In addition to the listed papers, I am also part of the Centre for Mathematical Modelling of Infectious Diseases COVID-19 Working Group, whose publications are listed here.


[70] Hodgson D, Koltai M, Krauer F, Flasche S, Jit M, Atkins KE (2022) Optimal Respiratory Syncytial Virus intervention programmes using Nirsevimab in England and Wales medRxiv link

[69] Jimenez-Silva C, Rivero R, Douglas J, Bouckaert R, Villabona-Arenas CJ, Atkins KE, Gastelbondo B, Calderon A, Guzman C, Echeverri-De la Hoz D, Muñoz M, Ballesteros N, Castañeda S, H. Patiño L, Ramirez A, Luna N, Paniz-Mondolfi A, Serrano-Coll H, Ramirez JD, Mattar S, Drummond A (2022) Genomic epidemiology of circulating SARS-CoV-2 variants during first two years of the pandemic in Colombia medRxiv link

[68] Atkins KE, Hodgson D, Jit M, Davies NG (2021) Evaluating the impact of RSV immunisation strategies on antibiotic use in England medRxiv link

[67] Baxter JAC, Langhorne S, Shi T, Tully DC, Villabona-Arenas CJ, Hué S, Albert J, Leigh Brown A, Atkins KE (2021) Inferring the multiplicity of founder variants initiating HIV-1 infection: a systematic review and individual patient data meta-analysis medRxiv link


[66] Endo A, CMMID COVID-19 Working Group, Uchida M, Liu Y, Atkins KE, Kucharski AJ, Funk S (2022) Simulating respiratory disease transmission within and between classrooms to assess pandemic management strategies at schools PNAS online here

[65] Villabona-Arenas CJ, Hue S, Baxter J, Hall M, Lythgoe K, Bradley J, Atkins KE (2022) Using phylogenetics to accurately infer HIV-1 transmission direction PNAS online here

[64] Pujol-Hodge E, Salazar-Gonzalez JF, Ssemwanga D, Charlebois ED, Ayieko J, Grant HE, Liegler T, Atkins KE, Kaleebu P, Kamya MR, Petersen M, Havlir DV, Leigh Brown A (2022) Detection of HIV-1 Transmission Clusters from Dried Blood Spots within a Universal Test-and-Treat Trial in East Africa Viruses online here

[63] Banks CJ, Colman E, Doherty T, Tearne O, Arnold M, Atkins KE, Balaz D, Beaunée G, Bessell PR, Enright J, Kleczkowski A, Rossi G, Ruget A-S, Kao RR (2022) SCoVMod – a spatially explicit mobility and deprivation adjusted model of first wave COVID-19 transmission dynamics Wellcome Open Res 7:161 online here

[62] Lindsey BB, Villabona-Arenas CJ, Campbell F, Keeley AJ, Parker MD, Shah DR, Parsons H, Zhang P, Kakkar N, Gallis M, Foulkes BH, Wolverson P, Louka SF, Christou S, State A, Johnson K, Raza M, Hsu S, Jombart T, Cori A, Sheffield COVID-19 Genomics Group, The COVID-19 Genomics UK (COG-UK) consortium, CMMID COVID-19 working group, Evans CM, Partridge DG, Atkins KE(1), Hué S(1), de Silva TI(1) (2022) Characterising within-hospital SARS-CoV-2 transmission events: a retrospective analysis integrating epidemiological and viral genomic data from a UK tertiary care setting across two pandemic waves Nature Communications 13:671 (1) contributed equally online here


[61] Munday JD, Pebody R, Atkins KE, van Hoek AJ (2021) Changing socio-economic and ethnic disparities in Influenza/A/H1N1 infection early in the 2009 UK epidemic: A descriptive analysis BMC Infectious Diseases online here

[60] Endo A, CMMID COVID-19 Working Group, Uchida M, Atkins KE, Kucharski AJ, Funk S (2020) Within and between classroom transmission patterns of seasonal influenza among primary school students in Matsumoto city, Japan Proceedings of the National Academy of Sciences online here

[59] Blassel, Zhukova A, Villabona-Arenas CJ, Atkins KE, Hué S, Gascuel O (2021) Drug Resistance Mutations in HIV: New Bioinformatics Approaches and Challenges Current Opinion in Virology 51:56-64

[58] Davies NJ, Flasche S, Jit M, Atkins KE. Modeling the effect of vaccination on selection for antibiotic resistance in Streptococcus pneumoniae Science Translational Medicine online here

[57] Leclerc Q, Fuller NM, Keogh RH, Diaz-Ordaz K, Sekula R, Semple MG, ISARIC4C Investigators, CMMID COVID-19 Working Group, Atkins KE, Procter SR, Knight GM (2021) Importance of patient bed pathways and length of stay differences in predicting COVID-19 bed occupancy in England. BMC Health Services Research online here

[56] Davies NG, Barnard RC, Jarvis CI, Kucharski AJ, Munday J, Pearson CAB, Russell TW, Tully DC, Abbott S, Gimma A, Waites W, Wong KLM, van Zandvoort K, CMMID COVID-19 Working Group, Eggo RM, Funk S, Jit M, Atkins KE, Edmunds WJ (2021) Estimated transmissibility and severity of novel SARS-CoV-2 Variant of Concern 202012/01 in England Science

[55] Munday JD, Sherratt K, Meakin S, Hellewell J, Abbott S, Bosse NI, CMMID COVID-19 Working Group, Atkins KE, Wallinga J, Edmunds WJ, van Hoek AJ, Funk S (2021) Implications of the school-household network structure on SARS-CoV-2 transmission under different school reopening strategies in England Nature Communications

[54] Wenzel N, Atkins KE, van Leeuwen E, Halloran ME, Baguelin M (2020) Cost-Effectiveness of Live-Attenuated Influenza Vaccination Among School-Age Children. Vaccine


[53] Endo A, LSHTM CMMID COVID-19 Working Group, Leclerc QJ, Knight GM, Medley G, Atkins KE, Funk S, Kucharski AJ (2020) Evaluating the effectiveness of backward contact-tracing to control COVID-19. Wellcome Open Research 5:239

[52] Hodgson D, Panovska-Griffiths J, Pebody R, Baguelin M, Atkins KE (2020) Cost-effectiveness of the next generation of RSV intervention strategies BMC Medicine 18 (1): 1-14

[51] Yi L, Hodgson D, Wang L, Atkins KE, Feikin D, Nair H (2020) The role of RSV seasonality on RSV prevention strategy planning for passive immunisation of infants in low- and middle-income countries: a modelling study. Lancet Infectious Diseases

[50] Wuerz T, Kassim S, Atkins KE (2020) Acquisition of extended-spectrum beta-lactamase-producing Enterobacteriaceae (ESBL-PE) carriage after exposure to systemic antimicrobials during travel: systematic review and meta-analysis. Travel Medicine and Infectious Disease 37: 101823

[49] Villabona-Arenas CJ, Hall M, Lythgoe KA, Gaffney SG, Regoes RR, Hué S, Atkins KE (2020) Number of HIV-1 founder variants is determined by the recency of source partner infection. Science

[48] Yang J, Atkins KE, Feng L, Baguelin M, Wu P, Yan H, Lau EHY, Wu JT, Liu Y, Cowling BJ, Jit M, Yu H (2020) Cost-effectiveness of introducing national seasonal influenza vaccination for adults aged 60 years and above in mainland China: a modelling analysis. BMC Medicine 18:90 doi: 10.1186/s12916-020-01545-6

[47] Jit M, Ng DHL, Luangasanatip N, Sandmann F, Atkins KE, Robotham JV, Pouwels KB (2020) Quantifying the economic cost of antibiotic resistance and the impact of related interventions: rapid methodological review, conceptual framework and recommendations for future studies. BMC Medicine *18:38 doi: 10.1186/s12916-020-1507-2

[46] Chae C, Davies NG, Jit M, Atkins KE (2020) Impact of pediatric influenza vaccination on antibiotic resistance in England and Wales. Emerging Infectious Diseases 26(1). doi: 10.3201/eid2601.191110

[45] Knight GM, Davies NG, Colijn C, Coll F, Donker T, Gifford DR, Glover RE, Jit M, Klemm E, Lehtinen S, Lindsay JA, Lipsitch M, Llewelyn MJ, Mateus ALP, Robotham JV, Sharland M, Stekel D, Yakob L, Atkins KE (2020) Mathematical modelling for antibiotic resistance control policy: do we know enough? BMC Infectious Diseases 19:1011. doi: 10.1186/s12879-019-4630-y


[44] Ndeffo-Mbah ML, Pandey A, Atkins KE, Askoy S, Galvani AP (2020) The potential impact of tsetse fly migration on Gambiense human African trypanosomiasis elimination efforts. PLOS Neglected Tropical Diseases 13(12):e0007903 doi:10.1371/journal.pntd.0007903

[43] Hodgson D, Atkins KE, Baguelin M, Panovska-Griffiths J, Fragaszy E, Thorrington D, van Hoek AJ, Hayward A, Pebody R (2019) Quality of life loss for Respiratory Syncytial Virus. Influenza and Other Respiratory Pathogens doi:10.1111/irv.12686

[42] Luyten J, Kessels R, Atkins KE, Jit M, van Hoek AJ (2019) Quantifying the public’s view on key value judgments in vaccine decision-making: a discrete choice experiment. Social Science and Medicine

[41] Capewell P, Atkins KE, Weir W, Clucas C, Garside P, Galvani AP, Bucheton B, MacLeod A. (2019) Resolving the apparent transmission paradox of African sleeping sickness. PLOS Biology 17(1):e3000105. doi:10.1371/journal.pbio.3000105

[40] Davies NG, Flasche S, Jit M, Atkins KE (2019) Within-host dynamics shape the coexistence of antibiotic-sensitive and resistant bacteria. Nature Ecology and Evolution doi:10.1038/s41559-018-0786-x Open access link — see commentary by Lehtinen (2019) Open access link


[39] Munday J, van Hoek AJ, Edmunds WJ, Atkins KE (2018) Vaccination drives infectious disease inequality. BMC Medicine

[38] Atkins KE, Lipsitch M (2018) Can antibotic resistance be reduced by vaccinating against respiratory disease? Lancet Respiratory Medicine

[37] Flasche S, Atkins KE (2018) Balancing benefits and risks of antibiotic use. Journal of Infectious Diseases

[36] Camacho A, Bouhenia M, de Radiguès X, Mohammed Naji AM, Abubakar A, Seguin C, Sagrad MJ, Poncin M, McRae M, Musoke M, Al-Mesbahy AR, Rakesh A, Cohuet S, Atkins KE, Eggo RM, Azman A, Broekhuijsen M, Quilici M-L, Olson D, Legros D, Zagaria N, Luquero FJ (2018) Cholera in the time of war: the 2017–8 epidemic in Yemen Lancet Global Health

[35] Rock KS, Ndeffo Mbah M, Castano S, Palmer C, Chitnis N, Pandey A, Atkins KE, Ndung’u JM, Hollingsworth TD, Galvani AP, Bever C, Chitnis N, Keeling MJ (2018) Refining strategies against Gambian sleeping sickness through new application of existing tools: Insights from mathematical modelling Clinical Infectious Diseases 66(suppl 4):S286–S292

[34] Atkins KE, Flasche S (2018) Vaccination to reduce antimicrobial resistance The Lancet Global Health 6(3):e252 doi:10.1016/S2214-109X(18)30043-3


[33] Atkins KE, Lafferty EI, Deeny SR, Davies NG, Robotham J, Jit M (2017) Using mathematical modelling to evaluate the impact of vaccines on antibiotic resistance: a mechanistic framework and literature review. The Lancet Infectious Diseases 18(6):e204-e213.

[32] Coltart CEM, Edmunds WJ, Atkins KE (2017) The 2013–2016 Ebola epidemic: multidisciplinary success conceals a missed opportunity Philosophical Transactions of the Royal Society B 372:20160292

[31] Piot P, Coltart CEM, Atkins KE (2017) Preface to “The 2013-16 Ebola epidemic: data, decision-making and disease control” Philosophical Transactions of the Royal Society B 372:20170020

[30] Rock KS, Pandey A, Ndeffo Mbah M, Atkins KE, Lumbala C, Galvani AP & Keeling M (2017) Data-driven models to predict the elimination of sleeping sickness in former Equateur province of DRC. Epidemics 18:101-112 doi:10.1016/j.epidem.2017.01.006

[29] Hodgson D, Baguelin M, van Leeuwen E, Panovska-Griffiths J, Ramsay M, Pebody R & Atkins KE (2017) Cost-effectiveness analysis of target vaccine groups in the presence of mass paediatric influenza vaccination The Lancet Public Health 2(2):74-81 doi:10.1016/ S2468-2667(16)30044-5 — see commentary by Fisman and Bogoch (2016) The Lancet Public Health doi:10.1016/ S2468-2667(17)30004-X


[28] Thomas SL, Walker JL, Fenty J, Atkins KE, Elliot AJ, Hughes HE, Stowe J, Ladhani S, Andrews NJ (2016) Impact of the national rotavirus vaccination programme on acute gastroenteritis in England Vaccine 35(4):680–686

[27] Yang J*, Atkins KE*, Feng L, (*contributed equally) Pang M, Zheng Y, Liu X, Cowling B, Yu H (2016) Seasonal influenza vaccination in China: landscape of diverse regional reimbursement policy, and budget impact analysis. Vaccine 11;34(47):5724-5735. doi: 10.1016/j.vaccine.2016.10.013

[26] Li M, Taylor E, Atkins KE, Chapman G & Galvani AP. Stimulating influenza vaccination via prosocial motives (2016) PLoS ONE 11(7): e0159780. doi: 10.1371/journal.pone.0159780

[25] Yamin D, Atkins KE, Remy V & Galvani A (2016) Economic evaluation of mass rotavirus vaccination in France Value in Health 19(6):811-9

[24] Fitzpatrick MC, Wenzel NS, Scarpino SV, Althouse BM, Atkins KE, Galvani AP & Townsend JP (2016) Cost-effectiveness of next-generation vaccines: The case of pertussis Vaccine 34(29):3405-11

[23] Atkins KE*, Pandey A*, (*contributed equally) Ndeffo-Mbah ML, Medlock JP, Wenzel N, Townsend JP, Altice F, Fallah M, Bawo L, Nyenswah TG & Galvani AP (2016) Retrospective Analysis of the 2014–5 Ebola Epidemic in Liberia American Journal for Tropical Medicine and Hygiene 94(4):833-9

[22] Atkins KE*, Fitzpatrick M*, (*contributed equally) Galvani AP, Townsend JP (2016) Cost-effectiveness of pertussis vaccination during pregnancy in the US. American Journal of Epidemiology doi:10.1093/aje/kwv347

[21] Atkins KE, Van Hoek AJ, Watson C, Baguelin M, Raj T, Patel A, Choga L, Jit M, Griffiths U (2016) Seasonal influenza vaccination delivery through community pharmacists in England: evaluation of the London pilot BMJ Open 2016;6:e009739 doi:10.1136/bmjopen-2015-009739


[20] Hollingsworth TD, Adams ER, Anderson RM, Atkins KE, Bartsch S, Basáñez MG, Behrend M, Blok DG, Chapman LAC, Coffeng L, Courtenay O, Crump RE, de Vlas SJ, Dobson A, Dyson L, Farkas H, Galvani AP, Gambhir M, Gurarie D, Irvine MA, Jervis S, Keeling MJ, Kelly-Hope L, King C, Lee BY, Le Rutte EA, Lietman TM, Ndeffo-Mbah M, Medley GF, Michael E, Pandey A, Peterson JK, Pinsent A, Porco TC, Richardus JH, Reimer L, Rock KS, Singh BK, Stolk W, Swaminathan S, Torr SJ, Townsend J, Truscott J, Walker M, Zoueva A and NTD Modelling Consortium (2015) Quantitative analyses and modelling to support achievement of the 2020 goals for nine neglected tropical diseases. Parasites & Vectors 8:630 doi:10.1186/s13071-015-1235-1

[19] Pandey A, Atkins KE, Bucheton B, Camara M, Aksoy S, Galvani AP, Ndeffo-Mbah ML (2015) Evaluating long-term effectiveness of sleeping sickness control measures in Guinea. Parasites and Vectors 8 (1), 1-10

[18] Ibuka Y, Ohkusa Y, Sugawara T, Chapman GB, Yamin D, Atkins KE, Taniguchi K, Okabe N, Galvani AP (2015) Social contacts, vaccination decisions and influenza in Japan. Journal of Epidemiology and Community Health doi:10.1136/jech-2015-205777

[17] Taylor E, Atkins KE, Medlock J, Li M, Chapman C, Galvani AP (2015) Cross-cultural household influence on vaccination decisions. Medical Decision Making 0272989X15591007

[16] Wells CR, Yamin D, Ndeffo Mbah ML, Wenzel N, Gaffney SG, Townsend JP, Meyers LA, Fallah M, Nyenswah T, Altice F, Atkins KE, Galvani AP (2015) Harnessing case isolation and ring vaccination to control Ebola. PLoS Neglected Tropical Diseases 9(5):e0003794

[15] Atkins KE, Wenzel N, Ndeffo-Mbah ML, Altice FL, Townsend JP, & Galvani AP (2015) Under-reporting and Case Fatality Estimates for Emerging Epidemics. BMJ 2015;350:h1115


[14] Pandey A*, Atkins KE*, (*contributed equally) Medlock JP, Wenzel N, Townsend JP, Childs JE, Nyenswah TG, Ndeffo-Mbah ML & Galvani AP (2014) Strategies for Containing Ebola in West Africa Science 21 (346) 6212:991-995 DOI: 10.1126/science.1260612

[13] Talbert-Slagle K, Atkins KE, Yan K-K, Khurana E, Gerstein M, Bradley E, Berg D, Galvani AP & Townsend JP (2014) Cellular superspreaders: an epidemiological view of within-host HIV infection. PLoS Pathogens 10(5): e1004092. doi: 10.1371/journal.ppat.1004092


[12] Atkins KE, Read AF, Savill NJ, Walkden-Brown SW & Woolhouse MEJ (2013) The effectiveness of mass vaccination on Marek’s disease virus (MDV) outbreaks and detection within a broiler barn: a modeling study. Epidemics 5(4):208-17. doi: 10.1016/j.epidem.2013.10.001

[11] Medlock J, Atkins KE, Thomas D, Aksoy S & Galvani AP (2013) Modeling wolbachia-induced cytoplasmic incompatibility as a driver for genes to combat African trypanosomiasis. PLoS Neglected Tropical Diseases 7(8): e2374 doi:10.1371/journal.pntd.0002374

[10] Ndeffo Mbah ML, Poolman E, Atkins KE, Orenstein EW, Meyers LA, Townsend JP & Galvani AP (2013) Cost-effectiveness of schistosomiasis treatment for reducing HIV transmission in Africa: case of Zimbabwean women. PLoS Neglected Tropical Diseases 7(8): e2346 doi:10.1371/journal.pntd.0002346

[9] Bocedi G, Atkins KE, Liao J, Henry R, Travis JMJ & Hellmann JJ (2013) Effects of local adaptation and interspecific interactions on species’ responses to climate change. Annals of the New York Academy of Sciences 1297:83–97

[8] Atkins KE, Townsend JP, Medlock J & Galvani AP (2013) Epidemiological mechanisms of genetic resistance to kuru. Royal Society Interface 10(85) doi:10.1098/rsif.2013.0331

[7] Ndeffo Mbah ML, Kjetland E, Atkins KE, Poolman E, Orenstein EW, Meyers LA, Townsend JP & Galvani AP (2013) Cost-effectiveness of a community-based intervention for reducing the transmission of Schistosoma haematobium and HIV in Africa. PNAS 110(19):7952-7957 doi:10.1073/pnas.1221396110

[6] Atkins KE, Read AF, Savill NJ, Renz KG, Islam AFMF, Walkden-Brown SW & Woolhouse MEJ (2013) Vaccination and Reduced Cohort Duration Can Drive Virulence Evolution: Marek’s Disease Virus and Industrialized Agriculture. Evolution 67(3):851-860. doi:10.1111/j.1558-5646.2012.01803.x


[5] Atkins KE, Shim E, Carroll S, Quilici S & Galvani AP (2012) The Cost-Effectiveness of Pentavalent Rotavirus Vaccination in England and Wales. Vaccine 30(48):6766–6776

[4] Pitzer VE, Atkins KE*, Freiesleben de Blasio B*, Van Effelterre T*,(*contributed equally) Atchison CJ, Harris JP, Shim E, Galvani AP, Edmunds WJ, Viboud C, Patel MM, Grenfell BT, Parashar U & Lopman BA (2012) Direct and Indirect Effects of Rotavirus Vaccination: Comparing Predictions from Transmission Dynamic Models PLoS ONE 7(8): e42320. doi:10.1371/journal.pone.0042320

[3] Atkins KE, Shim E, Pitzer VE & Galvani AP (2012) Impact of Rotavirus Vaccination on Epidemiological Dynamics in England and Wales. Vaccine 30:552-564. DOI:10.1016/j.vaccine2011.11.064


[2] Atkins KE, Read AF, Walkden-Brown SW, Savill NJ, Renz KM & Woolhouse MEJ (2011) Modelling Marek’s Disease Virus (MDV) Infection: Parameter Estimates For Mortality Rate And Infectiousness. BMC Veterinary Research 7(1):70. DOI:10.1186/1746-6148-7-70


[1] Atkins KE and Travis JMJ (2010) Local adaptation and the evolution of species’ ranges under climate change. Journal of Theoretical Biology 266(3): 449-457. DOI:10.1016/j.jtbi.2010.07.014