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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 Jun 19. doi: 10.1021/acssynbio.8b00062. [Epub ahead of print]


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 Jun 13. pii: JVI.00768-18. doi: 10.1128/JVI.00768-18. [Epub ahead of print]


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 Jun 6. pii: JVI.00323-18. doi: 10.1128/JVI.00323-18. [Epub ahead of print]


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.


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.


Reverse Engineering Field Isolates of Myxoma Virus Demonstrates that Some Gene Disruptions or Losses of Function Do Not Explain Virulence Changes Observed in the Field.

Liu J, Cattadori IM, Sim DG, Eden JS, Holmes EC, Read AF, Kerr PJ.

J Virol. 2017 Sep 27;91(20). pii: e01289-17. doi: 10.1128/JVI.01289-17. Print 2017 Oct 15.


Parasite Microbiome Project: Systematic Investigation of Microbiome Dynamics within and across Parasite-Host Interactions.

Dheilly NM, Bolnick D, Bordenstein S, Brindley PJ, Figuères C, Holmes EC, Martínez Martínez J, Phillips AJ, Poulin R, Rosario K.

mSystems. 2017 Jul 18;2(4). pii: e00050-17. doi: 10.1128/mSystems.00050-17. eCollection 2017 Jul-Aug.


Metabolic engineering of Rhodopseudomonas palustris for the obligate reduction of n-butyrate to n-butanol.

Doud DFR, Holmes EC, Richter H, Molitor B, Jander G, Angenent LT.

Biotechnol Biofuels. 2017 Jul 11;10:178. doi: 10.1186/s13068-017-0864-3. eCollection 2017.


Discovery of a highly divergent coronavirus in the Asian house shrew from China illuminates the origin of the alphacoronaviruses.

Wang W, Lin XD, Liao Y, Guan XQ, Guo WP, Xing JG, Holmes EC, Zhang YZ.

J Virol. 2017 Jun 21. pii: JVI.00764-17. doi: 10.1128/JVI.00764-17. [Epub ahead of print]


High-Resolution Metatranscriptomics Reveals the Ecological Dynamics of Mosquito-Associated RNA Viruses in Western Australia.

Shi M, Neville P, Nicholson J, Eden JS, Imrie A, Holmes EC.

J Virol. 2017 Aug 10;91(17). pii: e00680-17. doi: 10.1128/JVI.00680-17. Print 2017 Sep 1.


Francisella tularensis ssp. holarctica in Ringtail Possums, Australia.

Eden JS, Rose K, Ng J, Shi M, Wang Q, Sintchenko V, Holmes EC.

Emerg Infect Dis. 2017 Jul;23(7):1198-1201. doi: 10.3201/eid2307.161863.


The impact of migratory flyways on the spread of avian influenza virus in North America.

Fourment M, Darling AE, Holmes EC.

BMC Evol Biol. 2017 May 25;17(1):118. doi: 10.1186/s12862-017-0965-4.


Establishment and cryptic transmission of Zika virus in Brazil and the Americas.

Faria NR, Quick J, Claro IM, Thézé J, de Jesus JG, Giovanetti M, Kraemer MUG, Hill SC, Black A, da Costa AC, Franco LC, Silva SP, Wu CH, Raghwani J, Cauchemez S, du Plessis L, Verotti MP, de Oliveira WK, Carmo EH, Coelho GE, Santelli ACFS, Vinhal LC, Henriques CM, Simpson JT, Loose M, Andersen KG, Grubaugh ND, Somasekar S, Chiu CY, Muñoz-Medina JE, Gonzalez-Bonilla CR, Arias CF, Lewis-Ximenez LL, Baylis SA, Chieppe AO, Aguiar SF, Fernandes CA, Lemos PS, Nascimento BLS, Monteiro HAO, Siqueira IC, de Queiroz MG, de Souza TR, Bezerra JF, Lemos MR, Pereira GF, Loudal D, Moura LC, Dhalia R, França RF, Magalhães T, Marques ET Jr, Jaenisch T, Wallau GL, de Lima MC, Nascimento V, de Cerqueira EM, de Lima MM, Mascarenhas DL, Neto JPM, Levin AS, Tozetto-Mendoza TR, Fonseca SN, Mendes-Correa MC, Milagres FP, Segurado A, Holmes EC, Rambaut A, Bedford T, Nunes MRT, Sabino EC, Alcantara LCJ, Loman NJ, Pybus OG.

Nature. 2017 Jun 15;546(7658):406-410. doi: 10.1038/nature22401. Epub 2017 May 24.


A Diverse Range of Novel RNA Viruses in Geographically Distinct Honey Bee Populations.

Remnant EJ, Shi M, Buchmann G, Blacquière T, Holmes EC, Beekman M, Ashe A.

J Virol. 2017 Jul 27;91(16). pii: e00158-17. doi: 10.1128/JVI.00158-17. Print 2017 Aug 15.


Extensive diversity of rickettsiales bacteria in ticks from Wuhan, China.

Lu M, Tian JH, Yu B, Guo WP, Holmes EC, Zhang YZ.

Ticks Tick Borne Dis. 2017 Jun;8(4):574-580. doi: 10.1016/j.ttbdis.2017.03.006. Epub 2017 Mar 24.


Virus genomes reveal factors that spread and sustained the Ebola epidemic.

Dudas G, Carvalho LM, Bedford T, Tatem AJ, Baele G, Faria NR, Park DJ, Ladner JT, Arias A, Asogun D, Bielejec F, Caddy SL, Cotten M, D'Ambrozio J, Dellicour S, Di Caro A, Diclaro JW, Duraffour S, Elmore MJ, Fakoli LS, Faye O, Gilbert ML, Gevao SM, Gire S, Gladden-Young A, Gnirke A, Goba A, Grant DS, Haagmans BL, Hiscox JA, Jah U, Kugelman JR, Liu D, Lu J, Malboeuf CM, Mate S, Matthews DA, Matranga CB, Meredith LW, Qu J, Quick J, Pas SD, Phan MVT, Pollakis G, Reusken CB, Sanchez-Lockhart M, Schaffner SF, Schieffelin JS, Sealfon RS, Simon-Loriere E, Smits SL, Stoecker K, Thorne L, Tobin EA, Vandi MA, Watson SJ, West K, Whitmer S, Wiley MR, Winnicki SM, Wohl S, Wölfel R, Yozwiak NL, Andersen KG, Blyden SO, Bolay F, Carroll MW, Dahn B, Diallo B, Formenty P, Fraser C, Gao GF, Garry RF, Goodfellow I, Günther S, Happi CT, Holmes EC, Kargbo B, Keïta S, Kellam P, Koopmans MPG, Kuhn JH, Loman NJ, Magassouba N, Naidoo D, Nichol ST, Nyenswah T, Palacios G, Pybus OG, Sabeti PC, Sall A, Ströher U, Wurie I, Suchard MA, Lemey P, Rambaut A.

Nature. 2017 Apr 20;544(7650):309-315. doi: 10.1038/nature22040. Epub 2017 Apr 12.


Molecular Evolution and Emergence of H5N6 Avian Influenza Virus in Central China.

Du Y, Chen M, Yang J, Jia Y, Han S, Holmes EC, Cui J.

J Virol. 2017 May 26;91(12). pii: e00143-17. doi: 10.1128/JVI.00143-17. Print 2017 Jun 15.


Autochthonous Japanese Encephalitis with Yellow Fever Coinfection in Africa.

Simon-Loriere E, Faye O, Prot M, Casademont I, Fall G, Fernandez-Garcia MD, Diagne MM, Kipela JM, Fall IS, Holmes EC, Sakuntabhai A, Sall AA.

N Engl J Med. 2017 Apr 13;376(15):1483-1485. doi: 10.1056/NEJMc1701600. No abstract available.


Extensive diversity of coronaviruses in bats from China.

Lin XD, Wang W, Hao ZY, Wang ZX, Guo WP, Guan XQ, Wang MR, Wang HW, Zhou RH, Li MH, Tang GP, Wu J, Holmes EC, Zhang YZ.

Virology. 2017 Jul;507:1-10. doi: 10.1016/j.virol.2017.03.019. Epub 2017 Apr 3.


Benign Rabbit Calicivirus in New Zealand.

Nicholson LJ, Mahar JE, Strive T, Zheng T, Holmes EC, Ward VK, Duckworth JA.

Appl Environ Microbiol. 2017 May 17;83(11). pii: e00090-17. doi: 10.1128/AEM.00090-17. Print 2017 Jun 1.


Genome-scale rates of evolutionary change in bacteria.

Duchêne S, Holt KE, Weill FX, Le Hello S, Hawkey J, Edwards DJ, Fourment M, Holmes EC.

Microb Genom. 2016 Nov 30;2(11):e000094. doi: 10.1099/mgen.0.000094. eCollection 2016 Nov.


Multiple Sources of Genetic Diversity of Influenza A Viruses during the Hajj.

Cobbin JCA, Alfelali M, Barasheed O, Taylor J, Dwyer DE, Kok J, Booy R, Holmes EC, Rashid H; Hajj Research Team.

J Virol. 2017 May 12;91(11). pii: e00096-17. doi: 10.1128/JVI.00096-17. Print 2017 Jun 1.


Neanderthal behaviour, diet, and disease inferred from ancient DNA in dental calculus.

Weyrich LS, Duchene S, Soubrier J, Arriola L, Llamas B, Breen J, Morris AG, Alt KW, Caramelli D, Dresely V, Farrell M, Farrer AG, Francken M, Gully N, Haak W, Hardy K, Harvati K, Held P, Holmes EC, Kaidonis J, Lalueza-Fox C, de la Rasilla M, Rosas A, Semal P, Soltysiak A, Townsend G, Usai D, Wahl J, Huson DH, Dobney K, Cooper A.

Nature. 2017 Apr 20;544(7650):357-361. doi: 10.1038/nature21674. Epub 2017 Mar 8.


Genomic and phenotypic characterization of myxoma virus from Great Britain reveals multiple evolutionary pathways distinct from those in Australia.

Kerr PJ, Cattadori IM, Rogers MB, Fitch A, Geber A, Liu J, Sim DG, Boag B, Eden JS, Ghedin E, Read AF, Holmes EC.

PLoS Pathog. 2017 Mar 2;13(3):e1006252. doi: 10.1371/journal.ppat.1006252. eCollection 2017 Mar.

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