Peer-reviewed Publications.

2024

• [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
• [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