Broadly reactive real‐time reverse transcription‐polymerase chain reaction assay for the detection of human sapovirus genotypes

• Published in: Journal of medical virology Vol. 91; no. 3; pp. 370 - 377
• Main Authors: Oka, Tomoichiro, Iritani, Nobuhiro, Yamamoto, Seiji P., Mori, Kohji, Ogawa, Tomoko, Tatsumi, Chika, Shibata, Shinichiro, Harada, Seiya, Wu, Fang‐Tzy
• Format: Journal Article
• Language: English
• Published: United States Wiley Subscription Services, Inc 01.03.2019
• Subjects: Assaying; Caliciviridae Infections - diagnosis; Caliciviridae Infections - virology; Deoxyribonucleic acid; DNA; DNA Primers - genetics; DNA Probes; Feces - virology; Gastroenteritis; Gene sequencing; Genetic Variation; Genotype; Genotypes; Health and safety screening; Humans; Polymerase chain reaction; Real-Time Polymerase Chain Reaction; real‐time reverse transcription‐polymerase chain reaction (RT‐PCR); Reverse transcription; RNA, Viral - genetics; Rotavirus; sapovirus; Sapovirus - classification; Sapovirus - genetics; Sensitivity and Specificity; Shellfish; Strains (organisms); TaqMan probe; Virology; Viruses; Water analysis; Water sampling; sapovirus; real-time reverse transcription-polymerase chain reaction (RT-PCR); TaqMan probe
• ISSN: 0146-6615; 1096-9071
• DOI: 10.1002/jmv.25334

Sapoviruses are associated with acute gastroenteritis. Human sapoviruses are classified into four distinct genogroups (GI, GII, GIV, and GV) based on their capsid gene sequences. A TaqMan probe‐based real‐time reverse transcription‐polymerase chain reaction (RT‐PCR) assay that detects the representative strains of these four genogroups is widely used for screening fecal specimens, shellfish, and environmental water samples. However, since the development of this test, more genetically diverse sapovirus strains have been reported, which are not detectable by the previously established assays. In this study, we report the development of a broader‐range sapovirus real‐time RT‐PCR assay. The assay can detect 2.5 × 107 and 2.5 × 10 1 copies of sapovirus and therefore is as sensitive as the previous test. Analysis using clinical stool specimens or synthetic DNA revealed that the new system detected strains representative of all the 18 human sapovirus genotypes: GI.1‐7, GII.1‐8, GIV.1, and GV.1, 2. No cross‐reactivity was observed against other representative common enteric viruses (norovirus, rotavirus, astrovirus, and adenovirus). This new assay will be useful as an improved, broadly reactive, and specific screening tool for human sapoviruses.