Why it’s so difficult to trace the origin of COVID-19

That’s why scientists are backing a thorough, evidence-based investigation into the origins of COVID-19. But similar investigations in past epidemics have taken months, if not years, to provide answers, and in several cases the mystery remains unresolved.

“Science takes time,” says Arinjay Banerjee, a virologist at the University of Saskatchewan in Canada. “Going back and identifying the source with confidence is a difficult task. “

Earlier this year, an international team from the World Health Organization visited the city of Wuhan, China, to assess the evidence provided by China on the origin of SARS-CoV-2. In a report summarizing their findings, the WHO suggested that it was “probably very likely” that the virus first spread from infected bats to humans via an animal intermediate host.

This was the case with the SARS-CoV epidemic of 2002—the first pandemic of the 21st century; the virus has most likely spread from troglodyte horseshoe bats in China to palm civets sold in live animal markets, where it has reached humans. Likewise, the 2012 MERS-CoV outbreak is believed to have originated in bats and was later transmitted to camels, which infected humans.

This WHO report also considered that a laboratory leak from the Wuhan Institute of Virology, known for its work on coronaviruses, was “extremely unlikely”. But the finding drew backlash from scientists and governments around the world, who argued it was still too early to rule out a lab leak based on the available evidence. Other experts warn that political motives could lead people to hasty conclusions.

“There is a progenitor virus somewhere, and we should be looking for it,” says David Morens, senior scientific advisor in epidemiology to Anthony Fauci, director of the National Institute of Allergy and Infectious Diseases in the United States. “But at a At some point it goes from due diligence to wasting time and insanity We may have seen that point before.

Here’s what we know so far about the scientific investigation into the origin of the pandemic, and what remains to be done to find clear answers.

What evidence are virus detectives looking for?

Finding the origin of a virus requires extensive fieldwork, in-depth forensic expertise, and a bit of luck. The painstaking effort can take years until scientists have the evidence they need to point to a source.

For diseases of animal origin, this evidence is usually a genetic match between viral sequences obtained from an animal and those from some of the first confirmed patients. The match may not be 100% because viruses accumulate mutations or new genes over time and as they jump on hosts. But with enough investigation, scientists have found near perfect matches of around 99% or better for some viruses, including those responsible for two previous coronavirus outbreaks.

Cat-like arboreal civets, considered a delicacy and sold in street markets, quickly became the center of interest during the 2002-2004 Severe Acute Respiratory Syndrome (SARS) epidemic that emerged in China’s Guangdong Province, which resulted in more than 8,000 cases and nearly 800 deaths in 29 countries. Some of the early cases of SARS included several infected restaurant chefs handling a variety of animals. Blood tests from animal traders in the area showed a higher prevalence of antibodies to the SARS-associated coronavirus compared to healthy controls, with the the highest levels recorded among those who traded primarily in masked palmate civets.

A 2003 article also showed that a nasal swab from a masked palm kernel civet obtained from a live animal market in Guangdong gave a 99.8% match between the complete genome sequence of the SARS-CoV virus isolated from civet and the virus from a human. This indicated that the SARS-CoV-like virus had recently infected civets in the market.

But it became clear that these furry mammals were not the original sources, as the virus was mostly absent among farmed masked palm civets before reaching the markets, and it was little circulating in its wild populations. Suspecting bats to be the natural reservoirs, given that they harbor other zoonotic viruses, the researchers sampled blood, fecal and throat swabs from bats in parts of China and Hong Kong.

More than 10 years later, they identified horseshoe bats in an isolated cave in southwest China’s Yunnan province carrying strains of the virus that contain all genetic parts recorded in the viral genomes of human patients. It is possible that the strain that precipitated the 2002 epidemic was a recombination product of the different genetic strains found in these bats.

Scientists then used the lessons learned from researching the origins of the SARS virus to investigate the source of the 2012 Middle East Respiratory Syndrome (MERS) coronavirus outbreak, which infected more than 2,000 people in 37 countries and killed nearly 900.

The virus was first isolated of a 60-year-old businessman who died of severe pneumonia and multiple organ failure in June 2012 in a hospital in Jeddah, Saudi Arabia. Early efforts to trace the source focused on bats. In Saudi Arabia, throat swabs, urine, feces and blood samples taken from wild bats, including in the area where the first patient lived and worked, showed signs of MERS-type coronavirus in Egyptian bat fecal sample. But without a complete genome sequence, the role of bats could not be assessed.

During this time, anecdotal reports suggested that some patients had been exposed to camels or goats. A 2013 study found antibodies to MERS in blood samples taken from retired racing camels in Oman, which were missing in the blood of European sheep, goats and cattle. Similar blood surveys carried out in several countries in the Arabian Peninsula, Egypt and the Spanish Canary Islands have also shown the presence of antibodies in camel blood, indicating that hoofed mammals were once infected with the virus.

But the strongest evidence of camel involvement came from Qatar in October 2013, where a camel herd owner and his colleague were diagnosed with MERS. Nasal swab tests indicated five of 14 camels on their farm tested positive for MERS. In addition, entire viral genome sequences obtained from humans and camels have been 99.5 to 99.9 percent identical.

Scientists believe that camels are the intermediate hosts and bats suspect to be the original reservoirs of MERS-CoV. This is because some species of bats, like the vesper bats in South Africa, harbor viruses which are related to the one causing MERS. But there is still a evolutionary gap between these bat viruses and the human or camel versions.

“We still have not found these viruses which are very, very close,” says virologist Chantal Reusken of the Dutch Institute for Public Health and the Environment in the Netherlands.