COS 17-4 - Coronavirus dynamics in wildlife and trade contextualized from health and origin inference of seized Sunda pangolins (Manis javanica)

Abstract: The multifaceted challenge of understanding wildlife trade dynamics and how such trade might increase risk of disease emergence remains a major concern for public health and conservation. In the early months of 2020, pangolins were speculated to have a role in the emergence of SARS-CoV-2 following the detection of closely related viruses of pangolins in the trade. However, the precise role, if any, of pangolins in SARS-CoV-2 emergence remains unclear. We sampled 88 Sunda pangolin carcasses seized from a single enforcement event in Hong Kong in 2018. For all pangolins we performed detailed necropsies, analyzed the genomics of individuals, and sampled for virus presence and serology. Our objectives were to 1) determine whether evidence of coronavirus infections was evident for any of the individuals sampled, and 2) estimate approximate geographic origins of each of the individuals to characterize trade pathways. For the viral detection we implemented PCR screening for viruses and also looked for the presence of total antibodies cross-reactive with the SARS-CoV-2 spike protein using double antigen binding assays. For geographic origin analysis, we applied double digest restriction site-associated DNA sequencing (ddRADseq) to individual pangolins and compared to reference samples. All PCR screening for coronavirus and paramyxovirus RNA produced negative results while serology revealed six individuals were seropositive for SARSr-CoVs. We also discovered that individuals originated from across the distribution of Sunda pangolins – most (n=61) came from Borneo, while the rest were inferred as having come from Java (n=16) and Singapore/Sumatra (n=8). Our results point to a complex origin of coronavirus infection of Sunda pangolins and suggest that natural infection of coronavirus throughout their distribution is likely to be common (though we cannot rule out that infection may be trade-related). Furthermore, we highlight through this work how intensive and collaborative study from public health and ecological perspectives can advance One Health and conservation objectives for pangolin species and biodiversity affected by wildlife trade more broadly.