The UK's COVID-19 epidemic during early 2020 was one of world's largest and unusually well represented by virus genomic sampling. Here we reveal the fine-scale genetic lineage structure of this epidemic through analysis of 50,887 SARS-CoV-2 genomes,...
Spatiotemporal sampling gaps in existing pathogen genomic data limits their use in understanding epidemiological patterns. Here, the authors apply a phylogeographic approach with SARS-CoV-2 genomes to accurately reproduce pathogen spread by...
The Wellcome Trust 4-yearPhD programme in Hosts, Pathogens and Global Health was established at the University of Edinburgh in 2016. It provides broad, interdisciplinary training in all aspects of infectious disease research, from immunology to...
Andrew Rambaut 🦠🧬🌲🔮🤦♂️I am going to go out on a limb here but I assert that by far the best breading for a bacon roll is a fresh Scottish morning-roll. en.wikipedia.org/wiki/Morning_r… but note the picture is wrong.
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Genomic epidemiology has become an increasingly common tool for epidemic response. Recent technological advances have made it possible to sequence genomes rapidly enough to inform outbreak response, and cheaply enough to justify dense sampling of...
Genetic recombination processes, such as reassortment, make it complex or impossible to use standard phylogenetic and phylodynamic methods. This is due to the fact that the shared evolutionary history of individuals has to be represented by a...
The Chinese horseshoe bat (Rhinolophus sinicus), reservoir host of severe acute respiratory syndrome coronavirus (SARS-CoV), carries many bat SARS-related CoVs (SARSr-CoVs) with high genetic diversity, particularly in the spike gene. Despite these...
Accurate understanding of the global spread of emerging viruses is critically important for public health responses and for anticipating and preventing future outbreaks. Here, we elucidate when, where and how the earliest sustained SARS-CoV-2...
The origins and global spread of two recent, yet quite different, pandemic diseases is discussed and reviewed in depth: Candida auris, a eukaryotic fungal disease, and COVID-19 (SARS-CoV-2), a positive strand RNA viral respiratory disease. Both...
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Andrew Rambaut 🦠🧬🌲🔮🤦♂️Tweet from January quoted in a paper claiming SARS-CoV-2 came from space on an asteroid. ncbi.nlm.nih.gov/pmc/articles/P… Not sure space was the hypothesis I had in mind - all I was saying is it was clearly transmitting from human to human rather than repeated spillover.
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Amplicon sequencing protocol for SARS-CoV-2 v3 (LoCost)We thank the ARTIC network, Oxford Nanopore Technologies, New England Biolabs, BCCDC, COG-UK, CanCOGen and protocols.io commenters...
The rapid spread of the virus causing COVID-19, SARS-CoV-2, raises questions about the possibility of a universally effective vaccine. The virus can mutate in a given individual, and these variants can be propagated across populations and time. To...
Vaccines rarely provide full protection from disease. Nevertheless, partially effective (imperfect) vaccines may be used to protect both individuals and whole populations. We studied the potential impact of different types of imperfect vaccines on...
A study using Marek's disease virus in poultry shows that by reducing natural selection against highly virulent strains, imperfect vaccination enables the spread of viral strains that would otherwise be too lethal to persist.
Influenza viruses (family Orthomyxoviridae) infect a variety of vertebrates, including birds, humans, and other mammals. Recent metatranscriptomic studies have uncovered divergent influenza viruses in amphibians, fish and jawless vertebrates,...
On June 5th, 2020, we posted the first viral genome from the 2020 Equateur Province outbreak. Phylogenetic analysis indicated the cluster of cases was caused by a new spillover event and represented the 11th Ebola virus disease (EVD) outbreak in the...
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Andrew Rambaut 🦠🧬🌲🔮🤦♂️This is unexpected: “Two Ebola virus variants circulating during the 2020 Equateur Province outbreak”
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