Top 10: February 6

Copy-editor: Rob Camp


Paper of the Day

Kemp SA, Collier DA, Datir RP, et al. SARS-CoV-2 evolution during treatment of chronic infection. Nature 2021, published 5 February. Full-text:

In immune-suppressed patients, convalescent plasma therapy may lead to the emergence of viral variants with evidence of reduced susceptibility to neutralizing antibodies. Here, Ravinda Gupta, Steven Kemp and colleagues demonstrate that convalescent plasma therapy led to large, dynamic virus population shifts, with the emergence of a dominant viral strain bearing D796H in S2 and ΔH69/ΔV70 in the S1 N-terminal domain NTD of the Spike protein.



Quammen D. How viruses shape our world – COVID-19 is a reminder of their destructive power, but they’re crucial to humans’ development and survival. National Geographic 2021, published 14 January. Full-text:

“Although feared as agents of disease, viruses also work wonders, shaping evolution from the very beginning. About 8 percent of our DNA comes from viruses that infected our long-ago ancestors and patched viral genes into their genomes. Some of these genes now play crucial roles in the early stages of the developing embryo and the placenta that surrounds this 13-week-old fetus.”


Bruckner TA, Parker DM, Bartell SM, et al. Estimated seroprevalence of SARS-CoV-2 antibodies among adults in Orange County, California. Sci Rep 11, 3081 (2021). Full-text:

In Orange County, a densely populated and diverse county in southern California, the SARS-CoV-2 seroprevalence in July and August 2020 may have been approximately 12 percent, seven-fold greater than the reported cases.



Madera S. Crawford E, Langelier C, et al. Nasopharyngeal SARS-CoV-2 viral loads in young children do not differ significantly from those in older children and adults. Sci Rep 11, 3044 (2021). Full-text:

This study of 5544 children and adults did not demonstrate higher nasopharyngeal viral loads in children under five years of age.



Ren X, Wen W, Fan X, et al. COVID-19 immune features revealed by a large-scale single cell transcriptome atlas. Cell 2021, published 3 February. Full-text:

Zemin Zhang, Xianwen Ren and colleagues applied single-cell RNA sequencing to 284 samples from 196 COVID-19 patients and controls and created a comprehensive immune landscape with 1,46 million cells. The authors found SARS-CoV-2 RNAs in diverse epithelial and immune cell types, accompanied by dramatic transcriptomic changes within viral positive cells. Systemic up-regulation of S100A8/A9, mainly by megakaryocytes and monocytes in the peripheral blood, might contribute to the cytokine storms observed in severe COVID-19.



Rossman H, Shilo S, Meir T, Gorfine M, Shalit U, Segal E. Patterns of covid-19 pandemic dynamics following deployment of a broad national immunization program. GitHub 2021, posted 3 February. Full-text:

SARS-CoV-2 vaccines work under real-world conditions. Eran Segal, Hagai Rossman and colleagues show that there was a 41% drop in COVID-19 infections in people aged 60 or older from mid-January to early February. During the same period, there was also a 31% drop in hospitalizations (Rossmann 2021, Figure 11). In people aged 59 and younger who received the vaccine later, cases dropped by only 12% and hospitalizations by 5%.



Teo AKJ, Choudhury Y, Tan IB, et al. Saliva is more sensitive than nasopharyngeal or nasal swabs for diagnosis of asymptomatic and mild COVID-19 infection. Sci Rep 11, 3134 (2021). Full-text:

Li Yang Hsu, Alvin Kuo Jing Teo and colleagues recruited 200 subjects, of which 91 and 46 were tested twice and thrice respectively. In total, 62,0%, 44,5%, and 37,7% of saliva, nasopharyngeal (NP) swab and self-administered nasal (SN) swab samples were positive. The percentage of test-positive saliva was higher than NP and SN swabs. The authors conclude that saliva is an alternative sample for COVID-19 screening and diagnosis.


Du Z, Pandey A, Bai Y, et al. Comparative cost-effectiveness of SARS-CoV-2 testing strategies in the USA: a modelling study. Lancet Public Health 2021, published 4 February. Full-text:

In communities where the virus is spreading rapidly, weekly testing coupled with a 2-week isolation period after a positive test is advisable. Where non-pharmacological measures are substantially curtailing the spread of the virus, monthly testing with a 1-week isolation period after a positive test is expected to be the most optimal strategy, according to this paper.



Tesoriero JM, Swain CE, Pierce JL, et al. COVID-19 Outcomes Among Persons Living With or Without Diagnosed HIV Infection in New York State. JAMA Netw Open. 2021 Feb 1;4(2):e2037069. PubMed: Full-text:

Persons living with diagnosed HIV might experience poorer COVID-related outcomes relative to persons living without diagnosed HIV. In this study, previous HIV diagnosis was associated with higher rates of severe disease requiring hospitalization, and hospitalization risk increased with progression of HIV disease stage. Hospitalization risk increased with disease progression to HIV stage 2 (aRR, 1,29 [95% CI: 1,11-1,49]) and stage 3 (aRR, 1,69 [95% CI: 1,38-2,07]) relative to stage 1.



Hoertel N, Sánchez-Rico M, Vernet R, et al. Association between antidepressant use and reduced risk of intubation or death in hospitalized patients with COVID-19: results from an observational study. Mol Psychiatry (2021). Full-text:

Antidepressant use could be associated with lower risk of death or intubation in patients hospitalized for COVID-19. This is the result of an observational study which included 7230 adults hospitalized for COVID-19, 345 patients of whom (4.8%) received an antidepressant within 48 h of hospital admission. Nicolas Hoertel etal. report a reduced risk of intubation or death (HR, 0.56; 95% CI, 0.43–0.73, p < 0.001). Next step: controlled randomized clinical trials.



Thompson B, Baker N, Maxmen A. Coronapod: Variants – what you need to know. Nature Podcast 2021, published 5 February. Link:

Around the world, concern is growing about the impact that new, faster-spreading variants of the SARS-CoV-2 virus could have on the pandemic. In this episode of Coronapod, the authors discuss what these variants are, and the best way to respond to them, in the face of increasing evidence that some can evade the immunity produced by vaccination or previous infection.



BBC Sound. The Shapeshifting Virus. BBC 2021, published 30 January. Audio, 52:59. Link:

News that at least three new variants of SARS-CoV-2 have emerged in three separate continents have sent a chill throughout the scientific community. All viruses mutate but the speed and scale of the changes and the fact they occurred independently, is seen as a wake-up call.

News that at least three new variants of SARS-CoV-2 have emerged in three separate continents have sent a chill throughout the scientific community. All viruses mutate but the speed and scale of the changes and the fact they occurred independently, is seen as a wake-up call.

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