Virus hunter searches bat cave to predict next pandemic

“We collected more than 15,000 bat samples (which resulted in the identification of about 500 new coronaviruses),” he says.

One of the ones found in Chinese caves in 2013 was likely a Covid-19 ancestor.

Coronavirus research

Prior to the 2003 SARS epidemic, research on coronaviruses received little attention. “This wasn’t considered a sexy division of medical research,” said Wang Linfa, a virologist at Duke NUS in Singapore who develops the tools used to analyze samples collected by the EcoHealth Alliance. say.

Only two human coronaviruses were identified, both of which were discovered in the 1960s.

The initiative’s mission is to identify and address new zoonotic diseases such as coronaviruses before they are transmitted to humans. During the 10-year operational period, approximately $ 200 million was awarded.

Since its establishment, five more human coronaviruses have been identified, including Covid-19. Daszak estimates that bats carry up to 15,000 coronaviruses.

Dazak’s organization focuses on the aforementioned limestone cave system in southwestern China, and more specifically in Yunnan, which is known for its large number of bats.

“We were initially looking for China because we were looking for the origin of SARS,” he explains. “But I found that there were hundreds of other dangerous coronaviruses out there, so I decided to focus on finding them.”

Predict operates in 31 countries. Another team of virus hunters at the Smithsonian Institution has begun focusing on Myanmar and Kenya. “So far, we have identified six new coronaviruses in Myanmar,” says Susan Murray, head of the Smithsonian Institution’s Global Health Program.

“These are areas with a lot of wildlife biodiversity, increased populations invading natural habitats, good travel networks, and large numbers of livestock. This is a potential for interspecies viral spillover. Is part of a virus sampling expedition at Dawn Zimmerman Smithsonian Institution.

From bats to humans

Analyzing blood samples of people living near two bat caves in Jining County, Yunnan Province in 2015, Dazak’s team found that 3% had antibodies to the virus, which is commonly found only in bats. Yes-that is, they were already exposed to bats.

“They may have unknowingly been infected with these pathogens and recovered or had few somatic cells infected,” he says.

In order to jump into humans, coronaviruses need to be able to bind to cellular receptors that normally require an intermediate animal host, Wang explains. This could be a musk cat, a camel, a pangolin, or another mammal closely related to humans, he said.

However, it carries a very high percentage of viruses that are usually derived from bats and that can infect humans such as Marburg, Nipah, Ebola, and SARS, according to Daszak, who co-authored Nature’s research on this topic in 2017. according to,

“Because bats are flying mammals, their bodies are subject to a lot of stress, which usually causes a reaction in the immune system,” he explains. “To deal with this, they need to weaken their immune system, which makes them more susceptible to viruses and able to withstand higher viral loads.”

Bats, which make up about 20% of all mammalian species, also collect in large colonies of crowded caves, making it more likely that the virus will spread between them.

Coronavirus library

Once the Dazak team collects the samples, they are stored in liquid nitrogren and sent to partner labs around the world for analysis.

“We usually choose to work with the best laboratories in the country, and if it doesn’t, we will increase our local capacity,” Daszak says. Next, the strands of viral DNA found in the sample are compared to GenBank profiles, an open access database maintained by the National Center for Biotechnology Information (NCBI). This will determine “whether to deal with new viruses”.

The answer is not always clear.

“A virus is considered a new virus if 20% or more of its DNA differs from that of a known virus,” says a lab linked to Chulalongkorn University in Bangkok to study emerging diseases independently of Predict. Supaporn Watcharaprueksadee explains.

Researchers may also think that they actually discovered a new virus that had spread in the community for several years. Less than half of all viruses that cause pneumonia have been identified, according to Patrick Woo, an emerging disease expert at the University of Hong Kong. Often, the patient just gets better and his case is not investigated further, he said.

In 2005, Wu discovered a new coronavirus in two patients hospitalized in Hong Kong and called it HKU1. But he later discovered that the same virus had already infected patients in the United States, Australia, and France.

Another virus that may have spread to humans without being noticed by anyone is Nipah. Dazak believes that the virus, which was associated with 105 deaths in Malaysia in 1998, was escaping from bats to humans in rural Bangladesh.

“Every year, there were some outbreaks classified as anomalous measles,” he explains. “A survey of these patients revealed that they were actually infected with the Nipah virus.” None of these infections were detected. He added that most people living in those areas are poor or too far from hospitals to seek medical care.

The samples he and other Predict teams collect are meant to fill this knowledge gap.

COVID-19

When Covid-19 appeared, Shi Zhengli, a virologist at the Wuhan Virology Institute, immediately compared it to a database compiled using the 500 new coronaviruses identified by the EcoHealth Alliance.

There was a hit “The new coronavirus matched a sample taken from horseshoe bats in a cave in Yunnan in 2013,” says Daszak. “It was 96.2% identical.”

That is, the virus was either an ancestor or a close relative of the virus that is causing the current epidemic. “It’s very likely that an intermediate animal host was involved and transmitted the virus to humans, explaining a 3.8% difference in the genome,” he says.

Knowing where the new virus came from and how it was transmitted to humans is important information. Watcharaprueksadee says it can enable early detection of epidemics and the timely introduction of measures to curb its epidemic.

There is precedent. In January 2019, Columbia University School of Public Health and EcoHealth Alliance announced the discovery of a bat in Liberia that carries a Zaire strain of Ebola. This caused a 2013-16 outbreak in West Africa. An epidemic that caused over 11,000 deaths.

Next big thing

In addition to providing insight into the origins of Covid-19 and Ebola, virus hunters want to anticipate where the next big outbreak will occur and prevent it. By elaborating on where the virus poses the greatest risk to humans, it is believed that the progression of the virus can be mapped and the infection minimized.

“Our team of virologists uses samples collected in the field to determine which viruses are most likely to spill into humans and classify them according to their risk profile,” Murray said. say.

Coronaviruses, which are closely associated with SARS or MERS, are particularly dangerous because of their ability to jump into humans. “In the course of the research, we discovered 50 new pathogens that are only associated with SARS,” says Daszak. “It makes sense to focus preventive efforts on these high-risk viruses.”

In one cave, his team identified all the buildings needed to make a SARS.

According to a paper published in PLoS Pathogens, when combined, the resulting virus can directly infect humans without the need for intermediate hosts.

There are a range of precautions that can be taken to prevent it. Community education is especially important in areas where dangerous viruses are widespread. “In some parts of Kenya, we teach people to block roof holes to prevent bat invasion, or to boil camel milk before drinking to kill pathogens,” Zimmerman said. Says.

The EcoHealth Alliance is also raising awareness about the risk of human trafficking, such as pangolins that can infect viruses, and educating locals about the need to avoid the fruit that bats may bite.

Bats and other wildlife may also have trackers installed to understand patterns of transmission by analyzing their movements and frequency of contact with livestock and humans.

Local features built by Predict’s team may also play an important role in preventing the spread of epidemics. “In the lab we work in the field, we know all the ways to identify new pathogens,” Zimmermann explains. Predict has built or strengthened around 60 laboratories in Asia and Africa.

This knowledge can be used to develop vaccines and treatments against new pathogens.

“Blood samples taken from bats contain antibodies produced to fight off the virus,” Wang said. “These could serve as the basis for the development of vaccines or plasma therapies against new pathogens.”

Just before the pandemic, the future of Predict became uncertain because it was set to expire at the end of March 2020.

However, according to a UC Davis press release, showing how important virus hunter work is, Covid-19 is currently undergoing a six-month extension worth $ 2,260,000.

The virus hunter had to put on a chemo protective suit to cancel the sampling expedition, but provided emergency support to test Covid-19 cases in Africa, Asia and the Middle East, as well as UC. According to Davis’ notice these countries.

“We want to get back there as soon as possible,” Dazak says. “Then we’ll do our best to find out exactly where Covid-19 came from.”