Peer-reviewed Publications.

2025

• [39] Hong, S. L., Stockman, M., Nova Blanco, J. R., Van Cleemput, C., Ahouidi, A., Armién, B., Bento, A., Bollen, N., Conde Pereira, C., Freitas, C., Hofstra, M., Jordan, M. R., Kashima, S., Gonçalves, C. C. M., Campelo de Albuquerque e Melo, C. F., Nahata, K., de Oliveira, E. C., Parra, L., Saenz, C., … Vandamme, A.-M. (2025). Transdisciplinary training to address challenges in genomic epidemiology of infectious diseases. Frontiers in Public Health, 13, 1713182. https://doi.org/10.3389/fpubh.2025.1713182
• [38] Thibaut, J., Gámbaro, F., Geenen, C., Hong, S. L., Raymenants, J., Gorissen, S., Cuypers, L., Maes, P., Baele, G., Dellicour, S., & André, E. (2025). A novel methodology for assessing contact tracing precision: Phylogenetic validation of a contact tracing program for COVID-19 in Belgium. Journal of Virological Methods, 340, 115279. https://doi.org/10.1016/j.jviromet.2025.115279
• [37] Clessin, A., Briand, F.-X., Tornos, J., Lejeune, M., De Pasquale, C., Fischer, R., Souchaud, F., Hirchaud, E., Hong, S. L., Bralet, T., Guinet, C., McMahon, C. R., Grasland, B., Baele, G., & Boulinier, T. (2025). Circumpolar spread of avian influenza H5N1 to southern Indian Ocean islands. Nature Communications, 16(1), 8463. https://doi.org/10.1038/s41467-025-64297-y
• [36] Gallego-García, P., Hong, S. L., Bollen, N., Dellicour, S., Baele, G., Suchard, M. A., Lemey, P., & Posada, D. (2025). International importance and spread of SARS-CoV-2 variants Alpha, Delta, and Omicron BA.1 into Spain. Communications Medicine, 5(1), 209. https://doi.org/10.1038/s43856-025-00912-9
• [35] Bollen, N., Hong, S. L., Potter, B. I., Lienhard, R., Tritten, M.-L., Sierro, N., Guedj, E., Dulize, R., Bornand, D., Auberson, M., Berthouzoz, M., Duvoisin, P., Ivanov, N. V., Peitsch, M. C., Hill, V., Matheeussen, V., Bontems, S., Verhasselt, B., Degosserie, J., … Baele, G. (2025). Tracking down the origin and subsequent spread of SARS-CoV-2 lineage B.1.619. Virus Evolution, 11(1), veaf017. https://doi.org/10.1093/ve/veaf017

2024

• [34] Li, Y., Bollen, N., Hong, S. L., Brusselmans, M., Gambaro, F., Klaps, J., Suchard, M. A., Rambaut, A., Lemey, P., Dellicour, S., & Baele, G. (2024). spread. gl: visualizing pathogen dispersal in a high-performance browser application. Bioinformatics, 40(12), btae721. https://doi.org/10.1093/bioinformatics/btae721
• [33] Wawina-Bokalanga, T., Vanmechelen, B., Logist, A.-S., Bloemen, M., Laenen, L., Bontems, S., Hayette, M.-P., Meex, C., Meuris, C., Orban, C., André, E., Snoeck, R., Baele, G., Hong, S. L., Andrei, G., & Maes, P. (2024). A retrospective genomic characterisation of the 2022 mpox outbreak in Belgium, and in vitro assessment of three antiviral compounds. EBioMedicine, 110(105488), 105488. https://doi.org/10.1016/j.ebiom.2024.105488
• [32] Brusselmans, M., Carvalho, L. M.,Hong, S. L., Gao, J., Matsen, F. A., Iv, Rambaut, A., Lemey, P., Suchard, M. A., Dudas, G., & Baele, G. (2024). On the importance of assessing topological convergence in Bayesian phylogenetic inference. Virus Evolution, 10(1), veae081. https://doi.org/10.1093/ve/veae081
• [31] Sun, Y.*, Xing, J.*, Hong, S. L.*, Bollen, N., Xu, S., Li, Y., Zhong, J., Gao, X., Zhu, D., Liu, J., Gong, L., Zhou, L., An, T., Shi, M., Wang, H., Baele, G., & Zhang, G. (2024). Untangling lineage introductions, persistence and transmission drivers of HP-PRRSV sublineage 8.7. Nature Communications, 15(1), 8842. https://doi.org/10.1038/s41467-024-53076-w
• [30] Holtz, A., Van Weyenbergh, J., Hong, S. L., Cuypers, L., O’Toole, Á., Dudas, G., Gerdol, M., Potter, B. I., Ntoumi, F., Mapanguy, C. C. M., Vanmechelen, B., Wawina-Bokalanga, T., Van Holm, B., Menezes, S. M., Soubotko, K., Van Pottelbergh, G., Wollants, E., Vermeersch, P., Jacob, A.-S., … Baele, G. (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. BMC Infectious Diseases, 24(1), 1139. https://doi.org/10.1186/s12879-024-09967-w
• [29] Moussaoui, M. E., Bontems, S., Meex, C., Hayette, M.-P., Lejeune, M., Hong, S. L., Dellicour, S., Moutschen, M., Cambisano, N., Renotte, N., Bours, V., Darcis, G., Artesi, M., & Durkin, K. (2024). Intrahost evolution leading to distinct lineages in the upper and lower respiratory tracts during SARS-CoV-2 prolonged infection. Virus Evolution, veae073. https://doi.org/10.1093/ve/veae073
• [28] Pérez, L. J., Baele, G., Hong, S. L., Cloherty, G. A., & Berg, M. G. (2024). Ecological changes exacerbating the spread of invasive ticks has driven the dispersal of severe fever with thrombocytopenia syndrome virus throughout Southeast Asia. Molecular Biology and Evolution, 41(8), msae173. https://doi.org/10.1093/molbev/msae173
• [27] Gallego-García, P., Estévez-Gómez, N., De Chiara, L., Alvariño, P., Juiz-González, P. M., Torres-Beceiro, I., Poza, M., Vallejo, J. A., Rumbo-Feal, S., Conde-Pérez, K., Aja-Macaya, P., Ladra, S., Moreno-Flores, A., Gude-González, M. J., Coira, A., Aguilera, A., Costa-Alcalde, J. J., Trastoy, R., Barbeito-Castiñeiras, G., …, Hong, S.L., …, Posada, D. (2024). Dispersal history of SARS-CoV-2 in Galicia, Spain. Journal of Medical Virology, 96(7), e29773. https://doi.org/10.1002/jmv.29773

2023

• [26] Rudin, C.*, Bollen, N.*, Hong, S. L., Wegner, F., Politi, L., Mellou, K., Geenen, C., Gorissen, S., Verhasselt, B., Durkin, K., Henin, C., Logist, A.-S., Dellicour, S., Resa, T., Stadler, T., Maes, P., Cuypers, L., André, E., Egli, A., & Baele, G. (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. Euro Surveillance: Bulletin Europeen Sur Les Maladies Transmissibles = European Communicable Disease Bulletin, 28(45). https://doi.org/10.2807/1560-7917.ES.2023.28.45.2300018
• [25] Cuypers, L., Keyaerts, E., Hong, S. L., Gorissen, S., Menezes, S. M., Starick, M., Van Elslande, J., Weemaes, M., Wawina-Bokalanga, T., Marti-Carreras, J., Vanmechelen, B., Van Holm, B., Bloemen, M., Dogne, J.-M., Dufrasne, F., Durkin, K., Ruelle, J., De Mendonca, R., Wollants, E., … Van Weyenbergh, J. (2023). Immunovirological and environmental screening reveals actionable risk factors for fatal COVID-19 during post-vaccination nursing home outbreaks. Nature Aging. https://doi.org/10.1038/s43587-023-00421-1
• [24] Dellicour, S., Hong, S. L., Hill, V., Dimartino, D., Marier, C., Zappile, P., Harkins, G. W., Lemey, P., Baele, G., Duerr, R., & Heguy, A. (2023). Variant-specific introduction and dispersal dynamics of SARS-CoV-2 in New York City - from Alpha to Omicron. PLoS Pathogens, 19(4), e1011348. https://doi.org/10.1371/journal.ppat.1011348
• [23] Duerr, R., Zhou, H., Tada, T., Dimartino, D., Marier, C., Zappile, P., Wang, G., Plitnick, J., Griesemer, S. B., Girardin, R., Machowski, J., Bialosuknia, S., Lasek-Nesselquist, E., Hong, S. L., Baele, G., Dittmann, M., Ortigoza, M. B., Prasad, P. J., McDonough, K., … Heguy, A. (2023). Delta-Omicron recombinant escapes therapeutic antibody neutralization. iScience, 26(2), 106075. https://doi.org/10.1016/j.isci.2023.106075

2022

• [22] Cuypers, L., Dellicour, S., Hong, S. L., Potter, B. I., Verhasselt, B., Vereecke, N., Lambrechts, L., Durkin, K., Bours, V., Klamer, S., Bayon-Vicente, G., Vael, C., Ariën, K. K., De Mendonca, R., Soetens, O., Michel, C., Bearzatto, B., Naesens, R., Gras, J., … Baele, G. (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. Viruses, 14(10). https://doi.org/10.3390/v14102301
• [21] El Moussaoui, M., Maes, N., Hong, S.L., Lambert, N., Gofflot, S., Dellot, P., Belhadj, Y., Huynen, P., Hayette, M.-P., Meex, C., Bontems, S., Defêche, J., Godderis, L., Molenberghs, G., Meuris, C., Artesi, M., Durkin, K., Rahmouni, S., Grégoire, C., Beguin, Y., Moutschen, M., Dellicour, S., Darcis, G., 2022. Evaluation of Screening Program and Phylogenetic Analysis of SARS-CoV-2 Infections among Hospital Healthcare Workers in Liège, Belgium. Viruses 14, 1302. https://doi.org/10.3390/v14061302
• [20] Truong Nguyen, P., Kant, R., Van den Broeck, F., Suvanto, M.T., Alburkat, H., Virtanen, J., Ahvenainen, E., Castren, R., Hong, S.L., Baele, G., Ahava, M.J., Jarva, H., Jokiranta, S.T., Kallio-Kokko, H., Kekäläinen, E., Kirjavainen, V., Kortela, E., Kurkela, S., Lappalainen, M., Liimatainen, H., Suchard, M.A., Hannula, S., Ellonen, P., Sironen, T., Lemey, P., Vapalahti, O., Smura, T., 2022. The phylodynamics of SARS-CoV-2 during 2020 in Finland. Communications Medicine 2, 1–9. https://doi.org/10.1038/s43856-022-00130-7
• [19] Lefrancq, N., Bouchez, V., Fernandes, N., Barkoff, A.-M., Bosch, T., Dalby, T., Åkerlund, T., Darenberg, J., Fabianova, K., Vestrheim, D.F., Fry, N.K., González-López, J.J., Gullsby, K., Habington, A., He, Q., Litt, D., Martini, H., Piérard, D., Stefanelli, P., Stegger, M., Zavadilova, J., Armatys, N., Landier, A., Guillot, S., Hong, S.L., Lemey, P., Parkhill, J., Toubiana, J., Cauchemez, S., Salje, H., Brisse, S. (2022). Global spatial dynamics and vaccine-induced fitness changes of Bordetella pertussis. Science Translational Medicine. 14, eabn3253. https://doi.org/10.1126/scitranslmed.abn3253
• [18] Kaleta, T.*, Kern, L.*, Hong, S. L.*, Hölzer, M., Kochs, G., Beer, J., Schnepf, D., Schwemmle, M., Bollen, N., Kolb, P., Huber, M., Ulferts, S., Weigang, S., Dudas, G., Wittig, A., Jaki, L., Padane, A., Lagare, A., Salou, M., … Fuchs, J. (2022). Antibody escape and global spread of SARS-CoV-2 lineage A.27. Nature Communications, 13(1), 1–13. https://doi.org/10.1038/s41467-022-28766-y

2021

• [17] Dudas, G., Hong, S. L., Potter, B. I., Calvignac-Spencer, S., Niatou-Singa, F. S., Tombolomako, T. B., Fuh-Neba, T., Vickos, U., Ulrich, M., Leendertz, F. H., Khan, K., Huber, C., Watts, A., Olendraitė, I., Snijder, J., Wijnant, K. N., Bonvin, A. M. J. J., Martres, P., Behillil, S., … Baele, G. (2021). Emergence and spread of SARS-CoV-2 lineage B.1.620 with variant of concern-like mutations and deletions. Nature Communications, 12(1), 5769. https://doi.org/10.1038/s41467-021-26055-8
• [16] Butera, Y., Mukantwari, E., Artesi, M., Umuringa, J. D., O’Toole, Á. N., Hill, V., Rooke, S., Hong, S. L., Dellicour, S., Majyambere, O., Bontems, S., Boujemla, B., Quick, J., Resende, P. C., Loman, N., Umumararungu, E., Kabanda, A., Murindahabi, M. M., Tuyisenge, P., … Rujeni, N. (2021). Genomic sequencing of SARS-CoV-2 in Rwanda reveals the importance of incoming travelers on lineage diversity. Nature Communications, 12(1), 5705. https://doi.org/10.1038/s41467-021-25985-7
• [15] Bollen, N., Artesi, M., Durkin, K., Hong, S. L., Potter, B., Boujemla, B., Vanmechelen, B., Martí-Carreras, J., Wawina-Bokalanga, T., Meex, C., Bontems, S., Hayette, M.-P., André, E., Maes, P., Bours, V., Baele, G., & Dellicour, S. (2021). Exploiting genomic surveillance to map the spatio-temporal dispersal of SARS-CoV-2 spike mutations in Belgium across 2020. Scientific Reports, 11(1), 18580. https://doi.org/10.1038/s41598-021-97667-9
• [14] Pirnay, J.-P., Selhorst, P., Hong, S. L., Cochez, C., Potter, B., Maes, P., Petrillo, M., Dudas, G., Claes, V., Beken, Y. V. der, Verbeken, G., Degueldre, J., Dellicour, S., Cuypers, L., T’Sas, F., Van den Eede, G., Verhasselt, B., Weuts, W., Smets, C., … Baele, G. (2021). Variant Analysis of SARS-CoV-2 Genomes from Belgian Military Personnel Engaged in Overseas Missions and Operations. Viruses, 13(7), 1359. https://doi.org/10.3390/v13071359
• [13] Lemey, P., Ruktanonchai, N., Hong, S. L., Colizza, V., Poletto, C., Van den Broeck, F., Gill, M. S., Ji, X., Levasseur, A., Oude Munnink, B. B., Koopmans, M., Sadilek, A., Lai, S., Tatem, A. J., Baele, G., Suchard, M. A., & Dellicour, S. (2021). Untangling introductions and persistence in COVID-19 resurgence in Europe. Nature. https://doi.org/10.1038/s41586-021-03754-2
• [12] Dellicour S, Hong SL, Vrancken B, Chaillon A, Gill MS, et al. (2021) Dispersal dynamics of SARS-CoV-2 lineages during the first epidemic wave in New York City. PLOS Pathogens 17(5): e1009571. https://doi.org/10.1371/journal.ppat.1009571
• [11] Hong, S. L., Lemey, P., Suchard, M. A., & Baele, G. (2021). Bayesian phylogeographic analysis incorporating predictors and individual travel histories in BEAST. Current Protocols, 1, e98. http://dx.doi.org/10.1002/cpz1.98

2020

• [10] Elnekave, E., Hong, S. L., Lim, S., Boxrud, D., Rovira, A., Mather, A. E….Alvarez, J. (2020). Transmission of Multidrug-Resistant Salmonella enterica Subspecies enterica 4,[5],12:i:- Sequence Type 34 between Europe and the United States. Emerging Infectious Diseases, 26(12), 3034-3038. https://dx.doi.org/10.3201/eid2612.200336.
• [9] Dellicour, S., Durkin, K., Hong, S. L., Vanmechelen, B., Martí-Carreras, J., Gill, M. S., Meex, C., Bontems, S., André, E., Gilbert, M., Walker, C., De Maio, N., Hadfield, J., Hayette, M.-P., Bours, V., Wawina-Bokalanga, T., Artesi, M., Baele, G., & Maes, P. (2020). A phylodynamic workflow to rapidly gain insights into the dispersal history and dynamics of SARS-CoV-2 lineages. Molecular Biology and Evolution, , https://doi.org/10.1093/molbev/msaa284
• [8] Hayer, S. S., Lim, S., Hong, S., Elnekave, E., Johnson, T., Rovira, A., … Alvarez, J. (2020). Genetic Determinants of Resistance to Extended-Spectrum Cephalosporin and Fluoroquinolone in Escherichia coli Isolated from Diseased Pigs in the United States. mSphere, 5(5). https://doi.org/10.1128/msphere.00990-20
• [7] Lemey, P., Hong, S. L., Hill, V., Baele, G., Poletto, C., Colizza, V., O’Toole, Á., McCrone, J. T., Andersen, K. G., Worobey, M., Nelson, M. I., Rambaut, A., & Suchard, M. A. (2020). Accommodating individual travel history and unsampled diversity in Bayesian phylogeographic inference of SARS-CoV-2. Nature Communications, 11(1), 5110. https://doi.org/10.1038/s41467-020-18877-9
• [6] Elnekave, E., Hong, S. L., Lim, S., Johnson, T. J., Perez, A., & Alvarez, J. (2020). Comparing serotyping with whole-genome sequencing for subtyping of non-typhoidal Salmonella enterica: a large-scale analysis of 37 serotypes with a public health impact in the USA. Microbial Genomics, 8, 534. https://doi.org/10.1099/mgen.0.000425
• [5] Hong, S. L., Dellicour, S., Vrancken, B., Suchard, M. A., Pyne, M. T., Hillyard, D. R., Lemey, P., & Baele, G. (2020). In Search of Covariates of HIV-1 Subtype B Spread in the United States-A Cautionary Tale of Large-Scale Bayesian Phylogeography. Viruses, 12(2). https://doi.org/10.3390/v12020182

2019

• [4] Elnekave, E., Hong, S. L., Lim, S., Hayer, S. S., Boxrud, D., Taylor, A. J., Lappi, V., Noyes, N., Johnson, T. J., Rovira, A., Davies, P., Perez, A., & Alvarez, J. (2019). Circulation of Plasmids Harboring Resistance Genes to Quinolones and/or Extended-Spectrum Cephalosporins in Multiple Salmonella enterica Serotypes from Swine in the United States. Antimicrobial Agents and Chemotherapy, 63(4). https://doi.org/10.1128/AAC.02602-18

2018

• [3] Elnekave, E., Hong, S., Mather, A. E., Boxrud, D., Taylor, A. J., Lappi, V., Johnson, T. J., Vannucci, F., Davies, P., Hedberg, C., Perez, A., & Alvarez, J. (2018). Salmonella enterica Serotype 4,[5],12:i:- in Swine in the United States Midwest: An Emerging Multidrug-Resistant Clade. Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America, 66(6), 877–885. https://doi.org/10.1093/cid/cix909

2017

• [2] Ahlstrom, C., Muellner, P., Spencer, S. E. F., Hong, S., Saupe, A., Rovira, A., Hedberg, C., Perez, A., Muellner, U., & Alvarez, J. (2017). Inferring source attribution from a multiyear multisource data set of Salmonella in Minnesota. Zoonoses and Public Health, 64(8), 589–598. https://doi.org/10.1111/zph.12351

2016

• [1] Hong, S., Rovira, A., Davies, P., Ahlstrom, C., Muellner, P., Rendahl, A., Olsen, K., Bender, J. B., Wells, S., Perez, A., & Alvarez, J. (2016). Serotypes and Antimicrobial Resistance in Salmonella enterica Recovered from Clinical Samples from Cattle and Swine in Minnesota, 2006 to 2015. PloS One, 11(12), e0168016. https://doi.org/10.1371/journal.pone.0168016