Abstract
Despite the discovery of several closely related viruses in bats, the direct evolutionary progenitor of SARS-CoV-2 has not yet been identified. In this study, we investigated potential animal sources of SARS-related coronaviruses using archived specimens from Sunda pangolins (Manis javanica) and Chinese pangolins (Manis pentadactyla) confiscated from the illegal wildlife trade, and from common palm civets (Paradoxurus hermaphroditus) raised on wildlife farms in Viet Nam. A total of 696 pangolin and civet specimens were screened for the presence of viral RNA from five zoonotic viral families and from Sarbecoviruses using primers specifically designed for pangolin coronaviruses. We also performed a curated data collection of media reports of wildlife confiscation events involving pangolins in Viet Nam between January 2016 and December 2020, to illustrate the global pangolin supply chain in the context of Viet Nam where the trade confiscated pangolins were sampled for this study. All specimens from pangolins and civets sampled along the wildlife supply chains between February 2017 and July 2018, in Viet Nam and tested with conventional PCR assays designed to detect flavivirus, paramyxovirus, filovirus, coronavirus, and orthomyxovirus RNA were negative. Civet samples were also negative for Sarbecoviruses, but 12 specimens from seven live pangolins confiscated in Hung Yen province, northern Viet Nam, in 2018 were positive for Sarbecoviruses. Our phylogenetic trees based on two fragments of the RdRp gene revealed that the Sarbecoviruses identified in these pangolins were closely related to pangolin coronaviruses detected in pangolins confiscated from the illegal wildlife trade in Yunnan and Guangxi provinces, China. Our curated data collection of media reports of wildlife confiscation events involving pangolins in Viet Nam between January 2016 and December 2020, reflected what is known about pangolin trafficking globally. Pangolins confiscated in Viet Nam were largely in transit, moving toward downstream consumers in China. Confiscations included pangolin scales sourced originally from Africa (and African species of pangolins), or pangolin carcasses and live pangolins native to Southeast Asia (predominately the Sunda pangolin) sourced from neighboring range countries and moving through Viet Nam toward provinces bordering China.
Highlights
The role of animal intermediate hosts in the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and the role of the wildlife trade in facilitating the emergence of SARS-CoV-2 has not been determined
All specimens from pangolins and civets sampled along the wildlife supply chains in Viet Nam and tested with conventional PCR assays designed to detect flavivirus, paramyxovirus, filovirus, CoV, and orthomyxovirus RNA were negative [Table 3, Supplementary Material 1 and United States Agency for International Development (USAID) Development Data Library [33]]
All sequences obtained from pangolins confiscated in Viet Nam were identical or highly similar to sequences from SARS-CoV-2 and other Sarbecoviruses identified in bats and pangolins and were too short to discriminate among viral strains
Summary
The role of animal intermediate hosts in the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and the role of the wildlife trade in facilitating the emergence of SARS-CoV-2 has not been determined. Specific questions about the origins of the virus, the context of early transmission events, and the potential role of intermediate animal hosts in the emergence of SARS-CoV-2, were raised as the first cases of the coronavirus disease 2019 (COVID-19) pandemic were being described [3] and the outbreak was declared a “global health concern” [4, 5]. These questions remain pertinent 2 years later. The risk of rhinolophid-associated CoV emergence is not limited to China, and, likely, a large proportion of the bat CoV diversity in the region is yet to be discovered [12, 16]
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