Imperial College London


Faculty of MedicineSchool of Public Health

Senior Lecturer in Infectious Disease Modelling



+44 (0)20 7594 3229a.cori




G27Norfolk PlaceSt Mary's Campus





I am a mathematical and statistical modeller at the Medical Research Council (MRC) Centre for Global Infectious Disease Analysis. My research interests lie in developing statistical methods to understand the dynamics of epidemics and inform control policies, using a range of data. I have worked on a variety of infections including MERS, influenza, SARS-CoV-1, HIV, Ebola, and most recently SARS-CoV-2.

I am particularly interested in developing methods that can be used in real time, for a broad range of pathogens, to quickly characterise their transmissibility, detect potential changes in transmission patterns over time and space, and predict possible outbreak trajectories under a range of control measures. I am the author of the R package EpiEstim [1,2], which allows estimating the transmissibility of a pathogen in real time during an outbreak. We used this tool extensively during the 2013-16 West African Ebola epidemic but also in the more recent Ebola outbreaks in DRC and Guinea, to quantify the transmissibility at various points in the outbreak, forecast future incidence, and assess the impact of control measures [3-7]. EpiEstim has become particularly prominent during the COVID-19 pandemic and is being widely used by academics, public health agencies and governments worldwide to monitor SARS-CoV-2 transmission. 

Recent epidemics and the ongoing pandemic have highlighted the need for other tools, to clean outbreak data and analyse it to inform policy in a timely and robust manner [8,9]. I am currently involved in a range of projects trying to address these gaps. One of these projects, mRIIDS, is a collaboration with Dr. Pierre NouvelletProMED, HealthMap and, aiming at developing a tool for real-time mapping of disease transmission risk from one country to another [10].

As many colleagues, my research in the last year has focused primarily on COVID-19. I was involved in early efforts to characterise the magnitude of the epidemic as well as quantifying transmissibility and severity of SARS-CoV-2 [11, 12]. I contributed to work estimating the impact of interventions against COVID-19 [13-15] and examining the issue of nosocomial SARS-CoV-2 transmission [16]. Most recently, I co-led efforts to characterise the epidemic in England, and to assist the design, monitoring and evaluation of the "roadmap out of lockdown" [17,18]. 

Ongoing projects include extensions to EpiEstim and epidemic forecasting approaches with a particular focus on spatial spread of infectious diseases; as well as use of genetic and epidemiological data to better understand and control nosocomial outbreaks. 

[1] Cori et al. A new framework and software to estimate time-varying reproduction numbers during epidemics. AJE 2013

[2] Thompson et al. Improved inference of time-varying reproduction numbers during infectious disease outbreaks, Epidemics 2019

[3] WHOER Team. Ebola Virus Disease in West Africa — The First 9 Months of the Epidemic and Forward Projections. NEJM 2014

[4] WHOER Team. West African Ebola Epidemic after One Year — Slowing but Not Yet under Control. NEJM 2015

[5] WHOER Team. After Ebola in West Africa : unpredictable risks, preventable epidemics. NEJM 2016

[6] WHOER Team. Exposure patterns driving Ebola transmission in West Africa. PLoS Med 2016

[7] EOE Team. Outbreak of Ebola Virus Disease in the Democratic Republic of the Congo, April-May 2018: an epidemiological study. The Lancet 2018

[8] Cori et al. Key data for outbreak evaluation: building on the Ebola experience, Trans. R. Soc. B 2017

[9] Polonsky et al. Outbreak analytics: a developing data science for informing the response to emerging pathogens. Phil Trans R Soc B 2018

[10] Bhatia et al. Using digital surveillance tools for near real-time mapping of the risk of international infectious disease spread: Ebola as a case study. NPJ Digital Medicine 2021

[11] Bhatia et al. Estimating the number of undetected COVID-19 cases among travellers from mainland China. Wellcome Open Research 2020

[12] Verity et al. Estimates of the severity of coronavirus disease 2019: a model-based analysis. Lancet ID 2020

[13] Nouvellet P et al. Reduction in mobility and COVID-19 transmission. Nature communication 2020

[14] Mishra S et al. Comparing the responses of the UK, Sweden and Denmark to COVID-19 using counterfactual modelling Scientific reports 2021

[15] Ragonnet-Cronin M et al. Genetic evidence for the association between COVID-19 epidemic severity and timing of non-pharmaceutical interventions. Nature communication 2021

[16] Abbas M et al. Explosive nosocomial outbreak of SARS-CoV-2 in a rehabilitation clinic: the limits of genomics for outbreak reconstruction. Journal of Hospital Infection 2021

[17] Knock et al. The 2020 SARS-CoV-2 epidemic in England: key epidemiological drivers and impact of interventions. Science Translational Medicine 2021

[18] Sonabend et al. Non-pharmaceutical interventions, vaccination and the Delta variant: epidemiological insights from modelling England's COVID-19 roadmap out of lockdown – a mathematical modelling study. The Lancet 2021

Selected Publications

Journal Articles

Bhatia S, Imai N, Watson OJ, et al., 2023, Lessons from COVID-19 for re-scalable data collection, Lancet Infectious Diseases, Vol:23, ISSN:1473-3099, Pages:E383-E388

Cori A, Lassmann B, Nouvellet P, 2023, Data needs for better surveillance and response to infectious disease threats, Epidemics, Vol:43, ISSN:1755-4365

Imai N, Rawson T, Knock E, et al., 2023, Quantifying the impact of delaying the second COVID-19 vaccine dose in England: a mathematical modelling study, The Lancet Public Health, Vol:8, ISSN:2468-2667, Pages:e174-e183

Wardle J, Bhatia S, Kraemer MUG, et al., 2023, Gaps in mobility data and implications for modelling epidemic spread: a scoping review and simulation study, Epidemics, Vol:42, ISSN:1755-4365, Pages:1-11

Probert WJM, Sauter R, Pickles M, et al., 2022, Projected outcomes of universal testing and treatment in a generalised HIV epidemic in Zambia and South Africa (the HPTN 071 [PopART] trial): a modelling study, The Lancet Hiv, Vol:9, ISSN:2352-3018, Pages:e771-e780

Abbas M, Cori A, Cordey S, et al., 2022, Reconstruction of transmission chains of SARS-CoV-2 amidst multiple outbreaks in a geriatric acute-care hospital: a combined retrospective epidemiological and genomic study, Elife, Vol:11, ISSN:2050-084X

Nash RK, Nouvellet P, Cori A, 2022, Real-time estimation of the epidemic reproduction number: Scoping review of the applications and challenges, Plos Digital Health, Vol:1, ISSN:2767-3170, Pages:e0000052-e0000052

Green WD, Ferguson NM, Cori A, 2022, Inferring the reproduction number using the renewal equation in heterogeneous epidemics, Journal of the Royal Society Interface, Vol:19, ISSN:1742-5662

Sonabend R, Whittles LK, Imai N, et al., 2021, Non-pharmaceutical interventions, vaccination, and the SARS-CoV-2 delta variant in England: a mathematical modelling study, The Lancet, Vol:398, ISSN:0140-6736, Pages:1825-1835

Pickles M, Cori A, Probert WJM, et al., 2021, PopART-IBM, a highly efficient stochastic individual-based simulation model of generalised HIV epidemics developed in the context of the HPTN 071 (PopART) trial, PLOS Computational Biology, Vol:17, ISSN:1553-734X

Knock ES, Whittles LK, Lees JA, et al., 2021, Key epidemiological drivers and impact of interventions in the 2020 SARS-CoV-2 epidemic in England, Science Translational Medicine, Vol:13, ISSN:1946-6234, Pages:1-12

Bhatia S, Lassmann B, Cohn E, et al., 2021, Using digital surveillance tools for near real-time mapping of the risk of infectious disease spread, Npj Digital Medicine, Vol:4, ISSN:2398-6352

Djaafara B, Imai N, Hamblion E, et al., 2020, A quantitative framework for defining the end of an infectious disease outbreak: application to Ebola virus disease, American Journal of Epidemiology, Vol:190, ISSN:0002-9262, Pages:642-651

Thompson R, Stockwin J, van Gaalen R, et al., 2019, Improved inference of time-varying reproduction numbers during infectious disease outbreaks, Epidemics, Vol:29, ISSN:1755-4365, Pages:1-11

Campbell F, Cori A, Ferguson N, et al., 2019, Bayesian inference of transmission chains using timing of symptoms, pathogen genomes and contact data, PLOS Computational Biology, Vol:15, ISSN:1553-734X

Cori A, Nouvellet P, Garske T, et al., 2018, A graph-based evidence synthesis approach to detecting outbreak clusters: An application to dog rabies, PLOS Computational Biology, Vol:14, ISSN:1553-734X

The Ebola Outbreak Epidemiology Team, Bhatia S, Cori A, et al., 2018, Outbreak of Ebola virus disease in the Democratic Republic of the Congo, April–May, 2018: an epidemiological study, The Lancet, Vol:392, ISSN:0140-6736, Pages:213-221

Campbell F, Strang C, Ferguson N, et al., 2018, When are pathogen genome sequences informative of transmission events?, PLOS Pathogens, Vol:14, ISSN:1553-7366

Cori A, Donnelly CA, dorigatti, et al., 2017, Key data for outbreak evaluation: building on the Ebola experience, Philosophical Transactions of the Royal Society B: Biological Sciences, Vol:372, ISSN:1471-2970

International Ebola Response Team, Agua-Agum J, Ariyarajah A, et al., 2016, Exposure patterns driving Ebola transmissions in West Africa: a retrospective observational study, PLOS Medicine, Vol:13, ISSN:1549-1277

Heffernan A, Barber E, Thomas R, et al., 2016, Impact and Cost-Effectiveness of Point-Of-Care CD4 Testing on the HIV Epidemic in South Africa., PLOS One, Vol:11, ISSN:1932-6203

Cori A, Pickles M, van Sighem A, et al., 2015, CD4+ cell dynamics in untreated HIV-1 infection: overall rates, and effects of age, viral load, sex and calendar time., AIDS, Vol:29, ISSN:0269-9370, Pages:2435-2446

O'Reilly KM, cori A, Durry E, et al., 2015, A new method to estimate the coverage of mass vaccination campaigns against poliomyelitis from surveillance data., American Journal of Epidemiology, Vol:182, ISSN:1476-6256, Pages:961-970

Bezemer D, Cori A, Ratmann O, et al., 2015, Dispersion of the HIV-1 Epidemic in Men Who Have Sex with Men in the Netherlands: A Combined Mathematical Model and Phylogenetic Analysis., PLOS Medicine, Vol:12, ISSN:1549-1277, Pages:e1001898-e1001898

Agua-Agum J, Ariyarajah A, Aylward B, et al., 2015, West African Ebola epidemic after one year - slowing but not yet under control, New England Journal of Medicine, Vol:372, ISSN:1533-4406, Pages:584-587

Dye C, 2015, Goal-Directed Resuscitation in Septic Shock, New England Journal of Medicine, Vol:372, ISSN:0028-4793, Pages:189-189

WHO Ebola Response Team, 2014, Ebola virus disease in West Africa — The first 9 months of the epidemic and forward projections, New England Journal of Medicine, Vol:371, ISSN:0028-4793, Pages:1481-1495

Jombart T, Cori A, Didelot X, et al., 2014, Bayesian Reconstruction of Disease Outbreaks by Combining Epidemiologic and Genomic Data, PLOS Computational Biology, Vol:10, ISSN:1553-734X

Cori A, Ayles H, Beyers N, et al., 2014, HPTN 071 (PopART): A Cluster-Randomized Trial of the Population Impact of an HIV Combination Prevention Intervention Including Universal Testing and Treatment: Mathematical Model, PLOS One, Vol:9, ISSN:1932-6203

Cori A, Ferguson NM, Fraser C, et al., 2013, A New Framework and Software to Estimate Time-Varying Reproduction Numbers During Epidemics, American Journal of Epidemiology, Vol:178, ISSN:0002-9262, Pages:1505-1512

Cori A, Valleron AJ, Carrat F, et al., 2012, Estimating influenza latency and infectious period durations using viral excretion data, Epidemics, Vol:4, ISSN:1755-4365, Pages:132-138

Boelle P-Y, Ansart S, Cori A, et al., 2011, Transmission parameters of the A/H1N1 (2009) influenza virus pandemic: a review, Influenza and Other Respiratory Viruses, Vol:5, ISSN:1750-2640, Pages:306-316

Valleron A-J, Cori A, Valtat S, et al., 2010, Transmissibility and geographic spread of the 1889 influenza pandemic, Proceedings of the National Academy of Sciences of the United States of America, Vol:107, ISSN:0027-8424, Pages:8778-8781

Cori A, Boelle P-Y, Thomas G, et al., 2009, Temporal Variability and Social Heterogeneity in Disease Transmission: The Case of SARS in Hong Kong, PLOS Computational Biology, Vol:5, ISSN:1553-734X


Cori A, Kamvar ZN, Stockwin J, et al., 2020, mrc-ide/EpiEstim: 2.2-3, v.2.2-3

Cori A, Kamvar ZN, Stockwin J, et al., 2019, annecori/EpiEstim: EpiEstim Cran 2.2-1, v.2.2-0


Dorigatti I, Okell L, Cori A, et al., 2020, Report 4: Severity of 2019-novel coronavirus (nCoV)

Imai N, Cori A, Dorigatti I, et al., 2020, Report 3: Transmissibility of 2019-nCoV

Imai N, Dorigatti I, Cori A, et al., 2020, Report 2: Estimating the potential total number of novel Coronavirus cases in Wuhan City, China

Imai N, Dorigatti I, Cori A, et al., 2020, Report 1: Estimating the potential total number of novel Coronavirus cases in Wuhan City, China

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