Molecular Genotyping and Quantitation Assay for Rotavirus Surveillance

Details

• Alternative Title:
  J Virol Methods
• Personal Author:
  Liu, Jie ; Lurain, Kate ; Sobuz, Shihab U. ; Begum, Sharmin ; Kumburu, Happiness ; Gratz, Jean ; Kibiki, Gibson ; Toney, Denise ; Gautam, Rashi ; Bowen, Michael D. ; Petri, William A. ; Haque, Rashidul ; Houpt, Eric R.
  More +
• Description:
  Rotavirus genotyping is useful for surveillance purposes especially in areas where rotavirus vaccination has been or will be implemented. RT-PCR based molecular methods have been applied widely, but quantitative assays targeting a broad spectrum of genotypes have not been developed. Three real time RT-PCR panels were designed to identify G1, G2, G9, G12 (panel GI), G3, G4, G8, G10 (panel GII), and P4, P6, P8, P10, P11 (panel P), respectively. An assay targeting NSP3 was included in both G panels as an internal control. The cognate assays were also formulated as one RT-PCR-Luminex panel for simultaneous detection of all the genotypes listed above plus P9. The assays were evaluated with various rotavirus isolates and 89 clinical samples from Virginia, Bangladesh and Tanzania, and exhibited 95% (81/85) sensitivity compared with the conventional RT-PCR-Gel-electrophoresis method, and 100% concordance with sequencing. Real time assays identified a significantly higher rate of mixed genotypes in Bangladeshi samples than the conventional gel-electrophoresis-based RT-PCR assay (32.5% versus 12.5%, P<0.05). In these mixed infections, the relative abundance of the rotavirus types could be estimated by Cq values. These typing assays detect and discriminate a broad range of G/P types circulating in different geographic regions with high sensitivity and specificity and can be used for rotavirus surveillance.
• Subjects:
  • Bangladesh
  • Child, Preschool
  • Coinfection
  • Epidemiological Monitoring
  • Genotyping Techniques
  • Humans
  • Infant
  • Infant, Newborn
  • Molecular Epidemiology
  • Multiplex Polymerase Chain Reaction
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• Keywords:
  • rotavirus
  • diarrhea
  • genotyping
  • multiplex real time RT-PCR
• Source:
  J Virol Methods. 2014; 213:157-163
• Pubmed ID:
  25526999
• Pubmed Central ID:
  PMC4417650
• Document Type:
  Journal Article
• Funding:
  CC999999/Intramural CDC HHSUnited States/ ; R01 AI043596/AI/NIAID NIH HHSUnited States/
• Volume:
  213
• Download URL:
  https://stacks.cdc.gov/view/cdc/34822/cdc_34822_DS1.pdf
• File Type:
  [PDF - 362.14 KB]
• Collection(s):
  CDC Public Access
• Main Document Checksum:
  urn:sha-512:50a96aad1ef3eab911503b0ae11fd3684ed5cc5cc7c392cfe12f2d619f16f75aea66aee3f37282ad4f59e57d2053d3d5b191dfb3c69280391f2a3db9728f2d2e