title: Multiplexed one-step RT-PCR VP7 and VP4 genotyping assays for rotaviruses using updated primers.
abstract: The current two-step VP7 and VP4 genotyping RT-PCR assays for rotaviruses have been linked consistently to genotyping failure in an estimated 30% of RVA positive samples worldwide. We have developed a VP7 and VP4 multiplexed one-step genotyping assays using updated primers generated from contemporary VP7 and VP4 sequences. To determine assay specificity and sensitivity, 17 reference virus strains, 6 non-target gastroenteritis viruses and 725 clinical samples carrying the most common VP7 (G1, G2, G3, G4, G9, and G12) and VP4 (P[4], P[6], P[8], P[9] and P[10]) genotypes were tested in this study. All reference RVA strain targets yielded amplicons of the expected sizes and non-target genotypes and gastroenteritis viruses were not detected by either assay. Out of the 725 clinical samples tested, the VP7 and VP4 assays were able to assigned specific genotypes to 711 (98.1%) and 714 (98.5%), respectively. The remaining unassigned samples were re-tested for RVA antigen using EIA and qRT-PCR assays and all were found to be negative. The overall specificity, sensitivity and limit of detection of the VP7 assay were in the ranges of 99.0-100%, 94.0-100% and 8.6×10(1) to 8.6×10(2) copies of RNA/reaction, respectively. For the VP4 assay, the overall specificity, sensitivity and limit of detection assay were in the ranges of 100%, 94.0-100% and ≤1 to 8.6×10(2) copies of RNA/reaction, respectively. Here we report two highly robust, accurate, efficient, affordable and documentable gel-based genotyping systems which are capable of genotyping 97.8% of the six common VP7 and 98.3% of the five common VP4 genotypes of RVA strains which are responsible for approximately 88.2% of all RVA infections worldwide.
authors.affiliation: Gastroenteritis and Respiratory Viruses Laboratory Branch, Division of Viral Diseases, NCIRD, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA. Electronic address: mdi4@cdc.gov.
authors.forename: Mathew D
authors.initials: MD
authors.lastname: Esona
authors.affiliation: Gastroenteritis and Respiratory Viruses Laboratory Branch, Division of Viral Diseases, NCIRD, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA.
authors.forename: Rashi
authors.initials: R
authors.lastname: Gautam
authors.affiliation: Gastroenteritis and Respiratory Viruses Laboratory Branch, Division of Viral Diseases, NCIRD, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA.
authors.forename: Ka Ian
authors.initials: KI
authors.lastname: Tam
authors.affiliation: Furman University, Greenville, SC, USA.
authors.forename: Alice
authors.initials: A
authors.lastname: Williams
authors.affiliation: Gastroenteritis and Respiratory Viruses Laboratory Branch, Division of Viral Diseases, NCIRD, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA.
authors.forename: Slavica
authors.initials: S
authors.lastname: Mijatovic-Rustempasic
authors.affiliation: Gastroenteritis and Respiratory Viruses Laboratory Branch, Division of Viral Diseases, NCIRD, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA.
authors.forename: Michael D
authors.initials: MD
authors.lastname: Bowen
mesh_terms: D000956:Antigens, Viral / Q000235:genetics*; D036022:Capsid Proteins / Q000235:genetics*; D017931:DNA Primers / Q000235:genetics; D060005:Genotyping Techniques / Q000379:methods*; D006801:Humans; D060885:Multiplex Polymerase Chain Reaction / Q000379:methods*; D020133:Reverse Transcriptase Polymerase Chain Reaction / Q000379:methods*; D012401:Rotavirus / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D012680:Sensitivity and Specificity
chemical_list: D000956:Antigens, Viral; D036022:Capsid Proteins; D017931:DNA Primers; C060339:VP4 protein, Rotavirus; C050779:VP7 protein, Rotavirus
keywords: Rotavirus; Updated primers; VP7 and VP4 genes multiplexed gel-based genotyping