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Institut Pasteur du Cambodge identifies a betacoronavirus closely related to SARS-CoV-2 in bat samples from 2010


Southeast Asia, including Cambodia, is a hotspot of emerging and endemic infectious diseases, and the Institut Pasteur du Cambodge has been integral in searching for and combating these pathogens since its inception. The COVID-19 pandemic has returned the global spotlight to zoonotic emerging diseases caused by pathogens of wildlife origin. Numerous viruses, including coronaviruses, are widely distributed among mammals and birds, and have spilled over into human populations several times in history, often causing pandemics and establishing seasonal strains.

As part of the research for the global origins of COVID-19, the Institut Pasteur du Cambodge is screening its biobanks of historical samples from wildlife funded by the USAID PREDICT project. Restrospective screening identified a betacoronavirus that is closely related to SARS-CoV -2, the virus responsible for the pandemic. The virus was detected in two Shamel’s horseshoe bats (Rhinolophus shameli) captured in the Northern region of Cambodia in 2010 during a joint mission with the French National Museum of Natural History (MNHN). Recently, similar results have been found in Japan and in Thailand.

In collaboration with Institut Pasteur (Paris), full genome sequencing revealed the Cambodian viruses share 92,6% nucleotide identity with SARS-CoV-2, but are likely a cousin of the virus currently causing the global pandemic. This finding could be crucial in understanding the spillover transmission process from animals to humans, and in understanding the diversity in this virus family.

The discovery of these viruses in a bat species in Cambodia and in Thailand suggests 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.

At the current time, there is no demonstrated occurrence of direct transmission of SARS-CoV-2 or other coronaviruses from bats to humans in Cambodia. All laboratory-confirmed cases (470 as of February 4th, 2021) are imported or have a direct epidemiological link with an imported case.





The Virology Unit at IPC was established in 1996 and, since 2008, hosts a high-level (BSL-3) biosafety laboratory containing multiple diagnostic and research capacities to identify and understand endemic and emerging infectious diseases. IPC was prepared to test for COVID-19 by mid-January, 2020, and detected the first COVID-19 case in Cambodia on January 27th. In March 2020, scientists at IPC successfully isolated the virus and, in April 2020, IPC received designation as a WHO Global Referral Laboratory for COVID-19, a crucial role in addressing the public health risks emerging from the global COVID-19 pandemic. In addition to routine molecular testing, IPC is also actively involved in global validation and verification of novel testing protocols and diagnostic kits for SARS-CoV-2.

IPC is a Cambodian non-for-profit research institution established in 1953. IPC carries out life science and health research on infectious diseases, and supports public health surveillance through high-quality laboratories and epidemiology/clinical research capacities. As a member of the Institut Pasteur International Network (IPIN), IPC also works closely with several national and international partners to further increase capacity and capability in Cambodia and beyond.

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