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Advances in Virology
Volume 2016 (2016), Article ID 1412838, 12 pages
http://dx.doi.org/10.1155/2016/1412838
Research Article

Direct Detection and Identification of Enteroviruses from Faeces of Healthy Nigerian Children Using a Cell-Culture Independent RT-Seminested PCR Assay

1Department of Virology, College of Medicine, University of Ibadan, Ibadan, Oyo State, Nigeria
2Department of Microbiology, Faculty of Science, Ekiti State University, Ado Ekiti, Ekiti, Nigeria
3Department of Microbiology, Faculty of Science, University of Ibadan, Ibadan, Oyo State, Nigeria
4WHO National Polio Laboratory, University of Ibadan, Ibadan, Oyo State, Nigeria

Received 27 December 2015; Accepted 11 February 2016

Academic Editor: George N. Pavlakis

Copyright © 2016 Temitope Oluwasegun Cephas Faleye et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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.