Publications
* denotes equal contributions
Peer-reviewed
2022
- Archival influenza virus genomes from Europe reveal genomic variability during the 1918 pandemic L. V. Patrono*, B. Vrancken*, M. Budt*, A. Düx, S. Lequime, S. Boral, M. T. P. Gilbert, J. F. Gogarten, L. Hoffmann, D. Horst, K. Merkel, D. Morens, B. Prepoint, J. Schlotterbeck, V. Schuenemann, M. A. Suchard, J. K. Taubenberger, L. Tenkhoff, C. Urban, N. Widulin, E. Winter, M. Worobey, T. Schnalke, T. Wolff, P. Lemey, S. Calvignac-Spencer (2022) Nature Communications 13:2314
- Innate immune pathways act synergistically to constrain RNA virus evolution in Drosophila melanogaster V. Mongelli, S. Lequime, A. Kousathanas, V. Gausson, H. Blanc, L. Quintana-Murci, S. F. Elena & M.-C. Saleh (2022) Nature Ecology and Evolution 6:565–578
- Mutational analysis of Aedes aegypti Dicer 2 provides insights into the biogenesis of antiviral exogenous small interfering RNAs R. J. Gestuveo, R. Parry , L. B. Dickson, S. Lequime, V. B. Sreenu, M. J. Arnold, A. A. Khromykh, E. Schnettler, L. Lambrechts, M. Varjak & A. Kohl (2022) PLoS Pathogens 18(1): e1010202
2021
- Potential role of vector-mediated natural selection in dengue virus genotype/lineage replacements in two epidemiologically contrasted settings O. O’Connor, T. Putita Ou, F. Aubry, S. Dabo, S. Russet, D. Girault, S. In, M. Minier, S. Lequime, T. Hoem, S. Boyer, P. Dussart, N. Pocquet, V. Burtet-Sarramegna, L. Lambrechts, V. Duong & M. Dupont-Rouzeyrol (2021) Emerging Microbes & Infections 10(1): 1346-1357
- Molecular detection and genomic characterization of diverse hepaciviruses in African rodents M. Bletsa, B. Vrancken, S. Gryseels, I. Boonen, A. Fikatas, Y. Li, A. Laudisoit, S. Lequime, J. Bryja, R. Makundi, Y. Meheretu, B. Dudu Akaibe, S. Gambalemoke Mbalitini, F. Van de Perre, N. Van Houtte, J. Těšíková, E. Wollants, M. Van Ranst, J.F. Drexler, E. Verheyen, H. Leirs, J. Gouy de Bellocq, P. Lemey (2021) Virus Evolution 7(1): veab036
- Recent African strains of Zika virus display higher transmissibility and fetal pathogenicity than Asian strains F. Aubry*, S. Jacobs*, M. Darmuzey*, S. Lequime, L. Delang, A. Fontaine, N. Jupatanakul, E. F. Miot, S. Dabo, C. Manet, X. Montagutelli, A. Baidaliuk, F. Gambaro, E. Simon-Lorière, M. Gilsoul, C. M. Romero-Vivas, V.-M. Cao-Lormeau, R. G. Jarman, C. T. Diagne, O. Faye, O. Faye, A. A. Sall, L. Nguyen, J. Neyts, L. Nguyen, S. J. F. Kaptein** & L. Lambrechts** (2021) Nature Communications 12:916
2020
- Modeling intra-mosquito dynamics of Zika virus and its dose-dependence confirms the low epidemic potential of Aedes albopictus S. Lequime, J.-S. Dehecq, S. Matheus, F. de Laval, L. Almeras, S. Briolant & A. Fontaine (2020) PLoS Pathogens 16(12): e1009068
- Phylogeographic and phylodynamic approaches to epidemiological hypothesis testing S. Dellicour, S. Lequime, B. Vrancken, M. S. Gill, P. Bastide, K. Gangavarapu, N. Matteson, Y. Tan, L. du Plessis, A. A. Fisher, M. I. Nelson, M. Gilbert, M. A. Suchard, K. G. Andersen, N. D. Grubaugh, O. G. Pybus & P. Lemey (2020) Nature Communications 11:5620
- Experimental adaptation of dengue virus 1 to Aedes albopictus mosquitoes by in vivo selection R. Bellone*, S. Lequime*, H. Jupille*, G. P. Göertz, F. Aubry, L. Mousson, G. Piorkowski, P.-S. Yen, G. Gabiane, M. Vazeille, A. Sakuntabhai, G. P. Pijlman, X. de Lamballerie, L. Lambrechts & A.-B. Failloux (2020) Scientific Reports 10:18404
- Wolbachia modulates prevalence and viral load of Culex pipiens densoviruses in natural populations M. Altinli, S. Lequime, C. Atyame, F. Justy, M. Weill, M. Sicard (2020) Molecular Ecology 29(20):4000-4013
- Non-retroviral endogenous viral element limits cognate virus replication in Aedes aegypti ovaries Y. Suzuki, A. Baidaliuk, P. Miesen, L. Frangeul, A. B. Crist, S. H. Merkling, A. Fontaine, S. Lequime, I. Moltini-Conclois, H. Blanc, R. P. van Rij, L. Lambrechts & M.-C. Saleh (2020) Current Biology 30(18): 3495-3506
- Measles virus and rinderpest virus divergence dated to the sixth century BCE A. Düx*, S. Lequime*, L. V. Patrono, B. Vrancken, S. Boral, J. F. Gogarten, A. Hilbig, D. Horst, K. Merkel, B. Prepoint, S. Santibanez, J. Schlotterbeck, M. A. Suchard, M. Ulrich, N. Widulin, A. Mankertz, F. H. Leendertz, K. Harper, P. Lemey** & S. Calvignac-Spencer** (2020) Science 368(6497): 1367-1370
- nosoi: a stochastic agent-based transmission chain simulation framework in R S. Lequime, P. Bastide, S. Dellicour, P. Lemey & G. Baele (2020) Methods in Ecology and Evolution. 11:1002-1007
- Genomic epidemiology of 2015–2016 Zika virus outbreak in Cape Verde O. Faye*, M. de Lourdes Monteiro*, B. Vrancken*, M. Prot*, S. Lequime, M. Diarra, O. Ndiaye, T. Valdez, S. Tavarez, J. Ramos, S. Leal, C. Pires, A. Moreira, M. F. Tavares, L. Fernandes, J. N. Narreto, M. do Céu Teixeira, M. da Luz de Lima Mendonça, C. Cardosa da Sila Laite Gomes, M. S. Castellon, L. Ma, F. Lemoine, F. Gambaro, D. Delaune, G. Fall, M. Diop, A. Sakuntabhai, C. Loucoubar, P. Lemey, E. C. Holmes, O. Faye, A. A. Sall & E. Simon-Lorière. (2020) Emerging Infectious Diseases 26(6):1084-1090
- Novel genome sequences of cell-fusing agent virus allow comparison of virus phylogeny with the genetic structure of Aedes aegypti populations A. Baidaliuk, S. Lequime, I. Moltini-Conclois, S. Dabo, L. B. Dickson, M. Prot, V. Duong, P. Dussart, S. Boyer, C. Shi, J. Matthijnssens, J. Guglielmini, A. Gloria-Soria, E. Simon-Lorière & L. Lambrechts (2020) Virus Evol. 6(1): veaa018
2019
- Evolution and phylogeography of Culex pipiens densovirus M. Altinli, S. Lequime, M. Courcelle, S. François, F. Justy, A.-S. Gosselin-Grenet, M. Ogliastro, M. Weill & M. Sicard (2019) Virus Evol. 5(2): vez053
- Cell-fusing agent virus reduces arbovirus dissemination in Aedes aegypti mosquitoes in vivo A. Baidaliuk, E. Miot, S. Lequime, I. Moltini-Conclois, F. Delaigue, S. Dabo, L. Dickson, F. Aubry, S. Merkling, V.-M. Cao-Lormeau & L. Lambrechts (2019) J. Virol. 93:e00705-19
- RNA Structure Duplication in the Dengue Virus 3′ UTR: Redundancy or Host Specificity? L. de Borba, S. M. Villordo, F. L. Marsico, J. M. Carballeda, C. V. Filomatori, L. G. Gebhard, H. M. Pallarés, S. Lequime, L. Lambrechts, I. Sánchez Vargas, C. D. Blair & A. V. Gamarnik (2019) mBio 10(1) e02506-18
2018
- Epidemiological significance of dengue virus genetic variation in mosquito infection dynamics A. Fontaine, S. Lequime, I. Moltini-Conclois, D. Jiolle, I. Leparc-Goffart, R. C. Reiner Jr. & L. Lambrechts (2018) PLoS Pathog. 14(7): e1007187
- A survey of virus recombination uncovers canonical features of artificial chimeras generated during library preparation J. Peccoud, S. Lequime, I. Conclois, I. Giraud, L. Lambrechts & C. Gilbert (2018) G3 (Bethesda) 8(4): 1129-1138
2017
- Full-genome dengue virus sequencing in mosquito saliva shows lack of convergent positive selection during transmission by Aedes aegypti S. Lequime*, V. Richard*, V.-M. Cao-Lormeau & L. Lambrechts (2017) Virus Evol. 3(2): vex031
- Discovery of flavivirus-derived endogenous viral elements in Anopheles mosquito genomes supports the existence of Anopheles-associated insect-specific flaviviruses S. Lequime & L. Lambrechts (2017) Virus Evol. 3(1): vew035
2016
- Evolutionary dynamics of dengue virus populations within the mosquito vector. L. Lambrechts & S. Lequime (2016) Curr. Opin. Virol. 21: 47-53
- Genetic drift, purifying selection and vector genotype shape dengue virus intra-host genetic diversity in mosquitoes S. Lequime, A. Fontaine, M. Ar Gouilh, I. Conclois-Moltini & L. Lambrechts (2016) PLoS Genet. 12(6): e1006111
- Determinants of arbovirus vertical transmission in mosquitoes S. Lequime, R. E. Paul & L. Lambrechts (2016) PLoS Pathog. 12(5): e1005548
- Excretion of dengue virus RNA by Aedes aegypti allows non-destructive monitoring of viral dissemination in individual mosquitoes A. Fontaine, D. Jiolle, I. Moltini-Conclois, S. Lequime & L. Lambrechts (2016) Sci. Rep. 6: 24885
2014
- Vertical transmission of arboviruses in mosquitoes: a historical perspective S. Lequime & L. Lambrechts (2014) Infect. Genet. Evol. 28:681-90
2010
- Covering all bases in HIV research: unveiling a hidden world of viral evolution. B. Vrancken, S. Lequime, K. Theys & P. Lemey (2010) AIDS Reviews 12(2): 89-102.
Preprints
- Discovery of Flaviviridae-derived endogenous viral elements in shrew genomes provide novel insights into Pestivirus ancient history YQ. Li, M. Bletsa, Z. Zisi, I. Boonen, S. Gryseels, L. Kafetzopoulou, J. P. Webster, S. Catalano, O. G Pybus, F. Van de Perre, H. Li, YY. Li, YC. Li, A. Abramov, P. Lymberakis, P. Lemey, S. Lequime (2022) bioRxiv 2022.02.11.480044