Evidence of SARS-CoV-2 Related Coronaviruses Circulating in Sunda pangolins (Manis javanica) Confiscated From the Illegal Wildlife Trade in Viet Nam

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.

Virome in healthy pangolins reveals compatibility with multiple potentially zoonotic viruses

“…Although pangolin susceptibility to coronaviruses has been demonstrated many times, the positivity rates vary among populations, ranging from 25% to 81% in different batches of dead pangolins (e.g., 17/21 ( Xiao et al, 2020 ), 5/18 ( Lam et al, 2020 ), 3/12 ( Lam et al, 2020 ), and 7/15 ( Nga et al, 2022 )). Two large-scale surveys of pangolins found that only a few individuals tested positive for coronavirus among hundreds of pangolin samples (e.g., 1/161 ( Shi et al, 2022 ) and 4/163 ( Peng et al, 2021 )).…”

One Health Surveillance Highlights Circulation of Viruses with Zoonotic Potential in Bats, Pigs, and Humans in Viet Nam

“…In addition to these broadly reactive consensus PCR tests, 539 bat samples collected in the guano farms and the bat cave were additionally screened specifically for Sarbecoviruses and SARS-CoV-2 using a RT-PCR assay targeting the E gene and RdRp gene [ 42 ] and cDNA previously obtained for the consensus PCR assays ( Table S1 ). Samples with positive results for either the E gene or RdRp gene assay were then screened using conventional PCR and primers specifically designed to detect pangolin Sarbecoviruses [ 43 ].…”

“… a Includes 338 positive samples detected by the broadly reactive CoV consensus PCR [ 35 , 36 ] and one sample detected using the Sarbecovirus/SARS-CoV-2 assays [ 42 , 43 ]. b Porcine epidemic diarrhea virus was detected using the Sarbecovirus/SARS-CoV-2 assays [ 42 , 43 ] and was not detected by the broadly reactive CoV consensus PCR [ 35 , 36 ]. …”

A Study on the Nature of SARS-CoV-2 Using the Shell Disorder Models: Reproducibility, Evolution, Spread, and Attenuation

“…The samples have about 90% sequence homology with SARS-CoV-2. Recently, it was discovered that pangolins confiscated in Vietnam around 2017–2018 were also infected with a COVID-19-related virus [ 13 ]. Phylogenetic analysis revealed that the CoV is most closely related to the pangolin samples from Guangxi.…”