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Decoding noises in HIV computational genotyping
Virology ( IF 3.7 ) Pub Date : 2017-09-14 , DOI: 10.1016/j.virol.2017.08.031
MingRui Jia , Timothy Shaw , Xing Zhang , Dong Liu , Ye Shen , Amara E. Ezeamama , Chunfu Yang , Ming Zhang

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.



中文翻译:

HIV计算基因分型中的解码噪声

缺乏一致和可靠的基因分型系统会严重阻碍HIV基因组学的发病机理,适应性,毒力,耐药性以及基于基因组的医疗保健和治疗。目前,未知的基因分型,即分子基因分型中的背景噪声及其对流行病监测的影响尚不清楚。我们首次提出了对HIV基因分型质量的综合评估。从世界范围内公开的记录中检索HIV序列数据,并对其进行系统的基因分型评估。结果显示,基因分型错误的病例在全球发生率为4.6%,存在一些地区性和高风险人群异质性。结果还显示出gp120中存在一致的错误基因分型模式在所有研究的人群中,除了与男人发生性关系的男人群体之外。我们的研究还表明,在基因分型错误的病例中,新型病毒具有多样性。最后,本研究再次强调了实施标准化基因分型流程的重要性,以避免基因分型差异,并加深我们对各种流行病学背景下病毒进化的理解。

更新日期:2017-09-14
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