20 January 2021

Copy-editor: Rob Camp


* * * Paper of the Day * * *

Li F, Li YY, Liu MJ, et al. Household transmission of SARS-CoV-2 and risk factors for susceptibility and infectivity in Wuhan: a retrospective observational study. Lancet Infect Dis 2021, published 18 January. Full-text: https://www.thelancet.com/journals/laninf/article/PIIS1473-3099(20)30981-6/fulltext

Within households, children and adolescents are less susceptible to SARS-CoV-2 infection but may be more infectious than older individuals. This is the message by Shun-Qing Xu, Fang Li and colleagues who analyzed 27.101 households with 29.578 primary cases and 57.581 household contacts. The secondary attack rate was estimated at 15·6% (95% CI 15·2–16·0), assuming a mean incubation period of 5 days and a maximum infectious period of 22 days. Pre-symptomatic cases were more infectious and individuals with asymptomatic infection less infectious than symptomatic cases.

Figure. Spatial distribution of all confirmed COVID-19 cases and the retrospective cohort of contact-traced households reported during Dec 2, 2019–April 18, 2020, at the community level in Wuhan, China | (A) Distribution of all clinically or laboratory confirmed COVID-19 cases in Wuhan. (B) Distribution of all… | Continue reading at https://www.thelancet.com/journals/laninf/article/PIIS1473-3099(20)30981-6/fulltext


6th Edition – 453 pages



Mervosh S, Baker M, Mazzei P, Walker M. One Year, 400,000 Coronavirus Deaths: How the U.S. Guaranteed Its Own Failure. The New York Times 2021, published 17 January. Full-text: https://www.nytimes.com/2021/01/17/us/covid-deaths-2020.html

After the White House declined to pursue a unified national COVID strategy, governors faced off against lobbyists, health experts and a restless public consumed by misinformation.



Mahase E. Covid-19: What new variants are emerging and how are they being investigated? BMJ. 2021 Jan 18;372:n158. PubMed: https://pubmed.gov/33462092. Full-text: https://doi.org/10.1136/bmj.n158

What do we know about the new variant emerging from Brazil? What do we know about the South African variant? Do the current vaccines work against the Brazilian, English, and South African variants? Could the virus still mutate to escape the vaccines? Elisabeth Mahase gives the preliminary answers.


Corum J, Zimmer C. Inside the B.1.1.7 Coronavirus Variant. The New York Times 2021, published 18 January. Full-text: https://www.nytimes.com/interactive/2021/health/coronavirus-mutations-B117-variant.html

A short graphical guide to the B117 variant.

Figure 2. Mutations in the B.1.1.7 Lineage | A coronavirus variant first reported in Britain has 17 recent mutations that change or delete amino acids in viral proteins.


Rambaut A, Loman N, Pybus O, et al. Preliminary genomic characterisation of an emergent SARS-CoV-2 lineage in the UK defined by a novel set of spike mutations. Virological 2020, Full-text: https://virological.org/t/preliminary-genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-the-uk-defined-by-a-novel-set-of-spike-mutations/563/1

A paper we missed 4 weeks ago where Andrew Rambaut and colleagues describe the B117 lineage.

Figure 2 | Regression of root-to-tip genetic distances against sampling dates, for sequences belonging to lineage B.1.1.7 (blue) and those in its immediate outgroup in the global phylogenetic tree (brown). The regression lines are fitted to the two sets independently. The regression gradient is an estimate of the rate of sequence evolution. These rates are 5.6E-4 and 5.3E-4 nucleotide changes/site/year for the B.1.1.7 and outgroup data sets, respectively.


Tegally H, Wilkinson E, Giovanetti M, et al. Emergence and rapid spread of a new severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) lineage with multiple spike mutations in South Africa. Virological 2020, Full-text: doi: https://doi.org/10.1101/2020.12.21.20248640

Another paper we missed where Tulio de Oliveira, Houriiyah Tegally and colleagues describe the 501Y.V2 lineage characterized by eight mutations in the spike protein, including three at important residues in the receptor-binding domain (K417N, E484K and N501Y) that may have functional significance. This lineage emerged in South Africa and spread rapidly, becoming the dominant lineage within weeks in the Eastern Cape and Western Cape Provinces.

Figure 2. Evolution and spread of the S.501Y.V2 cluster in South Africa. A) Time-resolved maximum clade credibility phylogeny of 1350 SARS-CoV-2 sequences, 647 of which are from South Africa (red). The new SARS-CoV-2 cluster is highlighted in yellow. B) Time-resolved maximum clade credibility phylogeny of S.501Y.V2 cluster, with… | Continue reading at https://doi.org/10.1101/2020.12.21.20248640.



Kim JH, Marks F, Clemens JD. Looking beyond COVID-19 vaccine phase 3 trials. Nat Med (2021). Full-text: https://doi.org/10.1038/s41591-021-01230-y

After Phase III vaccine trials, a comprehensive program of prevention, continued work on vaccine optimization, new vaccines, correlates, long-term safety and continued surveillance will be needed simultaneously with the steady implementation of vaccination.

Figure 1. The next steps for a COVID-19 vaccine. | After a COVID-19 vaccine has demonstrated efficacy in a clinical trial, the vaccine must be approved and manufacturing scaled up, according to an international standard known as CGMP. The transportation of the vaccine must respect the cold-chain requirements. COVID-19 vaccines should be allocated with… | Continue reading at https://doi.org/10.1038/s41591-021-01230-y.


Glover RE, Urquhart R, Lukawska J, Blumenthal KG. Vaccinating against covid-19 in people who report allergies. BMJ. 2021 Jan 18;372:n120. PubMed: https://pubmed.gov/33461962. Full-text: https://doi.org/10.1136/bmj.n120

A history of severe allergy does not preclude vaccination unless that allergy is to the vaccine or its components. Discover the key facts and reassure your patients.



Naveca F, da Costa C, Nascimento V, et al. SARS-CoV-2 reinfection by the new Variant of Concern (VOC) P.1 in Amazonas, Brazil. Virological 2021, posted 18 January. Full-text: https://virological.org/t/sars-cov-2-reinfection-by-the-new-variant-of-concern-voc-p-1-in-amazonas-brazil/596

The lineage P.1 (alias of B. is an emerging variant that harbors several amino acid mutations including S:K417T, S:E484K, and S:N501Y. Paola Resende, Felipe Naveca and colleagues describe the first confirmed case of reinfection with the P.1 lineage in a 29-year-old woman in Manaus, Amazonas, Brazil, with no history of immunosuppression, who presented two clinical episodes of COVID-19 infection within a gap of nine months.

Figure 1. Timeline indicating the epidemiological, clinical, and laboratory events regarding the P.1 (alias of B. reinfection case in Manaus, Amazonas, Brazil. Mutation highlighted in pink indicates a new potential N-glycosylation site, and orange mutations indicate changes at the RBD.



Beyond Corona

Rothe C (Ed.). Clinical Cases in Tropical Medicine. Elsevier 2022, 2nd edition, 320 pages. Link: https://www.amazon.com/dp/0702078794/

We almost never recommend books (why not?), but this one, by Camilla Rothe and more than 100 contributors, is a worthy exception. Find 103 outstanding case reports for doctors and senior medical students who already have some background knowledge in tropical medicine.



If you read Spanish, read Gomollón-Bel F. El glaseado que camufla al coronavirus. El País 2021, published 19 January. Full-text: https://elpais.com/ciencia/2021-01-18/el-glaseado-que-camufla-al-coronavirus.html

Una capa de azúcares recubre al patógeno y ayuda a esconderlo de nuestro sistema inmunitario. Ahora, gracias a los superordenadores, podemos verlos por primera vez y pintar una imagen del coronavirus totalmente diferente.


González B. ¿Es exagerado el miedo a que la vacuna de la covid provoque alergia? El País 2021, published 18 January. Full-text: https://elpais.com/buenavida/salud/2021-01-18/es-exagerado-el-miedo-a-que-la-vacuna-de-la-covid-provoque-alergia.html

No es nada extraño que las vacunas tengan efectos secundarios. De hecho, todas los tienen, solo que unas más y otras menos. El peor efecto adverso que tiene la vacuna es no administrarla.


Sampedro J. Vuelve Manaos. El País 2021, published 18 January. Full-text: https://elpais.com/ciencia/2021-01-18/vuelve-manaos.html

No herd immunity in Manaus, Brazil.



If you read French, read Marc Gozlan. Covid-19 : le défi des nouveaux variants. Réalités Biomédicales 2021, published 18 January. Full-text : https://www.lemonde.fr/blog/realitesbiomedicales/2021/01/18/covid-19-le-defi-des-nouveaux-variants/

Depuis quelques jours, les données concernant les variants du coronavirus SARS-CoV-2, qu’ils soient britannique, sud-africain, brésilien, voire possiblement américain, se succèdent à un rythme soutenu. Ces nouveaux variants du SARS-CoV-2 inquiètent les autorités dans le monde entier. En effet, certains sont plus contagieux que les variants circulant actuellement, appelés variants historiques.

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