Genotype distribution and genetic variation analysis on human immunodeficiency virus-1 epidemic strains in Yunnan Province

Abstract

Objective To investigate the subtypes distribution of human immunodeficiency virus (HIV)-1 epidemic strains and the characteristics of amino acid variation in different areas of Yunnan Province. Methods Totally 800 HIV/AIDS plasma specimens and epidemiological information were collected between 2012 and 2015 from 14 areas of Yunnan. Viral RNA was extracted and amplified using RT-polymerase chain reaction (PCR). 4.5 kb 5′halves fragments were obtained and directly sequenced. Subtypes of strains were identified by Genotyping, MEGA 6.06 and BLAST. Grouping was analyzed by location and subtype. Entropy software was used to analyze the difference of amino acid sequences between different groups according to the sampling location and subtypes to analyze the regional distribution and genetic variation of HIV-1 subtypes in Yunnan Province. Results Of the 800 plasma specimens, a total of 446 genomic sequences from 12 areas were successfully amplified and sequenced. After genotypes were identified, the subtypes of HIV-l strains prevalent in Yunnan were CRF08_BC (58.3%), CRF01_AE (19.3%), CRF07_BC (11.6%), unknown recombinant forms (7.1%), B(B′) (1.7%) and C (1.3%). The geographical distribution in Yunnan was analyzed. The CRF01_AE predominated in Dehong, Xishuangbanna and Wenshan. The CRF08_BC predominated in Lincang, Honghe and Puer (more than 70.0%) and CRF08_BC was prevalent in the other areas. But CRF07_BC in Kunming, Yuxi and Dali accounted for more than 20%. The constitutions of amino acid of three majors CRF08_BC, CRF01_AE and CRF07_BC were different on 17, 14 and 18 amino acid sites with statistical differences in the eastern and western regions of Yunnan Province (均P<0.05). Conclusions HIV-1 strains transmit and vary genetically in the province widely. The amino acid mutation sites of eastern and western strains are different. This difference represents that the same subtype strains in different geographical distribution vary on different genetic background and are selected by immune responses. The epidemic trends need to be closely monitored. Key words: Human immunodeficiency virus type 1; Genetic subtype; Genovariation