1. Molecular genotyping and quantitation assay for rotavirus surveillance.
- Author
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Liu J, Lurain K, Sobuz SU, Begum S, Kumburu H, Gratz J, Kibiki G, Toney D, Gautam R, Bowen MD, Petri WA Jr, Haque R, and Houpt ER
- Subjects
- Bangladesh, Child, Preschool, Coinfection epidemiology, Coinfection virology, Humans, Infant, Infant, Newborn, Molecular Epidemiology methods, Multiplex Polymerase Chain Reaction methods, Real-Time Polymerase Chain Reaction methods, Reverse Transcriptase Polymerase Chain Reaction methods, Rotavirus isolation & purification, Sensitivity and Specificity, Tanzania, Virginia, Epidemiological Monitoring, Genotyping Techniques methods, Rotavirus classification, Rotavirus genetics, Rotavirus Infections epidemiology, Rotavirus Infections virology, Viral Load methods
- Abstract
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 P[4], P[6], P[8], P[10], P[11] (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 P[9]. 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., (Copyright © 2014 Elsevier B.V. All rights reserved.)
- Published
- 2015
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