Abstract
Several studies identified HIV-1 recombination in some distinct areas in Yunnan, China. However, no comprehensive studies had been fulfilled in the whole province up to now. To illustrate the epidemiology and recombination form of Unique Recombinant Forms (URFs) circulating in Yunnan, 788 HIV-1 positive individuals residing in 15 prefectures of Yunnan were randomly enrolled into the study. Full-length gag and pol genes were amplified and sequenced. Maximum likelihood tree was constructed for phylogenetic analysis. Recombinant breakpoints and genomic schematics were identified with online software jpHMM. 63 (10.2%) unique recombinant strains were identified from 617 strains with subtypes. The URFs distributed significantly differently among prefectures (Pearson chi-square test, P<0.05). IDUs contained more URFs than sexual transmitted population (Pearson chi-square test, P<0.05). Two main recombinant forms were identified by considering the presence of CRF01_AE segments in full length gag-pol genes, which were B′/C and B′/C/CRF01-AE recombinants. Three clusters were identified in the ML tree which contained more than three sequences and supported by high bootstrap values. One CRF was identified. Many of URFs contained identical breakpoints. The results will contribute to our understanding on HIV recombination and provide clues to the identification of potential CRFs in China.
Highlights
Human immunodeficiency viruses (HIV) were characterized with high level of genetic variation
High heterogeneity of HIV was always observed in infected individuals, which made it difficult for the amplification and sequencing of long gene segments
In most of previous studies, the determination of HIV subtypes prevalent in Yunnan province was always based on short gene segment, which could not conclude HIV-1 subtypes and identify recombination exactly
Summary
Human immunodeficiency viruses (HIV) were characterized with high level of genetic variation. Recombination is one of main mechanisms of HIV diversity. When a cell that was dually infected by two different viruses produced progeny virions with genomic. RNAs from each virus, strand-switching would take place during the round of reverse transcription [1,2,3]. Recombination would happen and unique variants with genome from two distinct parental viruses would be produced. Substantial studies showed that recombination contributed to viral escaping mutations under immune pressure, viral fitness and emergence of viral drug-resistance [4].
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