Publications
2024
(14) Geographical migration and fitness dynamics of Streptococcus pneumoniae
Sophie Belman, Noémie Lefrancq, Susan Nzenze, Sarah Downs, Mignon du Plessis, Stephanie Lo, The Global Pneumococcal Sequencing Consortium, Lesley McGee, Shabir A. Madhi, Anne von Gottberg, Stephen D. Bentley and Henrik Salje,
Nature, 2024.
(13) Antigenic distance between primary and secondary dengue infections correlates with disease risk
Lin Wang, Angkana T Huang, Leah C Katzelnick, Noémie Lefrancq, Ana Coello Escoto, Loréna Duret, Nayeem Chowdhury, Richard Jarman, Matthew A Conte, Irina Maljkovic Berry, Stefan Fernandez, Chonticha Klungthong, Butsaya Thaisomboonsuk, Piyarat Suntarattiwong, Warunee Vandepitte, Stephen Whitehead, Simon Cauchemez, Derek AT Cummings and Henrik Salje,
Science Translational Medicine, 2024.
(12) The genetic diversity of Nipah virus across spatial scales
Oscar Cortés Azuero, Noémie Lefrancq, Birgit Nikolay, Clifton McKee, Julien Cappelle, Vibol Hul, Tey Putita Ou, Thavry Hoem, Philippe Lemey, Mohammed Ziaur Rahman, Ausraful Islam, Emily S. Gurley, Veasna Duong and Henrik Salje,
The Journal of Infectious Diseases, 2024.
2023
(11) Learning the fitness dynamics of pathogens from phylogenies
Noémie Lefrancq, Loréna Duret, Valérie Bouchez, Sylvain Brisse, Julian Parkhill and Henrik Salje,
medRxiv, 2023.
(10) Association of poultry vaccination with the interspecies transmission and molecular evolution of H5 subtype avian influenza virus
Bingying Li, Jayna Raghwani, Sarah C. Hill, Sarah François, Noémie Lefrancq, Yilin Liang, Zengmiao Wang, Lu Dong, Phillipe Lemey, Oliver G. Pybus and Huaiyu Tian,
bioRxiv, 2023.
2022
(9) Global spatial dynamics and vaccine-induced fitness changes of Bordetella pertussis
Noémie Lefrancq & Valérie Bouchez, Nadia Fernandes, Alex-Mikael Barkoff, Thijs Bosch, Tine Dalby, Thomas Åkerlund, Jessica Darenberg, Katerina Fabianova, Didrik F Vestrheim, Norman K Fry, Juan José González-López, Karolina Gullsby, Adele Habington, Qiushui He, David Litt, Helena Martini, Denis Piérard, Paola Stefanelli, Marc Stegger, Jana Zavadilova, Nathalie Armatys, Annie Landier, Sophie Guillot, Samuel L Hong, Philippe Lemey, Julian Parkhill, Julie Toubiana, Simon Cauchemez, Henrik Salje and Sylvain Brisse,
Science Translational Medicine, 2022.
2021
(8) Evolution of outcomes for patients hospitalised during the first 9 months of the SARS-CoV-2 pandemic in France: a retrospective national surveillance data analysis
Noémie Lefrancq, Juliette Paireau, Nathanaël Hozé, Noémie Courtejoie, Yazdan Yazdanpanah, Lila Bouadma, Pierre-Yves Boëlle, Fanny Chereau, Henrik Salje and Simon Cauchemez,
Lancet Regional Health Europe, 2021.
(7) Emergence and global spread of Listeria monocytogenes main clinical clonal complex
Alexandra Moura, Noémie Lefrancq, Thierry Wirth, Alexandre Leclercq, Vítor Borges, Brent Gilpin, Timothy J Dallman, Joachim Frey, Eelco Franz, Eva M Nielsen, Juno Thomas, Arthur Pightling, Benjamin P Howden, Cheryl L Tarr, Peter Gerner-Smidt, Simon Cauchemez, Henrik Salje, Sylvain Brisse, Marc Lecuit, and the Listeria CC1 Study Group,
Science Advances, 2021.
(6) Ongoing diphtheria outbreak in Yemen: a cross-sectional and genomic epidemiology study
Edgar Badell, Abdulilah Alharazi, Alexis Criscuolo, Khaled Abdullah Ali Almoayed, Noémie Lefrancq, Valerie Bouchez, Julien Guglielmini, Melanie Hennart, Annick Carmi-Leroy, Nora Zidane, Marine Pascal-Perrigault, Manon Lebreton, Helena Martini, Henrik Salje, Julie Toubiana, Fekri Dureab, Ghulam Dhabaan, Sylvain Brisse, and the NCPHL diphtheria outbreak working group
The Lancet Microbe, 2021.
(5) Reconstructing unseen transmission events to infer dengue dynamics from viral sequences
Henrik Salje, Amy Wesolowski, Tyler S. Brown, Mathew V. Kiang, Irina Maljkovic Berry, Noémie Lefrancq, Stefan Fernandez, Richard G. Jarman, Kriangsak Ruchusatsawat, Sopon Iamsirithaworn, Warunee P. Vandepitte, Piyarat Suntarattiwong, Jonathan M. Read, Chonticha Klungthong, Butsaya Thaisomboonsuk, Kenth Engø-Monsen, Caroline Buckee, Simon Cauchemez and Derek A.T. Cummings,
Nature Communications, 2021.
(4) SARS-CoV-2 transmission across age groups in France and implications for control
Cécile Tran Kiem, Paolo Bosetti, Juliette Paireau, Pascal Crepey, Henrik Salje, Noémie Lefrancq, Arnaud Fontanet, Daniel Benamouzig, Pierre-Yves Boëlle, Jean-Claude Desenclos, Lulla Opatowski and Simon Cauchemez,
Nature Communications, 2021.
(3) Evaluating the impact of curfews and other measures on SARS-CoV-2 transmission in French Guiana
Alessio Andronico, Cécile Tran Kiem, Juliette Paireau, Tiphanie Succo, Paolo Bosetti, Noémie Lefrancq, Mathieu Nacher, Félix Djossou, Alice Sanna, Claude Flamand, Henrik Salje, Cyril Rousseau and Simon Cauchemez
Nature Communications, 2021.
2020
(2) Estimating the burden of SARS-CoV-2 in France
Henrik Salje, Cécile Tran Kiem, Noémie Lefrancq, Noémie Courtejoie, Paolo Bosetti, Juliette Paireau, Alessio Andronico, Nathanaël Hozé, Jehanne Richet, Claire-Lise Dubost, Yann Le Strat, Justin Lessler, Daniel Levy-Bruhl, Arnaud Fontanet, Lulla Opatowski, Pierre-Yves Boelle and Simon Cauchemez
Science, 2020.
2018
(1) Characterization of the spatial and temporal distribution of Nipah virus spillover events in Bangladesh, 2007–2013
Maria C. Cortes, Simon Cauchemez, Noémie Lefrancq, Stephen P. Luby, M Jahangir Hossain, Hossain MS Sazzad, Mahmudur Rahman, Peter Daszak, Henrik Salje, Emily S Gurley,
The Journal of infectious diseases, 2018.