Henrik Salje, Amy Wesolowski, Tyler S. Brown, Mathew V. Kiang, Irina Maljkovic Berry, Noemie 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 & Derek A. T. Cummings

Reconstructing unseen transmission events to infer dengue dynamics from viral sequences

Nature Communications, 2021; 12: 1810. https://doi.org/10.1038/s41467-021-21888-9
Bingyi Yang,Brooke A. Borgert,Barry W. Alto,Carl K. Boohene,Joe Brew,Kelly Deutsch,James T. DeValerio,Rhoel R. Dinglasan,Daniel Dixon,Joseph M. Faella,Sandra L. Fisher-Grainger,Gregory E. Glass,Reginald Hayes Jr.,David F. Hoel,Austin Horton,Agne Janusauskaite,Bill Kellner,Moritz U. G. Kraemer,Keira J. Lucas,Johana Medina,Rachel Morreale,William Petrie,Robert C. Reiner Jr.,Michael T. Riles,Henrik Salje,David L. Smith,John P. Smith,Amy Solis,Jason Stuck,Chalmers Vasquez,Katie F. Williams,Rui-De Xue,Derek A. T. Cummings

Modelling distributions of Aedes aegypti and Aedes albopictus using climate, host density and interspecies competition

PLOS Neglected Tropical Diseases, 2021; 15(3): e0009063. https://doi.org/10.1371/journal.pntd.0009063
Noemie Lefrancq, Juliette Paireau, Nathanael Hoze, Noemie Courtejoie, Yazdan Yazdanpanah, Lila Bouadma, Pierre-Yves Boelle, Fanny Chereau, Henrik Salje, Simon Cauchemez

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

The Lancet Regional Health - Europe, 2021; 5: 100087. https://doi.org/10.1016/j.lanepe.2021.100087
Cécile Kiem, Paolo Bosetti, Juliette Paireau, Pascal Crepey, Henrik Salje, Noémie Lefrancq, Arnaud Fontanet, Daniel Benamouzig, Pierre-Yves Boëlle, Jean-Claude Desenclos, Lulla Opatowski, Simon Cauchemez

SARS-CoV-2 transmission across age groups in France and implications for control

HAL, 2021; : .
C. Jessica E. Metcalf, Juliette Paireau, Megan O’Driscoll, Mathilde Pivette, Bruno Hubert, Isabelle Pontais, Derek Cummings, Simon Cauchemez, Henrik Salje

Comparing the age and sex trajectories of SARS-CoV-2 morbidity with other respiratory pathogens points to potential immune mechanisms

MedRxiv, 2021; : . https://doi.org/10.1101/2021.01.07.21249381
Clifton D McKee, Ausraful Islam, Stephen P Luby, Henrik Salje, Peter J Hudson, Raina K Plowright, Emily S Gurley

The Ecology of Nipah Virus in Bangladesh: A Nexus of Land-Use Change and Opportunistic Feeding Behavior in Bats

Viruses, 2021; 13: . https://doi.org/10.3390/v13020169
Hui-Jia Li, Lin Wang, Yan Zhang, Matjaž Perc

Optimization of identifiability for efficient community detection

New Journal of Physics, 2020; 22: 063035. https://doi.org/10.1088/1367-2630/ab8e5e
Xiao-Ke Xu, Xiao Fan Liu, Ye Wu, Sheikh Taslim Ali, Zhanwei Du, Paolo Bosetti, Eric H Y Lau, Benjamin J Cowling, Lin Wang

Reconstruction of Transmission Pairs for Novel Coronavirus Disease 2019 (COVID-19) in Mainland China: Estimation of Superspreading Events, Serial Interval, and Hazard of Infection

Clinical Infectious Diseases, 2020; 71 (12): 3163–3167. https://doi.org/10.1093/cid/ciaa790
Sheikh Taslim Ali, Lin Wang, Eric HY Lau, Xiao-Ke Xu, Zhanwei Du, Ye Wu, Gabriel M Leung, Benjamin J Cowling

Serial interval of SARS-CoV-2 was shortened over time by nonpharmaceutical interventions

Science, 2020; 369 (6507): 1106-1109. 10.1126/science.abc9004
Zhanwei Du, Xiaoke Xu, Lin Wang, Spencer J. Fox, Benjamin J. Cowling, Alison P. Galvani, and Lauren Ancel Meyers

Effects of Proactive Social Distancing on COVID-19 Outbreaks in 58 Cities, China

Emerging Infectious Diseases, 2020; 26 (9): 2267-2269. https://dx.doi.org/10.3201%2Feid2609.201932
Claude Flamand, Antoine Enfissi, Sarah Bailly, Christelle Alves Sarmento, Emmanuel Beillard, Mélanie Gaillet, Céline Michaud, Véronique Servas, Nathalie Clement, Anaïs Perilhou, Thierry Carage, Didier Musso, Jean-François Carod, Stéphanie Eustache, Céline Tourbillon, Elodie Boizon, Samantha James, Félix Djossou, Henrik Salje, Simon Cauchemez, Dominique Rousset

Seroprevalence of anti-SARS-CoV-2 IgG at the epidemic peak in French Guiana

MedRxiv, 2020; : . https://doi.org/10.1101/2020.09.27.20202465
Paolo Bosetti, Bich-Tram Huynh, Armiya Youssouf Abdou, Marie Sanchez, Catherine Eisenhauer, Noémie Courtejoie, Jérôme Accardo, Henrik Salje, Didier Guillemot, Mathieu Moslonka-Lefebvre, Pierre-Yves Boëlle, Guillaume Béraud, Simon Cauchemez, Lulla Opatowski

Lockdown impact on age-specific contact patterns and behaviours in France

MedRxiv, 2020; : . https://doi.org/10.1101/2020.10.07.20205104
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, Simon Cauchemez

Evaluating the impact of curfews and other measures on SARS-CoV-2 transmission in French Guiana

MedRxiv, 2020; : . https://doi.org/10.1101/2020.10.07.20208314
Juliette Paireau, Alexandra Mailles, Catherine Eisenauher, Franck de Laval, François Delon, Paolo Bosetti, Henrik Salje, Valérie Pontiès, Simon Cauchemez

Early chains of transmission of COVID-19 in France

MedRxiv, 2020; : . https://doi.org/10.1101/2020.11.17.20232264
Angkana T. Huang, Bernardo Garcia-Carreras, Matt D. T. Hitchings, Bingyi Yang, Leah C. Katzelnick, Susan M. Rattigan, Brooke A. Borgert, Carlos A. Moreno, Benjamin D. Solomon, Luke Trimmer-Smith, Veronique Etienne, Isabel Rodriguez-Barraquer, Justin Lessler, Henrik Salje, Donald S. Burke, Amy Wesolowski & Derek A. T. Cummings

A systematic review of antibody mediated immunity to coronaviruses: kinetics, correlates of protection, and association with severity

Nature Communications, 2020; 11: 4704. 10.1038/s41467-020-18450-4
Angkana T. Huang, Bernardo Garcia-Carreras, Matt D.T. Hitchings, Bingyi Yang, Leah C. Katzelnick, Susan M. Rattigan, Brooke A. Borgert, Carlos A. Moreno, Benjamin D. Solomon, Isabel Rodriguez-Barraquer, Justin Lessler, Henrik Salje, Donald Burke, Amy Wesolowski, and Derek A.T. Cummings

A systematic review of antibody mediated immunity to coronaviruses: antibody kinetics, correlates of protection, and association of antibody responses with severity of disease

MedRxiv, 2020; : . https://dx.doi.org/10.1101%2F2020.04.14.20065771
Hannah Clapham, James Hay, Isobel Routledge, Saki Takahashi, Marc Choisy, Derek Cummings, Bryan Grenfell, C. Jessica E. Metcalf, Michael Mina, Isabel Rodriguez Barraquer, Henrik Salje, and Clarence C. Tam

Seroepidemiologic Study Designs for Determining SARS-COV-2 Transmission and Immunity

Emerging Infectious Diseases, 2020; 26(9): 1978-1986. 10.3201/eid2609.201840
Megan O'Driscoll, Gabriel Ribeiro Dos Santos, Lin Wang, Derek A.T. Cummings, Andrew S Azman, Juliette Paireau, Arnaud Fontanet, Simon Cauchemez, Henrik Salje

Age-specific mortality and immunity patterns of SARS-CoV-2 infection in 45 countries

Nature, 2020; : . https://doi.org/10.1038/s41586-020-2918-0
Nabeel Abdur Rehman, Henrik Salje, Moritz U G Kraemer, Lakshminarayanan Subramanian, Umar Saif, Rumi Chunara

Quantifying the localized relationship between vector containment activities and dengue incidence in a real-world setting: A spatial and time series modelling analysis based on geo-located data from Pakistan

PLoS Neglected Tropical Diseases, 2020; 14(5): e0008273. 10.1371/journal.pntd.0008273
In-Kyu Yoon, Anon Srikiatkhachorn, Maria Theresa Alera, Stefan Fernandez, Derek A T Cummings, Henrik Salje

Pre-existing chikungunya virus neutralizing antibodies correlate with risk of symptomatic infection and subclinical seroconversion in a Philippine cohort

International Journal of Infectious Diseases, 2020; 95: 167-173. 10.1016/j.ijid.2020.03.073
Birgit Nikolay, Henrik Salje, A K M Dawlat Khan, Hossain M S Sazzad, Syed M Satter, Mahmudur Rahman, Stephanie Doan, Barbara Knust, Meerjady Sabrina Flora, Stephen P Luby, Simon Cauchemez, Emily S Gurley

A Framework to Monitor Changes in Transmission and Epidemiology of Emerging Pathogens: Lessons From Nipah Virus

Journal of Infectious Diseases, 2020; 221(Supplement_4): S363-S369. 10.1093/infdis/jiaa074
Kishor Kumar Paul, Henrik Salje, Muhammad W Rahman, Mahmudur Rahman, Emily S Gurley

Comparing insights from clinic-based versus community-based outbreak investigations: a case study of chikungunya in Bangladesh

International Journal of Infectious Diseases, 2020; 97: 306-312. 10.1016/j.ijid.2020.05.111
Nathanaël Hozé, Henrik Salje, Dominique Rousset, Camille Fritzell, Jessica Vanhomwegen, Sarah Bailly, Matthieu Najm, Antoine Enfissi, Jean-Claude Manuguerra, Claude Flamand, Simon Cauchemez

Reconstructing Mayaro virus circulation in French Guiana shows frequent spillovers

Nature Communications, 2020; 11: 2842. 10.1038/s41467-020-16516-x
Salje H, Tran Kiem C, Lefrancq N, Courtejoie N, Bosetti P, Paireau J, Andronico A, Hozé N, Richet J, Dubost CL, Le Strat Y, Lessler J, Levy-Bruhl D, Fontanet A, Opatowski L, Boelle PY, Cauchemez S

Estimating the burden of SARS-CoV-2 in France.

Science, 2020; 369: 208-211. 10.1126/science.abc3517
Teissier Y, Paul R, Aubry M, Rodo X, Dommar C, Salje H, Sakuntabhai A, Cazelles B, Cao-Lormeau VM

Long-term persistence of monotypic dengue transmission in small size isolated populations, French Polynesia, 1978-2014.

PLoS Neglected Tropical Diseases, 2020; 14: e0008110. 10.1371/journal.pntd.0008110
Lee KH, Nikolay B, Sazzad HMS, Hossain MJ, Khan AKMD, Rahman M, Satter SM, Nichol ST, Klena JD, Pulliam JRC, Kilpatrick AM, Sultana S, Afroj S, Daszak P, Luby S, Cauchemez S, Salje H, Gurley E

Changing contact patterns over disease progression: Nipah virus as a case study.

Journal of Infectious Diseases, 2020; 222(3): 438-442. 10.1093/infdis/jiaa091
David J Haw, Derek A T Cummings, Justin Lessler, Henrik Salje, Jonathan M Read, Steven Riley

Differential mobility and local variation in infection attack rate

PLoS Computational Biology, 2019; 15(1): e1006600. 10.1371/journal.pcbi.1006600
John R. Giles, Henrik Salje, and Justin Lessler

The IDSpatialStats R Package: Quantifying Spatial Dependence of Infectious Disease Spread

The R Journal, 2019; 11/2: 308-327.
K. Ruchusatsawat, P. Wongjaroen, A. Posanacharoen, I. Rodriguez-Barraquer, S. Sangkitporn, D. A.T. Cummings and H. Salje

Observational study into the long-term circulation of Zika in Thailand

Lancet Infectious Diseases, 2019; 19(4): 439-446. 10.1016/S1473-3099(18)30718-7
A. Cousien, S. Abel, A. Monthieux, A. Andronico, I. Calmont, M. Cervantes, R. Césaire, P. Gallian, X. de Lamballerie, C. Laouénan, F. Najioullah, S. Pierre-François, M. Pircher, H. Salje, Q. ten Bosch, A. Cabié, and S. Cauchemez

Assessing Zika virus transmission within households during an outbreak in Martinique, 2015-2016

American Journal of Epidemiology, 2019; 188(7): 1389-1396. 10.1093/aje/kwz091
Birgit Nikolay, Henrik Salje, M Jahangir Hossain, AKM Dawlat Khan, Hossain MS Sazzad, Mahmudur Rahman, Peter Daszak, Ute Ströher, Juliet RC Pulliam, A Marm Kilpatrick, Stuart T Nichol, John D Klena, Sharmin Sultana, Sayma Afroj, Stephen P Luby, Simon Cauchemez, Emily S Gurley

Transmission of Nipah virus: 14 years of investigations in Bangladesh

New England Journal of Medicine, 2019; 380(19): 1804-1814. 10.1056/NEJMoa1805376
S. Hegde, H. Salje, H. Sazzad, M. J. Hossain, M. Rahman, P. Daszak, S. Luby, E. S. Gurley

Using Healthcare Seeking Behaviors to Estimate the Number of Nipah Outbreaks Missed by Hospital-Based Surveillance in Bangladesh

Internation Journal of Epidemiology, 2019; 48(4): 1219-1227. 10.1093/ije/dyz057
Mikhail Churakov, Christian J. Villabona-Arenas, Moritz U. G. Kraemer, Henrik Salje, Simon Cauchemez

Spatio-temporal dynamics of dengue in Brazil: seasonal travelling waves and determinants of regional synchrony

PLoS Neglected Tropical Diseases, 2019; 13(4): e0007012. 10.1371/journal.pntd.0007012
A. M. Weaver, E. S. Gurley, C. Crabtree-Ide, H. Salje, E.-H. Yoo, L. Mu, N. Akter and P. K. Ram

Air pollution dispersion from biomass stoves to neighboring homes in Mirpur, Dhaka, Bangladesh

BMC Public Health, 2019; 19(1): 425. 10.1186/s12889-019-6751-z
I. Rodriguez-Barraquer, H. Salje and DAT Cummings

Opportunities for improved surveillance and control of dengue from age-specific case data

eLife, 2019; 8: e45474. 10.7554/eLife.45474
H. Salje, K. Paul, R. Paul, I. Rodriguez-Barraquer, Z. Rahman, M. S. Alam, M. Rahman, H. M. Al-Amin, J. Heffelfinger and E. Gurley

Nationally-representative serostudy of dengue in Bangladesh allows generalizable disease burden estimates

eLife, 2019; 8: e42869. 10.7554/eLife.42869
C. Flamand, S. Bailly, C. Fritzell, L. Berthelot, J. Vanhomwegen, H. Salje, J. Paireau, S. Matheus, A. Enfissi, S. Fernandes-Pellerin, F. Djossou, S. Linares, J.-F. Carod, M. Kazanji, J.-C. Manuguerra, S. Cauchemez and D. Rousset

Impact of Zika virus emergence in French Guiana: A large general population seroprevalence survey

Journal of Infectious Diseases , 2019; 220(12): 1915-1925. 10.1093/infdis/jiz396
I. Rodriguez-Barraquer, H. Salje and D. A. T. Cummings

Dengue pre-vaccination screening and positive predictive values

Lancet Infectious Diseases , 2019; 19(2): 132-134. 10.1016/S1473-3099(18)30799-0
T. Succo, H. Noël, B. Nikolay, M. Maquart, A. Cochet, I. Leparc-Goffart, O. Catelinois, H. Salje, C. Pelat, P. de Crouy-Chanel, H. de Valk, S. Cauchemez, and C. Rousseau

Dengue serosurvey after a 2-month long outbreak in Nîmes, France, 2015: was there more than met the eye?

Eurosurveillance, 2018; 23: 23. 10.2807/1560-7917.ES.2018.23.23.1700482
M. C. Cortes, S. Cauchemez, N. Lefrancq, S. Luby, M. Hossain, H. Sazzad, M. Rahman, P. Daszak, and H. Salje*, E. Gurley*

Characterization of the spatial and temporal distribution of Nipah virus spillover events in Bangladesh 2007 – 2013

Journal of Infectious Diseases, 2018; 217(9): 1390-1394. 10.1093/infdis/jiy015

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