标题：Decoding noises in HIV computational genotyping
作者：Jia, MingRui; Shaw, Timothy; Zhang, Xing; Liu, Dong; Shen, Ye; Ezeamama, Amara E.; Yang, Chunfu; Zhang, Ming
作者机构：[Jia, MingRui] Shandong Univ, Shandong Prov Hosp, Dept Pain Management, 324 Jingwu Rd, Jinan 250021, Shandong, Peoples R China.; [Jia, MingRui; Shaw 更多
通讯作者地址：[Zhang, M]Univ Georgia, Dept Epidemiol & Biostat, 101 Buck Rd, Athens, GA 30602 USA.
关键词：HIV; Molecular genotyping; Epidemic surveillance
摘要：Lack of a consistent and reliable genotyping system can critically impede HIV genomic research on pathogenesis, fitness, virulence, drug resistance, and genomic-based healthcare and treatment. At present, mis-genotyping, i.e., background noises in molecular genotyping, and its impact on epidemic surveillance is unknown. For the first time, we present a comprehensive assessment of HIV genotyping quality. HIV sequence data were retrieved from worldwide published records, and subjected to a systematic genotyping assessment pipeline. Results showed that mis-genotyped cases occurred at 4.6% globally, with some regional and high-risk population heterogeneities. Results also revealed a consistent mis-genotyping pattern in gp120 in all studied populations except the group of men who have sex with men. Our study also suggests novel virus diversities in the mis-genotyped cases. Finally, this study reemphasizes the importance of implementing a standardized genotyping pipeline to avoid genotyping disparity and to advance our understanding of virus evolution in various epidemiological settings.