Copy-editor: Rob Camp
Variants
Paper of the Day
Tegally H, Wilkinson E, Giovanetti M. et al. Emergence of a SARS-CoV-2 variant of concern with mutations in spike glycoprotein. Nature March 9, 2021. https://www.nature.com/articles/s41586-021-03402-9_reference.pdf
The future “reference” paper on the detection of B.1.351 (or 501Y.V2), characterized by eight lineage-defining mutations in the spike protein, including three at important residues in the receptor-binding domain (K417N, E484K and N501Y). This lineage was identified in South Africa after the first epidemic wave in a severely affected metropolitan area, and spread rapidly. The genomic data, showing the rapid expansion and displacement of other lineages in multiple regions, suggest that this lineage is associated with a selection advantage, most plausibly as a result of increased transmissibility or immune escape. Nevertheless, congrats to co-author Wolfgang Preiser!
Epidemiology
Agrawal S, Orschler L, Lackner S. Long-term monitoring of SARS-CoV-2 RNA in wastewater of the Frankfurt metropolitan area in Southern Germany. Sci Rep 11, 5372 (2021). https://www.nature.com/articles/s41598-021-84914-2
After monitoring the time course of the SARS-CoV-2 RNA concentration in raw sewage in the Frankfurt metropolitan area for several months, Shelesh Agrawal and colleagues believe that wastewater-based epidemiology has the potential to serve as an early warning system for SARS-CoV-2 infections and as a monitoring system to identify global hotspots.
Brault V, Mallein B, Rupprecht JF, et al. Group testing as a strategy for COVID-19 epidemiological monitoring and community surveillance. PLOS Computational Biology, March 4, 2021. https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008726
Group testing could provide the means for regular and massive screenings. In this paper, the authors do not address any diagnostic problems—e.g. how to use a minimal number of tests to obtain an individual diagnostic—but rather focus on population-scale application of pooling.
Immunology
Grzelak L, Velay A, Madec Y, et al. Sex differences in the evolution of neutralizing antibodies to SARS-CoV-2. Journal of Infectious Diseases 07 March 2021, jiab127, https://academic.oup.com/jid/advance-article/doi/10.1093/infdis/jiab127/6161322?searchresult=1
More robust humoral responses in women than in men? In 308 healthcare workers with mild disease, anti-S and anti-N antibodies were detected in 99% and 59% of individuals at 3-6 months, respectively. Anti-S antibodies and NAbs declined faster in males than in females, independently of age and BMI, suggesting an association of sex with evolution of the humoral response.
Vaccine
Saad-Roy CM, Morris SE, Metcalf JE, et al. Epidemiological and evolutionary considerations of SARS-CoV-2 vaccine dosing regimes. Science 09 Mar 2021: eabg8663. https://science.sciencemag.org/content/early/2021/03/08/science.abg8663
Delaying the second dose? Maybe easier said than done. Chadi Saad-Roy and colleagues urge caution. According to their models, a vaccine strategy with a very long inter-dose period could lead to marginal short-term benefits at the cost of a higher infection burden in the long term and substantially more potential for viral evolution and the development of new variants. However, current uncertainties surrounding the strength and duration of adaptive immunity in response to natural infection or vaccination lead to very broad range of possible outcomes of various dosing regimens.
Capetti AF, Stangalini CA, Borgonovo F, et al. Impressive boosting of anti-S1/S2 IgG production in COVID-19-experienced patients after the first shot of the BNT162b2 mRNA COVID-19 Vaccine. Clinical Infectious Diseases 06 March 2021, ciab214, https://doi.org/10.1093/cid/ciab214
But is one shot enough after infection? The next study, comparing COVID-19 naïve people versus asymptomatic/pauci-symptomatic (A/P) people versus symptomatic/hospitalized (S/H) COVID-19 patients. Titers (logarithmic scale!) before and after the first dose of the BNT162b2 vaccine.
Virology
Baggen J, Persoons L, Vanstreels E, et al. Genome-wide CRISPR screening identifies TMEM106B as a proviral host factor for SARS-CoV-2. Nat Genet March 8, 2021. https://www.nature.com/articles/s41588-021-00805-2.pdf
Jim Baggen and colleagues from Belgium have identified two new host factors required for coronavirus infection. The lysosomal protein TMEM106B serves as an essential specific host factor for SARS-CoV-2 infection in multiple human cell lines. The phosphoinositide 3-kinase (PI3K) type 3 appears to be a common host factor for SARS-CoV-2 that could be targeted by small molecules.
Diagnostics
Shrotri M, Harris RJ, Rodger A, Planche T, Sanderson F, Mahungu T, et al. Persistence of SARS-CoV-2 N-antibody response in healthcare workers, London, UK. Emerg Infect Dis. 2021 Apr [date cited]. https://wwwnc.cdc.gov/eid/article/27/4/20-4554_article
Nucleocapsid (N) antibodies appear more stable than Spike (S) antibodies in the short term. N antibody titers were stable and sustained for < 12 weeks in 312 seropositive participants. This was consistent across demographic and clinical variables and contrasts with reports of short-term antibody waning.
Van Elslande J, Gruwier L, Godderis P. Estimated half-life of SARS-CoV-2 anti-spike antibodies more than double the half-life of anti-nucleocapsid antibodies in healthcare workers. Clinical Infectious Diseases 08 March 2021, ciab219, https://academic.oup.com/cid/advance-article/doi/10.1093/cid/ciab219/6162856?searchresult=1
Oops, the opposite? See title. We would like to attend a Zoom meeting between Madhumita Shrotri and Jan Van Elslande. Different time periods, methods, participants? The debate goes on.
Noh JY, Kwak JE, Yang JS, et al. Longitudinal assessment of anti-SARS-CoV-2 immune responses for six months based on the clinical severity of COVID-19. Journal of Infectious Diseases 04 March 2021, jiab124, https://academic.oup.com/jid/advance-article/doi/10.1093/infdis/jiab124/6158870?searchresult=1
Ji Yun Noh and colleagues from Seoul have investigated the longitudinal profile of anti-SARS-CoV-2 antibodies in patients who recovered from COVID-19. Neutralizing antibodies were detected in 86.9% until six months after diagnosis of SARS-CoV-2 infection. Patients with pneumonia had significantly higher titers (and stronger T cell immunity) than patients without.