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A Divergent Hepatitis D-Like Agent in Birds.

Wille M, Netter HJ, Littlejohn M, Yuen L, Shi M, Eden JS, Klaassen M, Holmes EC, Hurt AC.

Viruses. 2018 Dec 17;10(12). pii: E720. doi: 10.3390/v10120720.


Tracking virus outbreaks in the twenty-first century.

Grubaugh ND, Ladner JT, Lemey P, Pybus OG, Rambaut A, Holmes EC, Andersen KG.

Nat Microbiol. 2019 Jan;4(1):10-19. doi: 10.1038/s41564-018-0296-2. Epub 2018 Dec 13. Review.


Evolutionary Virology at 40.

Geoghegan JL, Holmes EC.

Genetics. 2018 Dec;210(4):1151-1162. doi: 10.1534/genetics.118.301556.


Fogarty International Center collaborative networks in infectious disease modeling: Lessons learnt in research and capacity building.

Nelson MI, Lloyd-Smith JO, Simonsen L, Rambaut A, Holmes EC, Chowell G, Miller MA, Spiro DJ, Grenfell B, Viboud C.

Epidemics. 2018 Oct 23. pii: S1755-4365(18)30029-X. doi: 10.1016/j.epidem.2018.10.004. [Epub ahead of print] Review.


Extensive Diversity of RNA Viruses in Australian Ticks.

Harvey E, Rose K, Eden JS, Lo N, Abeyasuriya T, Shi M, Doggett SL, Holmes EC.

J Virol. 2018 Nov 7. pii: JVI.01358-18. doi: 10.1128/JVI.01358-18. [Epub ahead of print]


Hidden diversity and evolution of viruses in market fish.

Geoghegan JL, Di Giallonardo F, Cousins K, Shi M, Williamson JE, Holmes EC.

Virus Evol. 2018 Oct 31;4(2):vey031. doi: 10.1093/ve/vey031. eCollection 2018 Jul.


Virus-virus interactions and host ecology are associated with RNA virome structure in wild birds.

Wille M, Eden JS, Shi M, Klaassen M, Hurt AC, Holmes EC.

Mol Ecol. 2018 Dec;27(24):5263-5278. doi: 10.1111/mec.14918. Epub 2018 Nov 22.


The phylogenomics of evolving virus virulence.

Geoghegan JL, Holmes EC.

Nat Rev Genet. 2018 Dec;19(12):756-769. doi: 10.1038/s41576-018-0055-5. Review.


An Atypical Parvovirus Drives Chronic Tubulointerstitial Nephropathy and Kidney Fibrosis.

Roediger B, Lee Q, Tikoo S, Cobbin JCA, Henderson JM, Jormakka M, O'Rourke MB, Padula MP, Pinello N, Henry M, Wynne M, Santagostino SF, Brayton CF, Rasmussen L, Lisowski L, Tay SS, Harris DC, Bertram JF, Dowling JP, Bertolino P, Lai JH, Wu W, Bachovchin WW, Wong JJ, Gorrell MD, Shaban B, Holmes EC, Jolly CJ, Monette S, Weninger W.

Cell. 2018 Oct 4;175(2):530-543.e24. doi: 10.1016/j.cell.2018.08.013. Epub 2018 Sep 13.


Evolution of Human Respiratory Syncytial Virus (RSV) over Multiple Seasons in New South Wales, Australia.

Di Giallonardo F, Kok J, Fernandez M, Carter I, Geoghegan JL, Dwyer DE, Holmes EC, Eden JS.

Viruses. 2018 Sep 6;10(9). pii: E476. doi: 10.3390/v10090476.


Transcriptome Analysis and In Situ Hybridization for FcaGHV1 in Feline Lymphoma.

Aghazadeh M, Shi M, Pesavento PA, Durham AC, Polley T, Donahoe SL, Troyer RM, Barrs VR, Holmes EC, Beatty JA.

Viruses. 2018 Aug 30;10(9). pii: E464. doi: 10.3390/v10090464.


The diversity, evolution and origins of vertebrate RNA viruses.

Zhang YZ, Wu WC, Shi M, Holmes EC.

Curr Opin Virol. 2018 Aug;31:9-16. doi: 10.1016/j.coviro.2018.07.017. Epub 2018 Aug 13. Review.


Draft genome assembly of the invasive cane toad, Rhinella marina.

Edwards RJ, Tuipulotu DE, Amos TG, O'Meally D, Richardson MF, Russell TL, Vallinoto M, Carneiro M, Ferrand N, Wilkins MR, Sequeira F, Rollins LA, Holmes EC, Shine R, White PA.

Gigascience. 2018 Sep 1;7(9). doi: 10.1093/gigascience/giy095.


A Simple Method to Detect Candidate Overlapping Genes in Viruses Using Single Genome Sequences.

Schlub TE, Buchmann JP, Holmes EC.

Mol Biol Evol. 2018 Oct 1;35(10):2572-2581. doi: 10.1093/molbev/msy155.


No detectable effect of Wolbachia wMel on the prevalence and abundance of the RNA virome of Drosophila melanogaster.

Shi M, White VL, Schlub T, Eden JS, Hoffmann AA, Holmes EC.

Proc Biol Sci. 2018 Jul 25;285(1883). pii: 20181165. doi: 10.1098/rspb.2018.1165.


Low evolutionary rate of infectious pancreatic necrosis virus (IPNV) in Italy is associated with reduced virulence in trout.

Panzarin V, Holmes EC, Abbadi M, Zamperin G, Quartesan R, Milani A, Schivo A, Bille L, Dalla Pozza M, Monne I, Toffan A.

Virus Evol. 2018 Jul 18;4(2):vey019. doi: 10.1093/ve/vey019. eCollection 2018 Jul.


A complex mosaic of enteroviruses shapes community-acquired hand, foot and mouth disease transmission and evolution within a single hospital.

Cobbin JCA, Britton PN, Burrell R, Thosar D, Selvakumar K, Eden JS, Jones CA, Holmes EC.

Virus Evol. 2018 Jul 13;4(2):vey020. doi: 10.1093/ve/vey020. eCollection 2018 Jul.


Author Correction: The evolutionary history of vertebrate RNA viruses.

Shi M, Lin XD, Chen X, Tian JH, Chen LJ, Li K, Wang W, Eden JS, Shen JJ, Liu L, Holmes EC, Zhang YZ.

Nature. 2018 Sep;561(7722):E6. doi: 10.1038/s41586-018-0310-0.


The Biological Object Notation (BON): a structured file format for biological data.

Buchmann JP, Fourment M, Holmes EC.

Sci Rep. 2018 Jun 25;8(1):9644. doi: 10.1038/s41598-018-28016-6.


Fine-Tuned Protein Production in Methanosarcina acetivorans C2A.

Karim AA, Gestaut DR, Fincker M, Ruth JC, Holmes EC, Sheu W, Spormann AM.

ACS Synth Biol. 2018 Aug 17;7(8):1874-1885. doi: 10.1021/acssynbio.8b00062. Epub 2018 Jul 13.


Viral Discovery in the Invasive Australian Cane Toad (Rhinella marina) Using Metatranscriptomic and Genomic Approaches.

Russo AG, Eden JS, Enosi Tuipulotu D, Shi M, Selechnik D, Shine R, Rollins LA, Holmes EC, White PA.

J Virol. 2018 Aug 16;92(17). pii: e00768-18. doi: 10.1128/JVI.00768-18. Print 2018 Sep 1.


Pandemics: spend on surveillance, not prediction.

Holmes EC, Rambaut A, Andersen KG.

Nature. 2018 Jun;558(7709):180-182. doi: 10.1038/d41586-018-05373-w. No abstract available.


Multiple Incursions and Recurrent Epidemic Fade-Out of H3N2 Canine Influenza A Virus in the United States.

Voorhees IEH, Dalziel BD, Glaser A, Dubovi EJ, Murcia PR, Newbury S, Toohey-Kurth K, Su S, Kriti D, Van Bakel H, Goodman LB, Leutenegger C, Holmes EC, Parrish CR.

J Virol. 2018 Jul 31;92(16). pii: e00323-18. doi: 10.1128/JVI.00323-18. Print 2018 Aug 15.


Virological Sampling of Inaccessible Wildlife with Drones.

Geoghegan JL, Pirotta V, Harvey E, Smith A, Buchmann JP, Ostrowski M, Eden JS, Harcourt R, Holmes EC.

Viruses. 2018 Jun 2;10(6). pii: E300. doi: 10.3390/v10060300.


A Novel Hepadnavirus Identified in an Immunocompromised Domestic Cat in Australia.

Aghazadeh M, Shi M, Barrs VR, McLuckie AJ, Lindsay SA, Jameson B, Hampson B, Holmes EC, Beatty JA.

Viruses. 2018 May 17;10(5). pii: E269. doi: 10.3390/v10050269.


Publisher Correction: Sudden emergence of human infections with H7N9 avian influenza A virus in Hubei province, central China.

Liu J, Xu J, Liu L, Wei X, Song Y, Fang B, Yu X, Li X, Ye G, Du Y, Chen M, Shi W, Liu D, Holmes EC, Cui J.

Sci Rep. 2018 May 10;8(1):7588. doi: 10.1038/s41598-018-25257-3.


Complete genome of Aedes aegypti anphevirus in the Aag2 mosquito cell line.

Di Giallonardo F, Audsley MD, Shi M, Young PR, McGraw EA, Holmes EC.

J Gen Virol. 2018 Jun;99(6):832-836. doi: 10.1099/jgv.0.001079. Epub 2018 May 9.


N-hydroxy-pipecolic acid is a mobile metabolite that induces systemic disease resistance in Arabidopsis.

Chen YC, Holmes EC, Rajniak J, Kim JG, Tang S, Fischer CR, Mudgett MB, Sattely ES.

Proc Natl Acad Sci U S A. 2018 May 22;115(21):E4920-E4929. doi: 10.1073/pnas.1805291115. Epub 2018 May 7.


The evolutionary history of vertebrate RNA viruses.

Shi M, Lin XD, Chen X, Tian JH, Chen LJ, Li K, Wang W, Eden JS, Shen JJ, Liu L, Holmes EC, Zhang YZ.

Nature. 2018 Apr;556(7700):197-202. doi: 10.1038/s41586-018-0012-7. Epub 2018 Apr 4. Erratum in: Nature. 2018 Jun 26;:.


Using Metagenomics to Characterize an Expanding Virosphere.

Zhang YZ, Shi M, Holmes EC.

Cell. 2018 Mar 8;172(6):1168-1172. doi: 10.1016/j.cell.2018.02.043.


Estimating evolutionary rates in giant viruses using ancient genomes.

Duchêne S, Holmes EC.

Virus Evol. 2018 Feb 27;4(1):vey006. doi: 10.1093/ve/vey006. eCollection 2018 Jan.


A Single Amino Acid Change in the Response Regulator PhoP, Acquired during Yersinia pestis Evolution, Affects PhoP Target Gene Transcription and Polymyxin B Susceptibility.

Fukuto HS, Vadyvaloo V, McPhee JB, Poinar HN, Holmes EC, Bliska JB.

J Bacteriol. 2018 Apr 9;200(9). pii: e00050-18. doi: 10.1128/JB.00050-18. Print 2018 May 1.


Correction: The paradox of HBV evolution as revealed from a 16th century mummy.

Patterson Ross Z, Klunk J, Fornaciari G, Giuffra V, Duchêne S, Duggan AT, Poinar D, Douglas MW, Eden JS, Holmes EC, Poinar HN.

PLoS Pathog. 2018 Feb 9;14(2):e1006887. doi: 10.1371/journal.ppat.1006887. eCollection 2018 Feb.


Correction: Continental synchronicity of human influenza virus epidemics despite climactic variation.

Geoghegan JL, Saavedra AF, Duchêne S, Sullivan S, Barr I, Holmes EC.

PLoS Pathog. 2018 Feb 7;14(2):e1006903. doi: 10.1371/journal.ppat.1006903. eCollection 2018 Feb.


Sudden emergence of human infections with H7N9 avian influenza A virus in Hubei province, central China.

Liu J, Xu J, Liu L, Wei X, Song Y, Fang B, Yu X, Li X, Ye G, Du Y, Chen M, Shi W, Liu D, Holmes EC, Cui J.

Sci Rep. 2018 Feb 6;8(1):2486. doi: 10.1038/s41598-018-20988-9. Erratum in: Sci Rep. 2018 May 10;8(1):7588.


Interplay between co-divergence and cross-species transmission in the evolutionary history of bat coronaviruses.

Leopardi S, Holmes EC, Gastaldelli M, Tassoni L, Priori P, Scaravelli D, Zamperin G, De Benedictis P.

Infect Genet Evol. 2018 Mar;58:279-289. doi: 10.1016/j.meegid.2018.01.012. Epub 2018 Jan 30.


Continental synchronicity of human influenza virus epidemics despite climatic variation.

Geoghegan JL, Saavedra AF, Duchêne S, Sullivan S, Barr I, Holmes EC.

PLoS Pathog. 2018 Jan 11;14(1):e1006780. doi: 10.1371/journal.ppat.1006780. eCollection 2018 Jan. Erratum in: PLoS Pathog. 2018 Feb 7;14 (2):e1006903.


The paradox of HBV evolution as revealed from a 16th century mummy.

Patterson Ross Z, Klunk J, Fornaciari G, Giuffra V, Duchêne S, Duggan AT, Poinar D, Douglas MW, Eden JS, Holmes EC, Poinar HN.

PLoS Pathog. 2018 Jan 4;14(1):e1006750. doi: 10.1371/journal.ppat.1006750. eCollection 2018 Jan. Erratum in: PLoS Pathog. 2018 Feb 9;14 (2):e1006887.


Detection and Circulation of a Novel Rabbit Hemorrhagic Disease Virus in Australia.

Mahar JE, Read AJ, Gu X, Urakova N, Mourant R, Piper M, Haboury S, Holmes EC, Strive T, Hall RN.

Emerg Infect Dis. 2018 Jan;24(1):22-31. doi: 10.3201/eid2401.170412.


The impact of host genetic diversity on virus evolution and emergence.

Rodríguez-Nevado C, Lam TT, Holmes EC, Pagán I.

Ecol Lett. 2018 Feb;21(2):253-263. doi: 10.1111/ele.12890. Epub 2017 Dec 5.


Extensive diversity and evolution of hepadnaviruses in bats in China.

Nie FY, Lin XD, Hao ZY, Chen XN, Wang ZX, Wang MR, Wu J, Wang HW, Zhao G, Ma RZ, Holmes EC, Zhang YZ.

Virology. 2018 Jan 15;514:88-97. doi: 10.1016/j.virol.2017.11.005. Epub 2017 Nov 16.


Meta-transcriptomics and the evolutionary biology of RNA viruses.

Shi M, Zhang YZ, Holmes EC.

Virus Res. 2018 Jan 2;243:83-90. doi: 10.1016/j.virusres.2017.10.016. Epub 2017 Oct 27. Review.


Rabbit haemorrhagic disease virus 2 (GI.2) is replacing endemic strains of RHDV in the Australian landscape within 18 months of its arrival.

Mahar JE, Hall RN, Peacock D, Kovaliski J, Piper M, Mourant R, Huang N, Campbell S, Gu X, Read A, Urakova N, Cox T, Holmes EC, Strive T.

J Virol. 2017 Nov 1. pii: JVI.01374-17. doi: 10.1128/JVI.01374-17. [Epub ahead of print]


Emergence and Adaptation of a Novel Highly Pathogenic H7N9 Influenza Virus in Birds and Humans from a 2013 Human-Infecting Low-Pathogenic Ancestor.

Qi W, Jia W, Liu D, Li J, Bi Y, Xie S, Li B, Hu T, Du Y, Xing L, Zhang J, Zhang F, Wei X, Eden JS, Li H, Tian H, Li W, Su G, Lao G, Xu C, Xu B, Liu W, Zhang G, Ren T, Holmes EC, Cui J, Shi W, Gao GF, Liao M.

J Virol. 2018 Jan 2;92(2). pii: e00921-17. doi: 10.1128/JVI.00921-17. Print 2018 Jan 15.


Predicting virus emergence amid evolutionary noise.

Geoghegan JL, Holmes EC.

Open Biol. 2017 Oct;7(10). pii: 170189. doi: 10.1098/rsob.170189. Review.


Comment: Characterization of Two Historic Smallpox Specimens from a Czech Museum.

Porter AF, Duggan AT, Poinar HN, Holmes EC.

Viruses. 2017 Sep 28;9(10). pii: E276. doi: 10.3390/v9100276.


Characterizing the virome of Ixodes ricinus ticks from northern Europe.

Pettersson JH, Shi M, Bohlin J, Eldholm V, Brynildsrud OB, Paulsen KM, Andreassen Å, Holmes EC.

Sci Rep. 2017 Sep 7;7(1):10870. doi: 10.1038/s41598-017-11439-y.


Spread of Canine Influenza A(H3N2) Virus, United States.

Voorhees IEH, Glaser AL, Toohey-Kurth K, Newbury S, Dalziel BD, Dubovi EJ, Poulsen K, Leutenegger C, Willgert KJE, Brisbane-Cohen L, Richardson-Lopez J, Holmes EC, Parrish CR.

Emerg Infect Dis. 2017 Dec;23(12):1950-1957. doi: 10.3201/eid2312.170246. Epub 2017 Dec 17.


Next step in the ongoing arms race between myxoma virus and wild rabbits in Australia is a novel disease phenotype.

Kerr PJ, Cattadori IM, Liu J, Sim DG, Dodds JW, Brooks JW, Kennett MJ, Holmes EC, Read AF.

Proc Natl Acad Sci U S A. 2017 Aug 29;114(35):9397-9402. doi: 10.1073/pnas.1710336114. Epub 2017 Aug 14.


Persistent infections in immunocompromised hosts are rarely sources of new pathogen variants.

Eden JS, Chisholm RH, Bull RA, White PA, Holmes EC, Tanaka MM.

Virus Evol. 2017 Jul 28;3(2):vex018. doi: 10.1093/ve/vex018. eCollection 2017 Jul.

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