Defining the Enterovirus Diversity Landscape of a Fecal Sample: A Methodological Challenge?
Enteroviruses are a group of over 250 naked icosahedral virus serotypes that have been associated with clinical conditions that range from intrauterine enterovirus transmission withfataloutcome through encephalitis and meningitis, to paralysis. Classically, enterovirus detection was done by assaying...
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| Format: | Article |
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MDPI AG
2016-01-01
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| Series: | Viruses |
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| Online Access: | http://www.mdpi.com/1999-4915/8/1/18 |
| _version_ | 1818511907364012032 |
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| author | Temitope Oluwasegun Cephas Faleye Moses Olubusuyi Adewumi Johnson Adekunle Adeniji |
| author_facet | Temitope Oluwasegun Cephas Faleye Moses Olubusuyi Adewumi Johnson Adekunle Adeniji |
| author_sort | Temitope Oluwasegun Cephas Faleye |
| collection | DOAJ |
| description | Enteroviruses are a group of over 250 naked icosahedral virus serotypes that have been associated with clinical conditions that range from intrauterine enterovirus transmission withfataloutcome through encephalitis and meningitis, to paralysis. Classically, enterovirus detection was done by assaying for the development of the classic enterovirus-specific cytopathic effect in cell culture. Subsequently, the isolates were historically identified by a neutralization assay. More recently, identification has been done by reverse transcriptase-polymerase chain reaction (RT-PCR). However, in recent times, there is a move towards direct detection and identification of enteroviruses from clinical samples using the cell culture-independent RT semi-nested PCR (RT-snPCR) assay. This RT-snPCR procedure amplifies the VP1 gene, which is then sequenced and used for identification. However, while cell culture-based strategies tend to show a preponderance of certain enterovirus species depending on the cell lines included in the isolation protocol, the RT-snPCR strategies tilt in a different direction. Consequently, it is becoming apparent that the diversity observed in certain enterovirus species, e.g., enterovirus species B(EV-B), might not be because they are the most evolutionarily successful. Rather, it might stem from cell line-specific bias accumulated over several years of use of the cell culture-dependent isolation protocols. Furthermore, it might also be a reflection of the impact of the relative genome concentration on the result of pan-enterovirus VP1 RT-snPCR screens used during the identification of cell culture isolates. This review highlights the impact of these two processes on the current diversity landscape of enteroviruses and the need to re-assess enterovirus detection and identification algorithms in a bid to better balance our understanding of the enterovirus diversity landscape. |
| first_indexed | 2024-12-10T23:39:26Z |
| format | Article |
| id | doaj.art-83dc7d63289d4eeda25e598490aeb874 |
| institution | Directory Open Access Journal |
| issn | 1999-4915 |
| language | English |
| last_indexed | 2024-12-10T23:39:26Z |
| publishDate | 2016-01-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Viruses |
| spelling | doaj.art-83dc7d63289d4eeda25e598490aeb8742022-12-22T01:29:05ZengMDPI AGViruses1999-49152016-01-01811810.3390/v8010018v8010018Defining the Enterovirus Diversity Landscape of a Fecal Sample: A Methodological Challenge?Temitope Oluwasegun Cephas Faleye0Moses Olubusuyi Adewumi1Johnson Adekunle Adeniji2Department of Microbiology, Faculty of Science, Ekiti State University, Ado Ekiti, Ekiti State, NigeriaDepartment of Virology, College of Medicine, University of Ibadan, Ibadan, Oyo State, NigeriaWHO National Polio Laboratory, Department of Virology, College of Medicine, University of Ibadan, Ibadan, Oyo State, NigeriaEnteroviruses are a group of over 250 naked icosahedral virus serotypes that have been associated with clinical conditions that range from intrauterine enterovirus transmission withfataloutcome through encephalitis and meningitis, to paralysis. Classically, enterovirus detection was done by assaying for the development of the classic enterovirus-specific cytopathic effect in cell culture. Subsequently, the isolates were historically identified by a neutralization assay. More recently, identification has been done by reverse transcriptase-polymerase chain reaction (RT-PCR). However, in recent times, there is a move towards direct detection and identification of enteroviruses from clinical samples using the cell culture-independent RT semi-nested PCR (RT-snPCR) assay. This RT-snPCR procedure amplifies the VP1 gene, which is then sequenced and used for identification. However, while cell culture-based strategies tend to show a preponderance of certain enterovirus species depending on the cell lines included in the isolation protocol, the RT-snPCR strategies tilt in a different direction. Consequently, it is becoming apparent that the diversity observed in certain enterovirus species, e.g., enterovirus species B(EV-B), might not be because they are the most evolutionarily successful. Rather, it might stem from cell line-specific bias accumulated over several years of use of the cell culture-dependent isolation protocols. Furthermore, it might also be a reflection of the impact of the relative genome concentration on the result of pan-enterovirus VP1 RT-snPCR screens used during the identification of cell culture isolates. This review highlights the impact of these two processes on the current diversity landscape of enteroviruses and the need to re-assess enterovirus detection and identification algorithms in a bid to better balance our understanding of the enterovirus diversity landscape.http://www.mdpi.com/1999-4915/8/1/18enterovirusesenterovirus diversity landscapecell culturespecies bias |
| spellingShingle | Temitope Oluwasegun Cephas Faleye Moses Olubusuyi Adewumi Johnson Adekunle Adeniji Defining the Enterovirus Diversity Landscape of a Fecal Sample: A Methodological Challenge? Viruses enteroviruses enterovirus diversity landscape cell culture species bias |
| title | Defining the Enterovirus Diversity Landscape of a Fecal Sample: A Methodological Challenge? |
| title_full | Defining the Enterovirus Diversity Landscape of a Fecal Sample: A Methodological Challenge? |
| title_fullStr | Defining the Enterovirus Diversity Landscape of a Fecal Sample: A Methodological Challenge? |
| title_full_unstemmed | Defining the Enterovirus Diversity Landscape of a Fecal Sample: A Methodological Challenge? |
| title_short | Defining the Enterovirus Diversity Landscape of a Fecal Sample: A Methodological Challenge? |
| title_sort | defining the enterovirus diversity landscape of a fecal sample a methodological challenge |
| topic | enteroviruses enterovirus diversity landscape cell culture species bias |
| url | http://www.mdpi.com/1999-4915/8/1/18 |
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