2020 Publications

Selected publications of CREID investigators

Andersen KG, Rambaut A, Lipkin WI, Holmes EC, Garry RF. 2020. The proximal origin of SARS-CoV-2. Nature Medicine 26:450-452.

Cliff OM, McLean N, Sintchenko V, Fair KM, Sorrell TC, Kauffman S, Prokopenko M. 2020. Inferring evolutionary pathways and directed genotype networks of foodborne pathogens. PLoS Computational Biology 16:10, doi: 10.1371/journal.pcbi.1008401

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, Sintchenko V, Chen SC, Maddocks S, Sorrell TC, Holmes EC, Dwyer DE, Kok J. 2020. An emergent clade of SARS-CoV-2 linked to returned travellers from Iran. Virus Evolution 6: 1, doi: 10.1093/ve/veaa027

French RK, Holmes EC. 2020. An Ecosystems Perspective on Virus Evolution and Emergence. Trends in Microbiology 28:165-175.


Hayward JA, Tachedjian M, Kohl C, ...L, Poumbourios P, Drummer HE, Holmes EC, et al. 2020. Infectious KoRV-related retroviruses circulating in Australian bats. Proceedings of the National Academy of Sciences of the United States of America 117:9529-9536.

Kamruzzaman M, Iredell JR. 2020. CRISPR-Cas System in Antibiotic Resistance Plasmids in Klebsiella pneumoniae. Frontiers in Microbiology 10, doi: 10.3389/fmicb.2019.02934

Khalid A, Lubián AF, Ma L, Lin R, Iredell JR. 2020. Characterizing the role of porin mutations in susceptibility of beta lactamase producing Klebsiella pneumoniae isolates to ceftaroline and ceftaroline-avibactam. International Journal of Infectious Dis 93:252-257.


Lam TTY, Jia N, Zhang YW, … Leung GM, Holmes EC, Hu YL, Guan Y, Cao WC. 2020. Identifying SARS-CoV-2-related coronaviruses in Malayan pangolins. Nature 583:282-285.

Lu R, Zhao X, Li J, Niu P, …Wang D, Xu W, Holmes EC, et al. 2020. Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding. The Lancet 395:565-574.

Marais BJ, Sorrell TC. 2020. Pathways to COVID-19 ‘community protection’. International Journal of Infectious Diseases 96:496-499.


Marcelino V, Holmes EC, Sorrell TC. 2020. The use of taxon-specific reference databases compromises metagenomic classification. BMC Genomics 21:1, doi: 10.1186/s12864-020-6592-2

Marcelino VR, Clausen PTLC, Buchmann JP, Wille M, Iredell JR, Meyer W, Lund O, Sorrell TC, Holmes EC. 2020. CCMetagen: Comprehensive and accurate identification of eukaryotes and prokaryotes in metagenomic data. Genome Biology 21.

Peter Donnelly J, Chen SC and the Mycoses Study Group Education and Research Consortium including Sorrell TC. 2020. Revision and update of the consensus definitions of invasive fungal disease from the European organization for research and treatment of cancer and the mycoses study group education and research consortium. Clinical Infectious Diseases 71:1367-1376.

Petrovic Fabijan A, Lin RCY, Ho J, Maddocks S, Ben Zakour NL, Iredell JR, et al. 2020. Safety of bacteriophage therapy in severe Staphylococcus aureus infection. Nature Microbiology 5:465-472.

Rambaut A, Holmes EC, O’Toole Á, Hill V, McCrone JT, Ruis C, du Plessis L, Pybus OG. 2020. A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nature Microbiology 5:1403-1407.

Rockett RJ, Arnott A, Lam C, Sadsad R, Timms V, Gray KA, Eden JS, Chang S, Gall M, ... Carter I, Basile K, Byun R, O’Sullivan MV, Chen SCA, Maddocks S, Sorrell TC, Dwyer DE, Holmes EC, Kok J, Prokopenko M, Sintchenko V. 2020. Revealing COVID-19 transmission in Australia by SARS-CoV-2 genome sequencing and agent-based modeling. Nature Medicine 26:1398-1404.

Schlub TE, Holmes EC. 2020. Properties and abundance of overlapping genes in viruses. Virus Evolution 6:1, doi: 10.1093/ve/veaa009


Shaban RZ, Nahidi S, Sotomayor-Castillo C, Li C, Gilroy N, O'Sullivan MVN, Sorrell TC, White E, Hackett K, Bag S. 2020. SARS-CoV-2 infection and COVID-19: The lived experience and perceptions of patients in isolation and care in an Australian healthcare setting. American Journal of Infection Control 48:1445-1450.

Venturini C, Ben Zakour NL, Bowring B, Morales S, Cole R, Kovach Z, Branston S, Kettle E, Thomson N, Iredell JR. 2020. Fine capsule variation affects bacteriophage susceptibility in Klebsiella pneumoniae ST258. FASEB Journal 34:10801-10817.

Wu AY, Kamruzzaman M, Iredell JR. 2020. Specialised functions of two common plasmid mediated toxin-Antitoxin systems, ccdAB and pemIK, in Enterobacteriaceae. PLoS ONE 15, 10.1371/journal.pone.0230652

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. 2020. A new coronavirus associated with human respiratory disease in China. Nature 579:265-269.

Zhang YZ, Holmes EC. 2020. A Genomic Perspective on the Origin and Emergence of SARS-CoV-2. Cell 181:223-227.