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Article: SMRT sequencing revealed the diversity and characteristics of defective interfering RNAs in influenza A (H7N9) virus infection
Title | SMRT sequencing revealed the diversity and characteristics of defective interfering RNAs in influenza A (H7N9) virus infection |
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Authors | |
Keywords | Avian influenza A/H7N9 virus defective interfering viral genome Illumina sequencing single Molecule Real Time sequencing |
Issue Date | 2019 |
Publisher | Taylor & Francis Group, on behalf of Shanghai ShangyixunCultural Communication Co., Ltd. The Journal's web site is located at https://www.tandfonline.com/toc/temi20/current |
Citation | Emerging Microbes & Infections, 2019, v. 8 n. 1, p. 662-674 How to Cite? |
Abstract | 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. |
Persistent Identifier | http://hdl.handle.net/10722/274419 |
ISSN | 2023 Impact Factor: 8.4 2023 SCImago Journal Rankings: 2.316 |
PubMed Central ID | |
ISI Accession Number ID |
DC Field | Value | Language |
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dc.contributor.author | Lui, WY | - |
dc.contributor.author | Yuen, CK | - |
dc.contributor.author | Li, C | - |
dc.contributor.author | Wong, WM | - |
dc.contributor.author | Lui, PY | - |
dc.contributor.author | Lin, CH | - |
dc.contributor.author | Chan, KH | - |
dc.contributor.author | Zhao, H | - |
dc.contributor.author | Chen, H | - |
dc.contributor.author | To, KKW | - |
dc.contributor.author | Zhang, J | - |
dc.contributor.author | Yuen, KY | - |
dc.contributor.author | Kok, KH | - |
dc.date.accessioned | 2019-08-18T15:01:21Z | - |
dc.date.available | 2019-08-18T15:01:21Z | - |
dc.date.issued | 2019 | - |
dc.identifier.citation | Emerging Microbes & Infections, 2019, v. 8 n. 1, p. 662-674 | - |
dc.identifier.issn | 2222-1751 | - |
dc.identifier.uri | http://hdl.handle.net/10722/274419 | - |
dc.description.abstract | 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. | - |
dc.language | eng | - |
dc.publisher | Taylor & Francis Group, on behalf of Shanghai ShangyixunCultural Communication Co., Ltd. The Journal's web site is located at https://www.tandfonline.com/toc/temi20/current | - |
dc.relation.ispartof | Emerging Microbes & Infections | - |
dc.rights | This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License. | - |
dc.subject | Avian influenza A/H7N9 virus | - |
dc.subject | defective interfering viral genome | - |
dc.subject | Illumina sequencing | - |
dc.subject | single Molecule Real Time sequencing | - |
dc.title | SMRT sequencing revealed the diversity and characteristics of defective interfering RNAs in influenza A (H7N9) virus infection | - |
dc.type | Article | - |
dc.identifier.email | Li, C: canlee@hku.hk | - |
dc.identifier.email | Chan, KH: chankh2@hkucc.hku.hk | - |
dc.identifier.email | Zhao, H: hjzhao13@hku.hk | - |
dc.identifier.email | Chen, H: hlchen@hku.hk | - |
dc.identifier.email | To, KKW: kelvinto@hku.hk | - |
dc.identifier.email | Zhang, J: zhangajx@hkucc.hku.hk | - |
dc.identifier.email | Yuen, KY: kyyuen@hkucc.hku.hk | - |
dc.identifier.email | Kok, KH: khkok@hku.hk | - |
dc.identifier.authority | Chan, KH=rp01921 | - |
dc.identifier.authority | Chen, H=rp00383 | - |
dc.identifier.authority | To, KKW=rp01384 | - |
dc.identifier.authority | Zhang, J=rp00413 | - |
dc.identifier.authority | Yuen, KY=rp00366 | - |
dc.identifier.authority | Kok, KH=rp01455 | - |
dc.description.nature | published_or_final_version | - |
dc.identifier.doi | 10.1080/22221751.2019.1611346 | - |
dc.identifier.pmid | 31084471 | - |
dc.identifier.pmcid | PMC6534226 | - |
dc.identifier.scopus | eid_2-s2.0-85065774250 | - |
dc.identifier.hkuros | 301126 | - |
dc.identifier.volume | 8 | - |
dc.identifier.issue | 1 | - |
dc.identifier.spage | 662 | - |
dc.identifier.epage | 674 | - |
dc.identifier.isi | WOS:000474600100001 | - |
dc.publisher.place | United Kingdom | - |
dc.identifier.issnl | 2222-1751 | - |