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All Outputs (51)

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

Phylogenetic analysis of migration, differentiation, and class switching in B cells (2022)
Journal Article
Hoehn, K., Pybus, O., & Kleinstein, S. (2022). Phylogenetic analysis of migration, differentiation, and class switching in B cells. PLoS Computational Biology, 18(4), https://doi.org/10.1371/journal.pcbi.1009885

B cells undergo rapid mutation and selection for antibody binding affinity when producing antibodies capable of neutralizing pathogens. This evolutionary process can be intermixed with migration between tissues, differentiation between cellular subse... Read More about Phylogenetic analysis of migration, differentiation, and class switching in B cells.

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

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.

Assessing the impact of COVID-19 border restrictions on dengue transmission in Yunnan Province, China: an observational epidemiological and phylogenetic analysis (2021)
Journal Article
Li, N., Feng, Y., Vrancken, B., Chen, Y., Dong, L., Yang, Q., Kraemer, M., Pybus, O., Zhang, H., Brady, O., & Tian, H. (2021). Assessing the impact of COVID-19 border restrictions on dengue transmission in Yunnan Province, China: an observational epidemiological and phylogenetic analysis. The Lancet Regional Health, 14, https://doi.org/10.1016/j.lanwpc.2021.100259

Background: In response to the COVID-19 pandemic, China implemented strict restrictions on cross-border travel to prevent disease importation. Yunnan, a Chinese province that borders dengue-endemic countries in Southeast Asia, experienced unprecedent... Read More about Assessing the impact of COVID-19 border restrictions on dengue transmission in Yunnan Province, China: an observational epidemiological and phylogenetic analysis.

Generation and transmission of interlineage recombinants in the SARS-CoV-2 pandemic (2021)
Journal Article
COVID-19 Genomics UK COG-UK Consor, Jackson, B., Boni, M., Bull, M., Colleran, A., Colquhoun, R., Darby, A., Haldenby, S., Hill, V., Lucaci, A., McCrone, J., Nicholls, S., O'Toole, A., Pacchiarini, N., Poplawski, R., Scher, E., Todd, F., Webster, H., Whitehead, M., Wierzbicki, C., …Rambaut, A. (2021). Generation and transmission of interlineage recombinants in the SARS-CoV-2 pandemic. Cell, 184(20), 5179-+. https://doi.org/10.1016/j.cell.2021.08.014

We present evidence for multiple independent origins of recombinant SARS-CoV-2 viruses sampled from late 2020 and early 2021 in the United Kingdom. Their genomes carry single-nucleotide polymorphisms and deletions that are characteristic of the B.1.1... Read More about Generation and transmission of interlineage recombinants in the SARS-CoV-2 pandemic.

Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity (2021)
Journal Article
COG-UK Consortium, Volz, E., Hill, V., McCrone, J., Price, A., Jorgensen, D., O'Toole, A., Southgate, J., Johnson, R., Jackson, B., Nascimento, F., Rey, S., Nicholls, S., Colquhoun, R., Filipe, A., Shepherd, J., Pascall, D., Shah, R., Jesudason, N., Li, K., …Connor, T. (2021). Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity. Cell, 184(1), 64-+. https://doi.org/10.1016/j.cell.2020.11.020

Global dispersal and increasing frequency of the SARS-CoV-2 spike protein variant D614G are suggestive of a selective advantage but may also be due to a random founder effect. We investigate the hypothesis for positive selection of spike D614G in the... Read More about Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity.

Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK (2021)
Journal Article
COVID-19 Gcnomics UK COG-UK Consor, du Plessis, L., McCrone, J., Zarebski, A., Hill, V., Ruis, C., Gutierrez, B., Raghwani, J., Ashworth, J., Colquhoun, R., Connor, T., Faria, N., Jackson, B., Loman, N., O'Toole, A., Nicholls, S., Parag, K., Scher, E., Vasylyeva, T., Volz, E., …Pybus, O. (2021). Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK. Science, 371(6530), 708-+. https://doi.org/10.1126/science.abf2946

The United Kingdom's COVID-19 epidemic during early 2020 was one of world's largest and was unusually well represented by virus genomic sampling. We determined the fine-scale genetic lineage structure of this epidemic through analysis of 50,887 sever... Read More about Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK.

Molecular detection and genomic characterization of diverse hepaciviruses in African rodents (2021)
Journal Article
Bletsa, M., Vrancken, B., Gryseels, S., Boonen, I., Fikatas, A., Li, Y., Laudisoit, A., Lequime, S., Bryja, J., Makundi, R., Meheretu, Y., Akaibe, B., Mbalitini, S., Van de Perre, F., Van Houtte, N., Tesikova, J., Wollants, E., Van Ranst, M., Pybus, O., Drexler, J., …Lemey, P. (2021). Molecular detection and genomic characterization of diverse hepaciviruses in African rodents. Virus Evolution, 7(1), https://doi.org/10.1093/ve/veab036

Hepatitis C virus (HCV; genus Hepacivirus) represents a major public health problem, infecting about three per cent of the human population. Because no animal reservoir carrying closely related hepaciviruses has been identified, the zoonotic origins... Read More about Molecular detection and genomic characterization of diverse hepaciviruses in African rodents.

Spatiotemporal invasion dynamics of SARS-CoV-2 lineage B.1.1.7 emergence (2021)
Journal Article
COVID-19 Genomics UK COG-UK Consor, Kraemer, M., Hill, V., Ruis, C., Dellicour, S., Bajaj, S., McCrone, J., Baele, G., Parag, K., Battle, A., Gutierrez, B., Jackson, B., Colquhoun, R., O'Toole, A., Klein, B., Vespignani, A., Volz, E., Faria, N., Aanensen, D., Loman, N., …Pybus, O. (2021). Spatiotemporal invasion dynamics of SARS-CoV-2 lineage B.1.1.7 emergence. Science, 373(6557), 889-+. https://doi.org/10.1126/science.abj0113

Understanding the causes and consequences of the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern is crucial to pandemic control yet difficult to achieve because they arise in the context of variable human... Read More about Spatiotemporal invasion dynamics of SARS-CoV-2 lineage B.1.1.7 emergence.

Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil (2021)
Journal Article
Faria, N., Mellan, T., Whittaker, C., Claro, I., Candido, D., Mishra, S., Crispim, M., Sales, F., Hawryluk, I., McCrone, J., Hulswit, R., Franco, L., Ramundo, M., de Jesus, J., Andrade, P., Coletti, T., Ferreira, G., Silva, C., Manuli, E., Pereira, R., …Sabino, E. (2021). Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil. Science, 372(6544), 815-+. https://doi.org/10.1126/science.abh2644

Cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in Manaus, Brazil, resurged in late 2020 despite previously high levels of infection. Genome sequencing of viruses sampled in Manaus between November 2020 and January 202... Read More about Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil.

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., Bowden, T. A., & 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., Pigott, D. M., Gutierrez, B., Zarebski, A. E., Shrestha, M., Brownstein, J. S., Castro, M. C., Dye, C., Tian, H., Pybus, O. G., & 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.