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Article: Comparative analysis of six genome sequences of three novel picornaviruses, turdiviruses 1, 2 and 3, in dead wild birds, and proposal of two novel genera, Orthoturdivirus and Paraturdivirus, in the family Picornaviridae

TitleComparative analysis of six genome sequences of three novel picornaviruses, turdiviruses 1, 2 and 3, in dead wild birds, and proposal of two novel genera, Orthoturdivirus and Paraturdivirus, in the family Picornaviridae
Authors
Issue Date2010
PublisherSociety for General Microbiology. The Journal's web site is located at http://vir.sgmjournals.org
Citation
Journal of General Virology, 2010, v. 91 n. 10, p. 2433-2448 How to Cite?
AbstractIn this territory-wide molecular epidemiology study of picornaviruses, involving 6765 dead wild birds from 201 species in 50 families over a 12 month period, three novel picornaviruses, turdiviruses 1, 2 and 3 (TV1, TV2 and TV3), were identified from birds of different genera in the family Turdidae. In contrast to many other viruses in birds of the family Turdidae or viruses of the family Picornaviridae, TV1, TV2 and TV3 were found exclusively in the autumn and winter months. Two genomes each of TV1, TV2 and TV3 were sequenced. Regions P1, P2 and P3 of the three turdiviruses possessed, respectively, <40, <40 and <50% amino acid identities with those of other picornaviruses. Moreover, P1, P2 and P3 of TV1 also possessed, respectively, <40, <40 and <50% amino acid identities with those of TV2 and TV3. Phylogenetic analysis revealed that TV1, TV2 and TV3 were distantly related to members of the genus Kobuvirus. Among the three turdiviruses, TV2 and TV3 were always clustered together, with high bootstrap supports of 1000. The genomic features of TV2 and TV3 were also distinct from TV1, including lower G+C contents, shorter leader protein and a preference for codon sequence NNT rather than NNC for amino acids that can use either NNT or NNC as codons (P<0.001 by χ 2-test). Based on our results we propose two novel genera, Orthoturdivirus for TV1, and Paraturdivirus for TV2 and TV3, in the family Picornaviridae. The type of internal ribosomal entry site for TV1, TV2 and TV3 remains to be determined. © 2010 SGM.
Persistent Identifierhttp://hdl.handle.net/10722/157603
ISSN
2015 Impact Factor: 3.192
2015 SCImago Journal Rankings: 1.741
ISI Accession Number ID
Funding AgencyGrant Number
Research Grant Council
University Development Fund
Outstanding Young Researcher Award
The University of Hong Kong
The Tung Wah Group of Hospitals Fund for Research in Infectious Diseases
HKSAR
Shaw Foundation
Funding Information:

We thank Professor York Y N Chow, Secretary of Health, Welfare and Food, HKSAR, The Peoples' Republic of China, and Virology and Biotechnology laboratory staff of the Tat Lung Veterinary Laboratory of the AFCD of the HKSAR Views expressed in this paper are those of the authors only, and may not represent the opinion of the AFCD, the Government (lithe HKSAR We are grateful for the generous support of Mr Hui Hoy and Mr Hui Ming in the genomic sequencing platform The MRC-5 cell line was a gift from Dr Wilina Lim, ViroMed Laboratories, Centre for Health Protection, Hong Kong This work is partly supported by a Research Grant Council grant, a University Development Fund and Outstanding Young Researcher Award, The University of Hong Kong; The Tung Wah Group of Hospitals Fund for Research in Infectious Diseases; the HKSAR Research Fund for the Control of Infectious Diseases of the Health, Welfare and Food Bureau, and the Shaw Foundation

References

 

DC FieldValueLanguage
dc.contributor.authorWoo, PCYen_US
dc.contributor.authorLau, SKPen_US
dc.contributor.authorHuang, Yen_US
dc.contributor.authorLam, CSFen_US
dc.contributor.authorPoon, RWSen_US
dc.contributor.authorTsoi, HWen_US
dc.contributor.authorLee, Pen_US
dc.contributor.authorTse, Hen_US
dc.contributor.authorChan, ASLen_US
dc.contributor.authorLuk, Gen_US
dc.contributor.authorChan, KHen_US
dc.contributor.authorYuen, KYen_US
dc.date.accessioned2012-08-08T08:51:37Z-
dc.date.available2012-08-08T08:51:37Z-
dc.date.issued2010en_US
dc.identifier.citationJournal of General Virology, 2010, v. 91 n. 10, p. 2433-2448en_US
dc.identifier.issn0022-1317en_US
dc.identifier.urihttp://hdl.handle.net/10722/157603-
dc.description.abstractIn this territory-wide molecular epidemiology study of picornaviruses, involving 6765 dead wild birds from 201 species in 50 families over a 12 month period, three novel picornaviruses, turdiviruses 1, 2 and 3 (TV1, TV2 and TV3), were identified from birds of different genera in the family Turdidae. In contrast to many other viruses in birds of the family Turdidae or viruses of the family Picornaviridae, TV1, TV2 and TV3 were found exclusively in the autumn and winter months. Two genomes each of TV1, TV2 and TV3 were sequenced. Regions P1, P2 and P3 of the three turdiviruses possessed, respectively, <40, <40 and <50% amino acid identities with those of other picornaviruses. Moreover, P1, P2 and P3 of TV1 also possessed, respectively, <40, <40 and <50% amino acid identities with those of TV2 and TV3. Phylogenetic analysis revealed that TV1, TV2 and TV3 were distantly related to members of the genus Kobuvirus. Among the three turdiviruses, TV2 and TV3 were always clustered together, with high bootstrap supports of 1000. The genomic features of TV2 and TV3 were also distinct from TV1, including lower G+C contents, shorter leader protein and a preference for codon sequence NNT rather than NNC for amino acids that can use either NNT or NNC as codons (P<0.001 by χ 2-test). Based on our results we propose two novel genera, Orthoturdivirus for TV1, and Paraturdivirus for TV2 and TV3, in the family Picornaviridae. The type of internal ribosomal entry site for TV1, TV2 and TV3 remains to be determined. © 2010 SGM.en_US
dc.languageengen_US
dc.publisherSociety for General Microbiology. The Journal's web site is located at http://vir.sgmjournals.orgen_US
dc.relation.ispartofJournal of General Virologyen_US
dc.subject.meshAnimalsen_US
dc.subject.meshBird Diseases - Epidemiology - Virologyen_US
dc.subject.meshCluster Analysisen_US
dc.subject.meshGenome, Viralen_US
dc.subject.meshMolecular Epidemiologyen_US
dc.subject.meshMolecular Sequence Dataen_US
dc.subject.meshPhylogenyen_US
dc.subject.meshPicornaviridae - Classification - Genetics - Isolation & Purificationen_US
dc.subject.meshSeasonsen_US
dc.subject.meshSequence Analysis, Dnaen_US
dc.subject.meshSequence Homology, Amino Aciden_US
dc.subject.meshSongbirds - Virologyen_US
dc.subject.meshViral Structural Proteins - Geneticsen_US
dc.titleComparative analysis of six genome sequences of three novel picornaviruses, turdiviruses 1, 2 and 3, in dead wild birds, and proposal of two novel genera, Orthoturdivirus and Paraturdivirus, in the family Picornaviridaeen_US
dc.typeArticleen_US
dc.identifier.emailWoo, PCY: pcywoo@hkucc.hku.hken_US
dc.identifier.emailLau, SKP: skplau@hkucc.hku.hken_US
dc.identifier.emailHuang, Y: huangyi@hkucc.hku.hken_US
dc.identifier.emailLam, CSF: carollamsukfun@yahoo.com.hken_US
dc.identifier.emailPoon, RWS: rosana@hkucc.hku.hken_US
dc.identifier.emailTsoi, HW: hwtsoi@hkucc.hku.hk-
dc.identifier.emailLee, P: paullee1@hkucc.hku.hk-
dc.identifier.emailTse, H: htse@hkucc.hku.hk-
dc.identifier.emailYuen, KY: kyyuen@hkucc.hku.hk-
dc.identifier.authorityWoo, PCY=rp00430en_US
dc.identifier.authorityLau, SKP=rp00486en_US
dc.identifier.authorityTsoi, HW=rp00439en_US
dc.identifier.authorityTse, H=rp00519en_US
dc.identifier.authorityYuen, KY=rp00366en_US
dc.description.naturelink_to_OA_fulltexten_US
dc.identifier.doi10.1099/vir.0.021717-0en_US
dc.identifier.pmid20554801-
dc.identifier.scopuseid_2-s2.0-77956845187en_US
dc.identifier.hkuros178233-
dc.identifier.hkuros182537-
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-77956845187&selection=ref&src=s&origin=recordpageen_US
dc.identifier.volume91en_US
dc.identifier.issue10en_US
dc.identifier.spage2433en_US
dc.identifier.epage2448en_US
dc.identifier.isiWOS:000283004800004-
dc.publisher.placeUnited Kingdomen_US
dc.identifier.scopusauthoridWoo, PCY=7201801340en_US
dc.identifier.scopusauthoridLau, SKP=7401596211en_US
dc.identifier.scopusauthoridHuang, Y=36007277800en_US
dc.identifier.scopusauthoridLam, CSF=25950267400en_US
dc.identifier.scopusauthoridPoon, RWS=9334879200en_US
dc.identifier.scopusauthoridTsoi, HW=6603822102en_US
dc.identifier.scopusauthoridLee, P=36189338700en_US
dc.identifier.scopusauthoridTse, H=7006070596en_US
dc.identifier.scopusauthoridChan, ASL=36558880500en_US
dc.identifier.scopusauthoridLuk, G=7005143304en_US
dc.identifier.scopusauthoridChan, KH=7406034307en_US
dc.identifier.scopusauthoridYuen, KY=36078079100en_US
dc.identifier.citeulike10107604-
dc.customcontrol.immutablesml 130524-

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