Virus World

Horseshoe bats carry viruses closely related to SARS-CoV-2, but they probably can’t spread in people yet. Coronavirus hunters looking for the next pandemic threats have focused on China and southeast Asia, where wild bats carry SARS-CoV-2’s closest known relatives. But a survey of UK bat species suggests that researchers might want to cast a wider net. The trawl turned up new coronaviruses, and some from the same group as SARS-CoV-2. Laboratory studies with safe versions of these viruses suggest that some share key adaptations with SARS-CoV-2 — but are unlikely to spread in humans without further evolution. SARS-CoV-2 belongs to a group of coronaviruses called sarbecoviruses, which circulate in bats. But before the pandemic, efforts to find and characterize these viruses focused on Asia. “Europe and the UK had been totally overlooked,” says Vincent Savolainen, an evolutionary geneticist at Imperial College London who led the study, published on 27 June in Nature Communications. To help plug this gap, Savolainen and his colleagues teamed up with groups involved in bat rehabilitation and conservation to collect a total of 48 faecal samples from bats representing 16 of the 17 species that breed in the United Kingdom. Genetic sequencing turned up nine coronaviruses, including four sarbecoviruses and one related to the coronavirus responsible for Middle East Respiratory Syndrome, or MERS, which periodically spills over into camels and humans. 

Ties that bind — or not

To gauge the threat posed by the UK coronaviruses, the researchers created pseudoviruses: non-replicating forms of HIV that are engineered to carry the spike protein that coronaviruses use to infect cells. One sarbecovirus found in a lesser horseshoe bat (Rhinolophus hipposideros) had a spike protein that was able to infect human cells by attaching to a protein called ACE2, the same receptor used by SARS-CoV-2. But the UK sarbecovirus’s version of spike didn’t attach nearly as strongly as SARS-CoV-2’s, and pseudoviruses could infect only human cells with unnaturally high levels of ACE2. This makes it unlikely that the virus could readily infect people and spread, the researchers say. That’s reassuring, but other sarbecoviruses circulating in British bats could be able to bind to human ACE2 more efficiently, says Michael Letko, a molecular virologist at Washington State University in Pullman, who was not involved in the study. A February preprint surveyed UK lesser horseshoe bats and found signs that around half were infected with sarbecoviruses. Further adaptations that help these viruses to infect human cells more efficiently might not be hard to come by, Letko says. “Once the virus has its foot in the door, it’s easier to adapt further.” Tyler Starr, a molecular evolutionary biologist at the University of Utah in Salt Lake City, says that sarbecoviruses identified so far in Europe and in Africa probably represent the tip of the iceberg when it comes to the group’s true diversity and geographical distribution. He wouldn’t be surprised if the next sarbecovirus to spill over into humans came from an unprecedented location or branch of the family tree. “The next pandemic threat could very well be in our own backyard,” adds Letko.

Cited research published in Nat. Communications (June 27, 2023):

https://doi.org/10.1038/s41467-023-38717-w 

Long before COVID-19, scientists had been working to identify animal viruses that could potentially jump to people. These efforts have led to a Web-based platform called SpillOver, which ranks the risk that various viruses will make the leap. Developers hope the new tool will help public health experts and policymakers avoid future outbreaks. Jonna Mazet, an epidemiologist and disease ecologist at the University of California, Davis, has led this work for more than a decade. It began with the USAID PREDICT project, which sought to go beyond well-tracked influenza viruses and identify other emerging pathogens that pose a risk to humans. Thousands of scientists scoured more than 30 countries to locate and identify animal viruses, discovering many new ones in the process. But not every virus is equally threatening. So Mazet and her colleagues decided to create a framework to interpret their findings. “We wanted to move beyond scientific stamp collecting [simply finding viruses] to actual risk evaluation and reduction,” she says. The team was surprised to find very little existing research on categorizing threats from viruses that are currently found only in animals but are in viral families that can likely cause disease in people.

So the researchers started from scratch, identifying 31 factors pertaining to animal viruses (such as how they are transmitted), to their hosts (such as how many and varied they are), and to the environment (human population density, frequency of interaction with hosts, and more). These are summed up in a risk score out of 155; the higher the score, the more likelihood of spillover. Cornell University virologist Colin Parrish, who was not involved in the study, says the factors examined were important in previous spillovers. But he notes that other viruses' crossover risk may be heightened by unforeseeable factors that crop up later. “It's a bit like the stock market,” he says. The new study, published in the Proceedings of the National Academy of Sciences USA, ranks 887 animal-borne viruses. Twelve known human pathogens scored at the top—with the virus that causes COVID-19 in second place, just under the rat-carried Lassa virus. (Influenza would have topped the list if included, Mazet says, but flu variants are already tracked elsewhere.) Parrish notes that the list also omits insect-borne viruses and those from domesticated animals. “This is a work in progress,” he says. “I'm sure it will be iterated into a more powerful tool as more information and data become available. SpillOver is publicly editable, and scientists around the world are already contributing their own findings. Mazet hopes it catches the attention of public health practitioners and leaders, too. With targeted action, Mazet says, “we can ensure that we don't have these spillovers at all. Or if we do, we're ready for them—because we're watching.”

See also research published in P.N.A.S. (April 13, 2021):

https://doi.org/10.1073/pnas.2002324118

A second Ebola patient has died in northwestern Democratic Republic of Congo, the World Health Organization (WHO) said on Tuesday, days into a fresh outbreak of the deadly disease. Genetic testing showed an infection confirmed last week in the city of Mbandaka was a new "spillover event", a transmission from an infected animal, and not linked to any previous outbreaks, said the country's National Institute of Biomedical Research.  The second fatality was a 25-year-old woman who was the sister-in-law of the first case, the WHO said on Twitter. She began experiencing symptoms 12 days earlier, it said. The first patient began showing symptoms on April 5, but did not seek treatment for more than a week. He died in an Ebola treatment centre on April 21. The lag time has health workers rushing to identify contacts who may have been infected, the WHO said.

At least 145 people came into contact with the confirmed cases and their health is being closely monitored, the WHO said, noting later that one of the first cases was a health worker.  Mbandaka, a trading hub on the banks of the Congo River, is a city of over one million where people live in close proximity with road, water and air links to the capital Kinshasa. WHO emergencies director for Africa, Ibrahima Soce Fall, said there was a risk the disease could spread to neighbouring Central African Republic and Congo Brazzaville.  "This is concerning but taking into account the capacity build up and experience in Congo we believe it can be contained," Fall said at a press conference in Geneva. Congo has seen 13 previous outbreaks of Ebola, including one in 2018-2020 in the east that killed nearly 2,300 people, the second highest toll recorded in the history of the hemorrhagic fever. The most recent outbreak ended in December in the east after six deaths. Mbandaka, the capital of Equateur province, has also contended with two previous outbreaks - in 2018 and in 2020. The country's equatorial forests are a natural reservoir for the Ebola virus, which was discovered near the Ebola River in northern Congo in 1976.