title: Specific primer amplification of the VP1 region directed by 5' UTR sequence analysis: enterovirus testing and identification in clinical samples from hand-foot-and-mouth disease patients.
abstract: Many genotypes of the enterovirus (EV) pathogens can cause clinical hand-foot-and-mouth disease (HFMD). Therefore, rapid identification and monitoring of HFMD pathogens can be difficult, especially from the original clinical specimens. In this study, both universal pan-enterovirus and EV71/CA16 VP1-specific primer sets were designed and used to examine clinical specimens from HFMD patients. Based on the initial sequence analysis of the 5'-untanslated region (5'-UTR) and VP1 amplification products, additional primers for the VP1 region were redesigned for further genotyping of the remaining small portion non-EV71/non-CA16 specimens. With a known panel, it was possible to identify 15 out of 16 members using 5'-UTR sequence typing and VP1 typing, suggesting good detectability and genotyping of this method. One strain that was not typed by 5'-UTR was shown to be a recombinant virus. When this method was applied to examine clinical specimens from 44 suspected HFMD patients, 41 were detected as EV positive. In only one case, the VP1 sequence could not be identified. Four types of EVs, including CA16 (26/41, 63.4%), EV71-C4 (6/41, 14.6%), CA6 (5/41, 12.2%) and CA10 (3/41, 7.3%), were detected. In conclusion, 5' UTR amplification sequencing and subsequent VP1 specific primer amplification ensures a high detection rate and good genotyping accuracy in the examination of clinical samples. This detection strategy can be used for routine evaluation and monitoring of HFMD to follow local trends of EV infection.
authors.affiliation: National Institute of Diagnostics and Vaccine Development in Infectious Disease, Xiamen University, Xiamen, China.
authors.forename: Shengxiang
authors.initials: S
authors.lastname: Ge
authors.forename: Qiang
authors.initials: Q
authors.lastname: Yan
authors.forename: Shuizhen
authors.initials: S
authors.lastname: He
authors.forename: Sijie
authors.initials: S
authors.lastname: Zhuang
authors.forename: Jianjun
authors.initials: J
authors.lastname: Niu
authors.forename: Ningshao
authors.initials: N
authors.lastname: Xia
mesh_terms: D020121:5' Untranslated Regions; D000818:Animals; D002675:Child, Preschool; D017931:DNA Primers / Q000235:genetics; D004770:Enterovirus / Q000235:genetics / Q000302:isolation & purification*; D005260:Female; D005838:Genotype; D006232:Hand, Foot and Mouth Disease / Q000175:diagnosis* / Q000821:virology; D006801:Humans; D008297:Male; D025202:Molecular Diagnostic Techniques / Q000379:methods*; D017720:Molecular Epidemiology / Q000379:methods; D021141:Nucleic Acid Amplification Techniques / Q000379:methods*; D017421:Sequence Analysis; D015678:Viral Structural Proteins / Q000235:genetics*; D014773:Virology / Q000379:methods
chemical_list: D020121:5' Untranslated Regions; D017931:DNA Primers; D015678:Viral Structural Proteins
keywords: 5′ UTR; Enterovirus; HFMD; VP1