Newer Dominant COVID-19 Variant
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Newer Dominant COVID-19 Variant
Found to be More Infectious in the Lab

A specific change in the virus genome of SARS-CoV-2 coronavirus, previously associated with increased viral transmission and the spread of COVID-19, is shown to be more infectious in cell culture in new research by scientists published in the journal Cell. 

A small yet effective change in the ‘spike’ protein of the virus, which the virus uses to enter human cells, is made by the D614G, the variant in question.

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The lead author of the study and a theoretical biologist at Los Alamos National Laboratory, Bette Korber noted, ” We had observed a strikingly repetitive pattern and the D614G variant first came to our attention in early April. The D614G variant became the prevalent form soon after it was introduced into a region even when local epidemics had many cases of the original form circulating, all over the world.”

The tracking of this highly recurrent pattern, a shift in the viral population from the original form to the D614G variant, was enabled by the geographic information from samples from the GISAID COVID-19 viral sequence database. At every geographic level: city, county, and sub country, this occurred.

Supporting these initial results, there were two independent lines of experimental evidence included in the paper. At the La Jolla Institute, Professor Erica Ollmann Saphire, Ph.D., and Duke University Professor David Montefiori, Ph.D., led these additional experiments which showed that the virus’s infectivity in the laboratory is increased by the D614G change. The paper also included more extensive sequence and clinical data and improved statistical models, and these new experiments. To determine the full implications of the change, more in Vivo work remains to be done.

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Overall, the mutation rate of the SARS-CoV-2 virus is low (much lower than the viruses that cause HIV-AIDS and influenza). The D614G variant appears as part of a set of four linked mutations that appear to have emerged once and then moved together around the world as a regular set of variations. An author of the study, Will Fischer of Los Alamos commented, “By careful observation of sequence data alone, this increase in infectivity was detected and in such a short time, our experimental colleagues could confirm it with the live virus.”

The Gates Foundation-supported Coronavirus Immunotherapy Consortium (CoVIC) lead, Saphire said, “According to the clinical data in this paper from Sheffield, there wasn’t a corresponding increase in the severity of illness, even though patients with the new G virus carried more copies of the virus than patients infected with D.”

Korber noted, “The importance of maintaining social distancing and wearing masks is highlighted here these findings suggest that the newer form of the virus may be even more readily transmitted than the original form.”

On the bioRxiv site in an April 2020 preprint, research partners from the University of Sheffield, Duke University, and Los Alamos National Laboratory, initially published work on this analysis. Observations of COVID-19 patients from Sheffield that suggested an association of the D614G variant with higher viral loads in the upper respiratory tract were also included in that work.

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Korber said, “Through the GISAID viral sequence database, researchers worldwide are rapidly making their viral sequence data available making it possible to track SARS-CoV-2 evolution globally.” Korber and the research team were able to identify the emergence of the D614G variant as there are tens of thousands of sequences available through this project currently.

In order to encourage collaboration among influenza researchers, GISAID was established, however, the consortium established a SARS-CoV-2 database early in the epidemic, making it the de facto standard for sharing outbreak sequences among researchers globally.

The Medical Research Council (MRC) part of UK Research & Innovation (UKRI the National Institute of Health Research (NIHR); the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, under Interagency Agreement No. AAI12007-001-00000, and the Los Alamos Laboratory Directed Research and Development program; a FastGrant, from Emergent Ventures, in aid of COVID-19 research; private philanthropic support, as well as the Overton family; CoVIC, INV-006133 of the COVID-19 Therapeutics Accelerator, supported by the Bill and Melinda Gates Foundation, Mastercard, Wellcome; Genome Research Limited, operating as the Wellcome Sanger Institute; supported the study, “Tracking changes in SARS-CoV-2 Spike: evidence that D614G increases infectivity of the COVID-19 virus”.

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The study included additional authors: H. Yoon, S. Gnanakaran, C.C. LaBranche, S.P. Whelan, A. Moon-Walker, H. Tang, L.G. Perez, C. McDanal, T.I. de Silva, T.M. Freeman, C.M. Evans, D.G. Partridge, K.M. Hastie,  B. Foley, T. Bhattacharya, M.D. Parker, E.E. Giorgi, N. Hengartner, W. Abfalterer, J. Theiler.

 

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