Decoding Noises in HIV Computational Genotyping

Details

• Alternative Title:
  Virology
• Personal Author:
  Jia, MingRui ; Shaw, Timothy ; Zhang, Xing ; Liu, Dong ; Shen, Ye ; Ezeamama, Amara E. ; Yang, Chunfu ; Zhang, Ming
• Description:
  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.
• Subjects:
  Computational Biology Diagnostic Errors Genetic Variation Genotype Genotyping Techniques HIV Humans
• Keywords:
  Chlorination Epidemic Surveillance Household Water Treatment Molecular Genotyping Safe Water Storage
• Source:
  Virology. 511:249-255
• Pubmed ID:
  28918303
• Pubmed Central ID:
  PMC6443101
• Document Type:
  Journal Article
• Funding:
  CC999999/Intramural CDC HHSUnited States/ ; R03 AI104258/AI/NIAID NIH HHSUnited States/ ; R03 AI120203/AI/NIAID NIH HHSUnited States/
• Volume:
  511
• Collection(s):
  CDC Public Access
• Main Document Checksum:
  urn:sha256:0d2d9d3c71723e3f5074a2be459700cf437b18f61af3c00135839c149b609057
• Download URL:
  https://stacks.cdc.gov/view/cdc/77173/cdc_77173_DS1.pdf
• File Type:
  [PDF - 3.07 MB ]