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The Cambodian samples were taken from horseshoe bats. Photo: Handout

Coronavirus: Cambodian scientists find close match for pathogen in samples collected in 2010

  • Viral sequences in samples from horseshoe bats have 92 per cent similarity to Covid-19 pathogen, researchers say
  • Closest known relative to the coronavirus was a bat virus found in Yunnan province, which is a 96 per cent match
With a World Health Organization investigation into the origins of the coronavirus which causes the Covid-19 disease under way in China, a laboratory in Cambodia has discovered close relatives of the pathogen in samples that have been stored in a freezer for more than a decade.
Two viruses found in the samples, taken from horseshoe bats in northeastern Cambodia in 2010 and identified in research released on Tuesday, have a 92.6 per cent similarity to SARS-CoV-2 behind the Covid-19 pandemic. That makes them the closest relatives uncovered outside China and adds new information to the investigation into where the pathogen came from.
The closest known relative to the virus that causes Covid-19 is a bat virus found in southwest China’s Yunnan province, which has a 96.2 per cent similarity.

The latest discovery, by researchers at the Pasteur Institute in Cambodia in Phnom Penh, comes as the WHO-backed team is working to understand how the coronavirus began spreading in Wuhan, central China, where it was first identified in late 2019.

Little is known about how the outbreak started, but scientists suspect the virus may have originated in bats before passing to humans either directly or via an intermediary animal.

Chinese officials have suggested the virus may have come from overseas. The WHO has said it is too soon to jump to any conclusions.

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The hunt for the origin has led a number of labs to back-test stored animal samples for traces of similar viruses in an effort to provide more clues.

The findings from Phnom Penh, which have not been peer reviewed, “suggest that Southeast Asia represents a key area to consider in the ongoing search for the origins of SARS-CoV-2, and in future surveillance for coronaviruses’’, said the researchers, who include scientists from Sorbonne University and Pasteur Institute in France and the University of California, Davis in the US.

They also add new data to a body of evidence showing Southeast Asia and southern China as hotspots for this larger group of coronaviruses.

The Cambodian viruses were picked up in swabs taken from Shamel’s horseshoe bats as part of a project backed by Unesco, in which researchers were comparing species diversity on two sides of the Mekong River in northern Cambodia.

The samples were transported back to the institute, where they were stored at minus 80 degrees Celsius (minus 112 degrees Fahrenheit), the paper said.

Following the outbreak of Covid-19, the scientists began running additional tests on stored samples in search of related coronaviruses. Of the 430 samples they looked at, 16 tested positive for coronaviruses, and among those were two nearly identical strains that turned out to be the close SARS-CoV-2 relatives.

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In November, Veasna Duong, a virologist at the institute told the scientific publication Nature about early findings which indicated there could be a close relative. The team was still waiting for the genetic sequencing to understand exactly how close the virus might be to the one that caused Covid-19, the journal reported at the time.

Though the genetic results released on Tuesday did not reveal a closer match than the known relatives in China, the researchers said their analysis suggested SARS-CoV-2 related viruses had a much wider geographic distribution than previously understood. The Shamel’s horseshoe bat species carrying the Cambodian viruses is not known to live in China.

This “possibly reflects a lack of sampling in Southeast Asia”, they said, calling for more surveillance in the region, which is home to both a high diversity of bats and wildlife as well as wildlife trade and land-use change – known drivers of emerging infectious diseases.

Members of the WHO team in China have expressed similar opinions on the need for more regional data.

Virologist Marion Koopmans of the Erasmus University Medical Centre in the Netherlands said on Wednesday that the Cambodian findings were “adding to our knowledge on SARS-Cov (-2) like viruses in bats in the region”.

“Data from Laos, Vietnam, Myanmar would also be needed,” she said on Twitter, adding that the hunt for the closest relatives of the pandemic virus was like searching for a needle in a haystack.

This article appeared in the South China Morning Post print edition as: Close match for pathogen unearthed in 2010 samples