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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, …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., …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.

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., …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., …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., …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.

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.