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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.

Parallel evolution in the emergence of highly pathogenic avian influenza A viruses (2020)
Journal Article
Escalera-Zamudio, M., Golden, M., Gutiérrez, B., Thézé, J., Keown, J. R., Carrique, L., …Pybus, O. G. (2020). Parallel evolution in the emergence of highly pathogenic avian influenza A viruses. Nature Communications, 11(1), 5511. https://doi.org/10.1038/s41467-020-19364-x

Abstract: Parallel molecular evolution and adaptation are important phenomena commonly observed in viruses. Here, we exploit parallel molecular evolution to understand virulence evolution in avian influenza viruses (AIV). Highly-pathogenic AIVs evolv... Read More about Parallel evolution in the emergence of highly pathogenic avian influenza A viruses.

Crowding and the shape of COVID-19 epidemics (2020)
Journal Article
Rader, B., Scarpino, S. V., Nande, A., Hill, A. L., Adlam, B., Reiner, R. C., …Kraemer, M. U. G. (2020). Crowding and the shape of COVID-19 epidemics. Nature Medicine,

The coronavirus disease 2019 (COVID-19) pandemic is straining public health systems worldwide, and major non-pharmaceutical interventions have been implemented to slow its spread1,2,3,4. During the initial phase of the outbreak, dissemination of seve... Read More about Crowding and the shape of COVID-19 epidemics.

Identification of Common Deletions in the Spike Protein of Severe Acute Respiratory Syndrome Coronavirus 2 (2020)
Journal Article
Liu, Z., Zheng, H., Lin, H., Li, M., Yuan, R., Peng, J., …Pfeiffer, J. K. (2020). Identification of Common Deletions in the Spike Protein of Severe Acute Respiratory Syndrome Coronavirus 2. Journal of Virology, 94(17),

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a novel coronavirus first identified in December 2019. Notable features that make SARS-CoV-2 distinct from most other previously identified betacoronaviruses include a receptor binding d... Read More about Identification of Common Deletions in the Spike Protein of Severe Acute Respiratory Syndrome Coronavirus 2.

Epidemiological and clinical characteristics of the COVID-19 epidemic in Brazil (2020)
Journal Article
de Souza, W. M., Buss, L. F., Candido, D. A., Carrera, J. P., Li, S., Zarebski, A. E., …Faria, N. R. (2020). Epidemiological and clinical characteristics of the COVID-19 epidemic in Brazil. Nature Human Behaviour, 4(8), 856-865

The first case of COVID-19 was detected in Brazil on 25 February 2020. We report and contextualize epidemiological, demographic and clinical findings for COVID-19 cases during the first 3 months of the epidemic. By 31 May 2020, 514,200 COVID-19 cases... Read More about Epidemiological and clinical characteristics of the COVID-19 epidemic in Brazil.

Assessing the role of live poultry trade in community-structured transmission of avian influenza in China (2020)
Journal Article
Yang, Q., Zhao, X., Lemey, P., Suchard, M. A., Bi, Y., Shi, W., …Tian, H. (2020). Assessing the role of live poultry trade in community-structured transmission of avian influenza in China. Proceedings of the National Academy of Sciences, 117(11), 5949-5954. https://doi.org/10.1073/pnas.1906954117

The live poultry trade is thought to play an important role in the spread and maintenance of highly pathogenic avian influenza A viruses (HP AIVs) in Asia. Despite an abundance of small-scale observational studies, the role of the poultry trade in di... Read More about Assessing the role of live poultry trade in community-structured transmission of avian influenza in China.

Molecular evolution, diversity and adaptation of H7N9 viruses in China during 2013-2017 (2018)
Journal Article
Lu, J., Raghwani, J., Pryce, R., Bowden, T. A., Thézé, J., Huang, S., …Ke, C. (2018). Molecular evolution, diversity and adaptation of H7N9 viruses in China during 2013-2017. https://doi.org/10.3201/eid2410.171063

The substantial increase in prevalence and emergence of antigenically divergent or highly pathogenic influenza A(H7N9) viruses during 2016–17 raises concerns about the epizootic potential of these viruses. We investigated the evolution and adaptation... Read More about Molecular evolution, diversity and adaptation of H7N9 viruses in China during 2013-2017.

Establishment and cryptic transmission of Zika virus in Brazil and the Americas (2017)
Journal Article
Faria, N. R., Quick, J., Claro, I., Thézé, J., de Jesus, J. G., Giovanetti, M., …Pybus, O. G. (2017). Establishment and cryptic transmission of Zika virus in Brazil and the Americas. Nature, 546(7658), 406-410. https://doi.org/10.1038/nature22401

Transmission of Zika virus (ZIKV) in the Americas was first confirmed in May 2015 in northeast Brazil1. Brazil has had the highest number of reported ZIKV cases worldwide (more than 200,000 by 24 December 20162) and the most cases associated with mic... Read More about Establishment and cryptic transmission of Zika virus in Brazil and the Americas.

Antibody responses to avian influenza viruses in wild birds broaden with age (2016)
Journal Article
Hill, S. C., Manvell, R. J., Schulenburg, B., Shell, W., Wikramaratna, P. S., Perrins, C., …Pybus, O. G. (2016). Antibody responses to avian influenza viruses in wild birds broaden with age. https://doi.org/10.1098/rspb.2016.2159

For viruses such as avian influenza, immunity within a host population can drive the emergence of new strains by selecting for viruses with novel antigens that avoid immune recognition. The accumulation of acquired immunity with age is hypothesized t... Read More about Antibody responses to avian influenza viruses in wild birds broaden with age.

Role for migratory wild birds in the global spread of avian influenza (2016)
Journal Article
The Global Consortium For H5N8 And Related Influenza Viruses, . (2016). Role for migratory wild birds in the global spread of avian influenza. Science, 354(6309), 213-217. https://doi.org/10.1126/science.aaf8852

Avian influenza viruses affect both poultry production and public health. A subtype H5N8 (clade 2.3.4.4) virus, following an outbreak in poultry in South Korea in January 2014, rapidly spread worldwide in 2014–2015. Our analysis of H5N8 viral sequenc... Read More about Role for migratory wild birds in the global spread of avian influenza.

Wild waterfowl migration and domestic duck density shape the epidemiology of highly pathogenic H5N8 influenza in the Republic of Korea (2015)
Journal Article
Hill, S. C., Lee, Y., Song, B., Kang, H., Lee, E., Hanna, A., …Pybus, O. G. (2015). Wild waterfowl migration and domestic duck density shape the epidemiology of highly pathogenic H5N8 influenza in the Republic of Korea. https://doi.org/10.1016/j.meegid.2015.06.014

Highly pathogenic avian influenza (HPAI) viruses threaten human and animal health yet their emergence is poorly understood, partly because sampling of the HPAI Asian-origin H5N1 lineage immediately after its identification in 1996 was comparatively s... Read More about Wild waterfowl migration and domestic duck density shape the epidemiology of highly pathogenic H5N8 influenza in the Republic of Korea.

Comparative micro-epidemiology of pathogenic avian influenza virus outbreaks in a wild bird population
Journal Article
Hill, S. C., Hansen, R., Watson, S., Coward, V., Russell, C., Cooper, J., …Pybus, O. G. (in press). Comparative micro-epidemiology of pathogenic avian influenza virus outbreaks in a wild bird population. Philosophical Transactions of the Royal Society B: Biological Sciences, 374(1775), https://doi.org/10.1098/rstb.2018.0259

Understanding the epidemiological dynamics of highly pathogenic avian influenza virus (HPAIV) in wild birds is crucial for guiding effective surveillance and control measures. The spread of H5 HPAIV has been well characterized over large geographical... Read More about Comparative micro-epidemiology of pathogenic avian influenza virus outbreaks in a wild bird population.