Usefulness of the rapid determination system of viral genome sequences in human stool specimens

Masahiro Miyoshi; Shima Yoshizumi; Setsuko Ishida; Rika Komagome; Hideki Nagano; Shinichi Kudo; Motohiko Okano

doi:10.1016/j.jviromet.2011.11.013

Usefulness of the rapid determination system of viral genome sequences in human stool specimens

J Virol Methods. 2012 Jan;179(1):256-60. doi: 10.1016/j.jviromet.2011.11.013. Epub 2011 Nov 23.

Authors

Masahiro Miyoshi¹, Shima Yoshizumi, Setsuko Ishida, Rika Komagome, Hideki Nagano, Shinichi Kudo, Motohiko Okano

Affiliation

¹ Center for Infectious Diseases Control, Hokkaido Institute of Public Health, North 19 West 12, Kita-ku, Sapporo 060-0819, Japan. [email protected]

PMID: 22123408
DOI: 10.1016/j.jviromet.2011.11.013

Abstract

The rapid determination system of viral genome sequences (the RDV method) consists of detecting and determining the nucleotide sequences of viral genomes without using specific primers. To evaluate the usefulness of the RDV method, the detection of human norovirus (NV) genomes in stool specimens was investigated. In addition, the effect of nuclease treatment of the process was examined. A total of 23 human stool specimens were used, all of which were collected from patients with acute viral gastroenteritis, and were shown to contain NV genomes and also determined the cDNA copy numbers by the real-time reverse transcriptase-polymerase chain reaction. NV genomes were detected by the RDV method with nuclease treatment in nine specimens containing cDNA copies ranging between 6.2×10(9) and 9.8×10(11)/g stool. In contrast, NV genome was found by the method in 15 specimens without nuclease treatment and the number of NV cDNA copies ranged between 1.2×10(6) and 9.8×10(11)/g stool. These results suggest that the RDV method has potential for detecting viral genomes in stool specimens. The procedure without a step of nuclease treatment appears to be sensitive.

Publication types

Evaluation Study
Research Support, Non-U.S. Gov't

MeSH terms

Caliciviridae Infections / diagnosis*
Caliciviridae Infections / virology
Feces / virology*
Gastroenteritis / virology*
Genome, Viral*
Humans
Molecular Sequence Data
Norovirus / genetics
Norovirus / isolation & purification*
RNA, Viral / genetics
Sequence Analysis, DNA / methods*
Viral Load

Substances

RNA, Viral

Associated data

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