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Structural basis for catalysis and substrate specificity of a 3C-like cysteine protease from a mosquito mesonivirus.

Kanitz M, Blanck S, Heine A, Gulyaeva AA, Gorbalenya AE, Ziebuhr J, Diederich WE.

Virology. 2019 May 2;533:21-33. doi: 10.1016/j.virol.2019.05.001. [Epub ahead of print]


Additional changes to taxonomy ratified in a special vote by the International Committee on Taxonomy of Viruses (October 2018).

Siddell SG, Walker PJ, Lefkowitz EJ, Mushegian AR, Adams MJ, Dutilh BE, Gorbalenya AE, Harrach B, Harrison RL, Junglen S, Knowles NJ, Kropinski AM, Krupovic M, Kuhn JH, Nibert M, Rubino L, Sabanadzovic S, Sanfaçon H, Simmonds P, Varsani A, Zerbini FM, Davison AJ.

Arch Virol. 2019 Mar;164(3):943-946. doi: 10.1007/s00705-018-04136-2.


A planarian nidovirus expands the limits of RNA genome size.

Saberi A, Gulyaeva AA, Brubacher JL, Newmark PA, Gorbalenya AE.

PLoS Pathog. 2018 Nov 1;14(11):e1007314. doi: 10.1371/journal.ppat.1007314. eCollection 2018 Nov.


PCR assays for detection of human astroviruses: In silico evaluation and design, and in vitro application to samples collected from patients in the Netherlands.

Nijhuis RHT, Sidorov IA, Chung PK, Wessels E, Gulyaeva AA, de Vries JJ, Claas ECJ, Gorbalenya AE.

J Clin Virol. 2018 Nov;108:83-89. doi: 10.1016/j.jcv.2018.09.007. Epub 2018 Sep 13.


Increasing the number of available ranks in virus taxonomy from five to ten and adopting the Baltimore classes as taxa at the basal rank.

Gorbalenya AE.

Arch Virol. 2018 Oct;163(10):2933-2936. doi: 10.1007/s00705-018-3915-6. Epub 2018 Jun 26.


Changes to taxonomy and the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses (2018).

King AMQ, Lefkowitz EJ, Mushegian AR, Adams MJ, Dutilh BE, Gorbalenya AE, Harrach B, Harrison RL, Junglen S, Knowles NJ, Kropinski AM, Krupovic M, Kuhn JH, Nibert ML, Rubino L, Sabanadzovic S, Sanfaçon H, Siddell SG, Simmonds P, Varsani A, Zerbini FM, Davison AJ.

Arch Virol. 2018 Sep;163(9):2601-2631. doi: 10.1007/s00705-018-3847-1. Epub 2018 May 12.


ICTV Virus Taxonomy Profile: Picornaviridae.

Zell R, Delwart E, Gorbalenya AE, Hovi T, King AMQ, Knowles NJ, Lindberg AM, Pallansch MA, Palmenberg AC, Reuter G, Simmonds P, Skern T, Stanway G, Yamashita T, Ictv Report Consortium.

J Gen Virol. 2017 Oct;98(10):2421-2422. doi: 10.1099/jgv.0.000911. Epub 2017 Sep 8.


Changes to taxonomy and the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses (2017).

Adams MJ, Lefkowitz EJ, King AMQ, Harrach B, Harrison RL, Knowles NJ, Kropinski AM, Krupovic M, Kuhn JH, Mushegian AR, Nibert M, Sabanadzovic S, Sanfaçon H, Siddell SG, Simmonds P, Varsani A, Zerbini FM, Gorbalenya AE, Davison AJ.

Arch Virol. 2017 Aug;162(8):2505-2538. doi: 10.1007/s00705-017-3358-5. Epub 2017 Apr 22.


Consensus statement: Virus taxonomy in the age of metagenomics.

Simmonds P, Adams MJ, Benkő M, Breitbart M, Brister JR, Carstens EB, Davison AJ, Delwart E, Gorbalenya AE, Harrach B, Hull R, King AM, Koonin EV, Krupovic M, Kuhn JH, Lefkowitz EJ, Nibert ML, Orton R, Roossinck MJ, Sabanadzovic S, Sullivan MB, Suttle CA, Tesh RB, van der Vlugt RA, Varsani A, Zerbini FM.

Nat Rev Microbiol. 2017 Mar;15(3):161-168. doi: 10.1038/nrmicro.2016.177. Epub 2017 Jan 3.


50 years of the International Committee on Taxonomy of Viruses: progress and prospects.

Adams MJ, Lefkowitz EJ, King AM, Harrach B, Harrison RL, Knowles NJ, Kropinski AM, Krupovic M, Kuhn JH, Mushegian AR, Nibert ML, Sabanadzovic S, Sanfaçon H, Siddell SG, Simmonds P, Varsani A, Zerbini FM, Orton RJ, Smith DB, Gorbalenya AE, Davison AJ.

Arch Virol. 2017 May;162(5):1441-1446. doi: 10.1007/s00705-016-3215-y. Epub 2017 Jan 11.


Domain Organization and Evolution of the Highly Divergent 5' Coding Region of Genomes of Arteriviruses, Including the Novel Possum Nidovirus.

Gulyaeva A, Dunowska M, Hoogendoorn E, Giles J, Samborskiy D, Gorbalenya AE.

J Virol. 2017 Feb 28;91(6). pii: e02096-16. doi: 10.1128/JVI.02096-16. Print 2017 Mar 15.


Ratification vote on taxonomic proposals to the International Committee on Taxonomy of Viruses (2016).

Adams MJ, Lefkowitz EJ, King AM, Harrach B, Harrison RL, Knowles NJ, Kropinski AM, Krupovic M, Kuhn JH, Mushegian AR, Nibert M, Sabanadzovic S, Sanfaçon H, Siddell SG, Simmonds P, Varsani A, Zerbini FM, Gorbalenya AE, Davison AJ.

Arch Virol. 2016 Oct;161(10):2921-49. doi: 10.1007/s00705-016-2977-6. Epub 2016 Jul 16.


Mutations in Encephalomyocarditis Virus 3A Protein Uncouple the Dependency of Genome Replication on Host Factors Phosphatidylinositol 4-Kinase IIIα and Oxysterol-Binding Protein.

Dorobantu CM, Albulescu L, Lyoo H, van Kampen M, De Francesco R, Lohmann V, Harak C, van der Schaar HM, Strating JR, Gorbalenya AE, van Kuppeveld FJ.

mSphere. 2016 May 11;1(3). pii: e00068-16. doi: 10.1128/mSphere.00068-16. eCollection 2016 May-Jun.


Limited variation during circulation of a polyomavirus in the human population involves the COCO-VA toggling site of Middle and Alternative T-antigen(s).

Kazem S, Lauber C, van der Meijden E, Kooijman S, Kravchenko AA; TrichSpin Network, Feltkamp MC, Gorbalenya AE.

Virology. 2016 Jan;487:129-40. doi: 10.1016/j.virol.2015.09.013. Epub 2015 Nov 2.


Arterivirus RNA-dependent RNA polymerase: Vital enzymatic activity remains elusive.

Lehmann KC, Gorbalenya AE, Snijder EJ, Posthuma CC.

Virology. 2016 Jan;487:68-74. doi: 10.1016/j.virol.2015.10.002. Epub 2015 Oct 23.


Modulation of the Host Lipid Landscape to Promote RNA Virus Replication: The Picornavirus Encephalomyocarditis Virus Converges on the Pathway Used by Hepatitis C Virus.

Dorobantu CM, Albulescu L, Harak C, Feng Q, van Kampen M, Strating JR, Gorbalenya AE, Lohmann V, van der Schaar HM, van Kuppeveld FJ.

PLoS Pathog. 2015 Sep 25;11(9):e1005185. doi: 10.1371/journal.ppat.1005185. eCollection 2015 Sep.


Discovery of an essential nucleotidylating activity associated with a newly delineated conserved domain in the RNA polymerase-containing protein of all nidoviruses.

Lehmann KC, Gulyaeva A, Zevenhoven-Dobbe JC, Janssen GM, Ruben M, Overkleeft HS, van Veelen PA, Samborskiy DV, Kravchenko AA, Leontovich AM, Sidorov IA, Snijder EJ, Posthuma CC, Gorbalenya AE.

Nucleic Acids Res. 2015 Sep 30;43(17):8416-34. doi: 10.1093/nar/gkv838. Epub 2015 Aug 24.


[The prevalence of the human rhinoviruses and coronaviruses circulating in the Moscow region during 2007-2012].

Lobodanov SA, Kiselev IS, Ammour YI, Gorbalenya AE, Claas EC, Zverev VV, Faizuloev EB.

Vopr Virusol. 2015;60(3):31-6. Russian.


Arterivirus nsp12 versus the coronavirus nsp16 2'-O-methyltransferase: comparison of the C-terminal cleavage products of two nidovirus pp1ab polyproteins.

Lehmann KC, Hooghiemstra L, Gulyaeva A, Samborskiy DV, Zevenhoven-Dobbe JC, Snijder EJ, Gorbalenya AE, Posthuma CC.

J Gen Virol. 2015 Sep;96(9):2643-55. doi: 10.1099/vir.0.000209. Epub 2015 Jun 3.


Ratification vote on taxonomic proposals to the International Committee on Taxonomy of Viruses (2015).

Adams MJ, Lefkowitz EJ, King AM, Bamford DH, Breitbart M, Davison AJ, Ghabrial SA, Gorbalenya AE, Knowles NJ, Krell P, Lavigne R, Prangishvili D, Sanfaçon H, Siddell SG, Simmonds P, Carstens EB.

Arch Virol. 2015 Jul;160(7):1837-50. doi: 10.1007/s00705-015-2425-z.


Interspecific adaptation by binary choice at de novo polyomavirus T antigen site through accelerated codon-constrained Val-Ala toggling within an intrinsically disordered region.

Lauber C, Kazem S, Kravchenko AA, Feltkamp MC, Gorbalenya AE.

Nucleic Acids Res. 2015 May 26;43(10):4800-13. doi: 10.1093/nar/gkv378. Epub 2015 Apr 22.


What we know but do not understand about nidovirus helicases.

Lehmann KC, Snijder EJ, Posthuma CC, Gorbalenya AE.

Virus Res. 2015 Apr 16;202:12-32. doi: 10.1016/j.virusres.2014.12.001. Epub 2014 Dec 8. Review.


One severe acute respiratory syndrome coronavirus protein complex integrates processive RNA polymerase and exonuclease activities.

Subissi L, Posthuma CC, Collet A, Zevenhoven-Dobbe JC, Gorbalenya AE, Decroly E, Snijder EJ, Canard B, Imbert I.

Proc Natl Acad Sci U S A. 2014 Sep 16;111(37):E3900-9. doi: 10.1073/pnas.1323705111. Epub 2014 Sep 2.


Structural basis for the regulatory function of a complex zinc-binding domain in a replicative arterivirus helicase resembling a nonsense-mediated mRNA decay helicase.

Deng Z, Lehmann KC, Li X, Feng C, Wang G, Zhang Q, Qi X, Yu L, Zhang X, Feng W, Wu W, Gong P, Tao Y, Posthuma CC, Snijder EJ, Gorbalenya AE, Chen Z.

Nucleic Acids Res. 2014 Mar;42(5):3464-77. doi: 10.1093/nar/gkt1310. Epub 2013 Dec 24.


The footprint of genome architecture in the largest genome expansion in RNA viruses.

Lauber C, Goeman JJ, Parquet Mdel C, Nga PT, Snijder EJ, Morita K, Gorbalenya AE.

PLoS Pathog. 2013;9(7):e1003500. doi: 10.1371/journal.ppat.1003500. Epub 2013 Jul 18.


Middle East respiratory syndrome coronavirus (MERS-CoV): announcement of the Coronavirus Study Group.

de Groot RJ, Baker SC, Baric RS, Brown CS, Drosten C, Enjuanes L, Fouchier RA, Galiano M, Gorbalenya AE, Memish ZA, Perlman S, Poon LL, Snijder EJ, Stephens GM, Woo PC, Zaki AM, Zambon M, Ziebuhr J.

J Virol. 2013 Jul;87(14):7790-2. doi: 10.1128/JVI.01244-13. Epub 2013 May 15. No abstract available.


From Stockholm to Malawi: recent developments in studying human polyomaviruses.

Feltkamp MC, Kazem S, van der Meijden E, Lauber C, Gorbalenya AE.

J Gen Virol. 2013 Mar;94(Pt 3):482-96. doi: 10.1099/vir.0.048462-0. Epub 2012 Dec 19. Review.


Genetics-based classification of filoviruses calls for expanded sampling of genomic sequences.

Lauber C, Gorbalenya AE.

Viruses. 2012 Sep;4(9):1425-37. doi: 10.3390/v4091425. Epub 2012 Aug 31.


Genomic characterization of a newly discovered coronavirus associated with acute respiratory distress syndrome in humans.

van Boheemen S, de Graaf M, Lauber C, Bestebroer TM, Raj VS, Zaki AM, Osterhaus AD, Haagmans BL, Gorbalenya AE, Snijder EJ, Fouchier RA.

MBio. 2012 Nov 20;3(6). pii: e00473-12. doi: 10.1128/mBio.00473-12.


No novel coronaviruses identified in a large collection of human nasopharyngeal specimens using family-wide CODEHOP-based primers.

Zlateva KT, Coenjaerts FE, Crusio KM, Lammens C, Leus F, Viveen M, Ieven M, Spaan WJ, Claas EC, Gorbalenya AE.

Arch Virol. 2013 Jan;158(1):251-5. doi: 10.1007/s00705-012-1487-4. Epub 2012 Sep 28.


Comparative analysis of an expanded Clostridium difficile reference strain collection reveals genetic diversity and evolution through six lineages.

Knetsch CW, Terveer EM, Lauber C, Gorbalenya AE, Harmanus C, Kuijper EJ, Corver J, van Leeuwen HC.

Infect Genet Evol. 2012 Oct;12(7):1577-85. doi: 10.1016/j.meegid.2012.06.003. Epub 2012 Jun 15.


Antagonism of the interferon-induced OAS-RNase L pathway by murine coronavirus ns2 protein is required for virus replication and liver pathology.

Zhao L, Jha BK, Wu A, Elliott R, Ziebuhr J, Gorbalenya AE, Silverman RH, Weiss SR.

Cell Host Microbe. 2012 Jun 14;11(6):607-16. doi: 10.1016/j.chom.2012.04.011.


The "Bridge" in the Epstein-Barr virus alkaline exonuclease protein BGLF5 contributes to shutoff activity during productive infection.

Horst D, Burmeister WP, Boer IG, van Leeuwen D, Buisson M, Gorbalenya AE, Wiertz EJ, Ressing ME.

J Virol. 2012 Sep;86(17):9175-87. doi: 10.1128/JVI.00309-12. Epub 2012 Jun 13.


Mesoniviridae: a proposed new family in the order Nidovirales formed by a single species of mosquito-borne viruses.

Lauber C, Ziebuhr J, Junglen S, Drosten C, Zirkel F, Nga PT, Morita K, Snijder EJ, Gorbalenya AE.

Arch Virol. 2012 Aug;157(8):1623-8. doi: 10.1007/s00705-012-1295-x. Epub 2012 Apr 24.


Toward genetics-based virus taxonomy: comparative analysis of a genetics-based classification and the taxonomy of picornaviruses.

Lauber C, Gorbalenya AE.

J Virol. 2012 Apr;86(7):3905-15. doi: 10.1128/JVI.07174-11. Epub 2012 Jan 25.


Partitioning the genetic diversity of a virus family: approach and evaluation through a case study of picornaviruses.

Lauber C, Gorbalenya AE.

J Virol. 2012 Apr;86(7):3890-904. doi: 10.1128/JVI.07173-11. Epub 2012 Jan 25.


Discovery of the first insect nidovirus, a missing evolutionary link in the emergence of the largest RNA virus genomes.

Nga PT, Parquet Mdel C, Lauber C, Parida M, Nabeshima T, Yu F, Thuy NT, Inoue S, Ito T, Okamoto K, Ichinose A, Snijder EJ, Morita K, Gorbalenya AE.

PLoS Pathog. 2011 Sep;7(9):e1002215. doi: 10.1371/journal.ppat.1002215. Epub 2011 Sep 8.


Design and validation of consensus-degenerate hybrid oligonucleotide primers for broad and sensitive detection of corona- and toroviruses.

Zlateva KT, Crusio KM, Leontovich AM, Lauber C, Claas E, Kravchenko AA, Spaan WJ, Gorbalenya AE.

J Virol Methods. 2011 Nov;177(2):174-83. doi: 10.1016/j.jviromet.2011.08.005. Epub 2011 Aug 11.


Structural basis for antiviral inhibition of the main protease, 3C, from human enterovirus 93.

Costenaro L, Kaczmarska Z, Arnan C, Janowski R, Coutard B, Solà M, Gorbalenya AE, Norder H, Canard B, Coll M.

J Virol. 2011 Oct;85(20):10764-73. doi: 10.1128/JVI.05062-11. Epub 2011 Aug 10.


Picornavirus non-structural proteins as targets for new anti-virals with broad activity.

Norder H, De Palma AM, Selisko B, Costenaro L, Papageorgiou N, Arnan C, Coutard B, Lantez V, De Lamballerie X, Baronti C, Solà M, Tan J, Neyts J, Canard B, Coll M, Gorbalenya AE, Hilgenfeld R.

Antiviral Res. 2011 Mar;89(3):204-18. doi: 10.1016/j.antiviral.2010.12.007. Epub 2011 Jan 12. Review.


Identification of tolerated insertion sites in poliovirus non-structural proteins.

Teterina NL, Lauber C, Jensen KS, Levenson EA, Gorbalenya AE, Ehrenfeld E.

Virology. 2011 Jan 5;409(1):1-11. doi: 10.1016/j.virol.2010.09.028. Epub 2010 Oct 23.


The 2C putative helicase of echovirus 30 adopts a hexameric ring-shaped structure.

Papageorgiou N, Coutard B, Lantez V, Gautron E, Chauvet O, Baronti C, Norder H, de Lamballerie X, Heresanu V, Ferté N, Veesler S, Gorbalenya AE, Canard B.

Acta Crystallogr D Biol Crystallogr. 2010 Oct;66(Pt 10):1116-20. doi: 10.1107/S090744491002809X. Epub 2010 Sep 18.


Discovery of a new human polyomavirus associated with trichodysplasia spinulosa in an immunocompromized patient.

van der Meijden E, Janssens RW, Lauber C, Bouwes Bavinck JN, Gorbalenya AE, Feltkamp MC.

PLoS Pathog. 2010 Jul 29;6(7):e1001024. doi: 10.1371/journal.ppat.1001024.


Papain-like protease 1 from transmissible gastroenteritis virus: crystal structure and enzymatic activity toward viral and cellular substrates.

Wojdyla JA, Manolaridis I, van Kasteren PB, Kikkert M, Snijder EJ, Gorbalenya AE, Tucker PA.

J Virol. 2010 Oct;84(19):10063-73. doi: 10.1128/JVI.00898-10. Epub 2010 Jul 28.


Arterivirus Nsp1 modulates the accumulation of minus-strand templates to control the relative abundance of viral mRNAs.

Nedialkova DD, Gorbalenya AE, Snijder EJ.

PLoS Pathog. 2010 Feb 19;6(2):e1000772. doi: 10.1371/journal.ppat.1000772.


Practical application of bioinformatics by the multidisciplinary VIZIER consortium.

Gorbalenya AE, Lieutaud P, Harris MR, Coutard B, Canard B, Kleywegt GJ, Kravchenko AA, Samborskiy DV, Sidorov IA, Leontovich AM, Jones TA.

Antiviral Res. 2010 Aug;87(2):95-110. doi: 10.1016/j.antiviral.2010.02.005. Epub 2010 Feb 11. Review.


Structure of the X (ADRP) domain of nsp3 from feline coronavirus.

Wojdyla JA, Manolaridis I, Snijder EJ, Gorbalenya AE, Coutard B, Piotrowski Y, Hilgenfeld R, Tucker PA.

Acta Crystallogr D Biol Crystallogr. 2009 Dec;65(Pt 12):1292-300. doi: 10.1107/S0907444909040074. Epub 2009 Nov 17.


Euprosterna elaeasa virus genome sequence and evolution of the Tetraviridae family: emergence of bipartite genomes and conservation of the VPg signal with the dsRNA Birnaviridae family.

Zeddam JL, Gordon KH, Lauber C, Alves CA, Luke BT, Hanzlik TN, Ward VK, Gorbalenya AE.

Virology. 2010 Feb 5;397(1):145-54. doi: 10.1016/j.virol.2009.10.042. Epub 2009 Dec 1.


Permutation of the active site of putative RNA-dependent RNA polymerase in a newly identified species of plant alpha-like virus.

Sabanadzovic S, Ghanem-Sabanadzovic NA, Gorbalenya AE.

Virology. 2009 Nov 10;394(1):1-7. doi: 10.1016/j.virol.2009.08.006. Epub 2009 Sep 29.


SNAD: Sequence Name Annotation-based Designer.

Sidorov IA, Reshetov DA, Gorbalenya AE.

BMC Bioinformatics. 2009 Aug 14;10:251. doi: 10.1186/1471-2105-10-251.

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