But the new virus might be more distantly related, in which case, studying it will help scientists to learn more about the diversity in this virus family, says Etienne Simon-Loriere, a virologist at the Pasteur Institute in Paris, who plans to sequence the virus, after which it will be shared publicly.

That is the case with the other virus, called Rc-o319, identified in a little Japanese horseshoe bat (Rhinolophus cornutus) captured in 2013. That virus shares 81% of its genome with SARS-CoV-2, according to a paper1 published on 2 November — which makes it too distant to provide insights into the pandemic’s origin, says Edward Holmes, a virologist at the University of Sydney in Australia.

The virus in Cambodia was found in two Shamel’s horseshoe bats (Rhinolophus shameli) captured in the country’s north in 2010. The virus’s genome has not yet been fully sequenced — nor its discovery published — making its full significance to the pandemic hard to ascertain.

If the virus is very closely related to — or even an ancestor of — the pandemic virus, it could provide crucial information about how SARS-CoV-2 passed from bats to people, and inform the search for the pandemic’s origin, says Veasna Duong, a virologist at the Pasteur Institute in Cambodia in Phnom Penh, who led the search of the old samples in Cambodia and alerted Nature to the discovery in early November. To provide such insights, the virus would have to share more than 97% of its genome with SARS-CoV-2, which is more than its closest known relative, say researchers.

Two lab freezers in Asia have yielded surprising discoveries. Researchers have told Nature they have found a coronavirus that is closely related to SARS-CoV-2, the virus responsible for the pandemic, in horseshoe bats stored in a freezer in Cambodia. Meanwhile, a team in Japan has reported the discovery of another closely related coronavirus — also found in frozen bat droppings.

The viruses are the first known relatives of SARS-CoV-2 to be found outside China, which supports the World Health Organization’s search across Asia for the pandemic’s animal origin. Strong evidence suggests that SARS-CoV-2 originated in horseshoe bats

https://www.nature.com/articles/d41586-020-03217-0

“This means that other viruses that are capable of infecting humans are circulating in horseshoe bats in China,” David L Robertson, study author and professor of computational virology at MRC-University of Glasgow Centre for Virus Research, explained in a statement.

The findings also throw doubt on the theory that pangolins, scaly-skinned mammals from Asia and Africa, were the intermediary animal that harbored the virus before it jumped to humans. Previous research suggested SARS-CoV-2’s RBD sequence was more similar to pangolin viruses than RaTG13. However, the team found there was no evidence that pangolins helped to arm SARS-CoV-2 with the RBD during its evolutionary history. Although pangolins may have played a role in the transmission to humans, they are unlikely to be the chief intermediate host for the virus.

The study also highlights a final damning question: if these potentially deadly viruses have been circulating in bats for decades, then why did the Covid-19 pandemic catch the world off guard? To protect against the next coronavirus pandemic, the study authors say their findings further highlight how the world must carry out more research and surveillance to identify novel pathogens.

“We were too late in responding to the initial SARS-CoV-2 outbreak, but this will not be our last coronavirus pandemic. A much more comprehensive and real-time surveillance system needs to be put in place to catch viruses like this when case numbers are still in the double digits,” added Maciej Boni, study author and associate professor of biology at Penn State University.

According to the new findings, the lineage of viruses to which SARS-CoV-2 belongs to genetically is split between related bat coronaviruses that diverged in 1948, 1969, and 1982. One of these divergences, in 1969, eventually gave rise to RaTG13, a coronavirus that's 96.1 percent genetically similar to SARS-CoV-2. Researchers first identified this virus in 2013 after sampling a horseshoe bat in China’s Yunnan province.

Another key feature analyzed by the researchers was the receptor-binding domain (RBD) on the virus’ spike protein, an important part of the virus that's effectively the “key” used by the pathogen to recognize and enter host cells. The researchers found that SARS-CoV-2 and its relatives — such as RaTG13 and a pangolin virus sampled in Guangdong in 2019, Pangolin-2019 — all share a similar RBD and spike protein. However, these features do not appear to be the product of recombination. This suggests the protein and its RBD are an ancestral trait of the lineage leading to SARS-CoV-2, RaTG13, and Pangolin-2019.

It also hints that there could be other members of this family that are capable of infecting humans.

The family of SARS-CoV-2, the virus responsible for the Covid-19 pandemic, has been lurking in the bat caves of China for decades and most likely includes other relatives that could infect humans. That’s according to a new study published in the journal Nature Microbiology this week.

An international team of scientists from the UK, Belgium, China, and the US traced the evolutionary history of SARS-CoV-2 by studying genetically related coronaviruses found in bats and pangolins. Understanding the evolutionary origins of the novel coronavirus can be fiddly as they undergo a process known as recombination, in which two different viruses both infect the same host cell and interact during replication, resulting in genetic material being swapped. This means their genome does not have a straight-forward lineage and can come from multiple sources.

https://www.iflscience.com/health-and-medicine/family-the-novel-coronavirus-belongs-to-has-been-lurking-in-bats-for-decades/

In studies like these, false positives are a concern, particularly when the prevalence of viral infections is low, as was the case in the early days of the U.S. epidemic. Researchers in this study followed CDC guidance to use sequential testing on two separate platforms to minimize false positive results.

All of Us worked with Quest Diagnostics to test samples on the Abbott Architect SARS-CoV-2 IgG ELISA and the EUROIMMUN SARS-CoV-2 ELISA (IgG) platforms. For a sample to be considered “positive” by the research team, it had to have positive results on both platforms, which target antibodies that bind to different parts of the virus. Both tests have emergency use authorization from the FDA.

“Antibody testing of blood samples helps us better understand the spread of SARS-CoV-2 in the U.S. in the early days of the U.S. epidemic, when testing was restricted and public health officials could not see that the virus had already spread outside of recognized initial points of entry,” said Keri N. Althoff, Ph.D., lead author and associate professor of epidemiology at the Johns Hopkins Bloomberg School of Public Health, Baltimore. “This study also demonstrates the importance of using multiple serology platforms, as recommended by the CDC.”

In the All of Us study, researchers analyzed more than 24,000 stored blood samples contributed by program participants across all 50 states between Jan. 2 and March 18, 2020. Researchers detected antibodies against SARS-CoV-2 using two different serology tests in nine participants’ samples. These participants were from outside the major urban hotspots of Seattle and New York City, believed to be key points of entry of the virus in the U.S. The positive samples came as early as Jan. 7 from participants in Illinois, Massachusetts, Mississippi, Pennsylvania and Wisconsin. Most positive samples were collected prior to the first reported cases in those states, demonstrating the importance of expanding testing as quickly as possible in an epidemic setting.

“This study allows us to uncover more information about the beginning of the U.S. epidemic and highlights the real-world value of longitudinal research in understanding dynamics of emerging diseases like COVID-19,” said Josh Denny, M.D., M.S., chief executive officer of All of Us and an author of the study. “Our participants come from diverse communities across the U.S. and give generously of themselves to drive a wide range of biomedical discoveries, which are vital for informing public health strategies and preparedness.”

A new antibody testing study examining samples originally collected through the National Institutes of Health’s All of Us Research Program found evidence of SARS-CoV-2 infections in five states earlier than had initially been reported. These findings were published in the journal Clinical Infectious Diseases. The results expand on findings from a Centers for Disease Control and Prevention study that suggested SARS-CoV-2, the virus that causes COVID-19, was present in the U.S. as far back as December 2019.

The sample could also have been contaminated in the lab in which it was stored and tested, Jonathan Ball, a professor of molecular virology at the University of Nottingham, tells the AP. “If he was infected (with COVID-19), then you would expect a more rapid and earlier spread of the virus in France than was seen,” he says in a statement.

Other experts say it’s possible the virus was spreading weeks before the first cases were confirmed in France on January 24, 2020.

“This gives a whole new picture on everything,” WHO spokesman Christian Lindmeier told a UN briefing in Geneva, according to Reuters. “The findings help to better understand the potential virus circulation of COVID-19,” he explained, and urged doctors in countries around the world to test unspecified cases of pneumonia for SARS-CoV-2.

As cases of COVID-19 spread worldwide, Cohen and his colleagues decided to analyze samples taken from patients visiting the hospital who were diagnosed with influenza-like illness between December 2, 2019, and January 16, 2020. Of the 14 samples described in the study, only one, Hammar’s, was positive for SARS-CoV-2. Cohen and his team called Hammar after they got this result and learned he had not traveled before getting sick and that one of his children had fallen ill with similar symptoms around the same time. Both Hammar’s children ended up becoming sick while his wife showed no symptoms of illness. Hammar’s wife worked in a local market selling fish. She may have been an asymptomatic carrier, contracting the virus at the market, Cohen tells BF-MTV.

Cohen and his colleagues caution that the work is tentative. The study was done retrospectively, “medical records were not exhaustive and some relevant information might have been missing,” Cohen tells the AP.

A man living in France may have been infected with SARS-CoV-2, the virus that causes COVID-19, as early as December 27, weeks before the first official coronavirus cases were reported in the country, according to a study published online Sunday (May 3) in the International Journal of Antimicrobial Agents.

When the man, Amirouche Hammar, a 42-year-old fishmonger, visited a hospital north of Paris on December 27, he suffered from chest pains and had difficulty breathing. Doctors diagnosed him with viral pneumonia and treated him with antibiotics. “We told ourselves, ‘It’s a virus that we haven’t discovered,’ but we stopped there,” Yves Cohen, one of Hammar’s doctors who works at Avicenne and Jean Verdier hospitals, told BFM-TV, according to the Associated Press.

https://www.the-scientist.com/news-opinion/doctors-date-first-covid-19-case-in-france-to-late-december-67510

Still, there is one theory that can be dismissed. From the earliest days of the pandemic, there has been speculation that the new virus had escaped, or even been deliberately released, from the Wuhan Institute of Virology. At a White House press conference on May 1, 2020, US President Donald Trump declined to assert that SARS-CoV-2 had occurred naturally. When asked what gave him a “high degree of confidence that this [virus] originated from the Wuhan Institute of Virology”, Trump replied “I can't tell you that. I'm not allowed to tell you that.”

“If the virus had been human-made, that would show in its genome”, counters Robertson. “Besides, if you were going to create a coronavirus that can be transmitted by humans, you would almost certainly start with the first SARS virus. SARS-CoV-2 is like nothing we have seen before. It really is highly unlikely that someone created it; it is not put together from pieces we know about.” SARS-CoV-2 is closely related to other beta coronaviruses such as RaTG13, a bat virus that the Wuhan Institute of Virology has been working on. But it only shares 96% of its genome sequence with RaTG13, which makes them roughly as similar as human beings and chimpanzees, and points to a common ancestor rather than one springing from the other.

“The generalist property of the virus means an intermediate host is not required for any evolutionary change”, said Robertson. “As the virus has been around for decades it may have emerged in another host and this could be the missing intermediate species but we are inferring that this would only facilitate transmission.” The fact that SARS-CoV-2 was first detected in Wuhan, China, far from where the horseshoe bat is found, hints at the presence of an intermediary.

Some have posited that the pangolin could be this missing link. Pangolins have reportedly fallen sick as a result of coronavirus infection, which would mean they are not a natural reservoir. But that leaves the possibility that the pangolin is facilitating transmission to humans. SARS-CoV-2 can jump to other animals such ferrets and cats. “The virus would not need to evolve in the pangolin, it would just need to be brought into contact with humans”, explains Robertson. And it is still too soon to rule out direct bat–human transmission.

The fact that severe acute respiratory syndrome coronavirus 2 derived from bat coronaviruses highlights inherent issues of the way we interact with the environment.

A paper published in July, 2020, traced the origins of SARS-CoV-2. The researchers concluded that it came from a virus with relatively generalist properties circulating in horseshoe bats. “Everything points to a bat sarbecovirus reservoir; we are very confident about this”, said David Robertson, head of bioinformatics at the Medical Research Council–University of Glasgow Centre for Virus Research, Scotland, UK, and co-author of the paper. The evolutionary analysis suggested that the lineage from which SARS-CoV-2 emerged has been present in bats for several decades.

"Secret service reports usually have the property that they are secret and will remain secret. So we cannot check whether such a report actually exists, what is really there and what evidence is included, if any. The bottom line is that the current debate is based on hearsay," said Glaubrecht.

When asked about the origin of the coronavirus, Glaubrecht said it is difficult for scientists to give conclusive evidence where the virus came from.

"We only have to estimate what is more plausible," Glaubrecht said.

So far the most impeccable hypothesis is from the World Health Organization that COVID-19 jumped to humans via intermediate hosts, according to the biologist.

"In nature, new virus variants are constantly emerging, (and) genes are changing. Even the best experts cannot tell where new sequences come from," Glaubrecht told Der Spiegel.

He questioned some media reports that cited U.S. intelligence information suggesting that the virus is man-made and leak from a laboratory in Wuhan.

The COVID-19 lab leak theory is falsely claimed and some media reports from the United States are based on hearsay, a German biologist has said.

Matthias Glaubrecht, scientific director and professor from the Department of Animal Diversity at the University of Hamburg, made the remarks in a recent interview with German media Der Spiegel.

But the fact that these bits of coronavirus RNA can be found in untreated wastewater (known as “influent”) is useful for tracking outbreaks. Indeed, they can predict where an outbreak is likely to occur a week to ten days before they show up in official figures – the reason being that people shed coronavirus before symptoms become evident. These “pre-symptomatic” people then have to get sick enough to be tested, get the results, and be admitted to a hospital as an official “case”, hence the week or so lag.

As a result, many countries, including Spain, are now monitoring wastewater for traces of coronavirus. In this particular study, wastewater epidemiologists were examining frozen samples of influent between January 2018 and December 2019 to see when the virus made its debut in the city.

So, how was the experiment conducted and what exactly did the scientists find?

One of the early findings about SARS-CoV-2 is that it is found in the faeces of infected people. As the virus makes its way through the gut – where it can cause gastrointestinal symptoms – it loses its outer protein layer, but bits of genetic material called RNA survive the journey intact and are “shed” in faeces. At this point, it is no longer infectious – as far as current evidence tells us.