Researchers in the Virology Unit have recently published papers on the search for coronaviruses and have been integral in searching for and combating emerging and endemic viruses for 25 years. 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 human 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 with funding from the USAID PREDICT project. Screening of retrospective samples identified a betacoronavirus that is closely related to SARS-CoV-2, the virus responsible for the COVID-19 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).

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 sister or 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. These viruses detected in bats do not contain the same spike domain as human SARS-CoV-2 and are not able to bind to human ACE2 receptor. They also do not include the furin cleavage site, a key component of the pandemic virus. Hence, they are not able to cause infection in human.

Recently, similar results have been found in Thailand, Yunnan province of China, and Lao People’s Democratic Republic. The discovery of these viruses in Rhinolophus species in several parts of Southeast Asia, specifically the Greater Mekong Subregion, pinpoints a key geographic 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.