000289663 001__ 289663
000289663 005__ 20241111103815.0
000289663 0247_ $$2doi$$a10.1371/journal.ppat.1012163
000289663 0247_ $$2pmid$$apmid:38648214
000289663 0247_ $$2ISSN$$a1553-7366
000289663 0247_ $$2ISSN$$a1553-7374
000289663 0247_ $$2altmetric$$aaltmetric:162805029
000289663 037__ $$aDKFZ-2024-00845
000289663 041__ $$aEnglish
000289663 082__ $$a610
000289663 1001_ $$aLauber, Chris$$b0
000289663 245__ $$aDeep mining of the Sequence Read Archive reveals major genetic innovations in coronaviruses and other nidoviruses of aquatic vertebrates.
000289663 260__ $$aLawrence, Kan.$$bPLoS$$c2024
000289663 3367_ $$2DRIVER$$aarticle
000289663 3367_ $$2DataCite$$aOutput Types/Journal article
000289663 3367_ $$0PUB:(DE-HGF)16$$2PUB:(DE-HGF)$$aJournal Article$$bjournal$$mjournal$$s1713876179_20489
000289663 3367_ $$2BibTeX$$aARTICLE
000289663 3367_ $$2ORCID$$aJOURNAL_ARTICLE
000289663 3367_ $$00$$2EndNote$$aJournal Article
000289663 500__ $$a#LA:F170#LA:D430#
000289663 520__ $$aVirus discovery by genomics and metagenomics empowered studies of viromes, facilitated characterization of pathogen epidemiology, and redefined our understanding of the natural genetic diversity of viruses with profound functional and structural implications. Here we employed a data-driven virus discovery approach that directly queries unprocessed sequencing data in a highly parallelized way and involves a targeted viral genome assembly strategy in a wide range of sequence similarity. By screening more than 269,000 datasets of numerous authors from the Sequence Read Archive and using two metrics that quantitatively assess assembly quality, we discovered 40 nidoviruses from six virus families whose members infect vertebrate hosts. They form 13 and 32 putative viral subfamilies and genera, respectively, and include 11 coronaviruses with bisegmented genomes from fishes and amphibians, a giant 36.1 kilobase coronavirus genome with a duplicated spike glycoprotein (S) gene, 11 tobaniviruses and 17 additional corona-, arteri-, cremega-, nanhypo- and nangoshaviruses. Genome segmentation emerged in a single evolutionary event in the monophyletic lineage encompassing the subfamily Pitovirinae. We recovered the bisegmented genome sequences of two coronaviruses from RNA samples of 69 infected fishes and validated the presence of poly(A) tails at both segments using 3'RACE PCR and subsequent Sanger sequencing. We report a genetic linkage between accessory and structural proteins whose phylogenetic relationships and evolutionary distances are incongruent with the phylogeny of replicase proteins. We rationalize these observations in a model of inter-family S recombination involving at least five ancestral corona- and tobaniviruses of aquatic hosts. In support of this model, we describe an individual fish co-infected with members from the families Coronaviridae and Tobaniviridae. Our results expand the scale of the known extraordinary evolutionary plasticity in nidoviral genome architecture and call for revisiting fundamentals of genome expression, virus particle biology, host range and ecology of vertebrate nidoviruses.
000289663 536__ $$0G:(DE-HGF)POF4-314$$a314 - Immunologie und Krebs (POF4-314)$$cPOF4-314$$fPOF IV$$x0
000289663 588__ $$aDataset connected to CrossRef, PubMed, , Journals: inrepo02.dkfz.de
000289663 7001_ $$aZhang, Xiaoyu$$b1
000289663 7001_ $$0P:(DE-He78)ce8b5b2120dc1f88ab3a0448db16a862$$aVaas, Josef$$b2$$udkfz
000289663 7001_ $$0P:(DE-He78)3c16d6c55b6685b47eda28e64d5cdc8e$$aKlingler, Franziska$$b3$$udkfz
000289663 7001_ $$0P:(DE-He78)ef6607c4f6cbe71fd65ed9424177c77a$$aMutz, Pascal$$b4
000289663 7001_ $$aDubin, Arseny$$b5
000289663 7001_ $$aPietschmann, Thomas$$b6
000289663 7001_ $$aRoth, Olivia$$b7
000289663 7001_ $$aNeuman, Benjamin W$$b8
000289663 7001_ $$aGorbalenya, Alexander E$$b9
000289663 7001_ $$0P:(DE-He78)1d3968d2f0ff3eae55f6b2ea4c474387$$aBartenschlager, Ralf$$b10$$udkfz
000289663 7001_ $$0P:(DE-He78)ceac1da6bb3c2176c2be7ef93a1e54cc$$aSeitz, Stefan$$b11$$eLast author$$udkfz
000289663 773__ $$0PERI:(DE-600)2205412-1$$a10.1371/journal.ppat.1012163$$gVol. 20, no. 4, p. e1012163 -$$n4$$pe1012163 -$$tPLoS pathogens$$v20$$x1553-7366$$y2024
000289663 8564_ $$uhttps://inrepo02.dkfz.de/record/289663/files/journal.ppat.1012163.pdf
000289663 8564_ $$uhttps://inrepo02.dkfz.de/record/289663/files/journal.ppat.1012163.pdf?subformat=pdfa$$xpdfa
000289663 909CO $$ooai:inrepo02.dkfz.de:289663$$pVDB
000289663 9101_ $$0I:(DE-588b)2036810-0$$6P:(DE-He78)ce8b5b2120dc1f88ab3a0448db16a862$$aDeutsches Krebsforschungszentrum$$b2$$kDKFZ
000289663 9101_ $$0I:(DE-588b)2036810-0$$6P:(DE-He78)3c16d6c55b6685b47eda28e64d5cdc8e$$aDeutsches Krebsforschungszentrum$$b3$$kDKFZ
000289663 9101_ $$0I:(DE-588b)2036810-0$$6P:(DE-He78)ef6607c4f6cbe71fd65ed9424177c77a$$aDeutsches Krebsforschungszentrum$$b4$$kDKFZ
000289663 9101_ $$0I:(DE-588b)2036810-0$$6P:(DE-He78)1d3968d2f0ff3eae55f6b2ea4c474387$$aDeutsches Krebsforschungszentrum$$b10$$kDKFZ
000289663 9101_ $$0I:(DE-588b)2036810-0$$6P:(DE-He78)ceac1da6bb3c2176c2be7ef93a1e54cc$$aDeutsches Krebsforschungszentrum$$b11$$kDKFZ
000289663 9131_ $$0G:(DE-HGF)POF4-314$$1G:(DE-HGF)POF4-310$$2G:(DE-HGF)POF4-300$$3G:(DE-HGF)POF4$$4G:(DE-HGF)POF$$aDE-HGF$$bGesundheit$$lKrebsforschung$$vImmunologie und Krebs$$x0
000289663 9141_ $$y2024
000289663 915__ $$0StatID:(DE-HGF)0100$$2StatID$$aJCR$$bPLOS PATHOG : 2022$$d2023-10-25
000289663 915__ $$0StatID:(DE-HGF)0200$$2StatID$$aDBCoverage$$bSCOPUS$$d2023-10-25
000289663 915__ $$0StatID:(DE-HGF)0300$$2StatID$$aDBCoverage$$bMedline$$d2023-10-25
000289663 915__ $$0StatID:(DE-HGF)0320$$2StatID$$aDBCoverage$$bPubMed Central$$d2023-10-25
000289663 915__ $$0StatID:(DE-HGF)0501$$2StatID$$aDBCoverage$$bDOAJ Seal$$d2023-01-04T15:23:16Z
000289663 915__ $$0StatID:(DE-HGF)0500$$2StatID$$aDBCoverage$$bDOAJ$$d2023-01-04T15:23:16Z
000289663 915__ $$0StatID:(DE-HGF)0030$$2StatID$$aPeer Review$$bDOAJ : Anonymous peer review$$d2023-01-04T15:23:16Z
000289663 915__ $$0LIC:(DE-HGF)CCBYNV$$2V:(DE-HGF)$$aCreative Commons Attribution CC BY (No Version)$$bDOAJ$$d2023-01-04T15:23:16Z
000289663 915__ $$0StatID:(DE-HGF)0600$$2StatID$$aDBCoverage$$bEbsco Academic Search$$d2023-10-25
000289663 915__ $$0StatID:(DE-HGF)0030$$2StatID$$aPeer Review$$bASC$$d2023-10-25
000289663 915__ $$0StatID:(DE-HGF)0199$$2StatID$$aDBCoverage$$bClarivate Analytics Master Journal List$$d2023-10-25
000289663 915__ $$0StatID:(DE-HGF)1050$$2StatID$$aDBCoverage$$bBIOSIS Previews$$d2023-10-25
000289663 915__ $$0StatID:(DE-HGF)0113$$2StatID$$aWoS$$bScience Citation Index Expanded$$d2023-10-25
000289663 915__ $$0StatID:(DE-HGF)0150$$2StatID$$aDBCoverage$$bWeb of Science Core Collection$$d2023-10-25
000289663 915__ $$0StatID:(DE-HGF)1030$$2StatID$$aDBCoverage$$bCurrent Contents - Life Sciences$$d2023-10-25
000289663 915__ $$0StatID:(DE-HGF)1190$$2StatID$$aDBCoverage$$bBiological Abstracts$$d2023-10-25
000289663 915__ $$0StatID:(DE-HGF)0160$$2StatID$$aDBCoverage$$bEssential Science Indicators$$d2023-10-25
000289663 915__ $$0StatID:(DE-HGF)9905$$2StatID$$aIF >= 5$$bPLOS PATHOG : 2022$$d2023-10-25
000289663 915__ $$0StatID:(DE-HGF)0561$$2StatID$$aArticle Processing Charges$$d2023-10-25
000289663 915__ $$0StatID:(DE-HGF)0700$$2StatID$$aFees$$d2023-10-25
000289663 9202_ $$0I:(DE-He78)F170-20160331$$kF170$$lVirus-assoziierte Karzinogenese$$x0
000289663 9202_ $$0I:(DE-He78)D430-20160331$$kD430$$lVirus-assoziierte Karzinogenese$$x1
000289663 9201_ $$0I:(DE-He78)F170-20160331$$kF170$$lVirus-assoziierte Karzinogenese$$x0
000289663 9201_ $$0I:(DE-He78)D430-20160331$$kD430$$lVirus-assoziierte Karzinogenese$$x1
000289663 980__ $$ajournal
000289663 980__ $$aVDB
000289663 980__ $$aI:(DE-He78)F170-20160331
000289663 980__ $$aI:(DE-He78)D430-20160331
000289663 980__ $$aUNRESTRICTED