New software based on statistical probability principles is helping forecast our flu season, and could also identify the level of threat of a bioterrorist attack. A forecasting tool that uses data routinely collected by state health departments could be used to forecast disease in the event of a bioterrorist attack or new influenza pandemic. EpiFX,…
Guernier V, Diefenbach-Elstob T, Pelowa D, Pollard S, Burgess G, McBryde E and Warner J (2018) Molecular diagnosis of suspected tuberculosis from archived smear slides from the Balimo region, Papua New Guinea. International Journal of Infectious Diseases, 67. pp. 75-81.
Indigenous Australian household structure: a simple data collection tool and implications for close contact transmission of communicable diseases. Thiripura Vino 1 , Gurmeet R. Singh 2,3 , Belinda Davison 2 , Patricia T. Campbell 4,5 , Michael J. Lydeamore 4,5 , Andrew Robinson 1,6,7 , Jodie McVernon 5 , Steven Y.C. Tong 2,8 and Nicholas Geard9,10 . PeerJ October 2017 5:e3958; DOI 10.7717/peerj.3958
Inference of epidemiological parameters from household stratified data. James N. Walker, Joshua V. Ross, Andrew J. Black. PLOS One October 2017. https://doi.org/10.1371/journal.pone.0185910
The Impact of Antimalarial Use on the Emergence and Transmission of Plasmodium falciparum Resistance: A Scoping Review of Mathematical Models . Aleisha R. Brock1, Carole A. Gibbs2, Joshua V. Ross 3 and Adrian Esterman 4,5 Trop. Med. Infect. Dis. 2017, 2(4), 54; doi:10.3390/tropicalmed2040054
Who’s holding the baby? A prospective diary study of the contact patterns of mothers with an infant. Patricia Therese Campbell, Jodie McVernon, Niraj Shrestha, Paula M. Nathan and Nicholas Geard. BMC Infectious Diseases September 2017. https://doi.org/10.1186/s12879-017-2735-8.
Hybrid Markov chain models of S–I–R disease dynamics. Nicholas P. Rebuli, N.G.Beanm J.V.Ross. Journal of Mathematical Biology September 2017, Volume 75 Issue 3, pp 52. https://doi.org/10.1186/s12879-017-2735-8.
Vaccine efficacy against Indonesian Highly Pathogenic Avian Influenza H5N1: systematic review and meta-analysis. Villanueva-Cabezas JP, Coppo MJC, Durr PA, McVernon J. Vaccine September 2017 DOI: 10.1016/j.vaccine.2017.07.059
Predicting the Risk of Biological Invasions Using Environmental Similarity and Transport Network Connectedness. Robert C. Cope, Joshua V. Ross, Talia A. Wittmann, Michael J. Watts, Phillip Cassey. Risk Analysis Aug 2017. DOI: 10.1111/risa.12870.
The Mechanisms for Within-Host Influenza Virus Control Affect Model-Based Assessment and Prediction of Antiviral Treatment. Pengxing Cao 1 , James McCaw 1,2,3,*. Viruses 2017, 9(8), 197; doi:10.3390/v9080197
The Mechanisms for Within-Host Influenza Virus Control Affect Model-Based Assessment and Prediction of Antiviral Treatment. Pengxing Cao 1 and James M. McCaw 1,2,3 .Viruses 2017, 9(8), 197; doi:10.3390/v9080197
A mechanistic model quantifies artemisinin-induced parasite growth retardation in blood-stage Plasmodium falciparum infection. Pengxing Caoa, Nectarios Klonisb, Sophie Zaloumisc, David S. Khouryd, Deborah Cromerd, Miles P. Davenportd, Leann Tilleyb, Julie A. Simpsonc, James M. McCaw a, c, e,. https://doi.org/10.1016/j.jtbi.2017.07.017
Influenza as a trigger for cardiovascular disease: An investigation of serotype, subtype and geographic location. D.C.Pearce ab, J.M.McCaw acd, J.McVernon ac , J.D.Mathews a. Environmental Research Volume 156 July 2017, pages 688-696. https://doi.org/10.1016/j.envres.2017.04.024
Modelling the impact of antimalarial quality on the transmission of sulfadoxine-pyrimethamine resistance in Plasmodium falciparum. Aleisha R.Brock a , Joshua V. Ross b , Scott Greenhalgh c , David P.Durham d , Alison Galvani d , Sunil Parikh e , Adrian Esterman f g . Infectious Disease Modelling 2 (2017) 161e187. https://doi.org/10.1016/j.idm.2017.04.001
Determining best strategies for maternally-targeted pertussis vaccination using an individual based model. Campbell PT, McVernon J, Geard N. American Journal of Epidemiology 186 (1):109-117. https://doi.org/10.1093/aje/kwx002.
Is Australia prepared for the next pandemic? Jodie McVernon, Tania C Sorrell, Jenny Firman, Brendan Murphy and Sharon R Lewin. Med J Aust 2017; 206 (7): 284-286. || doi: 10.5694/mja16.01451
High rates of latent tuberculosis infection in contacts and the wider community in South India. P Narasimhan, CR MacIntyre, D Mathai, JG Wood. Transactions of the Royal Society of Tropical Medicine and Hygiene (accepted, Feb 2017).
Measuring Transitions in Sexual Risk Among Men Who Have Sex With Men: The Novel Use of Latent Class and Latent Transition Analysis in HIV Sentinel Surveillance. Wilkinson AL, El-Hayek C, Fairley CK, Roth N, Tee BK, McBryde E, Hellard M, Stoové M. Am J Epidemiol (2017) 185 (8): 627-635, Mar 10:1-9. doi: 10.1093/aje/kww239.
Wilkinson et al. Respond to “Latent Transition Analyses in Clinical Cohorts”. Wilkinson AL, El-Hayek C, Fairley CK, Roth N, Tee BK, McBryde E, Hellard M, Stoové M. Am J Epidemiol. 2017 Mar 10:1-2. doi: 10.1093/aje/kww238.
Treatment outcomes in patients with multidrug-resistant tuberculosis in north-west Ethiopia. Kefyalew Addis Alene, Kerri Viney, Emma S. McBryde, Adino Tesfahun Tsegaye, Archie C. A. Clements. Tropical Medicine and International Health. First published: 6 January 2017. Volume 22, Issue 3 March 2017, pages 351–362. doi: 10.1111/tmi.12826
Mycobacteria-specific IL-1RA response as a potential correlate of treatment success in active and latent tuberculosis infection. Vanessa Clifford, Marc Tebruegge, Christel Zufferey, Susie Germano, Ben Forbes, Lucy Cosentino, Elizabeth Matchett, Emma McBryde, Damon Eisen, Roy Robins-Browne, Alan Street, Justin Denholm, Nigel Curtis. Pathology 49 (Feb 2017): S59.
Spatial patterns of multidrug resistant tuberculosis and relationships to socio-economic, demographic and household factors in northwest Ethiopia. Kefyalew Addis Alene , Kerri Viney, Emma S. McBryde, Archie C. A. Clements.Published: February 9, doi.org/10.1371/journal.pone.0171800
The risk of global epidemic replacement with drug-resistant Mycobacterium tuberculosis strains. Emma S. McBryde, Michael T. Meehan, Tan N. Doan, Romain Ragonnet, Ben J. Marais, Vanina Guernier, James M. Trauer. International Journal of Infectious Diseases Vol 56, P 14-20. doi: http://dx.doi.org/10.1016/j.ijid.2017.01.031
Andrew J. Blacka , Nicholas Geardb, c, James M. McCawb, d, e, Jodie McVernonb, e, f, Joshua V. Rossa . Characterising pandemic severity and transmissibility from data collected during first few hundred studies. | Epidemics, 19th January 2017 doi: 10.3389/fimmu.2016.00611.
Model selection for seasonal influenza forecasting. Zarebski AE, Dawson P, McCaw JM, Moss R, Infectious Disease Modelling. (accepted 16 December 2016) doi.org/10.1016/j.idm.2016.12.004
High rates of multidrug-resistant and rifampicin-resistant tuberculosis among re-treatment cases: where do they come from? Romain Ragonnet, James M. Trauer, Justin T. Denholm, Ben J. Marais and Emma S. McBryde. BMC Infectious Diseases:36, doi: 10.1186/s12879-016-2171-1 Published: 6 January 2017
Is IPT more effective in high-burden settings? Modelling the effect of tuberculosis incidence on IPT impact. Ragonnet, R, Trauer J, McBryde E, Houben R. M. G. J, Denholm, J, Handel A, Sumner, T. The International Journal of Tuberculosis and Lung Disease, Volume 21, Nr 1, 1 January 2017, pp. 60-66(7). doi:10.5588/ijtld.16.0297
Heterogeneity of distribution of tuberculosis in Sheka Zone, Ethiopia: drivers and temporal trends. Shaweno, D, Shaweno, T, Trauer J.M, Denholm J, McBryde, E. The International Journal of Tuberculosis and Lung Disease, Volume 21, Number 1, 1 January 2017, pp. 79-85(7)
Pengxing Cao1, Zhongfang Wang 2, 3, Ada W. Yan1, Jodie McVernon 4, 6, Jianqing Xu2, Jane M. Heffernan5, Katherine Kedzierska3 and James M. McCaw1, 4, 6*,
On the role of CD8+ T cells in determining recovery time from influenza virus infection. Front. Immunol. | doi: 10.3389/fimmu.2016.00611.
Cost-effectiveness and resource implications of aggressive action on tuberculosis in China, India, and South Africa: a combined analysis of nine models. Nicolas A Menzies, Gabriela B Gomez, , Emma S McBryde, James M Trauer, et al. The Lancet Global Health Volume 4, Issue 11, November 2016, Pages e816–e826. doi.org/10.1016/S2214-109X(16)30265-0
Jodie McVernon, Pursuit:WORLD-CHANGING RESEARCH MADE POSSIBLE BY MELBOURNE, 18 November 2016.
Modelling the effect of short-course multidrug-resistant tuberculosis treatment in Karakalpakstan, Uzbekistan. James M. Trauer, Jay Achar, Nargiza Parpieva, Atadjan Khamraev, Justin T. Denholm, Dennis Falzon, Ernesto Jaramillo, Anita Mesic, Philipp du Cros and Emma S. McBryde BMC Medicine2016 14:187. doi: 10.1186/s12916-016-0723-2. Published: 18 November 2016
Patricia Therese Campbell1,2, Jodie McVernon1,2,3, Peter McIntyre4, and Nicholas Geard1,Influence of Population Demography and Immunization History on the Impact of an Antenatal Pertussis Program. Clinical Infectious Diseases Volume 63, Issue suppl 4Pp. S213-S220, doi: 10.1093/cid/ciw520.
Ada W. C. Yana , Pengxing Caoa , Jane M. Heffernan b,c, Jodie McVernond,e,f, Kylie M. Quinn g,h, Nicole L. La Grutag,h, Karen L. Laurie i,j,g, James M. McCaw a,e,f.Modelling cross-reactivity and memory in the cellular adaptive immune response to influenza infection in the host. Journal of Theoretical Biology. Accepted 2016 Nov 8.
Furuya-Kanamori L1, Riley TV2,3, Paterson DL4, Foster NF2,3, Huber CA4, Hong S2, Harris-Brown T4, Robson J5, Clements AC6. A comparison of Clostridium difficile ribotypes circulating in Australian hospitals and communities. J Clin Microbiol 2016; Epub ahead of print. doi:10.1128/JCM.01779-16
The impact of active surveillance and health education on an Ebola virus disease cluster – Kono District, Sierra Leone, 2014-2015. Stehling-Ariza T, Wood JG, Manso D et. al. BMC Infectious Diseases, Oct 2016(1). doi:10.1186/s12879-016-1941-0
A data-driven model for influenza transmission incorporating media effects. Mitchell L, Ross JV. 2016 A R. Soc. open sci.3: 160481..doi.org/10.1098/rsos.160481
Robert Moss,1 James M. McCaw,1,2,3 Allen C. Cheng,4,5 Aeron C. Hurt,6 and Jodie McVernon1,3.Reducing disease burden in an influenza pandemic by targeted delivery of neuraminidase inhibitors: mathematical models in the Australian context.Published online 2016 Oct 10, BMC Infectious Diseases.doi:10.1186/s12879-016-1866-7
Feasibility of achieving the 2025 WHO global tuberculosis targets in South Africa, China, and India: a combined analysis of 11 mathematical models. Rein M G J Houben, Nicolas A Menzies, Tom Sumner, Grace H Huynh, Nimalan Arinaminpathy, Jeremy D Goldhaber-Fiebert, James M Trauer, Justin T Denholm, Emma S McBryde, Anna Vassall, Richard G White, et al. Lancet Glob Health 2016;4: e806–15 Published Online October 6, 2016. doi.org/10.1016/ S2214-109X(16)30199-1
R. MOSS (a1), A. ZAREBSKI (a2), P. DAWSON (a3) and J. M. McCAW (a1) (a2) (a4).Retrospective forecasting of the 2010–2014 Melbourne influenza seasons using multiple surveillance systems. Epidemiology and Infection, 145(1), 156-169. doi:10.1017/S0950268816002053. Published online: 27 September 2016
Robert Moss, Roslyn I. Hickson, Jodie McVernon, James M. McCaw, Krishna Hort, Jim Black, John R. Madden, Nhi H. Tran, Emma S. McBryde, Nicholas Geard. Model-Informed Risk Assessment and Decision Making for an Emerging Infectious Disease in the Asia-Pacific Region. PLOS Neglected Tropical Diseases. 2016 Sep 23;DOI:10.1371/journal.pntd.0005018
Furuya-Kanamori L, Yakob L, Riley TV, Paterson DL, Baker P, McKenzie SJ, Robson J, Clements AC. Community-acquired Clostridium difficile infections in Queensland, Australia. Emerg Infect Dis 2016; 22(9):1659-61.DOI: http://dx.doi.org/10.3201/eid2209.151115
Furuya-Kanamori L1, Clements AC2, Foster NF3, Huber CA4, Hong S5, Harris-Brown T4, Yakob L6, Paterson DL4, Riley TV3.Asymptomatic Clostridium difficile colonisation in two Australian tertiary hospitals, 2012-2014: A prospective, repeated cross-sectional study. Clin Microb Infect 2016. doi: 10.1016/j.cmi.2016.08.030
Problematic Dichotomization of Risk for Intensive Care Unit (ICU)–Acquired Invasive Candidiasis: Results Using a Risk-Predictive Model to Categorize 3 Levels of Risk From a Multicenter Prospective Cohort of Australian ICU Patients. E. Geoffrey Playford Jeffrey Lipman Michael Jones Anna F. Lau Masrura Kabir Sharon C.-A. Chen Deborah J. Marriott Ian Seppelt Thomas Gottlieb Winston Cheung Jonathan R. Iredell Emma S. McBryde, Tania C. Sorrell. Clin Infect Dis (2016) 63 (11): 1463-1469. doi.org/10.1093/cid/ciw610 .Published: 06 September 2016
This guide is intended as an introduction to interpreting the results of mathematical modelling studies in epidemiology. Such studies are increasingly used to support decision-making related to immunisation policy and the control of vaccine preventable diseases. The guide is designed to be read either in full or on a section by section basis, with these sections closely relating to the ordering of material in published modelling papers. Where it has been essential to use more technical terms to convey a precise message, these have been italicized to indicate inclusion in the attached glossary found on pages 24-26 of this document.
The guidance has been kept fairly general as we could not cover the large variety of specific details that appear in the literature. References for further reading are provided at the end of the document.
Tiffany Leung a, Barry D. Hughes a, Federico Frascoli b, James M. McCaw a, c, d,Periodic solutions in an SIRWS model with immune boosting and cross-immunity. Journal of Theoretical Biology 410, December 2016, 55-64.http://dx.doi.org/10.1016/j.jtbi.2016.08.034
McBride WJH, Abhayaratna WP, Barr I, Booy R, Carapetis J, Carson S, De Looze F, Ellis-Pegler R, Heron L, Karrasch J, Marshall H, McVernon J, Nolan T, Rawlinson W, Reid J, Richmond P, Shakib S, Basser RL, Hartel GF, Lai MH, Rockman S, Greenberg ME. Efficacy of a trivalent influenza vaccine against seasonal strains and against 2009 pandemic H1N1: a randomized placebo-controlled trial. Vaccine 34 (2016) 4991–4997. http://dx.doi.org/10.1016/j.vaccine.2016.08.038.
Managing the risk of wildlife disease introduction: pathway-level biosecurity for preventing the introduction of alien ranaviruses. Pablo García-Díaz, Joshua V. Ross, Andrew P. Woolnough, Phillip Cassey. Vol54, Issue 1 Feb 2017 P 234–241. First published: 9 August 2016. doi: 10.1111/1365-2664.12749
Yang T, Xie SC, Cao P, Giannangelo C, McCaw J, Creek DJ, Charman SA, Klonis N, Tilley L. Comparison of the Exposure Time Dependence of the Activities of Synthetic Ozonide Antimalarials and Dihydroartemisinin against K13 Wild-Type and Mutant Plasmodium falciparum Strains. Antimicrobial Agents and Chemotherapy. 2016 Jul 22;60(8):4501-10.2016 Aug; 60(8): 4501–4510. DOI:10.1128/AAC.00574-16
The Zika outbreak, arriving on the heels of Ebola and just in time for the Rio Olympics, has challenged global health agencies to respond rapidly and effectively. Determining the appropriate response is far from straightforward, though, as there is much we don’t yet know about the Zika virus.
A pair of papers published recently in the journal Science have reviewed current evidence about the spread and control of Zika. These studies use mathematical models to help understand how the virus may spread.
Read the full article here.
Millions of people suffer each year from infectious diseases which are responsible for about a quarter of all deaths worldwide. But tracking the cause of such illness and trying to avoid their spread is always a challenge.
Read the full article here.
Quinones-Parra S, Clemens B, Wang Z, Croom H, Kedzierski L, McVernon J, Vijaykrishna D, Kedzierska K. A role of influenza exposure history in determining pandemic susceptibility and CD8+ T cell responses. Journal of Virology, August 2016 vol. 90 no. 15 6936-6947. doi:10.1128/JVI.00349-16 Abstract Novel influenza viruses often cause differential infection patterns across different age groups, an effect…
Alexandra B. Hogan a, Robert S. Anderssen b, Stephanie Davis a, Hannah C. Moore c, Faye J. Lim c, Parveen Fathima c, Kathryn Glass a.Time series analysis of RSV and bronchiolitis seasonality in temperate and tropical Western Australia. Epidemics 16 (2016) 49–55. http://dx.doi.org/10.1016/j.epidem.2016.05.001 Abstract Respiratory syncytial virus (RSV) causes respiratory illness in young children and is…
The Potential Impact of a Hepatitis C Vaccine for People Who Inject Drugs: Is a Vaccine Needed in the Age of Direct-Acting Antivirals? Jack Stone , Natasha K. Martin, Matthew Hickman, Margaret Hellard, Nick Scott, Emma McBryde, Heidi Drummer, Peter Vickerman. PLOS one.Published: May 25, 2016. http://dx.doi.org/10.1371/journal.pone.0156213
On the efficient determination of optimal Bayesian experimental designs using ABC: A case study in optimal observation of epidemics. David J. Price, Nigel G. Bean, Joshua V. Ross, Jonathan Tuke. Journal of Statistical Planning and Inference.Vol 172, May 2016, Pages 1–15. doi.org/10.1016/j.jspi.2015.12.008
Scenario Analysis for Programmatic Tuberculosis Control in Western Province, Papua New Guinea. James M. Trauer Justin T. Denholm Saba Waseem, Romain Ragonnet, Emma S. McBryde. Am J Epidemiol (2016) 183 (12): 1138-1148. doi.org/10.1093/aje/kwv323. Published: 19 May 2016
Alexandra B. Hogan , Kathryn Glass, Hannah C. Moore, Robert S. Anderssen. Exploring the dynamics of respiratory syncytial virus (RSV) transmission in children. Theoretical Population Biology, May 2016. doi:10.1016/j.tpb.2016.04.003
Feasibiliy of Recruiting People who Inject Drugs into a Nurse-Led Model of Care Trial: The Tap Study. S. von Bibra, J.S. Doyle, P. Higgs, P. Dietze, P. Desmond, M. Stoove, E. McBryde, L. Burke, J. Lupi, M. Bryant, A.J. Thompson, M.E. Hellard. Journal of Hepatology Vol 64-2. doi: 10.1016/S0168-8278(16)01598-1
Hepatic Fibrosis Measured by Elastography among People who Inject Drugs with Chronic HCV in Community Settings: The Tap Study. J.S. Doyle, P. Dietze, P. Desmond, D.M. Iser, M. Stoove, E. McBryde, P. Higgs, M.E. Hellard, A.J. Thompson. 16 April 2016: Viral hepatitis: Hepatitis C – Clinical (therapy). Journal of Hepatology, 2016 Vol 64-2. doi: 10.1016/S0168-8278(16)01526-9
Treatment scale-up to achieve global HCV incidence and mortality elimination targets: a cost-effectiveness model. Nick Scott, Emma S McBryde, Alexander Thompson, Joseph S Doyle, Margaret E Hellard. BMJ Journal.doi.org/10.1136/gutjnl-2016-311504
Ndii MZ, Allingham D, Hickson RI, Glass K. (2016) The effect of Wolbachia on dengue dynamics in the presence of two serotypes of dengue: symmetric and asymmetric epidemiological characteristics. Epidemiology & Infection March2016. doi:10.1017/S0950268816000753
Komadina N, Quinones-Parra SM, Kedzierska K, McCaw JM, Kelso A, Leder K, McVernon J. High conservation level of CD8+ T cell immunogenic regions within an unusual H1N2 human influenza variant. Journal Med Virol Mar 2016. DOI: 10.1002/jmv.24516
The probability of epidemic fade-out is non-monotonic in transmission rate for the Markovian SIR model with demography. P.G. Ballard, N.G. Bean, J.V. Ross. Journal of Theoretical Biology. Volume 393, 2016, Pages 170–178 doi/10.1016/j.jtbi.2016.01.012
Ballard, P.G., Bean, N.G. and Ross, J.V. (2016) The probability of epidemic fade-out is non-monotonic in transmission rate for the Markovian SIR model with demography. Journal of Theoretical Biology 393, 170-178. doi:10.1016/j.jtbi.2016.01.012
McKinley, T.J., Ross, J.V., Deardon, R. and Cook, A.R. (2014) Simulation-based Bayesian inference for epidemic models. Computational Statistics and Data Analysis 71, 434-447. doi:10.1016/j.csda.2012.12.012
Furuya-Kanamori L, Doi SA, Paterson DL, Helms SK, Yakob L, McKenzie SJ, Garborg K, Emanuelsson F, Stollman N, Kronman MP, Clark J, Huber CA, Riley TV, Clements AC. Upper versus lower-gastrointestinal delivery for transplantation of fecal microbiota in recurrent or refractory Clostridium difficile infection – A collaborative analysis of individual patient data from 14 studies. J Clin Gastroenterol 2016; Epub ahead of print.DOI:10.1097/MCG.0000000000000511
Lokuge K, Caleo G, Greig J, Duncombe J, McWilliam N, Squire J, Lamin M, Wolz A, Kobinger G,de la Vega M-A, Gbabai O, Nabieu S, Lamin M, Kremer R, Danis K, Banks E, Glass K. (2016) Successful control of Ebola Virus Disease: analysis of service based data from rural Sierra Leone. Plos Neglected Tropical Diseases 10(3):e0004498. doi: 10.1371/journal.pntd.0004498
Dirmesropian S; Wood JG; MacIntyre CR; Beutels P; Newall AT, 2016, ‘Economic Evaluation of Vaccination Programmes in Older Adults and the Elderly: Important Issues and Challenges.’,PharmacoEconomics, http://dx.doi.org/10.1007/s40273-016-0393-0
Choice of Antiviral Allocation Scheme for Pandemic Influenza Depends on Strain Transmissibility, Delivery Delay and Stockpile Size. Lydeamore, M., Bean, N., Black, A.J., Ross J.V. Bull Math Biol (2016) 78: 293. doi:10.1007/s11538-016-0144-6
Risk of Active Tuberculosis in the Five Years Following Infection . . . 15%? James M. Trauer, Nompilo Moyo, Ee-Laine Tay, Katie Dale, Romain Ragonnet, Emma S. McBryde, Justin T. Denholm. Chest. 2016;149(2):516-525. doi:10.1016/j.chest.2015.11.017
Doan TN, Kong DC, Marshall C, Kirkpatrick CM, McBryde ES. Modeling the impact of interventions against Acinetobacter baumannii transmission in intensive care units. Virulence.2015:112. doi:10.1080/21505594.2015.1076615
Lydeamore, M., Bean, N., Black, A.J. and Ross, J.V. (2016) Choice of antiviral allocation scheme for pandemic influenza depends on strain transmissibility, delivery delay and stockpile size. Bulletin of Mathematical Biology 78, 293-321. DOI 10.1007/s11538-016-0144-6
Bowen AC, Harris T, Holt DC, Giffard PM, Carapetis JR, Campbell PT, McVernon J, Tong SYC. Whole genomesequencing reveals extensive community-level transmission of Group AStreptococcus in remote communities. Epidemiol Infect.doi.org/10.1017/S095026881500326X
Cope, R.C., Ross, J.V., Wittmann, T.A. and Cassey, P. (2016) Integrative analysis of the physical transport network into Australia. PLOS ONE 11, e0148831. http://dx.doi.org/10.1371/journal.pone.0148831
, , , . Forecasting inﬂuenza outbreak dynamics in Melbourne from Internet search query surveillance data. Influenza and other respiratory viruses 7 MAR 2016. DOI:10.1111/irv.12376
Wilkinson AL, El-Hayek C, Spelman T, Fairley CK, Leslie D, McBryde ES, et al. A ‘test and treat’ prevention strategy in Australia requires innovative HIV testing models: a cohort study of repeat testing among ‘high-risk’ men who have sex with men. Sex Transm Infect. 2016. doi:10.1136/sextrans-2015-052421
Newall AT, Reyes JF, McIntyre P., Menzies R, Beutels P, & Wood, JG (2016). Retrospective economic evaluation of childhood 7-valent pneumococcal conjugate vaccination in Australia: Uncertain herd impact on pneumonia critical. Vaccine, 34(3), 320-327. doi:10.1016/j.vaccine.2015.11.053
Yan AWC, Cao P, McCaw JM, On the extinction probability in models of within-host infection: the role of latency and immunity, Journal of Mathematical Biology 9 Jan 2016 doi:10.1007/s00285-015-0961-5
Furuya-Kanamori L, Wangdi K, Yakob L, McKenzie SJ, Doi SA, Clark J, Paterson DL, Riley TV, Clements AC. 25-Hydroxyvitamin D concentrations and Clostridium difficile infection – A meta-analysis. JPEN Parenter Enter 2015; Epub ahead of print.DOI:10.1177/0148607115623457
Quinn KM, Zaloumis SG, Cukalac T, Kan W-T, Sng X, Mirams M, Watson K, McCaw JM, Doherty PC, Thomas PG, Handel A, La Gruta NL, Heightened self-reactivity associated with selective survival, but not expansion, of naïve virus-specific CD8+ T cells in aged mice, PNAS January 19, 2016, doi: 10.1073/pnas.1525167113
Fielding JE, Kelly HA, Glass K (2015) Transmission of the first influenza A(H1N1)pdm09 pandemic wave in Australia was driven by undetected infections: pandemic response implications. PLoS One 10(12): e0144331.http://dx.doi.org/10.1371/journal.pone.0144331
Arden KE, Beatson SA, Lambert SB, Wang CYT, McVernon J, Nissen MD, Nolan T, Sloots TP, Mackay IM. Deep sequence characterization of a divergent HPIV-4a from an adult with prolonged influenza-like illness. Virology Reports, 2015 February 18. doi:10.1016/j.virep.2015.02.001
Scott N, McBryde E, Kirwan A, Stoove M. Modelling the Impact of Condom Distribution on the Incidence and Prevalence of Sexually Transmitted Infections in an Adult Male Prison System. PLoS One. 2015;10(12):e0144869. DOI: 10.1371/journal.pone.0144869
The recent outbreak of chickenpox in a Melbourne primary school is a reminder that even in a country like Australia where immunisation rates are high, children and adults are still at risk of vaccine-preventable diseases.
Outbreaks such as this one occur from time to time for two main reasons. Read the full article here.
Geard N, Glass K, McCaw JM, McBryde E, Korb, K, Keeling MJ, McVernon J (2015) The effects of demographic change on disease transmission and vaccine impact in a household structured population. Epidemics, 13:56-64. doi:10.1016/j.epidem.2015.08.002
Furuya-Kanamori L, Marquess J, Yakob L, Riley TV, Paterson DL, Foster NF, Huber C, Clements AC. Asymptomatic Clostridium difficile colonization – Epidemiology and Clinical Implications. BMC Infect Dis2015; 15:516.DOI:10.1186/s12879-015-1258-4
Regan DG, Wood JG, Benevent C. et. al. (2016). Estimating the critical immunity threshold for preventing hepatitis A outbreaks in men who have sex with men. Epidemiology and Infection. 144(7):1528-37.http://dx.doi.org/10.1017/S0950268815002605
Fondation Merieux webcast 2015. Pertussis modeling: contributions of natural and vaccines immunity on the epidemiology. http://www.fondation-merieux.org/pertussis-biology-epidemiology-and-prevention-2015-webcasts
Rolls DA, Wang P, McBryde E, Pattison P, Robins G. A Simulation Study Comparing Epidemic Dynamics on Exponential Random Graph and Edge-Triangle Configuration Type Contact Network Models. PLoS One. 2015;10(11):e0142181. DOI: 10.1371/journal.pone.0142181
Rolls D, Geard N, Warr DJ, Nathan PM, Robins GL, Pattison PE, McCaw JM, McVernon J (2015) Social encounter profiles of greater Melbourne residents, by location – a telephone survey.BMC Infectious Diseases, 15:494. doi:10.1186/s12879-015-1237-9
Patricia Campbell, James McCaw, Peter McIntyre , Jodie McVernon. Defining long-term drivers of pertussis resurgence, and optimal vaccine control strategies. Vaccine, 19 September 2015. doi:10.1016/j.vaccine.2015.09.025
Ragonnet R, Trauer JM, Denholm JT, Geard N, Hellard M, McBryde ES (2015) Vaccination programs for endemic infections: modelling real versus apparent impacts of vaccine and infection characteristics. Scientific Reports, 15:15468. doi:10.1038/srep15468
Perrett, K.P., McVernon, J., Richmond, P.C., Marshall, H., Nissen, M., August, A., Percell, S., Toneatto, D., Nolan, T.: Immune responses to a recombinant, four-component, meningococcal serogroup B vaccine (4CMenB) in adolescents: a phase III, randomized, multicentre, lot-to-lot consistency study.Vaccine, 2015; 33(39):5217-24. doi:10.1016/j.vaccine.2015.06.103
Ross, J.V. and Black, A.J. (2015) Contact tracing and antiviral prophylaxis in the early stages of a pandemic: The probability of a major outbreak. Mathematical Medicine and Biology 32, 331-343. doi: 10.1093/imammb/dqu014
Wilkinson AL, El-Hayek C, Spelman T, Fairley C, Leslie D, McBryde E, et al. “Seek, Test, Treat” Lessons From Australia: A Study of HIV Testing Patterns From a Cohort of Men Who Have Sex With Men. J Acquir Immune Defic Syndr. 2015;69(4):460-5. doi: 10.1097/QAI.0000000000000613.
Sharmin S, Viennet E, Glass K, Harley D. (2015) The emergence and decline of dengue in Bangladesh: Epidemiology, challenges, and future disease risk. Trans. Roy. Soc. Trop. Med. Hyg. 109(10):619-627. doi: 10.1093/trstmh/trv067
Scott N, Hellard M, McBryde E. Modelling hepatitis C virus transmission among people who inject drugs: assumptions, limitations and future challenges. Virulence. 2015. doi:10.1080/21505594.2015.1085151
Cao P, Yan AWC, Heffernan JM, Petrie S, Moss RG, Carolan LA, Guarnaccia TA, Kelso A, Barr IG, McVernon J, Laurie KL, McCaw JM, Innate immunity and the inter-exposure interval determine the dynamics of secondary influenza virus infection and explain observed viral hierarchies, PLoS Computational Biology 11(8): e1004334 (2015). doi:10.1371/journal.pcbi.1004334.
We humans have an innate tendency to recognise patterns. This ability has helped us survive by learning important skills such as how to distinguish danger (predators and poisonous plants, for instance) from important resources (food sources and safe shelter) and knowing the right time of year to plant crops.
But the same ability can sometimes convince us we’re seeing a meaningful pattern when it isn’t there.
Read the full article here.
Brown CR, McCaw JM, Fairmaid EJ, Brown LE, Leder K, Sinclair M, McVernon J, Factors associated with transmission of influenza-like illness in a cohort of households containing multiple children, Influenza Other Respi Viruses 9(5): 247-254 (2015). doi:10.1111/irv.12331.
Scott N, McBryde E, Vickerman P, Martin NK, Stone J, Drummer H, et al. The role of a hepatitis C virus vaccine: modelling the benefits alongside direct-acting antiviral treatments. BMC medicine. 2015;13(1):198. DOI: 10.1186/s12916-015-0440-2
Yakob L., Riley T.V., Paterson D.L., Marquess J., Soares Magalhaes R., Furuya Kanamori L.,Clements A.C.A. (2015) Modelled mechanisms of hypervirulent Clostridium difficile ribotype 027 displacement of endemic strains. Scientific Reports. 5:12666. doi: 10.1038/srep12666
Bean, N.G., Elliott, R.J., Eshragh, A. and Ross, J.V. On binomial observations of continuous-time Markovian population models. Journal of Applied Probability 52, 457-472. doi:10.1239/jap/1437658609
Petrie SM, Butler J, Bar IG, McVernon J, Hurt AC, McCaw JM, Quantifying relative within-host replication fitness in influenza virus competition experiments, Journal of Theoretical Biology 382: 259-271 (2015). doi:10.1016/j.jtbi.2015.07.003
Sharmin S, Glass K, Viennet E, Harley D. (2015) Interaction of mean temperature and daily fluctuation influences dengue incidence in Dhaka, Bangladesh. PLOS Neglected Tropical Diseases 9(7):e0003901.http://dx.doi.org/10.1371/journal.pntd.0003901
Viruses have been described as “organisms at the edge of life”, unable to reproduce outside the cells of those they infect. But this status has not impeded their evolutionary success. Children, in particular, experience a multitude of viral illnesses during their early years, which gradually reduce over time as their natural immunity develops.
Viral infections may be fleeting (think influenza) or chronic (HIV, for instance), affecting various parts of the body to cause a diverse array of symptoms. These differences have important implications for the spread of that particular viral disease.
Read full article here.
Doan TN, Kong DC, Marshall C, Kirkpatrick CM, McBryde ES. Characterising the Transmission Dynamics of Acinetobacter baumannii in Intensive Care Units Using Hidden Markov Models. PLoS One. 2015;10(7):e0132037. DOI: 10.1371/journal.pone.0132037
Keeling, M.J. and Ross, J.V. (2015) Optimal prophylactic vaccination in segregated populations: When can we improve on the equalising strategy? Epidemics 11, 7-13.doi:10.1016/j.epidem.2015.01.002
Laurie KL, Guarnaccia TA, Carolan LA, Yan AWC, Aban M, Petrie S, Cao P, Heffernan JM, McVernon J, Mosse J, Kelso A, McCaw JM, Barr IG, The time-interval between infections and viral hierarchies are determinants of viral interference following influenza virus infection in a ferret model, Journal of Infectious Diseases (accepted 24th March 2015). doi:10.1093/infdis/jiv260
Wood JG; Goeyvaerts N; Raina MacIntyre C; Menzies RI; McIntyre PB; Hens N, 2015. Estimating vaccine coverage from serial trivariate serologic data in the presence of waning immunity. Epidemiology. vol. 26, no. 3, pp. 381 – 389, http://dx.doi.org/10.1097/eDe.0000000000000278
Hellard M, McBryde E, Sacks Davis R, Rolls DA, Higgs P, Aitken C, et al. Hepatitis C transmission and treatment as prevention – The role of the injecting network. Int J Drug Policy. 2015. doi.org/10.1016/j.drugpo.2015.05.006
Dirmesropian S; Wood JG; Macintyre CR; Newall AT, 2015, ‘A review of economic evaluations of 13-valent pneumococcal conjugate vaccine (PCV13) in adults and the elderly‘, Human Vaccines and Immunotherapeutics, vol. 11, no. 4, pp. 818 – 825, http://dx.doi.org/10.1080/21645515.2015.1011954
Dogovski C, Xie SC, Burgio G, Bridgford J, Mok S, McCaw JM, Chotivanich K, Kenny S, Gnadig N, Straimer J, Bozdech Z, Fidock DA, Simpson JA, Dondorp AM, Foote S, Klonis N, Tilley L, Targeting the cell stress response of plasmodium falciparum to overcome artemisinin resistance, PLoS Biology 13(4): e1002132 (2015). doi:10.1371/journal.pbio.1002132
Korostil, I. A., Wood, J. G., & Regan, D. G. (2015). Periodicity of varicella-zoster virus in the presence of immune boosting and clinical reinfection with varicella. Theoretical Biology and Medical Modelling, 12(1).DOI: 10.1186/s12976-015-0002-5
Bolton KJ, McCaw JM, Brown L, Jackson D, Kedzierska K, McVernon J, Prior population immunity reduces the expected impact of CTL-inducing vaccines for pandemic influenza control, PLoS ONE 10(3): e0120138 (2015). doi:10.1371/journal.pone.0120138
Perrett K, Richmond P, Borrow R, Nolan T, McVernon J. Antibody persistence in Australian adolescents following meningococcal C conjugate vaccination. Pediatric Infect Dis J 2015; 34(3):279-85. doi: 10.1097/INF.0000000000000541
Furuya-Kanamori L., McKenzie S.J., Yakob L., Clark J., Paterson D.L., Riley T.V., Clements A.C. (2015) Clostridium difficile infection seasonality: Patterns across hemispheres and continents. PLoS One. doi: 10.1371/journal.pone.0120730
Davey, H. M., Muscatello, D. J., Wood, J. G., Snelling, T. L., Ferson, M. J., & Macartney, K. K. (2015). Impact of high coverage of monovalent human rotavirus vaccine on Emergency Department presentations for rotavirus gastroenteritis. Vaccine, 33(14), 1726-1730. doi: 10.1016/j.vaccine.2015.01.082
Wood, J. G., Heywood, A. E., Menzies, R. I., McIntyre, P. B., & MacIntyre, C. R. (2015). Predicting localised measles outbreak potential in Australia. Vaccine, 33(9), 1176-1181. doi: 10.1016/j.vaccine.2014.12.071
Doan, Tan N, Kong, David, Kirkpatrick, Carl MJ, McBryde, Emma S. Optimizing Hospital Infection Control: The Role of Mathematical Modeling. Infection Control & Hospital Epidemiology / Volume 35 / Issue 12 / December 2014, pp 1521-1530. dx.doi.org/10.1086/678596
Ali H, Cameron E, Drovandi CC, McCaw JM, Guy RJ, Middleton M, El -Hayek C, Hocking JS, Kaldor JM, Donovan B, Wilson DP, on behalf of the Australian chlamydia incidence estimation group, A new approach to estimating trends in chlamydia incidence,Sexually Transmitted InfectionsSexually Transmitted Infections 91: 513-519 (2015).doi:10.1136/sextrans-2014-051631
Furuya-Kanamori L., Stone J.C., Clark J., McKenzie S.J., Yakob L., Paterson D.L., Riley T.V., Doi S.A.R., Clements A.C. (2015) Comorbidities, exposure to medications and the risk of community-acquired Clostridium difficile infection – A systematic review and meta-analysis. Infection Control and Hospital Epidemiology. 36:132–141. doi: 10.1017/ice.2014.39
Cope, R.C., Cassey, P., Hugo, G.J. and Ross, J.V. (2014) Assessment of the Risk of Ebola Importation to Australia. PLoS Curents Outbreaks 2014 Dec 10. Edition 1. doi:10.1371/currents.outbreaks.aa0375fd48a92c7c9422aa543a88711f.
Sacks-Davis R, McBryde E, Grebely J, Hellard M, Vickerman P. Many hepatitis C reinfections that spontaneously clear may be undetected: Markov-chain Monte Carlo analysis of observational study data. J R Soc Interface. 2015;12(104):20141197. doi: 10.1098/rsif.2014.1197.
Dafilis MP, Frascoli F, McVernon J, Heffernan JM, McCaw JM, The dynamical consequences of seasonal forcing, immune boosting and demographic change in a model of disease transmission, J Theor Biol 361: 124-132 (2014). doi:10.1016/j.jtbi.2014.07.028
Hellard, Margaret; Rolls, David A; Sacks-Davis, Rachel; Robins, Garry; Pattison, Philippa; Higgs, Peter; Aitken, Campbell; McBryde, Emma; The impact of injecting networks on hepatitis C transmission and treatment in people who inject drugs, Hepatology Vol 60, 1861-1870 (2014).
Black, A.J., House, T., Keeling, M.J. and Ross, J.V. (2014) The effect of clumped population structure on the variability of spreading dynamics. Journal of Theoretical Biology359, 45-53. doi:10.1016/j.jtbi.2014.05.042
Trauer JM, Denholm JT, McBryde ES. Construction of a mathematical model for tuberculosis transmission in highly endemic regions of the Asia-pacific. J Theor Biol. 2014;358(7 October 2014):74–84. doi:10.1016/j.jtbi.2014.05.023
Dafilis MP, Frascoli F, McVernon J, Heffernan JM, McCaw JM, Dynamical crises, multistability and the influence of the duration of immunity in a seasonally-forced model of disease transmission, Theoretical Biology and Medical Modelling 11:43 (2014). doi:10.1186/1742-4682-11-43
Begun M; Newall AT; Marks GB; Wood JG, 2015, ‘Revisiting Styblo’s law: Could mathematical models aid in estimating incidence from prevalence data?‘, Epidemiology and Infection, vol. 143, no. 7, pp. 1556 – 1565, http://dx.doi.org/10.1017/S0950268814002428
Gao, Z., Wood, J. G., Gidding, H. F., Newall, A. T., Menzies, R. I., Wang, H., . . . MacIntyre, C. R. (2015). Control of varicella in the post-vaccination era in Australia: A model-based assessment of catch-up and infant vaccination strategies for the future. Epidemiology and Infection, 143(7), 1467-1476. http://dx.doi.org/10.1017/S0950268814002222
Johnston, S.T., Simpson, M.J., McElwain, D.L.S., Binder, B.J. and Ross, J.V. (2014)Interpreting scratch assays using pair density dynamics and approximate Bayesian computation. Open Biology 4: 140097. DOI: 10.1098/rsob.140097
Simpson JA, Zaloumis S, DelIvera AM, Price RN, McCaw JM, Making the most of clinical data: reviewing the role of pharmacokinetic-pharmacodynamic models of anti-malarial drugs, AAPS Journal 16(5): 962-974 (2014) doi: 10.1208/s12248-014-9647-y
Davies, K.J., Green, J.E.F., Bean, N.G., Binder, B.J. and Ross, J.V. (2014) On the derivation of approximations to cellular automata models and the assumption of independence. Mathematical Biosciences 253, 63-71.doi:10.1016/j.mbs.2014.04.004
Gardner LM; Rey D; Heywood AE; Toms R; Wood J; Travis Waller S; Raina MacIntyre C, 2014, ‘A scenario-based evaluation of the Middle East respiratory syndrome coronavirus and the Hajj’, Risk Analysis: an international journal, vol. 34, no. 8, pp. 1391 – 1400, http://dx.doi.org/10.1111/risa.12253
Furuya-Kanamori L., Robson J., Soares Magalhaes R.J., Yakob L., McKenzie S., Paterson D.L., Riley T.V., Clements A.C. (2014) A population-based spatio-temporal analysis of Clostridium difficile infection in Queensland, Australia over a 10-year period. Journal of Infection. 69:447–455. doi:10.1016/j.jinf.2014.06.014
Moore HC, Jacoby P, Hogan AB, Blyth CC, Mercer GN (2014) Modelling the seasonal epidemics of respiratory syncytial virus in young children.(2014) PLOS One 9(6):e100422.
Yakob L., Riley T.V., Paterson D.L., Marquess J., Clements A.C.A.(2014) Assessing control bundles for Clostridium difficile: a review and mathematical model. Emerging Microbes and Infections. doi: 10.1038/emi.2014.43
Ross, J.V. and Binder, B.J. (2014) Approximating spatially-exclusive invasion processes.Physical Review E 89, 052709. http://dx.doi.org/10.1103/PhysRevE.89.052709
Thomas EG, McCaw JM, Kelly H, Grant K, McVernon J, Quantifying differences in the epidemic curves from three influenza surveillance systems: a nonlinear regression analysis, Epidemiology and Infection 43(2): 427-439 (2015). doi:10.1017/S0950268814000764
McVernon J,Laurie K, Faddy H, Irving D, Nolan T, Barr I, Kelso A, Seroprevalence of antibody to influenza A(H1N1)pdm09 attributed to vaccination or infection, before and after the second (2010) pandemic wave in Australia, Influenza Other Resp Vir 8(2): 194-200 (2014). doi:10.1111/irv.12225
Hellard, Margaret, Doyle, Joseph S, Sacks-Davis, Rachel, Thompson, Alexander J,McBryde, Emma. Eradication of hepatitis C infection: the importance of targeting people who inject drugs. Hepatology 2014 Vol 59 nr 2. 366-369, DOI: 10.1002/hep.26623
Chiew M; Gidding HF; Dey A; Wood J; Martin N; Davis S; McIntyre P, 2014, ‘Estimating the measles effective reproduction number in Australia from routine notification data.’, Bulletin of the World Health Organization, vol. 92, no. 3, pp. 171 – 177, http://dx.doi.org/10.2471/BLT.13.125724
Newall, A. T., Reyes, J. F., Wood, J. G., Beutels, P., McIntyre, P., & Menzies, R. (2014). Economic evaluations of implemented vaccination programmes: key methodological challenges in retrospective analyses. Vaccine. 32(7):759-65. doi: 10.1016/j.vaccine.2013.11.067
Fielding JE, Kelly HA, Mercer GN, Glass K (2014) Systematic review of influenza A (H1N1)pdm09 virus shedding: duration is affected by severity but not age. Influenza and Other Respiratory Viruses DOI: 10.1111/irv.12216.
Yakob L., Riley T.V., Paterson D.L., Clements A.C.A. (2013) Clostridium difficile exposure as an insidious source of infection in healthcare settings: An epidemiologic model. BMC Infectious Diseases. 13:376. doi:10.1186/1471-2334-13-376
Dafilis MP, Frascoli F, Wood JG, McCaw JM, The influence of increasing life expectancy on the dynamics of SIRS systems with immune boosting, Australian New Zealand Industrial and Applied Mathematics Journal 54:50-63 (2012). doi:10.1017/S1446181113000023.
Campbell P, McIntyre P, Quinn H, Hueston L, Gilbert GL, McVernon J, Increased population prevalence of low pertussis toxin antibody levels preceding a record epidemic in Australia. PLoS ONE 7(4): e35874 (2012). doi:10.1371/journal.pone.0035874.