Publications

Dispersal history of SARS-CoV-2 in Galicia, Spain
P. Gallego-García, N. Estévez-Gómez, L. De Chiara, P. Alvariño, P. M. Juiz-González, I. Torres-Beceiro, M. Poza, J. A. Vallejo, S. Rumbo-Feal, K. Conde-Pérez, P. Aja-Macaya, S. Ladra, A. Moreno-Flores, M. J. Gude-González, A. Coira, A. Aguilera, J. J. Costa-Alcalde, R. Trastoy, G. Barbeito-Castiñeiras, D. García-Souto, J. M. C. Tubio, M. Trigo-Daporta, P. Camacho-Zamora, J. G. Costa, M. González-Domínguez, L. Canoura-Fernández, D. Glez-Peña, S. Pérez-Castro, J. J. Cabrera, C. Daviña-Núñez, M. Godoy-Diz, A. B. Treinta-Álvarez, M. I. Veiga, J. C. Sousa, N. S. Osório, I. Comas, F. González-Candelas, S. L. Hong, N. Bollen, S. Dellicour, G. Baele, M. A. Suchard, P. Lemey, A. Agulla, G. Bou, P. Alonso-García, M. L. Pérez-del-Molino, M. García-Campello, I. Paz-Vidal, B. Regueiro, and D. Posada. "Journal of Medical Virology", Vol. 96, Issue 7, Pages e29773, 2024.

Integrating indicator-based and event-based surveillance data for risk mapping of West Nile virus, Europe, 2006 to 2021
K. Serres, D. Erazo, G. Despréaux, M. F. Vincenti-González, W. V. Bortel, E. Arsevska, and S. Dellicour. "Eurosurveillance", Vol. 29, Issue 44, Pages 2400084, 2024.

Emergence of the B.1.214.2 SARS-CoV-2 lineage with an Omicron-like spike insertion and a unique upper airway immune signature
A. Holtz, J. Van Weyenbergh, S. L. Hong, L. Cuypers, Á. O’Toole, G. Dudas, M. Gerdol, B. I. Potter, F. Ntoumi, C. C. M. Mapanguy, B. Vanmechelen, T. Wawina-Bokalanga, B. Van Holm, S. M. Menezes, K. Soubotko, G. Van Pottelbergh, E. Wollants, P. Vermeersch, A.-S. Jacob, B. Maes, D. Obbels, V. Matheeussen, G. Martens, J. Gras, B. Verhasselt, W. Laffut, C. Vael, T. Goegebuer, R. van der Kant, F. Rousseau, J. Schymkowitz, L. Serrano, J. Delgado, T. Wenseleers, V. Bours, E. André, M. A. Suchard, A. Rambaut, S. Dellicour, P. Maes, K. Durkin, and G. Baele. "BMC Infectious Diseases", Vol. 24, Issue 1, Pages 1139, 2024.

A spatially-heterogeneous impact of fencing on the African swine fever wavefront in the Korean wild boar population
J.-S. Lim, T. Vergne, E. Kim, C. Guinat, S. Dellicour, and M. Andraud. "Veterinary Research", 2024.

Intrahost evolution leading to distinct lineages in the upper and lower respiratory tracts during SARS-CoV-2 prolonged infection
M. El Moussaoui, S. Bontems, C. Meex, M.-P. Hayette, M. Lejeune, S. L. Hong, S. Dellicour, M. Moutschen, N. Cambisano, N. Renotte, V. Bours, G. Darcis, M. Artesi, and K. Durkin. "Virus Evolution", Vol. 10, Issue 1, Pages veae073, 2024.

Modeling the velocity of evolving lineages and predicting dispersal patterns
P. Bastide, P. Rocu, J. Wirtz, G. W. Hassler, F. Chevenet, D. Fargette, M. A. Suchard, S. Dellicour, P. Lemey, and S. Guindon. "Proceedings of the National Academy of Sciences USA", 2024.

Impact of Quaternary Amazonian river dynamics on the diversification of uakari monkeys (genus Cacajao)
F. E. Silva, L. W. Luna, R. Batista, F. Röhe, C. Gubili, I. P. Farias, T. Hrbek, J. Valsecchi, C. C. Ribas, A. D. McDevitt, S. Dellicour, J.-F. Flot, and J. P. Boubli. "Journal of Biogeography", Vol. 51, Issue 8, Pages 1505-1517, 2024.

Emergence and dissemination of SARS-CoV-2 XBB.1.5 in New York
F. Gámbaro, R. Duerr, D. Dimartino, C. Marier, E. Iturrate, M. J. Mulligan, A. Heguy, and S. Dellicour. "Virus Evolution", Vol. 10, Issue 1, Pages veae035, 2024.

Comparative population genetics of habitat-forming octocorals in two marine protected areas: eco-evolutionary and management implications
M. Horaud, R. Arizmendi-Meija, E. Nebot-Colomer, P. López-Sendino, A. Antunes, S. Dellicour, F. Viard, R. Leblois, C. Linares, J. Garrabou, and J.-B. Ledoux. "Conservation Genetics", Vol. 25, Issue 2, Pages 319-334, 2024.

Genetic insights of H9N2 avian influenza viruses circulating in Mali and phylogeographic patterns in Northern and Western Africa
I. N. Sanogo, C. Guinat, S. Dellicour, M. A. Diakité, M. Niang, O. A. Koita, C. Camus, and M. Ducatez. "Virus Evolution", Vol. 10, Issue 1, Pages veae011, 2024.

Projected decline in European bumblebee populations in the twenty-first century
G. Ghisbain, W. Thiery, F. Massonnet, D. Erazo, P. Rasmont, D. Michez, and S. Dellicour. "Nature", Vol. 628, Issue 8007, Pages 337-341, 2024.

Dispersion patterns of SARS-CoV-2 variants Gamma, Lambda and Mu in Latin America and the Caribbean
T. Gräf, A. A. Martinez, G. Bello, S. Dellicour, P. Lemey, V. Colizza, M. Mazzoli, C. Poletto, V. L. O. Cardoso, A. F. da Silva, F. C. Motta, P. C. Resende, M. M. Siqueira, L. Franco, L. Gresh, J.-M. Gabastou, A. Rodriguez, A. Vicari, S. Aldighieri, J. Mendez-Rico, and J. A. Leite. "Nature Communications", Vol. 15, Issue 1, Pages 1837, 2024.

Contribution of climate change to the spatial expansion of West Nile virus in Europe
D. Erazo, L. Grant, G. Ghisbain, G. Marini, F. J. Colón-González, W. Wint, A. Rizzoli, W. Van Bortel, C. B. F. Vogels, N. D. Grubaugh, M. Mengel, K. Frieler, W. Thiery, and S. Dellicour. "Nature Communications", Vol. 15, Issue 1, Pages 1196, 2024.

Application of phylodynamic tools to inform the public health response to COVID-19: qualitative analysis of expert opinions
S. N. Rich, V. Richards, C. Mavian, B. R. Magalis, N. Grubaugh, S. A. Rasmussen, S. Dellicour, B. Vrancken, C. Carrington, R. Fisk-Hoffman, D. Danso-Odei, D. Chacreton, J. Shapiro, M. N. Seraphin, C. Hepp, A. Black, A. Dennis, N. S. Trovão, A.-M. Vandamme, A. Rasmussen, M. Lauzardo, N. Dean, M. Salemi, and M. Prosperi. "JMIR Formative Research", Vol. 7, Issue 1, Pages e39409, 2023.

Impact and mitigation of sampling bias to determine viral spread: Evaluating discrete phylogeography through CTMC modeling and structured coalescent model approximations
M. Layan, N. F. Müller, S. Dellicour, N. De Maio, H. Bourhy, S. Cauchemez, and G. Baele. "Virus Evolution", Vol. 9, Issue 1, Pages vead010, 2023.

Phylogeographic reconstruction of the emergence and spread of Powassan virus in the northeastern United States
C. B. F. Vogels, D. E. Brackney, A. P. Dupuis, R. M. Robich, J. R. Fauver, A. F. Brito, S. C. Williams, J. F. Anderson, C. B. Lubelczyk, R. E. Lange, M. A. Prusinski, L. D. Kramer, J. L. Gangloff-Kaufmann, L. B. Goodman, G. Baele, R. P. Smith*, P. M. Armstrong*, A. T. Ciota*, S. Dellicour*, and N. D. Grubaugh*. *Equal contribution
"Proceedings of the National Academy of Sciences USA", Vol. 120, Issue 16, Pages e2218012120, 2023.

Genomic assessment of invasion dynamics of SARS-CoV-2 Omicron BA.1
J.-H. Tsui, J. T. McCrone, B. Lambert, S. Bajaj, R. P. D. Inward, P. Bosetti, R. E. Pena, H. Tegally, V. Hill, A. E. Zarebski, T. P. Peacock, L. Liu, N. Wu, M. Davis, I. I. Bogoch, K. Khan, M. Kall, N. I. B. Abdul Aziz, R. Colquhoun, Á. O’Toole, B. Jackson, A. Dasgupta, E. Wilkinson, T. de Oliveira, The COVID-19 Genomics UK (COG-UK) consortium, T. R. Connor, N. J. Loman, V. Colizza, C. Fraser, E. Volz, X. Ji, B. Gutierrez, M. Chand, S. Dellicour, S. Cauchemez, J. Raghwani, M. A. Suchard, P. Lemey, A. Rambaut, O. G. Pybus, and M. U. G. Kraemer. "Science", Vol. 381, Issue 6655, Pages 336-343, 2023.

Comparing the evolutionary dynamics of predominant SARS-CoV-2 virus lineages co-circulating in Mexico
H. G. Castelán-Sánchez*, L. Delaye*, R. P. Inward*, S. Dellicour*, B. Gutierrez*, N. Martinez de la Vina, C. Boukadida, O. G. Pybus, G. de Anda Jáuregui, P. Guzmán, M. Flores-Garrido, Ó. Fontanelli, M. Hernández Rosales, A. Meneses, G. Olmedo-Alvarez, A. H. Herrera-Estrella, A. Sánchez-Flores, J. E. Muñoz-Medina, A. Comas-García, B. Gómez-Gil, S. Zárate, B. Taboada, S. López, C. F. Arias, M. U. Kraemer, A. Lazcano, and M. Escalera Zamudio. *Equal contribution
"eLife", Vol. 12, Pages e82069, 2023.

Uncovering the endemic circulation of rabies in Cambodia
M. Layan, L. Dacheux, P. Lemey, K. Brunker, L. Ma, C. Troupin, P. Dussart, V. Chevalier, J. L. N. Wood, S. Ly, V. Duong, H. Bourhy, and S. Dellicour. "Molecular Ecology", Vol. 32, Issue 18, Pages 5140-5155, 2023.

Genomic monitoring of SARS-CoV-2 variants using sentinel SARI hospital surveillance
S. Denayer, F. E. Dufrasne, B. Monsieurs, R. van Eycken, S. Houben, L. Seyler, T. Demuyser, E. van Nedervelde, M. Bourgeois, B. Delaere, K. Magerman, D. Jouck, B. Lissoir, C. Sion, M. Reynders, E. Petit, N. Dauby, M. Hainaut, L. Laenen, P. Maes, G. Baele, S. Dellicour, L. Cuypers, E. André, S. Couvreur, R. Brondeel, C. Barbezange, N. Bossuyt, and S. van Gucht. "Influenza and Other Respiratory Viruses", Vol. 17, Issue 10, Pages e13202, 2023.

Dispersal history and bidirectional human-fish host switching of invasive, hypervirulent Streptococcus agalactiae sequence type 283
D. Schar, Z. Zhang, J. Pires, B. Vrancken, M. A. Suchard, P. Lemey, M. Ip, M. Gilbert, T. V. Boeckel, and S. Dellicour. "PLoS Global Public Health", Vol. 3, Issue 10, Pages e0002454, 2023.

Investigation of an international water polo tournament in Czechia as a potential source for early introduction of the SARS-CoV-2 Omicron variant into Belgium, Switzerland and Germany, November 2021
C. Rudin, N. Bollen, S. L. Hong, F. Wegner, L. Politi, K. Mellou, C. Geenen, S. Gorissen, B. Verhasselt, K. Durkin, C. Henin, A.-S. Logist, S. Dellicour, T. Resa, T. Stadler, P. Maes, L. Cuypers, E. André, A. Egli, and G. Baele. "Eurosurveillance", Vol. 28, Issue 45, Pages 2300018, 2023.

Genomic epidemiology of West Nile virus in Europe
R. T. Koch, D. Erazo, A. J. Folly, N. Johnson, S. Dellicour, N. D. Grubaugh, and C. B. F. Vogels. "One Health", Vol. 18, Pages 100664, 2023.

Complete genome reconstruction of the global and European regional dispersal history of the lumpy skin disease virus
S. Van Borm*, S. Dellicour*, D. P. Martin, P. Lemey, E. I. Agianniotaki, E. D. Chondrokouki, D. Vidanovic, N. Vaskovic, T. Petroviċ, S. Laziċ, X. Koleci, A. Vodica, I. Djadjovski, K. Krstevski, F. Vandenbussche, A. Haegeman, K. De Clercq, and E. Mathijs. *Equal contribution
"Journal of Virology", Vol. 97, Issue 11, Pages e01394-23, 2023.

Unravelling the effect of New Year’s Eve celebrations on SARS-CoV-2 transmission
C. Geenen, J. Thibaut, L. Laenen, J. Raymenants, L. Cuypers, P. Maes, S. Dellicour, and E. André. "Scientific Reports", Vol. 13, Issue 1, Pages 22195, 2023.

Variant-specific introduction and dispersal dynamics of SARS-CoV-2 in New York City – from Alpha to Omicron
S. Dellicour, S. L. Hong, V. Hill, D. Dimartino, C. Marier, P. Zappile, G. W. Harkins, P. Lemey, G. Baele, R. Duerr, and A. Heguy. "PLoS Pathogens", Vol. 19, Issue 4, Pages e1011348, 2023.

Combined phylogeographic analyses and epidemiologic contact tracing to characterize atypically pathogenic avian influenza (H3N1) epidemic, Belgium, 2019
S. Van Borm*, G. Boseret*, S. Dellicour*, M. Steensels, V. Roupie, F. Vandenbussche, E. Mathijs, A. Vilain, M. Driesen, M. Dispas, A. W. Delcloo, P. Lemey, I. Mertens, M. Gilbert, B. Lambrecht, and T. v. d. Berg. *Equal contribution
"Emerging Infectious Diseases", Vol. 29, Issue 2, Pages 351, 2023.

Immunovirological and environmental screening reveals actionable risk factors for fatal COVID-19 during post-vaccination nursing home outbreaks
L. Cuypers, E. Keyaerts, S. L. Hong, S. Gorissen, S. M. Menezes, M. Starick, J. Van Elslande, M. Weemaes, T. Wawina-Bokalanga, J. Marti-Carreras, B. Vanmechelen, B. Van Holm, M. Bloemen, J.-M. Dogne, F. Dufrasne, K. Durkin, J. Ruelle, R. De Mendonca, E. Wollants, P. Vermeersch, C. Boulouffe, A. Djiena, C. Broucke, B. Catry, K. Lagrou, M. Van Ranst, J. Neyts, G. Baele, P. Maes*, E. André*, S. Dellicour*, and J. Van Weyenbergh*. *Equal contribution
"Nature Aging", Vol. 3, Issue 6, Pages 722-733, 2023.

SPREAD 4: online visualisation of pathogen phylogeographic reconstructions
K. D. Nahata, F. Bielejec, J. Monetta, S. Dellicour, A. Rambaut, M. A. Suchard, G. Baele, and P. Lemey. "Virus Evolution", Vol. 8, Issue 2, Pages veac088, 2022.

Context-specific emergence and growth of the SARS-CoV-2 Delta variant
J. T. McCrone, V. Hill, S. Bajaj, R. E. Pena, B. C. Lambert, R. Inward, S. Bhatt, E. Volz, C. Ruis, S. Dellicour, G. Baele, A. E. Zarebski, A. Sadilek, N. Wu, A. Schneider, X. Ji, J. Raghwani, B. Jackson, R. Colquhoun, Á. O’Toole, T. P. Peacock, K. Twohig, S. Thelwall, G. Dabrera, R. Myers, N. R. Faria, C. Huber, I. I. Bogoch, K. Khan, L. du Plessis, J. C. Barrett, D. M. Aanensen, W. S. Barclay, M. Chand, T. Connor, N. J. Loman, M. A. Suchard, O. G. Pybus, A. Rambaut, and M. U. G. Kraemer. "Nature", Vol. 610, Issue 7930, Pages 154-160, 2022.

Two years of genomic surveillance in Belgium during the SARS-CoV-2 pandemic to attain country-wide coverage and monitor the introduction and spread of emerging variants
L. Cuypers, S. Dellicour, S. L. Hong, B. I. Potter, B. Verhasselt, N. Vereecke, L. Lambrechts, K. Durkin, V. Bours, S. Klamer, G. Bayon-Vicente, C. Vael, K. K. Ariën, R. De Mendonca, O. Soetens, C. Michel, B. Bearzatto, R. Naesens, J. Gras, A. Vankeerberghen, V. Matheeussen, G. Martens, D. Obbels, A. Lemmens, B. Van den Poel, E. Van Even, K. De Rauw, L. Waumans, M. Reynders, J. Degosserie, P. Maes, E. André, and G. Baele. "Viruses", Vol. 14, Issue 10, Pages 2301, 2022.

Spatially explicit phylogeographical reconstruction sheds light on the history of the forest cover in the Congo Basin
K. Matvijev, S. Dellicour, E. Kaymak, and O. J. Hardy. "Journal of Biogeography", Vol. 49, Issue 12, Pages 2256-2268, 2022.

Genome-associations of extended-spectrum ß-lactamase producing (ESBL) or AmpC producing E. coli in small and medium pig farms from Khon Kaen province, Thailand
J. Pires, L. Huber, R. A. Hickman, S. Dellicour, K. Lunha, T. Leangapichart, J. Jiwakanon, U. Magnusson, M. Sunde, J. D. Järhult, and T. P. Van Boeckel. "BMC Microbiology", Vol. 22, Issue 1, Pages 253, 2022.

Molecular epidemiology of HIV-1 subtype B infection across Florida reveals few Large superclusters with metropolitan origin
S. N. Rich, M. C. F. Prosperi, S. Dellicour, B. Vrancken, R. L. Cook, E. C. Spencer, M. Salemi, and C. Mavian. "Microbiology Spectrum", Vol. 10, Issue 6, Pages e01889-22, 2022.

Early genomic surveillance and phylogeographic analysis of Getah virus, a reemerging arbovirus, in livestock in China
J. Zhao*, S. Dellicour*, Z. Yan, M. Veit, M. S. Gill, W.-T. He, X. Zhai, X. Ji, M. A. Suchard, P. Lemey, and S. Su. *Equal contribution
"Journal of Virology", Vol. 97, Issue 1, Pages e01091-22, 2022.

Phylogeographic analysis of Tula hantavirus highlights a single introduction to central Europe
V. Cirkovic, S. Dellicour, G. Stamenkovic, M. Siljic, A. Gligic, and M. Stanojevic. "Virus Evolution", Vol. 8, Issue 2, Pages veac112, 2022.

Predicting the evolution of the Lassa virus endemic area and population at risk over the next decades
R. Klitting, L. E. Kafetzopoulou, W. Thiery, G. Dudas, S. Gryseels, A. Kotamarthi, B. Vrancken, K. Gangavarapu, M. Momoh, J. D. Sandi, A. Goba, F. Alhasan, D. S. Grant, S. Okogbenin, E. Ogbaini-Emovo, R. F. Garry, A. R. Smither, M. Zeller, M. G. Pauthner, M. McGraw, L. D. Hughes, S. Duraffour, S. Günther, M. A. Suchard, P. Lemey, K. G. Andersen, and S. Dellicour. "Nature Communications", Vol. 13, Issue 1, Pages 5596, 2022.

Transmission networks of SARS-CoV-2 in Coastal Kenya during the first two waves: A retrospective genomic study
C. N. Agoti, L. I. Ochola-Oyier, S. Dellicour, K. S. Mohammed, A. W. Lambisia, Z. R. de Laurent, J. M. Morobe, M. W. Mburu, D. O. Omuoyo, E. M. Ongera, L. Ndwiga, E. Maitha, B. Kitole, T. Suleiman, M. Mwakinangu, J. K. Nyambu, J. Otieno, B. Salim, J. Musyoki, N. Murunga, E. Otieno, J. N. Kiiru, K. Kasera, P. Amoth, M. Mwangangi, R. Aman, S. Kinyanjui, G. Warimwe, M. Phan, A. Agweyu, M. Cotten, E. Barasa, B. Tsofa, D. J. Nokes, P. Bejon, and G. Githinji. "eLife", Vol. 11, Pages e71703, 2022.

Genome-wide diversity of Zika virus: exploring spatio-temporal dynamics to guide a new nomenclature proposal
S. G. Seabra, P. J. K. Libin, K. Theys, A. Zhukova, B. I. Potter, H. Nebenzahl-Guimaraes, A. E. Gorbalenya, I. A. Sidorov, V. Pimentel, M. Pingarilho, A. T. R. de Vasconcelos, S. Dellicour, R. Khouri, O. Gascuel, A.-M. Vandamme, G. Baele, L. Cuypers, and A. B. Abecasis. "Virus Evolution", Vol. 8, Issue 1, Pages veac029, 2022.

Evaluation of screening program and phylogenetic analysis of SARS-CoV-2 infections among hospital healthcare workers in Liège, Belgium
M. El Moussaoui, N. Maes, S. L. Hong, N. Lambert, S. Gofflot, P. Dellot, Y. Belhadj, P. Huynen, M.-P. Hayette, C. Meex, S. Bontems, J. Defêche, L. Godderis, G. Molenberghs, C. Meuris, M. Artesi, K. Durkin, S. Rahmouni, C. Grégoire, Y. Beguin, M. Moutschen, S. Dellicour, and G. Darcis. "Viruses", Vol. 14, Issue 6, Pages 1302, 2022.

Investigating COVID-19 vaccine impact on the risk of hospitalisation through the analysis of national surveillance data collected in Belgium
D. Erazo, M. F. Vincenti-González, J. A. F. van Loenhout, P. Hubin, M. Vandromme, P. Maes, M. Taquet, J. Van Weyenbergh, L. Catteau, and S. Dellicour. "Viruses", Vol. 14, Issue 6, Pages 1315, 2022.

Accommodating sampling location uncertainty in continuous phylogeography
S. Dellicour, P. Lemey, M. A. Suchard, M. Gilbert, and G. Baele. "Virus Evolution", Vol. 8, Issue 1, Pages veac041, 2022.

Hunting alters viral transmission and evolution in a large carnivore
N. M. Fountain-Jones, S. Kraberger, R. B. Gagne, M. L. J. Gilbertson, D. R. Trumbo, M. Charleston, P. E. Salerno, W. Chris Funk, K. Crooks, K. Logan, M. Alldredge, S. Dellicour, G. Baele, X. Didelot, S. VandeWoude, S. Carver, and M. E. Craft. "Nature Ecology & Evolution", Vol. 6, Issue 2, Pages 174-182, 2022.

Phylogeography reveals association between swine trade and the spread of porcine epidemic diarrhea virus in China and across the world
W.-T. He, N. Bollen, Y. Xu, J. Zhao, S. Dellicour, Z. Yan, W. Gong, C. Zhang, L. Zhang, M. Lu, A. Lai, M. A. Suchard, X. Ji, C. Tu, P. Lemey, G. Baele, and S. Su. "Molecular Biology and Evolution", Vol. 39, Issue 2, Pages msab364, 2022.

Considerable escape of SARS-CoV-2 Omicron to antibody neutralization
D. Planas, N. Saunders, P. Maes, F. Guivel-Benhassine, C. Planchais, J. Buchrieser, W.-H. Bolland, F. Porrot, I. Staropoli, F. Lemoine, H. Péré, D. Veyer, J. Puech, J. Rodary, G. Baele, S. Dellicour, J. Raymenants, S. Gorissen, C. Geenen, B. Vanmechelen, T. Wawina-Bokalanga, J. Martí-Carreras, L. Cuypers, A. Sève, L. Hocqueloux, T. Prazuck, F. A. Rey, E. Simon-Loriere, T. Bruel, H. Mouquet, E. André, and O. Schwartz. "Nature", Vol. 602, Issue 7898, Pages 671-675, 2022.

Phycova – a tool for exploring covariates of pathogen spread
T. Blokker, G. Baele, P. Lemey, and S. Dellicour. "Virus Evolution", Vol. 8, Issue 1, Pages veac015, 2022.

Genomic sequencing of SARS-CoV-2 in Rwanda reveals the importance of incoming travelers on lineage diversity
Y. Butera, E. Mukantwari, M. Artesi, J. d. Umuringa, Á. N. O’Toole, V. Hill, S. Rooke, S. L. Hong, S. Dellicour, O. Majyambere, S. Bontems, B. Boujemla, J. Quick, P. C. Resende, N. Loman, E. Umumararungu, A. Kabanda, M. M. Murindahabi, P. Tuyisenge, M. Gashegu, J. P. Rwabihama, R. Sindayiheba, D. Gikic, J. Souopgui, W. Ndifon, R. Rutayisire, S. Gatare, T. Mpunga, D. Ngamije, V. Bours, A. Rambaut, S. Nsanzimana, G. Baele, K. Durkin, L. Mutesa, and N. Rujeni. "Nature Communications", Vol. 12, Issue 1, Pages 1-11, 2021.

SARS-CoV-2 genomic characterization and clinical manifestation of the COVID-19 outbreak in Uruguay
V. Elizondo, G. W. Harkins, B. Mabvakure, S. Smidt, P. Zappile, C. Marier, M. T. Maurano, V. Perez, N. Mazza, C. Beloso, S. Ifran, M. Fernandez, A. Santini, V. Perez, V. Estevez, M. Nin, G. Manrique, L. Perez, F. Ross, S. Boschi, M. N. Zubillaga, R. Balleste, S. Dellicour, A. Heguy, and R. Duerr. "Emerging Microbes & Infections", Vol. 10, Issue 1, Pages 51-65, 2021.

Host relatedness and landscape connectivity shape pathogen spread in the puma, a large secretive carnivore
N. M. Fountain-Jones, S. Kraberger, R. B. Gagne, D. R. Trumbo, P. E. Salerno, W. Chris Funk, K. Crooks, R. Biek, M. Alldredge, K. Logan, G. Baele, S. Dellicour, H. B. Ernest, S. VandeWoude, S. Carver, and M. E. Craft. "Communications Biology", Vol. 4, Issue 1, Pages 1-9, 2021.

High dispersal capacity of Culicoides obsoletus (Diptera: Ceratopogonidae), vector of bluetongue and Schmallenberg viruses, revealed by landscape genetic analyses
A. Mignotte, C. Garros, S. Dellicour, M. Jacquot, M. Gilbert, L. Gardès, T. Balenghien, M. Duhayon, I. Rakotoarivony, M. de Wavrechin, and K. Huber. "Parasites and Vectors", Vol. 14, Issue 1, Pages 93, 2021.

Dispersal dynamics of SARS-CoV-2 lineages during the first epidemic wave in New York City
S. Dellicour, S. L. Hong, B. Vrancken, A. Chaillon, M. S. Gill, M. T. Maurano, S. Ramaswami, P. Zappile, C. Marier, G. W. Harkins, G. Baele, R. Duerr, and A. Heguy. "PLoS Pathogens", Vol. 17, Issue 5, Pages e1009571, 2021.

Massive parallelization boosts big Bayesian multidimensional scaling
A. J. Holbrook, P. Lemey, G. Baele, S. Dellicour, D. Brockmann, A. Rambaut, and M. A. Suchard. "Journal of Computational and Graphical Statistics", Vol. 30, Issue 1, Pages 11-24, 2021.

A phylodynamic workflow to rapidly gain insights into the dispersal history and dynamics of SARS-CoV-2 lineages
S. Dellicour, K. Durkin, S. L. Hong, B. Vanmechelen, J. Martí-Carreras, M. S. Gill, C. Meex, S. Bontems, E. André, M. Gilbert, C. Walker, N. D. Maio, N. R. Faria, J. Hadfield, M.-P. Hayette, V. Bours, T. Wawina-Bokalanga, M. Artesi, G. Baele, and P. Maes. "Molecular Biology and Evolution", Vol. 38, Issue 4, Pages 1608-1613, 2021.

Investigating the drivers of the spatio-temporal heterogeneity in COVID-19 hospital incidence — Belgium as a study case
S. Dellicour, C. Linard, N. Van Goethem, D. Da Re, J. Artois, J. Bihin, P. Schaus, F. Massonnet, H. Van Oyen, S. O. Vanwambeke, N. Speybroeck, and M. Gilbert. "International Journal of Health Geographics", Vol. 20, Issue 1, Pages 29, 2021.

Variant analysis of SARS-CoV-2 genomes from Belgian military personnel engaged in overseas missions and operations
J.-P. Pirnay, P. Selhorst, S. L. Hong, C. Cochez, B. Potter, P. Maes, M. Petrillo, G. Dudas, V. Claes, Y. Van der Beken, G. Verbeken, J. Degueldre, S. Dellicour, L. Cuypers, F. T’Sas, G. Van den Eede, B. Verhasselt, W. Weuts, C. Smets, J. Mertens, P. Geeraerts, K. K. Ariën, E. André, P. Neirinckx, P. Soentjens, and G. Baele. "Viruses", Vol. 13, Issue 7, Pages 1359, 2021.

Untangling introductions and persistence in COVID-19 resurgence in Europe
P. Lemey, N. Ruktanonchai, S. L. Hong, V. Colizza, C. Poletto, F. Van den Broeck, M. S. Gill, X. Ji, A. Levasseur, B. B. Oude Munnink, M. Koopmans, A. Sadilek, S. Lai, A. J. Tatem, G. Baele, M. A. Suchard, and S. Dellicour. "Nature", Vol. 595, Issue 7869, Pages 713-717, 2021.

Spatiotemporal invasion dynamics of SARS-CoV-2 lineage B.1.1.7 emergence
M. U. G. Kraemer*, V. Hill*, C. Ruis*, S. Dellicour*, S. Bajaj*, J. T. McCrone, G. Baele, K. V. Parag, A. L. Battle, B. Gutierrez, B. Jackson, R. Colquhoun, Á. O’Toole, B. Klein, A. Vespignani, COVID-19 Genomics UK (COG-UK) Consortium, E. Volz, N. R. Faria, D. M. Aanensen, N. J. Loman, L. du Plessis, S. Cauchemez, A. Rambaut, S. V. Scarpino, and O. G. Pybus. *Equal contribution
"Science", Vol. 373, Issue 6557, Pages 889-895, 2021.

Relax, keep walking – a practical guide to continuous phylogeographic inference with BEAST
S. Dellicour, M. S. Gill, N. R. Faria, A. Rambaut, O. G. Pybus, M. A. Suchard, and P. Lemey. "Molecular Biology and Evolution", Vol. 38, Issue 8, Pages 3486-3493, 2021.

On the use of phylogeographic inference to Infer the dispersal history of rabies virus: a review study
K. D. Nahata, N. Bollen, M. S. Gill, M. Layan, H. Bourhy, S. Dellicour*, and G. Baele*. *Equal contribution
"Viruses", Vol. 13, Issue 8, Pages 1628, 2021.

Phylogeographic analysis of foot-and-mouth disease virus serotype O dispersal and associated drivers in East Africa
A. Munsey, F. N. Mwiine, S. Ochwo, L. Velazquez-Salinas, Z. Ahmed, F. Maree, L. L. Rodriguez, E. Rieder, A. Perez, S. Dellicour, and K. VanderWaal. "Molecular Ecology", Vol. 30, Issue 15, Pages 3815-3825, 2021.

Mathematical modelling and phylodynamics for the study of dog rabies dynamics and control: A scoping review
M. Layan, S. Dellicour, G. Baele, S. Cauchemez, and H. Bourhy. "PLoS Neglected Tropical Diseases", Vol. 15, Issue 5, Pages e0009449, 2021.

The evolution of ant worker polymorphism correlates with multiple social traits
N. Lecocq de Pletincx, S. Dellicour, and S. Aron. "Behavioral Ecology and Sociobiology", Vol. 75, Issue 8, Pages 113, 2021.

Rivers and landscape ecology of a plant virus, Rice yellow mottle virus along the Niger Valley
S. Issaka, O. Traoré, R. D. S. Longué, A. Pinel-Galzi, M. S. Gill, S. Dellicour, P. Bastide, S. Guindon, E. Hébrard, M.-J. Dugué, Y. Séré, S. Semballa, S. Aké, P. Lemey, and D. Fargette. "Virus Evolution", Vol. 7, Issue 2, 2021.

Early introductions and transmission of SARS-CoV-2 variant B.1.1.7 in the United States
T. Alpert, A. F. Brito, E. Lasek-Nesselquist, J. Rothman, A. L. Valesano, M. J. MacKay, M. E. Petrone, M. I. Breban, A. E. Watkins, C. B. F. Vogels, C. C. Kalinich, S. Dellicour, A. Russell, J. P. Kelly, M. Shudt, J. Plitnick, E. Schneider, W. J. Fitzsimmons, G. Khullar, J. Metti, J. T. Dudley, M. Nash, N. Beaubier, J. Wang, C. Liu, P. Hui, A. Muyombwe, R. Downing, J. Razeq, S. M. Bart, A. Grills, S. M. Morrison, S. Murphy, C. Neal, E. Laszlo, H. Rennert, M. Cushing, L. Westblade, P. Velu, A. Craney, L. Cong, D. R. Peaper, M. L. Landry, P. W. Cook, J. R. Fauver, C. E. Mason, A. S. Lauring, K. St. George, D. R. MacCannell, and N. D. Grubaugh. "Cell", Vol. 184, Issue 10, Pages 2595-2604.e13, 2021.

Exploiting genomic surveillance to map the spatio-temporal dispersal of SARS-CoV-2 spike mutations in Belgium across 2020
N. Bollen, M. Artesi, K. Durkin, S. L. Hong, B. Potter, B. Boujemla, B. Vanmechelen, J. Martí-Carreras, T. Wawina-Bokalanga, C. Meex, S. Bontems, M.-P. Hayette, E. André, P. Maes, V. Bours, G. Baele, and S. Dellicour. "Scientific Reports", Vol. 11, Issue 1, Pages 18580, 2021.

Global effects of extreme temperatures on wild bumblebees
B. Martinet, S. Dellicour, G. Ghisbain, K. Przybyla, E. Zambra, T. Lecocq, M. Boustani, R. Baghirov, D. Michez, and P. Rasmont. "Conservation Biology", Vol. 35, Issue 5, Pages 1507-1518, 2021.

Estimating migration of Gonioctena quinquepunctata (Coleoptera: Chrysomelidae) Inside a mountain range in a spatially explicit context
C. Kastally, S. Dellicour, O. J. Hardy, M. Gilbert, and P. Mardulyn. "Insect Systematics and Diversity", Vol. 5, Issue 5, 2021.

Leveraging of SARS-CoV-2 PCR cycle thresholds values to forecast COVID-19 trends
N. Yin, S. Dellicour, V. Daubie, N. Franco, M. Wautier, C. Faes, D. Van Cauteren, L. Nymark, N. Hens, M. Gilbert, M. Hallin, and O. Vandenberg. "Frontiers in Medicine", Vol. 8, Pages 2036, 2021.

A world apart: Levels and determinants of excess mortality due to COVID-19 in care homes: The case of the Belgian region of Wallonia during the spring 2020 wave
O. J. Hardy, D. Dubourg, M. Bourguignon, S. Dellicour, T. Eggerickx, M. Gilbert, J.-P. Sanderson, A. Scohy, E. Vandael, and J.-M. Decroly. "Demographic Research", Vol. 45, Issue 33, Pages 1011-1040, 2021.

Split it up and see: using proxies to highlight divergent inter-populational performances in aquaculture standardised conditions
L. Toomey, S. Dellicour, A. Kapusta, D. Żarski, F. Buhrke, S. Milla, P. Fontaine, and T. Lecocq. "BMC Ecology & Evolution", Vol. 21, Issue 1, Pages 206, 2021.

Dynamics and dispersal of local human immunodeficiency virus epidemics within San Diego and across the San Diego–Tijuana border
B. Vrancken, S. R. Mehta, S. Ávila-Ríos, C. García-Morales, D. Tapia-Trejo, G. Reyes-Terán, S. Navarro-Álvarez, S. J. Little, M. Hoenigl, H. A. Pines, T. Patterson, S. A. Strathdee, D. M. Smith, S. Dellicour*, and A. Chaillon*. *Equal contribution
"Clinical Infectious Diseases", Vol. 73, Issue 7, Pages e2018-e2025, 2021.

SARS-CoV-2 emergence and diffusion: a new disease manifesting human-environment interactions and a global geography of health
S. O. Vanwambeke, C. Linard, M. Gilbert, and S. Dellicour. "Current Opinion in Environmental Sustainability", Vol. 46, Pages 43-45, 2020.

Comparative circulation dynamics of the five main HIV types in China
B. Vrancken, B. Zhao, X. Li, X. Han, H. Liu, J. Zhao, P. Zhong, Y. Lin, J. Zai, M. Liu, D. M. Smith, S. Dellicour*, and A. Chaillon*. *Equal contribution
"Journal of Virology", Vol. 94, Issue 23, Pages e00683-20, 2020.

Unravelling the dispersal dynamics and ecological drivers of the African swine fever outbreak in Belgium
S. Dellicour, D. Desmecht, J. Paternostre, C. Malengreaux, A. Licoppe, M. Gilbert, and A. Linden. "Journal of Applied Ecology", Vol. 57, Issue 8, Pages 1619-1629, 2020.

Sampling bias and incorrect rooting make phylogenetic network tracing of SARS-COV-2 infections unreliable
C. Mavian, S. K. Pond, S. Marini, B. R. Magalis, A.-M. Vandamme, S. Dellicour, S. V. Scarpino, C. Houldcroft, J. Villabona-Arenas, T. K. Paisie, N. S. Trovão, C. Boucher, Y. Zhang, R. H. Scheuermann, O. Gascuel, T.-Y. Lam, M. A. Suchard, A. Abecasis, E. Wilkinson, T. de Oliveira, A. I. Bento, H. A. Schmidt, D. Martin, J. Hadfield, N. Faria, N. D. Grubaugh, R. A. Neher, G. Baele, P. Lemey, T. Stadler, J. Albert, K. A. Crandall, T. Leitner, A. Stamatakis, M. Prosperi, and M. Salemi. "Proceedings of the National Academy of Sciences, USA", Vol. 117, Issue 23, Pages 12522, 2020.

Epidemiological hypothesis testing using a phylogeographic and phylodynamic framework
S. Dellicour, S. Lequime, B. Vrancken, M. S. Gill, P. Bastide, K. Gangavarapu, N. L. 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, and P. Lemey. "Nature Communications", Vol. 11, Pages 5620, 2020.

NOSOI: a stochastic agent-based transmission chain simulation framework in R
S. Lequime, P. Bastide, S. Dellicour, P. Lemey, and G. Baele. "Methods in Ecology and Evolution", Vol. 11, Issue 8, Pages 1002-1007, 2020.

Genomic epidemiology, evolution, and transmission dynamics of porcine deltacoronavirus
W.-T. He*, X. Ji*, W. He*, S. Dellicour*, S. Wang, G. Li, L. Zhang, M. Gilbert, H. Zhu, G. Xing, M. Veit, Z. Huang, G.-Z. Han, Y. Huang, M. A. Suchard, G. Baele, P. Lemey, and S. Su. *Equal contribution
"Molecular Biology and Evolution", Vol. 37, Pages 2641-2654, 2020.

Symptom evolution following the emergence of maize streak virus
A. L. Monjane*, S. Dellicour*, P. Hartnady, K. A. Oyeniran, B. E. Owor, M. Bezeidenhout, D. Linderme, R. A. Syed, L. Donaldson, S. Murray, E. P. Rybicki, A. Kvarnheden, E. Yazdkhasti, P. Lefeuvre, R. Froissart, P. Roumagnac, D. N. Shepherd, G. W. Harkins, M. A. Suchard, P. Lemey, A. Varsani, and D. P. Martin. *Equal contribution
"eLife", Vol. 9, Pages e51984, 2020.

In search of covariates of HIV-1 subtype B spread in the United States — A cautionary tale of large-scale Bayesian phylogeography
S. L. Hong, S. Dellicour, B. Vrancken, M. A. Suchard, M. T. Pyne, D. R. Hillyard, P. Lemey, and G. Baele. "Viruses", Vol. 12, Issue 2, Pages 182, 2020.

Incorporating heterogeneous sampling probabilities in continuous phylogeographic inference — Application to H5N1 spread in the Mekong region
S. Dellicour, P. Lemey, J. Artois, T. T. Lam, A. Fusaro, I. Monne, G. Cattoli, D. Kuznetsov, I. Xenarios, G. Dauphin, W. Kalpravidh, S. Von Dobschuetz, F. Claes, S. H. Newman, M. A. Suchard, G. Baele, and M. Gilbert. "Bioinformatics", Vol. 36, Issue 7, Pages 2098-2104, 2020.

HIV persists throughout deep tissues with repopulation from multiple anatomical sources
A. Chaillon, S. Gianella, S. Dellicour, S. A. Rawlings, T. E. Schlub, M. F. D. Oliveira, C. Ignacio, M. Porrachia, B. Vrancken, and D. M. Smith. "The Journal of Clinical Investigation", Vol. 130, Issue 4, Pages 1699-1712, 2020.

Getting off on the right foot: Integration of spatial distribution of genetic variability for aquaculture development and regulations, the European perch case
L. Toomey, S. Dellicour, T. Vanina, J. Pegg, Z. Kaczkowski, J. Kouřil, F. Teletchea, M. Bláha, P. Fontaine, and T. Lecocq. "Aquaculture", Vol. 521, Pages 734981, 2020.

Genomic and epidemiological surveillance of Zika virus in the Amazon region
M. Giovanetti, N. R. Faria, J. Lourenço, J. G. d. Jesus, J. Xavier, I. M. Claro, M. U. G. Kraemer, V. Fonseca, S. Dellicour, J. Thézé, F. d. S. Salles, T. Gräf, P. P. Silveira, V. A. d. Nascimento, V. C. d. Souza, F. C. d. M. Iani, E. A. Castilho-Martins, L. N. Cruz, G. Wallau, A. Fabri, F. Levy, J. Quick, V. d. Azevedo, R. S. Aguiar, T. d. Oliveira, C. B. d. Menezes, M. d. C. Castilho, T. M. Terra, M. S. d. Silva, A. M. B. d. Filippis, A. L. d. Abreu, W. K. Oliveira, J. Croda, C. F. C. d. Albuquerque, M. R. T. Nunes, E. C. Sabino, N. Loman, F. G. Naveca, O. G. Pybus, and L. C. Alcantara. "Cell Reports", Vol. 30, Issue 7, Pages 2275-2283.e7, 2020.

The impact of anthropogenic and environmental factors on human rabies cases in China
J. Yu, H. Xiao, W. Yang, S. Dellicour, M. U. G. Kraemer, Y. Liu, J. Cai, Z. X. Huang, Y. Zhang, Y. Feng, W. Huang, H. Zhang, M. Gilbert, and H. Tian. "Transboundary and Emerging Diseases", Vol. 67, Pages 2544-2553, 2020.

Evolution and epidemic spread of SARS-CoV-2 in Brazil
D. S. Candido*, I. M. Claro*, J. G. d. Jesus*, W. M. Souza*, F. R. R. Moreira*, S. Dellicour*, T. A. Mellan*, L. d. Plessis, R. H. M. Pereira, F. C. S. Sales, E. R. Manuli, J. Thézé, L. Almeida, M. T. Menezes, C. M. Voloch, M. J. Fumagalli, T. M. Coletti, C. A. M. d. Silva, M. S. Ramundo, M. R. Amorim, H. H. Hoeltgebaum, S. Mishra, M. S. Gill, L. M. Carvalho, L. F. Buss, C. A. Prete, J. Ashworth, H. I. Nakaya, P. S. Peixoto, O. J. Brady, S. M. Nicholls, A. Tanuri, Á. D. Rossi, C. K. V. Braga, A. L. Gerber, A. P. d. C. Guimarães, N. Gaburo, C. S. Alencar, A. C. S. Ferreira, C. X. Lima, J. E. Levi, C. Granato, G. M. Ferreira, R. S. Francisco, F. Granja, M. T. Garcia, M. L. Moretti, M. W. Perroud, T. M. P. P. Castiñeiras, C. S. Lazari, S. C. Hill, A. A. d. S. Santos, C. L. Simeoni, J. Forato, A. C. Sposito, A. Z. Schreiber, M. N. N. Santos, C. Z. d. Sá, R. P. Souza, L. C. Resende-Moreira, M. M. Teixeira, J. Hubner, P. A. F. Leme, R. G. Moreira, M. L. Nogueira, D. Brazil-UK Centre for Arbovirus Discovery, N. M. Ferguson, S. F. Costa, J. L. Proenca-Modena, A. T. R. Vasconcelos, S. Bhatt, P. Lemey, C.-H. Wu, A. Rambaut, N. J. Loman, R. S. Aguiar, O. G. Pybus, E. C. Sabino, and N. R. Faria. *Equal contribution
"Science", Vol. 369, Pages 1255-1260, 2020.

Genomic surveillance of yellow fever virus epizootic in São Paulo, Brazil, 2016 – 2018
S. C. Hill, R. de Souza, J. Thézé, I. Claro, R. S. Aguiar, L. Abade, F. C. P. Santos, M. S. Cunha, J. S. Nogueira, F. C. S. Salles, I. M. Rocco, A. Y. Maeda, F. G. S. Vasami, L. du Plessis, P. P. Silveira, J. G. de Jesus, J. Quick, N. C. C. A. Fernandes, J. M. Guerra, R. A. Réssio, M. Giovanetti, L. C. J. Alcantara, C. S. Cirqueira, J. Díaz-Delgado, F. L. L. Macedo, M. d. C. S. T. Timenetsky, R. de Paula, R. Spinola, J. Telles de Deus, L. F. Mucci, R. M. Tubaki, R. M. T. de Menezes, P. L. Ramos, A. L. de Abreu, L. N. Cruz, N. Loman, S. Dellicour, O. G. Pybus, E. C. Sabino, and N. R. Faria. "PLoS Pathogens", Vol. 16, Issue 8, Pages e1008699, 2020.

Wildlife conservation strategies should be taxon-specific - further evidence with bumblebees
G. Ghisbain, D. Michez, L. Marshall, P. Rasmont, and S. Dellicour. "Diversity and Distribution", Vol. 26, Pages 1741-1751, 2020.

HIV rebound Is predominantly fueled by genetically identical viral expansions from diverse reservoirs
M.-A. De Scheerder, B. Vrancken*, S. Dellicour*, T. Schlub, E. Lee, W. Shao, S. Rutsaert, C. Verhofstede, T. Kerre, T. Malfait, D. Hemelsoet, M. Coppens, A. Dhondt, D. De Looze, F. Vermassen, P. Lemey, S. Palmer, and L. Vandekerckhove. *Equal contribution
"Cell Host & Microbe", Vol. 26, Pages 347-358, 2019.

Distinct rates and patterns of spread of the major HIV-1 subtypes in Central and East Africa
N. R. Faria, N. Vidal, J. Lourenco, J. Raghwani, K. C. E. Sigaloff, A. J. Tatem, D. A. M. v. d. Vijver, A.-C. Pineda-Peña, R. Rose, C. L. Wallis, S. Ahuka-Mundeke, J.-J. Muyembe-Tamfum, J. Muwonga, M. A. Suchard, T. F. R. d. Wit, R. L. Hamers, N. Ndembi, G. Baele, M. Peeters, O. G. Pybus, P. Lemey, and S. Dellicour. "PLoS Pathogens", Vol. 15, Issue 12, Pages e1007976, 2019.

Comparing patterns and scales of plant virus phylogeography: Rice yellow mottle virus in Madagascar and in continental Africa
M. Rakotomalala, B. Vrancken, A. Pinel-Galzi, P. Ramavovololon, E. Hébrard, S. Randrianangaly, S. Dellicour, Lemey P, and D. Fargette. "Virus Evolution", Vol. 5, Issue 2, Pages vez023, 2019.

Phylogeography of Lassa virus in Nigeria
D. U. Ehichioya, S. Dellicour, M. Pahlmann, T. Rieger, L. Oestereich, B. Becker-Ziaja, D. Cadar, Y. Ighodalo, T. Olokor, E. Omomoh, J. Oyakhilome, R. Omiunu, J. Agbukor, B. Ebo, J. Aiyepada, P. Ebhodaghe, B. Osiemi, S. Ehikhametalor, P. Akhilomen, M. Airende, R. Esumeh, E. Muoebonam, R. Giwa, A. Ekanem, G. Igenegbale, G. Odigie, G. Okonofua, R. Enigbe, E. O. Yerumoh, E. Pallasch, S. Bockholt, L. E. Kafetzopoulou, S. Duraffour, P. O. Okokhere, G. O. Akpede, S. A. Okogbenin, I. Odia, C. Aire, N. Akpede, E. Tobin, E. Ogbaini-Emovon, P. Lemey, D. I. Adomeh, D. A. Asogun, and S. Günther. "Journal of Virology", Vol. 93, Pages e00929-19, 2019.

Using phylogeographic approaches to analyse the dispersal history, velocity, and direction of viral lineages – application to rabies virus spread in Iran
S. Dellicour, C. Troupin, F. Jahanbakhsh, A. Salama, S. Massoudi, M. K. Moghaddam, G. Baele, P. Lemey, A. Gholami, and H. Bourhy. "Molecular Ecology", Vol. 28, Pages 4335-4350, 2019.

Identifying the patterns and drivers of Puumala hantavirus enzootic dynamics using reservoir sampling
L. Laenen, V. Vergote, B. Vanmechelen, K. Tersago, G. Baele, P. Lemey, H. Leirs, S. Dellicour, B. Vrancken, and P. Maes. "Virus Evolution", Vol. 5, Issue 1, 2019.

Landscape genetic analyses of Cervus elaphus and Sus scrofa: comparative study and analytical developments
S. Dellicour, J. G. Prunier, S. Piry, M.-C. Eloy, S. Bertouille, A. Licoppe, A. C. Frantz, and M.-C. Flamand. "Heredity", Vol. 123, Issue 2, Pages 228-241, 2019.

Mass migration to Europe: an opportunity for elimination of hepatitis B virus?
M. Thijssen, P. Lemey, S. Amini-Bavil-Olyaee, S. Dellicour, S. M. Alavian, F. Tacke, C. Verslype, F. Nevens, and M. R. Pourkarim. "The Lancet Gastroenterology and Hepatology", Vol. 4, Issue 4, Pages 315-323, 2019.

Recent advances in computational phylodynamics
G. Baele, S. Dellicour, M. A. Suchard, P. Lemey, and B. Vrancken. "Current Opinion in Virology", Vol. 31, Pages 24-32, 2018.

Molecular archaeoparasitology identifies cultural changes in the Medieval Hanseatic trading centre of Lübeck
P. G. Flammer, S. Dellicour, S. G. Preston, D. Rieger, S. Warren, C. K. W. Tan, R. Nicholson, R. Přichystalová, N. Bleicher, J. Wahl, N. R. Faria, O. G. Pybus, M. Pollard, and A. L. Smith. "Proceedings of the Royal Society of London B: Biological Sciences", Vol. 285, Issue 1888, 2018.

Genomic and epidemiological monitoring of yellow fever virus transmission potential
N. R. Faria, M. U. G. Kraemer, S. C. Hill, J. Goes de Jesus, R. S. Aguiar, F. C. M. Iani, J. Xavier, J. Quick, L. du Plessis, S. Dellicour, J. Thézé, R. D. O. Carvalho, G. Baele, C.-H. Wu, P. P. Silveira, M. B. Arruda, M. A. Pereira, G. C. Pereira, J. Lourenço, U. Obolski, L. Abade, T. I. Vasylyeva, M. Giovanetti, D. Yi, D. J. Weiss, G. R. W. Wint, F. M. Shearer, S. Funk, B. Nikolay, V. Fonseca, T. E. R. Adelino, M. A. A. Oliveira, M. V. F. Silva, L. Sacchetto, P. O. Figueiredo, I. M. Rezende, E. M. Mello, R. F. C. Said, D. A. Santos, M. L. Ferraz, M. G. Brito, L. F. Santana, M. T. Menezes, R. M. Brindeiro, A. Tanuri, F. C. P. dos Santos, M. S. Cunha, J. S. Nogueira, I. M. Rocco, A. C. da Costa, S. C. V. Komninakis, V. Azevedo, A. O. Chieppe, E. S. M. Araujo, M. C. L. Mendonça, C. C. dos Santos, C. D. dos Santos, A. M. Mares-Guia, R. M. R. Nogueira, P. C. Sequeira, R. G. Abreu, M. H. O. Garcia, A. L. Abreu, O. Okumoto, E. G. Kroon, C. F. C. de Albuquerque, K. Lewandowski, S. T. Pullan, M. Carroll, T. de Oliveira, E. C. Sabino, R. P. Souza, M. A. Suchard, P. Lemey, G. S. Trindade, B. P. Drumond, A. M. B. Filippis, N. J. Loman, S. Cauchemez, L. C. J. Alcantara, and O. G. Pybus. "Science", Vol. 361, Issue 6405, Pages 894-899, 2018.

Divergent geographic patterns of genetic diversity among wild bees: conservation implications
T. Lecocq, D. Michez, M. Gérard, N. J. Vereecken, J. Delangre, P. Rasmont, S. Vray, M. Dufrêne, P. Mardulyn, and S. Dellicour. "Diversity and Distributions", Vol. 24, Issue 12, Pages 1860-1868, 2018.

Phylodynamic assessment of intervention strategies for the West African Ebola virus outbreak
S. Dellicour, G. Baele, G. Dudas, N. R. Faria, O. G. Pybus, M. A. Suchard, A. Rambaut, and P. Lemey. "Nature Communications", Vol. 9, Issue 1, Pages 2222, 2018.

The hitchhiker's guide to single-locus species delimitation
S. Dellicour, and J.-F. Flot. "Molecular Ecology Resources", Vol. 18, Pages 1234-1246, 2018.

Geographical and historical patterns in the emergences of novel highly pathogenic avian influenza (HPAI) H5 and H7 viruses in poultry
M. S. Dhingra, J. Artois, S. Dellicour, P. Lemey, G. Dauphin, S. Von Dobschuetz, T. P. Van Boeckel, D. M. Castellan, S. Morzaria, and M. Gilbert. "Frontiers in Veterinary Science", Vol. 5, Issue 84, 2018.

Transmission dynamics of re-emerging rabies in domestic dogs of rural China
H. Tian, Y. Feng, B. Vrancken, B. Cazelles, H. Tan, M. S. Gill, Q. Yang, Y. Li, W. Yang, Y. Zhang, Y. Zhang, P. Lemey, O. G. Pybus, N. C. Stenseth, H. Zhang, and S. Dellicour. "PLoS Pathogens", Vol. 14, Issue 12, Pages e1007392, 2018.

On the importance of negative controls in viral landscape phylogeography
S. Dellicour, B. Vrancken, N. S. Trovão, D. Fargette, and P. Lemey. "Virus Evolution", Vol. 4, Issue 2, 2018.

Ecological niche modelling and coalescent simulations to explore the recent geographical range history of five widespread bumblebee species in Europe
S. Dellicour, C. Kastally, S. Varela, D. Michez, P. Rasmont, P. Mardulyn, and T. Lecocq. "Journal of Biogeography", Vol. 44, Issue 1, Pages 39-50, 2017.

Glacial survival of trophically linked boreal species in northern Europe
M. C. Quinzin, S. Normand, S. Dellicour, J.-C. Svenning, and P. Mardulyn. "Proceedings of the Royal Society B: Biological Sciences", Vol. 284, Issue 1856, 2017.

Host genetic variation does not determine spatio-temporal patterns of European bat 1 lyssavirus
C. Troupin, E. Picard-Meyer, S. Dellicour, I. Casademont, L. Kergoat, A. Lepelletier, L. Dacheux, G. Baele, E. Monchâtre-Leroy, F. Cliquet, P. Lemey, and H. Bourhy. "Genome Biology and Evolution", Vol. 9, Issue 11, Pages 3202-3213, 2017.

Cross-border spread, lineage displacement and evolutionary rate estimation of rabies virus in Yunnan Province, China
Y. Zhang, B. Vrancken, Y. Feng, S. Dellicour, Q. Yang, W. Yang, Y. Zhang, L. Dong, O. G. Pybus, H. Zhang, and H. Tian. "Virology Journal", Vol. 14, Issue 1, Pages 102, 2017.

Conservation genetics of European bees: new insights from the continental scale
T. Lecocq, M. Gérard, D. Michez, and S. Dellicour. "Conservation Genetics", Vol. 18, Issue 3, Pages 585-596, 2017.

Distribution and predictors of wing shape and size variability in three sister species of solitary bees
S. Dellicour, M. Gerard, J. G. Prunier, A. Dewulf, M. Kuhlmann, and D. Michez. "PLoS One", Vol. 12, Issue 3, 2017.

Using viral gene sequences to compare and explain the heterogeneous spatial dynamics of virus epidemics
S. Dellicour, R. Rose, N. R. Faria, L. F. P. Vieira, H. Bourhy, M. Gilbert, P. Lemey, and O. G. Pybus. "Molecular Biology and Evolution", Vol. 34, Issue 10, Pages 2563-2571, 2017.

Virus genomes reveal factors that spread and sustained the Ebola epidemic
G. Dudas, L. M. Carvalho, T. Bedford, A. J. Tatem, G. Baele, N. R. Faria, D. J. Park, J. T. Ladner, A. Arias, D. Asogun, F. Bielejec, S. L. Caddy, M. Cotten, J. D'Ambrozio, S. Dellicour, A. Di Caro, J. W. Diclaro, S. Duraffour, M. J. Elmore, L. S. Fakoli, O. Faye, M. L. Gilbert, S. M. Gevao, S. Gire, A. Gladden-Young, A. Gnirke, A. Goba, D. S. Grant, B. L. Haagmans, J. A. Hiscox, U. Jah, J. R. Kugelman, D. Liu, J. Lu, C. M. Malboeuf, S. Mate, D. A. Matthews, C. B. Matranga, L. W. Meredith, J. Qu, J. Quick, S. D. Pas, M. V. T. Phan, G. Pollakis, C. B. Reusken, M. Sanchez-Lockhart, S. F. Schaffner, J. S. Schieffelin, R. S. Sealfon, E. Simon-Loriere, S. L. Smits, K. Stoecker, L. Thorne, E. A. Tobin, M. A. Vandi, S. J. Watson, K. West, S. Whitmer, M. R. Wiley, S. M. Winnicki, S. Wohl, R. Wölfel, N. L. Yozwiak, K. G. Andersen, S. O. Blyden, F. Bolay, M. W. Carroll, B. Dahn, B. Diallo, P. Formenty, C. Fraser, G. F. Gao, R. F. Garry, I. Goodfellow, S. Günther, C. T. Happi, E. C. Holmes, B. Kargbo, S. Keïta, P. Kellam, M. P. G. Koopmans, J. H. Kuhn, N. J. Loman, N. Magassouba, D. Naidoo, S. T. Nichol, T. Nyenswah, G. Palacios, O. G. Pybus, P. C. Sabeti, A. Sall, U. Ströher, I. Wurie, M. A. Suchard, P. Lemey, and A. Rambaut. "Nature", Vol. 544, Issue 7650, Pages 309-315, 2017.

Explaining the geographic spread of emerging epidemics: a framework for comparing viral phylogenies and environmental landscape data
S. Dellicour, R. Rose, and O. G. Pybus. "BMC Bioinformatics", Vol. 17, Issue 1, 2016.

Rapid outbreak sequencing of Ebola virus in Sierra Leone identifies transmission chains linked to sporadic cases
A. Arias, S. J. Watson, D. Asogun, E. A. Tobin, J. Lu, M. V. T. Phan, U. Jah, R. E. G. Wadoum, L. Meredith, L. Thorne, S. Caddy, A. Tarawalie, P. Langat, G. Dudas, N. R. Faria, S. Dellicour, A. Kamara, B. Kargbo, B. O. Kamara, S. Gevao, D. Cooper, M. Newport, P. Horby, J. Dunning, F. Sahr, T. Brooks, A. J. H. Simpson, E. Groppelli, G. Liu, N. Mulakken, K. Rhodes, J. Akpablie, Z. Yoti, M. Lamunu, E. Vitto, P. Otim, C. Owilli, I. Boateng, L. Okoror, E. Omomoh, J. Oyakhilome, R. Omiunu, I. Yemisis, D. Adomeh, S. Ehikhiametalor, P. Akhilomen, C. Aire, A. Kurth, N. Cook, J. Baumann, M. Gabriel, R. Wölfel, A. Di Caro, M. W. Carroll, S. Günther, J. Redd, D. Naidoo, O. G. Pybus, A. Rambaut, P. Kellam, I. Goodfellow, and M. Cotten. "Virus Evolution", Vol. 2, Issue 1, 2016.

SERAPHIM: studying environmental rasters and phylogenetically informed movements
S. Dellicour, R. Rose, N. R. Faria, P. Lemey, and O. G. Pybus. "Bioinformatics", Vol. 32, Issue 20, Pages 3204-3206, 2016.

Spatio-temporal analysis of Nova virus, a divergent hantavirus circulating in the European mole in Belgium
L. Laenen, S. Dellicour, V. Vergote, I. Nauwelaers, S. De Coster, I. Verbeeck, B. Vanmechelen, P. Lemey, and P. Maes. "Molecular Ecology", Vol. 25, Issue 23, Pages 5994-6008, 2016.

Methods for species delimitation in bumblebees (Hymenoptera, Apidae, Bombus): towards an integrative approach
T. Lecocq, S. Dellicour, D. Michez, M. Dehon, A. Dewulf, T. De Meulemeester, N. Brasero, I. Valterová, J. Y. Rasplus, and P. Rasmont. "Zoologica Scripta", Vol. 44, Issue 3, Pages 281-297, 2015.

Delimiting species-poor data sets using single molecular markers: A study of barcode gaps, haplowebs and GMYC
S. Dellicour, and J. F. Flot. "Systematic Biology", Vol. 64, Issue 6, Pages 900-908, 2015.

Comparative phylogeography of five bumblebees: Impact of range fragmentation, range size and diet specialization
S. Dellicour, D. Michez, and P. Mardulyn. "Biological Journal of the Linnean Society", Vol. 116, Issue 4, Pages 926-939, 2015.

Impact of past climatic changes and resource availability on the population demography of three food-specialist bees
S. Dellicour, D. Michez, J.-Y. Rasplus, and P. Mardulyn. "Molecular Ecology", Vol. 24, Issue 5, Pages 1074-1090, 2015.

An integrative taxonomic approach to assess the status of Corsican bumblebees: implications for conservation
T. Lecocq, N. Brasero, T. De Meulemeester, D. Michez, S. Dellicour, P. Lhomme, R. de Jonghe, I. Valterová, K. Urbanová, and P. Rasmont. "Animal Conservation", Vol. 18, Issue 3, Pages 236-248, 2015.

Inferring the past and present connectivity across the range of a north american leaf beetle: combining ecological niche modeling and a geographically explicit model of coalescence
S. Dellicour, S. Fearnley, A. Lombal, S. Heidl, E. P. Dahlhoff, N. E. Rank, and P. Mardulyn. "Evolution", Vol. 68, Issue 8, Pages 2371-2385, 2014.

Inferring the mode of colonization of the rapid range expansion of a solitary bee from multilocus DNA sequence variation
S. Dellicour, P. Mardulyn, O. J. Hardy, C. Hardy, S. P. M. Roberts, and N. J. Vereecken. "Journal of Evolutionary Biology", Vol. 27, Issue 1, Pages 116-132, 2014.

SPADS 1.0: a toolbox to perform spatial analyses on DNA sequence data sets
S. Dellicour, and P. Mardulyn. "Molecular Ecology Resources", Vol. 14, Issue 3, Pages 647-651, 2014.

Molecular phylogeny, biogeography, and host plant shifts in the bee genus Melitta (Hymenoptera: Anthophila)
S. Dellicour, T. Lecocq, M. Kuhlmann, P. Mardulyn, and D. Michez. "Molecular Phylogenetics and Evolution", Vol. 70, Issue 1, Pages 412-419, 2014.

Comparing phylogeographic hypotheses by simulating DNA sequences under a spatially explicit model of coalescence
S. Dellicour, C. Kastally, O. J. Hardy, and P. Mardulyn. "Molecular Biology and Evolution", Vol. 31, Issue 12, Pages 3359-3372, 2014.

GCALIGNER 1.0: an alignment program to compute a multiple sample comparison data matrix from large eco-chemical datasets obtained by GC
S. Dellicour, and T. Lecocq. "Journal of Separation Science", Vol. 36, Issue 19, Pages 3206-3209, 2013.

Patterns of genetic and reproductive traits differentiation in mainland vs. Corsican populations of bumblebees
T. Lecocq, N. J. Vereecken, D. Michez, S. Dellicour, P. Lhomme, I. Valterová, J. Y. Rasplus, and P. Rasmont. "PLoS One", Vol. 8, Issue 6, 2013.

Scent of a break-up: phylogeography and reproductive trait divergences in the red-tailed bumblebee (Bombus lapidarius)
T. Lecocq, S. Dellicour, D. Michez, P. Lhomme, M. Vanderplanck, I. Valterová, J. Y. Rasplus, and P. Rasmont. "BMC Evolutionary Biology", Vol. 13, Issue 1, 2013.

Molecular and chemical characters to evaluate species status of two cuckoo bumblebees: Bombus barbutellus and Bombus maxillosus (Hymenoptera, Apidae, Bombini)
T. Lecocq, P. Lhomme, D. Michez, S. Dellicour, I. Valterova, and P. Rasmont. "Systematic Entomology", Vol. 36, Issue 3, Pages 453-469, 2011.

Population structure and genetic diversity of red deer (Cervus elaphus) in forest fragments in north-western France
S. Dellicour, A. C. Frantz, M. Colyn, S. Bertouille, F. Chaumont, and M. C. Flamand. "Conservation Genetics", Vol. 12, Issue 5, Pages 1287-1297, 2011.