Copy-editor: Rob Camp
Transmission
European Centre for Disease Prevention and Control. Threat Assessment Brief: Rapid increase of a SARS-CoV-2 variant with multiple spike protein mutations observed in the United Kingdom. ECDC 2020, published 20 December. Full-text: https://www.ecdc.europa.eu/en/publications-data/threat-assessment-brief-rapid-increase-sars-cov-2-variant-united-kingdom
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European Centre for Disease Prevention and Control. Rapid increase of a SARS-CoV-2 variant with multiple spike protein mutations observed in the United Kingdom. ECDC 2020, published 20 December. Full-text: https://www.ecdc.europa.eu/sites/default/files/documents/SARS-CoV-2-variant-multiple-spike-protein-mutations-United-Kingdom.pdf
South East England has recently faced a rapid increase in COVID-19 cases. Analysis of viral genome sequence data showed that a large proportion of cases belonged to a new single phylogenetic cluster. The new variant is defined by multiple spike protein mutations (deletion 69-70, deletion 144, N501Y, A570D, D614G, P681H, T716I, S982A, D1118H) present as well as mutations in other genomic regions. Preliminary analysis in the UK suggests that this variant is more transmissible than previously circulating variants, with an estimated potential to increase the reproductive number (R) by 0.4 or greater with an estimated increased transmissibility of up to 70%. There is no indication at this point of increased infection severity associated with the new variant.
Virology
Pickering BS, Smith G, Pinette MM, et al. Susceptibility of domestic swine to experimental infection with severe acute respiratory syndrome coronavirus 2. Emerg Infect Dis December 17, 2020. Full-text: https://doi.org/10.3201/eid2701.200339
Domestic swine are susceptible to low levels of SARS-CoV-2 viral infection. Among 16 experimentally inoculated animals, 5 (31,3%) displayed some level of exposure or elicited an immune response to the virus. Only 1 pig in the study retained live virus, but 2 other animals had detectible RNA measured in nasal wash, and another 2 developed antibodies. Of note, Brad Pickering from the Canadian Food Inspection Agency and colleagues used a 10-fold higher viral dose for experimental infection than was used in previous studies.
Immunology
Singh DK, Singh B, Ganatra SR. et al. Responses to acute infection with SARS-CoV-2 in the lungs of rhesus macaques, baboons and marmosets. Nat Microbiol December 18, 2020. Full-text: https://doi.org/10.1038/s41564-020-00841-4
Rhesus macaques, baboons and marmosets can all be infected with SARS-CoV-2 but show differential progression to COVID-19. Whereas older marmosets have a mild infection, macaques developed moderate progressive pneumonia that resolves, accompanied by a marked reduction in lung and nasal viral loads. Baboons have the most severe lung pathology, and the greatest viral load.
Vaccine
Dai L, Gao GF. Viral targets for vaccines against COVID-19. Nat Rev Immunol 18 December 2020. Full-text: https://doi.org/10.1038/s41577-020-00480-0
Which viral elements are used in COVID-19 vaccine candidates, why might they act as good targets for the immune system and what are the implications for protective immunity? This review addresses these questions.
Ewer KJ, Barrett JR, Belij-Rammerstorfer S. et al. T cell and antibody responses induced by a single dose of ChAdOx1 nCoV-19 (AZD1222) vaccine in a phase 1/2 clinical trial. Nat Med December 18, 2020. Full-text: https://doi.org/10.1038/s41591-020-01194-5
A detailed description of the immune response after administration of one dose of ChAdOx1 nCoV-19 in 88 adults (ages 18-55 years). The authors define, in detail, the isotypes, subclasses and antibody avidity induced after vaccination. They also performed multiplex cytokine profiling and intracellular cytokine staining analysis, demonstrating that ChAdOx1 nCoV-19 vaccination induces a predominantly Th1-type response (that appears to be good).
Prevention
Spaccaferri G, Larrieu S, Pouey J, et al. Early assessment of the impact of mitigation measures to control COVID-19 in 22 French metropolitan areas, October to November 2020. Euro Surveill 2020;25(50):pii=2001974. Full-text: https://doi.org/10.2807/1560-7917.ES.2020.25.50.2001974
In France, measures including curfew and lockdown were implemented to control the COVID-19 pandemic second wave in 2020. This study found a considerable decrease in incidence of COVID-19 cases and hospital admissions 7 to 10 days after mitigation measures were put in place, occurring earlier in metropolitan areas.
Transmission
Sayampanathan AA, Heng CS, Pin PH, et al. Infectivity of asymptomatic versus symptomatic COVID-19. Lancet December 18, 2020. Full-text: https://doi.org/10.1016/S0140-6736(20)32651-9
Some evidence of a lower infectivity of asymptomatic patients. Andrew Sayampanathan and colleagues looked at 628 people with COVID-19 and 3790 close contacts in Singapore. Overall, 89 (2%) of 3790 close community contacts developed COVID-19 while in quarantine. Binomial regression revealed that when adjusted for age, gender, and serology of index case, the incidence of COVID-19 among close contacts of a symptomatic index case was 3,85 times higher than for close contacts of an asymptomatic index case (95% CI 2.06–7.19; p < 0·0001).
Heinrich F, Meißner K, Langenwalder F, et al. Postmortem stability of SARS-CoV-2 in nasopharyngeal mucosa. Emerg Infect Dis December 16, 2020. Full-text: https://wwwnc.cdc.gov/eid/article/27/1/20-3112_article
Be careful with human corpses: Fabian Heinrich and colleagues from Hamburg found that nasopharyngeal viral RNA stability in 79 corpses showed no time-dependent decrease. Maintained infectivity was supported by virus isolation up to 35 hours post-mortem. There was no correlation between the post-mortem interval (time of death until cooling at 4°C; median 17,8 hours) and the viral RNA loads of corpses. According to the authors, their data indicate potentially high infectivity of human corpses, requiring hazard assessments in professional fields concerned and careful and conscious handling.
Comorbidities
Goodman KE, Magder LS, Baghdadi JD, et al. Impact of Sex and Metabolic Comorbidities on COVID-19 Mortality Risk Across Age Groups: 66,646 Inpatients Across 613 U.S. Hospitals. Clin Infect Dis 2020, December 19. Full-text: https://doi.org/10.1093/cid/ciaa1787
Among 66.646 (6,5%) admissions with a COVID-19 diagnosis across 613 US hospitals, 12.388 (18,6%) died in-hospital. In multivariable analysis, male sex was independently associated with 30% higher mortality risk (aRR, 1.30, 95% CI: 1.26 – 1.34). Of note, diabetes without chronic complications was not a risk factor at any age (aRR 1.01, 95% CI: 0.96 – 1.06), and hypertension without chronic complications was only a risk factor in younger people (20-39 year-olds) (aRR, 1.68, 95% CI: 1.17 – 2.40). Diabetes with chronic complications, hypertension with chronic complications, and obesity were risk factors in most age groups, with highest relative risks among 20-39 year-olds (respective aRRs 1.79, 2.33, 1.92; p ≤ 0.002).
Hyrich KL, Machado PM. Rheumatic disease and COVID-19: epidemiology and outcomes. Nat Rev Rheumatol December 18, 2020. Full-text: https://doi.org/10.1038/s41584-020-00562-2
According to this brief review, many questions about COVID-19 in patients with rheumatic diseases remain unanswered. These patients, when analyzed as a combined group, might have a slightly increased risk of death, although the role of disease activity and treatment was not taken into account in most studies. Chronic use of glucocorticoids at moderate or high doses is associated with hospitalization for severe COVID-19. Treatment with cytokine inhibitors could reduce the risk of SARS-CoV-2 infection, although the mechanisms of this protective effect are not clear.