Direct Detection and Identification of Enteroviruses from Faeces of Healthy Nigerian Children Using a Cell-Culture Independent RT-Seminested PCR Assay
Open Access
- 20 March 2016
- journal article
- research article
- Published by Hindawi Limited in Advances in Virology
- Vol. 2016, 1-12
- https://doi.org/10.1155/2016/1412838
Abstract
Recently, a cell-culture independent protocol for detection of enteroviruses from clinical specimen was recommended by the WHO for surveillance alongside the previously established protocols. Here, we investigated whether this new protocol will show the same enterovirus diversity landscape as the established cell-culture dependent protocols. Faecal samples were collected from sixty apparently healthy children in Ibadan, Nigeria. Samples were resuspended in phosphate buffered saline, RNA was extracted, and the VP1 gene was amplified using WHO recommended RT-snPCR protocol. Amplicons were sequenced and sequences subjected to phylogenetic analysis. Fifteen (25%) of the 60 samples yielded the expected band size. Of the 15 amplicons sequenced, 12 were exploitable. The remaining 3 had electropherograms with multiple peaks and were unexploitable. Eleven of the 12 exploitable sequences were identified as Coxsackievirus A1 (CVA1), CVA3, CVA4, CVA8, CVA20, echovirus 32 (E32), enterovirus 71 (EV71), EVB80, and EVC99. Subsequently, the last exploitable sequence was identified as enterobacteriophage baseplate gene by nucleotide BLAST. The results of this study document the first description of molecular sequence data on CVA1, CVA8, and E32 strains present in Nigeria. The result further showed that species A enteroviruses were more commonly detected in the region when cell-culture bias is bypassed.Keywords
This publication has 30 references indexed in Scilit:
- High Frequency and Diversity of Species C Enteroviruses in Cameroon and Neighboring CountriesJournal of Clinical Microbiology, 2013
- Antigenic Diversity of Enteroviruses Associated with Nonpolio Acute Flaccid Paralysis, India, 2007–2009Emerging Infectious Diseases, 2012
- Molecular Characterization of Human Enteroviruses in the Central African Republic: Uncovering Wide Diversity and Identification of a New Human Enterovirus A71 GenogroupJournal of Clinical Microbiology, 2012
- MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony MethodsMolecular Biology and Evolution, 2011
- An automated genotyping tool for enteroviruses and norovirusesJournal of Clinical Virology, 2011
- From Emergence to Eradication: The Epidemiology of Poliomyelitis DeconstructedAmerican Journal of Epidemiology, 2010
- Eight Years of Experience with Molecular Identification of Human EnterovirusesJournal of Clinical Microbiology, 2008
- Sensitive, Seminested PCR Amplification of VP1 Sequences for Direct Identification of All Enterovirus Serotypes from Original Clinical SpecimensJournal of Clinical Microbiology, 2006
- Species-specific RT-PCR amplification of human enteroviruses: a tool for rapid species identification of uncharacterized enterovirusesJournal of General Virology, 2006
- A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequencesJournal of Molecular Evolution, 1980