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

Emerging Microbes & Infections
Wing-Yu LuiKin-Hang Kok

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-R...Continue Reading

References

Jul 1, 1979·Proceedings of the National Academy of Sciences of the United States of America·A R Davis, D P Nayak
Apr 1, 1982·Proceedings of the National Academy of Sciences of the United States of America·D P NayakJ Sung
Jan 1, 1980·Annual Review of Microbiology·D P Nayak
Aug 4, 1999·Proceedings of the National Academy of Sciences of the United States of America·G NeumannY Kawaoka
Oct 6, 2009·Journal of Clinical Virology : the Official Publication of the Pan American Society for Clinical Virology·I W S LiK Y Yuen
Dec 31, 2009·Reviews in Medical Virology·A C Marriott, N J Dimmock
Sep 2, 2010·Proceedings of the National Academy of Sciences of the United States of America·Alina BaumAdolfo García-Sastre
Apr 13, 2013·The New England Journal of Medicine·Rongbao GaoYuelong Shu
May 17, 2013·Journal of Virology·Kazima SairaINSIGHT FLU003 Study Group
Feb 21, 2018·The Journal of General Virology·Zizhang ShengDan Wang
May 17, 2018·Methods in Molecular Biology·Anthony BayegaJiannis Ragoussis
Sep 19, 2018·Nature Microbiology·Aartjan J W Te VelthuisErvin Fodor

Datasets Mentioned

BETA
SRP126530

Methods Mentioned

BETA
Illumina sequencing
electrophoresis
PCR
chip

Related Concepts

Metazoa
Lobar Bronchus Structure
Defective Viruses
Epithelial Cells
Influenza
Structure of Choanae
Orthomyxoviridae Infections
RNA, Viral
Viral Genome
Deletion Mutation

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Lipidomics & Rhinovirus Infection

Lipidomics can be used to examine the lipid species involved with pathogenic conditions, such as viral associated inflammation. Discovered the latest research on Lipidomics & Rhinovirus Infection.

Spatio-Temporal Regulation of DNA Repair

DNA repair is a complex process regulated by several different classes of enzymes, including ligases, endonucleases, and polymerases. This feed focuses on the spatial and temporal regulation that accompanies DNA damage signaling and repair enzymes and processes.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Torsion Dystonia

Torsion dystonia is a movement disorder characterized by loss of control of voluntary movements appearing as sustained muscle contractions and/or abnormal postures. Here is the latest research.

Archaeal RNA Polymerase

Archaeal RNA polymerases are most similar to eukaryotic RNA polymerase II but require the support of only two archaeal general transcription factors, TBP (TATA-box binding protein) and TFB (archaeal homologue of the eukaryotic general transcription factor TFIIB) to initiate basal transcription. Here is the latest research on archaeal RNA polymerases.

Alzheimer's Disease: MS4A

Variants within the membrane-spanning 4-domains subfamily A (MS4A) gene cluster have recently been implicated in Alzheimer's disease in genome-wide association studies. Here is the latest research on Alzheimer's disease and MS4A.

Central Pontine Myelinolysis

Central Pontine Myelinolysis is a neurologic disorder caused most frequently by rapid correction of hyponatremia and is characterized by demyelination that affects the central portion of the base of the pons. Here is the latest research on this disease.