Top 10: December 13

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Buss LF, Prete Jr A, Abrahim CMM, et al. Three-quarters attack rate of SARS-CoV-2 in the Brazilian Amazon during a largely unmitigated epidemic. Science 2020, published 8 December. Full-text:

Brazil has experienced one of the world’s most rapidly-growing COVID-19 epidemics, with the Amazon being the worst hit region. Here, Ester Sabino, Nuno Faria, Lewis Buss and colleagues show that one month after the epidemic peak in Manaus, capital of Amazonas state, 44% of the population had detectable IgG antibodies. Correcting for cases without a detectable antibody response and antibody waning, the authors estimate a 66% attack rate in June, rising to 76% in October. The authors conclude that when poorly controlled, COVID-19 can infect a high fraction of the population causing high mortality.

Figure 2. Monthly antibody prevalence and signal-to-cutoff (S/C) reading in Manaus and São Paulo. | (A and C) SARS-CoV-2 antibody prevalence estimates in Manaus (A) and São Paulo (C) with a range of corrections, from left to right: re-weighting positive tests, at positivity threshold of… | Continue reading at


Geoghegan JL, Ren X, Storey M, et al. Genomic epidemiology reveals transmission patterns and dynamics of SARS-CoV-2 in Aotearoa New Zealand. Nat Commun 11, 6351 (2020). Full-text:

New Zealand is one of a handful of countries that aimed to eliminate coronavirus disease 19 (COVID-19). Here, Jemma L. Geoghegan generated 649 SARS-CoV-2 genome sequences from infected patients with samples collected during the ‘first wave’, representing 56% of all confirmed cases in this time period. The authors found that only 19% of virus introductions into New Zealand resulted in ongoing transmission of more than one additional case. They conclude that ongoing genomic surveillance should be an integral part of the national response to monitor any re-emergence of the virus, particularly when border restrictions might eventually be eased.

Figure 2. Number and distribution of cases and genomes. | a Root-to-tip regression analysis of New Zealand (blue) and global (grey) SARS-CoV-2 sequences, with the determination coefficient, r2 (an asterisk indicates statistical significance; p = 0.049). b Maximum-likelihood time-scaled phylogenetic analysis of 649 viruses sampled from… | Continue reading at



Lemieux JE, Siddle KJ, Shaw BM, et al. Phylogenetic analysis of SARS-CoV-2 in Boston highlights the impact of superspreading events. Science 2020, published 10 December. Full-text:

Understanding the role of superspreading events in transmission is critical for prioritizing public health interventions. Here, Jacob Lemieux et al. report the analysis of 772 complete SARS-CoV-2 genomes from early in the Boston area epidemic. They found numerous introductions of the virus, a small number of which led to most cases. Find more about two superspreading events in a skilled nursing facility and at an international business conference and varying transmission dynamics in superspreading events.

Figure 4. SARS-CoV-2 superspreading events. | (A) Minimal spanning network showing genetic similarity of SARS-CoV-2 genomes in the MA dataset, with genomes from major known superspreading events highlighted. (B and C) Gene graphs showing clusters of… | Continue reading at



The SARS-CoV-2 pandemic is a colossal challenge for healthcare systems and societies. It is also the time of the ‘Great Rehearsal’. By coordinating global resources and supra-national structures to react swiftly, science is currently creating the infrastructure to fight any other new and potentially far deadlier viral disease that emerges in the future. SARS-CoV-2 is not the last pathogen humanity will have to deal with in the 21st century and more enzootic viruses will jump from their animal reservoirs to humans. However, after this pandemic, hopefully we will be better prepared for future challenges, with new vaccine platforms that can quickly be adapted to newly emerging viral diseases. There is even a final twist to the unexpected events of 2020: the SARS-CoV-2 pandemic is opening up a new era of vaccine development. In 10 years we can expect to have a wide range of new and innovative vaccines we would not have dared to previously dream of. (Source:



Soltan ASS, Kouchaki S, Zhu T, et al. Rapid triage for COVID-19 using routine clinical data for patients attending hospital: development and prospective validation of an artificial intelligence screening test. Lancet Digital Health 2020, published 11 December. Full-text:

The early clinical course of COVID-19 can be difficult to distinguish from other illnesses driving presentation to hospital and PCR testing can take up to 72 h. Here, David Clifton, Andrew Soltan and colleagues from Radcliffe, Oxford, trained linear and non-linear machine learning classifiers to distinguish patients with COVID-19 from pre-pandemic controls. Their models excluded COVID-19 with high-confidence by use of clinical data routinely available within 1 h of presentation to hospital. The authors suggest that their approach could be rapidly scalable, fitting within the existing laboratory testing infrastructure and standard of care of hospitals in high-income and middle-income countries.

Figure. Receiver operating characteristic curves (A) and relative importance of features (B) for the ED and admissions models



Kalil A, Patterson TF, Mehta AK, et al. Baricitinib plus Remdesivir for Hospitalized Adults with Covid-19. N Engl J Med 2020, published 11 December. Full-text:

Baricitinib plus remdesivir was superior to remdesivir alone in reducing recovery time and accelerating improvement in clinical status among hospitalized adults with COVID-19, notably among those receiving high-flow oxygen or noninvasive ventilation. This is the result of double-blind, randomized, placebo-controlled trial involving 1033 patients. The 216 patients receiving high-flow oxygen or noninvasive ventilation at enrollment had a time to recovery of 10 days with combination treatment (n=103) and 18 days with control (n=103) (rate ratio for recovery, 1.51; 95% CI, 1.10 to 2.08). The 28-day mortality was 5.1% in the combination group and 7.8% in the control group (hazard ratio for death, 0.65; 95% CI, 0.39 to 1.09). We still need better drugs.

Figure 2. Kaplan–Meier Estimates of Cumulative Recoveries. | Cumulative recovery estimates are shown in the overall population (Panel A), in patients with a baseline score of 4 on the ordinal scale… | Continue reading at


An EUA for Bamlanivimab—A Monoclonal Antibody for COVID-19. JAMA 2020, puublished 11 December. Full-text:

JAMA published a Medical Letter about the investigational neutralizing IgG1 monoclonal antibody bamlanivimab (LY-CoV555; Lilly) which has been granted an FDA Emergency Use Authorization (EUA) for treatment of recently diagnosed mild to moderate COVID-19 in patients who are ≥12 years old, weigh at least 40 kg, and are at high risk for progressing to severe disease and/or hospitalization. See also the FDA fact sheet of bamlanivimab at



Bhaskaran K, Rentsch CT, MacKenna B, et al. HIV infection and COVID-19 death: a population-based cohort analysis of UK primary care data and linked national death registrations within the OpenSAFELY platform. Lancet HIV 2020, published 11 December. Full-text:

Should people with HIV in the UK be at increased risk of COVID-19 mortality? This would be the suggestion of a retrospective cohort study by Ben Goldacre, Krishnan Bhaskaran and colleagues who analyzed the data of 17 282 905 adults, of whom 27 480 (0·16%) had HIV recorded. 14,882 COVID-19 deaths occurred during the study period, with 25 among people with HIV. People living with HIV had higher risk of COVID-19 death than those without HIV after adjusting for age and sex: hazard ratio (HR) 2·90 (95% CI 1·96–4·30; p<0·0001). In a comment, Laura Waters and  Anton Pozniak urge for caution in interpretating the results of this study. (Waters LJ, Pozniak AL. COVID-19 death in people with HIV: interpret cautiously. Lancet HIV 2020, published 11 December. Full-text: They emphasize a low absolute mortality of less than 0·1% and recall that 23 (92%) of 25 people with HIV who died had comorbidities.



O’Leary ST, Trefren L, Roth H, et al. Number of Childhood and Adolescent Vaccinations Administered Before and After the COVID-19 Outbreak in Colorado. JAMA Pediatr 2020, published 7 December. Full-text:

As a consequence of the social distancing measures, medical visits to primary care physicians have dropped, including preventive visits and scheduled vaccinations.  In Colorado, after March 15 (weeks 12-18), the mean immunization rate dropped 31% for individuals aged 0 to 2 years, 78% for those aged 3 to 9 years, and 82% for those aged 10 to 17 years.

Figure 1.  Interrupted Time Series Analysis for Total Vaccine Doses Administered, January 5 Through May 2, 2020, by Age Group. Find the corresponding figures for individuals aged 3 to 9 years and aged 10 to 17 years at


Beyond Corona

Marshall M. How the first life on Earth survived its biggest threat — water. Nature 2020, published 9 December. Full-text:

Living things depend on water, but it breaks down DNA and other key molecules. So how did the earliest cells deal with the water paradox? In this News Feature, Michael Marshall goes back to the beginning of life. Listen also to the Nature podcast at 00:46: A shallow start to life on Earth? | It’s long been thought that life on Earth first appeared in the oceans. However, the chemical complexities involved in creating biopolymers in water has led some scientists to speculate that shallow pools on land were actually the most likely location for early life.

NASA’s Perseverance rover will search for signs of life in Jezero Crater on Mars.Credit: ESA/FU-Berlin



If you read Spanish, read Limón R. ¿Por qué los niños contagian menos, se infectan menos y sufren menos la covid? El País 2020, published 11 December. Full-text:

Las investigaciones señalan a una respuesta más rápida y eficaz del sistema inmune como causa de la menor incidencia de la pandemia entre los menores



If you read French, read Dagorn G. Ce que l’on sait de la sûreté des vaccins à ARN messager. Le Monde 2020, published 11 December. Full-text :

Bien qu’étudiés depuis longtemps, les vaccins à ARN ont atteint une maturité technique plutôt récente, ce qui soulève craintes et questionnements.



If you read German, read Feldenkirchen M. Todesfalle Glühweinstand. Der Spiegel 2020, published 12 December. Full-text:

Die deutsche Politik hat einen neuen Pandemietreiber ausfindig gemacht. Erst der Karneval, dann Kirchenchöre, Fetischpartys oder Großhochzeiten im migrantischen Milieu. Jetzt kommt der Glühweinstand. In der Not trinkt der Deutsche Glühwein.


Copy-editor: Rob Camp


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