Metagenomic analysis of Sichuan takin fecal sample viromes reveals novel enterovirus and astrovirus

Guan, Tian-Pei; Teng, Jade L. L.; Yeong, Kai Yan; You, Zhangqiang; Liu, Hao; Wong, Samson S. Y.; Lau, Susanna K.P.; Woo, Patrick C. Y.

doi:10.1016/j.virol.2018.05.027

Cited by 22 publications

(20 citation statements)

References 42 publications

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“…The phylogenetic trees of the ORF2 genes of AstV SLO/D5-14 and AstV SLO/D12-14 strains and other AstV strains showed that the roe deer AstV strains were also related to other bovine AstVs, porcine AstV2 strains, yak AstV, porcupine AstV and dromedary AstVs forming a highly supported group of sequences distantly related to MAstV genogroups I and II, that might constitute a new MAstV genogroup, as proposed by Guan et al [34].…”

Section: Discussionmentioning

confidence: 55%

“…According to the latter authors, the MAstV genus consists of at least 33 species, of which only 19 are currently officially recognized as genotype/species by the ICTV. The phylogenetic and aa pairwise distance analysis of ORF2 sequences revealed a cluster of closely related AstV sequences, namely the two bovine strains from Hong Kong (BAstV-B18 and BAstV-B76-2) described by Tse et al [28], the four bovine strains (BAstGX-G1, BAstGX-J22, BAstGX-J27, BAstGX-J8 and BAstGX-J7) and two water buffalo strains (BufAstGX-M552 and BufAstGX-M541) from China, described by Alfred et al [31], two bovine strains from China (BAstV-GX7 and BAstV-GX27), one bovine strain BoAstV/JPN/Kago-shima1-7/2014 from Japan described by Nagai et al [33], the Sichuan takin AstV strain [34], two deer strains (CcAstV-1/DNK/2010 and CcAstV-2/DNK/2010) described by Smits et al [16] and the two roe deer strains (SLO/D5-14 and SLO/D12-14) described in this study. The aa identities of AstV strains SLO/D5-14 and SLO/ D12-14 compared to those of other AstV sequences from the described cluster were greater than 75.4 and 74.9%, respectively.…”

Section: Discussionmentioning

confidence: 99%

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A molecular survey, whole genome sequencing and phylogenetic analysis of astroviruses from roe deer

et al. 2020

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Background: Although astroviruses (AstV) have been detected in a variety of host species, there are only limited records of their occurrence in deer. One of the most important game species in Europe, due to its meat and antlers, is roe deer. Infected game animals can pose a threat to the health of other animals and of humans, so more attention needs to be focused on understanding the diversity of viruses in wildlife. The complete genome and organization of the roe deer AstV genome have not so far been described. Results: In our study, 111 game animals were screened for the presence of AstV. While no AstVs were detected in red deer, wild boar, chamois and mouflon, AstV RNA was present in three samples of roe deer. They were further subjected to whole genome sequencing with next generation sequencing. In this study, two AstV genomes were assembled; one in sample D5-14 and one in sample D12-14, while, in sample D45-14, no AstV sequences were identified. The complete coding sequences of the AstV SLO/D5-14 strain genome and of the almost complete genome of the AstV SLO/D12-14 strain were determined. They showed a typical Mamastrovirus organization. Phylogenetic analyses and amino acid pairwise distance analysis revealed that Slovenian roe deer AstV strains are closely related to each other and, also, related to other deer, bovine, water buffalo, yak, Sichuan takin, dromedary, porcine and porcupine AstV strains -thus forming a highly supported group of currently unassigned sequences. Conclusions: Our findings suggest the existence of a new Mamastrovirus genogroup might be constituted while this aforementioned group is distantly related to Mamastrovirus genogroups I and II. In this study, additional data supporting a novel taxonomic classification are presented.

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Section: Discussionmentioning

confidence: 55%

Section: Discussionmentioning

confidence: 99%

A molecular survey, whole genome sequencing and phylogenetic analysis of astroviruses from roe deer

et al. 2020

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“…Based on phylogenetic position, most viruses identified in the caecal content are likely to be associated with the rabbit diet or other commensal microorganisms, such as fungi and protozoa (Figure 2). To our knowledge, equivalent viral meta-transcriptomics analyses on caecal content have not been reported, although an abundance of plant and microorganism-associated viruses is consistent with the faecal viromes of other herbivores (Guan et al, 2018; Woo et al, 2014; Zhang et al, 2017). Importantly, we identified diverse novel viruses in rabbits – Racaecavirus and Orycavirus - that cluster with other vertebrate-associated viruses (in the Caliciviridae and the Picornaviridae , respectively) suggesting that the most likely hosts are the rabbits from which they were sampled.…”

Section: Discussionmentioning

confidence: 77%

Limited overlap in RNA virome composition among rabbits and their ectoparasites reveals barriers to virus transmission

Mahar

Shī

Hall

et al. 2019

Preprint

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Ectoparasites play an important role in virus transmission among vertebrates. However, little is known about the extent and composition of viruses that pass between invertebrates and vertebrates. In Australia, flies and fleas support the mechanical transmission of viral biological controls against wild rabbits - rabbit haemorrhagic disease virus (RHDV) and myxoma virus. We compared virome structure and composition in rabbits and these associated ectoparasites, sequencing total RNA from multiple tissues and gut contents of wild rabbits, fleas collected from these rabbits, and flies trapped sympatrically. Meta-transcriptomic analyses identified 50 novel viruses from multiple RNA virus families. Rabbits and their ectoparasites were characterised by markedly different viromes: although viral contigs from six virus families/groups were found in both rabbits and ectoparasites, none were vertebrate-associated. A novel calicivirus and picornavirus detected in rabbit caecal content were vertebrate-specific: the newly detected calicivirus was distinct from known rabbit caliciviruses, while the novel picornavirus clustered with the Sapeloviruses. Several Picobirnaviridae were also identified, falling in diverse phylogenetic positions suggestive of an association with co-infecting bacteria. The remaining viruses found in rabbits, and all those from ectoparasites, were likely associated with invertebrates, plants and co-infecting endosymbionts. While no full genomes of vertebrate-associated viruses were detected in ectoparasites, suggestive of major barriers to biological transmission with active replication, small numbers of reads from rabbit astrovirus, RHDV and other lagoviruses were present in flies. This supports the role of flies in the mechanical transmission of RHDV and implies that they may assist the spread of astroviruses.

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“…In recent years a wide variety of mammalian domestic animal species were found positive for astroviruses in their feces; e.g. cattle (Woode & Bridger 1978), sheep (Snodgrass & Gray 1977), red deer (Tzipori et al 1981), takins (Guan et al 2018) and also domestic carnivores (Hoshino et al 1981;Williams 1980), mice (Kjeldsberg & Hem 1985) and pigs (Bridger 1980), but their role in the context of disease remained largely unclear.…”

Section: Introductionmentioning

confidence: 99%

Peer Review #1 of "Discovery of novel astrovirus genotype species in small ruminants (v0.2)"

2019

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Astroviruses are single-stranded, positive-sense RNA viruses, best known for causing diarrhea in humans and are also found in many other mammals; in those, the relevance in gastroenteritis remains unclear. Recently described neurotropic astroviruses showed associations with encephalitis in humans as well as in other mammals. In Switzerland, two different neurotropic astroviruses were identified in cattle, as well as one in a sheep. The high genetic similarity between the ovine and one of the bovine astroviruses strengthens the hypothesis of an interspecies transmission. In humans, astroviruses associated with encephalitis were found also in human stool samples, suggesting that in these patients the infection spreads from the gastrointestinal tract to the brain under certain conditions, such as immunosuppression. Whether a similar pathogenesis occurs in ruminants remains unknown. The aims of this study were 1) the investigation of the potential occurrence of neurotropic astroviruses in feces samples, 2) the discovery and analysis of so far unknown astroviruses in small ruminants and other ruminant species' fecal samples and 3) the examination of a potential interspecies transmission of astroviruses. To achieve the aims, RNA extraction out of 164 fecal samples from different ruminant species was performed and all samples were screened for known neurotropic astroviruses occurring in Switzerland, as well as for various astroviruses using RT-PCR. Positive tested samples were submitted to next generation sequencing (NGS). The generated sequences were compared to nucleotide-and amino acid databases, virus properties were identified, and phylogenetic analyses as well as recombination analysis were performed. The excretion of neurotropic astroviruses in small ruminants' feces could not be demonstrated, but this work suggests the first identification of astroviruses in goats as well as the discovery of multiple and highly diverse new genetic variants in small ruminants, which lead to a classification into novel genotype-species. Additionally, the prediction of multiple recombination events in four of five newly discovered full or almost full-length genome

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Metagenomic analysis of Sichuan takin fecal sample viromes reveals novel enterovirus and astrovirus

Cited by 22 publications

References 42 publications

A molecular survey, whole genome sequencing and phylogenetic analysis of astroviruses from roe deer

A molecular survey, whole genome sequencing and phylogenetic analysis of astroviruses from roe deer

Limited overlap in RNA virome composition among rabbits and their ectoparasites reveals barriers to virus transmission

Peer Review #1 of "Discovery of novel astrovirus genotype species in small ruminants (v0.2)"

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