Identification of signature amino acids in the env V3-V4 and flanking regions of human immunodeficiency virus type 1 predominant strains in China

Abstract

To identify signature amino acids in the V3-V4 and flanking regions of the env gene from human immunodeficiency virus type 1 (HIV-1) predominant strains in China and to elucidate the role of these signature amino acids on epidemiologic tracking and the development of vaccine. Fragments of the HIV-1 env gene were amplified by nested-PCR from the whole blood of HIV-1 infected individuals from 12 provinces in China. Then, the PCR products were directly sequenced by using ABI 377 DNA SEQUENCER. The sequences covering the env V3-V4 region of the strains were used for the analyses described here. Envelope sequence subtypes were assigned using BLAST (http://www.HIV-Web.lanl.gov). Phylogenetic analyses were performed using GCG and MEGA as well as signature amino acids were identified using VESPA. Subtype B' strains and two recombinants (B'/C and CRF01-AE) were discovered among 157 currently circulating strains in China. The most prevalent subtypes were B'/C (38.85%), followed by B' (34.40%), and CRF01-AE (26.75%). Phylogenetic tree analysis of env V3-V4 region showed that subtype B' strains were closely related to B.CN.RL42, while most of B'/C strains clustered with 97CN54A and 97CNGX6F, CRF01-AE strains clustered into two distinct subgroups, which were closely related to THCM240 and 97CNGX2F. Analysis of signature amino acids revealed that eight of positions were identified as conserved signature amino acid sites in the env V3-V4 and flanking regions of the subtype B' and B'/C strains and almost all signature amino acids were found in their reference strains. Interestingly, eleven signature amino acids were demonstrated in the same regions of the CRF01-AE strains, but nine out of 11 signature amino acid sites were distinct from the same positions of the reference strains 97CNGX2F and TH.CM240. It is noteworthy that these 9 signature amino acids were found in the strains from all of the selected provinces except those from Yunnan province. Analysis of the signature amino acids suggest that much of the current Chinese epidemics of subtype B' and B'/C strains are descended from a single introduction into China, while the epidemic caused by the CRF01-AE strain is caused by multiple introductions into China from Thailand. These results will contribute to the policy of AIDS prevention and control as well as the ongoing development of AIDS vaccine.