Trafficked Malayan pangolins contain viral pathogens of humans

Abstract

Pangolins are the most trafficked wild animal in the world according to the World Wildlife Fund. The discovery of SARS-CoV-2-related coronaviruses in Malayan pangolins has piqued interest in the viromes of these wild, scaly-skinned mammals. We sequenced the viromes of 161 pangolins that were smuggled into China and assembled 28 vertebrate-associated viruses, 21 of which have not been previously reported in vertebrates. We named 16 members of Hunnivirus, Pestivirus and Copiparvovirus pangolin-associated viruses. We report that the l-protein has been lost from all hunniviruses identified in pangolins. Sequences of four human-associated viruses were detected in pangolin viromes, including respiratory syncytial virus, Orthopneumovirus, RotavirusA and Mammalian orthoreovirus. The genomic sequences of five mammal-associated and three tick-associated viruses were also present. Notably, a coronavirus related to HKU4-CoV, which was originally found in bats, was identified. The presence of these viruses in smuggled pangolins identifies these mammals as a potential source of emergent pathogenic viruses.

Virome Analysis of Normal and Growth Retardation Disease-Affected Macrobrachiumrosenbergii

“…To confirm the relative abundance of viral contigs, clean reads were mapped back to the nonredundant contigs using Bowtie2 (version 2.4.2) ( 73 ) and inspected using Integrative Genomics Viewer (IGV [version 2.5.0]) ( 74 ). To identify and eliminate possible contamination, we used the following steps to exclude false positives of these viral contigs suggested by previous study ( 75 ). The relative abundance of each viral contig was quantified as the number of mapped reads per million total reads (RPM), and we set RPM at ≥1 and the number of identified reads at ≥10 for a positive virus hit.…”

Discovery of novel papillomaviruses in the critically-endangered Malayan and Chinese pangolins

“…We also found reads with significant matches (e-values: 9·10 −29 −2·10 −3 ) to the Pangolin papillomavirus 1 genome in the samples from five individuals described in the meta-transcriptomic study of the Malayan pangolin by Shi et al (15) (Table S3). The difference in the number of matching reads we obtained from the genomic and transcriptomic SRA samples may be attributed to latent papillomavirus infections and differences in sampling (different tissues were pooled together for the meta-transcriptomic work).…”

“…Pangolins have recently gained attention as a potential host of emerging viral diseases after coronaviruses related to SARS-CoV-2 were reported in the Malayan pangolin (5–10). Pangolins have also been recognised as hosts for several other RNA viruses such as Canine distemper virus ( Paramyxoviridae ), which is associated with respiratory, digestive and neurological illness in pangolins (11), flaviviruses, reoviruses, pneumoviruses and picornaviruses (12–15). Overall, the diversity of DNA viruses and their disease association in pangolins is less well known; so far anellovirus, parvovirus, circovirus and genomovirus genomes have been described (15,16).…”

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 )). In the current study, we did not detect the presence of coronavirus in the pangolin samples.…”