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Why are bats the source of dangerous coronavirus pandemics?

Why are bats the source of dangerous coronavirus pandemics?



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Why do coronaviruses come from bats?

I mean, why precisely coronaviruses and not (for instance) herpesviruses? It looks like bats host more zoonotic viruses (per species) than rodents, although they don't develop any sign of disease.

The article above says that rodents host more zoonotic viruses than bats overall (68 against 61), but at the same time most of the latest pandemics originated from bats.

It also seems that bats could be involved in the maintenance of ebola viruses.

My question is: why did these major pandemics originate from bats and not from rodents, although rodents host more zoonotic viruses overall?

We should also take into consideration that human-rodent interaction is usually more likely than human-bat interaction, except for people who consume bats (like Chinese people; this would (partially) explain why both SARS and 2019-nCoV developed in China).


The preponderance of links between bat and human pathogens has led to a debate about whether bats disproportionately contribute to emerging viral infections crossing the species barrier into humans (26-30). Given the diversity of the Chiroptera order (Figure ​(Figure1),1), we may simply see more bat viruses because there are so many (>1,300) species of bats (31). However, even when accounting for the fact that they make up ~20% of extant terrestrial mammals, bats are overrepresented as reservoir hosts of pathogens with a high potential for spilling into human populations (32, 33). In fact, no known predictors that have been described to impact the likelihood of crossing the species barrier, including reservoir host ecology, phylogenetic relatedness to humans or frequency of reservoir-human contact, explain this pattern (32). Thus, why bats are such a frequent source of pathogenic human viruses remains a tantalizing mystery.

--Going to Bat(s) for Studies of Disease Tolerance

Other references that debate whether bats are special, generally conclude that they might somehow be, and argue about causes, include

  • Brook CE, Dobson AP. Bats as 'special' reservoirs for emerging zoonotic pathogens. Trends Microbiol. (2015) 23:172-80. This may be the best of the group, going into more detail and including more recent data

  • Dobson AP. Virology. What links bats to emerging infectious diseases? Science (2005) 310:628-9.

  • Wang LF, Walker PJ, Poon LL. Mass extinctions, biodiversity and mitochondrial function: are bats 'special' as reservoirs for emerging viruses? Curr Opin Virol. (2011) 1:649-57.

  • Olival K, Epstein JH, Wang LF, Field HE, Daszak P. Are bats exceptional viral reservoirs? In: Aguirre AA, Ostfeld R, Daszak P, editors. editors. New Directions in Conservation Medicine. Oxford, UK: Oxford University Press; (2012). p. 195-212.

  • Luis AD, Hayman DT, O'Shea TJ, Cryan PM, Gilbert AT, Pulliam JR, et al… A comparison of bats and rodents as reservoirs of zoonotic viruses: are bats special? Proc Biol Sci. (2013) 280:20122753.


The following paper proposes that the bat borne viruses evolve to rapidly-transmit as a response to their robust immune systems:

We carried out virus infectivity assays on bat cell lines expressing induced and constitutive immune phenotypes, then developed a theoretical model of our in vitro system, which we fit to empirical data. Best fit models recapitulated expected immune phenotypes for representative cell lines, supporting robust antiviral defenses in bat cells that correlated with higher estimates for within-host viral propagation rates. In general, heightened immune responses limit pathogen-induced cellular morbidity, which can facilitate the establishment of rapidly-propagating persistent infections within-host. Rapidly-transmitting viruses that have evolved with bat immune systems will likely cause enhanced virulence following emergence into secondary hosts with immune systems that diverge from those unique to bats.

  • Accelerated viral dynamics in bat cell lines, with implications for zoonotic emergence, eLife Sciences (2020)

Leap from bats to humans was easy for SARS-CoV-2 — study

All data and statistics are based on publicly available data at the time of publication. Some information may be out of date. Visit our coronavirus hub and follow our live updates page for the most recent information on the COVID-19 pandemic.

Health officials quickly traced the initial outbreak of COVID-19 in December 2019 to a seafood market in the Chinese city of Wuhan.

Exactly how the virus passed from its original animal host into humans remains a mystery, however.

Viruses closely related to SARS-CoV-2 — the virus that causes COVID-19 — have been found in horseshoe bats and pangolins, but previous research suggests that its lineage diverged from theirs several decades ago.

Scientists are keen to find out more about the origins of the virus, because it will help them assess the risk of similar viruses emerging that could cause future pandemics.

  • How much evolutionary adaptation was required to make the jump into humans?
  • How fast did the virus evolve once it had established in the human population?

According to new research by scientists in the United States, the United Kingdom, and Belgium, the transition from bats to people was one small step for the virus.

The researchers have published their results in the journal PLOS Biology.

The scientists drew upon their experience of tracing the evolutionary origins of HIV and other viruses.

They scoured the genomes of more than 130,000 samples of SARS-CoV-2 collected between December 2019 and October 2020 for signs of evolutionary adaptations. They then contrasted these with the molecular signatures of adaptation in 69 related bat viruses.

Their analysis suggests that most of the adaptations that allowed the SARS-CoV-2 lineage to jump from bats to humans and spread across the world arose in bats many years ago.

They note that many sarbecoviruses — which are the group of bat and pangolin viruses to which SARS-CoV-2 belongs — are “generalists.” This means that they have adaptations that allow them to skip from one mammalian host species to another relatively easily.

The research also revealed that there were few evolutionarily significant changes in the genome of the virus during the first 11 months of the pandemic. This implies that the virus was already well adapted to its new host and could “hit the ground running.”

“What has been so surprising is just how transmissible SARS-CoV-2 has been from the outset,” says co-lead author Prof. Sergei Pond from the Institute for Genomics and Evolutionary Medicine at Temple University in Philadelphia, PA.

“Usually viruses that jump to a new host species take some time to acquire adaptations to be as capable as SARS-CoV-2 at spreading, and most never make it past that stage, resulting in dead-end spillovers or localized outbreaks,” he adds.

The researchers explain that this does not mean there were no changes in the virus’s genome over this period.

Random mutations occur in the genetic sequences of viruses all the time. Mutations with negative consequences for the virus are weeded out by natural selection, whereas beneficial ones proliferate.

However, “neutral” mutations that are neither beneficial nor detrimental for the virus can persist by default.

There were some significant changes during this period, say the researchers. For example, a mutation called D614G that affected its spike protein allowed the virus to infect host cells more easily.

This made the virus more transmissible, but it did not appear to make the disease any more severe.

The majority of mutations that arose during this early phase of the pandemic were neutral, however.

“This stasis can be attributed to the highly susceptible nature of the human population to this new pathogen, with limited pressure from population immunity, and lack of containment, leading to exponential growth, making almost every virus a winner,” says co-first author Dr. Oscar MacLean from the University of Glasgow Centre for Virus Research (CVR) in the U.K.

This free-for-all appeared to end in late 2020 with the emergence of new “variants of concern,” such as the U.K. and South African strains.

A growing proportion of the human population became immune to the virus as a result of previous infections, which increased selective pressure on the virus and accelerated its evolution.

Mutations that allowed the virus to spread — despite increasing immunity within the population — began to come to the fore.

“The reason for the ‘shifting of gears’ of SARS-CoV-2 in terms of its increased rate of evolution at the end of 2020, associated with more heavily mutated lineages, is because the immunological profile of the human population has changed,” says senior author Prof. David L. Robertson from CVR.

In addition, some significant mutations may have had time to evolve during infections that became long-term and chronic — for example, in patients with weakened immune systems.

The vaccines currently in use were designed to provoke a strong immune response to the strain of the virus that was prevalent at the start of the pandemic.

As time passes, and the evolution of the virus gathers pace, there is an increased risk that the virus could mutate in a way that would allow it to evade immunity from previous infection or vaccination with current vaccines.

“The first race was to develop a vaccine. The race now is to get the global population vaccinated as quickly as possible,” says Prof. Robertson.

For live updates on the latest developments regarding the novel coronavirus and COVID-19, click here.


Why are bats the source of dangerous coronavirus pandemics? - Biology

Scientists believe bats are the source of the novel coronavirus and that it jumped to an intermediate host before spreading to humans in Hubei Province in China in mid November.

A lab at the Wuhan Institute of Virology had previously experimented with human coronaviruses derived from bats, including SARS. Some scientists outside China had voiced concerns that pathogens could escape from the lab.

Reporting from several media outlets suggests that U.S. officials were concerned before the outbreak about safety problems at the Wuhan Institute. Officially, the U.S. government says it&rsquos still investigating root causes.

Research shows that the virus&rsquo genetic makeup precludes it from being man-made. The Chinese government has denied the notion that the coronavirus escaped from a lab.

Since the beginning of the coronavirus pandemic, theories have swirled online about its source. Many early posts claimed the virus originated in a Chinese lab as a bioweapon.

PolitiFact and other fact-checkers debunked those conspiracies. Now, there is new reporting that suggests the virus could have come from a lab in Wuhan, China, the epicenter of the outbreak.

Washington Post columnist Josh Rogin reported April 14 that officials at the United States Embassy in Beijing sent two official warnings to Washington about safety problems in the Wuhan Institute of Virology. In 2015, the facility became China&rsquos first lab to achieve the highest level of international bioresearch safety. That designation meant the lab could experiment with the world&rsquos most dangerous pathogens &mdash including coronaviruses that come from bats, like the novel coronavirus and Severe Acute Respiratory Syndrome.

Yahoo News published a similar story on April 14. A day later, Fox News cited anonymous sources to report that the researchers at the Wuhan Institute of Virology may have been studying the novel coronavirus, and that patient zero worked at the lab.

"There is increasing confidence that the COVID-19 outbreak likely originated in a Wuhan laboratory, though not as a bioweapon but as part of China's attempt to demonstrate that its efforts to identify and combat viruses are equal to or greater than the capabilities of the United States," the network wrote.

When asked about the reporting during the April 15 coronavirus press briefing, President Donald Trump said the federal government is "doing a very thorough examination of this horrible situation that happened."

The media reports emphasize that there is still no conclusive proof that the coronavirus came from the lab. But they present new information about the potential source of the pandemic, so we wanted to review publicly available evidence about the source and spread of the coronavirus &mdash and what is still unproven.

Scientists widely believe that bats are the source of the novel coronavirus.

SARS-CoV-2, the official name of the virus that causes COVID-19, is a betacoronavirus, like Middle East Respiratory Syndrome and Severe Acute Respiratory Syndrome. All three viruses have their origins in bats, according to the U.S. Centers for Disease Control and Prevention.

Specifically, scientists have linked the genetic structure of the novel coronavirus to the horseshoe bat, which is common in southern and central China. The virus is "zoonotic," meaning it spread from animals to humans, according to a report from 25 international experts, including some from China and the U.S., convened by the World Health Organization.

Although betacoronaviruses originate in bats, they sometimes can jump to another species before infecting humans. Chinese researchers have found a possible link between COVID-19 and pangolins, a mammal covered in scales.

Scientists still aren&rsquot sure how the novel coronavirus made the jump from its intermediate host to humans. Despite a popular narrative online, there is no evidence that eating meat was part of the equation.

Past epidemics could offer some clues. Scientists first thought the Ebola outbreak started with the consumption of bat meat in Guinea. But Time reported that patient zero was likely infected by bat droppings that contaminated something she put in her mouth. MERS was also primarily spread through contact with live camels as opposed to camel meat.

The coronavirus outbreak was first documented in Wuhan in December. But the first actual case of COVID-19 was in November, according to Chinese government data.

The South China Morning Post reported March 13 that, based on government data it had obtained, the earliest case of the novel coronavirus was Nov. 17 in a 55-year-old resident of Hubei Province. From that point on, one to five new cases were reported each day, but health care workers did not know they were dealing with a new virus until December.

"Chinese authorities have so far identified at least 266 people who were infected last year, all of whom came under medical surveillance at some point," the newspaper reported. "Some of the cases were likely backdated after health authorities had tested specimens taken from suspected patients."

The Wuhan Huanan Wholesale Seafood Market, where a number of people related to the market fell ill with a virus, sits closed in Wuhan, China, on Jan. 21, 2020. (AP)

One of the earliest coronavirus cases in Wuhan was in early December. At first, many of the patients in the city had some link to a large seafood and live animal market, suggesting animal-to-person spread, according to the CDC. Later, a growing number of patients reportedly did not have exposure to animal markets, indicating person-to-person spread.

On Dec. 27, Wuhan health officials were told that the disease was a new coronavirus. Four days later, China notified the WHO about the outbreak.

As the number of coronavirus cases ballooned in China and spread to other countries, social media users and bloggers started to speculate that the virus escaped from a lab near Wuhan.

At the time, there was no evidence to back up those claims, and health officials are still investigating the source of the pandemic. But given recent media reports, let&rsquos review what we know about a lab that conducts infectious disease research near Wuhan.

The Wuhan National Biosafety Laboratory is a maximum-security biolab that deals with some of the world&rsquos most dangerous pathogens. It is housed within the Wuhan Institute of Virology, which is part of the larger Chinese Academy of Sciences and has been the subject of reporting from outlets like the Washington Post and Fox News.

The lab is located southeast of central Wuhan &mdash about 8.5 miles from the animal market connected to the earliest reported cases in the city. The Chinese government started building it in 2005 after the 2003 SARS epidemic to prepare for and respond to future outbreaks, according to a CDC report. The lab was completed in 2015.

The Wuhan National Biosafety Laboratory has experimented with human betacoronaviruses in the past. In 2017, researchers published a study of SARS-related coronaviruses based on five years of surveillance in "a cave inhabited by multiple species of horseshoe bats in Yunnan Province, China."

Nature magazine reported in February 2017 that some scientists outside China were concerned about pathogens escaping from the lab given the fact that it had happened elsewhere in the country. A 2004 outbreak of SARS was linked to a Beijing research lab, from which the WHO said the virus spread to the public.

American intelligence agencies are investigating whether the novel coronavirus could have originated in a lab, despite denials from the Chinese government and the Wuhan Institute of Virology.

"We know that this virus originated in Wuhan, China. We know that there is the Wuhan Institute of Virology just a handful of miles away from where the wet market was," Secretary of State Mike Pompeo said during an April 15 interview on Fox News. "There&rsquos still lots to learn. The United States government is working diligently to figure it out."

Despite the speculation, the Trump administration officials have been careful to say that all evidence points to the fact that the coronavirus occurred naturally. When asked during an April 14 press briefing about the possibility that the coronavirus leaked from a lab, Joint Chiefs of Staff Chairman Gen. Mark Milley said the evidence is "inconclusive."

Research shows that the virus could not have been created in a lab, as many conspiracy theories have suggested. An article published March 17 says the genetic makeup of the coronavirus, documented by researchers from several public health organizations, does not indicate it was altered.

However, that finding does not preclude the possibility that Chinese researchers were studying the novel coronavirus in a lab when it managed to spread outside the lab, although the government has denied that notion.

The Wuhan Institute of Virology said in a February statement that the rumors had "caused severe damage to our researchers who have been dedicated to working on the front line." When asked about Fox News&rsquo reporting during an April 16 press briefing, Zhao Lijian, a spokesman for China&rsquos Foreign Ministry, denied it.

"China's position with regard to the origin and transmission routes of the novel coronavirus is clear," he said. "It is a matter of science on which we should only rely on the findings of scientists and medical experts."


Bombshell: Fauci Said Risk of Manipulating Bat Viruses Was Worth a Potential Pandemic

Things keep getting worse for NIH Director Dr. Anthony Fauci, who continues to say during testimony on Capitol Hill that he didn't fund Frankenstein gain-of-function research at the Wuhan Institute of Virology.

According to The Weekend Australian, Fauci wrote in 2012 that continuing dangerous gain-of-function research was worth the risk of a pandemic.

In previously unreported remarks, Dr Fauci supported the contentious gain-of-­function experiments that some now fear might have led to an escape from a Wuhan laboratory causing the Covid-19 pandemic, calling them &ldquoimportant work&rdquo.

An investigation by The Weekend Australian has also confirmed Dr Fauci, the director of the Nat­ional Institute of Allergy and Infectious Diseases, did not alert senior White House officials before lifting the ban on gain-of-function research in 2017.

Writing in the American Society for Microbiology in October 2012, Dr Fauci acknowledged the controversial scientific research could spark a pandemic.

&ldquoIn an unlikely but conceivable turn of events, what if that scientist becomes infected with the virus, which leads to an outbreak and ultimately triggers a pandemic?&rdquo he wrote. &ldquoMany ask reasonable questions: given the possibility of such a scenario &ndash however remote &ndash should the initial experiments have been performed and/or published in the first place, and what were the processes involved in this decision?

&ldquoScientists working in this field might say &ndash as indeed I have said &ndash that the benefits of such experiments and the resulting knowledge outweigh the risks.

EXCLUSIVE: Anthony Fauci argued the benefits of gain-of-function research was worth the risk of a laboratory accident sparking a pandemic. https://t.co/TPPmeHNjBL

&mdash Sharri Markson (@SharriMarkson) May 28, 2021

After telling Republican Senator Rand Paul two weeks ago that he "never" approved grant funding through the NIH for gain-of-function research at the Wuhan Institute of Virology, Fauci changed his tune this week and said he simply told Chinese Communist Party controlled scientists not to conduct the research.

From Fauci's exchange with Republican Senator John Kennedy:

Kennedy: &ldquoHere&rsquos where I&rsquom getting at: You gave them money, and you said, &lsquoDon&rsquot do gain-of-function research.&rsquo&rdquo

Fauci: &ldquoCorrect.&rdquo

Kennedy: &ldquoAnd they said, &lsquoWe won&rsquot.&rsquo&rdquo

Fauci: &ldquoCorrect.&rdquo

Kennedy: &ldquoAnd you have no way of knowing whether they did or not, except you trust them. Is that right?&rdquo

Fauci: &ldquoWell, we generally always trust the grantee to do what they say, and you look at the results&mdash&rdquo

Kennedy: &ldquoHave you ever had a grantee lie to you?&rdquo

Fauci: &ldquoI cannot guarantee that a grantee has not lied to us because you never know.&rdquo


Wet markets--a continuing source of severe acute respiratory syndrome and influenza?

Context: Live-animal markets (wet markets) provide a source of vertebrate and invertebrate animals for customers in tropical and subtropical regions of the world. Wet markets sell live poultry, fish, reptiles, and mammals of every kind. Live-poultry markets (mostly chicken, pigeon, quail, ducks, geese, and a wide range of exotic wild-caught and farm-raised fowl) are usually separated from markets selling fish or red-meat animals, but the stalls can be near each other with no physical separation. Despite the widespread availability of affordable refrigeration, many Asian people prefer live animals for fresh produce. Wet markets are widespread in Asian countries and in countries where Asian people have migrated. Live-poultry markets were the source of the H5N1 bird-influenza virus that transmitted to and killed six of 18 people in Hong Kong.

Starting point: Yi Guan and colleagues (Science 2003 302: 276-78) recently reported the isolation of severe acute respiratory syndrome (SARS) coronavirus (CoV) from Himalayan palm civets (Paguna larvata) in wet markets in Shenzen, southern China. These researchers also found serological evidence of infection in raccoon dogs (Nyctereutes procuyoinboides). Serological evidence for SARS CoV in human beings working in these markets, taken together with the earliest cases of SARS in restaurant workers, supports the contention of a potential zoonotic origin for SARS. WHERE NEXT? Will SARS reappear? This question confronts public-health officials worldwide, particularly infectious disease personnel in those regions of the world most affected by the disease and the economic burden of SARS, including China, Taiwan, and Canada. Will the virus re-emerge from wet markets or from laboratories working with SARS CoV, or are asymptomatic infections ongoing in human beings? Similar questions can be asked about a pandemic of influenza that is probably imminent. Knowledge of the ecology of influenza in wet markets can be used as an early-warning system to detect the reappearance of SARS or pandemic influenza.


Diverse and Unique

Humans are more closely related to bats than we are to dogs, cows or whales. But bats seem more alien, which can make it harder for people to relate to them.

Bats are the most unusual of the world’s 26 mammal orders , or large groups, such as rodents and carnivores. They are the only land mammals that navigate by echolocation, and the only mammals capable of true flight.

Many bats are small and have rapid metabolisms, but they reproduce slowly and live long lives. That’s more typical of large animals like sharks and elephants.

And a bat’s internal body temperatures can fluctuate by more than 60 degrees Fahrenheit in response to external conditions. This is more typical of cold-blooded animals that take on the temperature of their surroundings, like turtles and lizards.

Bats carry a range of viruses that can sicken other mammals when they jump species. These include at least 200 coronaviruses, some of which cause human respiratory diseases like SARS and MERS . Bats also host several filoviruses , including some that in humans manifest as deadly hemorrhagic fevers like Marburg and probably even Ebola .

Normally, these viruses remain hidden in bats’ bodies and ecosystems without harming humans. People raise the risk of transmission between species when they encroach on bats’ habitats or harvest bats for medicine or food . In particular, humans pack live bats into unsanitary conditions with other wild species that may serve as intermediate hosts. This is what happened at the Wuhan wet market where many experts believe COVID-19 emerged .

With a few exceptions, such as rabies, bats host their pathogens without getting sick . Recent media coverage attempting to explain this riddle has focused on a 2019 study suggesting that bats carry a gene mutation, which may enable them to remain healthy while harboring such viruses . But while the mutation may be of interest from a public health perspective, understanding where this novel coronavirus came from requires understanding what makes a bat a bat.

Why do bats carry so many diseases but seem unaffected by them? Genetic mutations that boost their immune systems may help. But a better answer is that bats are the only mammals that fly.

With thousands of bats crowded together licking, breathing and pooping on one another, bat caves are ideal environments for breeding and transmitting germs. But when bats fly, they generate so much internal heat that, according to many scientists, their bodies are able to fight off the germs they carry. This is known as the “ flight as fever hypothesis .”


We still don’t know for sure where the coronavirus came from. Here’s why

Researchers are studying the viruses that bats, such as this wrinkle-lipped bat (Chaerephon plicata), carry to better understand which ones might pose a threat to human health.

Smithsonian Conservation Biology Institute, PREDICT/Myanmar

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More than a year after the novel coronavirus had spread to all corners of the globe, officially becoming a pandemic, we still don’t know where it came from (SN: 3/11/20).

Many researchers agree the virus most likely came from nature, probably harbored in bats. Even so, conspiracy theories claiming that the virus came from a lab arose shortly after the first genetic blueprint for SARS-CoV-2 was unveiled in January 2020. Using that very genetic blueprint, multiple studies have refuted the lab-borne hypothesis and continue to point to bats as the original source of the virus.

But even after more than a year of sleuthing, many questions remain. It’s unclear where those bats lived. Nor do researchers know whether another animal was responsible for helping the virus jump from bats to people. Answering these questions could take years. Viruses often take labyrinthian journeys as they hop from host to host, so tracing their origins is time-consuming. And with myriad versions of coronaviruses circulating in bats, finding the ones that gave rise to SARS-CoV-2 will require both luck and skill.

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Still, identifying the source of SARS-CoV-2 is important, says virologist Chee Wah Tan of the Duke-NUS Medical School in Singapore. Knowing the virus’s origin could help researchers figure out ways to keep an eye out for similar viruses and, hopefully, prevent future outbreaks.

Essential clues

Two types of clues are crucial for tracing a virus back to its source: viral genetic material and evidence of past infections.

Genetic material, such as viral DNA or RNA, is the more revealing of the two. As a virus spreads among hosts, it mutates in unique ways (SN: 5/26/20). By tracking the changes that viruses accumulate, scientists can infer how a virus spread from host to host, from animal to human. The more virus blueprints from people and animals that researchers have, the clearer the picture becomes — like how knowing all of a person’s grandparents helps trace ancestry.

Such analyses led researchers to discover SARS-CoV-2’s closest coronavirus relative, called RaTG13, in bat droppings found in 2013 near a cave in Yunnan, China (SN: 7/28/20). More recently, scientists found a bat virus collected in 2020 from the same region that is more closely related to the new human coronavirus than RaTG13 in some genes.

Evidence of an infection that has already cleared can also help researchers retrace a virus’s steps. Those signs typically come from antibodies, proteins the immune system leaves behind after eliminating a virus from the body. Finding antibodies that recognize SARS-CoV-2 tells researchers that a person or animal had been previously infected, and researchers can use that information along with contact tracing to reveal the pathogen’s early days (SN: 4/28/20).

But some people with COVID-19, the disease caused by the coronavirus, never develop symptoms. That makes the virus harder to track, because those people might never know that they were infected, says Jonna Mazet, an epidemiologist at the University of California, Davis and director of the university’s One Health Institute. And if the immune proteins wane in the blood, that evidence of infection can slowly disappear.

See all our coverage of the coronavirus outbreak

Both the virus’s genetic material and signs of antibodies in people infected with COVID-19 have been important to tracking SARS-CoV-2’s origins. So far, though, there’s no clear record of the first human cases. The world learned about COVID-19 in the wake of a cluster of cases at the Hunan Seafood Market in Wuhan, China. But in time, reports revealed cases not associated with the market from mid-December 2019, a hint that the virus may have gained a foothold elsewhere.

Several teams of researchers have been working to track the virus and its origins for months and in January, the World Health Organization sent a team to China to search for clues to where it came from. Though the visit did not answer major questions about the beginnings of the pandemic, the team concluded that the virus was not likely to have been leaked from a lab it might have even come from outside of China, the scientists say.

An analysis of viruses found in samples from humans compared with viral material from other animals shows that coronaviruses similar to SARS-CoV-2 are also circulating in bats and pangolins in Thailand, virologist Tan and his colleagues reported February 9 in Nature Communications. A separate preliminary study posted January 26 at bioRxiv.org found related coronaviruses in bats from Cambodia.

After SARS-CoV-2 began spreading, researchers identified related viruses in pangolins, such as this Malayan pangolin (Manis javanica) confiscated in an animal smuggling ring in Kuala Lumpur. The finding led some experts to suspect that infected pangolins may have helped the coronavirus jump to people, but subsequent studies suggest pangolins are not directly involved. JIMIN LAI/AFP via Getty Images

These findings bolster work from last year that found that the novel coronavirus has some features that could come only from viruses circulating in animals, making lab-origin hypotheses less probable (SN: 3/26/20).

Tracing viruses takes time

Though researchers have been scrutinizing the source of SARS-CoV-2 since the outbreak began, one of the biggest challenges is time, Mazet says. “Going back and re-creating [a transmission event] more than a year later is incredibly difficult,” she says. “But it is possible to collect a body of evidence that points in the right direction.”

That’s what happened with the first SARS outbreak in 2003. The virus began spreading widely in February, but the first cases appeared in late 2002 in people who had contact with wildlife, a hint that the virus came from animals. By October 2003, after the worst of the outbreak was over, researchers reported another hint: Some masked palm civets sold at a live animal market had been infected.

Later it became clear that wild palm civets (Paguma larvata) didn’t carry the virus in nature. Only ones sold at the market had been infected — meaning the animals were probably not the natural hosts of the virus. Researchers ultimately pinpointed horseshoe bats (Rhinolophus) as a potential source. That genetic detective work revealed that civets most likely got the virus from bats and then passed it onto the people who handled civets.

Coronavirus-infected masked palm civets, such as this Paguma larvata spotted in Myanmar, from a live animal market were initially linked to the 2003–2004 SARS outbreak. Rejoice Gassah/iNaturalist.org (CC BY 4.0)

Even still, the search continued. In 2017, genetic analyses revealed several bat coronaviruses carried bits of RNA that constituted the original SARS coronavirus that sparked the 2003 outbreak and could recombine to form similar viruses (SN: 11/30/17). The research moved slowly and took time. The search for the origins of the newly emerged SARS-CoV-2 is following the same format. This time, at least, researchers already know that bats harbor SARS-like coronaviruses.

Nature’s black box

Having bats as the prime suspect isn’t enough to trace the virus’s origins. There’s essential information about bats’ biology and ecology that researchers don’t yet have, which makes it harder to home in on how humans contracted SARS-CoV-2. Researchers don’t fully understand how bats interact with the viruses they carry and therefore how they might transmit viruses to other animals. It’s also largely unknown how the environment where bats live might make them more likely to transmit a virus to another animal.

To get a better sense for how bat viruses might spark a pandemic, researchers need to study how those viruses might get their start in natural habitats, says Raina Plowright, a disease ecologist at Montana State University in Bozeman. “There are all these drivers that we need to be thinking about — what’s bringing humans into those landscapes and what’s driving the pathogen circulating in bats?”

Researchers take a blood sample from a wrinkle-lipped bat to test for new viruses. Smithsonian Conservation Biology Institute, PREDICT/Myanmar

The search for the animal viruses that sparked an outbreak in another species is like hunting for a specific stalk of hay in a haystack, says Colin Parrish, a virologist at Cornell University. Bats carry lots of viruses — coronaviruses and others — so researchers have to look in the right geographic location to find identify viruses similar to SARS-CoV-2. And to complicate the search, a virus might be there one season and gone the next, so timing matters. “It’s possible that this is the wrong time,” Parrish says.

It’s unclear why viruses come and go, says Plowright. Studies have shown that stressed bats are more likely to shed viruses into the environment, kind of like stressed people getting cold sores from herpes viruses. So one possibility is that persistently infected bats may become contagious because of stressors like habitat loss, and then stop shedding the virus when the threat is gone.

Another possibility is that coronaviruses sweep through bat populations much like measles does through people: short periods of infectiousness with fast transmission. In that scenario, a virus in bats might burn through a population until all the animals are recovered, then jump to the next group of bats.

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It’s hard to figure out which scenario occurs in nature. Doing so requires heaps of data about the health and immune status of bats as well as the environmental conditions. And there could be different answers for the different viruses that bats carry.

What’s clear is that data collected on the effects humans have on the environment, and the animals that live there, could help officials make decisions that protect the public from future outbreaks, Plowright and her colleagues write March 5 in Lancet Planetary Health. Cutting down swaths of dense rainforest to make room for agriculture or building a road could bring people in closer proximity to stressed animals infected with viruses. Knowing when bats are more likely to shed viruses could help mitigate the risk of transmission.

It might also help fill in some of the gaps on the origins of the novel coronavirus. “I don’t think we will ever be able to say with 100 percent confidence what happened [with SARS-CoV-2] because a year’s gone by,” Mazet says. But, she adds, we may be able to get to an answer in which “we’re all reasonably confident.”

Questions or comments on this article? E-mail us at [email protected]

Editor's Note:

This story was updated March 22, 2021 to correct the spelling of Chee Wah Tan's name.


The Bats Behind the Pandemic

The coronavirus has been found in horseshoe bats in China.

RaTG13 is the name, rank and serial number of an individual horseshoe bat of the species Rhinolophus affinis, or rather of a sample of its feces collected in 2013 in a cave in Yunnan, China. The sample was collected by hazmat-clad scientists from the Institute of Virology in Wuhan that year. Stored away and forgotten until January this year, the sample from the horseshoe bat contains the virus that causes Covid-19.

The scientists were mostly sampling a very similar species with slightly shorter wings, called Rhinolophus sinicus, in a successful search for the origin of the virus responsible for the SARS epidemic of 2002-03. That search had alarming implications, which were largely ignored.

In Shitou Cave, south of Kunming, the capital of Yunnan, they found viruses in the bats’ droppings and anal swabs that were more similar to human SARS than anything found in palm civets, the small mammals that until then were presumed to be the source of human infection. Back in the laboratory, they found that one of the viruses from bat droppings, called WIV1, could thrive in monkey and human cells specially engineered to activate the gene for ACE2 receptors, the lock to which a coronavirus’s spike protein can fit as a key. This suggested that people could catch SARS directly from a bat dropping.

Then in 2016, Ralph Baric and colleagues at the University of North Carolina at Chapel Hill showed that the same bat virus could infect live mice that had been engineered to express the human gene for the ACE2 receptor. The virus was “poised for human emergence,” as the title of Dr. Baric’s paper put it.

When Covid-19 broke out, attention focused on pangolins, mammals often called scaly anteaters. Early analyses of the pangolin version of the virus seemed to indicate it was even more closely related to the human version than the RaTG13 bat sample was. The illegal pangolin trade for traditional Chinese medicine brings people into contact with sick animals. Just over a year ago, 21 live Malayan pangolins destined for sale in China were intercepted by anti-smuggling officers in Guangdong. Despite the best efforts of a local wildlife rescue center, 16 died with swollen, flooded lungs, rich in coronaviruses.


Lab Leaks And Covid-19: Why The Lab Leak Hypothesis Doesn’t Mean The Virus Was Engineered

Security personnel stand guard outside the Wuhan Institute of Virology in Wuhan as members of the . [+] World Health Organization (WHO) team investigating the origins of the COVID-19 coronavirus make a visit to the institute in Wuhan in China's central Hubei province on February 3, 2021. (Photo by Hector RETAMAL / AFP) (Photo by HECTOR RETAMAL/AFP via Getty Images)

The “lab leak” hypothesis about the origin of Covid-19 has been getting a lot of attention lately, and deservedly so. This is the idea that the SARS-CoV-2 virus accidentally escaped from a laboratory in Wuhan, China, that conducts research on coronaviruses. Just a few weeks ago, a group of highly respected virologists and epidemiologists published a letter in the journal Science calling for a more thorough investigation, stating that the lab leak hypothesis was not taken seriously enough in earlier investigations.

The coincidence of having a major virus research facility, the Wuhan Institute of Virology (WIV), just a short distance from the live animal food market that was originally believed to be the source of the outbreak is too great to ignore. Even more curious is that WIV was actively doing research on coronaviruses in bats, including the bats that carry a strain of SARS-CoV-2 that is the closest known relative to the Covid-19 virus itself.

From the beginning of the outbreak, attention was focused on WIV, and various conspiracy theorists suggested, without any evidence, that the Covid-19 virus was either intentionally engineered, intentionally released, or both. Let me just say right off the bat that I don’t believe either of those claims.

However, I do think the lab leak hypothesis is credible, and it’s also possible that “gain of function” research (more about this below) might be responsible.

In arguing against (unsupported) claims that the Chinese released the virus on purpose, a group of virologists published a paper very early in the pandemic, in March 2020, which looked at the genome sequence of the virus and concluded that “SARS-CoV-2 is not a laboratory construct or a purposefully manipulated virus.” Other studies since then have come to similar conclusions: the virus is very similar to naturally-occurring coronaviruses, and it is possible that it simply evolved naturally in the wild, probably in bats.

Even so, the lab leak hypothesis remains highly credible, regardless of whether or not the virus was genetically engineered. Here’s why. First, we know that lab accidents can happen and viruses can escape, even if these accidents are rare. We also know that the Wuhan Institute of Virology had thousands of viruses, including coronaviruses, in its facility. And despite claims that viruses couldn’t possibly have escaped accidentally, a 2017 Nature article describing the then-new Wuhan Institute reported, perhaps prophetically, that “worries surround the [Wuhan Institute of Virology], too. The SARS virus has escaped from high-level containment facilities in Beijing multiple times.”

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The secrecy of the Chinese government, which has not yet allowed independent, outside scientists full access to WIV to investigate, hasn’t helped matters. We need to know if any viruses in WIV are similar to the Covid-19 virus, and at this point we can’t trust the Chinese government’s assurances on this question. Of course, even if they allow outsiders to investigate now, we cannot know that they have preserved all the viruses that were present in the lab in the winter of 2019-2020.

Now let’s talk about gain-of-function research. Gain of function, or GoF, refers to research that tries to make viruses or bacteria more harmful, by making them more infectious. This seems crazy, right? And yet it’s been going on for years, despite the efforts of many scientists to stop it. In the past, GoF research focused on the influenza virus, and in particular on a small number of scientists (highly irresponsible ones, in my view) who were trying to give avian influenza–bird flu–the ability to jump from birds into humans. I wrote about this in 2013, and in 2017, and again in 2019, each time calling on the US government to stop funding this extremely dangerous work. The NIH did put a “pause” on gain-of-function research for a few years, but the work resumed in 2019.

Now, let me explain why GoF research does not require artificially engineering a virus. Viruses mutate very rapidly all by themselves, and RNA viruses like influenza and SARS-CoV-2 mutate even more rapidly than DNA viruses. So a GoF experiment doesn’t need to engineer a virus to make it more infectious: instead, scientists can simply grow a few trillion viral particles, which is easy, and design experiments to select the ones that are more infectious. For example, some GoF research on bird flu simply sprays an aerosol mixture of viruses into a ferret’s nose (influenza research often uses ferrets, since you can’t ethically do this with people), and waits to see if the ferret comes down with the flu. If it does (and this has been done, successfully), the strain that succeeds now has a new function, because it can infect mammals. The viruses that are artificially selected (as opposed to natural selection) in these experiments will appear completely natural no genetic engineering required.

We know that WIV was conducting gain-of-function experiments, and we know that its work included coronaviruses. Was the Wuhan Institute of Virology running GoF experiments on SARS-CoV-2 viruses from bats? Possibly. And if it was, these experiments could easily have produced a strain that infected humans. If a lab employee was accidentally infected with such a strain, that could have started the pandemic. And even if SARS-CoV-2 wasn’t the subject of GoF experiments, a naturally-occurring strain being studied at WIV could still have infected one of their scientists and thereby leaked out into the population.

I’m not saying that any of these events is likely. I am, however, agreeing with the scientists who, in their recent letter to Science, called for a deeper investigation into the cause of the Covid-19 pandemic.

Finally, let me echo a sentiment they expressed in their letter, which is best said by simply quoting them: “in this time of unfortunate anti-Asian sentiment in some countries, we note that at the beginning of the pandemic, it was Chinese doctors, scientists, journalists, and citizens who shared with the world crucial information about the spread of the virus—often at great personal cost.” Rather than seeking to cast blame, we need to uncover the origin of the Covid-19 pandemic, and any behaviors that led to it, as a means to help all societies prevent future pandemics.


Bats May Be Carrying the Next SARS Pandemic

In November 2002, a deadly new virus emerged suddenly in the south of China. In less than a year, the disease it caused, known as SARS, spread to 33 countries, sickening more than 8000 people and killing more than 700. Then it disappeared. Now, researchers say, they have for the first time isolated a closely related virus from bats in China that can infect human cells. "This shows, that right now in China, there are bats carrying a virus that can directly infect people, and cause another SARS pandemic," says Peter Daszak, one of the authors and president of EcoHealth Alliance in New York City.

Scientists have long suspected bats to be the natural reservoir for coronaviruses such as the one responsible for SARS (severe acute respiratory syndrome). The animals have been identified as the source of many dangerous viruses, such as Nipah and Hendra, and have also been linked to Ebola and the new coronavirus causing a SARS-like illness, dubbed MERS. In 2005, Daszak and others found viral DNA closely resembling the SARS virus in three species of Chinese horseshoe bats. However, while the sequences of those viral genomes were 88% to 92% identical with that of the SARS coronavirus, they showed marked differences in a region coding for the so-called spike protein. In the SARS virus, this protein binds to a receptor on the surface of human cells mediating its entry. The differences meant that the bat viruses would not be able to infect human cells. And because some palm civets were found to carry a virus almost identical to the human SARS virus, most researchers have come to believe that SARS spread from bats to civets—probably in a Chinese market, where these and other animals come into close contact—and then to humans.

Now, new research suggests that civets may not be necessary to start a SARS pandemic. For more than a year, scientists from China, Australia, and the United States collected anal swabs or fecal samples from horseshoe bats at a cave in Kunming, in the south of China. They found coronavirus RNA in 27 of 117 sampled animals. Among the viruses were two new strains of coronavirus that resemble the SARS strain more closely than those previously identified in bats, especially in the part of the genome coding for the important spike protein. The scientists also managed to isolate live virus from one of the animals. In experiments, reported online today in Nature, they showed that the virus infected pig and bat kidney cells, and perhaps more important, cells lining the human lung.

The new results cannot resolve whether the original SARS virus moved directly from bats into humans or via an intermediate host, says Columbia University virologist Ian Lipkin, who was not involved in the work. But it shows that a similar coronavirus "has the potential to infect people without an intermediate host."

That should be a warning to everyone, Daszak says. Even if the SARS virus did jump to humans via civets, that intermediate stop was not necessary, he argues. Bats are still hunted and eaten in large numbers in China, he notes with concern. "I think people should stop hunting bats and stop eating bats."

But Michael Osterholm, director at the Center for Infectious Disease Research and Policy at the University of Minnesota, Twin Cities, says scientists should be careful to distinguish between what is possible and what is likely in nature. Bat rabies, for instance, readily infects human tissue, and many bats carry the virus, he says. "If that was enough for transmission we should all be dying of bat rabies in the U.S." But the virus can be transmitted only if an infected bat bites a human. That rarely happens and there are very few cases of bat rabies in the United States.

Christian Drosten, a coronavirus expert at the University of Bonn in Germany, also cautions against overinterpreting the results. Laboratory experiments do not necessarily mean that the virus can actually infect human beings, he says. "Receptor studies and cell culture aren't everything. You would have to take this virus and see in an animal experiment whether it can, for instance, infect a primate."

What fascinates Drosten most about the paper is a parallel to the coronavirus causing MERS, an illness that was first reported in the Middle East in 2012 and has killed 62 people so far. That virus has also been shown to infect various species' cells in cell culture. "We thought that was a special characteristic of MERS, but now this virus shows a similar pattern," Drosten says. That suggests that the coronaviruses present in bats and other animals differ in ways that may make them more or less likely to jump to humans. In trying to predict future pandemics, such characteristics may guide virologists to the pathogens most likely to cause a pandemic, he hopes, and may one day help prevent another SARS pandemic from happening.

Kai Kupferschmidt

Kai is a contributing correspondent for Science magazine based in Berlin, Germany. He is the author of a book about the color blue, published in 2019.