SMRT sequencing revealed the diversity and characteristics of defective interfering RNAs in influenza A (H7N9) virus infection
Influenza defective interfering (DI) particles are replication-incompetent viruses carrying large internal deletion in the genome. The loss of essential genetic information causes abortive viral replication, which can be rescued by co-infection with a helper virus that possesses an intact genome. De...
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Taylor & Francis Group
2019-01-01
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| Series: | Emerging Microbes and Infections |
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| Online Access: | https://www.tandfonline.com/doi/10.1080/22221751.2019.1611346 |
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| author | Wing-Yu Lui Chun-Kit Yuen Can Li Wan Man Wong Pak-Yin Lui Chi-Ho Lin Kwok-Hung Chan Hanjun Zhao Honglin Chen Kelvin K. W. To Anna J. X Zhang Kwok-Yung Yuen Kin-Hang Kok |
| author_facet | Wing-Yu Lui Chun-Kit Yuen Can Li Wan Man Wong Pak-Yin Lui Chi-Ho Lin Kwok-Hung Chan Hanjun Zhao Honglin Chen Kelvin K. W. To Anna J. X Zhang Kwok-Yung Yuen Kin-Hang Kok |
| author_sort | Wing-Yu Lui |
| collection | DOAJ |
| description | Influenza defective interfering (DI) particles are replication-incompetent viruses carrying large internal deletion in the genome. The loss of essential genetic information causes abortive viral replication, which can be rescued by co-infection with a helper virus that possesses an intact genome. Despite reports of DI particles present in seasonal influenza A H1N1 infections, their existence in human infections by the avian influenza A viruses, such as H7N9, has not been studied. Here we report the ubiquitous presence of DI-RNAs in nasopharyngeal aspirates of H7N9-infected patients. Single Molecule Real Time (SMRT) sequencing was first applied and long-read sequencing analysis showed that a variety of H7N9 DI-RNA species were present in the patient samples and human bronchial epithelial cells. In several abundantly expressed DI-RNA species, long overlapping sequences have been identified around at the breakpoint region and the other side of deleted region. Influenza DI-RNA is known as a defective viral RNA with single large internal deletion. Beneficial to the long-read property of SMRT sequencing, double and triple internal deletions were identified in half of the DI-RNA species. In addition, we examined the expression of DI-RNAs in mice infected with sublethal dose of H7N9 virus at different time points. Interestingly, DI-RNAs were abundantly expressed as early as day 2 post-infection. Taken together, we reveal the diversity and characteristics of DI-RNAs found in H7N9-infected patients, cells and animals. Further investigations on this overwhelming generation of DI-RNA may provide important insights into the understanding of H7N9 viral replication and pathogenesis. |
| format | Article |
| id | doaj-art-f33b858fe2994e339e8ecd9c7eb0e18f |
| institution | OA Journals |
| issn | 2222-1751 |
| language | English |
| publishDate | 2019-01-01 |
| publisher | Taylor & Francis Group |
| record_format | Article |
| series | Emerging Microbes and Infections |
| spelling | doaj-art-f33b858fe2994e339e8ecd9c7eb0e18f2025-08-20T01:54:18ZengTaylor & Francis GroupEmerging Microbes and Infections2222-17512019-01-018166267410.1080/22221751.2019.1611346SMRT sequencing revealed the diversity and characteristics of defective interfering RNAs in influenza A (H7N9) virus infectionWing-Yu Lui0Chun-Kit Yuen1Can Li2Wan Man Wong3Pak-Yin Lui4Chi-Ho Lin5Kwok-Hung Chan6Hanjun Zhao7Honglin Chen8Kelvin K. W. To9Anna J. X Zhang10Kwok-Yung Yuen11Kin-Hang Kok12Department of Microbiology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, People’s Republic of ChinaDepartment of Microbiology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, People’s Republic of ChinaDepartment of Microbiology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, People’s Republic of ChinaDepartment of Microbiology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, People’s Republic of ChinaDepartment of Microbiology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, People’s Republic of ChinaCenter for Genome Sciences, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, People’s Republic of ChinaDepartment of Microbiology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, People’s Republic of ChinaDepartment of Microbiology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, People’s Republic of ChinaDepartment of Microbiology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, People’s Republic of ChinaDepartment of Microbiology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, People’s Republic of ChinaDepartment of Microbiology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, People’s Republic of ChinaDepartment of Microbiology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, People’s Republic of ChinaDepartment of Microbiology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, People’s Republic of ChinaInfluenza defective interfering (DI) particles are replication-incompetent viruses carrying large internal deletion in the genome. The loss of essential genetic information causes abortive viral replication, which can be rescued by co-infection with a helper virus that possesses an intact genome. Despite reports of DI particles present in seasonal influenza A H1N1 infections, their existence in human infections by the avian influenza A viruses, such as H7N9, has not been studied. Here we report the ubiquitous presence of DI-RNAs in nasopharyngeal aspirates of H7N9-infected patients. Single Molecule Real Time (SMRT) sequencing was first applied and long-read sequencing analysis showed that a variety of H7N9 DI-RNA species were present in the patient samples and human bronchial epithelial cells. In several abundantly expressed DI-RNA species, long overlapping sequences have been identified around at the breakpoint region and the other side of deleted region. Influenza DI-RNA is known as a defective viral RNA with single large internal deletion. Beneficial to the long-read property of SMRT sequencing, double and triple internal deletions were identified in half of the DI-RNA species. In addition, we examined the expression of DI-RNAs in mice infected with sublethal dose of H7N9 virus at different time points. Interestingly, DI-RNAs were abundantly expressed as early as day 2 post-infection. Taken together, we reveal the diversity and characteristics of DI-RNAs found in H7N9-infected patients, cells and animals. Further investigations on this overwhelming generation of DI-RNA may provide important insights into the understanding of H7N9 viral replication and pathogenesis.https://www.tandfonline.com/doi/10.1080/22221751.2019.1611346Avian influenza A/H7N9 virusdefective interfering viral genomeSingle Molecule Real Time sequencingIllumina sequencing |
| spellingShingle | Wing-Yu Lui Chun-Kit Yuen Can Li Wan Man Wong Pak-Yin Lui Chi-Ho Lin Kwok-Hung Chan Hanjun Zhao Honglin Chen Kelvin K. W. To Anna J. X Zhang Kwok-Yung Yuen Kin-Hang Kok SMRT sequencing revealed the diversity and characteristics of defective interfering RNAs in influenza A (H7N9) virus infection Emerging Microbes and Infections Avian influenza A/H7N9 virus defective interfering viral genome Single Molecule Real Time sequencing Illumina sequencing |
| title | SMRT sequencing revealed the diversity and characteristics of defective interfering RNAs in influenza A (H7N9) virus infection |
| title_full | SMRT sequencing revealed the diversity and characteristics of defective interfering RNAs in influenza A (H7N9) virus infection |
| title_fullStr | SMRT sequencing revealed the diversity and characteristics of defective interfering RNAs in influenza A (H7N9) virus infection |
| title_full_unstemmed | SMRT sequencing revealed the diversity and characteristics of defective interfering RNAs in influenza A (H7N9) virus infection |
| title_short | SMRT sequencing revealed the diversity and characteristics of defective interfering RNAs in influenza A (H7N9) virus infection |
| title_sort | smrt sequencing revealed the diversity and characteristics of defective interfering rnas in influenza a h7n9 virus infection |
| topic | Avian influenza A/H7N9 virus defective interfering viral genome Single Molecule Real Time sequencing Illumina sequencing |
| url | https://www.tandfonline.com/doi/10.1080/22221751.2019.1611346 |
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