New detection of coronavirus from horseshoe bats in Vietnam and surrounding areas

19/12/2024

Recently, scientists from Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, and colleagues from Hungarian Academy of Sciences and National Museum of Natural History, French Republic, have published new findings on the diversity and emergence of coronavirus species. These viruses were collected from horseshoe bat populations (Rhinolophus sp.) in Vietnam and neighboring countries.

These data not only provide important insights into the origins of the SARS-CoV-1 virus (which causes SARS, 2002-2004) and SARS-CoV-2 (which causes COVID-19, from December 2019 to the present), but also provides an important foundation for the development of surveillance and prevention strategies for coronavirus and other pathogens in the future. The research is based on an interdisciplinary approach One Health – combining the fields of health, veterinary medicine and the environment to ensure the holistic health of humans, animals and ecosystems.

Origin and risk of outbreaks of infectious diseases associated with bats

Since the beginning of the 21st century, humanity has faced three global pandemics caused by the coronavirus, including Severe Acute Respiratory Syndrome (SARS, 2002-2004) caused by the SARS-CoV-1 virus, Middle East Respiratory Syndrome (MERS, from 2012 to the present) caused by the MERS-CoV virus, and COVID-19 (from December 2019 to the present) caused by the SARS-CoV-2 virus. In particular, the COVID-19 pandemic, with more than 700 million infections and 7 million deaths globally, clearly shows the serious threat from the outbreak or re-outbreak of coronavirus infectious diseases. This poses a major challenge in ensuring global health security. Therefore, understanding the origin and epidemiological characteristics of potentially pathogenic coronaviruses in humans remains a priority research topic in medicine and biology.

Therefore, Dr. Vuong Tan Tu and his team of scientists conducted a study to evaluate the diversity and evolutionary relationship of coronaviruses that are closely related to two strains of SARS-CoV-1 and SARS-CoV-2 viruses in horseshoe bats in Vietnam. The study was carried out with the support of part of an international cooperation mission between the Vietnam Academy of Science and Technology and the Hungarian Academy of Sciences: "To study the evolutionary relationships of bats, ectoparasites and viruses from them based on data collected in Hungary and Vietnam" (code: QTHU01.01/22-23).

Figure 1. Dr. Vuong Tan Tu and Dr. Alexandre Hassanin (Two directors standing on the far left) with the research team and forest rangers in Dien Bien province

Results and new findings

According to scientific studies, SARS-CoV-1 and SARS-CoV-2 viruses are related and both belong to the subgroup Sarbecovirus, the genus Betacoronavirus, but belong to different evolutionary clades. Scientists have detected coronaviruses that are closely related to SARS-CoV-1 and SARS-CoV-2 in some wild animals but mainly horseshoe bats (Rhinolophus sp.). These findings suggest that both strains of the virus originated from horseshoe bats that live in Southeast Asia and southern China.

Within the framework of the study, the scientists collected fecal samples from 1218 individuals of 13 out of 19 species of horseshoe bats living at 19 selected research sites across Vietnam (Figure 2). The results of screening by Realtime RT-PCR technique from 547 pooled samples of 1218 samples collected (by location and gender) showed that the positivity rate for virus strains of the subgenus Sarbecovirus was 11%, corresponding to 59 out of 547, of which 46 samples belonged to Rhinolophus thomasi (n = 99; 46%), 10 specimens of R. affinis (n = 99; 10%), two specimens of R. pusillus (n = 99; 2%) and one specimen of R. malayanus (n = 36; 3%).

Figure 2. Location of sample collection points and photos of the field sample collection process and four species of horseshoe bats that have been recorded to carry coronavirus strains similar to SARS-CoV-1 and SARS-CoV-2

Next, the researchers sequenced the positive samples using next-generation gene sequencing (NGS) technology and synthesized 38 complete genomes of 17 coronavirus strains of the Sarbecovirus subgenus. Genetic relationship analysis showed that 32 viruses were closely related to SARS-CoV viruses (SARSCoVr clade), four SARS-CoV-2-like viruses (SARSCoV2r clade) and two recombinant viruses from strains of two clades SARSCoVr and SARSCoV2r (RecSar clade) (Figure 3).

Figure 3: Evolutionary relationships of 38 samples of 17 strains of the subgenus Sarbecovirus (symbols A-Q) detected in horseshoe bats in Vietnam
The host specimen collection location is numbered as shown in Figure 2 (symbols (L1, L2, L3,...) (Hassanin et al. 2024a)

Further analysis of the phylogeny of viruses in the subgenus Sarbecovirus, scientists have found more evidence that the ancestors of the SARS-CoV virus originated from horseshoe bats living in the Yunnan region of China, while the precursors of the SARS-CoV-2 virus may have circulated on populations of horseshoe bats living along the border the boundary between Yunnan (China) and Southeast Asian countries such as Dien Bien (Vietnam), Phongsaly (northern Lao People's Democratic Republic) and possibly including the Shan region (Burma).

In this study, scientists found that coronavirus strains belonging to the subgenus Sarbecovirus on bats evolved at a high rate of mutation and genetic recombination. In the context of increased interaction between humans, pets and bats in Vietnam, the risk of hybrid coronavirus strains between humans and bats is increasing when a host is infected with multiple viruses at the same time. The emergence of new strains has the potential to spread to many animals and people that could pose a risk to public health, so we need to be prepared to prevent future pandemic outbreaks.

Monitoring and prevention of bat-related diseases in Vietnam

From the above scientific evidence, it can be seen that Vietnam is one of the countries that needs to be prioritized in programs to monitor and prevent the risk of outbreaks or re-outbreaks of infectious diseases caused by coronavirus strains (and other pathogens) related to bats. However, Dr. Vuong Tan Tu also noted that we need to correct the misinformation about the unnecessary negative association between bats and infectious diseases in humans and pets.

This is because the route of transmission of infectious pathogens from bats to humans and pets has not been fully studied. Meanwhile, the increase in human encroachment on the natural habitat of bats not only causes a decline in their diversity and ecological role, but also increases the risk of outbreaks or re-outbreaks of bat-related infectious diseases.

Figure 4. Dr. Vuong Tan Tu and Dr. Gábor Földvári in Hungary

Given the strong link between ecology, nature conservation, and public health globally, these studies (along with other studies in the international collaborative mission) provide the scientific basis for calling for cooperation from domestic and foreign scientists and organizations. The involvement of experts and the community is necessary to improve the capacity to respond to wildlife-borne diseases and strengthen biodiversity conservation in Vietnam in general.

Translated by Phuong Ha
Link to Vietnamese version

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