Genomic comparison of MERS-CoV & SARS-CoV

The Baric laboratory studies lethal human coronaviruses, specifically Middle East Respiratory Syndrome Coronavirus (MERS-CoV) and Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV). These viruses are positive-sense, single-stranded RNA viruses that cause severe to lethal atypical pneumonias in humans. Overall mortality in the SARS-CoV epidemic was 9%; however, this rate increased to ~50% in males over the age of 50. The overall mortality of the MERS-CoV epidemic is ~40% of currently reported cases, although underreporting of the total number of cases is suspected.

...

https://www.med.unc.edu/orfeome/projects/genomic-comparison-of-mers-cov-sars-cov/

A review of studies on animal reservoirs of the SARS coronavirus
Zhengli Shi, Zhihong Hu

Abstract

In this review, we summarize the researches on animal reservoirs of the SARS coronavirus (SARS-CoV). Masked palm civets were suspected as the origin of the SARS outbreak in 2003 and was confirmed as the direct origin of SARS cases with mild symptom in 2004. Sequence analysis of the SARS-CoV-like virus in masked palm civets indicated that they were highly homologous to human SARS-CoV with nt identity over 99.6%, indicating the virus has not been circulating in the population of masked palm civets for a very long time. Alignment of 10 complete viral genome sequences from masked palm civets with those of human SARS-CoVs revealed 26 conserved single-nucleotide variations (SNVs) in the viruses from masked palm civets. These conserved SNVs were gradually lost from the genomes of viruses isolated from the early phase to late phase human patients of the 2003 SARS epidemic. In 2005, horseshoe bats were identified as the natural reservoir of a group of coronaviruses that are distantly related to SARS-CoV. The genome sequences of bat SARS-like coronavirus had about 88-92% nt identity with that of the SARS-CoV. The prevalence of antibodies and viral RNA in different bat species and the characteristics of the bat SARS-like coronavirus were elucidated. Apart from masked palm civets and bats, 29 other animal species had been tested for the SARS-CoV, and the results are summarized in this paper.

...

A breakthrough came in May of 2003 when viruses related to SARS were identified in animals. A team led by Yi Guan (Hong Kong University) and colleagues from the Center for Disease Control (CDC) Shenzhen, studied 25 individuals from 8 different species including 6 masked palm civets (Paguma larvata), 1 raccoon dog (Nyctereutes procyonoides), 2 Chinese ferret-badgers (Melogale moschata), 3 hog-badgers (Arctonyx collaris), 3 beavers (Castor fiber), 4 domestic cats (Felis catus), 3 Chinese hares (Lepus sinensis) and 2 Chinese muntjac (Muntiacus reevesi) gathered in Dongmen Market, Shenzhen, Guangdong Province (Guan et al., 2003).

...


https://www.sciencedirect.com/science/article/pii/S0168170207001050?via%3Dihub

TWiV 762: SARS-CoV-2 origins with Robert Garry

May 30, 2021

Robert Garry joins TWiV to explain how the molecular biology of SARS-CoV-2 shows that it came from Nature and not a lab, including the receptor binding domain, the furin cleavage site, and the two lineages circulating in Wuhan wildlife markets.



https://www.microbe.tv/twiv/twiv-762/

Public Health | Opinion
Why We Don’t Know the Animal Origins of the Coronavirus
Viruses that “spill over” to people do not stick around in animals, so finding true sources takes years of careful work, an expert says

By Christine K. Johnson on June 9, 2021

Over the past century, many notable viruses have emerged from animals to cause widespread illness and death in people. The list includes the pathogens behind pandemic influenza, Ebola, Zika, West Nile fever, SARS and now COVID, brought on by the virus SARS-CoV-2. For all of these microbes, the animal species that served as the original source of spillover was hard to find. And for many, that source still has not been conclusively identified. Confirming the circumstances and key participants involved in the early emergence of an infectious disease is a holy grail of this type of scientific inquiry: difficult to track and even more difficult to prove.

In ideal conditions, the first human cases involved in a zoonotic disease spillover (when a pathogen jumps from animals to humans) are reported in connection to animals present at the time of the event. This happens when the cluster of cases is large enough to be investigated and reported. But it is not necessarily the first time spillover occurred. Most spillovers are limited to more narrow animal-to-human cases. Once pathogens start to spread by human-to-human transmission, the tracks leading back to the initial animal source grow faint and become nearly impossible to follow.

Thus, animal sources for viruses that cause pandemics often remain shrouded in mystery. For some viruses, animal sources have been implicated after years or decades of large-scale international investigations. For other viruses, animal sources are highly suspected, but enough evidence has yet to be produced to pinpoint an exact species or range of species. Typically, lines of evidence are drawn over time through a trove of peer-reviewed publications, each building on the research that came before it, using more precise methods to narrow the field of possible sources. The scientific process is naturally self-correcting. Often seemingly contradictory hypotheses can initially flood the field, especially for high-impact outbreaks. But eventually, some of them are ruled out, and lines of investigation are narrowed.

Frequently, this investigative research only points to a group of suspected species, possibly a few most likely genera or, more often, an entire taxonomic order. That is because the virus has not actually been found in the suspected animal source in such cases. The evidence instead revolves around closely related viruses or their most recent common ancestors, based on inferred evolutionary history. If a virus was found in animal samples after the same pathogen caused widespread transmission among humans, it is possible that the virus spilled from humans back into animals. That happens often enough with viruses that can infect a range of animal species that the possibility needs to be presumed until it is ruled out.

...

https://www.scientificamerican.com/article/finding-conclusive-animal-origins-of-the-coronavirus-will-take-time/

"We needed this information rapidly, from the PRC, while the pandemic was still new."