PMC:7151644 / 14674-17271
Annnotations
{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/7151644","sourcedb":"PMC","sourceid":"7151644","source_url":"https://www.ncbi.nlm.nih.gov/pmc/7151644","text":"3.3 Identification of viral agents by meta-transcriptomics and PCR\nTo identify the possible etiologic agents of disease in the four pangolins, eight meta-transcriptomic libraries from blood, liver, spleen, lung, kidney, and fecal samples were constructed, generating a total of 306,908,179 paired-end sequence reads. De novo assembly revealed the high abundance of a pestivirus- and coltivirus-like virus in all the meta-transcriptomic libraries of the pangolin 1-Dongyang and 2-Lishui, representing 6–80 and 1–29 per cent of total viral contigs, respectively (Supplementary Table S2). Notably, despite the presence of other putative viruses (Supplementary Table S2), only the pestivirus- and coltivirus-like virus could be successfully identified by PCR. As those putative viral sequences could not be confirmed by PCR and probably were from contamination; hence, they were not possible etiologic agents of disease in four pangolins. Additional assays revealed that the novel pestivirus was only present in 1-Dongyang, whereas the novel coltivirus was only present in 2-Lishui. No potential bacterial and fungal pathogens were found in the libraries generated from 1-Dongyang and 2-Lishui. Finally, no abundant viral, bacterial and fungal sequences were found in the libraries generated from blood and tissue samples of 3-Ruian and 4-Wucheng (Supplementary Table S2).\nGenetic analysis revealed that the novel pestivirus shared \u003c57 per cent nt similarity to known pestiviruses, while the novel coltivirus showed \u003c68 per cent nt similarity to known coltiviruses. Considering that they are related, yet clearly genetically distinct, from known members of Pestivirus and Coltivirus (see below), we designated these two newly identified viruses as Dongyang pangolin virus (DYPV) and Lishui pangolin virus (LSPV), respectively, reflecting their hosts species and the geographic location of sampling. Attempts at virus isolation by cell culture (BHK-21, Vero-E6, and DH82) and inoculation of suckling mice proved unsuccessful.\nTo determine the distribution of the newly identified viruses, each organ was tested by PCR. Consequently, DYPV was identified in the heart, liver, spleen, lung, kidney, brain, blood, throat swab, and fecal sampled from pangolin 1-Dongyang, as well as the nymph ticks (Amblyomma javanense) collected from this animal. Interestingly, the virus was not identified in the adult ticks also sampled from 1-Dongyang. Similarly, LSPV was also identified in a broad range of tissue organs including heart, liver, spleen, lung, kidney, blood, throat swab, and fecal matter of 2-Lishui.","divisions":[{"label":"title","span":{"begin":0,"end":66}},{"label":"p","span":{"begin":67,"end":1368}},{"label":"p","span":{"begin":1369,"end":2020}}],"tracks":[]}