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Institute of Human Virology and Italian Researchers identify a SARS-CoV-2 Viral Strain with Deletion in a Protein, Possibly Reducing Fatalities

August 21, 2020 | Nora Samaranayake

(left to right) Francesca Benedetti, PhD, Davide Zella, PhD, and Robert Gallo, MD

A deletion in a protein, NSP1, which is important for reducing innate immune response may signal emergence of a less pathogenic viral strain

The Institute of Human Virology (IHV) at the University of Maryland School of Medicine, a Global Virus Network (GVN) Center of Excellence, in collaboration with scientists from Campus Biomedico in Rome, Italy announced today the results of studies showing the emergence of a SARS-CoV-2 viral strain with a deletion in a protein known as nsp1. These data, accepted for publication today by the Journal of Translational Medicine, may indicate the emergence of a less pathogenic viral strain.

“Nsp1 plays a central role in hampering the anti-viral innate immune response,” said Robert C. Gallo, MD, The Homer & Martha Gudelsky Distinguished Professor, Co-founder & Director at the Institute of Human Virology, University of Maryland School of Medicine and Co-Founder and Chairman of the International Scientific Leadership Board of the Global Virus Network (GVN).  “Our data indicate that a small percentage of SARS-CoV-2 viruses is harboring a deletion in an important protein responsible for hampering the innate immune response, possibly adapting toward a decrease in pathogenicity. Scientists, including those within the Global Virus Network, will be able to expand on these data to confirm how widespread this deletion is.”

The researchers analyzed SARS-CoV-2 genome sequences from several countries and discovered a previously unknown deletion that is widespread and spans varying geographical areas. Modelling analysis of the newly identified deletion of SARS-CoV-2 nsp1 suggests that this deletion could affect the structure of the C-terminal region of the protein, important for both regulating viral replication and hampering the innate immune system response. The research indicates that the virus may become less pathogenic.

“SARS-CoV-2 seems to be undergoing profound genomic changes, but the effect of such changes on viral pathogenesis may become visible over a long period of time”, said Davide Zella, PhD, Assistant Professor of Biochemistry and Molecular Biology at the Institute of Human Virology, University of Maryland School of Medicine and member of the Global Virus Network (GVN).  “We need to confirm the spreading of this particular viral strain and research potential strains with other deletions in the nsp1 protein, both in the population of asymptomatic and pauci-symptomatic subjects, and correlate these changes in nsp1 with decreased viral pathogenicity. Also, the spreading of this deletion needs to be evaluated over time”.

“The percentage of deletions found in the cases analyzed did not seem to be geographically homogenous, possibly due to the low number of available sequences for analysis,” said Francesca Benedetti, PhD, Research Associate of Biochemistry and Molecular Biology at the Institute of Human Virology, University of Maryland School of. Medicine “The percentage was higher in Sweden with 1.89% while in certain parts of the United States was about 1%.”

“Our modeling of nsp1 protein of SARS-CoV-2 indicates that this deletion may influence potential structure in this region, thereby altering its activity and ability to interact with other proteins of the host,” says Greg Snyder, PhD, Assistant Professor of Microbiology and Immunology at the Institute of Human Virology, University of Maryland School of Medicine.

“We are pleased to work with our colleagues at the Institute of Human Virology to identify and characterize the profound alterations in the SARS-CoV-2 genomic sequences spanning the globe, and to evaluate their biological significance,” said Massimo Ciccozzi, PhD, Associate Professor of Medical Statistics, Universita’ Campus Biomedico in Rome, Italy.

About the Institute of Human Virology

Formed in 1996 as a partnership between the State of Maryland, the City of Baltimore, the University System of Maryland, and the University of Maryland Medical System, the IHV is an institute of the University of Maryland School of Medicine and is home to some of the most globally-recognized and world-renowned experts in all of virology. The IHV combines the disciplines of basic research, epidemiology, and clinical research in a concerted effort to speed the discovery of diagnostics and therapeutics for a wide variety of chronic and deadly viral and immune disorders - most notably, HIV the virus that causes AIDS. For more information, visit www.ihv.org and follow us on Twitter @IHVmaryland.

Contact

Institute of Human Virology
Nora Samaranayake
Director of Marketing and Public Relations
(410) 706-8614 (phone)
(410) 706-1952 (fax)
nsamaranayake@ihv.umaryland.edu

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