New research published in the journal Cell is evaluating viromes of 18 different game species across China to predict potential severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-like pathogens that could infect human populations.
Cases of SARS-CoV-2 infections were first identified in animal handlers in Hubei provinces of China, while similar virus strains were detected in civet cats, raccoon dogs and pangolins which were among the popular game animals and used for human consumption and world trade. However, there are no significant data on these wild animals despite their close contact with human populations and their potential to infect humans with a variety of pathogens.
About the study
The present study conducted a systematic meta-transcriptomic survey of 18 game animal species to assess the diversity and potential of vertebra-associated pathogens in these animals to infect human populations.
A total of 3,111 game samples were collected from June 2017 to December 2021 from the animals’ natural habitats, zoos and artificial breeding sites in 20 Chinese provinces. Samples were obtained from mammalian species, including Hystrix brachyura, Myocastor coypus, Rhizomys pruinosus, Marmota himalayana, Cynomys ludovicianus, Spermophilus dauricus, Callosciurus erythraeus, Sciurus vulgaris, Manis javanica, Manis pentadactyla, Paguma larvata, Nyctereutes procyonoides, Arctonyx collaris, Meles leucurus, Melogale moschata and Oryctolagus cuniculus. Nasal, pharyngeal, anal and fecal swabs from live animals and tissue samples from deceased animals were collected.
Marmota himalayana Image Credit: ErezFri/Shutterstock
Sample library construction and ribonucleic acid (RNA) extraction were performed by classifying samples according to species, health status, location, and environmental conditions. food. RNA extraction was followed by removal of genomic deoxyribonucleic acid (DNA) using deoxyribonuclease I (DNase I) and host ribosomal RNA to facilitate library preparation of meta-transcriptomes from each pool. The quality of sequencing reads in each library was controlled according to defined parameters, while the remaining reads were staged de novo and against the National Center for Biotechnology Information (NCBI) non-redundant (nr) protein database. The first explosion hit in each library was recognized as a probable virus hit, and taxonomic lineage information was obtained.
Viral presence on RNA samples was verified by reverse transcription-polymerase chain reaction (RT-PCR) and nested RT-PCR. The resulting PCR products were sequenced and compared to the original template.
The relative abundance of a virus species in each library was estimated based on the number of mapped reads per million total reads (RPM) using reads adjusted according to quality control. These were first mapped to separate reads related to ribosomal RNA, while unmapped reads were then mapped to verify viral genomes.
Paguma larvata. Image Credit: Ibenk_88 / Shutterstock
The results of the study showed samples of 18 species belonging to five orders of mammals, namely Pholidota, Rodentia, Eulipotyphla, Carnivora and Lagomorpha. Fecal and respiratory samples taken from the selected species provided more than 3 trillion nucleotide bases which aided in the discovery of the virus and its characterization. A total of 13 viral families, including 102 vertebrate-related viral species and 16 viral DNA species, were detected by meta-transcriptomic sequencing and verified by RT-PCR. Viruses belonging to Picornaviridae, Astroviridae and Parvovirdae were the most common and had higher abundance and prevalence compared to other viral species.
Notably, coronaviruses have been detected in Asian badgers, bamboo rats and civet cats; however, viruses related to SARS-CoV or SARS-CoV-2 were not found in any of the animal species examined in this study. Over 80% of nucleotide sequence identities were detected between viruses found in animal species and known pathogenic viruses, namely influenza A virus, influenza B virus, human parainfluenza virus 2, l orthohepevirus A, Norwalk virus, mammalian orthoreovirus and rotavirus A and C
Of the 102 vertebra-related viruses detected in this study, 21 viruses that were thought to pose a significant risk of infection were examined for epidemiological patterns such as perceived zoonotic potential and/or likelihood of crossing species barriers and to infect other animal species. A tendency of high-risk viruses to form geographic clusters has been observed in the Chinese province, as shown in the bat coronavirus Miniopterus in Hunan province, influenza B virus in Zhejiang province, the bovine respirovirus 3 in Hebei province and mammalian orthorubulavirus 5 in Yunnan. Province.
High prevalence of particular viruses and the presence of cross-species transmission signature markers in different libraries of the same or different species have been observed in several viruses. Furthermore, the greatest number of pathogens with an increased risk of zoonotic infection were found in civet cats, followed by porcupines, nutria, bamboo rats, Malayan pangolins and raccoon dogs.
The results of the study showed that wild game could act as crucial hosts for viruses and lead to related diseases in humans as well as domestic animals. In addition, the ability of these animal hosts to carry pathogenic viruses can promote chains of viral transmission and the emergence of new viral variants.
- He, W.-T., Hou, X., Zhao, J., Sun, J., He, H., Si, W., Wang, J., Jiang, Z., Yan, Z., Xing, G., Lu, M., Suchard, MA, Ji, X., Gong, W., He, B., Li, J., Lemey, P., Guo, D., Tu, C., Holmes, EC , Shi, M., Su, S., Characterization of game viromes in China reveals a spectrum of emerging pathogens, Cell (2022), do I: https://doi.org/10.1016/j.cell.2022.02.014, https://www.sciencedirect.com/science/article/pii/S0092867422001945