Publications

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.

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.

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.

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.

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. D. Akaibe, S. G. Mbalitini, F. Van de Perre, N. Van Houtte, J. Těšíková, E. Wollants, M. Van Ranst, O. G. Pybus, J. F. Drexler, E. Verheyen, H. Leirs, J. Gouy de Bellocq, and P. Lemey. "Virus Evolution", Vol. 7, Issue 1, 2021.

A Comprehensive molecular epidemiological analysis of SARS-CoV-2 infection in Cyprus from April 2020 to January 2021: Evidence of a highly polyphyletic and evolving epidemic
A. C. Chrysostomou, B. Vrancken, G. Koumbaris, G. Themistokleous, A. Aristokleous, C. Masia, C. Eleftheriou, C. Iοannou, D. C. Stylianou, M. Ioannides, P. Petrou, V. Georgiou, A. Hatziyianni, P. Lemey, A.-M. Vandamme, P. P. Patsalis, and L. G. Kostrikis. "Viruses", Vol. 13, Issue 6, Pages 1098, 2021.

Phylogenomic characterization of Lopma virus and Praja virus, two novel rodent-borne Arteriviruses
B. Vanmechelen, Z. Zisi, S. Gryseels, J. Goüy de Bellocq, B. Vrancken, P. Lemey, P. Maes, and M. Bletsa. "Viruses", Vol. 13, Issue 9, Pages 1842, 2021.

In vivo therapy with M2e-specific IgG selects for an influenza A virus mutant with delayed matrix protein 2 expression
S. Van den Hoecke, M. Ballegeer, B. Vrancken, L. Deng, E. R. Job, K. Roose, B. Schepens, L. Van Hoecke, P. Lemey, and X. Saelens. "mBio", Vol. 12, Issue 4, Pages e0074521, 2021.

Assessing the impact of COVID-19 border restrictions on dengue transmission in Yunnan Province, China: an observational epidemiological and phylogenetic analysis
N. Li, Y. Feng, B. Vrancken, Y. Chen, L. Dong, Q. Yang, M. U. G. Kraemer, O. G. Pybus, H. Zhang, O. J. Brady, and H. Tian. "The Lancet Regional Health – Western Pacific", Vol. 14, 2021.

A systematic review on global RSV genetic data: Identification of knowledge gaps
A. C. Langedijk, E. R. Harding, B. Konya, B. Vrancken, R. J. Lebbink, A. Evers, J. Willemsen, P. Lemey, and L. J. Bont. "Reviews in Medical Virology", Pages e2284, 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.

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.

A paucigranulocytic asthma host environment promotes the emergence of virulent influenza viral variants
K. D. Hulme, A. C. Karawita, C. Pegg, M. J. Bunte, H. Bielefeldt-Ohmann, C. J. Bloxham, S. Van den Hoecke, Y. X. Setoh, B. Vrancken, M. Spronken, L. E. Steele, N. A. Verzele, K. R. Upton, A. A. Khromykh, K. Y. Chew, M. Sukkar, S. Phipps, and K. R. Short. "eLife", Vol. 10, Pages e61803, 2021.

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. da Veiga Leal, C. Pires, A. Moreira, M. F. Tavares, L. Fernandes, J. N. Barreto, M. do Céu Teixeira, M. d. L. de Lima Mendonça, C. C. d. S. L. Gomes, M. S. Castellon, L. Ma, F. Lemoine, F. Gámbaro-Roglia, D. Delaune, G. Fall, I. S. Fall, M. Diop, A. Sakuntabhai, C. Loucoubar, P. Lemey, E. Holmes, O. Faye, A. A. Sall, and E. Simon-Loriere. "Emerging Infectious Disease", Vol. 26, Issue 6, Pages 1084, 2020.

Accounting for population structure reveals ambiguity in the Zaire Ebolavirus reservoir dynamics
B. Vrancken, T. Wawina-Bokalanga, B. Vanmechelen, J. Martí-Carreras, M. W. Carroll, J. Nsio, J. Kapetshi, S. Makiala-Mandanda, J.-J. Muyembe-Tamfum, G. Baele, K. Vermeire, V. Vergote, S. Ahuka-Mundeke, and P. Maes. "PLoS Neglected Tropical Diseases", Vol. 14, Issue 3, Pages e0008117, 2020.

Evaluating predictive markers for viral rebound and safety assessment in blood and lumbar fluid during HIV-1 treatment interruption
M.-A. De Scheerder, C. Van Hecke, H. Zetterberg, D. Fuchs, N. De Langhe, S. Rutsaert, B. Vrancken, W. Trypsteen, Y. Noppe, B. Van Der Gucht, J. Pelgrom, F. Van Wanzeele, S. Palmer, P. Lemey, M. Gisslén, and L. Vandekerckhove. "The Journal of Antimicrobial Chemotherapy", Vol. 75, Issue 5, Pages 1311-1320, 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.

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.

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.

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.

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, T. Schnalke, P. Lemey, and S. Calvignac-Spencer. "Science (New York, N.Y.)", Vol. 368, Issue 6497, Pages 1367-1370, 2020.

Cross-country migration linked to people who inject drugs challenges the long-term impact of national HCV elimination programmes
B. Vrancken, L. Cuypers, A. B. Pérez, N. Chueca, J. Anton-Basantas, A. de la Iglesia, J. Fuentes, J. A. Pineda, F. Téllez, E. Bernal, P. Rincón, M. A. Von Wichman, A. Fuentes, F. Vera, A. Rivero-Juárez, M. Jiménez, A.-M. Vandamme, and F. García. "Journal of Hepatology", Vol. 71, Issue 6, Pages 1270-1272, 2019.

Divergence dating using mixed effects clock modelling: An application to HIV-1
M. Bletsa, M. A. Suchard, X. Ji, S. Gryseels, B. Vrancken, G. Baele, M. Worobey, and P. Lemey. "Virus Evolution", Vol. 5, Issue 2, 2019.

Disentangling the role of Africa in the global spread of H5 highly pathogenic avian influenza
A. Fusaro, B. Zecchin, B. Vrancken, C. Abolnik, R. Ademun, A. Alassane, A. Arafa, J. A. Awuni, E. Couacy-Hymann, M. ’. B. Coulibaly, N. Gaidet, E. Go-Maro, T. Joannis, S. D. Jumbo, G. Minoungou, C. Meseko, M. M. Souley, D. B. Ndumu, I. Shittu, A. Twabela, A. Wade, L. Wiersma, Y. P. Akpeli, G. Zamperin, A. Milani, P. Lemey, and I. Monne. "Nature Communications", Vol. 10, Issue 1, Pages 5310, 2019.

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.

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.

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.

Limited evolution of the yellow fever virus 17d in a mouse infection model
D. B. Kum, N. Mishra, B. Vrancken, H. J. Thibaut, A. Wilder-Smith, P. Lemey, J. Neyts, and K. Dallmeier. "Emerging Microbes & Infections", Vol. 8, Issue 1, Pages 1734-1746, 2019.

New evidence for the east–west spread of the highly pathogenic avian influenza H5N1 virus between Central Asian and east Asian-Australasian flyways in China
W. Meng, Q. Yang, B. Vrancken, Z. Chen, D. Liu, L. Chen, X. Zhao, S. François, T. Ma, R. Gao, W. Ru, Y. Li, H. He, G. Zhang, H. Tian, and J. Lu. "Emerging Microbes & Infections", Vol. 8, Issue 1, Pages 823-826, 2019.

Increasing importance of European lineages in seeding the hepatitis C virus subtype 1a epidemic in Spain
A. B. Pérez, B. Vrancken, N. Chueca, A. Aguilera, G. Reina, M.-d. Toro, F. Vera, M. A. V. Wichman, J. I. Arenas, F. Téllez, J. A. Pineda, M. Omar, E. Bernal, A. Rivero-Juárez, E. Fernández-Fuertes, A. d. l. Iglesia, J. M. Pascasio, P. Lemey, F. Garcia, and L. Cuypers. "Eurosurveillance", Vol. 24, Issue 9, Pages 1800227, 2019.

Drivers of HIV-1 transmission: The Portuguese case
A.-C. Pineda-Peña, M. Pingarilho, G. Li, B. Vrancken, P. Libin, P. Gomes, R. J. Camacho, K. Theys, A. B. Abecasis, and o.-1. Group. "PLoS One", Vol. 14, Issue 9, Pages e0218226, 2019.

Why comprehensive datasets matter when inferring epidemic links or subgenotyping
B. Vrancken, S. M. Alavian, A. Aminy, S. Amini-Bavil-Olyaee, and M. R. Pourkarim. "Infection, Genetics and Evolution", Vol. 65, Pages 350-351, 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.

Discovery and genome characterization of three new Jeilongviruses, a lineage of paramyxoviruses characterized by their unique membrane proteins
B. Vanmechelen, M. Bletsa, L. Laenen, A. R. Lopes, V. Vergote, L. Beller, W. Deboutte, M. Korva, T. Avšič Županc, J. Goüy de Bellocq, S. Gryseels, H. Leirs, P. Lemey, B. Vrancken, and P. Maes. "BMC Genomics", Vol. 19, Issue 1, Pages 617, 2018.

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.

Proposal for a new subtype of the zoonotic genotype 3 Hepatitis E virus: HEV-3l
L. De Sabato, P. Lemey, B. Vrancken, L. Bonfanti, L. Ceglie, G. Vaccari, and I. Di Bartolo. "Virus Research", Vol. 248, Pages 1-4, 2018.

Phylogenetic relationships of the HA and NA genes between vaccine and seasonal influenza A(H3N2) strains in Korea
J. I. Kim, I. Lee, S. Park, J.-Y. Bae, K. Yoo, H. J. Cheong, J. Y. Noh, K. W. Hong, P. Lemey, B. Vrancken, J. Kim, M. Nam, S.-H. Yun, W. I. Cho, J. Y. Song, W. J. Kim, M. S. Park, J.-W. Song, S.-H. Kee, K.-J. Song, and M.-S. Park. "PLoS One", Vol. 12, Issue 3, Pages e0172059, 2017.

Implications of hepatitis C virus subtype 1a migration patterns for virus genetic sequencing policies in Italy
L. Cuypers, B. Vrancken, L. Fabeni, N. Marascio, V. Cento, V. C. Di Maio, M. Aragri, A. C. Pineda-Peña, Y. Schrooten, K. Van Laethem, D. Balog, A. Focà, C. Torti, F. Nevens, C. F. Perno, A.-M. Vandamme, and F. Ceccherini-Silberstein. "BMC Evolutionary Biology", Vol. 17, Issue 1, Pages 70, 2017.

The multi-faceted dynamics of HIV-1 transmission in Northern Alberta: A combined analysis of virus genetic and public health data
B. Vrancken, D. Adachi, M. Benedet, A. Singh, R. Read, S. Shafran, G. D. Taylor, K. Simmonds, C. Sikora, P. Lemey, C. L. Charlton, and J. W. Tang. "Infection, Genetics and Evolution", Vol. 52, Pages 100-105, 2017.

The epidemic dynamics of hepatitis C virus subtypes 4a and 4d in Saudi Arabia
A. A. Al-Qahtani, G. Baele, N. Khalaf, M. A. Suchard, M. R. Al-Anazi, A. A. Abdo, F. M. Sanai, H. I. Al-Ashgar, M. Q. Khan, M. N. Al-Ahdal, P. Lemey, and B. Vrancken. "Scientific Reports", Vol. 7, Issue 1, Pages 44947, 2017.

Accurate quantification of within- and between-host HBV evolutionary rates requires explicit transmission chain modelling
B. Vrancken, M. A. Suchard, and P. Lemey. "Virus Evolution", Vol. 3, Issue 2, 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.

Detection of natural resistance-associated substitutions by ion semiconductor technology in HCV1b positive, direct-acting antiviral agents-naïve patients
N. Marascio, G. Pavia, A. Strazzulla, T. Dierckx, L. Cuypers, B. Vrancken, G. S. Barreca, T. Mirante, D. Malanga, D. M. Oliveira, A.-M. Vandamme, C. Torti, M. C. Liberto, A. Focà, and The SINERGIE-UMG Study Group. "International Journal of Molecular Sciences", Vol. 17, Issue 9, Pages 1416, 2016.

Quantifying next generation sequencing sample pre-processing bias in HIV-1 complete genome sequencing
B. Vrancken, N. S. Trovão, G. Baele, E. van Wijngaerden, A.-M. Vandamme, K. van Laethem, and P. Lemey. "Viruses", Vol. 8, Issue 1, Pages E12, 2016.

Distinct effects of T-705 (Favipiravir) and Ribavirin on influenza virus replication and viral RNA synthesis
E. Vanderlinden, B. Vrancken, J. Van Houdt, V. K. Rajwanshi, S. Gillemot, G. Andrei, P. Lemey, and L. Naesens. "Antimicrobial Agents and Chemotherapy", Vol. 60, Issue 11, Pages 6679-6691, 2016.

SpreaD3: interactive visualization of spatiotemporal history and trait evolutionary processes
F. Bielejec, G. Baele, B. Vrancken, M. A. Suchard, A. Rambaut, and P. Lemey. "Molecular Biology and Evolution", Vol. 33, Issue 8, Pages 2167-2169, 2016.

Simultaneously estimating evolutionary history and repeated traits phylogenetic signal: applications to viral and host phenotypic evolution
B. Vrancken, P. Lemey, A. Rambaut, T. Bedford, B. Longdon, H. F. Günthard, and M. A. Suchard. "Methods in Ecology and Evolution", Vol. 6, Issue 1, Pages 67-82, 2015.

Disentangling the impact of within-host evolution and transmission dynamics on the tempo of HIV-1 evolution
B. Vrancken, G. Baele, A.-M. Vandamme, K. Van Laethem, M. A. Suchard, and P. Lemey. "AIDS", Vol. 29, Issue 12, Pages 1549-1556, 2015.

Contribution of epidemiological predictors in unraveling the phylogeographic history of HIV-1 subtype C in Brazil
T. Gräf, B. Vrancken, D. Maletich Junqueira, R. M. de Medeiros, M. A. Suchard, P. Lemey, S. Esteves de Matos Almeida, and A. R. Pinto. "Journal of Virology", Vol. 89, Issue 24, Pages 12341-12348, 2015.

A near-full length genotypic assay for HCV1b
L. Cuypers, J. Snoeck, B. Vrancken, L. Kerremans, G. Vuagniaux, J. Verbeeck, F. Nevens, R. J. Camacho, A.-M. Vandamme, and S. Van Dooren. "Journal of Virological Methods", Vol. 209, Pages 126-135, 2014.

The genealogical population dynamics of HIV-1 in a large transmission chain: Bridging within and among host evolutionary rates
B. Vrancken, A. Rambaut, M. A. Suchard, A. Drummond, G. Baele, I. Derdelinckx, E. V. Wijngaerden, A.-M. Vandamme, K. V. Laethem, and P. Lemey. "PLoS Computational Biology", Vol. 10, Issue 4, Pages e1003505, 2014.

HIV-1 evolution in patients undergoing immunotherapy with Tat, Rev, and Nef expressing dendritic cells followed by treatment interruption
A. L. de Goede, H. W. M. van Deutekom, B. Vrancken, M. Schutten, S. D. Allard, C. A. van Baalen, A. D. M. E. Osterhaus, K. Thielemans, J. L. Aerts, C. Keşmir, P. Lemey, and R. A. Gruters. "AIDS", Vol. 27, Issue 17, Pages 2679-2689, 2013.

High-throughput HIV sequencing: evolution in 2D
B. Vrancken, and P. Lemey. "Future Virology", Vol. 6, Issue 4, Pages 417-420, 2011.

Covering all bases in HIV research: unveiling a hidden world of viral evolution
B. Vrancken, S. Lequime, K. Theys, and P. Lemey. "AIDS reviews", Vol. 12, Issue 2, Pages 89-102, 2010.