Imperial College London

Professor Neil Ferguson

Faculty of MedicineSchool of Public Health

Vice-Dean (Academic Development)
 
 
 
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Contact

 

+44 (0)20 7594 3296neil.ferguson Website

 
 
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Location

 

Medical SchoolSt Mary's Campus

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Summary

 

Publications

Publication Type
Year
to

233 results found

Campbell F, Cori A, Ferguson N, Jombart Tet al., 2019, Bayesian inference of transmission chains using timing of symptoms, pathogen genomes and contact data., PLoS Comput Biol, Vol: 15

There exists significant interest in developing statistical and computational tools for inferring 'who infected whom' in an infectious disease outbreak from densely sampled case data, with most recent studies focusing on the analysis of whole genome sequence data. However, genomic data can be poorly informative of transmission events if mutations accumulate too slowly to resolve individual transmission pairs or if there exist multiple pathogens lineages within-host, and there has been little focus on incorporating other types of outbreak data. We present here a methodology that uses contact data for the inference of transmission trees in a statistically rigorous manner, alongside genomic data and temporal data. Contact data is frequently collected in outbreaks of pathogens spread by close contact, including Ebola virus (EBOV), severe acute respiratory syndrome coronavirus (SARS-CoV) and Mycobacterium tuberculosis (TB), and routinely used to reconstruct transmission chains. As an improvement over previous, ad-hoc approaches, we developed a probabilistic model that relates a set of contact data to an underlying transmission tree and integrated this in the outbreaker2 inference framework. By analyzing simulated outbreaks under various contact tracing scenarios, we demonstrate that contact data significantly improves our ability to reconstruct transmission trees, even under realistic limitations on the coverage of the contact tracing effort and the amount of non-infectious mixing between cases. Indeed, contact data is equally or more informative than fully sampled whole genome sequence data in certain scenarios. We then use our method to analyze the early stages of the 2003 SARS outbreak in Singapore and describe the range of transmission scenarios consistent with contact data and genetic sequence in a probabilistic manner for the first time. This simple yet flexible model can easily be incorporated into existing tools for outbreak reconstruction and should permit a bet

JOURNAL ARTICLE

Hamlet A, Jean K, Yactayo S, Benzler J, Cibrelus L, Ferguson N, Garske Tet al., 2019, POLICI: A web application for visualising and extracting yellow fever vaccination coverage in Africa, VACCINE, Vol: 37, Pages: 1384-1388, ISSN: 0264-410X

JOURNAL ARTICLE

Wilder-Smith A, Hombach J, Ferguson N, Selgelid M, Brien KO, Vannice K, Barrett A, Ferdinand E, Flasche S, Guzman M, Novaes HM, Ng L-C, Smith PG, Tharmaphornpilas P, Yoon I-K, Cravioto A, Farrar J, Nolan TMet al., 2019, Deliberations of the Strategic Advisory Group of Experts on Immunization on the use of CYD-TDV dengue vaccine, LANCET INFECTIOUS DISEASES, Vol: 19, Pages: E31-E38, ISSN: 1473-3099

JOURNAL ARTICLE

Campbell F, Didelot X, Fitzjohn R, Ferguson N, Cori A, Jombart Tet al., 2018, outbreaker2: a modular platform for outbreak reconstruction, BMC BIOINFORMATICS, Vol: 19, ISSN: 1471-2105

JOURNAL ARTICLE

Dorigatti I, Donnelly CA, Laydon DJ, Small R, Jackson N, Coudeville L, Ferguson NMet al., 2018, Refined efficacy estimates of the Sanofi Pasteur dengue vaccine CYD-TDV using machine learning, NATURE COMMUNICATIONS, Vol: 9, ISSN: 2041-1723

JOURNAL ARTICLE

Anders KL, Cutcher Z, Kleinschmidt I, Donnelly CA, Ferguson NM, Indriani C, Ryan PA, O'Neill SL, Jewell NP, Simmons CPet al., 2018, Cluster-Randomized Test-Negative Design Trials: A Novel and Efficient Method to Assess the Efficacy of Community-Level Dengue Interventions, AMERICAN JOURNAL OF EPIDEMIOLOGY, Vol: 187, Pages: 2021-2028, ISSN: 0002-9262

JOURNAL ARTICLE

Ferguson NM, 2018, Challenges and opportunities in controlling mosquito-borne infections, NATURE, Vol: 559, Pages: 490-497, ISSN: 0028-0836

JOURNAL ARTICLE

Ahuka-Mundeke S, Ahmed YA, Allarangar Y, Anoko J, Archer BN, Abedi AA, Bagaria J, Barry A, Bathe NT, Belizaire MRD, Bhatia S, Bokenge T, Bruni E, Cori A, Dabire E, Diallo AM, Diallo B, Donnelly CA, Dorigatti I, Dorji TC, Waeber AREC, Fall IS, Ferguson NM, FitzJohn RG, Tengomo GLF, Formenty PBH, Forna A, Fortin A, Garske T, Gaythorpe KAM, Gurry C, Hamblion E, Djingarey MH, Haskew C, Hugonnet SAL, Imai N, Impouma B, Kabongo G, Kabamba GK, Kalenga OI, Kibangou E, Kitenge E, Lay Y, Lee TM-H, Lubula L, Lukoya CO, Mwati JDDL, Ly O, Makiala-Mandanda S, Mamba A, Mbala-Kingebeni P, Mboussou FFR, Mbuy G, Mlanda T, Makuma VM, Mavila O, Morgan O, Mulumba AM, Mukadi-Bamuleka D, Kakoni PM, Mutombo A, Muyembe J-J, Ngamala PN, Ngom R, Ngoy G, Nouvellet P, Nsio J, Ousman KB, Peron E, Polonsky JA, Ryan MJ, Salama P, Toure A, Towner R, Tshapenda G, Van de Weerdt R, Van Kerkhove M, Wendland A, Yao NKM, Yoti Z, Yuma Eet al., 2018, Outbreak of Ebola virus disease in the Democratic Republic of the Congo, April-May, 2018: an epidemiological study, LANCET, Vol: 392, Pages: 213-221, ISSN: 0140-6736

JOURNAL ARTICLE

Miglianico M, Eldering M, Slater H, Ferguson N, Ambrose P, Lees RS, Koolen KMJ, Pruzinova K, Jancarova M, Volf P, Koenraadt CJM, Duerr H-P, Trevitt G, Yang B, Chatterjee AK, Wisler J, Sturm A, Bousema T, Sauerwein RW, Schultz PG, Tremblay MS, Dechering KJet al., 2018, Repurposing isoxazoline veterinary drugs for control of vector-borne human diseases, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, Vol: 115, Pages: E6920-E6926, ISSN: 0027-8424

JOURNAL ARTICLE

Marshall JM, Wu SL, Sanchez HMC, Kiware SS, Ndhlovu M, Ouedraogo AL, Toure MB, Sturrock HJ, Ghani AC, Ferguson NMet al., 2018, Mathematical models of human mobility of relevance to malaria transmission in Africa, SCIENTIFIC REPORTS, Vol: 8, ISSN: 2045-2322

JOURNAL ARTICLE

Hamlet A, Jean K, Perea W, Yactayo S, Biey J, Van Kerkhove M, Ferguson N, Garske Tet al., 2018, The seasonal influence of climate and environment on yellow fever transmission across Africa, PLOS NEGLECTED TROPICAL DISEASES, Vol: 12, ISSN: 1935-2735

JOURNAL ARTICLE

Pople D, 2018, The effect of social networks on the participation by those with parental responsibility in the baby immunisation programme in the UK

THESIS DISSERTATION

Nouvellet P, Cori A, Garske T, Blake IM, Dorigatti I, Hinsley W, Jombart T, Mills HL, Nedjati-Gilani G, Van Kerkhove MD, Fraser C, Donnelly CA, Ferguson NM, Riley Set al., 2018, A simple approach to measure transmissibility and forecast incidence, EPIDEMICS, Vol: 22, Pages: 29-35, ISSN: 1755-4365

JOURNAL ARTICLE

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

JOURNAL ARTICLE

Dorigatti I, McCormack C, Nedjati-Gilani G, Ferguson NMet al., 2018, Using Wolbachia for Dengue Control: Insights from Modelling, TRENDS IN PARASITOLOGY, Vol: 34, Pages: 102-113, ISSN: 1471-4922

JOURNAL ARTICLE

Katzelnick LC, Harris E, Participants in the Summit on Dengue Immune Correlates of Protection, 2017, Immune correlates of protection for dengue: State of the art and research agenda., Pages: 4659-4669

Dengue viruses (DENV1-4) are mosquito-borne flaviviruses estimated to cause up to ∼400 million infections and ∼100 million dengue cases each year. Factors that contribute to protection from and risk of dengue and severe dengue disease have been studied extensively but are still not fully understood. Results from Phase 3 vaccine efficacy trials have recently become available for one vaccine candidate, now licensed for use in several countries, and more Phase 2 and 3 studies of additional vaccine candidates are ongoing, making these issues all the more urgent and timely. At the "Summit on Dengue Immune Correlates of Protection", held in Annecy, France, on March 8-9, 2016, dengue experts from diverse fields came together to discuss the current understanding of the immune response to and protection from DENV infection and disease, identify key unanswered questions, discuss data on immune correlates and plans for comparison of results across assays/consortia, and propose a research agenda for investigation of dengue immune correlates, all in the context of both natural infection studies and vaccine trials.

CONFERENCE PAPER

Dorigatti I, Hamlet A, Aguas R, Cattarino L, Cori A, Donnelly CA, Garske T, Imai N, Ferguson NMet al., 2017, International risk of yellow fever spread from the ongoing outbreak in Brazil, December 2016 to May 2017, EUROSURVEILLANCE, Vol: 22, Pages: 10-13, ISSN: 1560-7917

JOURNAL ARTICLE

Cori A, Donnelly CA, Dorigatti I, Ferguson NM, Fraser C, Garske T, Jombart T, Nedjati-Gilani G, Nouvellet P, Riley S, Van Kerkhove MD, Mills HL, Blake IMet al., 2017, Key data for outbreak evaluation: building on the Ebola experience, PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, Vol: 372, ISSN: 0962-8436

JOURNAL ARTICLE

Garske T, Cori A, Ariyarajah A, Blake IM, Dorigatti I, Eckmanns T, Fraser C, Hinsley W, Jombart T, Mills HL, Nedjati-Gilani G, Newton E, Nouvellet P, Perkins D, Riley S, Schumacher D, Shah A, Van Kerkhove MD, Dye C, Ferguson NM, Donnelly CAet al., 2017, Heterogeneities in the case fatality ratio in the West African Ebola outbreak 2013-2016, PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, Vol: 372, ISSN: 0962-8436

JOURNAL ARTICLE

McCormack C, Ghani AC, Ferguson NM, 2017, THE EFFECTS OF METAPOPULATION STRUCTURE ON FINE-SCALE MOSQUITO POPULATION DYNAMICS AND POTENTIAL CONSEQUENCES FOR THE TRANSMISSION DYNAMICS OF DENGUE AND MALARIA, 66th Annual Meeting of the American-Society-of-Tropical-Medicine-and-Hygiene (ASTMH), Publisher: AMER SOC TROP MED & HYGIENE, Pages: 191-191, ISSN: 0002-9637

CONFERENCE PAPER

Hamlet A, Jean K, Ferguson N, Van Kerkhove M, Yactayo S, Perea W, Biey J, Sall A, Garske Tet al., 2017, POLICI: AN ONLINE TOOL FOR VISUALIZATION OF POPULATION-LEVEL YELLOW FEVER IMMUNIZATION COVERAGE IN AFRICA, 66th Annual Meeting of the American-Society-of-Tropical-Medicine-and-Hygiene (ASTMH), Publisher: AMER SOC TROP MED & HYGIENE, Pages: 257-257, ISSN: 0002-9637

CONFERENCE PAPER

Imai N, Rodriguez-Barraquer I, Hinsley W, Cummings DA, Ferguson NMet al., 2017, MAPPING THE GLOBAL ESTIMATES OF DENGUE SEROPREVALENCE AND TRANSMISSION INTENSITY, 66th Annual Meeting of the American-Society-of-Tropical-Medicine-and-Hygiene (ASTMH), Publisher: AMER SOC TROP MED & HYGIENE, Pages: 193-193, ISSN: 0002-9637

CONFERENCE PAPER

Cattarino L, Rodriguez-Barraquer I, Cummings D, Imai N, Ferguson Net al., 2017, MAPPING GLOBAL VARIATION IN DENGUE TRANSMISSION INTENSITY AND ASSESSING THE IMPACT OF CONTROL STRATEGIES, 66th Annual Meeting of the American-Society-of-Tropical-Medicine-and-Hygiene (ASTMH), Publisher: AMER SOC TROP MED & HYGIENE, Pages: 193-193, ISSN: 0002-9637

CONFERENCE PAPER

Jean K, Donnelly CA, Ferguson NM, Garske Tet al., 2016, A Meta-Analysis of Serological Response Associated with Yellow Fever Vaccination, AMERICAN JOURNAL OF TROPICAL MEDICINE AND HYGIENE, Vol: 95, Pages: 1435-1439, ISSN: 0002-9637

JOURNAL ARTICLE

Agua-Agum J, Ariyarajah A, Aylward B, Bawo L, Bilivogui P, Blake IM, Brennan RJ, Cawthorne A, Cleary E, Clement P, Conteh R, Cori A, Dafae F, Dahl B, Dangou J-M, Diallo B, Donnelly CA, Dorigatti I, Dye C, Eckmanns T, Fallah M, Ferguson NM, Fiebig L, Fraser C, Garske T, Gonzalez L, Hamblion E, Hamid N, Hersey S, Hinsley W, Jambei A, Jombart T, Kargbo D, Keita S, Kinzer M, George FK, Godefroy B, Gutierrez G, Kannangarage N, Mills HL, Moller T, Meijers S, Mohamed Y, Morgan O, Nedjati-Gilani G, Newton E, Nouvellet P, Nyenswah T, Perea W, Perkins D, Riley S, Rodier G, Rondy M, Sagrado M, Savulescu C, Schafer IJ, Schumacher D, Seyler T, Shah A, Van Kerkhove MD, Wesseh CS, Yoti Zet al., 2016, Exposure Patterns Driving Ebola Transmission in West Africa: A Retrospective Observational Study, PLOS MEDICINE, Vol: 13, ISSN: 1549-1676

JOURNAL ARTICLE

Flasche S, Jit M, Rodriguez-Barraquer I, Coudeville L, Recker M, Koelle K, Milne G, Hladish TJ, Perkins TA, Cummings DAT, Dorigatti I, Laydon DJ, Espana G, Kelso J, Longini I, Lourenco J, Pearson CAB, Reiner RC, Mier-y-Teran-Romero L, Vannice K, Ferguson Net al., 2016, The Long-Term Safety, Public Health Impact, and Cost-Effectiveness of Routine Vaccination with a Recombinant, Live-Attenuated Dengue Vaccine (Dengvaxia): A Model Comparison Study, PLOS MEDICINE, Vol: 13, ISSN: 1549-1676

JOURNAL ARTICLE

Ferguson NM, Rodriguez-Barraquer I, Dorigatti I, Mier-y-Teran-Romero L, Laydon DJ, Cummings DATet al., 2016, Benefits and risks of the Sanofi-Pasteur dengue vaccine: Modeling optimal deployment, SCIENCE, Vol: 353, Pages: 1033-1036, ISSN: 0036-8075

JOURNAL ARTICLE

Metcalf CJE, Farrar J, Cutts FT, Basta NE, Graham AL, Lessler J, Ferguson NM, Burke DS, Grenfell BTet al., 2016, Use of serological surveys to generate key insights into the changing global landscape of infectious disease, LANCET, Vol: 388, Pages: 728-730, ISSN: 0140-6736

JOURNAL ARTICLE

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