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Research GELIFES GREEN Lequime Lab

Publications

2023

Brait, N., Hackl, T., Morel, C., Exbrayat, A., Gutierrez, S., & Lequime, S. (2023). A tale of caution: How endogenous viral elements affect virus discovery in transcriptomic data. Virus evolution. Advance online publication. 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

2022

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

2021

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

2020

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
Lequime, S. (Author), Harrivelle, P.-B. (Designer), & Louis, T. (Developer). (2020). Épisode 1 - La Lumière de l'Évolution. Digital or Visual Products, VirEvo @virevo6268. https://www.youtube.com/watch?v=NOzPcPjy7gw
Lequime, S. (Author), Harrivelle, P.-B. (Designer), & Louis, T. (Developer). (2020). Épisode 2 - Reconstruire le Passé. Digital or Visual Products, VirEvo @virevo6268. https://www.youtube.com/watch?v=5Mijs_Q-G9I
Lequime, S. (Author), Harrivelle, P.-B. (Designer), & Louis, T. (Developer). (2020). Épisode 3 - Comprendre les Épidémies. Digital or Visual Products, VirEvo @virevo6268. https://www.youtube.com/watch?v=LlwhVtVRZpo
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
Lequime, S. (Developer), Bastide, P. (Photographer), Dellicour, S. (Photographer), Lemey, P. (Photographer), & Baele, G. (Photographer). (2020). nosoi package for R: stochastic agent-based transmission chain simulator. Software
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

2019

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

2018

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

2017

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

2016

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

2014

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

2010

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.
Last modified:09 June 2023 8.36 p.m.