28 February 
Copy-editor: Rob Camp
Variants
Paper of the Day
WHO 20210223. Weekly epidemiological update – 23 February 2021. WHO 2021, published 23 February. Full-text: https://www.who.int/publications/m/item/weekly-epidemiological-update—23-february-2021
If you are interested in variants, read the Special Focus: Update on SARS-CoV-2 Variants of Concern on page 7 to 13 with an excellent table on the current information we have on B.1.1.7, B.1.351 and P.1.
Epidemiology
Global.health 2021. Link: https://global.health/
This initiave by people from Oxford, Harvard, Northeastern, Boston Children’s Hospital, Georgetown, University of Washington, and Johns Hopkins is meant to be an easy-to-use global data repository and visualization platform that collects anonymized information about individual cases from around the world in one place. The goal: open access to real-time epidemiological anonymized data. See also Maxmen A. Massive Google-funded COVID database will track variants and immunity. Nature. 2021 Feb 24. PubMed: https://pubmed.gov/33627862. Full-text: https://doi.org/10.1038/d41586-021-00490-5
Virology
FT 2021026. The same covid-19 mutations are appearing in different places. Financial Times 2021, published 26 February. Link: https://www.economist.com/graphic-detail/2021/02/27/the-same-covid-19-mutations-are-appearing-in-different-places
Excellent ancestry tree of SARS-CoV-2. The Financial Times argues that convergent evolution might make travel restrictions redundant.
Variants
Naveca F, Nascimento V, Souza V, et al. COVID-19 epidemic in the Brazilian state of Amazonas was driven by long-term persistence of endemic SARS-CoV-2 lineages and the recent emergence of the new Variant of Concern P.1. Research Square 2021, posted 25 February. Full-text: https://doi.org/10.21203/rs.3.rs-275494/v1
The second wave in the Northern Brazilian state of Amazonas coincides with the emergence of the P.1 variant in late November 2020. P.1 replaced the parental lineage in less than two months. The authors report that successive lineage replacements in Amazonas were driven by a complex combination of variable levels of social distancing measures and the emergence of a more transmissible VOC P.1 virus. They provide insights to understanding the mechanisms that underlie COVID-19 waves and the risk of disseminating P.1 in Brazil and potentially worldwide.
Figure 2. Origin of major SARS-CoV-2 lineages circulating in the state of Amazonas. a-b) ML phylogeographic analysis of lineages B.1.1.28 and B.1.1.33 in Brazil. Graphs depict the estimated numbers of introductions into Amazonas colored by region of origin. c) Bayesian phylogeographic analysis of… | Continue reading at https://doi.org/10.21203/rs.3.rs-275494/v1.
Faria NR, Mellan TA, Whittaker C, et al. Genomics and epidemiology of a novel SARS-CoV-2 lineage in Manaus. GitHub 2021, posted 27 February. Full-text: https://github.com/CADDE-CENTRE/Novel-SARS-CoV-2-P1-Lineage-in-Brazil/blob/main/manuscript/FINAL_P1_MANUSCRIPT_25-02-2021_combined.pdf
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. These data need to be confirmed by further studies.
Figure 4. Estimates of P.1’s epidemiological characteristics inferred from a multicategory Bayesian transmission model fitted to data from Manaus, Brazil (A) Joint posterior distribution of the cross-immunity and transmissibility increase inferred through fitting the model to mortality and genomic data. Grey contours refer to posterior density intervals ranging from the 95% and 50% isoclines. Marginal posterior distributions for each parameter shown along each axis. (B) As for (A)… | Continue reading at https://github.com/CADDE-CENTRE/Novel-SARS-CoV-2-P1-Lineage-in-Brazil/blob/main/manuscript/FINAL_P1_MANUSCRIPT_25-02-2021_combined.pdf.
Transmission
Davis AC, Zee M, Clark AD, et al. Computational Fluid Dynamics Modeling of Cough Transport in an Aircraft Cabin. medRxiv 2021, posted 17 February. Full-text: https://doi.org/10.1101/2021.02.15.431324
Track particles released by coughing from a passenger seated in different seats on a Boeing 737 aircraft. The authors report that 80% of the particles were removed from the cabin in 1.3 to 2.6 minutes, depending on conditions, and 95% of the particles were removed in 2.3 to 4.5 minutes. We know from other reports that this is not sufficient to prevent SARS-CoV-2 transmission onboard aircraft. Remember the paper we presented on 23 February: Wang Z, Galea ER, Grandison A, et al. Inflight Transmission of COVID-19 Based on Experimental Aerosol Dispersion Data. Journal of Travel Medicine, February 19, 2021. taab023, https://doi.org/10.1093/jtm/taab023
Figure 1. Airflow design in narrow-body aircraft. (a) Airflow delivery features in the 737 Boeing Sky Interior cabin used in simulations. (b) Idealized airflow pattern in the passenger cabin.
Vaccine
WHO 20210223. Weekly epidemiological update – 23 February 2021. WHO 2021, published 23 February. Full-text: https://www.who.int/publications/m/item/weekly-epidemiological-update—23-february-2021
Three pages about WHO’s current COVID-19 vaccine policy recommendations (page 4 to 6): age requirements, pregnant women, breastfeeding mothers, people with compromised immune system, living with HIV, or previously infected with SARS-CoV-2, people with a history of severe allergic reaction.
Table 2. Who can be vaccinated with which vaccine against COVID-19?
FDA 20210226. Vaccines and Related Biological Products Advisory Committee February 26, 2021 Meeting Announcement. FDA 2021, published 26 February. Documents: https://www.fda.gov/advisory-committees/advisory-committee-calendar/vaccines-and-related-biological-products-advisory-committee-february-26-2021-meeting-announcement#event-materials
Find here the documents that will lead to the approval of vaccine #4 – the one-shot adenovirus vector vaccine by Johnson & Johnson. The best news of the day: the vaccine had only a slightly reduced overall efficacy rate in South Africa (64% vs 72% in the US). Most importantly, the J&J vaccine showed 86% and 82% efficacy against severe disease of COVID-19 in the US and South Africa, respectively.
Diagnostics
Carreño JM, Mendu DR, Simon V, et al. Longitudinal analysis of SARS-CoV-2 seroprevalence using multiple serology platforms. medRxiv 2021, posted 26 February. Full-text: https://doi.org/10.1101/2021.02.24.21252340
Florian Krammer, Juan Manuel Carreño and colleagues look at longitudinal SARS-CoV-2 seroprevalence using multiple serology platforms. Good correlation was observed between the MS and Kantaro RBD ELISAs and between the MS and Kantaro spike ELISAs. By contrast, modest correlations were observed between the Abbott Architect and both RBD and spike-based assays.
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