Title |
Decoding noises in HIV computational genotyping
|
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Published in |
Virology, September 2017
|
DOI | 10.1016/j.virol.2017.08.031 |
Pubmed ID | |
Authors |
MingRui Jia, Timothy Shaw, Xing Zhang, Dong Liu, Ye Shen, Amara E. Ezeamama, Chunfu Yang, Ming Zhang |
Abstract |
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. |
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Demographic breakdown
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Other | 0 | 0% |
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