{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,6]],"date-time":"2026-07-06T03:16:16Z","timestamp":1783307776129,"version":"3.54.6"},"reference-count":32,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2026,7,6]],"date-time":"2026-07-06T00:00:00Z","timestamp":1783296000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2026,7,6]],"date-time":"2026-07-06T00:00:00Z","timestamp":1783296000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"name":"Collaborative Research Fund","award":["C5079-21G"],"award-info":[{"award-number":["C5079-21G"]}]},{"name":"Theme-based Research Scheme","award":["T11-705\/21-N"],"award-info":[{"award-number":["T11-705\/21-N"]}]},{"name":"Innovation and Technology Commission\u2019s InnoHK initiative of the Hong Kong SAR Government"},{"name":"Hong Kong Jockey Club Global Health Institute"},{"name":"Health Bureau\u2019s Health and Medical Research Fund","award":["COVID1903011-WP1"],"award-info":[{"award-number":["COVID1903011-WP1"]}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Urban Info"],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>The urban system is believed to play a role in transmission of human respiratory disease such as COVID-19 in densely populated cities. Hong Kong experienced five significant local infection waves of COVID-19 during 2020\u20132022, caused by different SARS-CoV-2 variants. Viral genomic data capture the footprint of transmission history, offering insights that are invisible to incidence data, such as resolving fine-scale transmission chains, distinguishing between multiple independent introductions and local superspreading events, and revealing cryptic transmission links. Building on this, our study aimed to investigate the impact of urban demography and connectivity on SARS-CoV-2 transmission by integrating genomic surveillance and urban mobility data into Bayesian phylodynamics analysis to examine the spatiotemporal spread of SARS-CoV-2 across epidemic waves three to five in Hong Kong. Using 1,725 viral genomes linked to their patients\u2019 residential addresses, we reconstructed variant-specific dispersal patterns and quantified the impact of human demographic and behavioral factors on inter-district transmission. Results revealed that these three outbreak waves initially concentrated in high-density districts, Wong Tai Sin, Yau Tsim Mong, and Kwai Tsing, respectively. Population density and Mass Transit Railway (MTR) usage consistently predicted transmission rates among districts. The early seeding districts acted as epicenters and main exporters of regional spread. These findings demonstrated that synthesizing pathogen genomic, spatial, and urban mobility data can effectively identify transmission hotspots and optimize targeted interventions. This inter-disciplinary approach provides a multi-data-source framework for monitoring pathogen spread in cities, improving outbreak response in high-density urban environments.<\/jats:p>","DOI":"10.1007\/s44212-026-00108-z","type":"journal-article","created":{"date-parts":[[2026,7,6]],"date-time":"2026-07-06T03:01:26Z","timestamp":1783306886000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Geographical dispersion and transmission of multiple SARS-CoV-2 variants in Hong Kong"],"prefix":"10.1007","volume":"5","author":[{"given":"Zoe Yi","family":"Song","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jinjin","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marcus H. H.","family":"Shum","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Haogao","family":"Gu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wenzhong","family":"Shi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gilman K. H.","family":"Siu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Leo L. M.","family":"Poon","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joseph T.","family":"Wu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kathy S. M.","family":"Leung","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tommy T. Y.","family":"Lam","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,7,6]]},"reference":[{"issue":"8","key":"108_CR1","doi-asserted-by":"publisher","first-page":"2167","DOI":"10.1093\/molbev\/msw082","volume":"33","author":"F Bielejec","year":"2016","unstructured":"Bielejec, F., Baele, G., Vrancken, B., Suchard, M. A., Rambaut, A., & Lemey, P. (2016). Sprea D3: Interactive visualization of spatiotemporal history and trait evolutionary processes. Molecular Biology and Evolution, 33(8), 2167\u20132169.","journal-title":"Molecular Biology and Evolution"},{"key":"108_CR2","doi-asserted-by":"publisher","DOI":"10.1016\/j.buildenv.2022.109323","author":"VCC Cheng","year":"2022","unstructured":"Cheng, V. C. C., Wong, S. C., Au, A. K. W., Zhang, C., Chen, J. H. K., So, S. Y. C., Li, X., Wang, Q., Lu, K. K., Lung, D. C., Chuang, V. W. M., Schuldenfrei, E., Siu, G. K. H., To, K. K. W., Li, Y. G., & Yuen, K. Y. (2022). Explosive outbreak of SARS-CoV-2 Omicron variant is associated with vertical transmission in high-rise residential buildings in Hong Kong. Building and Environment. https:\/\/doi.org\/10.1016\/j.buildenv.2022.109323","journal-title":"Building and Environment"},{"issue":"1","key":"108_CR3","doi-asserted-by":"publisher","first-page":"1072","DOI":"10.1080\/22221751.2022.2060137","volume":"11","author":"PH Cheung","year":"2022","unstructured":"Cheung, P. H., Chan, C. P., & Jin, D. Y. (2022). Lessons learned from the fifth wave of COVID-19 in Hong Kong in early 2022. Emerging Microbes & Infections, 11(1), 1072\u20131078.","journal-title":"Emerging Microbes & Infections"},{"key":"108_CR4","unstructured":"De Maio, N., Walker, C., Borges, R., Weilguny, L., Slodkowicz, G., & Goldman, N. (2020). Issues with SARS-CoV-2 sequencing data. Retrieved 6th April 2025 from https:\/\/virological.org\/t\/issues-with-sars-cov-2-sequencing-data\/473"},{"issue":"5","key":"108_CR5","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1009571","volume":"17","author":"S Dellicour","year":"2021","unstructured":"Dellicour, S., Hong, S. L., Vrancken, B., Chaillon, A., Gill, M. S., Maurano, M. T., Ramaswami, S., Zappile, P., Marier, C., Harkins, G. W., Baele, G., Duerr, R., & Heguy, A. (2021). Dispersal dynamics of SARS-CoV-2 lineages during the first epidemic wave in New York City. PLoS Pathogens, 17(5), Article e1009571.","journal-title":"PLoS Pathogens"},{"key":"108_CR6","doi-asserted-by":"publisher","DOI":"10.1016\/j.jth.2022.101356","volume":"26","author":"N Gartland","year":"2022","unstructured":"Gartland, N., Fishwick, D., Coleman, A., Davies, K., Hartwig, A., Johnson, S., & van Tongeren, M. (2022). Transmission and control of SARS-CoV-2 on ground public transport: A rapid review of the literature up to May 2021. Journal of Transport & Health, 26, Article 101356.","journal-title":"Journal of Transport & Health"},{"issue":"1","key":"108_CR7","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-022-28420-7","volume":"13","author":"H Gu","year":"2022","unstructured":"Gu, H., Xie, R., Adam, D. C., Tsui, J. L., Chu, D. K., Chang, L. D. J., Cheuk, S. S. Y., Gurung, S., Krishnan, P., Ng, D. Y. M., Liu, G. Y. Z., Wan, C. K. C., Cheng, S. S. M., Edwards, K. M., Leung, K. S. M., Wu, J. T., Tsang, D. N. C., Leung, G. M., Cowling, B. J., & Poon, L. L. M. (2022). Genomic epidemiology of SARS-CoV-2 under an elimination strategy in Hong Kong. Nature Communications, 13(1), Article 736.","journal-title":"Nature Communications"},{"issue":"1","key":"108_CR8","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-022-12941-8","volume":"12","author":"MK Gurram","year":"2022","unstructured":"Gurram, M. K., Wang, M. X., Wang, Y.-C., & Pang, J. (2022). Impact of urbanisation and environmental factors on spatial distribution of COVID-19 cases during the early phase of epidemic in Singapore. Scientific Reports, 12(1), Article 9758.","journal-title":"Scientific Reports"},{"issue":"4","key":"108_CR9","doi-asserted-by":"publisher","DOI":"10.1002\/jmv.70318","volume":"97","author":"E Gustani-Buss","year":"2025","unstructured":"Gustani-Buss, E., Buss, C. E., Biagi, C. AOd., Oliveira, IMd., Peronni, K. C., Vitiello, G. A. F., Fermino, B. L., Ivanski, F., Chao, B. M. P., Tuon, F. F. B., Follador, F. A. C., Lucio, L. C., Ferreto, L. E. D., Pillegi, M., Visentainer, J. E. L., Consolaro, M. E. L., Ter\u00eancio, M. L., Bertolini, D. A., Jorge, A. S., & Figueiredo, D. L. A. (2025). Unveiling the dynamics of SARS-CoV-2 Gamma and Delta waves in Paran\u00e1, Brazil \u2013 Delta displacing a persistent Gamma through alternative routes of dispersal. Journal of Medical Virology, 97(4), Article e70318.","journal-title":"Journal of Medical Virology"},{"issue":"1","key":"108_CR10","doi-asserted-by":"publisher","DOI":"10.1038\/s42005-021-00679-0","volume":"4","author":"S Hazarie","year":"2021","unstructured":"Hazarie, S., Soriano-Pa\u00f1os, D., Arenas, A., G\u00f3mez-Garde\u00f1es, J., & Ghoshal, G. (2021). Interplay between population density and mobility in determining the spread of epidemics in cities. Communications Physics, 4(1), Article 191.","journal-title":"Communications Physics"},{"issue":"4","key":"108_CR11","doi-asserted-by":"publisher","first-page":"772","DOI":"10.1093\/molbev\/mst010","volume":"30","author":"K Katoh","year":"2013","unstructured":"Katoh, K., & Standley, D. M. (2013). MAFFT multiple sequence alignment software version 7: Improvements in performance and usability. Molecular Biology and Evolution, 30(4), 772\u2013780.","journal-title":"Molecular Biology and Evolution"},{"issue":"6490","key":"108_CR12","doi-asserted-by":"publisher","first-page":"493","DOI":"10.1126\/science.abb4218","volume":"368","author":"MUG Kraemer","year":"2020","unstructured":"Kraemer, M. U. G., Yang, C.-H., Gutierrez, B., Wu, C.-H., Klein, B., Pigott, D. M., Group\u2020, O. C.-D. W., du Plessis, L., Faria, N. R., Li, R., Hanage, W. P., Brownstein, J. S., Layan, M., Vespignani, A., Tian, H., Dye, C., Pybus, O. G., & Scarpino, S. V. (2020). The effect of human mobility and control measures on the COVID-19 epidemic in China. Science, 368(6490), 493\u2013497.","journal-title":"Science"},{"issue":"8","key":"108_CR13","doi-asserted-by":"publisher","first-page":"544","DOI":"10.1016\/j.tig.2020.05.009","volume":"36","author":"TT-Y Lam","year":"2020","unstructured":"Lam, T.T.-Y. (2020). Tracking the genomic footprints of SARS-CoV-2 transmission. Trends in Genetics, 36(8), 544\u2013546.","journal-title":"Trends in Genetics"},{"key":"108_CR14","doi-asserted-by":"publisher","DOI":"10.1038\/s41591-023-02219-5","author":"JJ Lau","year":"2023","unstructured":"Lau, J. J., Cheng, S. M. S., Leung, K., Lee, C. K., Hachim, A., Tsang, L. C. H., Yam, K. W. H., Chaothai, S., Kwan, K. K. H., Chai, Z. Y. H., Lo, T. H. K., Mori, M., Wu, C., Valkenburg, S. A., Amarasinghe, G. K., Lau, E. H. Y., Hui, D. S. C., Leung, G. M., Peiris, M., & Wu, J. T. (2023). Real-world COVID-19 vaccine effectiveness against the Omicron BA.2 variant in a SARS-CoV-2 infection-naive population. Nature Medicine. https:\/\/doi.org\/10.1038\/s41591-023-02219-5","journal-title":"Nature Medicine"},{"key":"108_CR15","doi-asserted-by":"crossref","unstructured":"Lee, S., Lee, D. W., Kim, J. M., Kim, D. W., Kim, J. Y., Kim, J. A., Kim, I. H., Rhee, J. E., Min, K. D., Cho, S. I., Kim, E. J., & Kwon, J. H. (2023). Phylodynamic analysis revealed that human mobility and vaccination were correlated to the local spread of SARS-CoV-2 in Republic of Korea. Emerging Microbes & Infections, 12(2), 2228934.","DOI":"10.1080\/22221751.2023.2228934"},{"issue":"9","key":"108_CR16","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1000520","volume":"5","author":"P Lemey","year":"2009","unstructured":"Lemey, P., Rambaut, A., Drummond, A. J., & Suchard, M. A. (2009). Bayesian phylogeography finds its roots. PLOS Computational Biology, 5(9), Article e1000520.","journal-title":"PLOS Computational Biology"},{"issue":"8","key":"108_CR17","doi-asserted-by":"publisher","first-page":"1877","DOI":"10.1093\/molbev\/msq067","volume":"27","author":"P Lemey","year":"2010","unstructured":"Lemey, P., Rambaut, A., Welch, J. J., & Suchard, M. A. (2010). Phylogeography takes a relaxed random walk in continuous space and time. Molecular Biology and Evolution, 27(8), 1877\u20131885.","journal-title":"Molecular Biology and Evolution"},{"issue":"9","key":"108_CR18","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgph.0000577","volume":"2","author":"P Liu","year":"2022","unstructured":"Liu, P., Song, Y., Colijn, C., & MacPherson, A. (2022a). The impact of sampling bias on viral phylogeographic reconstruction. PLOS Global Public Health, 2(9), Article e0000577.","journal-title":"PLOS Global Public Health"},{"issue":"3","key":"108_CR19","doi-asserted-by":"publisher","DOI":"10.1016\/j.multra.2022.100030","volume":"1","author":"X Liu","year":"2022","unstructured":"Liu, X., Korto\u00e7i, P., Motlagh, N. H., Nurmi, P., & Tarkoma, S. (2022b). A survey of COVID-19 in public transportation: Transmission risk, mitigation and prevention. Multimodal Transportation, 1(3), Article 100030.","journal-title":"Multimodal Transportation"},{"key":"108_CR20","doi-asserted-by":"publisher","DOI":"10.1016\/j.eclinm.2021.100929","volume":"36","author":"Y Liu","year":"2021","unstructured":"Liu, Y., Gu, Z., & Liu, J. (2021). Uncovering transmission patterns of COVID-19 outbreaks: A region-wide comprehensive retrospective study in Hong Kong. EClinicalMedicine, 36, Article 100929.","journal-title":"EClinicalMedicine"},{"issue":"4","key":"108_CR21","doi-asserted-by":"publisher","DOI":"10.1093\/nsr\/nwac004","volume":"9","author":"L Luo","year":"2022","unstructured":"Luo, L., Yang, Z., Liang, J., Ma, Y., Wang, H., Hon, C., Jiang, M., Lin, Z., Guan, W., Mai, Z., Li, Y., Mai, K., Zeng, Z., Tu, C., Song, J., Liu, B., Liu, Y., He, J., Li, H., & Zhong, N. (2022). Crucial control measures to contain China\u2019s first Delta variant outbreak. National Science Review, 9(4), Article nwac004.","journal-title":"National Science Review"},{"issue":"1","key":"108_CR22","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-021-81806-3","volume":"11","author":"Y Murano","year":"2021","unstructured":"Murano, Y., Ueno, R., Shi, S., Kawashima, T., Tanoue, Y., Tanaka, S., Nomura, S., Shoji, H., Shimizu, T., Nguyen, H., Miyata, H., Gilmour, S., & Yoneoka, D. (2021). Impact of domestic travel restrictions on transmission of COVID-19 infection using public transportation network approach. Scientific Reports, 11(1), Article 3109.","journal-title":"Scientific Reports"},{"key":"108_CR23","doi-asserted-by":"publisher","DOI":"10.1016\/j.scitotenv.2023.166099","volume":"902","author":"Y Pan","year":"2023","unstructured":"Pan, Y., Huang, W., Dai, H. K., Bian, Y., Ho, K. F., & Chen, C. (2023). Evaluation of intervention measures in reducing the driver\u2019s exposure to respiratory particles in a taxi with infected passengers. Science of the Total Environment, 902, Article 166099.","journal-title":"Science of the Total Environment"},{"key":"108_CR24","unstructured":"Population Census Office. (2022). 2021 Population Census \u2013 Main Results."},{"issue":"1","key":"108_CR26","doi-asserted-by":"publisher","DOI":"10.1093\/ve\/vey016","volume":"4","author":"MA Suchard","year":"2018","unstructured":"Suchard, M. A., Lemey, P., Baele, G., Ayres, D. L., Drummond, A. J., & Rambaut, A. (2018). Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10. Virus Evolution, 4(1), Article vey016.","journal-title":"Virus Evolution"},{"issue":"15","key":"108_CR27","doi-asserted-by":"publisher","first-page":"3277","DOI":"10.1016\/j.cell.2023.06.001","volume":"186","author":"H Tegally","year":"2023","unstructured":"Tegally, H., Wilkinson, E., Tsui, J. L. H., Moir, M., Martin, D., Brito, A. F., Giovanetti, M., Khan, K., Huber, C., Bogoch, I. I., San, J. E., Poongavanan, J., Xavier, J. S., Candido, Dd. S., Romero, F., Baxter, C., Pybus, O. G., Lessells, R. J., Faria, N. R., & de Oliveira, T. (2023). Dispersal patterns and influence of air travel during the global expansion of SARS-CoV-2 variants of concern. Cell, 186(15), 3277-3290.e3216.","journal-title":"Cell"},{"key":"108_CR28","unstructured":"The Centre for Health Protection. (2023). Archives of Latest situation of cases of COVID-19. Retrieved October 31 2023 from https:\/\/www.chp.gov.hk\/en\/features\/102997.html"},{"key":"108_CR29","doi-asserted-by":"publisher","DOI":"10.3389\/fpubh.2022.978052","volume":"10","author":"C Tong","year":"2022","unstructured":"Tong, C., Shi, W., Siu, G. K., Zhang, A., & Shi, Z. (2022). Understanding spatiotemporal symptom onset risk of Omicron BA.1, BA.2 and hamster-related Delta AY.127. Frontiers in Public Health, 10, Article 978052.","journal-title":"Frontiers in Public Health"},{"key":"108_CR30","unstructured":"Transport Department. (2022). The annual traffic census 2022. Retrieved Jul 27 2023 from https:\/\/atc.td.gov.hk\/2021\/AnnualTrafficCensus2021.pdf"},{"issue":"2","key":"108_CR31","doi-asserted-by":"publisher","DOI":"10.3390\/ijerph20021422","volume":"20","author":"Y Xu","year":"2023","unstructured":"Xu, Y., Guo, C., Yang, J., Yuan, Z., & Ho, H. C. (2023). Modelling impact of high-rise, high-density built environment on COVID-19 risks: Empirical results from a case study of two Chinese cities. International Journal of Environmental Research and Public Health, 20(2), Article 1422.","journal-title":"International Journal of Environmental Research and Public Health"},{"key":"108_CR32","doi-asserted-by":"publisher","DOI":"10.1016\/j.lanwpc.2023.100969","author":"B Yang","year":"2024","unstructured":"Yang, B., Lin, Y., Xiong, W., Liu, C., Gao, H., Ho, F., Zhou, J., Zhang, R., Wong, J. Y., Cheung, J. K., Lau, E. H. Y., Tsang, T. K., Xiao, J., Wong, I. O. L., Mart\u00edn-S\u00e1nchez, M., Leung, G. M., Cowling, B. J., & Wu, P. (2024). Comparison of control and transmission of COVID-19 across epidemic waves in Hong Kong: An observational study. The Lancet Regional Health. https:\/\/doi.org\/10.1016\/j.lanwpc.2023.100969","journal-title":"The Lancet Regional Health"},{"key":"108_CR33","doi-asserted-by":"publisher","DOI":"10.1016\/j.tbs.2025.101015","volume":"40","author":"L Zheng","year":"2025","unstructured":"Zheng, L., Kwan, M.-P., Huang, J., & Liu, D. (2025). Exploring the interaction between perceived risk and travel flexibility in daily mobility change: Evidence from Hong Kong\u2019s COVID-19 pandemic. Travel Behaviour and Society, 40, Article 101015.","journal-title":"Travel Behaviour and Society"}],"container-title":["Urban Informatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s44212-026-00108-z.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1007\/s44212-026-00108-z","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s44212-026-00108-z.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,7,6]],"date-time":"2026-07-06T03:01:40Z","timestamp":1783306900000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/s44212-026-00108-z"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,7,6]]},"references-count":32,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2026,12]]}},"alternative-id":["108"],"URL":"https:\/\/doi.org\/10.1007\/s44212-026-00108-z","relation":{},"ISSN":["2731-6963"],"issn-type":[{"value":"2731-6963","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,7,6]]},"assertion":[{"value":"5 August 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"29 December 2025","order":2,"name":"revised","label":"Revised","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"11 February 2026","order":3,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"6 July 2026","order":4,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"The authors declare no competing interests.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interest"}}],"article-number":"20"}}