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Detection and Typing of Human Enteroviruses from Clinical Samples by Entire-Capsid Next Generation Sequencing
There are increasing concerns of infections by enteroviruses (EVs) causing severe disease in humans. EV diagnostic laboratory methods show differences in sensitivity and specificity as well as the level of genetic information provided. We examined a detection method for EVs based on next generation...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8070635/ https://www.ncbi.nlm.nih.gov/pubmed/33918088 http://dx.doi.org/10.3390/v13040641 |
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author | Majumdar, Manasi Celma, Cristina Pegg, Elaine Polra, Krunal Dunning, Jake Martin, Javier |
author_facet | Majumdar, Manasi Celma, Cristina Pegg, Elaine Polra, Krunal Dunning, Jake Martin, Javier |
author_sort | Majumdar, Manasi |
collection | PubMed |
description | There are increasing concerns of infections by enteroviruses (EVs) causing severe disease in humans. EV diagnostic laboratory methods show differences in sensitivity and specificity as well as the level of genetic information provided. We examined a detection method for EVs based on next generation sequencing (NGS) analysis of amplicons covering the entire capsid coding region directly synthesized from clinical samples. One hundred and twelve clinical samples from England; previously shown to be positive for EVs, were analyzed. There was high concordance between the results obtained by the new NGS approach and those from the conventional Sanger method used originally with agreement in the serotypes identified in the 83 samples that were typed by both methods. The sensitivity and specificity of the NGS method compared to those of the conventional Sanger sequencing typing assay were 94.74% (95% confidence interval, 73.97% to 99.87%) and 97.85% (92.45% to 99.74%) for Enterovirus A, 93.75% (82.80% to 98.69%) and 89.06% (78.75% to 95.49%) for Enterovirus B, 100% (59.04% to 100%) and 98.10% (93.29% to 99.77%) for Enterovirus C, and 100% (75.29% to 100%) and 100% (96.34% to 100%) for Enterovirus D. The NGS method identified five EVs in previously untyped samples as well as additional viruses in some samples, indicating co-infection. This method can be easily expanded to generate whole-genome EV sequences as we show here for EV-D68. Information from capsid and whole-genome sequences is critical to help identifying the genetic basis for changes in viral properties and establishing accurate spatial-temporal associations between EV strains of public health relevance. |
format | Online Article Text |
id | pubmed-8070635 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-80706352021-04-26 Detection and Typing of Human Enteroviruses from Clinical Samples by Entire-Capsid Next Generation Sequencing Majumdar, Manasi Celma, Cristina Pegg, Elaine Polra, Krunal Dunning, Jake Martin, Javier Viruses Article There are increasing concerns of infections by enteroviruses (EVs) causing severe disease in humans. EV diagnostic laboratory methods show differences in sensitivity and specificity as well as the level of genetic information provided. We examined a detection method for EVs based on next generation sequencing (NGS) analysis of amplicons covering the entire capsid coding region directly synthesized from clinical samples. One hundred and twelve clinical samples from England; previously shown to be positive for EVs, were analyzed. There was high concordance between the results obtained by the new NGS approach and those from the conventional Sanger method used originally with agreement in the serotypes identified in the 83 samples that were typed by both methods. The sensitivity and specificity of the NGS method compared to those of the conventional Sanger sequencing typing assay were 94.74% (95% confidence interval, 73.97% to 99.87%) and 97.85% (92.45% to 99.74%) for Enterovirus A, 93.75% (82.80% to 98.69%) and 89.06% (78.75% to 95.49%) for Enterovirus B, 100% (59.04% to 100%) and 98.10% (93.29% to 99.77%) for Enterovirus C, and 100% (75.29% to 100%) and 100% (96.34% to 100%) for Enterovirus D. The NGS method identified five EVs in previously untyped samples as well as additional viruses in some samples, indicating co-infection. This method can be easily expanded to generate whole-genome EV sequences as we show here for EV-D68. Information from capsid and whole-genome sequences is critical to help identifying the genetic basis for changes in viral properties and establishing accurate spatial-temporal associations between EV strains of public health relevance. MDPI 2021-04-08 /pmc/articles/PMC8070635/ /pubmed/33918088 http://dx.doi.org/10.3390/v13040641 Text en © 2021 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Majumdar, Manasi Celma, Cristina Pegg, Elaine Polra, Krunal Dunning, Jake Martin, Javier Detection and Typing of Human Enteroviruses from Clinical Samples by Entire-Capsid Next Generation Sequencing |
title | Detection and Typing of Human Enteroviruses from Clinical Samples by Entire-Capsid Next Generation Sequencing |
title_full | Detection and Typing of Human Enteroviruses from Clinical Samples by Entire-Capsid Next Generation Sequencing |
title_fullStr | Detection and Typing of Human Enteroviruses from Clinical Samples by Entire-Capsid Next Generation Sequencing |
title_full_unstemmed | Detection and Typing of Human Enteroviruses from Clinical Samples by Entire-Capsid Next Generation Sequencing |
title_short | Detection and Typing of Human Enteroviruses from Clinical Samples by Entire-Capsid Next Generation Sequencing |
title_sort | detection and typing of human enteroviruses from clinical samples by entire-capsid next generation sequencing |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8070635/ https://www.ncbi.nlm.nih.gov/pubmed/33918088 http://dx.doi.org/10.3390/v13040641 |
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