SMRT #sequencing revealed the #diversity and characteristics of defective interfering #RNAs in #influenza A (#H7N9) virus infection (Emerg Microbes Infect., abstract)

[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.

 

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.

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.

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gimi69

I am an Italian blogger, active since 2005 with main focus on emerging infectious diseases such as avian influenza, SARS, antibiotics resistance, and many other global Health issues. Other fields of interest are: climate change, global warming, geological and biological sciences. My activity consists mainly in collection and analysis of news, public services updates, confronting sources and making decision about what are the 'signals' of an impending crisis (an outbreak, for example). When a signal is detected, I follow traces during the entire course of an event. I started in 2005 my blog ''A TIME'S MEMORY'', now with more than 40,000 posts and 3 millions of web interactions. Subsequently I added an Italian Language blog, then discontinued because of very low traffic and interest. I contributed for seven years to a public forum (FluTrackers.com) in the midst of the Ebola epidemic in West Africa in 2014, I left the site to continue alone my data tracking job.

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