Main GCEID Publications


Alexandersen, S., Chamings, A., Bhatta, T.R.: SARS-CoV-2 genomic and subgenomic RNAs in diagnostic samples are not an indicator of active replication.
Nature Communications 11, 6059, 2020.

Vibin, J., Chamings, A., Klaassen, M., and Alexandersen, S.: Metagenomic characterisation of additional and novel avian viruses from Australian wild ducks.
Scientific Reports 10: 22284, 2020.

Khatami, A., Burrell, R., McMullan, B.J., Rawlinson, W., Givney, R.C., Kok, J., Alexandersen, S., Jones, C.A., Macartney, K.K., Britton, P.N.  Epidemic and inter-epidemic burden of paediatric human parechovirus infection in New South Wales, Australia, 2017-2018. Paediatric  Infectious Diseases Journal. 2020; 39:507-511.  doi:10.1097/INF.0000000000002615

Bhatta, T.R., Ryt-Hansen, P., Nielsen, J.P., Larsen, L.E., Larsen, I., Chamings, A., Goecke, N.B., Alexandersen, S.  Infection Dynamics of swine Influenza Virus in a Danish Pig Herd Reveals Recurrent Infections with Different Variants of the H1N2 Swine Influenza A Virus Subtype. Viruses 2020, 12, 1013.

Vibin, J., Chamings, A., Klaassen, M., Bhatta, T.R., Alexandersen, S. Metagenomic characterisation of avian parvoviruses and picornaviruses from Australian Wild ducks  Scientific Reports  2020; 10, 12800.

Bhatta, T.R., Chamings, A., Vibin, J., Klaassen, M., and Alexandersen, S.: Detection of a reassortant H9N2 avian influenza virus with intercontinental gene segments in a resident Australian Chestnut teal. Viruses 2020; 12: 88.


Chamings, A., Liew,K.C., Reid, E., Athan, E., Raditsis, A., Vuillermin, P., Yoga, Y., Caly, L., Druce, J., and Alexandersen, S.: An emerging human parechovirus type 5 causing sepsis-like illness in infants in Australia. Viruses 2019; 11: 913.

Chamings, A., Druce, J., Caly, L., Yoga, Y., Britton, P.N., Macartney, K.K., Alexandersen, S.  Evolutionary analysis of human parechovirus type 3 and clinical outcomes of infection during the 2017-18 Australian epidemic.  Sci Rep. 2019 Jun 20;9(1):8906. https://doi: 10.1038/s41598-019-45445-z

Bhatta, T., Chamings, A., Vibin, J. and Alexandersen, S. Detection and characterisation of canine astrovirus, canine parvovirus and canine papillomavirus in puppies using next generation sequencing. Sci. Rep. 2019 March; 9:4602. https://doi:10.1038/s41598-019-41045-z.


Simon Coghlan & Benjamin Coghlan.  One Health, Bioethics, and Nonhuman Ethics. The American Journal of Bioethics. 2018, 18:11, 3-5. https://doi:10.1080/15265161.2018.1524224

Vibin, J., Chamings, A., Collier, F., Klaassen, M., Nelson,T.M. and Alexandersen, S. Metagenomics detection and characterisation of viruses in faecal samples from Australian wild birds. Sci. Rep. 2018 June; 8:8686. https://doi:10.1038/s41598-018-26851-1.

Chamings, A., Nelson, T., Vibin, J., Wille, M., Klaassen, M. and Alexandersen, S. Detection and characterisation of coronaviruses in migratory and non-migratory Australian wild birds. Sci. Rep. 2018 April 13; 8:5980. https://doi:10.1038/s41598-018-24407-x.


Anderson H, Vuillermin P, Jachno K, Allen KJ, Tang ML, Collier F, Kemp A, Ponsonby AL, Burgner D; Barwon Infant Study Investigator Group. Prevalence and determinants of antibiotic exposure in infants: A population-derived Australian birth cohort study. J Paediatr Child Health. 2017 Jul 27. https://doi: 10.1111/jpc.13616. PMID: 28749577.

Alexandersen, S., Nelson, T.M., Hodge, J. and Druce, Julian: Evolutionary and network analysis of virus sequences from infants infected with an Australian recombinant strain of human parechovirus type 3. Sci. Rep. 2017 June 20; 7:3861. https://doi:10.1038/s41598-017-04145-2.

Nelson, T.M., Vuillermin,P., Hodge,J., Druce, J. Williams, D.T., Jasrotia, R., and Alexandersen, S.: An outbreak of severe infections among Australian infants caused by a novel recombinant strain of human parechovirus type 3. Sci. Rep. 2017 March 14; 7:44423. https://doi: 10.1038/srep44423.

Nfon, C., Lung, O., Embury-Hyatt, C., and Alexandersen, S.: Clinical Signs and Pathology of Foot-and-Mouth Disease. Page 171-178 Chapter 8 in Foot-and-Mouth Disease Virus: Current Research and Emerging Trends, Editors Francisco Sobrino and Esteban Domingo. Wymondham, Caister Academic Press. January 2017.

The Geelong Centre for Emerging Infectious Diseases (GCEID): Strategic Plan 2017-2021


Xu, W., Berhane, Y., Dubé, C., Liang, B., Pasick, J., VanDomselarr, G., and Alexandersen, S.: Epidemiological and Evolutionary Inference of the Transmission Network of the 2014 Highly Pathogenic Avian Influenza H5N2 Outbreak in British Columbia, Canada. Sci Rep. 2016 Aug 4; 6:3085. https://doi:10.1038/srep30858.


Cowan, R., E. Athan, N. D. Friedman, A. J. Hughes, A. McDonald, P. Callan, J. Fyfe, and D. P. O’Brien. 2015. Mycobacterium ulcerans treatment–can antibiotic duration be reduced in selected patients? PLoS neglected tropical diseases 9.

Florido, M., R. Pillay, C. M. Gillis, Y. Xia, S. J. Turner, J. A. Triccas, J. Stambas, and W. J. Britton. 2015. Epitope-specific cd4(+), but not cd8(+), t-cell responses induced by recombinant influenza a viruses protect against mycobacterium tuberculosis infection. European Journal of Immunology 45:780-793.

Goossens, K. E., A. J. Karpala, A. Rohringer, A. Ward, and A. G. D. Bean. 2015. Characterisation of chicken viperin. Molecular Immunology 63:373-380.

Jacquelyn, H., Zhang, Z., Bittner, H., Hole, K., Singanallur, N.B., Alexandersen, S., and Vosloo, W.: Early protection in sheep against intra-typic heterologous challenge with serotype O foot-and-mouth disease virus using high-potency, emergency vaccine. Vaccine. 33:422-429, 2015.

Kittelberger, R., Nfon, C., Swekla, K., Zhang, Z., Hole, K., Bittner, H., Salo, T., Goolia, M., Embury-Hyatt, C., Bueno, R., Hannah, M., Swainsbury, R., O’Sullivan, C., Spence, R., Clough, R., McFadden, A., Rawdon, T., and Alexandersen, S.: Foot-and-Mouth Disease in Red Deer – Experimental Infection and Test Methods Performance. Transbound. Emerg. Dis. 2015.

Ojkic, D., Hazlett, M., Fairles, J., Marom, A., Slavic, D., Maxie, G., Alexandersen, S., Pasick, J., Alsop, J., Burlatschenko, S.: The first case of porcine epidemic diarrhea in Canada. Can Vet J. 56:149-152, 2015.

Pasick, J., Berhane, Y., Joseph, T., Bowes, V., Hisanaga, T., Handel, K., and Alexandersen. S.: Reassortant Highly Pathogenic Influenza A H5N2 Virus Containing Gene Segments Related to Eurasian H5N8 in British Columbia, Canada, 2014. Sci Rep. 2015 Mar 25;5:9484.

Plowright, R. K., P. Eby, P. J. Hudson, I. L. Smith, D. Westcott, W. L. Bryden, D. Middleton, P. A. Reid, R. A. McFarlane, G. Martin, G. M. Tabor, L. F. Skerratt, D. L. Anderson, G. Crameri, D. Quammen, D. Jordan, P. Freeman, L.-F. Wang, J. H. Epstein, G. A. Marsh, N. Y. Kung, and H. McCallum. 2015. Ecological dynamics of emerging bat virus spillover. Proceedings of the Royal Society B-Biological Sciences 282.

Rogers, B. A., P. R. Ingram, N. Runnegar, M. C. Pitman, J. T. Freeman, E. Athan, S. Havers, H. E. Sidjabat, E. Gunning, M. De Almeida, K. Styles, D. L. Paterson, and C. R. N. Asid. 2015. Sequence type 131fimh30 and fimh41 subclones amongst escherichia coil isolates in australia and new zealand. International Journal of Antimicrobial Agents 45:351-358.

Stuart, R. L., C. Marshall, E. Orr, N. Bennett, E. Athan, D. Friedman, M. Reilly, and Racrig. 2015b. Survey of infection control and antimicrobial stewardship practices in australian residential aged-care facilities. Internal Medicine Journal 45:576-580.

van Dijk, J. G. B., R. A. M. Fouchier, M. Klaassen, and K. D. Matson. 2015. Minor differences in body condition and immune status between avian influenza virus-infected and noninfected mallards: A sign of coevolution? Ecology and Evolution 5:436-449.

Ye, S., S. Lowther, and J. Stambas. 2015. Inhibition of reactive oxygen species production ameliorates inflammation induced by influenza a viruses via upregulation of socs1 and socs3. Journal of Virology 89:2672-2683.


Ching, P. K. G., V. Carr de los Reyes, M. Nemia Sucaldito, E. Tayag, A. Baby Columna-Vingno, F. F. Malbas, Jr., G. C. Bolo, Jr., J. J. Sejvar, D. Eagles, G. Playford, E. Dueger, Y. Kaku, S. Morikawa, M. Kuroda, G. A. Marsh, S. McCullough, and A. R. Foxwell. 2015. Outbreak of henipavirus infection, Philippines, 2014. Emerging Infectious Diseases 21:328-331.