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Article: SMRT sequencing revealed the diversity and characteristics of defective interfering RNAs in influenza A (H7N9) virus infection

TitleSMRT sequencing revealed the diversity and characteristics of defective interfering RNAs in influenza A (H7N9) virus infection
Authors
KeywordsAvian influenza A/H7N9 virus
defective interfering viral genome
Illumina sequencing
single Molecule Real Time sequencing
Issue Date2019
PublisherTaylor & 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?
AbstractInfluenza 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 Identifierhttp://hdl.handle.net/10722/274419
ISSN
2018 Impact Factor: 6.212
2015 SCImago Journal Rankings: 1.774
PubMed Central ID
ISI Accession Number ID

 

DC FieldValueLanguage
dc.contributor.authorLui, WY-
dc.contributor.authorYuen, CK-
dc.contributor.authorLi, C-
dc.contributor.authorWong, WM-
dc.contributor.authorLui, PY-
dc.contributor.authorLin, CH-
dc.contributor.authorChan, KH-
dc.contributor.authorZhao, H-
dc.contributor.authorChen, H-
dc.contributor.authorTo, KKW-
dc.contributor.authorZhang, J-
dc.contributor.authorYuen, KY-
dc.contributor.authorKok, KH-
dc.date.accessioned2019-08-18T15:01:21Z-
dc.date.available2019-08-18T15:01:21Z-
dc.date.issued2019-
dc.identifier.citationEmerging Microbes & Infections, 2019, v. 8 n. 1, p. 662-674-
dc.identifier.issn2222-1751-
dc.identifier.urihttp://hdl.handle.net/10722/274419-
dc.description.abstractInfluenza 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.languageeng-
dc.publisherTaylor & 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.ispartofEmerging Microbes & Infections-
dc.rightsThis work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.-
dc.subjectAvian influenza A/H7N9 virus-
dc.subjectdefective interfering viral genome-
dc.subjectIllumina sequencing-
dc.subjectsingle Molecule Real Time sequencing-
dc.titleSMRT sequencing revealed the diversity and characteristics of defective interfering RNAs in influenza A (H7N9) virus infection-
dc.typeArticle-
dc.identifier.emailLi, C: canlee@hku.hk-
dc.identifier.emailChan, KH: chankh2@hkucc.hku.hk-
dc.identifier.emailZhao, H: hjzhao13@hku.hk-
dc.identifier.emailChen, H: hlchen@hku.hk-
dc.identifier.emailTo, KKW: kelvinto@hku.hk-
dc.identifier.emailZhang, J: zhangajx@hkucc.hku.hk-
dc.identifier.emailYuen, KY: kyyuen@hkucc.hku.hk-
dc.identifier.emailKok, KH: khkok@hku.hk-
dc.identifier.authorityChan, KH=rp01921-
dc.identifier.authorityChen, H=rp00383-
dc.identifier.authorityTo, KKW=rp01384-
dc.identifier.authorityZhang, J=rp00413-
dc.identifier.authorityYuen, KY=rp00366-
dc.identifier.authorityKok, KH=rp01455-
dc.description.naturepublished_or_final_version-
dc.identifier.doi10.1080/22221751.2019.1611346-
dc.identifier.pmid31084471-
dc.identifier.pmcidPMC6534226-
dc.identifier.scopuseid_2-s2.0-85065774250-
dc.identifier.hkuros301126-
dc.identifier.volume8-
dc.identifier.issue1-
dc.identifier.spage662-
dc.identifier.epage674-
dc.identifier.isiWOS:000474600100001-
dc.publisher.placeUnited Kingdom-

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