Research & papers

Inference of epidemic dynamics in the COVID-19 era and beyond

Cori A and Kucharski AJ. Epidemics.

High SARS-CoV-2 incidence and asymptomatic fraction during Delta and Omicron BA.1 waves in The Gambia

Jarju S,..., Kucharski AJ et al. Nature Communications.

Detecting changes in generation and serial intervals under varying pathogen biology, contact patterns and outbreak response

Pung R, ..., Kucharski AJ. PLOS Comp Biol.

Predicting subnational incidence of COVID-19 cases and deaths in EU countries

Robert R,..., Kucharski AJ et al. Virus Evol.

Within-host SARS-CoV-2 viral kinetics informed by complex life course exposures reveals different intrinsic properties of Omicron and Delta variants

Russell T,..., Kucharski AJ. PLOS Biol.

Impact of vaccinations, boosters and lockdowns on COVID-19 waves in French Polynesia

Chapman L,..., Kucharski AJ. Nature Communications.

Real-time surveillance of international SARS-CoV-2 prevalence using systematic traveller arrival screening: an observational study

Kucharski AJ et al. PLOS Medicine.

Quantifying the value of viral genomics when inferring who infected whom in the 2014–16 Ebola virus outbreak in Guinea

Robert R,..., Kucharski AJ et al. Virus Evol.

Quantifying the relationship between climatic indicators and leptospirosis incidence in Fiji: A modelling study

Rees E,..., Kucharski AJ et al. PLOS Global Public Health.

Colonization and transmission of Staphylococcus aureus in schools: a citizen science project

Van Tonder AJ,..., Kucharski AJ, Conland AJK. Microb Genom.

Relative role of border restrictions, case finding and contact tracing in controlling SARS-CoV-2 in the presence of undetected transmission: a mathematical modelling study

Pung P,..., Kucharski AJ. BMC Med.

Monitoring Temporal Changes in SARS-CoV-2 Spike Antibody Levels and Variant-Specific Risk for Infection, Dominican Republic, March 2021–August 2022 .

Nilles E,..., Kucharski AJ et al. EID.

Using high-resolution contact networks to evaluate SARS- CoV-2 transmission and control in large-scale multi-day events

Pung R, Firth JA,..., Kucharski AJ. Nature Communications.

Tracking immune correlates of protection for emerging SARS-CoV-2 variants

Nilles E, Paulino CT,..., Kucharski AJ. Lancet Inf Dis.

SARS-CoV-2 antibodies protect against reinfection for at least 6 months in a multicentre seroepidemiological workplace cohort

Finch E, Lowe R,..., Kucharski AJ. PLOS Biol.

SARS-CoV-2 seroprevalence, cumulative infec- tions, and immunity to symptomatic infection – a multistage national household survey and modeling study, Dominican Republic, June–October 2021

Nilles E,..., Kucharski AJ et al. Lancet Regional Health – Americas.

Does repeated influenza vaccination attenuate effectiveness? A systematic review and meta-analysis

Jones-Gray E,..., Kucharski AJ et al. Lancet Resp Med.

Estimating the duration of antibody positivity and likely time of Leptospira infection using data from a cross-sectional serological study in Fiji

Rees E, Lau CL,..., Kucharski AJ. PLOS NTD.

The impact of local vaccine coverage and recent incidence on measles transmission in France between 2009 and 2018

Robert A,..., Kucharski AJ et al. BMC Medicine.

Simulating respiratory disease trans- mission within and between classrooms to assess pandemic management strategies at schools

Endo A,..., Kucharski AJ et al. PNAS.

Sharing, synthesis and sustainability of data analysis for epidemic preparedness in Europe

Kucharski AJ, Hodcroft E, Kramer MUG. Lancet Regional Health Europe.

Serial intervals observed in SARS-CoV-2 B.1.617.2 variant cases

Pung R, Mak TM,..., Kucharski AJ, Lee V. The Lancet.

Estimating the effectiveness of routine asymptomatic PCR testing at different frequencies for the detection of SARS-CoV-2 infections

Hellewell J, Russell TW, Beale R,..., Kucharski AJ. BMC Medicine.

The potential for vaccination-induced herd immunity against the SARS-CoV-2 B.1.1.7 variant

Hodgson D, Flasche S, Jit M, Kucharski AJ. Eurosurveillance.

Within and between classroom trans- mission patterns of seasonal influenza among primary school students in Matsumoto city, Japan

Endo A,..., Kucharski AJ et al. PNAS.

Estimated transmissibility and severity of novel SARS-CoV-2 Variant of Concern 202012/01 in England

Davies NG, Abbott S, Barnard RC, Jarvis CI, Kucharski AJ et al. Science.

Interactions between timing and transmissibility explain diverse flavivirus dynamics in Fiji

Henderson AD, Kama M, Aubry M,..., Kucharski AJ. Nature Communications.

Quarantine and testing strategies in contact tracing for SARS-CoV-2: a modelling study

Quilty BJ, Clifford S, Hellewell J, Russell TW, Kucharski AJ et al. Lancet Public Health.

Implication of backward contact tracing in the presence of overdispersed transmission in COVID-19 outbreaks

Endo A, ..., Funk S, Kucharski AJ. Wellcome Open Research.

Reconstructing the early global dynamics of under-ascertained COVID-19 cases and infections

Russell TW, Golding N, Hellewell J, ..., Kucharski AJ. BMC Medicine.

Using serological data to understand unobserved SARS-CoV-2 risk in health-care settings

Kucharski AJ, Nilles EJ. Lancet Infectious Diseases.

Using a real-world network to model localized COVID-19 control strategies

Firth J, Hellewell J, Klepac P, ..., Kucharski AJ, Spurgin LG. Nature Medicine.

The effectiveness of social bubbles as part of a Covid-19 lockdown exit strategy: a modelling study

Leng T, White C, Hilton J, Kucharski AJ et al. Wellcome Open Research.

Effectiveness of isolation, testing, contact tracing and physical distancing on reducing transmission of SARS-CoV-2 in different settings: a mathematical modelling study

Kucharski AJ, Klepac P, Conlan AJK, Kissler S, Tang M et al. Lancet Infect Dis.

Estimating the time-varying reproduction number of SARS-CoV-2 using national and subnational case counts

Abbott S, Hellewell J, Thompson RN, ..., Kucharski AJ, Eggo RM, Funk S. Wellcome Open Research.

Estimating the overdispersion in COVID-19 transmission using outbreak sizes outside China

Endo A, CMMID COVID-19 Working Group, ..., Kucharski AJ, Funk S. Wellcome Open Research.

The effect of non-pharmaceutical interventions on COVID-19 cases, deaths and demand for hospital services in the UK: a modelling study

Davies NG, Kucharski AJ, Eggo RM et al. Lancet Public Health.

Inferring the number of COVID-19 cases from recently reported deaths

Jombart T, van Zandvoort K, Russell TW, ..., Kucharski AJ, Edmunds WJ. Wellcome Open Research.

Contacts in context: large-scale setting-specific social mixing matrices from the BBC Pandemic project

Klepac P, Kucharski AJ, Conlan AJK, Kissler S, Tang M et al. MedRxiv preprint.

School’s out—balancing childcare needs of key workers with COVID infection control

Flasche S, Proctor S, Emery J, Kucharski AJ, Liu Y et al. BMJ.

Estimating the infection and case fatality ratio for COVID-19 using age-adjusted data from the outbreak on the Diamond Princess cruise ship

Russell TW, Hellewell J, Jarvis C, ..., Kucharski AJ. Eurosurveillance.

The effect of control strategies that reduce social mixing on outcomes of the COVID-19 epidemic in Wuhan, China

Prem K, Liu Yang, Russell TW, Kucharski AJ, Eggo RM et al. Lancet Public Health.

Secondary attack rate and superspreading events for SARS-CoV-2

Liu Y, Eggo RM, Kucharski AJ. The Lancet.

Early dynamics of transmission and control of COVID-19: a mathematical modelling study

Kucharski AJ, Russell TW, Diamond C et al. Lancet Infect Dis.

Feasibility of controlling 2019-nCoV outbreaks by isolation of cases and contacts

Hellewell J, Abbott S, Gimma A, ...., Kucharski AJ et al. Lancet Global Health.

Probabilistic reconstruction of measles transmission clusters from routinely collected surveillance data

Robert A, Kucharski AJ, Gastanaduy PA, Paul P, Funk S. J R Soc Interface (in press).

serosolver: an R package to infer viral epidemiological and immunological dynamics from serological data

Hay J, Minter A, Ainslie K, Lessler J, Kucharski AJ*, Riley S*. PLOS Comp Biol.

Comparison of effectiveness of various live poultry market interventions on the epidemic of human infection with avian influenza A H7N9 virus across five waves

Wang W, Artois J, Wang X, Kucharski AJ, Pei Y et al. Emerg Infect Dis.

Estimated effectiveness of traveller screening to prevent international spread of COVID-19

Gostic K, Gomez ACR, Mummah RO, Kucharski AJ, Lloyd-Smith JO. eLife.

Zika virus seroprevalence declines and neutralizing antibodies wane in adults following outbreaks in French Polynesia and Fiji

Henderson AD*, Aubry M*, Kama M, ..., Cao-Lormeau VM*, Kucharski AJ*. eLife.

Bias correction methods for test-negative designs in the presence of misclassification

Endo A, Funk S, Kucharski AJ. MedRxiv preprint.

Quantifying transmission of emerging zoonoses: Using mathematical models to maximize the value of surveillance data

Ambrose M, Kucharski AJ, Formenty P, Muyembe-Tamfum JJ, Rimoin A et al. BioRxiv preprint.

Fine-scale family structure shapes influenza transmission risk in households: insights from a study of primary school students in Matsumoto city, 2014/15

Endo A, Uchida M, Kucharski AJ, Funk S. PLOS Comput Biol.

Low chikungunya virus seroprevalence two years after emergence in Fiji

Aubry M, Kama K, Henderson AD, ..., Kucharski AJ, Cao-Lormeau VM. International Journal of Infectious Diseases.

The measles crisis in Europe — the need for a joined-up approach

Robert A, Funk S, Kucharski AJ. The Lancet.

Estimating the burden of dengue in Indonesia and the impact of Wolbachia.

O'Reilly K, Hendrickx E, Kharisma D, ..., Kucharski AJ et al. BMC Medicine.

Guiding vaccine efficacy trial design during public health emergencies: an interactive web-based decision support tool

Bellan SE, Eggo RM, Gsell PS, Kucharski AJ, Dean N et al. Vaccine.

Sustained low-level transmission of Zika and chikungunya viruses following emergence in the Fiji Islands

Kama M*, Aubry M*, Naivalu T, ..., Kucharski AJ*, Cao-Lormeau VM*. Emerg Infect Dis.

Determinants of transmission risk during the late stage of the West African Ebola epidemic

Robert A, Edmunds WJ, Watson CH, ..., Kucharski AJ et al. AJE.

Ross River virus antibody prevalence in the Fiji Islands, 2013-2015

Aubry M, Kama K, Vanhomwegen J, ..., Kucharski AJ, Cao-Lormeau VM. Emerg Infect Dis.

Assessing the performance of real-time epidemic forecasts: A case study of Ebola in the Western Area region of Sierra Leone, 2014-15

Funk S, Camacho A, Kucharski AJ, Lowe R, Eggo RM, Edmunds WJ. PLOS Comput Biol.

Real-time analysis of the diphtheria outbreak in forcibly displaced Myanmar nationals in Bangladesh

Finger F, Funk S, White K, Siddiqui R, Edmunds WJ, Kucharski AJ. BMC Medicine.

Projecting the end of the Zika virus epidemic in Latin America: a modelling analysis

O'Reilly K, Lowe R, Edmunds WJ, Mayaud P, Kucharski AJ et al. BMC Medicine.

Timescales of influenza A/H3N2 antibody dynamics

Kucharski AJ, Lessler J, Cummings DATC, Riley S. PLOS Biology.

Using paired serology and surveillance data to quantify dengue transmission and control during a large outbreak in Fiji

Kucharski AJ, Kama M, Watson CH, Aubry M, Funk S et al. eLife.

Identifying human encounters that shape the transmission of streptococcus pneumoniae and other respiratory infections

Le Polain de Waroux O, Flasche S, Kucharski AJ, Langendorf C, Ndazima D, Mwanga-Amumpaire J, Grais R, Cohuet S, Edmunds WJ. Epidemics.

Structure and consistency of self-reported social contact networks in British secondary schools

Kucharski AJ, Wenham C, Brownlee P, Racon L, Widmer N, Eames KTD, Conlan AJK. PLOS ONE.

Characteristics of human encounters and social mixing patterns relevant to infectious diseases spread by close contact: a survey in southwest Uganda

Le Polain de Waroux O, Cohuet S, Ndazima D, Kucharski AJ, Juan-Giner A et al. BMC Infect Dis

High Zika virus seroprevalence in Salvador, Northeastern Brazil limits the potential for further outbreaks

Netto EM, Moreira-Soto A, Pedroso C, Hoser C, Funk S, Kucharski AJ et al. mBio.

Social mixing in Fiji: who-eats-with-whom contact patterns and implications of age and ethnic heterogeneity for disease dynamics in Pacific Islands

Watson CH, Coriakula J, Ngoc DTT, Flasche S, Kucharski AJ et al. PLOS ONE.

Expected duration of adverse pregnancy outcomes following a Zika epidemic

Eggo R, Kucharski AJ. Emerg Infect Dis.

Ring vaccination of adults and children with rVSV-ZEBOV under Expanded Access in response to an outbreak of Ebola virus disease in Guinea, 2016: an operational and vaccine safety report

Gsell PS*, Camacho C*, Kucharski AJ*, Watson CH*, Bagayoko A et al. Lancet Infect Dis.

The RAPIDD Ebola forecasting challenge: synthesis and lessons learnt

Viboud C, Sun K, Gaffey R, Ajelli M, Fumanelli L, Merler S et al. Epidemics.

The role of human immunity and social behavior in shaping influenza evolution

Kucharski AJ and Baguelin M. PLOS Pathogens.

The impact of control strategies and behavioural changes on the elimination of Ebola from Lofa County, Liberia

Funk S, Ciglenecki I, Tiffany A, Gignoux E, Camacho A et al. Phil Trans R Soc B.

Reducing uncertainty about flavivirus infections

Kucharski AJ, Riley S. Lancet Infect Dis.

Real-time dynamic modelling for the design of a cluster-randomized phase 3 Ebola vaccine trial in Sierra Leone

Camacho A, Eggo RM, Goeyvaerts N, Vandebosch A, Mogg R, Funk S, Kucharski AJ, Watson CH, Vangeneugden T, Edmunds WJ. Vaccine.

Comparative analysis of dengue and Zika outbreaks reveals differences by setting and virus

Funk S, Kucharski AJ, Camacho A, Eggo RM, Yakob L, Edmunds WJ. PLOS Negl Trop Dis.

Real-time forecasting of infectious disease dynamics with a stochastic semi-mechanistic model

Funk S, Camacho A, Kucharski AJ, Eggo RM, Edmunds WJ. Epidemics.

Study epidemiology of fake news

Kucharski AJ. Nature.

Modelling the transmission dynamics of online social contagion

Kucharski AJ. ArXiv preprint.

Low risk of a sexually-transmitted Zika virus outbreak

Yakob L, Kucharski AJ, Hué S, Edmunds WJ. Lancet Infect Dis.

Transmission dynamics of Zika virus in island populations: a modelling analysis of the 2013–14 French Polynesia outbreak

Kucharski AJ, Funk S, Eggo RM, Mallet HP, Edmunds WJ, Nilles EJ. PLOS Negl Trop Dis.

The effect of community-based prevention and care on Ebola transmission in Sierra Leone

Pronyk P, Rogers B, Lee S, Bhatnagar A, Wolman Y, Monasch R, Hipgrave D, Salama P, Kucharski AJ, Chopra M, and on behalf of the UNICEF Sierra Leone Ebola Response Team. Am. J. Public Health.

Effectiveness of ring vaccination as control strategy for Ebola virus disease

Kucharski AJ, Eggo RM, Watson CH, Camacho A, Funk S, Edmunds WJ. Emerg Infect Dis.

Estimating the probability of demonstrating vaccine efficacy in the declining Ebola epidemic: a Bayesian modelling approach

Camacho A, Eggo RM, Funk S, Watson CH, Kucharski AJ, Edmunds WJ. BMJ Open.

Duration of Ebola virus RNA persistence in semen of survivors: population-level estimates and projections

Eggo RM, Watson CH, Camacho A, Kucharski AJ, Funk S, Edmunds WJ. Eurosurveillance.

Ebola virus disease in the Democratic Republic of the Congo, 1976-2014

Rosello A, Mossoko M, Flasche S, Van Hoek AJ, Mbala P, Camacho A, Funk S, Kucharski AJ, Illunga BK, Edmunds WJ, Piot P, Baguelin M, Muyembe Tamfum JJ. eLife.

Measuring the impact of Ebola control measures in Sierra Leone

Kucharski AJ, Camacho A, Flasche S, Glover RE, Edmunds WJ, Funk S. Proc Natl Acad Sci.

The role of superspreading in Middle East respiratory syndrome coronavirus (MERS-CoV) transmission

Kucharski AJ and Althaus CL. Eurosurveillance.

School’s Out: Seasonal Variation in the Movement Patterns of School Children

Kucharski AJ, Conlan AJK, Eames KTD. PLOS ONE.

Characterizing the Transmission Potential of Zoonotic Infections from Minor Outbreaks

Kucharski AJ and Edmunds WJ. PLOS Comput Biol.

Transmission Potential of Influenza A(H7N9) Virus, China, 2013–2014

Kucharski AJ*, Mills HL*, Donnelly CA, Riley S. Emerg Infect Dis.

Capturing the dynamics of pathogens with many strains

Kucharski AJ, Andreasen V, Gog JR. J Math Biol.

Estimating the life course of influenza A(H3N2) antibody responses from cross-sectional data

Kucharski AJ, Lessler J, Read JM, Zhu H, Jiang CQ, Guan Y, Cummings DA, Riley S. PLOS Biology.

Effectiveness of traveller screening for emerging pathogens is shaped by epidemiology and natural history of infection

Gostic KM*, Kucharski AJ*, Lloyd-Smith JO. eLife.

Temporal changes in Ebola transmission in Sierra Leone and implications for control requirements: a real-time modelling study

Camacho A, Kucharski AJ, Aki-Sawyerr Y, White MA, Flasche S, Baguelin M, Pollington TM, Carney J, Glover R, Smout E, Tiffany A, Edmunds WJ, Funk S. PLOS Currents Outbreaks.

Evaluation of the Benefits and Risks of Introducing Ebola Community Care Centers, Sierra Leone

Kucharski AJ, Camacho A, Checchi F, Waldman R, Grais RF, Cabrol JC, Briand S, Baguelin M, Flasche S, Funk S, Edmunds WJ. Emerg Infect Dis.

Five challenges in modelling interacting strain dynamics

Wikramaratna P, Kucharski AJ, Gupta S, Andreasen V, McLean AR, Gog JR. Epidemics.

Potential for large outbreaks of Ebola virus disease

Camacho A*, Kucharski AJ*, Funk S, Breban J, Piot P, Edmunds WJ. Epidemics.

Case fatality rate for Ebola virus disease in west Africa

Kucharski AJ and Edmunds WJ. The Lancet.

Cross-immunity and age patterns of influenza A(H5N1) infection

Kucharski AJ and Edmunds WJ. Epidemiology & Infection.

The contribution of social behaviour to the transmission of influenza A in a human population

Kucharski AJ, Kwok KO, Wei VWI, Cowling BJ, Read JM, Lessler J, Cummings DA, Riley S. PLOS Pathogens.

Distinguishing Between Reservoir Exposure and Human-to-Human Transmission for Emerging Pathogens Using Case Onset Data

Kucharski AJ*, Mills HL*, Pinsent A, Fraser C, Van Kerkhove MD, Donnelly CA, Riley S. PLOS Currents Outbreaks.

The role of social contacts and original antigenic sin in shaping the age pattern of immunity to seasonal influenza.

Kucharski AJ and Gog JR. PLOS Comput Biol.

Age profile of immunity to influenza: Effect of original antigenic sin

Kucharski AJ and Gog JR. Theor. Popul. Biol.

Influenza emergence in the face of evolutionary constraints

Kucharski AJ and Gog JR. Proc. R. Soc. B.

*Joint contribution.