Top 10: February 8

Copy-editor: Rob Camp


Paper of the Day

Washington NL, Gangavarapu K, Zeller M, et al. Genomic epidemiology identifies emergence and rapid transmission of SARS-CoV-2 B.1.1.7 in the United States. medRxiv 2021, posted 7 February. Full-text:

Kristian Andersen, Nicole L. Washington, Karthik Gangavarapu and colleagues from Helix and the Scripps Research Institute, La Jolla, sequenced 212 B117 genomes collected in the U.S. from December 2020 to January 2021. They found a doubling rate of a little over a week and an increased transmission rate of 35-45%. The authors show that the U.S. is on a similar trajectory as other countries where B117 rapidly became the dominant SARS-CoV-2 variant and warn that immediate and decisive action to minimize COVID-19 morbidity and mortality. Authorities in Germany, France, Italy, Spain and other countries should listen too.



News from Oxford

University of Oxford 20210207. ChAdOx1 nCov-19 provides minimal protection against mild-moderate COVID-19 infection from B.1.351 coronavirus variant in young South African adults. University of Oxford 2021, published 7 Febuary. Full-text:

In an analysis, submitted as a pre-print prior to peer-review publication, a two-dose regimen of the ChAdOx1 nCoV-19 vaccine provides minimal protection against mild-to-moderate COVID-19 infection from the B1351 coronavirus variant first identified in South Africa.



Mohanan M, Malani A, Krishnan K, Acharya A. Prevalence of SARS-CoV-2 in Karnataka, India. JAMA. 2021 Feb 4. PubMed: Full-text:

The adjusted seroprevalence of SARS-CoV-2 across Karnataka, India, was 46,7%, suggesting approximately 31,5 million residents were infected, far greater than the 327.076 cases reported by August 29, 2020.


Gaudart J, Landier J, Huiart L, et al. Factors associated with the spatial heterogeneity of the first wave of COVID-19 in France: a nationwide geo-epidemiological study. Lancet Public Health 2021, published 5 February. Full-text:

From March 19 to May 11, 2020, hospitals in metropolitan France notified a total of 100.988 COVID-19 cases, including 16.597 people who were admitted to intensive care and 17.062 deaths. Mortality and case fatality rates were higher in regions with older populations. Jean Gaudart et al. found no association between climate and in-hospital COVID-19 incidence, or between economic indicators and in-hospital COVID-19 incidence or mortality rates.


Roederer T, Mollo B, Vincent C, et al. Seroprevalence and risk factors of exposure to COVID-19 in homeless people in Paris, France: a cross-sectional study. Lancet Public Health 2021, published 5 February. Full-text:

During the COVID-19 lockdown period from March 17 to May 11, 2020, French authorities in Paris and its suburbs relocated people experiencing recurrent homelessness to emergency shelters, hotels, and large venues. In this study by Thomas Roederer et al., more than half of surveyed individuals (426 of 818, 52%) tested positive by any serological test. Seroprevalence was highest among those living in workers’ residences (88,7%), followed by emergency shelters (50,5%), and food distribution sites (27,8%). More than two thirds of COVID-19 seropositive individuals (68%) did not report any symptoms during the recall period. Living in crowded conditions was the strongest factor associated with exposure level. This study underscores the importance of providing safe, uncrowded accommodation, alongside adequate testing and public health information.



Koutsakos M, Rowntree LC, Hensen L, et al. Integrated immune dynamics define correlates of COVID-19 severity and antibody responses. Cell Rep Med 2021, published 4 February. Full-text:

Katherine Kedzierska, Marios Koutsakos and colleagues provide a comprehensive map of longitudinal immunological responses in COVID-19 patients. ICU patients with severe COVID-19 displayed higher levels of soluble IL-6, IL-6R, IL-18, and hyperactivation of innate, adaptive and myeloid compartments than patients with moderate disease.



Feld JJ, Kandel C, Biondi MJ, et al. Peginterferon lambda for the treatment of outpatients with COVID-19: a phase 2, placebo-controlled randomised trial. Lancet Respir Dis 2021, published 5 February. Full-text:

Interferon lambda-1 is a type III interferon involved in innate antiviral responses with activity against respiratory pathogens. Here, Jordan Feld et al. randomly assigned (1:1) 30 patients to a single subcutaneous injection of peg-interferon lambda 180 μg or placebo within 7 days of symptom onset or first positive swab if asymptomatic. Of those with baseline viral load above 106 copies per mL, 15 (79%) of 19 patients in the peg-interferon lambda group had undetectable virus on day 7, compared with six (38%) of 16 in the placebo group (OR 6,25 [95% CI: 1,49–31,06]; p = 0,012).


Collateral Effects

Dorward J, Khubone T, Gate K, et al. The impact of the COVID-19 lockdown on HIV care in 65 South African primary care clinics: an interrupted time series analysis. Lancet HIV 2021, published 4 February. Full-text:

The study describes the impact of the 2020 national COVID-19 lockdown on HIV testing and treatment in KwaZulu-Natal, South Africa, where 1,7 million people are living with HIV. While antiretroviral therapy (ART) provision was generally maintained, HIV testing and ART initiations were heavily impacted.



If you read Spanish, read Gorospe P, Linde P, Catalán N, Sevillano EG. Arquitectura de un supercontagio: cómo el virus se instaló dos semanas en un edificio de Bilbao. El País 2021, published 7 February. Full-text:

Varios expertos creen que los dos ascensores de un bloque de viviendas del barrio de Santutxu aceleraron un brote letal con 33 infectados, cinco de los cuales fallecieron.



If you read French, read Dagorn G. Grippe, gastro ou bronchite : les mesures anti-Covid-19 ont éteint presque toutes les autres épidémies hivernales. Le Monde 2021, published 7 February. Full-text :

Lavage des mains, port du masque et distanciation physique ont considérablement réduit le niveau de circulation des virus saisonniers habituels.


Berthou E. « Psychologiquement déstabilisante, la pandémie de Covid-19 a renforcé le complotisme ». Le Monde 2021, published 7 February. Full-text :

Un cerveau intuitif, peu porté sur l’analyse, adhère à des croyances infondées qui font le lit des théories du complot. Thierry Ripoll, chercheur en psychologie cognitive, dissèque ce mécanisme dans « Pourquoi croit-on ? ».


Charrel M. La pandémie de Covid-19 creuse le fossé en Europe, entre le Sud dépendant du tourisme et le Nord. Le Monde 2021, published 7 February. Full-text :

Tous les pays de la zone euro ne sont pas affectés de la même façon par la crise sanitaire. Les déséquilibres déjà existants entre l’Italie, le Portugal, l’Espagne ou la Grèce, et un Nord plus industriel, sont exacerbés.


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