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All Outputs (10)

Global disparities in SARS-CoV-2 genomic surveillance (2022)
Journal Article
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, Brito, A., Semenova, E., Dudas, G., Hassler, G., Kalinich, C., Kraemer, M., Ho, J., Tegally, H., Githinji, G., Agoti, C., Matkin, L., Whittaker, C., …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.

Endogenous Viral Elements in Shrew Genomes Provide Insights into Pestivirus Ancient History (2022)
Journal Article
Li, Y., Bletsa, M., Zisi, Z., Boonen, I., Gryseels, S., Kafetzopoulou, L., Webster, J., Catalano, S., Pybus, O., Van de Perre, F., Li, H., Li, Y., Li, Y., Abramov, A., Lymberakis, P., Lemey, P., & Lequime, S. (2022). Endogenous Viral Elements in Shrew Genomes Provide Insights into Pestivirus Ancient History. Molecular Biology and Evolution, 39(10), https://doi.org/10.1093/molbev/msac190

As viral genomic imprints in host genomes, endogenous viral elements (EVEs) shed light on the deep evolutionary history of viruses, ancestral host ranges, and ancient viral-host interactions. In addition, they may provide crucial information for cali... Read More about Endogenous Viral Elements in Shrew Genomes Provide Insights into Pestivirus Ancient History.

Evolutionary features of a prolific subtype of avian influenza A virus in European waterfowl (2022)
Journal Article
Wille, M., Tolf, C., Latorre-Margalef, N., Fouchier, R., Halpin, R., Wentworth, D., Ragwani, J., Pybus, O., Olsen, B., & Waldenstrom, J. (2022). Evolutionary features of a prolific subtype of avian influenza A virus in European waterfowl. Virus Evolution, 8(2), https://doi.org/10.1093/ve/veac074

Avian influenza A virus (AIV) is ubiquitous in waterfowl and is detected annually at high prevalence in waterfowl during the Northern Hemisphere autumn. Some AIV subtypes are globally common in waterfowl, such as H3N8, H4N6, and H6N2, and are detecte... Read More about Evolutionary features of a prolific subtype of avian influenza A virus in European waterfowl.

The origins and molecular evolution of SARS-CoV-2 lineage B.1.1.7 in the UK (2022)
Journal Article
Hill, V., Du Plessis, L., Peacock, T., Aggarwal, D., Colquhoun, R., Carabelli, A., Ellaby, N., Gallagher, E., Groves, N., Jackson, B., McCrone, J., O'Toole, A., Price, A., Sanderson, T., Scher, E., Southgate, J., Volz, E., Barclay, W., Barrett, J., Chand, M., …Rambaut, A. (2022). The origins and molecular evolution of SARS-CoV-2 lineage B.1.1.7 in the UK. Virus Evolution, 8(2), https://doi.org/10.1093/ve/veac080

The first SARS-CoV-2 variant of concern (VOC) to be designated was lineage B.1.1.7, later labelled by the World Health Organization as Alpha. Originating in early autumn but discovered in December 2020, it spread rapidly and caused large waves of inf... Read More about The origins and molecular evolution of SARS-CoV-2 lineage B.1.1.7 in the UK.

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

The relationship between rising temperatures and malaria incidence in Hainan, China, from 1984 to 2010: a longitudinal cohort study (2022)
Journal Article
Wang, Z., Liu, Y., Li, Y., Wang, G., Lourenco, J., Kraemer, M., He, Q., Cazeiles, B., Li, Y., Wang, R., Gao, D., Li, Y., Song, W., Sun, D., Dong, L., Pybus, O., Stenseth, N., & Tian, H. (2022). The relationship between rising temperatures and malaria incidence in Hainan, China, from 1984 to 2010: a longitudinal cohort study. The Lancet Planetary Health, 6(4), E350-E358. https://doi.org/10.1016/S2542-5196%2822%2900039-0