A universal primer-independent next-generation sequencing approach for investigations of norovirus outbreaks and novel variants

Abstract Norovirus (NoV) is the most common cause of non-bacterial gastroenteritis and is a major agent associated with outbreaks of gastroenteritis. Conventional molecular genotyping analysis of NoV, used for the identification of transmission routes, relies on standard typing methods (STM) by Sang...

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Main Authors:	Jannik Fonager, Marc Stegger, Lasse Dam Rasmussen, Mille Weismann Poulsen, Jesper Rønn, Paal Skytt Andersen, Thea Kølsen Fischer
Format:	article
Language:	EN
Published:	Nature Portfolio 2017
Subjects:	Medicine R Science Q
Online Access:	https://doaj.org/article/464482d500ad46929117eb437f8421f3
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spelling	oai:doaj.org-article:464482d500ad46929117eb437f8421f32021-12-02T12:31:48ZA universal primer-independent next-generation sequencing approach for investigations of norovirus outbreaks and novel variants10.1038/s41598-017-00926-x2045-2322https://doaj.org/article/464482d500ad46929117eb437f8421f32017-04-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-00926-xhttps://doaj.org/toc/2045-2322Abstract Norovirus (NoV) is the most common cause of non-bacterial gastroenteritis and is a major agent associated with outbreaks of gastroenteritis. Conventional molecular genotyping analysis of NoV, used for the identification of transmission routes, relies on standard typing methods (STM) by Sanger-sequencing of only a limited part of the NoV genome, which could lead to wrong conclusions. Here, we combined a NoV capture method with next generation sequencing (NGS), which increased the proportion of norovirus reads by ~40 fold compared to NGS without prior capture. Of 15 NoV samples from 6 single-genotype outbreaks, near full-genome coverage (>90%) was obtained from 9 samples. Fourteen polymerase (RdRp) and 15 capsid (cap) genotypes were identified compared to 12 and 13 for the STM, respectively. Analysis of 9 samples from two mixed-genotype outbreaks identified 6 RdRp and 6 cap genotypes (two at >90% NoV genome coverage) compared to 4 and 2 for the STM, respectively. Furthermore, complete or partial sequences from the P2 hypervariable region were obtained from 7 of 8 outbreaks and a new NoV recombinant was identified. This approach could therefore strengthen outbreak investigations and could be applied to other important viruses in stool samples such as hepatitis A and enterovirus.Jannik FonagerMarc SteggerLasse Dam RasmussenMille Weismann PoulsenJesper RønnPaal Skytt AndersenThea Kølsen FischerNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-11 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Jannik Fonager Marc Stegger Lasse Dam Rasmussen Mille Weismann Poulsen Jesper Rønn Paal Skytt Andersen Thea Kølsen Fischer A universal primer-independent next-generation sequencing approach for investigations of norovirus outbreaks and novel variants
description	Abstract Norovirus (NoV) is the most common cause of non-bacterial gastroenteritis and is a major agent associated with outbreaks of gastroenteritis. Conventional molecular genotyping analysis of NoV, used for the identification of transmission routes, relies on standard typing methods (STM) by Sanger-sequencing of only a limited part of the NoV genome, which could lead to wrong conclusions. Here, we combined a NoV capture method with next generation sequencing (NGS), which increased the proportion of norovirus reads by ~40 fold compared to NGS without prior capture. Of 15 NoV samples from 6 single-genotype outbreaks, near full-genome coverage (>90%) was obtained from 9 samples. Fourteen polymerase (RdRp) and 15 capsid (cap) genotypes were identified compared to 12 and 13 for the STM, respectively. Analysis of 9 samples from two mixed-genotype outbreaks identified 6 RdRp and 6 cap genotypes (two at >90% NoV genome coverage) compared to 4 and 2 for the STM, respectively. Furthermore, complete or partial sequences from the P2 hypervariable region were obtained from 7 of 8 outbreaks and a new NoV recombinant was identified. This approach could therefore strengthen outbreak investigations and could be applied to other important viruses in stool samples such as hepatitis A and enterovirus.
format	article
author	Jannik Fonager Marc Stegger Lasse Dam Rasmussen Mille Weismann Poulsen Jesper Rønn Paal Skytt Andersen Thea Kølsen Fischer
author_facet	Jannik Fonager Marc Stegger Lasse Dam Rasmussen Mille Weismann Poulsen Jesper Rønn Paal Skytt Andersen Thea Kølsen Fischer
author_sort	Jannik Fonager
title	A universal primer-independent next-generation sequencing approach for investigations of norovirus outbreaks and novel variants
title_short	A universal primer-independent next-generation sequencing approach for investigations of norovirus outbreaks and novel variants
title_full	A universal primer-independent next-generation sequencing approach for investigations of norovirus outbreaks and novel variants
title_fullStr	A universal primer-independent next-generation sequencing approach for investigations of norovirus outbreaks and novel variants
title_full_unstemmed	A universal primer-independent next-generation sequencing approach for investigations of norovirus outbreaks and novel variants
title_sort	universal primer-independent next-generation sequencing approach for investigations of norovirus outbreaks and novel variants
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/464482d500ad46929117eb437f8421f3
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A universal primer-independent next-generation sequencing approach for investigations of norovirus outbreaks and novel variants

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