A universal primer-independent next-generation sequencing approach for investigations of norovirus outbreaks and novel variants
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.
| Medienart: |
E-Artikel |
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| Erscheinungsjahr: |
2017 |
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| Erschienen: |
2017 |
| Enthalten in: |
Zur Gesamtaufnahme - volume:7 |
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| Enthalten in: |
Scientific reports - 7(2017), 1 vom: 11. Apr., Seite 813 |
| Sprache: |
Englisch |
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| Beteiligte Personen: |
Fonager, Jannik [VerfasserIn] |
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| Anmerkungen: |
Date Completed 18.09.2018 Date Revised 12.11.2023 published: Electronic Citation Status MEDLINE |
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| doi: |
10.1038/s41598-017-00926-x |
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| Förderinstitution / Projekttitel: |
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NLM270879897 |
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| 520 | |a 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 | ||
| 650 | 4 | |a Journal Article | |
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| 700 | 1 | |a Rasmussen, Lasse Dam |e verfasserin |4 aut | |
| 700 | 1 | |a Poulsen, Mille Weismann |e verfasserin |4 aut | |
| 700 | 1 | |a Rønn, Jesper |e verfasserin |4 aut | |
| 700 | 1 | |a Andersen, Paal Skytt |e verfasserin |4 aut | |
| 700 | 1 | |a Fischer, Thea Kølsen |e verfasserin |4 aut | |
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