Genomic and epidemiological monitoring of yellow fever virus transmission potential

Faria, N. R.; Kraemer, M. U. G.; Hill, S. C.; Goes de Jesus, J.; Aguiar, R. S.; Iani, F. C. M.; Xavier, J.; Quick, J.; du Plessis, L.; Dellicour, S.; Thézé, J.; Carvalho, R. D. O.; Baele, G.; Wu, C.-H.; Silveira, P. P.; Arruda, M. B.; Pereira, M. A.; Pereira, G. C.; Lourenço, J.; Obolski, U.; Abade, L.; Vasylyeva, T. I.; Giovanetti, M.; Yi, D.; Weiss, D. J.; Wint, G. R. W.; Shearer, F. M.; Funk, S.; Nikolay, B.; Fonseca, V.; Adelino, T. E. R.; Oliveira, M. A. A.; Silva, M. V. F.; Sacchetto, L.; Figueiredo, P. O.; Rezende, I. M.; Mello, E. M.; Said, R. F. C.; Santos, D. A.; Ferraz, M. L.; Brito, M. G.; Santana, L. F.; Menezes, M. T.; Brindeiro, R. M.; Tanuri, A.; dos Santos, F. C. P.; Cunha, M. S.; Nogueira, J. S.; Rocco, I. M.; da Costa, A. C.; Komninakis, S. C. V.; Azevedo, V.; Chieppe, A. O.; Araujo, E. S. M.; Mendonça, M. C. L.; dos Santos, C. C.; dos Santos, C. D.; Mares-Guia, A. M.; Nogueira, R. M. R.; Sequeira, P. C.; Abreu, R. G.; Garcia, M. H. O.; Abreu, A. L.; Okumoto, O.; Kroon, E. G.; de Albuquerque, C. F. C.; Lewandowski, K.; Pullan, S. T.; Carroll, M.; de Oliveira, T.; Sabino, E. C.; Souza, R. P.; Suchard, M. A.; Lemey, P.; Trindade, G. S.; Drumond, B. P.; Filippis, A. M. B.; Loman, N. J.; Cauchemez, S.; Alcantara, L. C. J.; Pybus, O. G.

doi:10.1126/science.aat7115

Characterisation of the genomic sequence of a circo-like virus and of three chaphamaparvoviruses detected in mute swan (Cygnus olor) (2024)
Journal Article
Francois, S., Hill, S., Perrins, C., & Pybus, O. (2024). Characterisation of the genomic sequence of a circo-like virus and of three chaphamaparvoviruses detected in mute swan (Cygnus olor). Microbiology Resource Announcements, https://doi.org/10.1128/mra.01186-23

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., …Escalera-Zamudio, M. (2023). Convergent trends and spatiotemporal patterns of Aedes-borne arboviruses in Mexico and Central America. PLoS Neglected Tropical Diseases, https://doi.org/10.1371/journal.pntd.0011169

Genetic diversity, recombination and cross-species transmission of a waterbird gammacoronavirus in the wild (2023)
Journal Article
François, S., Nazki, S., Vickers, S. H., Fournié, G., Perrins, C. M., Broadbent, A. J., …Hill, S. C. (2023). Genetic diversity, recombination and cross-species transmission of a waterbird gammacoronavirus in the wild. Journal of General Virology, https://doi.org/10.1099/jgv.0.001883

Phylodynamic approaches to studying avian influenza virus: a review (2023)
Journal Article
Carnegie, L., Raghwani, J., Fournié, G., & Hill, S. (2023). Phylodynamic approaches to studying avian influenza virus: a review. Avian Pathology, https://doi.org/10.1080/03079457.2023.2236568

H9N2 avian influenza virus dispersal along Bangladeshi poultry trading networks (2023)
Journal Article
Carnegie, L., Hasan, M., Mahmud, R., Hoque, M. A., Debnath, N., Uddin, M. H., …Hill, S. C. (in press). H9N2 avian influenza virus dispersal along Bangladeshi poultry trading networks. Virus Evolution, https://doi.org/10.1093/ve/vead014

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., …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., …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., …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

Seasonal dynamics of the wild rodent faecal virome (2022)
Journal Article
Raghwani, J., Faust, C. L., François, S., Nguyen, D., Marsh, K., Raulo, A., …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., …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., …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., …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

Phylogenetic and phylodynamic approaches to understanding and combating the SARS-CoV-2 pandemic. (2022)
Journal Article
Attwood, S., Hill, S., David, A., Connor, T., & Pybus, O. (2022). Phylogenetic and phylodynamic approaches to understanding and combating the SARS-CoV-2 pandemic. Nature Reviews Genetics, https://doi.org/10.1038/+s41576-022-00483-8

Genomic epidemiology of early SARS-CoV-2 transmission dynamics in Gujarat, India (2022)
Journal Article
Raghwani, J., du Plessis, L., McCrone, J. T., Hill, S. C., Parag, K. V., Thézé, J., …Joshi, C. (2022). Genomic epidemiology of early SARS-CoV-2 transmission dynamics in Gujarat, India. Emerging Infectious Disease, https://doi.org/10.1101/2021.08.31.21262680

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., …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. J., Omodei, E., Kraemer, M. U. G., Casteneda-Orjuela, C. A., Cruz-Rivera, E., Misnaza-Castrillon, S., …Perkins, A. (2021). Trade-offs between individual and ensemble forecasts of an emerging infectious disease. Nature Communications, 12, https://doi.org/10.1101/2021.02.25.21252363

Molecular epidemiology of peste des petits ruminants virus emergence in critically endangered Mongolian saiga antelope and other wild ungulates (2021)
Journal Article
Benfield, C. T. O., Hill, S., Shatar, M., Shiilegdamba, E., Damdinjav, B., Fine, A., …Bataille, A. (in press). Molecular epidemiology of peste des petits ruminants virus emergence in critically endangered Mongolian saiga antelope and other wild ungulates. Virus Evolution, https://doi.org/10.1093/ve/veab062

Genomic Surveillance of Yellow Fever Virus Epizootic in São Paulo, Brazil, 2016 – 2018 (2020)
Journal Article
Lauring, A. S., Hill, S. C., de Souza, R., Thézé, J., Claro, I., Aguiar, R. S., …Faria, N. R. (2020). Genomic Surveillance of Yellow Fever Virus Epizootic in São Paulo, Brazil, 2016 – 2018. PLoS Pathogens, 16(8), e1008699. https://doi.org/10.1371/journal.ppat.1008699

São Paulo, a densely inhabited state in southeast Brazil that contains the fourth most populated city in the world, recently experienced its largest yellow fever virus (YFV) outbreak in decades. YFV does not normally circulate extensively in São Paul... Read More about Genomic Surveillance of Yellow Fever Virus Epizootic in São Paulo, Brazil, 2016 – 2018.

Evolution and epidemic spread of SARS-CoV-2 in Brazil (2020)
Journal Article
Candido, D. S., Claro, I. M., de Jesus, J. G., Souza, W. M., Moreira, F. R. R., Dellicour, S., …Faria, N. (2020). Evolution and epidemic spread of SARS-CoV-2 in Brazil. Science, eabd2161. https://doi.org/10.1126/science.abd2161

Brazil currently has one of the fastest growing SARS-CoV-2 epidemics in the world. Owing to limited available data, assessments of the impact of non-pharmaceutical interventions (NPIs) on virus spread remain challenging. Using a mobility-driven trans... Read More about Evolution and epidemic spread of SARS-CoV-2 in Brazil.

Genomic and epidemiological monitoring of yellow fever virus transmission potential (2018)
Journal Article
Faria, N. R., Kraemer, M. U. G., Hill, S. C., Goes de Jesus, J., Aguiar, R. S., Iani, F. C. M., …Pybus, O. G. (2018). Genomic and epidemiological monitoring of yellow fever virus transmission potential. Science, 361(6405), 894-899. https://doi.org/10.1126/science.aat7115

The yellow fever virus (YFV) epidemic in Brazil is the largest in decades. The recent discovery of YFV in Brazilian Aedes species mosquitos highlights a need to monitor the risk of reestablishment of urban YFV transmission in the Americas. We use a s... Read More about Genomic and epidemiological monitoring of yellow fever virus transmission potential.

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