RNA viromes from terrestrial sites across China expand environmental viral diversity

Chen, Yanmei; Sadiq, Sabrina; Tian, Jingkui; Chen, Xiao; Lin, Xian-Dan; Shen, Jinjin; Chen, Hao; Hao, Zong-yu; Wille, Michelle; Zhou, Zien; Wu, Jun; Feng, Li; Wang, Hongwei; Yang, Weidi; Xu, Quangang; Wang, Wen; Gao, Wen-Hua; Holmes, Edward C.; Zhang, Yong-Zhen

doi:10.1038/s41564-022-01180-2

Cited by 82 publications

(103 citation statements)

References 47 publications

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“…Two full genome sequences have been identified by metatranscriptomics of environmental samples, namely cattle feces and soil from China ( Chen et al, 2022 ). They have been putatively named Guangdong jingmen-like virus and Hainan jingmen-like virus, respectively.…”

Section: Tick- and Vertebrate-associated Jingmenvirusesmentioning

confidence: 99%

Jingmenviruses: Ubiquitous, understudied, segmented flavi-like viruses

2022

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Jingmenviruses are a group of viruses identified recently, in 2014, and currently classified by the International Committee on Taxonomy of Viruses as unclassified Flaviviridae. These viruses closely related to flaviviruses are unique due to the segmented nature of their genome. The prototype jingmenvirus, Jingmen tick virus (JMTV), was discovered in Rhipicephalus microplus ticks collected from China in 2010. Jingmenviruses genomes are composed of four to five segments, encoding for up to seven structural proteins and two non-structural proteins, both of which display strong similarities with flaviviral non-structural proteins (NS2B/NS3 and NS5). Jingmenviruses are currently separated into two phylogenetic clades. One clade includes tick- and vertebrate-associated jingmenviruses, which have been detected in ticks and mosquitoes, as well as in humans, cattle, monkeys, bats, rodents, sheep, and tortoises. In addition to these molecular and serological detections, over a hundred human patients tested positive for jingmenviruses after developing febrile illness and flu-like symptoms in China and Serbia. The second phylogenetic clade includes insect-associated jingmenvirus sequences, which have been detected in a wide range of insect species, as well as in crustaceans, plants, and fungi. In addition to being found in various types of hosts, jingmenviruses are endemic, as they have been detected in a wide range of environments, all over the world. Taken together, all of these elements show that jingmenviruses correspond exactly to the definition of emerging viruses at risk of causing a pandemic, since they are already endemic, have a close association with arthropods, are found in animals in close contact with humans, and have caused sporadic cases of febrile illness in multiple patients. Despite these arguments, the vast majority of published data is from metagenomics studies and many aspects of jingmenvirus replication remain to be elucidated, such as their tropism, cycle of transmission, structure, and mechanisms of replication and restriction or epidemiology. It is therefore crucial to prioritize jingmenvirus research in the years to come, to be prepared for their emergence as human or veterinary pathogens.

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Section: Tick- and Vertebrate-associated Jingmenvirusesmentioning

confidence: 99%

Jingmenviruses: Ubiquitous, understudied, segmented flavi-like viruses

2022

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“…Yunnan emara-like virus In a metatranscriptomic approach investigating the virus diversity in different environmental samples, partial sequence information of seven RNAs of a putative emaravirus were identified from cattle faeces obtained in the province Yunnan (China) [76]. The authors reported closest relation to RLBV (RNA 1-RNA 6 and RNA8) in Diamond blastX from 34.3 % (partial P6) to 72.3 % (partial NC) on amino acid level suggesting a novel species in the genus related to clade C. However, as no additional biological information for instance on host species or confirmation of sequences are reported, further studies are required to confirm this novel virus as a plant infecting emaravirus.…”

Section: Putative Emaravirusesmentioning

confidence: 99%

The Complex World of Emaraviruses – Challenges, Insights and Prospects

Rehanek¹,

Karlin²,

Bandte³

et al. 2022

Preprint

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: Emaravirus (Order Bunyavirales; Family Fimoviridae) is a genus comprising over 20 emerging plant viruses with a worldwide distribution and economic impact. Emaraviruses infect a variety of host plants and have especially become prevalent in important long-living woody plants. These viruses are enveloped, with a segmented, single-stranded, negative-sense RNA genome and are transmitted by eriophyid mites or mechanical transmission. Emaraviruses have four core genome segments encoding an RNA-dependent RNA polymerase, a glycoprotein precursor, a nucleocapsid protein, and a movement protein. They also have additional genome segments, whose number varies widely. We report here that the proteins encoded by these segments form three main homology groups: a homolog of the sadwavirus Glu2 Pro glutamic protease; a protein involved in pathogenicity, which we named “ABC”; and a protein of unknown function, which we named “P55”. The distribution of these proteins parallels the emaravirus phylogeny and suggests, with other analyses, that emaraviruses should be split into at least two genera. Reliable diagnosis systems are urgently needed to detect emaraviruses, assess their economic and ecological importance, and take appropriate measures to prevent their spread (such as routine testing, hygiene measures, and control of mite vectors). Additional research needs include understanding the function of emaravirus proteins, breeding resistant plants and clarifying transmission modes.

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“…Viruses can be found wherever a potential host cell is present, and their numbers vary depending on the environment. For instance, an average of 10 7 virus-like particles (VLPs) have been identified in a milliliter (mL) of sea water and urine (1, 2), while an average of 10 7 , 10 8 , and 10 8 to 10 9 VLPs have been identified in one mL of saliva (3), one gram of stool (4), and one gram of soil (5)(with new viruses increasingly being identified in soil) (6), respectively. Viruses are obligate intracellular parasites, with singlestranded (ss) or double-stranded (ds) DNA or RNA genomes (7), that replicate through a series of steps generally involving attachment to host surface receptors followed by replication and host cell lysis.…”

Section: Introductionmentioning

confidence: 99%

Unraveling the viral dark matter through viral metagenomics

Santiago-Rodríguez

Hollister

2022

Front. Immunol.

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Viruses are part of the microbiome and have essential roles in immunology, evolution, biogeochemical cycles, health, and disease progression. Viruses influence a wide variety of systems and processes, and the continued discovery of novel viruses is anticipated to reveal new mechanisms influencing the biology of diverse environments. While the identity and roles of viruses continue to be discovered and understood through viral metagenomics, most of the sequences in virome datasets cannot be attributed to known viruses or may be only distantly related to species already described in public sequence databases, at best. Such viruses are known as the viral dark matter. Ongoing discoveries from the viral dark matter have provided insights into novel viruses from a variety of environments, as well as their potential in immunological processes, virus evolution, health, disease, therapeutics, and surveillance. Increased understanding of the viral dark matter will continue with a combination of cultivation, microscopy, sequencing, and bioinformatic efforts, which are discussed in the present review.

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RNA viromes from terrestrial sites across China expand environmental viral diversity

Cited by 82 publications

References 47 publications

Jingmenviruses: Ubiquitous, understudied, segmented flavi-like viruses

Jingmenviruses: Ubiquitous, understudied, segmented flavi-like viruses

The Complex World of Emaraviruses – Challenges, Insights and Prospects

Unraveling the viral dark matter through viral metagenomics

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