Total virome characterizations of game animals in China reveals a spectrum of emerging viral pathogens
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Abstract
Game animals are wildlife species often traded and consumed as exotic food, and are potential reservoirs for SARS-CoV and SARS-CoV-2. We performed a meta-transcriptomic analysis of 1725 game animals, representing 16 species and five mammalian orders, sampled across China. From this we identified 71 mammalian viruses, with 45 described for the first time. Eighteen viruses were considered as potentially high risk to humans and domestic animals. Civets ( Paguma larvata ) carried the highest number of potentially high risk viruses. We identified the transmission of Bat coronavirus HKU8 from a bat to a civet, as well as cross-species jumps of coronaviruses from bats to hedgehogs and from birds to porcupines. We similarly identified avian Influenza A virus H9N2 in civets and Asian badgers, with the latter displaying respiratory symptoms, as well as cases of likely human-to-wildlife virus transmission. These data highlight the importance of game animals as potential drivers of disease emergence.
Highlights
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1725 game animals from five mammalian orders were surveyed for viruses
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71 mammalian viruses were discovered, 18 with a potential risk to humans
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Civets harbored the highest number of potential ‘high risk’ viruses
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A species jump of an alphacoronavirus from bats to a civet was identified
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H9N2 influenza virus was detected in a civet and an Asian badger
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Humans viruses were also identified in game animals
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SciScore for 10.1101/2021.11.10.467646: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Software and Algorithms Sentences Resources The remaining reads were assembled de novo using MEGAHIT61 (version 1.2.6) deploying default parameters. MEGAHIT61suggested: NoneAmong the virus contigs described here, those likely associated with vertebrates, specifically vertebrate-specific viruses and vector-borne vertebrate viruses, were preliminarily identified based on the taxonomic lineage information of the blastx results and confirmed by phylogenetic analyses. blastxsuggested: (BLASTX, RRID:SCR_001653)To estimate the relative abundance of each virus species in each library, quality-trimmed reads were firstly mapped to the SILIVA … SciScore for 10.1101/2021.11.10.467646: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Software and Algorithms Sentences Resources The remaining reads were assembled de novo using MEGAHIT61 (version 1.2.6) deploying default parameters. MEGAHIT61suggested: NoneAmong the virus contigs described here, those likely associated with vertebrates, specifically vertebrate-specific viruses and vector-borne vertebrate viruses, were preliminarily identified based on the taxonomic lineage information of the blastx results and confirmed by phylogenetic analyses. blastxsuggested: (BLASTX, RRID:SCR_001653)To estimate the relative abundance of each virus species in each library, quality-trimmed reads were firstly mapped to the SILIVA database (www.arb-silva.de, version 132.1) using Bowtie2 (version 2.3.5.1)65 to remove reads associated with ribosomal RNA. Bowtie2suggested: (Bowtie 2, RRID:SCR_016368)Following sequence alignment, all ambiguous aligned regions were removed using TrimAL67 (version 1.2). TrimAL67suggested: NonePhylogenetic trees were then estimated for the sequence alignment of each family using the maximum likelihood method available in PhyML (version 3.1)68, employing the LG model of amino acid substitution and a subtree pruning and the regrafting (SPR) branch swapping algorithm. PhyMLsuggested: (PhyML, RRID:SCR_014629)Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- No funding statement was detected.
- No protocol registration statement was detected.
Results from scite Reference Check: We found no unreliable references.
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