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da Silva Filipe A, Shepherd JG, Williams T, et al. Genomic epidemiology reveals multiple introductions of SARS-CoV-2 from mainland Europe into Scotland. Nat Microbiol 6, 112–122 (2021). Full-text: https://doi.org/10.1038/s41564-020-00838-z
During the first month of the SARS-CoV-2 outbreak in Scotland, 2641 cases of COVID-19 led to 1832 hospital admissions, 207 intensive care admissions and 126 deaths. Here, Emma Thomson, Ana da Silva Filipe and colleagues sequenced 1314 SARS-CoV-2 viral genomes and show that SARS-CoV-2 was introduced to Scotland on at least 283 occasions during February and March 2020. Early introductions of SARS-CoV-2 originated from mainland Europe (the majority from Italy and Spain). The authors identified subsequent early outbreaks in the community, within healthcare facilities and at an international conference. The authors conclude that the risk of multiple reintroduction events in future waves of infection remains high in the absence of population immunity.
Li T, Liu D, Yang Y, et al. Phylogenetic supertree reveals detailed evolution of SARS-CoV-2. Sci Rep 10, 22366 (2020), published 22 December. Full-text: https://doi.org/10.1038/s415
The origin of SARS-CoV-2 and its evolutionary relationship is still being discussed. Here, Jie Feng, Tingting Li and colleagues applied the matrix representation with parsimony (MRP) pseudo-sequence supertree analysis to study the origin and evolution of SARS-CoV-2.
Malone B, Simovski B, Moliné C, et al. Artificial intelligence predicts the immunogenic landscape of SARS-CoV-2 leading to universal blueprints for vaccine designs. Sci Rep 10, 22375 (2020). Full-text: https://doi.org/10.1038/s41598-020-78758-5
In order to effectively combat the SARS-CoV-2 pandemic, a vaccine will need to protect the vast majority of the human population and stimulate diverse T cell responses against multiple viral targets including, but not limited to, the S protein. Here, Travor Clancy, Brandon Malone and colleagues profiled the entire SARS-CoV-2 proteome across the most frequent 100 HLA-A, HLA-B and HLA-DR alleles in the human population and generated comprehensive epitope maps. They identified a subset of epitope hotspots that could be harnessed in a vaccine formulation to provide broad coverage across the global population.
Larsen MD, de Graaf EL, Sonneveld ME, et al. Afucosylated IgG characterizes enveloped viral responses and correlates with COVID-19 severity. Science 2020, published 23 December. Full-text: https://doi.org/10.1126/science.abc8378
Afucosylated IgG (~6% of total IgG in humans) are specifically formed against enveloped viruses but generally not against other antigens. Here, Gestur Vidarsson, Mads Delbo Larsen and colleagues report that critically ill COVID-19 patients, but not those with mild symptoms, had high levels of afucosylated IgG antibodies against SARS-CoV-2, amplifying pro-inflammatory cytokine release and acute phase responses.
Schmidt N, Lareau CA, Keshishian H, et al. The SARS-CoV-2 RNA–protein interactome in infected human cells. Nat Microbiol (2020). Full-text: https://doi.org/10.1038/s41564-020-00846-z
Mathias Munschauer, Nora Schmidt and colleagues provide detailed molecular insights into the identity of host factors and cellular machinery that directly and specifically bind SARS-CoV-2 RNAs during infection of human cells. They integrated CRISPR perturbation data and performed genetic and pharmacological validation experiments that together suggest functional roles for 18 RNA interactome proteins in SARS-CoV-2 infections.
Pollard AJ, Bijker EM. A guide to vaccinology: from basic principles to new developments. Nat Rev Immunol (2020). Full-text: https://doi.org/10.1038/s41577-020-00479-7
2021 may be the perfect time for immunologists to be involved in designing the next generation of powerful immunogens. In this review, Andrew Pollard and Else Bijker provide an overview of vaccines, immunization and related issues.
Rosado J, Pelleau S, Cockram C, et al. Multiplex assays for the identification of serological signatures of SARS-CoV-2 infection: an antibody-based diagnostic and machine learning study. Lancet Microbe 2020, published 21 December. Full-text: https://doi.org/10.1016/S2666-5247(20)30197-X
Would you like to classify individuals who were infected more than 6 months ago and measure perform serological surveys in very low transmission settings? Then measure IgG and IgM antibody responses to 1) seven SARS-CoV-2 spike or nucleoprotein antigens, 2) two antigens for the nucleoproteins of the 229E and NL63 seasonal coronaviruses, and 3) three non-coronavirus antigens up to 39 days after symptom onset from 215 adults – and start your machine learning algorithms. A paper by Michael White, Jason Rosado and colleagues from the Pasteur Institute in Paris.
ACTIV-3/TICO LY-CoV555 Study Group. A Neutralizing Monoclonal Antibody for Hospitalized Patients with Covid-19. N Engl J Med 2020, publshed 22 December. Full-text: https://doi.org/10.1056/NEJMoa2033130
The Lilly monoclonal antibody LY-CoV555, when co-administered with remdesivir, did not demonstrate efficacy among hospitalized patients who had COVID-19 without end organ failure. This is the result of a randomized study involving 314 hospitalized patients by Jens D. Lundgren and colleagues of the ACTIV-3/TICO LY-CoV555 Study Group.
Henderson LA, Yeung RSM. MIS-C: early lessons from immune profiling. Nat Rev Rheumatol (2020). Full-text: https://doi.org/10.1038/s41584-020-00566-y
A brief summary of what we have learned in 9 months about the multisystem inflammatory syndrome in children (MIS-C), a rare complication of SARS-CoV-2 infection.
Steindl D, Boehmerle W, Körner R, et al. Novichok nerve agent poisoning. Lancet 2020, published 22 December. Full-text: https://doi.org/10.1016/S0140-6736(20)32644-1
Kai-Uwe Eckardt, David Steindl and colleagues report the clinical details of 44-year-old Alexei Navalny’s poisoning. Two weeks after the poisoning, a laboratory of the German armed forces identified an organophosphorus nerve agent from the novichok group in blood samples collected immediately after Navalny’s admission to Charité clinic in Berlin.
Editors. A review of 2020 through Nature’s editorials. Nature 2020, published 22 December. Full-text: https://www.nature.com/articles/d41586-020-03560-2
Nature’s first editorial of 2020 marked the beginning of what was expected to be a super-year for the environment and sustainable development. Then, on 21 January, Nature’s first editorial on the coronavirus appeared.
A virus is born: scanning electron micrograph of a dying cell (green) heavily infected with SARS-CoV-2 virus particles (orange), isolated from a patient sample.Credit: NIAID (CC BY 4.0).
Copy-editor: Rob Camp