Publications

Mateescu, I., & Lequime, S. (2024). Dengue-mediated changes in the vectorial capacity of Aedes aegypti (Diptera: Culicidae): Manipulation of transmission or infection by-product? Journal of medical entomology. Advance online publication. https://doi.org/10.1093/jme/tjae134

Ritsch, M., Brait, N., Harvey, E., Marz, M., & Lequime, S. (2024). Endogenous viral elements: insights into data availability and accessibility. Virus Evolution, 10(1), veae099. https://doi.org/10.1093/ve/veae099

Brait, N., Hackl, T., Morel, C., Exbrayat, A., Gutierrez, S., & Lequime, S. (2024). A tale of caution: How endogenous viral elements affect virus discovery in transcriptomic data. Virus Evolution, 10(1), Article vead088. https://doi.org/10.1093/ve/vead088

Viginier, B., Cappuccio, L., Garnier, C., Martin, E., Maisse, C., Valiente moro, C., Minard, G., Fontaine, A., Lequime, S., Ratinier, M., Arnaud, F., & Raquin, V. (2023). Chikungunya intra-vector dynamics in Aedes albopictus from Lyon (France) upon exposure to a human viremia-like dose range reveals vector barrier’s permissiveness and supports local epidemic potential. Peer Community Journal, 3, Article e96. https://doi.org/10.24072/pcjournal.326

van der Loos, L. M., De Coninck, L., Zell, R., Lequime, S., Willems, A., De Clerck, O., & Matthijnssens, J. (2023). Highly divergent CRESS DNA and picorna-like viruses associated with bleached thalli of the green seaweed Ulva. Microbiology Spectrum, 11(5), Article e0025523. https://doi.org/10.1128/spectrum.00255-23

Selhorst, P., Lequime, S., Dudas, G., Proesmans, S., Lutumba, P., Katshongo, F., Ramadan, K., Micalessi, I., Ahuka-Mundeke, S., Vanlerberghe, V., Van Esbroeck, M., & Ariën, K. (2023). Phylogeographic analysis of dengue virus serotype 1 and cosmopolitan serotype 2 in Africa. International Journal of Infectious Diseases, 133, 46-52. https://doi.org/10.1016/j.ijid.2023.04.391

Lequime, S. (2023). The sociality continuum of viruses: A commentary on Leeks et al. 2023. Journal of Evolutionary Biology, 36(11), 1568-1570. https://doi.org/10.1111/jeb.14247

Lensink, M. J., Li, Y., & Lequime, S. (2022). Aquatic flaviviruses. Journal of Virology, 96(17), Article e0043922. https://doi.org/10.1128/jvi.00439-22

Patrono, L. V., Vrancken, B., Budt, M., Düx, A., Lequime, S., Boral, S., Gilbert, M. T. P., Gogarten, J. F., Hoffmann, L., Horst, D., Merkel, K., Morens, D., Prepoint, B., Schlotterbeck, J., Schuenemann, V. J., Suchard, M. A., Taubenberger, J. K., Tenkhoff, L., Urban, C., ... Calvignac-Spencer, S. (2022). Archival influenza virus genomes from Europe reveal genomic variability during the 1918 pandemic. Nature Communications, 13(1), 2314. https://doi.org/10.1038/s41467-022-29614-9

Li, Y. Q., Bletsa, M., Zisi, Z., Boonen, I., Gryseels, S., Kafetzopoulou, L. E., Webster, J. P., Catalano, S., Pybus, O. G., Van de Perre, F., Li, H. T., Li, Y. Y., Li, Y. C., Abramov, A., Lymberakis, P., Lemey, P., & Lequime, S. (2022). Endogenous viral elements in shrew genomes provide insights into Pestivirus ancient history. Molecular Biology and Evolution, 39(10), Article msac190. https://doi.org/10.1093/molbev/msac190

Masika, F. B., Lequime, S., Alicai, T., Athman, S. Y., Ipulet, P., Ddamulira, G., & Tugume, A. K. (2022). First report of Pepo aphid-borne yellows virus infecting watermelon (Citrullus lanatus) in Uganda. New Disease Reports, 46(1), Article e12110. https://doi.org/10.1002/ndr2.12110

Mongelli, V., Lequime, S., Kousathanas, A., Gausson, V., Blanc, H., Nigg, J., Quintana-Murci, L., Elena, S. F., & Saleh, M.-C. (2022). Innate immune pathways act synergistically to constrain RNA virus evolution in Drosophila melanogaster. Nature Ecology & Evolution, 6, 565–578. https://doi.org/10.1038/s41559-022-01697-z

Gestuveo, R. J., Parry, R., Dickson, L. B., Lequime, S., Sreenu, V. B., Arnold, M. J., Khromykh, A. A., Schnettler, E., Lambrechts, L., Varjak, M., & Kohl, A. (2022). Mutational analysis of Aedes aegypti Dicer 2 provides insights into the biogenesis of antiviral exogenous small interfering RNAs. PLoS Pathogens, 18(1), Article e1010202. https://doi.org/10.1371/journal.ppat.1010202

Sourrouille, Z. A., Schwarzer, S., Lequime, S., Oksanen, H. M., & Quax, T. E. F. (2022). The viral susceptibility of the Haloferax species. Viruses, 14(6), Article 1344. https://doi.org/10.3390/v14061344

Bletsa, M., Vrancken, B., Gryseels, S., Boonen, I., Fikatas, A., Li, Y., Laudisoit, A., Lequime, S., Bryja, J., Makundi, R., Meheretu, Y., Akaibe, B. D., Mbalitini, S. G., Van de Perre, F., Van Houtte, N., Těšíková, J., Wollants, E., Van Ranst, M., Pybus, O. G., ... Lemey, P. (2021). Molecular detection and genomic characterization of diverse hepaciviruses in African rodents. Virus Evolution, 7(1), Article veab036. https://doi.org/10.1093/ve/veab036

O’Connor, O., Ou, T. P., Aubry, F., Dabo, S., Russet, S., Girault, D., In, S., Minier, M., Lequime, S., Hoem, T., Boyer, S., Dussart, P., Pocquet, N., Burtet-Sarramegna, V., Lambrechts, L., Duong, V., & Dupont-Rouzeyrol, M. (2021). Potential role of vector-mediated natural selection in dengue virus genotype/lineage replacements in two epidemiologically contrasted settings. Emerging Microbes and Infections, 10(1), 1346-1357. https://doi.org/10.1080/22221751.2021.1944789

Aubry, F., Jacobs, S., Darmuzey, M., Lequime, S., Delang, L., Fontaine, A., Jupatanakul, N., Miot, E. F., Dabo, S., Manet, C., Montagutelli, X., Baidaliuk, A., Gámbaro, F., Simon-Lorière, E., Gilsoul, M., Romero-Vivas, C. M., Cao-Lormeau, V.-M., Jarman, R. G., Diagne, C. T., ... Lambrechts, L. (2021). Recent African strains of Zika virus display higher transmissibility and fetal pathogenicity than Asian strains. Nature Communications, 12(1), 1-14. Article 916. https://doi.org/10.1038/s41467-021-21199-z

Vrancken, B., & Lequime, S. (2020). Een verhelderende kijk in het duistere verleden. Analyse, 75(5).

Dellicour, S., Lequime, S., Vrancken, B., Gill, M. S., Bastide, P., Gangavarapu, K., Matteson, N. L., Tan, Y., du Plessis, L., Fisher, A. A., Nelson, M. I., Gilbert, M., Suchard, M. A., Andersen, K. G., Grubaugh, N. D., Pybus, O. G., & Lemey, P. (2020). Epidemiological hypothesis testing using a phylogeographic and phylodynamic framework. Nature Communications, 11(1), Article 5620. https://doi.org/10.1038/s41467-020-19122-z

Bellone, R., Lequime, S., Jupille, H., Göertz, G. P., Aubry, F., Mousson, L., Piorkowski, G., Yen, P.-S., Gabiane, G., Vazeille, M., Sakuntabhai, A., Pijlman, G. P., de Lamballerie, X., Lambrechts, L., & Failloux, A.-B. (2020). Experimental adaptation of dengue virus 1 to Aedes albopictus mosquitoes by in vivo selection. Scientific Reports, 10(1), Article 18404. https://doi.org/10.1038/s41598-020-75042-4

Faye, O., de Lourdes Monteiro, M., Vrancken, B., Prot, M., Lequime, S., Diarra, M., Ndiaye, O., Valdez, T., Tavarez, S., Ramos, J., da Veiga Leal, S., Pires, C., Moreira, A., Tavares, M. F., Fernandes, L., Barreto, J. N., do Céu Teixeira, M., de Lima Mendonça, M. D. L., Gomes, C. C. D. S. L., ... Simon-Loriere, E. (2020). Genomic epidemiology of 2015-2016 Zika virus outbreak in Cape Verde. Emerging Infectious Diseases, 26(6), 1084-1090. https://doi.org/10.3201/eid2606.190928

Altinli, M., Lequime, S., Atyame, C., Justy, F., Weill, M., & Sicard, M. (2020). Wolbachia modulates prevalence and viral load of Culex pipiens densoviruses in natural populations. Molecular Ecology, 29(20), 4000-4013. https://doi.org/10.1111/mec.15609

Düx, A., Lequime, S., Patrono, L. V., Vrancken, B., Boral, S., Gogarten, J. F., Hilbig, A., Horst, D., Merkel, K., Prepoint, B., Santibanez, S., Schlotterbeck, J., Suchard, M. A., Ulrich, M., Widulin, N., Mankertz, A., Leendertz, F. H., Harper, K., Schnalke, T., ... Calvignac-Spencer, S. (2020). Measles virus and rinderpest virus divergence dated to the sixth century BCE. Science, 368(6497), 1367-1370. https://doi.org/10.1126/science.aba9411

Lequime, S., Dehecq, J.-S., Matheus, S., de Laval, F., Almeras, L., Briolant, S., & Fontaine, A. (2020). Modeling intra-mosquito dynamics of Zika virus and its dose-dependence confirms the low epidemic potential of Aedes albopictus. PLoS Pathogens, 16(12), Article e1009068. https://doi.org/10.1371/journal.ppat.1009068

Suzuki, Y., Baidaliuk, A., Miesen, P., Frangeul, L., Crist, A. B., Merkling, S. H., Fontaine, A., Lequime, S., Moltini-Conclois, I., Blanc, H., van Rij, R. P., Lambrechts, L., & Saleh, M.-C. (2020). Non-retroviral endogenous viral element limits cognate virus replication in Aedes aegypti ovaries. Current Biology, 30(18), 3495-3506.e6. https://doi.org/10.1016/j.cub.2020.06.057

Lequime, S., Paul, B., Dellicour, S., Lemey, P., & Baele, G. (2020). nosoi: A stochastic agent-based transmission chain simulation framework in R. Methods in ecology and evolution, 11(8), 1002-1007. https://doi.org/10.1111/2041-210X.13422

Baidaliuk, A., Lequime, S., Moltini-Conclois, I., Dabo, S., Dickson, L. B., Prot, M., Duong, V., Dussart, P., Boyer, S., Shi, C., Matthijnssens, J., Guglielmini, J., Gloria-Soria, A., Simon-Lorière, E., & Lambrechts, L. (2020). Novel genome sequences of cell-fusing agent virus allow comparison of virus phylogeny with the genetic structure of Aedes aegypti populations. Virus Evolution, 6(1), Article veaa018. https://doi.org/10.1093/ve/veaa018

Baidaliuk, A., Miot, E. F., Lequime, S., Moltini-Conclois, I., Delaigue, F., Dabo, S., Dickson, L. B., Aubry, F., Merkling, S. H., Cao-Lormeau, V.-M., & Lambrechts, L. (2019). Cell-fusing agent virus reduces arbovirus dissemination in Aedes aegypti mosquitoes in vivo. Journal of Virology, 93(18). https://doi.org/10.1128/JVI.00705-19

Altinli, M., Lequime, S., Courcelle, M., François, S., Justy, F., Gosselin-Grenet, A.-S., Ogliastro, M., Weill, M., & Sicard, M. (2019). Evolution and phylogeography of Culex pipiens densovirus. Virus Evolution, 5(2), Article vez053. https://doi.org/10.1093/ve/vez053

de Borba, L., Villordo, S. M., Marsico, F. L., Carballeda, J. M., Filomatori, C. V., Gebhard, L. G., Pallarés, H. M., Lequime, S., Lambrechts, L., Sánchez Vargas, I., Blair, C. D., & Gamarnik, A. V. (2019). RNA structure duplication in the dengue virus 3' UTR: Redundancy or host specificity? mBio, 10(1). https://doi.org/10.1128/mBio.02506-18

Peccoud, J., Lequime, S., Moltini-Conclois, I., Giraud, I., Lambrechts, L., & Gilbert, C. (2018). A survey of virus recombination uncovers canonical features of artificial chimeras generated during deep sequencing library preparation. G3 : Genes, Genomes, Genetics, 8(4), 1129-1138. https://doi.org/10.1534/g3.117.300468

Fontaine, A., Lequime, S., Moltini-Conclois, I., Jiolle, D., Leparc-Goffart, I., Reiner, R. C., & Lambrechts, L. (2018). Epidemiological significance of dengue virus genetic variation in mosquito infection dynamics. PLoS Pathogens, 14(7), Article e1007187. https://doi.org/10.1371/journal.ppat.1007187

Lequime, S., & Lambrechts, L. (2017). Discovery of flavivirus-derived endogenous viral elements in Anopheles mosquito genomes supports the existence of Anopheles-associated insect-specific flaviviruses. Virus Evolution, 3(1), Article vew035. https://doi.org/10.1093/ve/vew035

Lequime, S., Richard, V., Cao-Lormeau, V.-M., & Lambrechts, L. (2017). Full-genome dengue virus sequencing in mosquito saliva shows lack of convergent positive selection during transmission by Aedes aegypti. Virus Evolution, 3(2), Article vex031. https://doi.org/10.1093/ve/vex031

Lequime, S., Paul, R. E., & Lambrechts, L. (2016). Determinants of arbovirus vertical transmission in mosquitoes. PLoS Pathogens, 12(5), Article e1005548. https://doi.org/10.1371/journal.ppat.1005548

Lambrechts, L., & Lequime, S. (2016). Evolutionary dynamics of dengue virus populations within the mosquito vector. Current opinion in virology, 21, 47-53. https://doi.org/10.1016/j.coviro.2016.07.013

Fontaine, A., Jiolle, D., Moltini-Conclois, I., Lequime, S., & Lambrechts, L. (2016). Excretion of dengue virus RNA by Aedes aegypti allows non-destructive monitoring of viral dissemination in individual mosquitoes. Scientific Reports, 6, Article 24885. https://doi.org/10.1038/srep24885

Lequime, S., Fontaine, A., Ar Gouilh, M., Moltini-Conclois, I., & Lambrechts, L. (2016). Genetic drift, purifying selection and vector genotype shape dengue virus intra-host genetic diversity in mosquitoes. PLoS genetics, 12(6), e1006111. https://doi.org/10.1371/journal.pgen.1006111

Lequime, S., & Lambrechts, L. (2014). Vertical transmission of arboviruses in mosquitoes: A historical perspective. Infection genetics and evolution, 28, 681-90. https://doi.org/10.1016/j.meegid.2014.07.025

Vrancken, B., Lequime, S., Theys, K., & Lemey, P. (2010). Covering all bases in HIV research: Unveiling a hidden world of viral evolution. Aids reviews, 12(2), 89-102.