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Estimating epidemic dynamics with genomic and time series data (2025)
Journal Article
Zarebski, A., Zwaans, A., Gutierrez, B., du Plessis, L., & Pybus, O. (2025). Estimating epidemic dynamics with genomic and time series data. Journal of the Royal Society, Interface, 22(227), https://doi.org/10.1098/rsif.2024.0632

Accurately estimating the prevalence and transmissibility of an infectious disease is an important task in genetic infectious disease epidemiology. However, generating accurate estimates of these quantities, that make use of both epidemic time series... Read More about Estimating epidemic dynamics with genomic and time series data.

Artificial intelligence for modelling infectious disease epidemics (2025)
Journal Article
Kraemer, M. U. G., Tsui, L.-H., Chang, S. Y., Lytras, S., Khurana, M. P., Vanderslott, S., Bajaj, S., Scheidwasser, N., Curran-Sebastian, J. L., Semenova, E., Zhang, M., Unwin, H. J. T., Watson, O. J., Mills, C., Dasgupta, A., Ferretti, L., Scarpino, S. V., Koua, E., Morgan, O., Tegally, H., …Bhatt, S. (2025). Artificial intelligence for modelling infectious disease epidemics. Nature, 638(8051), 623-635. https://doi.org/10.1038/s41586-024-08564-w

Infectious disease threats to individual and public health are numerous, varied and frequently unexpected. Artificial intelligence (AI) and related technologies, which are already supporting human decision making in economics, medicine and social sci... Read More about Artificial intelligence for modelling infectious disease epidemics.

Anthropogenic land consolidation intensifies zoonotic host diversity loss and disease transmission in human habitats (2024)
Journal Article
Pei, S., Yu, P., Raghwani, J., Wang, Y., Liu, Z., Li, Y., Cheng, Y., Lin, Q., Song, C., Dharmarajan, G., Faust, C. L., Tian, Y., Xu, Y., Liang, Y., Qu, J., Wei, J., Li, S., Zhang, T., Ma, C., Bharti, N., …Tian, H. (in press). Anthropogenic land consolidation intensifies zoonotic host diversity loss and disease transmission in human habitats. Nature Ecology and Evolution, 9(1), 99-110. https://doi.org/10.1038/s41559-024-02570-x

Routes of importation and spatial dynamics of SARS-CoV-2 variants during localized interventions in Chile (2024)
Journal Article
Gutierrez, B., Tsui, J., Pullano, G., Mazzoli, M., Gangavarapu, K., Inward, R., Bajaj, S., Pena, R., Busch-Moreno, S., Suchard, M., Pybus, O., Dunner, A., Puentes, R., Ayala, S., Fernandez, J., Araos, R., Ferres, L., Colizza, V., & Kraemer, M. (2024). Routes of importation and spatial dynamics of SARS-CoV-2 variants during localized interventions in Chile. PNAS Nexus, 3(11), https://doi.org/10.1093/pnasnexus/pgae483

Human mobility is strongly associated with the spread of SARS-CoV-2 via air travel on an international scale and with population mixing and the number of people moving between locations on a local scale. However, these conclusions are drawn mostly fr... Read More about Routes of importation and spatial dynamics of SARS-CoV-2 variants during localized interventions in Chile.

Dispersal patterns and influence of air travel during the global expansion of SARS-CoV-2 variants of concern (2024)
Journal Article
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, D. D. S., Romero, F. R., Baxter, C., Pybus, O., Lessells,, R. J., Faria,, N. R., Kraemer,, M. U., & de Oliveira, T. (2024). Dispersal patterns and influence of air travel during the global expansion of SARS-CoV-2 variants of concern. Cell, https://doi.org/10.1016/j.cell.2023.06.001

Synchrony of Bird Migration with Global Dispersal of Avian Influenza Reveals Exposed Bird Orders (2024)
Journal Article
Yang, Q., Wang, B., Lemey, P., Dong, L., Mu, T., Wiebe, R. A., Guo, F., Trovão, N. S., Park, S. W., Lewis, N., Tsui, J. L.-H., Bajaj, S., Cheng, Y., Yang, L., Haba, Y., Li, B., Zhang, G., Pybus, O. G., Tian, H., & Grenfell, B. (2024). Synchrony of Bird Migration with Global Dispersal of Avian Influenza Reveals Exposed Bird Orders. Nature Communications, 15(1), https://doi.org/10.1038/s41467-024-45462-1

Highly pathogenic avian influenza virus (HPAIV) A H5, particularly clade 2.3.4.4, has caused worldwide outbreaks in domestic poultry, occasional spillover to humans, and increasing deaths of diverse species of wild birds since 2014. Wild bird migrati... Read More about Synchrony of Bird Migration with Global Dispersal of Avian Influenza Reveals Exposed Bird Orders.

Ancient chicken remains reveal the origins of virulence in Marek's disease virus (2023)
Journal Article
Fiddaman, S., Dimopoulos, E., Lebrasseur, O., du Plessis, L., Vrancken, B., Charlton, S., Haruda, A., Tabbada, K., Flammer, P., Dascalu, S., Markovic, N., Li, H., Franklin, G., Symmons, R., Baron, H., Daróczi-Szabó, L., Shaymuratova, D., Askeyev, I., Putelat, O., Sana, M., …Frantz, L. (2023). Ancient chicken remains reveal the origins of virulence in Marek's disease virus. Science, 382(6676), 1276-1281. https://doi.org/10.1126/science.adg2238

The pronounced growth in livestock populations since the 1950s has altered the epidemiological and evolutionary trajectory of their associated pathogens. For example, Marek's disease virus (MDV), which causes lymphoid tumors in chickens, has experien... Read More about Ancient chicken remains reveal the origins of virulence in Marek's disease virus.

SARS-CoV-2 evolution in the Omicron era (2023)
Journal Article
Roemer, C., Sheward, D., Hisner, R., Gueli, F., Sakaguchi, H., Frohberg, N., Schoenmakers, J., Sato, K., O'Toole, A., Rambaut, A., Pybus, O., Ruis, C., Murrell, B., & Peacock, T. (2023). SARS-CoV-2 evolution in the Omicron era. Nature Microbiology, 8(11), 1952-1959. https://doi.org/10.1038/s41564-023-01504-w

Since SARS-CoV-2 BA.5 (Omicron) emerged and spread in 2022, Omicron lineages have markedly diversified. Here we review the evolutionary trajectories and processes that underpin the emergence of these lineages, and identify the most prevalent sublinea... Read More about SARS-CoV-2 evolution in the Omicron era.

Comparing the evolutionary dynamics of predominant SARS-CoV-2 virus lineages co-circulating in Mexico (2023)
Journal Article
Castelán-Sánchez, H., Delaye, L., Inward, R., Dellicour, S., Gutierrez, B., de la Vina, N., Boukadida, C., Pybus, O., Jáuregui, G., Guzmán, P., Flores-Garrido, M., Fontanelli, O., Rosales, M., Meneses, A., Olmedo-Alvarez, G., Herrera-Estrella, A., Sánchez-Flores, A., Muñoz-Medina, J., Comas-García, A., Gómez-Gil, B., …Zamudio, M. (2023). Comparing the evolutionary dynamics of predominant SARS-CoV-2 virus lineages co-circulating in Mexico. eLife, 12, https://doi.org/10.7554/eLife.82069

Over 200 different SARS-CoV-2 lineages have been observed in Mexico by November 2021. To investigate lineage replacement dynamics, we applied a phylodynamic approach and explored the evolutionary trajectories of five dominant lineages that circulated... Read More about Comparing the evolutionary dynamics of predominant SARS-CoV-2 virus lineages co-circulating in Mexico.

Genomic assessment of invasion dynamics of SARS-CoV-2 Omicron BA.1 (2023)
Journal Article
Tsui, J. L.-H., McCrone, J. T., Lambert, B., Bajaj, S., Inward, R. P. D., Bosetti, P., Pena, R. E., Tegally, H., Hill, V., Zarebski, A. E., Peacock, T. P., Liu, L., Wu, N., Davis, M., Bogoch, I. I., Khan, K., Kall, M., Abdul Aziz, N. I. B., Colquhoun, R., O’Toole, Á., …The COVID-19 Genomics UK (COG-UK) consortium¶. (2023). Genomic assessment of invasion dynamics of SARS-CoV-2 Omicron BA.1. Science, 381(6655), 336-343. https://doi.org/10.1126/science.adg6605

Identification of Evolutionary Trajectories Shared across Human Betacoronaviruses (2023)
Journal Article
Escalera-Zamudio, M., Kosakovsky Pond, S. L., Martínez de la Viña, N., Gutiérrez, B., Inward, R. P. D., Thézé, J., van Dorp, L., Castelán-Sánchez, H. G., Bowden, T. A., Pybus, O. G., & Hulswit, R. J. G. (2023). Identification of Evolutionary Trajectories Shared across Human Betacoronaviruses. Genome Biology and Evolution, 15(6), https://doi.org/10.1093/gbe/evad076

Comparing the evolution of distantly related viruses can provide insights into common adaptive processes related to shared ecological niches. Phylogenetic approaches, coupled with other molecular evolution tools, can help identify mutations informati... Read More about Identification of Evolutionary Trajectories Shared across Human Betacoronaviruses.

Implementation of Genomic Surveillance of SARS-CoV-2 in the Caribbean: Lessons Learned for Sustainability in Resource-Limited Settings (2023)
Journal Article
Sahadeo, N. S. D., Nicholls, S., Moreira, F. R. R., O'Toole, Á., Ramkissoon, V., Whittaker, C., Hill, V., McCrone, J. T., Mohammed, N., Ramjag, A., Brown-Jordan, A., Hill, S. C., Singh, R., Nathaniel-Girdharrie, S.-M., Hinds, A., Ramkissoon, N., Parag, K. V., Nandram, N., Parasram, R., Khan-Mohammed, Z., …Carrington, C. V. F. (2023). Implementation of Genomic Surveillance of SARS-CoV-2 in the Caribbean: Lessons Learned for Sustainability in Resource-Limited Settings. The Lancet Global Health, https://doi.org/10.1371/journal.pgph.0001455

Bidirectional Movement of Emerging H5N8 Avian Influenza Viruses Between Europe and Asia via Migratory Birds Since Early 2020 (2023)
Journal Article
Zhang, G., Li, B., Raghwani, J., Vrancken, B., Jia, R., Hill, S., Fournié, G., Cheng, Y., Yang, Q., Wang, Y., Wang, Z., Dong, L., Pybus, O. G., & Tian, H. (2023). Bidirectional Movement of Emerging H5N8 Avian Influenza Viruses Between Europe and Asia via Migratory Birds Since Early 2020. Molecular Biology and Evolution, 40(2), https://doi.org/10.1093/molbev/msad019

Global disparities in SARS-CoV-2 genomic surveillance (2022)
Journal Article
Brito, A. F., Semenova, E., Dudas, G., Hassler, G. W., Kalinich, C. C., Kraemer, M. U., Ho, J., Tegally, H., Githinji, G., Agoti, C. N., Matkin, L. E., Whittaker, C., Howden, B. P., Sintchenko, V., Zuckerman, N. S., Mor, O., Blankenship, H. M., Oliveira, T. D., Lin, R. T. P., Siqueira, M. M., …GISAID core curation team. (in press). Global disparities in SARS-CoV-2 genomic surveillance. Nature Communications, https://doi.org/10.1101/2021.08.21.21262393

Global disparities in SARS-CoV-2 genomic surveillance (2022)
Journal Article
Brito, A., Semenova, E., Dudas, G., Hassler, G., Kalinich, C., Kraemer, M., Ho, J., Tegally, H., Githinji, G., Agoti, C., Matkin, L., Whittaker, C., Bulgarian SARS-CoV-2 Sequencing Gr, Communicable Dis Genomics Network, COVID-19 Impact Project, Danish Covid-19 Genome Consortium, Fiocruz COVID-19 Genomic Surveilla, GISAID Core Curation Team, Network Genomic Surveillance South, Swiss SARS-CoV-2 Sequencing Consor, …Faria, N. (2022). Global disparities in SARS-CoV-2 genomic surveillance. Nature Communications, 13(1), https://doi.org/10.1038/s41467-022-33713-y

Genomic sequencing is essential to track the evolution and spread of SARS-CoV-2, optimize molecular tests, treatments, vaccines, and guide public health responses. To investigate the global SARS-CoV-2 genomic surveillance, we used sequences shared vi... Read More about Global disparities in SARS-CoV-2 genomic surveillance.

Seasonal dynamics of the wild rodent faecal virome (2022)
Journal Article
Raghwani, J., Faust, C. L., François, S., Nguyen, D., Marsh, K., Raulo, A., Hill, S. C., Parag, K. V., Simmonds, P., Knowle1, S. C., & Pybus, O. G. (2023). Seasonal dynamics of the wild rodent faecal virome. Molecular Ecology, https://doi.org/10.1111/mec.16778

Viral discovery studies in wild animals often rely on cross-sectional surveys at a single time point. As a result, our understanding of the temporal stability of wild animal viromes remains poorly resolved. While studies of single host-virus systems... Read More about Seasonal dynamics of the wild rodent faecal virome.