Taxonomy of the family Arenaviridae and the order Bunyavirales: update 2018

Maes, Piet; Alkhovsky, Sergey V.; Bào, Yīmíng; Beer, Martin; Birkhead, Monica; Briese, Thomas; Buchmeier, Michael J.; Calisher, Charles H.; Charrel, Rémi N.; Choi, Il Ryong; Clegg, Christopher; Torre, Juan Carlos de la; Delwart, Eric; DeRisi, Joseph L.; Bello, Patrick L. Di; Serio, Francesco Di; Digiaro, M.; Dolja, Valerian V.; Drosten, Christian; Druciarek, Tobiasz; Du, Jie; Ebihara, Hideki; Elbeaino, Toufic; Gergerich, R. C.; Gillis, Amethyst; Gonzalez, Jean‐Paul; Haenni, Anne‐Lise; Hepojoki, Jussi; Hetzel, Udo; Hồ, Thiện; Hóng, Ní; Jain, Rakesh; Vuren, Petrus Jansen van; Jin, Qi; Jonson, Miranda Gilda; Junglen, Sandra; Keller, Karen E.; Kemp, Alan C.; Kipar, Anja; Kondov, Nikola O.; Koonin, Eugene V.; Kormelink, Richard; Korzyukov, Yegor; Krupovìč, Mart; Lambert, Amy J.; Laney, Alma G.; LeBreton, Matthew; Lukashevich, Igor S.; Marklewitz, Marco; Markotter, Wanda; Martelli, G. P.; Martín, Robert R.; Mielke-Ehret, Nicole; Mühlbach, Hans‐Peter; Navarro, Beatriz; Ng, Terry Fei Fan; Nunes, Márcio Roberto Teixeira; Palacios, Gustavo; Pawęska, Janusz T.; Peters, C. J.; Plyusnin, Alexander; Radoshitzky, Sheli R.; Romanowski, Vı́ctor; Salmenperä, Pertteli; Salvato, María S.; Sanfaçon, Hélène; Sasaya, Takahide; Schmaljohn, Connie S.; Schneider, Bradley S.; Shirako, Yukio; Siddell, Stuart G.; Sironen, Tarja; Stenglein, Mark D.; Storm, Nadia; Sudini, Harikishan; Tesh, Robert B.; Tzanetakis, Ioannis E.; Uppala, Mangala; Vapalahti, Olli; Vasilakis, Nikos; Walker, Peter; Wáng, Guópíng; Wáng, Lìpíng; Wáng, Yànxiăng; Wèi, Tàiyún; Wiley, Michael R.; Wolf, Yuri I.; Wolfe, Nathan; Wú, Zhìqiáng; Xú, Wénxìng; Yang, Li; Yang, Zuokun; Yeh, Shyi-Dong; Zhāng, Yǒng-Zhèn; Zhèng, Yàzhōu; Zhou, Xueping; Zhū, Chénxī; Zirkel, Florian; Kuhn, Jens H.

doi:10.1007/s00705-018-3843-5

Cited by 175 publications

(125 citation statements)

References 26 publications

Supporting

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120

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“…6B). The second clade combines the family Orthomyxoviridae, the genus Tilapinevirus (101), and the large order Bunyavirales (394 viruses) (102). The latter order consists of two branches, one of which is the sister group to the orthomyxovirus/tilapinevirus clade (albeit with weak support).…”

Section: Evolution Of the 5 Major Branches Of Rna Viruses And Reconstmentioning

confidence: 99%

Origins and Evolution of the Global RNA Virome

Wolf

Kazlauskas

Iranzo

et al. 2018

mBio

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442

333

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Viruses with RNA genomes dominate the eukaryotic virome, reaching enormous diversity in animals and plants. The recent advances of metaviromics prompted us to perform a detailed phylogenomic reconstruction of the evolution of the dramatically expanded global RNA virome. The only universal gene among RNA viruses is the gene encoding the RNA-dependent RNA polymerase (RdRp). We developed an iterative computational procedure that alternates the RdRp phylogenetic tree construction with refinement of the underlying multiple-sequence alignments. The resulting tree encompasses 4,617 RNA virus RdRps and consists of 5 major branches; 2 of the branches include positive-sense RNA viruses, 1 is a mix of positive-sense (ϩ) RNA and double-stranded RNA (dsRNA) viruses, and 2 consist of dsRNA and negative-sense (Ϫ) RNA viruses, respectively. This tree topology implies that dsRNA viruses evolved from ϩRNA viruses on at least two independent occasions, whereas ϪRNA viruses evolved from dsRNA viruses. Reconstruction of RNA virus evolution using the RdRp tree as the scaffold suggests that the last common ancestors of the major branches of ϩRNA viruses encoded only the RdRp and a single jelly-roll capsid protein. Subsequent evolution involved independent capture of additional genes, in particular, those encoding distinct RNA helicases, enabling replication of larger RNA genomes and facilitating virus genome expression and virus-host interactions. Phylogenomic analysis reveals extensive gene module exchange among diverse viruses and horizontal virus transfer between distantly related hosts. Although the network of evolutionary relationships within the RNA virome is bound to further expand, the present results call for a thorough reevaluation of the RNA virus taxonomy. IMPORTANCE The majority of the diverse viruses infecting eukaryotes have RNA genomes, including numerous human, animal, and plant pathogens. Recent advances of metagenomics have led to the discovery of many new groups of RNA viruses in a wide range of hosts. These findings enable a far more complete reconstruction of the evolution of RNA viruses than was attainable previously. This reconstruction reveals the relationships between different Baltimore classes of viruses and indicates extensive transfer of viruses between distantly related hosts, such as plants and animals. These results call for a major revision of the existing taxonomy of RNA viruses.

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Section: Evolution Of the 5 Major Branches Of Rna Viruses And Reconstmentioning

confidence: 99%

Origins and Evolution of the Global RNA Virome

Wolf

Kazlauskas

Iranzo

et al. 2018

mBio

Self Cite

442

333

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“…The most closely related strains are the Zhejiang and Cambodian viriants of WENV, with L and the S segment nucleotide identities of 85.4-87.0% and 83.0-87.7%, respectively. Based on the International Taxonomy Committee on Viruses (ICTV) Arenaviridae Study Group guidelines for new mammarenavirus species, the Yunnan strains examined here are strain of WENV (species Wenzhou mammarenavirus) [1,39]…”

Section: Genome Characterizationmentioning

confidence: 99%

Prevalence of Wēnzhōu virus in small mammals in Yunnan Province, China

et al. 2019

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Background Mammarenaviruses are associated with human hemorrhagic fever diseases in Africa and America. Recently, a rodent mammarenavirus, Wēnzhōu virus (WENV) and related viruses, have been reported in China, Cambodia, and Thailand. Moreover, in Cambodia, these viruses were suspected to be associated with human disease. In China, Yunnan Province is famous for its abundant animal and plant diversity and is adjacent to several South-eastern Asia countries. Therefore, it is necessary to know whether WENV-related viruses, or other mammarenaviruses, are prevalent in this province. Methodology/Principal findings Small mammals were trapped, euthanized, and sampled. Mammarenavirus RNA was detected using a nested reverse transcription polymerase chain reaction (RT-PCR) and quantified by real-time RT-PCR. A total of 1040 small mammals belonging to 13 genera and 26 species were trapped in Yunnan Province. WENV-related mammarenaviruses were detected in 41 rodent liver samples, mainly in brown rats ( Rattus norvegicus ) and oriental house rats ( R . tanezumi ).Viral nucleocapsid protein was detected in liver sections by indirect immunofluorescence assay. Full-length-genomes were amplified by RT-PCR and used for phylogenetic analysis with the MEGA package. Recombination analysis was performed using the SimPlot and Recombination Detection Program. Conclusions/Significance WENV related viruses circulated in small mammals in Yunnan Province. Whole genome sequence analysis of five selected viral strains showed that these viruses are closely related to WENVs discovered in Asia and form an independent branch in the phylogenetic tree in the WENV clade. Paying attention to investigate the influence of these viruses to public health is essential in the epidemic regions.

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“…Crimean-Congo hemorrhagic fever is caused by Crimean-Congo hemorrhagic fever virus (CCHFV; order Bunyavirales: family Nairoviridae). 4,5 Depending on the available health-care system infrastructure, the case fatality rate of CCHF can range from 5% up to 80% during limited outbreaks. 6,7 Most cases of CCHF are reported from the Western and Southern Asia, with incidences increasing during the past two decades.…”

Section: Introductionmentioning

confidence: 99%

An Emerging Biothreat: Crimean-Congo Hemorrhagic Fever Virus in Southern and Western Asia

Blair

Kuhn

Pecor

et al. 2019

The American Journal of Tropical Medicine and Hygiene

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Tick-borne Crimean-Congo hemorrhagic fever virus (CCHFV) is endemic in numerous countries, but the epidemiology and epizoology of Crimean-Congo hemorrhagic fever (CCHF) remain to be defined for most regions of the world. Using a broad database search approach, we reviewed the literature on CCHF and CCHFV in Southern and Western Asia to better define the disease burden in these areas. We used a One Health approach, moving beyond a focus solely on human disease burden to more comprehensively define this burden by reviewing CCHF case reports, human and animal CCHFV seroprevalence studies, and human and animal CCHFV isolations. In addition, we used published literature to estimate the distribution of Hyalomma ticks and infection of these ticks by CCHFV. Using these data, we propose a new classification scheme for organizing the evaluated countries into five categories by level of evidence for CCHF endemicity. Twelve countries have reported CCHF cases, five from Southern Asia and seven from Western Asia. These were assigned to level 1 or 2. Eleven countries that have evidence of vector circulation but did not report confirmed CCHF cases were assigned to level 3 or 4. This classification scheme was developed to inform policy toward strengthening CCHF disease surveillance in the Southern and Western Asia regions. In particular, the goal of this review was to inform international organizations, local governments, and health-care professionals about current shortcomings in CCHFV surveillance in these two high-prevalence regions.

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Taxonomy of the family Arenaviridae and the order Bunyavirales: update 2018

Cited by 175 publications

References 26 publications

Origins and Evolution of the Global RNA Virome

Origins and Evolution of the Global RNA Virome

Prevalence of Wēnzhōu virus in small mammals in Yunnan Province, China

An Emerging Biothreat: Crimean-Congo Hemorrhagic Fever Virus in Southern and Western Asia

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