CRF08, and one inter CRF recombinant ICR07/08 in 99 HIV-1 infected individuals of Liaoning province. Thai B subtype was the main subtype epidemic in Liaoning, next were CRF01_AE. In gag-pol region, the genetic distances of p17, p2-p6 were higher than p24, protease and RT coding region. The genetic distance of p24 region in B subtype strains were relative high compared with other subtypes. The genetic distance and the value of Ks and Ka were rather low in each region of CRF07 and CRF08. The ratio of Ks/Ka of p2-p6 region was the lowest in each subtype, the mean value was below 1. The ratio of Ks/Ka of RT region was as high as 10.45.

Conclusion: The HIV-1 genetic subtypes in Liaoning province were rather complex. The p24, protease and RT coding region coding region were more conserved in gag-pol region. P24 region of B subtype strains received more positive selective pressure, while the RT region of CRF01_AE strains received more negative selective pressure. CRF07_BC and CRF08_BC were the youngest strains transmitted to Liaoning province and showed strong founder effect.