[Source: US National Library of Medicine, full page: (LINK). Abstract, edited.]
Emerg Microbes Infect. 2019;8(1):662-674. doi: 10.1080/22221751.2019.1611346.
SMRT sequencing revealed the diversity and characteristics of defective interfering RNAs in influenza A (H7N9) virus infection.
Lui WY1, Yuen CK1, Li C1, Wong WM1, Lui PY1, Lin CH2, Chan KH1,3,4,5, Zhao H1,3,4,5, Chen H1, To KKW1,3,4,5, Zhang AJX1,3,4,5, Yuen KY1,3,4,5, Kok KH1.
Author information: 1a Department of Microbiology, Li Ka Shing Faculty of Medicine , University of Hong Kong , Hong Kong , People’s Republic of China. 2 b Center for Genome Sciences, Li Ka Shing Faculty of Medicine , University of Hong Kong , Hong Kong , People’s Republic of China. 3 c State Key Laboratory for Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine , University of Hong Kong , Hong Kong , People’s Republic of China. 4 d Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine , University of Hong Kong , Hong Kong , People’s Republic of China. 5 e Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Li Ka Shing Faculty of Medicine , University of Hong Kong , Hong Kong , People’s Republic of China.
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.
KEYWORDS: Avian influenza A/H7N9 virus; Illumina sequencing; Single Molecule Real Time sequencing; defective interfering viral genome
PMID: 31084471 DOI: 10.1080/22221751.2019.1611346
Keywords: Influenza A; Avian Influenza; H7N9.