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Convergent trends and spatiotemporal patterns of Aedes-borne arboviruses in Mexico and Central America (2023)
Journal Article
Gutierrez, B., da Silva Candido, D., Bajaj, S., Paulina Rodriguez Maldonado, A., Garces Ayala, F., de la Luz Torre Rodriguez, M., Araiza Rodriguez, A., Wong Arámbula, C., Ramírez González, E., López Martínez, I., Alberto Díaz-Quiñónez, J., Vázquez Pichardo, M., Hill, S. C., Thézé, J., Faria, N. R., Pybus, O. G., Preciado-Llanes, L., Reyes-Sandoval, A., Kraemer, M. U., & Escalera-Zamudio, M. (2023). Convergent trends and spatiotemporal patterns of Aedes-borne arboviruses in Mexico and Central America. PLoS Neglected Tropical Diseases, 17(9), https://doi.org/10.1371/journal.pntd.0011169

BackgroundAedes-borne arboviruses cause both seasonal epidemics and emerging outbreaks with a significant impact on global health. These viruses share mosquito vector species, often infecting the same host population within overlapping geographic reg... Read More about Convergent trends and spatiotemporal patterns of Aedes-borne arboviruses in Mexico and Central America.

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.

Impact of host age on viral and bacterial communities in a waterbird population (2022)
Journal Article
Hill, S. C., François, S., Thézé, J., Smith, A., Simmonds, P., Perrins, C., Van Der Hoek, L., & Pybus, O. (in press). Impact of host age on viral and bacterial communities in a waterbird population. ISME Journal,

Wildlife harbour pathogens that can harm human or livestock health and are the source of most emerging infectious diseases. It is rarely considered how changes in wildlife population age-structures or how age-stratified behaviours might alter the lev... Read More about Impact of host age on viral and bacterial communities in a waterbird population.

Molecular and genomic investigation of an urban outbreak of dengue serotype 2 in Angola, 2017-2019 (2022)
Journal Article
Neto, Z., Martinez, P., Hill, S., Jandondo, D., Thézé, J., Mirandela, M., Aguiar, R. S., Xavier, J., dos Santos Sebastião, C., Candido, A. L. M., Vaz, F., Reyes Castro, G., Paixão, J. P., Loman, N. L., Lemey, P., Pybus, O., Vasconcelos, J., Faria, N. R., & Afonso, J. (2022). Molecular and genomic investigation of an urban outbreak of dengue serotype 2 in Angola, 2017-2019. PLoS Neglected Tropical Diseases, https://doi.org/10.1371/journal.pntd.0010255

Understanding Sabiá virus infections (Brazilian mammarenavirus) (2022)
Journal Article
Nastri, A. C., Duarte-Neto, A. N., Casadio, L. V. B., Souza, W. M. D., Claro, I. M., Manuli, E. R., Selegatto, G., Salomão, M. C., Fialkovitz, G., Taborda, M., Almeida, B. L. D., Magri, M. C., Guedes, A. R., Perdigão Neto, L. V., Sataki, F. M., Guimarães, T., Mendes-Correa, M. C., Tozetto-Mendoza, T. R., Fumagalli, M. J., Ho, Y.-L., …Levin, A. S. (2022). Understanding Sabiá virus infections (Brazilian mammarenavirus). Travel Medicine and Infectious Disease, 48, 102351. https://doi.org/10.1016/j.tmaid.2022.102351

Genomic Epidemiology of Early SARS-CoV-2 Transmission Dynamics, Gujarat, India (2022)
Journal Article
Raghwani, J., du Plessis, L., McCrone, J., Hill, S., Parag, K., Theze, J., Kumar, D., Puvar, A., Pandit, R., Pybus, O., Fournie, G., Joshi, M., & Joshi, C. (2022). Genomic Epidemiology of Early SARS-CoV-2 Transmission Dynamics, Gujarat, India. Emerging Infectious Disease, 28(4), 751-758. https://doi.org/10.3201/eid2804.212053

Limited genomic sampling in many high-incidence countries has impeded studies of severe respiratory syndrome coronavirus 2 (SARS-CoV-2) genomic epidemiology. Consequently, critical questions remain about the generation and global distribution of viru... Read More about Genomic Epidemiology of Early SARS-CoV-2 Transmission Dynamics, Gujarat, India.

Mapping environmental suitability of Haemagogus and Sabethes spp. mosquitoes to understand sylvatic transmission risk of yellow fever virus in Brazil (2022)
Journal Article
Li, S. L., Acosta, A. L., Hill, S. C., Brady, O. J., de Almeida, M. A., Cardoso, J. D. C., Hamlet, A., Mucci, L. F., Telles de Deus, J., Iani, F. C., Alexander, N. S., William Wint, G., Pybus, O. G., Kraemer, M. U., Faria, N. R., & Messina, J. P. (2022). Mapping environmental suitability of Haemagogus and Sabethes spp. mosquitoes to understand sylvatic transmission risk of yellow fever virus in Brazil. PLoS Neglected Tropical Diseases,

Trade-offs between individual and ensemble forecasts of an emerging infectious disease (2021)
Journal Article
Oidtman, R., Omodei, E., Kraemer, M., Castaneda-Orjuela, C., Cruz-Rivera, E., Misnaza-Castrillon, S., Cifuentes, M., Rincon, L., Canon, V., de Alarcon, P., Espana, G., Huber, J., Hill, S., Barker, C., Johansson, M., Manore, C., Reiner, R., Rodriguez-Barraquer, I., Siraj, A., Frias-Martinez, E., …Perkins, T. (2021). Trade-offs between individual and ensemble forecasts of an emerging infectious disease. Nature Communications, 12(1), https://doi.org/10.1038/s41467-021-25695-0

Newly emerged pathogens are inherently difficult to forecast, due to many unknowns about their biology early in an epidemic. Here, the authors assess forecasts of a suite of models during the Zika epidemic in Colombia, finding that the models that pe... Read More about Trade-offs between individual and ensemble forecasts of an emerging infectious disease.

Trade-offs between individual and ensemble forecasts of an emerging infectious disease (2021)
Journal Article
Oidtman, R. J., Omodei, E., Kraemer, M. U. G., Casteneda-Orjuela, C. A., Cruz-Rivera, E., Misnaza-Castrillon, S., Cifuentes, M. P., Rincon, L. E., Canon, V., de Alarcon, P., Espana, G., Huber, J. H., Hill, S. C., Barker, C. M., Johansson, M. A., Manore, C. A., Reiner, R. C., Rodriguez-Barraquer, I., Siraj, A. S., Frias-Martinez, E., …Perkins, A. (2021). Trade-offs between individual and ensemble forecasts of an emerging infectious disease. Nature Communications, 12, Article 5379. https://doi.org/10.1101/2021.02.25.21252363