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Enhancement of detection and quantification of rotavirus in stool using a modified real-time RT-PCR assay

✍ Scribed by Molly M. Freeman; Tara Kerin; Jennifer Hull; Karen McCaustland; Jon Gentsch

Publisher
John Wiley and Sons
Year
2008
Tongue
English
Weight
129 KB
Volume
80
Category
Article
ISSN
0146-6615

No coin nor oath required. For personal study only.

✦ Synopsis

Abstract

A sensitive and specific real‐time RT‐PCR assay to detect rotavirus in stool samples was optimized and validated using a wide range of rotavirus genotypes. The target of the original TaqMan® assay is an 87 bp fragment of the highly conserved non‐structural protein 3 (NSP3) gene. Here we modified the original assay by introducing degeneracy into the forward primer to account for sequence variation between rotavirus genotypes, added four nucleotides at the 3′ end of the reverse primer to reduce its stability, and modified the probe label. Amplification and detection conditions were optimized using purified dsRNA from two cultivated strains. The limit of detection of the modified assay was calculated to be approximately 44 genome copies per reaction. To validate the reactivity of the assay, 103 archived RNAs that had been extracted from stools and genotyped during routine U.S. surveillance were tested. Samples were selected to represent both rare and common genotypes that have been detected in U.S. children. Nine genotypes known to be circulating in the United States were detected by the real‐time assay demonstrating broad reactivity. In addition, other enteric viruses were not detected demonstrating that the assay is specific for rotavirus and does not cross‐react with other viruses potentially present in stool samples. This real‐time assay is an important addition to the arsenal of molecular tools available to quickly identify rotavirus in stool samples during routine surveillance. J. Med. Virol. 80:1489–1496, 2008. © 2008 Wiley‐Liss, Inc.

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