Researchers in Cambodia, France and the United States have conducted a study indicating that viruses related to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) – the agent that causes coronavirus disease 2019 (COVID-19) – are far more geographically widespread than previously thought.
The closest relatives to SARS-CoV-2 that have been detected to date were identified in Rhinolophus bats sampled in Yunnan province, China.
Now, Veasna Duong from the International Network of Pasteur Institutes in Phnom Penh, Cambodia and colleagues have identified two coronaviruses in Rhinolophus bats that were sampled in Cambodia.
These viruses, which were identified in archived samples from 2010, share 92.6% genomic identity with SARS-CoV-2. Some genomic sections are closer to SARS-CoV-2 than any other related viruses discovered to date.
The discovery of these viruses in a bat species not found in China indicates that SARS-CoV-2-related viruses have a much wider geographic distribution than previously understood, and 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," writes the team.
A pre-print version of the research paper is available on the bioRxiv server, while the article undergoes peer review.
More about the close relatives identified so far
Although more than a year has passed since SARS-CoV-2 was first identified in Wuhan, China, in late 2019, information regarding the origin, reservoir, diversity, and circulation of its ancestors remains scarce.
To date, the closest relatives to SARS-CoV-2 have been detected in the Yunnan province, China. One relative – RaTG13 – was isolated from the intermediate horseshoe bat (Rhinolophus affinis) in 2013 and another – RmYN02 – was isolated from the Malayan horseshoe bat (Rhinolophus malayanus) in 2019.
Two close relatives were also identified in Sunda pangolins (Manis javanica) in two provinces of southern China.
Where does Southeast Asia come in?
The researchers point out that Southeast Asia (which lies south of China) is considered a hotspot for emerging diseases and is home to more than 25% of the world's diverse bat population.
SARS-CoV-2 is a single-stranded RNA virus belonging to the genus Betacoronavirus and the subgenus Sarbecovirus. The betacoronaviruses are one of four (alpha, beta, gamma, and delta) genera that make up the coronavirus subfamily of the coronaviridae family.
To search for putative SARS-CoV-2-like betacoronavirus, Duong and colleagues retrospectively performed pan-coronavirus polymerase chain rection (PCR) sequencing of 430 archived samples (162 oral swabs and 268 rectal swabs) taken from six bat families and two carnivorous mammal families.
Sixteen (3.72%) of the 430 samples tested positive for coronavirus, eleven of which were alphacoronaviruses, and five were betacoronaviruses.
Further sequencing of the five betacoronaviruses samples by reverse transcription-quantitative PCR (RT-qPCR) revealed that two were members of the Sarbecoviruses subgenus.
Both of these sarbecoviruses were from Shamel's horseshoe bats (Rhinolophus shameli) that were sampled in Steung Treng province of northeastern Cambodia in December 2010.
The viral genomes were almost identical to that of SARS-CoV-2
Next-generation metagenomic sequencing of RNA extracted from the samples identified two almost identical near-full-length coronavirus genomes, named RshSTT182 and RshSTT200.
The genomes exhibited 92.6% nucleotide identity with SARS-CoV-2 and identical genomic organization.
Phylogenetic analysis further showed that RshSTT182 and RshSTT200 represent a new sublineage of SARS-CoV-2-related viruses.
Genetic similarity was maintained across the genome, with several genomic regions of RshSTT182 and RshSTT200 being genetically closer to SARS-CoV-2 than any other close relatives identified to date.
All these elements suggest a co-circulation of ancestors to these viral sublineages with both a wider geographic area and more distinct bat species than those previously identified," writes Duong and colleagues.
Geographic distribution of Rhinolophus shameli bats does not include China
The team says it should be noted that the current geographic distribution of R. shameli bats does not include China. However, the distribution of R. affinis bats and R. malayanus bats overlaps with the distribution area of R. shameli in Southeast Asia and extends into China. This includes Yunnan province, where the other two close relatives (RaTG13 and RmYN02) of SARS-CoV2 were identified.
Further risk assessment is needed to understand the host range (including Humans) and pathogenesis associated with this novel sublineage," say the researchers.
What are the study implications?
Duong and colleagues say the findings suggest that SARS-CoV-2-related viruses have a much wider geographic distribution than previously thought and that they likely circulate via multiple Rhinolophus species.
Southeast Asia, with its rich diversity of wildlife and regular trading of animals that host SARS-CoV-2-like viruses, may represent an important area in the ongoing search for the origins of SARS-CoV-2 and in the broader surveillance of coronaviruses, advises the team.
The region is undergoing dramatic land-use changes such as infrastructure development, urban development, and agricultural expansion, that can increase contacts between bats and humans," say Ho and colleagues.
"Continued surveillance of bats and other key wild animals in Southeast Asia is thus crucial, not only to find the SARS-CoV-2 reservoir, but to also be better prepared for the next pandemic," they conclude.
bioRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.