A global dataset of sequence, diversity and biosafety recommendation of arbovirus and arthropod-specific virus

Huang, Ye; Wang, Shunlong; Li, Hong; Atoni, Evans; Wang, Fei; Chen, Wei; Li, Zhaolin; Rodrı́guez, Sergio; Yuan, Zhi Ming; Ming, Zhaoyan; Xia, Han

doi:10.1038/s41597-023-02226-8

Cited by 4 publications

(8 citation statements)

References 25 publications

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“…Genera with cross-phylum or cross-kingdom host ranges are typically characterised by well-established transmission routes between arthropod vectors and animal or plant hosts. For example, arboviruses in the genera Orthoflavivirus , Alphavirus , Coltivirus , and Orbivirus replicate in their vertebrate hosts as well as the arthropod vectors that transmit them (Huang et al ., 2023). Similarly, plant-infecting genera in the families Tospoviridae , Tymoviridae ( Marafivirus ), Rhabdoviridae , and order Reovirales also replicate in their arthropod vectors (Gray and Banerjee, 1999).…”

Section: Discussionmentioning

confidence: 99%

Genomic and phylogenetic features of thePicobirnaviridaesuggest microbial rather than animal hosts

Sadiq,

Holmes,

Mahar

2024

Preprint

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The RNA virus familyPicobirnaviridaehas traditionally been associated with the gastrointestinal systems of terrestrial mammals and birds, with the majority of viruses detected in animal stool samples. Metatranscriptomic studies of vertebrates, invertebrates, microbial communities, and environmental samples have resulted in an enormous expansion of the genomic and phylogenetic diversity of this family. Yet picobirnaviruses remain poorly classified, with only one genus and three species formally ratified by the International Committee of Virus Taxonomy. Additionally, an inability to culture picobirnaviruses in a laboratory setting or isolate them in animal tissue samples, combined with the presence of bacterial genetic motifs in their genomes, suggests these viruses may represent RNA bacteriophage rather than being associated with animal infection. Utilising a data set of 2,286 picobirnaviruses sourced from mammals, birds, reptiles, fish, invertebrates, microbial communities, and environmental samples, we identified seven consistent phylogenetic clusters likely representing picobirnavirus genera that we tentatively nameAlpha-, Beta-, Gamma-, Delta-, Epsilon-, Zeta-,andEtapicobirnavirus. A statistical analysis of topological congruence between virus-host phylogenies revealed more frequent cross-species transmission than any other RNA virus family. In addition, bacterial ribosomal binding site motifs were more enriched in picobirnavirus genomes than in the two groups of established RNA bacteriophage – theLeviviricetesandCystoviridae. Overall, our findings support the hypothesis that thePicobirnaviridaehave bacterial hosts and provide a lower-level taxonomic classification for this highly diverse and ubiquitous family of RNA viruses.

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Section: Discussionmentioning

confidence: 99%

Genomic and phylogenetic features of thePicobirnaviridaesuggest microbial rather than animal hosts

Sadiq,

Holmes,

Mahar

2024

Preprint

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Section: Discussionmentioning

confidence: 99%

Genomic and phylogenetic features of the Picobirnaviridae suggest microbial rather than animal hosts

Sadiq,

Holmes,

Mahar

2024

Virus Evolution

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The RNA virus family Picobirnaviridae has traditionally been associated with the gastrointestinal systems of terrestrial mammals and birds, with the majority of viruses detected in animal stool samples. Metatranscriptomic studies of vertebrates, invertebrates, microbial communities, and environmental samples have resulted in an enormous expansion of the genomic and phylogenetic diversity of this family. Yet picobirnaviruses remain poorly classified, with only one genus and three species formally ratified by the International Committee of Virus Taxonomy. Additionally, an inability to culture picobirnaviruses in a laboratory setting or isolate them in animal tissue samples, combined with the presence of bacterial genetic motifs in their genomes, suggests these viruses may represent RNA bacteriophage rather than being associated with animal infection. Utilising a data set of 2,286 picobirnaviruses sourced from mammals, birds, reptiles, fish, invertebrates, microbial communities, and environmental samples, we identified seven consistent phylogenetic clusters likely representing picobirnavirus genera that we tentatively name “Alpha-”, “Beta-”, “Gamma-”, “Delta-”, “Epsilon-”, “Zeta-”, and Etapicobirnavirus”. A statistical analysis of topological congruence between virus-host phylogenies revealed more frequent cross-species transmission than any other RNA virus family. In addition, bacterial ribosomal binding site motifs were more enriched in picobirnavirus genomes than in the two groups of established RNA bacteriophage – the Leviviricetes and Cystoviridae. Overall, our findings support the hypothesis that the Picobirnaviridae have bacterial hosts and provide a lower-level taxonomic classification for this highly diverse and ubiquitous family of RNA viruses.

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“…Firstly, data on TBVs in China was from a database named “global dataset of sequence, diversity and biosafety recommendation of arbovirus and arthropod-specific virus” recently published by Huang et al This database contains taxonomic, genomic, sequence, host, biosafety, and isolation source information for arboviruses and arthropod-specific viruses ( Huang Y et al, 2023 ). The literature on TBVs in China was searched in PubMed, Web of Science, and CNKI with the keywords “China” and “tick-borne viruses,” “TBVs” or specific virus names such as “Crimean Congo hemorrhagic fever virus” or “CCHFV” to collect more data.…”

Section: Methodsmentioning

confidence: 99%

Diversity of species and geographic distribution of tick-borne viruses in China

Wu,

Zhou,

Mao

et al. 2024

Front. Microbiol.

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IntroductionTick-borne pathogens especially viruses are continuously appearing worldwide, which have caused severe public health threats. Understanding the species, distribution and epidemiological trends of tick-borne viruses (TBVs) is essential for disease surveillance and control.MethodsIn this study, the data on TBVs and the distribution of ticks in China were collected from databases and literature. The geographic distribution of TBVs in China was mapped based on geographic locations of viruses where they were prevalent or they were detected in vector ticks. TBVs sequences were collected from The National Center for Biotechnology Information and used to structure the phylogenetic tree.ResultsEighteen TBVs from eight genera of five families were prevalent in China. Five genera of ticks played an important role in the transmission of TBVs in China. According to phylogenetic analysis, some new viral genotypes, such as the Dabieshan tick virus (DTV) strain detected in Liaoning Province and the JMTV strain detected in Heilongjiang Province existed in China.DiscussionTBVs were widely distributed but the specific ranges of viruses from different families still varied in China. Seven TBVs belonging to the genus Orthonairovirus of the family Nairoviridae such as Nairobi sheep disease virus (NSDV) clustered in the Xinjiang Uygur Autonomous Region (XUAR) and northeastern areas of China. All viruses of the family Phenuiviridae except Severe fever with thrombocytopenia syndrome virus (SFTSV) were novel viruses that appeared in the last few years, such as Guertu virus (GTV) and Tacheng tick virus 2 (TcTV-2). They were mainly distributed in the central plains of China. Jingmen tick virus (JMTV) was distributed in at least fourteen provinces and had been detected in more than ten species of tick such as Rhipicephalus microplus and Haemaphysalis longicornis, which had the widest distribution and the largest number of vector ticks among all TBVs. Parainfluenza virus 5 (PIV5) and Lymphatic choriomeningitis virus (LCMV) were two potential TBVs in Northeast China that could cause serious diseases in humans or animals. Ixodes persulcatus carried the highest number of TBVs, followed by Dermacentor nuttalli and H. longicornis. They could carry as many as ten TBVs. Three strains of Tick-borne encephalitis (TBEV) from Inner Mongolia Province clustered with ones from Russia, Japan and Heilongjiang Province, respectively. Several SFTSV strains from Zhejiang Province clustered with strains from Korea and Japan. Specific surveillance of dominant TBVs should be established in different areas in China.

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A global dataset of sequence, diversity and biosafety recommendation of arbovirus and arthropod-specific virus

Cited by 4 publications

References 25 publications

Genomic and phylogenetic features of thePicobirnaviridaesuggest microbial rather than animal hosts

Genomic and phylogenetic features of thePicobirnaviridaesuggest microbial rather than animal hosts

Genomic and phylogenetic features of the Picobirnaviridae suggest microbial rather than animal hosts

Diversity of species and geographic distribution of tick-borne viruses in China

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