Characterisation of human astrovirus in a diarrhoea outbreak using nanopore and Sanger sequencing protocols
Abstract Human astroviruses (HAstV) are etiologic agents of acute gastroenteritis that most often afflict young children and elderly adults. Most studies of HAstV have focused on epidemiology. In this study, we collected 10 stool samples from a diarrhea outbreak from a diarrhea sentinel surveillance...
| Main Authors: | , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2023-11-01
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| Series: | Virology Journal |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12985-023-02224-7 |
| _version_ | 1797578174615257088 |
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| author | Jinhui Li Lang Yang Kaiying Wang Zhiyong Gao Peihan Li Yanfeng Lin Leili Jia Quanyi Wang Hongbin Song Peng Li |
| author_facet | Jinhui Li Lang Yang Kaiying Wang Zhiyong Gao Peihan Li Yanfeng Lin Leili Jia Quanyi Wang Hongbin Song Peng Li |
| author_sort | Jinhui Li |
| collection | DOAJ |
| description | Abstract Human astroviruses (HAstV) are etiologic agents of acute gastroenteritis that most often afflict young children and elderly adults. Most studies of HAstV have focused on epidemiology. In this study, we collected 10 stool samples from a diarrhea outbreak from a diarrhea sentinel surveillance hospital in Beijing. Samples were evaluated immediately using parallel multiplex RT-qPCR and nanopore sequencing, and were then amplified by designed primers and Sanger sequencing to obtain whole genome sequences. Six isolates were categorized as HAstV-5 and subjected to whole genome analysis to characterize their genetic variation and evolution. Full genome analysis revealed low genetic variation (99.38–100% identity) among isolates. Phylogenetic analysis showed that all isolates were closely related to domestic strains Yu/1-CHN and 2013/Fuzhou/85. The recombination breakpoint of the six isolates was located at 2741 bp in the overlap region of ORF1a and ORF1b, similar to those of Yu/1-CHN and 2013/Fuzhou/85. Overall, our study highlights the combined use of RT-qPCR and sequencing as an important tool in rapid diagnosis and acquisition of whole genome sequences of HAstV. |
| first_indexed | 2024-03-10T22:18:25Z |
| format | Article |
| id | doaj.art-735e25822e38457885dc5d73af87ebd8 |
| institution | Directory Open Access Journal |
| issn | 1743-422X |
| language | English |
| last_indexed | 2024-03-10T22:18:25Z |
| publishDate | 2023-11-01 |
| publisher | BMC |
| record_format | Article |
| series | Virology Journal |
| spelling | doaj.art-735e25822e38457885dc5d73af87ebd82023-11-19T12:21:26ZengBMCVirology Journal1743-422X2023-11-012011810.1186/s12985-023-02224-7Characterisation of human astrovirus in a diarrhoea outbreak using nanopore and Sanger sequencing protocolsJinhui Li0Lang Yang1Kaiying Wang2Zhiyong Gao3Peihan Li4Yanfeng Lin5Leili Jia6Quanyi Wang7Hongbin Song8Peng Li9Chinese PLA Center for Disease Control and PreventionChinese PLA Center for Disease Control and PreventionChinese PLA Center for Disease Control and Prevention Beijing Center for Disease Prevention and ControlChinese PLA Center for Disease Control and PreventionChinese PLA Center for Disease Control and PreventionChinese PLA Center for Disease Control and Prevention Beijing Center for Disease Prevention and ControlChinese PLA Center for Disease Control and PreventionChinese PLA Center for Disease Control and PreventionAbstract Human astroviruses (HAstV) are etiologic agents of acute gastroenteritis that most often afflict young children and elderly adults. Most studies of HAstV have focused on epidemiology. In this study, we collected 10 stool samples from a diarrhea outbreak from a diarrhea sentinel surveillance hospital in Beijing. Samples were evaluated immediately using parallel multiplex RT-qPCR and nanopore sequencing, and were then amplified by designed primers and Sanger sequencing to obtain whole genome sequences. Six isolates were categorized as HAstV-5 and subjected to whole genome analysis to characterize their genetic variation and evolution. Full genome analysis revealed low genetic variation (99.38–100% identity) among isolates. Phylogenetic analysis showed that all isolates were closely related to domestic strains Yu/1-CHN and 2013/Fuzhou/85. The recombination breakpoint of the six isolates was located at 2741 bp in the overlap region of ORF1a and ORF1b, similar to those of Yu/1-CHN and 2013/Fuzhou/85. Overall, our study highlights the combined use of RT-qPCR and sequencing as an important tool in rapid diagnosis and acquisition of whole genome sequences of HAstV.https://doi.org/10.1186/s12985-023-02224-7Diarrhea outbreakHuman astrovirusesNanopore sequencingSanger sequencingWhole genome |
| spellingShingle | Jinhui Li Lang Yang Kaiying Wang Zhiyong Gao Peihan Li Yanfeng Lin Leili Jia Quanyi Wang Hongbin Song Peng Li Characterisation of human astrovirus in a diarrhoea outbreak using nanopore and Sanger sequencing protocols Virology Journal Diarrhea outbreak Human astroviruses Nanopore sequencing Sanger sequencing Whole genome |
| title | Characterisation of human astrovirus in a diarrhoea outbreak using nanopore and Sanger sequencing protocols |
| title_full | Characterisation of human astrovirus in a diarrhoea outbreak using nanopore and Sanger sequencing protocols |
| title_fullStr | Characterisation of human astrovirus in a diarrhoea outbreak using nanopore and Sanger sequencing protocols |
| title_full_unstemmed | Characterisation of human astrovirus in a diarrhoea outbreak using nanopore and Sanger sequencing protocols |
| title_short | Characterisation of human astrovirus in a diarrhoea outbreak using nanopore and Sanger sequencing protocols |
| title_sort | characterisation of human astrovirus in a diarrhoea outbreak using nanopore and sanger sequencing protocols |
| topic | Diarrhea outbreak Human astroviruses Nanopore sequencing Sanger sequencing Whole genome |
| url | https://doi.org/10.1186/s12985-023-02224-7 |
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