Edward C Holmes

Institutionthe University of Sydney
AddressAustralia
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    Publication Timeline
    COVID-19 publications
    Bar chart showing 37 Covid-19 publications, with a maximum of 5 publications in December 2020
    All Publications
    Bar chart showing 438 publications over 20 distinct years, with a maximum of 32 publications in 2013 and 2018
    These graphs show COVID-19 publications by month since August 2019 and all publications written by authors of COVID-19 publications over the past 30 years.

    To see the data from both graphs as text, click here.
    Publication Field Summary
    This graph shows the number and percent of publications by field. Fields are based on how the National Library of Medicine (NLM) classifies the publications' journals and might not represent the specific topics of the publications. Note that an individual publication can be assigned to more than one field. As a result, the publication counts in this graph might add up to more than the number of publications the person has written. To see the data as text, click here.
    Publication List
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications.
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    PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Neira V, Brito B, Agüero B, Berrios F, Valdés V, Gutierrez A, Ariyama N, Espinoza P, Retamal P, Holmes EC, Gonzalez-Reiche AS, Khan Z, van de Guchte A, Dutta J, Miorin L, Kehrer T, Galarce N, Almonacid LI, Levican J, van Bakel H, García-Sastre A, Medina RA. A household case evidences shorter shedding of SARS-CoV-2 in naturally infected cats compared to their human owners. Emerg Microbes Infect. 2021 Dec; 10(1):376-383. PMID: 33317424.
      Citations: 25     Fields:    Translation:HumansAnimals
    2. Wagner CE, Saad-Roy CM, Morris SE, Baker RE, Mina MJ, Farrar J, Holmes EC, Pybus OG, Graham AL, Emanuel EJ, Levin SA, Metcalf CJE, Grenfell BT. Vaccine nationalism and the dynamics and control of SARS-CoV-2. Science. 2021 09 24; 373(6562):eabj7364. PMID: 34404735.
      Citations: 6     Fields:    Translation:Humans
    3. Telenti A, Arvin A, Corey L, Corti D, Diamond MS, García-Sastre A, Garry RF, Holmes EC, Pang PS, Virgin HW. After the pandemic: perspectives on the future trajectory of COVID-19. Nature. 2021 08; 596(7873):495-504. PMID: 34237771.
      Citations: 7     Fields:    Translation:HumansAnimalsPHPublic Health
    4. Citations: 24     Fields:    Translation:Humans
    5. Zhou H, Ji J, Chen X, Bi Y, Li J, Wang Q, Hu T, Song H, Zhao R, Chen Y, Cui M, Zhang Y, Hughes AC, Holmes EC, Shi W. Identification of novel bat coronaviruses sheds light on the evolutionary origins of SARS-CoV-2 and related viruses. Cell. 2021 08 19; 184(17):4380-4391.e14. PMID: 34147139.
      Citations: 32     Fields:    Translation:HumansAnimalsCells
    6. Chappell JG, Tsoleridis T, Clark G, Berry L, Holmes N, Moore C, Carlile M, Sang F, Debebe BJ, Wright V, Irving WL, Thomson BJ, Boswell TCJ, Willingham I, Joseph A, Smith W, Khakh M, Fleming VM, Lister MM, Howson-Wells HC, Holmes EC, Loose MW, Ball JK, McClure CP. Retrospective screening of routine respiratory samples revealed undetected community transmission and missed intervention opportunities for SARS-CoV-2 in the United Kingdom. J Gen Virol. 2021 06; 102(6). PMID: 34130773.
      Citations: 3     Fields:    Translation:HumansPHPublic Health
    7. O'Toole Á, Hill V, Pybus OG, Watts A, Bogoch II, Khan K, Messina JP, Tegally H, Lessells RR, Giandhari J, Pillay S, Tumedi KA, Nyepetsi G, Kebabonye M, Matsheka M, Mine M, Tokajian S, Hassan H, Salloum T, Merhi G, Koweyes J, Geoghegan JL, de Ligt J, Ren X, Storey M, Freed NE, Pattabiraman C, Prasad P, Desai AS, Vasanthapuram R, Schulz TF, Steinbrück L, Stadler T, Parisi A, Bianco A, García de Viedma D, Buenestado-Serrano S, Borges V, Isidro J, Duarte S, Gomes JP, Zuckerman NS, Mandelboim M, Mor O, Seemann T, Arnott A, Draper J, Gall M, Rawlinson W, Deveson I, Schlebusch S, McMahon J, Leong L, Lim CK, Chironna M, Loconsole D, Bal A, Josset L, Holmes E, St George K, Lasek-Nesselquist E, Sikkema RS, et al. Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2. Wellcome Open Res. 2021; 6:121. PMID: 34095513.
      Citations: 25     
    8. Geoghegan JL, Douglas J, Ren X, Storey M, Hadfield J, Silander OK, Freed NE, Jelley L, Jefferies S, Sherwood J, Paine S, Huang S, Sporle A, Baker MG, Murdoch DR, Drummond AJ, Welch D, Simpson CR, French N, Holmes EC, de Ligt J. Use of Genomics to Track Coronavirus Disease Outbreaks, New Zealand. Emerg Infect Dis. 2021 05; 27(5):1317-1322. PMID: 33900175.
      Citations: 6     Fields:    Translation:HumansPHPublic Health
    9. Di Giallonardo F, Puglia I, Curini V, Cammà C, Mangone I, Calistri P, Cobbin JCA, Holmes EC, Lorusso A. Emergence and Spread of SARS-CoV-2 Lineages B.1.1.7 and P.1 in Italy. Viruses. 2021 04 29; 13(5). PMID: 33946747.
      Citations: 12     Fields:    Translation:HumansPHPublic Health
    10. Saad-Roy CM, Morris SE, Metcalf CJE, Mina MJ, Baker RE, Farrar J, Holmes EC, Pybus OG, Graham AL, Levin SA, Grenfell BT, Wagner CE. Partial immunity and SARS-CoV-2 mutations-Response. Science. 2021 04 23; 372(6540):354-355. PMID: 33888633.
      Citations: 2     Fields:    Translation:Humans
    11. Yang R, Peng J, Zhai J, Xiao K, Zhang X, Li X, Chen X, Chen ZJ, Holmes EC, Irwin DM, Shan F, Shen X, Chen W, Shen Y. Pathogenicity and transmissibility of a novel respirovirus isolated from a Malayan pangolin. J Gen Virol. 2021 04; 102(4). PMID: 33843572.
      Citations:    Fields:    Translation:AnimalsCells
    12. Hu T, Li J, Zhou H, Li C, Holmes EC, Shi W. Bioinformatics resources for SARS-CoV-2 discovery and surveillance. Brief Bioinform. 2021 03 22; 22(2):631-641. PMID: 33416890.
      Citations: 3     Fields:    Translation:HumansPHPublic Health
    13. Saad-Roy CM, Morris SE, Metcalf CJE, Mina MJ, Baker RE, Farrar J, Holmes EC, Pybus OG, Graham AL, Levin SA, Grenfell BT, Wagner CE. Epidemiological and evolutionary considerations of SARS-CoV-2 vaccine dosing regimes. Science. 2021 04 23; 372(6540):363-370. PMID: 33688062.
      Citations: 29     Fields:    Translation:HumansPHPublic Health
    14. Rambaut A, Holmes EC, O'Toole Á, Hill V, McCrone JT, Ruis C, du Plessis L, Pybus OG. Addendum: A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nat Microbiol. 2021 03; 6(3):415. PMID: 33514928.
      Citations: 19     Fields:    Translation:Humans
    15. Swadi T, Geoghegan JL, Devine T, McElnay C, Sherwood J, Shoemack P, Ren X, Storey M, Jefferies S, Smit E, Hadfield J, Kenny A, Jelley L, Sporle A, McNeill A, Reynolds GE, Mouldey K, Lowe L, Sonder G, Drummond AJ, Huang S, Welch D, Holmes EC, French N, Simpson CR, de Ligt J. Genomic Evidence of In-Flight Transmission of SARS-CoV-2 Despite Predeparture Testing. Emerg Infect Dis. 2021 03; 27(3):687-693. PMID: 33400642.
      Citations: 15     Fields:    Translation:HumansPHPublic Health
    16. Di Giallonardo F, Duchene S, Puglia I, Curini V, Profeta F, Cammà C, Marcacci M, Calistri P, Holmes EC, Lorusso A. Genomic Epidemiology of the First Wave of SARS-CoV-2 in Italy. Viruses. 2020 12 14; 12(12). PMID: 33327566.
      Citations: 10     Fields:    Translation:Humans
    17. Chen YM, Zheng Y, Yu Y, Wang Y, Huang Q, Qian F, Sun L, Song ZG, Chen Z, Feng J, An Y, Yang J, Su Z, Sun S, Dai F, Chen Q, Lu Q, Li P, Ling Y, Yang Z, Tang H, Shi L, Jin L, Holmes EC, Ding C, Zhu TY, Zhang YZ. Blood molecular markers associated with COVID-19 immunopathology and multi-organ damage. EMBO J. 2020 12 15; 39(24):e105896. PMID: 33140861.
      Citations: 16     Fields:    Translation:Humans
    18. Geoghegan JL, Ren X, Storey M, Hadfield J, Jelley L, Jefferies S, Sherwood J, Paine S, Huang S, Douglas J, Mendes FK, Sporle A, Baker MG, Murdoch DR, French N, Simpson CR, Welch D, Drummond AJ, Holmes EC, Duchêne S, de Ligt J. Genomic epidemiology reveals transmission patterns and dynamics of SARS-CoV-2 in Aotearoa New Zealand. Nat Commun. 2020 12 11; 11(1):6351. PMID: 33311501.
      Citations: 34     Fields:    Translation:HumansPHPublic Health
    19. Zhou H, Li C, Hu T, Liu T, Ni N, Chen W, Zhao H, Ruan S, Li J, Wu H, François S, Pybus OG, Holmes EC, Kang D, Hou P, Shi W. Total infectomes of 162 SARS-CoV-2 cases using meta-transcriptomic sequencing. J Infect. 2021 Jan; 82(1):e44-e48. PMID: 33307139.
      Citations: 3     Fields:    Translation:HumansAnimalsCells
    20. Xavier J, Giovanetti M, Adelino T, Fonseca V, Barbosa da Costa AV, Ribeiro AA, Felicio KN, Duarte CG, Ferreira Silva MV, Salgado Á, Lima MT, de Jesus R, Fabri A, Soares Zoboli CF, Souza Santos TG, Iani F, Ciccozzi M, Bispo de Filippis AM, Teixeira de Siqueira MAM, de Abreu AL, de Azevedo V, Ramalho DB, Campelo de Albuquerque CF, de Oliveira T, Holmes EC, Lourenço J, Junior Alcantara LC, Assunção Oliveira MA. The ongoing COVID-19 epidemic in Minas Gerais, Brazil: insights from epidemiological data and SARS-CoV-2 whole genome sequencing. Emerg Microbes Infect. 2020 Dec; 9(1):1824-1834. PMID: 32726185.
      Citations: 15     Fields:    Translation:HumansCellsPHPublic Health
    21. Di Teodoro G, Valleriani F, Puglia I, Monaco F, Di Pancrazio C, Luciani M, Krasteva I, Petrini A, Marcacci M, D'Alterio N, Curini V, Iorio M, Migliorati G, Di Domenico M, Morelli D, Calistri P, Savini G, Decaro N, Holmes EC, Lorusso A. SARS-CoV-2 replicates in respiratory ex vivo organ cultures of domestic ruminant species. Vet Microbiol. 2021 Jan; 252:108933. PMID: 33278734.
      Citations: 17     Fields:    Translation:Animals
    22. Wang W, Lin XD, Zhang HL, Wang MR, Guan XQ, Holmes EC, Zhang YZ. Extensive genetic diversity and host range of rodent-borne coronaviruses. Virus Evol. 2020 Jul; 6(2):veaa078. PMID: 33318860.
      Citations: 7     
    23. Zhou H, Chen X, Hu T, Li J, Song H, Liu Y, Wang P, Liu D, Yang J, Holmes EC, Hughes AC, Bi Y, Shi W. A Novel Bat Coronavirus Closely Related to SARS-CoV-2 Contains Natural Insertions at the S1/S2 Cleavage Site of the Spike Protein. Curr Biol. 2020 Oct 05; 30(19):3896. PMID: 33022232.
      Citations: 17     Fields:    
    24. Song ZG, Chen YM, Wu F, Xu L, Wang BF, Shi L, Chen X, Dai FH, She JL, Chen JM, Holmes EC, Zhu TY, Zhang YZ. Identifying the Risk of SARS-CoV-2 Infection and Environmental Monitoring in Airborne Infectious Isolation Rooms (AIIRs). Virol Sin. 2020 Dec; 35(6):785-792. PMID: 32986229.
      Citations: 1     Fields:    Translation:HumansPHPublic Health
    25. Wille M, Holmes EC. Wild birds as reservoirs for diverse and abundant gamma- and deltacoronaviruses. FEMS Microbiol Rev. 2020 09 01; 44(5):631-644. PMID: 32672814.
      Citations: 14     Fields:    Translation:AnimalsCells
    26. Pollock DD, Castoe TA, Perry BW, Lytras S, Wade KJ, Robertson DL, Holmes EC, Boni MF, Kosakovsky Pond SL, Parry R, Carlton EJ, Wood JLN, Pennings PS, Goldstein RA. Viral CpG Deficiency Provides No Evidence That Dogs Were Intermediate Hosts for SARS-CoV-2. Mol Biol Evol. 2020 09 01; 37(9):2706-2710. PMID: 32658964.
      Citations: 7     Fields:    Translation:HumansAnimalsCellsPHPublic Health
    27. Rambaut A, Holmes EC, O'Toole Á, Hill V, McCrone JT, Ruis C, du Plessis L, Pybus OG. A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nat Microbiol. 2020 11; 5(11):1403-1407. PMID: 32669681.
      Citations: 560     Fields:    Translation:HumansCellsPHPublic Health
    28. Rockett RJ, Arnott A, Lam C, Sadsad R, Timms V, Gray KA, Eden JS, Chang S, Gall M, Draper J, Sim EM, Bachmann NL, Carter I, Basile K, Byun R, O'Sullivan MV, O'Sullivan MV, Chen SC, Maddocks S, Sorrell TC, Dwyer DE, Holmes EC, Kok J, Prokopenko M, Sintchenko V. Revealing COVID-19 transmission in Australia by SARS-CoV-2 genome sequencing and agent-based modeling. Nat Med. 2020 09; 26(9):1398-1404. PMID: 32647358.
      Citations: 85     Fields:    Translation:HumansCellsPHPublic Health
    29. Zhou H, Chen X, Hu T, Li J, Song H, Liu Y, Wang P, Liu D, Yang J, Holmes EC, Hughes AC, Bi Y, Shi W. A Novel Bat Coronavirus Closely Related to SARS-CoV-2 Contains Natural Insertions at the S1/S2 Cleavage Site of the Spike Protein. Curr Biol. 2020 06 08; 30(11):2196-2203.e3. PMID: 32416074.
      Citations: 177     Fields:    Translation:AnimalsCells
    30. Eden JS, Rockett R, Carter I, Rahman H, de Ligt J, Hadfield J, Storey M, Ren X, Tulloch R, Basile K, Wells J, Byun R, Gilroy N, O'Sullivan MV, O'Sullivan MV, Sintchenko V, Chen SC, Maddocks S, Sorrell TC, Holmes EC, Dwyer DE, Kok J. An emergent clade of SARS-CoV-2 linked to returned travellers from Iran. Virus Evol. 2020 Jan; 6(1):veaa027. PMID: 32296544.
      Citations: 55     
    31. Grubaugh ND, Petrone ME, Holmes EC. We shouldn't worry when a virus mutates during disease outbreaks. Nat Microbiol. 2020 04; 5(4):529-530. PMID: 32071422.
      Citations: 48     Fields:    Translation:HumansAnimalsCellsPHPublic Health
    32. Andersen KG, Rambaut A, Lipkin WI, Holmes EC, Garry RF. The proximal origin of SARS-CoV-2. Nat Med. 2020 04; 26(4):450-452. PMID: 32284615.
      Citations: 1400     Fields:    Translation:HumansAnimalsCellsPHPublic Health
    33. Wu F, Zhao S, Yu B, Chen YM, Wang W, Song ZG, Hu Y, Tao ZW, Tian JH, Pei YY, Yuan ML, Zhang YL, Dai FH, Liu Y, Wang QM, Zheng JJ, Xu L, Holmes EC, Zhang YZ. Author Correction: A new coronavirus associated with human respiratory disease in China. Nature. 2020 04; 580(7803):E7. PMID: 32296181.
      Citations: 58     Fields:    
    34. Lam TT, Jia N, Zhang YW, Shum MH, Jiang JF, Zhu HC, Tong YG, Shi YX, Ni XB, Liao YS, Li WJ, Jiang BG, Wei W, Yuan TT, Zheng K, Cui XM, Li J, Pei GQ, Qiang X, Cheung WY, Li LF, Sun FF, Qin S, Huang JC, Leung GM, Holmes EC, Hu YL, Guan Y, Cao WC. Identifying SARS-CoV-2-related coronaviruses in Malayan pangolins. Nature. 2020 07; 583(7815):282-285. PMID: 32218527.
      Citations: 575     Fields:    Translation:HumansAnimalsCellsPHPublic Health
    35. Zhang YZ, Holmes EC. A Genomic Perspective on the Origin and Emergence of SARS-CoV-2. Cell. 2020 Apr 16; 181(2):223-227. PMID: 32220310.
      Citations: 261     Fields:    Translation:AnimalsCellsPHPublic Health
    36. Wu F, Zhao S, Yu B, Chen YM, Wang W, Song ZG, Hu Y, Tao ZW, Tian JH, Pei YY, Yuan ML, Zhang YL, Dai FH, Liu Y, Wang QM, Zheng JJ, Xu L, Holmes EC, Zhang YZ. A new coronavirus associated with human respiratory disease in China. Nature. 2020 03; 579(7798):265-269. PMID: 32015508.
      Citations: 3001     Fields:    Translation:HumansCells
    37. Lu R, Zhao X, Li J, Niu P, Yang B, Wu H, Wang W, Song H, Huang B, Zhu N, Bi Y, Ma X, Zhan F, Wang L, Hu T, Zhou H, Hu Z, Zhou W, Zhao L, Chen J, Meng Y, Wang J, Lin Y, Yuan J, Xie Z, Ma J, Liu WJ, Wang D, Xu W, Holmes EC, Gao GF, Wu G, Chen W, Shi W, Tan W. Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding. Lancet. 2020 02 22; 395(10224):565-574. PMID: 32007145.
      Citations: 3751     Fields:    Translation:HumansCells
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