Sequencing of Gag/Env association with HIV genotyping resolution and HIV-related epidemiologic studies of HIV in China.
HIV genotyping has led to conflicting results between laboratories. Therefore, identifying the most accurate gene combinations to sequence remains a priority. Datasets of Chinese HIV subtypes based on several markers and deposited in PubMed, Metstr, CNKI, and VIP databases between 2000 and 2015 were studied. In total, 9177 cases of amplification-positive samples from 26 provinces of China were collected and used to classify HIV subtypes based on eight individual genes or a combination thereof. CRF01_AE, CRF07_BC, CRF08_BC and B were the prevalent HIV subtypes in China, accounting for 84.07% of all genotypes. Gag/Env sequencing classified a greater number of HIV subtypes compared to other genes or combination of gene fragments. The geographical distribution of Gag and Gag/Env genotypes was similar to that observed with all genetic markers. Further principal component analysis showed a significantly different geographical distribution pattern of HIV in China for HIV genotypes detected with Gag/Env, which was in line with the distribution of all HIV genotypes in China. Gag/Env sequences had the highest diversity of the eight markers studied, followed by Gag and Gag/Pol/Env; Pol/Env polymorphisms were the least divergent. Gag/Env can serve as a high-resolution marker for HIV genotyping.
The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan Province, China.|The First People's Hospital of Yunnan Province, Kunming, Yunnan Province, China.|Medical Faculty of Kunming University of Science and Technology, Kunming, Yunnan Province, China.
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Ren
Yunnan Institute of Digestive Disease, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan Province, China.
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Wang
Yunnan Institute of Digestive Disease, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan Province, China.
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Xu
The First People's Hospital of Yunnan Province, Kunming, Yunnan Province, China.
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Feng
The First People's Hospital of Yunnan Province, Kunming, Yunnan Province, China.
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Zhang
The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan Province, China kunhuawangProf@163.com.|Yunnan Institute of Digestive Disease, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan Province, China kunhuawangProf@163.com.
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Wang
D002681:China; D016021:Epidemiologic Studies; D005838:Genotype; D006678:HIV / Q000235:genetics* / Q000472:pathogenicity; D015658:HIV Infections / Q000235:genetics* / Q000821:virology; D006801:Humans; D054299:env Gene Products, Human Immunodeficiency Virus / Q000235:genetics*; D054301:gag Gene Products, Human Immunodeficiency Virus / Q000235:genetics*; D054302:pol Gene Products, Human Immunodeficiency Virus / Q000235:genetics*
D054299:env Gene Products, Human Immunodeficiency Virus; D054301:gag Gene Products, Human Immunodeficiency Virus; D054302:pol Gene Products, Human Immunodeficiency Virus