ddRADseq of trafficked Manis javanica individuals

Early in the COVID-19 pandemic, Sunda pangolins (Manis javanica) involved in the illegal wildlife trade in mainland China were identified as hosts of SARS-related coronaviruses (SARSr-CoVs). Using a combination of virological and wildlife forensics tools, we investigated 89 Sunda pangolin carcasses seized by Hong Kong authorities during anti-smuggling operations in the territory conducted in 2013 (n=1) and 2018 (n=88). Swabs, organ tissues, blood, and other body fluids were collected during post-mortem examination. Using two double-antigen sandwich assays to detect antibodies reactive against SARSr-CoVs, one individual was found to be seropositive with support from both methods, while five individuals exhibited inconclusive results. PCR screening for coronavirus and paramyxovirus RNA did not yield any positives. Based on genomic data, the seropositive individual was determined to have likely originated from Java, while the putatively seropositive individuals were determined to have originated from populations in Borneo, Java, and Sumatra. While the role of pangolins in evolution and ecology of SARS-CoV-2 is uncertain, our results suggest susceptibility and potential widespread natural exposure of pangolins to SARSr-CoVs, although this exposure may also occur during the illegal trafficking of these animals. Complex dynamics between natural populations, traded individuals, and pathogen susceptibility complicate conclusions about the role of pangolins, as well as other host species, in the origins of COVID-19 and future emerging zoonoses.