Copy-editor: Rob Camp
7 March
Variants
Paper of the Day
De Souza WM, Amorm MR, Sesti-Costa R, et al. Levels of SARS-CoV-2 Lineage P.1 Neutralization by Antibodies Elicited after Natural Infection and Vaccination. Lancet Preprints 2021, posted 1 March. Full-text: https://papers.ssrn.com/sol3/papers.cfm?abstract_id=3793486
William de Souza and colleagues isolated two P.1-containing specimens from nasopharyngeal and bronchoalveolar lavage samples of patients in Manaus, Brazil. They found that the immune plasma of COVID-19 convalescent blood donors had 6-fold less neutralizing capacity against the P.1 than against the B lineage. Moreover, five months after booster immunization with the Chinese CoronaVac vaccine, plasma from vaccinated individuals failed to efficiently neutralize P.1 lineage isolates.
Faria NR, Mellan TA, Whittaker C, et al. Genomics and epidemiology of a novel SARS-CoV-2 lineage in Manaus, Brazil. MedRxiv 2021, posted 3 March. Full-text: https://doi.org/10.1101/2021.02.26.21252554
Using a combination of genomic and epidemiological data, Nuno Faria and colleagues characterize the emergence and characteristics of P.1 that acquired 17 mutations, including the trio in the spike protein (K417T, E484K and N501Y) associated with increased binding to the human ACE2 receptor. The authors show that P.1 emerged around early November 2020. They estimate that P.1 could be 1.4–2.2 times more transmissible and able to evade 25-61% of protective immunity elicited by previous infection with non-P.1 lineages.
Wang P, Wang M, Yu J, et al. Increased Resistance of SARS-CoV-2 Variant P.1 to Antibody Neutralization. bioRxiv 2021, posted 2 March. Full-text: https://doi.org/10.1101/2021.03.01.433466
David D. Ho, Pengfei Wang and colleagues report that P.1 is not only refractory to multiple neutralizing monoclonal antibodies, but also more resistant to neutralization by convalescent plasma (6.5-fold) and vaccinee sera (2.2-2.8-fold).
Cele S, Gazy I, Jackson L, et al. Escape of SARS-CoV-2 501Y.V2 from neutralization by convalescent plasma. MedRxiv 2021, posted 27 February. Full-text: https://doi.org/10.1101/2021.01.26.21250224
We already knew that people previously infected with the non-B.1.351 variant don’t neutralize B.1.351 very effectively. Now Alex Sigal, Tulio de Oliveira, Sandile Cele and colleagues show that people infected with B.1.351 can neutralize both B.1.351 and (to a slightly lesser extent) ‘regular’ non-B.1.351 viruses (Cele 2021). If these data are confirmed, a variant B.1.351-targeted booster vaccine could be a solution for countries where B.1.351 is the dominant strain.
Starr TN, Greaney AJ, Dingens AS, Bloom JD. Complete map of SARS-CoV-2 RBD mutations that escape the monoclonal antibody LY-CoV555 and its cocktail with LY-CoV016. bioRxiv 2021, posted 21 February. Full-text: https://doi.org/10.1101/2021.02.17.431683
Jesse Bloom, Tyler Starr and colleagues completely map all mutations to the SARS-CoV-2 spike receptor binding domain (RBD) that escape binding by LY-CoV555 (bamlanivimab, a monoclonal antibody manufactured by Lilly), and its cocktail combination with LY-CoV016. Individual mutations that escape binding are present in B.1.351 and P.1 (E484K escapes LY-CoV555, K417N/T escape LY-CoV016). Additionally, the L452R mutation in the B.1.429 lineage escapes LY-CoV555.
Transmission
Dinklage F, Ehmann A, Erdmann E, et al. Why Is the Risk of Coronavirus Transmission so High Indoors? Die Zeit 2020, published 26 November. Full-text: https://www.zeit.de/wissen/gesundheit/2020-11/coronavirus-aerosols-infection-risk-hotspot-interiors
Whenever people gather in closed spaces, the infection risk climbs. This interactive tool shows how the coronavirus spreads. Find out how safe your environment is. See also the German version.
Immunology
Tarke A, Sidney J, Methot N, et al. Negligible impact of SARS-CoV-2 variants on CD4+ and CD8+ T cell reactivity in COVID-19 exposed donors and vaccinees. bioRxiv 2021, posted 1 March. Full-text: https://doi.org/10.1101/2021.02.27.433180
Good news from the T cell front. Alessandro Sette, Alba Grifoni, Shane Crotty, Alison Tarke and colleagues did a comprehensive analysis of SARS-CoV-2-specific CD4+ and CD8+ T cell responses from COVID-19 convalescent subjects recognizing the ancestral strain, compared to variant lineages B.1.1.7, B.1.351, P.1, and CAL.20C as well as recipients of the Moderna (mRNA-1273) or the Pfizer/BioNTech (BNT162b2) COVID-19 vaccines. The comfortable result: CD4+ and CD8+ T cell responses in convalescent COVID-19 subjects or COVID-19 mRNA vaccinees are not substantially affected by mutations found in the SARS-CoV-2 variants.
Vaccines
Vasileiou E, Simpson CR, Robertson C, et al. Effectiveness of First Dose of COVID-19 Vaccines Against Hospital Admissions in Scotland: National Prospective Cohort Study of 5.4 Million People. Lancet Preprints 2021, posted 19 February. Full-text: https://papers.ssrn.com/sol3/papers.cfm?abstract_id=3789264
A single dose of the Pfizer-BioNTech or AstraZeneca vaccine results in substantial reductions in the risk of COVID-19 related hospitalization. In a study from Scotland, the first vaccine dose protected well over 80% of vaccinees against COVID-19 related hospitalization at 28-34 days post-vaccination (Pfizer-BioNTech: 85%; AstraZeneca: 94%). Comparable results (81%) were seen in people aged ≥ 80 years (Vasileiou 2021).
Hall VJ, Foulkes S, Saei A, et al. Effectiveness of BNT162b2 mRNA Vaccine Against Infection and COVID-19 Vaccine Coverage in Healthcare Workers in England, Multicentre Prospective Cohort Study (the SIREN Study) Victoria Jane Hall. Lancet Preprints 2021, published 22 February. Full-text: https://papers.ssrn.com/sol3/papers.cfm?abstract_id=3790399
These data from the SIREN (Sarscov2 Immunity and REinfection EvaluatioN) study suggest that the Pfizer-BioNTech vaccine effectively prevents both symptomatic and asymptomatic infection in working age adults. (The SIREN study is a prospective cohort study among staff working in publicly funded hospitals.) The vaccine was 72% effective (95% CI 58-86) 21 days after first dose and 86% effective (95% CI 76-97) seven days after two doses in the antibody negative cohort (Hall 2021).
French
If you read French, read Covid-19 : « A court terme, l’effet positif des vaccins risque de ne pas suffire pour compenser l’impact délétère des variants ». Le Monde 2021, published 6 March. Full-text : https://www.lemonde.fr/planete/article/2021/03/06/covid-19-a-court-terme-l-effet-positif-des-vaccins-risque-de-ne-pas-suffire-pour-compenser-l-impact-deletere-des-variants_6072159_3244.html
Simon Cauchemez, modélisateur à l’Institut Pasteur, doute que les mesures actuelles permettent une amélioration à la mi-avril, comme espéré par le gouvernement.
Mandard S. Covid-19 : les pics de pollution aux particules fines soupçonnés de jouer un rôle dans le rebond épidémique. Le Monde 2021, published 6 March. Full-text : https://www.lemonde.fr/planete/article/2021/03/06/covid-19-les-pics-de-pollution-aux-particules-fines-soupconnes-de-jouer-un-role-dans-le-rebond-epidemique_6072189_3244.html
Pour l’épidémiologiste Antoine Flahault, les épisodes de pollution liés aux sables du Sahara pourraient expliquer la reprise des contaminations et des hospitalisations.
Editorial. Covid-19 : changer le regard sur le vaccin. Le Monde 2021, published 5 March. Full-text : https://www.lemonde.fr/idees/article/2021/03/05/covid-19-changer-le-regard-sur-le-vaccin_6072064_3232.html
Cinq semaines après avoir exclu le reconfinement général du pays que de nombreux médecins appelaient de leurs vœux, Emmanuel Macron peut se targuer de deux résultats. A ce jour, l’épidémie n’a pas connu de hausse exponentielle, comme certains modèles le laissaient craindre. Et aucun de ses opposants politiques ne lui fait grief d’avoir fait ce choix risqué. Compte tenu de la fragilité économique et psychologique du pays, il existe désormais un quasi-consensus pour rejeter cette solution radicale. La partie, cependant, est encore loin d’être gagnée.