Copy-editor: Rob Camp
Virology
Chen Y, Li S, Wu W, Geng S, Mao M. Distinct mutations and lineages of SARS-CoV-2 virus in the early phase of COVID-19 pandemic and subsequent global expansion. bioRxiv 2021, published 8 January. Full-text: https://doi.org/10.1101/2021.01.05.425339
Mao Mao, Yan Chen and colleagues analyzed 4013 full-length SARS-CoV-2 genomes from different continents over a 14-week timespan since the outbreak in Wuhan. 2954 unique nucleotide substitutions were identified with 31 of the 4013 genomes remaining as ancestral type, and 952 (32,2%) mutations recurring in more than one genome. The authors used the same approach to analyze 261.350 full-length SARS-CoV-2 genomes available in the GISAID database as of 25 December 2020. They suggest that viral genotypes can be utilized as molecular barcodes in combination with epidemiologic data to monitor the spreading routes of the pandemic and evaluate the effectiveness of control measures.
Zahradnik J, Marciano S, Shemesh M, et al. SARS-CoV-2 RBD in vitro evolution follows contagious mutation spread, yet generates an able infection inhibitor. bioRxiv 2021, posted 8 January. Full-text: https://www.biorxiv.org/content/10.1101/2021.01.06.425392v2
SARS-CoV-2 is constantly evolving, with more contagious mutations spreading rapidly, in particular in England and South Africa. Here, Gideon Schreiber, Jiří Zahradník and colleagues show that the naturally selected mutations S477N, E484K, and N501Y of the Spike protein RBD, which show higher infectivity, were also selected by yeast surface display affinity maturation already in the first round, giving rise to the South African, E484K, N501Y, and British variants that bind ACE2 13 and 3,5-fold tighter than RBD-WT.
Prevention
Meidan D, Schulmann N, Cohen R, et al. Alternating quarantine for sustainable epidemic mitigation. Nat Commun 12, 220 (2021). Full-text: https://doi.org/10.1038/s41467-020-20324-8
To ease the potentially devastating socioeconomic consequences of pharmaceutical interventions, social distancing, lock-downs and mobility restrictions, Baruch Barzel, Dror Meidan and colleagues, propose an alternative alternaitng quarantine strategy: at any moment, half of the population remains under lockdown while the other half continues to be active – maintaining a routine of weekly alternation of activity and quarantine. This regime would minimize infectious interactions, as it allows only half of the population to interact for just half of the time. Dramatic reduction in transmission despite sustaining socioeconomic continuity at ~50% capacity?
Pathogenesis
Grant RA, Morales-Nebreda L, Markov NS, et al. Circuits between infected macrophages and T cells in SARS-CoV-2 pneumonia. Nature 2021, published 11 January. Full-text: https://doi.org/10.1038/s41586-020-03148-w
SARS-CoV-2 might cause a slowly unfolding, spatially limited alveolitis in which alveolar macrophages harboring SARS-CoV-2 and T cells form a positive feedback loop that drives persistent alveolar inflammation. This is the result of a study that collected bronchoalveolar lavage fluid samples from 88 patients with SARS-CoV-2-induced respiratory failure and 211 patients with known or suspected pneumonia from other pathogens and subjected them to flow cytometry and bulk transcriptomic profiling.
Vaccine
Bordon, Y. Immune readouts from the Oxford COVID-19 vaccine. Nat Rev Immunol 2021, published 11 January. Full-text: https://doi.org/10.1038/s41577-021-00503-4
Yvonne Bordon comments on two recent reports from the Oxford COVID-19 vaccine team which detail the immune outcomes observed in a Phase I/II trial of their ChAdOx1 nCoV-19 vaccine. In one of the papers we presented on 21 December, the authors give a detailed description of the immune response after administration of one dose of ChAdOx1 nCoV-19 in 88 adults (ages 18-55 years) (Ewer 2020). They define the isotypes, subclasses and antibody avidity induced after vaccination. They also performed multiplex cytokine profiling and intracellular cytokine staining analysis, demonstrating that ChAdOx1 nCoV-19 vaccination induces a predominantly Th1-type response (that appears to be good). See also Barrett JR, Belij-Rammerstorfer S, Dold C, et al. Phase 1/2 trial of SARS-CoV-2 vaccine ChAdOx1 nCoV-19 with a booster dose induces multifunctional antibody responses. Nat Med. 2020 Dec 17. PubMed: https://pubmed.gov/33335322. Full-text: https://doi.org/10.1038/s41591-020-01179-4
Clinical
McGonagle D, Bridgewood C, Ramanan AV, Meaney JFM, Watad A. COVID-19 vasculitis and novel vasculitis mimics. Lancet Rheumatology 2021, published 7 January. Full-text: https://doi.org/10.1016/S2665-9913(20)30420-3
In this Viewpoint article, Dennis McGonagle et al. highlight how imaging and post-mortem findings point to a novel vasculitis mimic related to COVID-19 that might lead to cryptogenic strokes across multivessel territories, acute kidney injury with hematuria, a skin vasculitis mimic, intestinal ischemia, and other organ ischemic manifestations.
Solomon T. Neurological infection with SARS-CoV-2 — the story so far. Nat Rev Neurol 2021, published 7 January. Full-text: https://doi.org/10.1038/s41582-020-00453-w
As the COVID-19 pandemic developed and neurological manifestations were reported, concern grew that SARS-CoV-2 might directly invade neuronal cells. However, research throughout the year to address this concern has revealed a different story with inflammatory processes at its center.
Treatment
Garber, K. Hunt for improved monoclonals against coronavirus gathers pace. Nat Biotechnol 39, 9–12 (2021). Full-text: https://doi.org/10.1038/s41587-020-00791-6
Bamlanivimab (Lilly) and the double-antibody cocktail casirivimab + imdevimab (Regeneron) have been recently given an Emergency Use Authorization (EUA) for use in high-risk COVID-19 patients with mild or moderate disease. Though both drugs represent new options for treating the coronavirus infection, neither is ideal. The future of monoclonals remains uncertain.
Cohen JB, Hanff TC, William P, et al. Continuation versus discontinuation of renin–angiotensin system inhibitors in patients admitted to hospital with COVID-19: a prospective, randomised, open-label trial. Lancet Respir Health 2021, published 7 January. Full-text: https://doi.org/10.1016/S2213-2600(20)30558-0
Consistent with international society recommendations, angiotensin-converting enzyme inhibitors (ACEIs) and angiotensin receptor blockers (ARBs), inhibitors of the renin–angiotensin system, can be safely continued in patients admitted to hospital with COVID-19. A confirmation from a small study that enrolled 152 participants randomly assigned them to either continue or discontinue renin–angiotensin system inhibitor therapy. There were 16 (21%) of 75 participants in the continuation arm versus 14 (18%) of 77 in the discontinuation arm who required intensive care unit admission or invasive mechanical ventilation, and 11 (15%) of 75 participants in the continuation group versus ten (13%) of 77 in the discontinuation group who died.
Severe COVID
Co-morbidities
Accili D. Can COVID-19 cause diabetes? Nat Metab 2021 published 11 January. Full-text: https://doi.org/10.1038/s42255-020-00339-7
Whether a separate entity of post-COVID-19 diabetes possibly associated with lasting β-cell damage also exists is not yet clear.
Spanish
If you read Spanish, read Jericó P. Reducir la fatiga pandémica. El País 2021, published 10 January. Full-text: https://elpais.com/elpais/2021/01/08/eps/1610126355_684003.html
Casi un año enfrentándonos al coronavirus pasa factura. El cansancio puede hacer que relajemos las medidas preventivas. Pero también hay remedio para ello.
French
If you read French, read Gatinois C, Aeberhardt C. Comment le français Sanofi s’est retrouvé distancé dans la course au vaccin. Le Monde 2021, published 11 January. Full-text : https://www.lemonde.fr/economie/article/2021/01/11/covid-19-le-destin-contrarie-du-vaccin-de-sanofi_6065825_3234.html
Après des débuts prometteurs, une erreur de laboratoire a fait perdre cinq à six mois au groupe. Nouveau rebondissement, vendredi 8 janvier : sous la pression de Bercy, le groupe français pourrait mettre son outil industriel à disposition de ses concurrents les plus avancés, et dont les capacités de production sont limitées.