The Proximal Origin of SARS-CoV-2

[Shiloh]

Source: http://virological.org/t/the-proxima...sars-cov-2/398

The Proximal Origin of SARS-CoV-2

Kristian G. Andersen1,2*, Andrew Rambaut3, W. Ian Lipkin4, Edward C. Holmes5 & Robert F. Garry6,7

1Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.

2Scripps Research Translational Institute, La Jolla, CA 92037, USA.

3Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK.

4Center for Infection and Immunity, Mailman School of Public Health of Columbia University, New York, New York, USA.

5Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, Australia.

6Tulane University, School of Medicine, Department of Microbiology and Immunology, New Orleans, LA, USA.

7Zalgen Labs, LCC, Germantown, MD, USA.

*Corresponding author:

Kristian G. Andersen
Department of Immunology and Microbiology,
The Scripps Research Institute,
La Jolla, CA 92037,
USA.

Since the first reports of a novel pneumonia (COVID-19) in Wuhan city, Hubei province, China there has been considerable discussion and uncertainty over the origin of the causative virus, SARS-CoV-2. Infections with SARS-CoV-2 are now widespread in China, with cases in every province. As of 14 February 2020, 64,473 such cases have been confirmed, with 1,384 deaths attributed to the virus. These official case numbers are likely an underestimate because of limited reporting of mild and asymptomatic cases, and the virus is clearly capable of efficient human-to-human transmission. Based on the possibility of spread to countries with weaker healthcare systems, the World Health Organization has declared the COVID-19 outbreak a Public Health Emergency of International Concern (PHEIC). There are currently neither vaccines nor specific treatments for this disease....

[Gert van der Hoek]

Updated version

• Correspondence
• Published: 17 March 2020

The proximal origin of SARS-CoV-2

• Kristian G. Andersen,
• Andrew Rambaut,
• W. Ian Lipkin,
• Edward C. Holmes &
• Robert F. Garry

Nature Medicine (2020)

To the Editor — Since the first reports of novel pneumonia (COVID-19) in Wuhan, Hubei province, China^1,2, there has been considerable discussion on the origin of the causative virus, SARS-CoV-2³ (also referred to as HCoV-19)⁴. Infections with SARS-CoV-2 are now widespread, and as of 11 March 2020, 121,564 cases have been confirmed in more than 110 countries, with 4,373 deaths⁵.

SARS-CoV-2 is the seventh coronavirus known to infect humans; SARS-CoV, MERS-CoV and SARS-CoV-2 can cause severe disease, whereas HKU1, NL63, OC43 and 229E are associated with mild symptoms⁶. Here we review what can be deduced about the origin of SARS-CoV-2 from comparative analysis of genomic data. We offer a perspective on the notable features of the SARS-CoV-2 genome and discuss scenarios by which they could have arisen. Our analyses clearly show that SARS-CoV-2 is not a laboratory construct or a purposefully manipulated virus.

Notable features of the SARS-CoV-2 genome

Our comparison of alpha- and betacoronaviruses identifies two notable genomic features of SARS-CoV-2: (i) on the basis of structural studies^7,8,9 and biochemical experiments^1,9,10, SARS-CoV-2 appears to be optimized for binding to the human receptor ACE2; and (ii) the spike protein of SARS-CoV-2 has a functional polybasic (furin) cleavage site at the S1–S2 boundary through the insertion of 12 nucleotides⁸, which additionally led to the predicted acquisition of three O-linked glycans around the site.

https://www.nature.com/articles/s41591-020-0820-9

[Gert van der Hoek]

Short explanation in newspaper SCMP

Coronavirus: pathogen could have been spreading in humans for decades, study says

• Virus may have jumped from animal to humans long before the first detection in Wuhan, according to research by an international team of scientists
• Findings significantly reduce the possibility of the virus having a laboratory origin, director of the US National Institute of Health says

Thecoronavirus that causes Covid-19 might have been quietly spreading among humans for years or even decades before the sudden outbreak that sparked a global health crisis, according to an investigation by some of the world’s top virus hunters.
Researchers from the United States ,Britain and Australia looked at piles of data released by scientists around the world for clues about the virus’ evolutionary past, and found it might have made the jump from animal to humans long before the first detection in the central China city of Wuhan.

Though there could be other possibilities, the scientists said the coronavirus carried a unique mutation that was not found in suspected animal hosts, but was likely to occur during repeated, small-cluster infections in humans.

Dr Francis Collins, director of the US National Institute of Health, who was not involved in the research, said the study suggested a possible scenario in which the coronavirus crossed from animals into humans before it became capable of causing disease in people.

“Then, as a result of gradual evolutionary changes over years or perhaps decades, the virus eventually gained the ability to spread from human to human and cause serious, often life-threatening disease,”