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By Christian Hoffmann &
Bernd S. Kamps
31 August
Epidemiology
Westhaus S, Weber FA, Schiwy S, et al. Detection of SARS-CoV-2 in raw and treated wastewater in Germany – Suitability for COVID-19 surveillance and potential transmission risks. Sci Total Environ 2020 August 18;751:141750. PubMed: https://pubmed.gov/32861187. Full-text: https://doi.org/10.1016/j.scitotenv.2020.141750
Detailed Analysis of a set of samples from nine wastewater treatment plants in North Rhine-Westphalia, Germany. Main conclusions: Yes, SARS-CoV-2 can be detected in wastewater in Germany using RT-qPCR. The total load of gene equivalents in wastewater correlated with the cumulative and the acute number of COVID-19 cases reported in the respective catchment areas. Thus, wastewater-based epidemiology can be regarded as a complementary measure to survey the outbreak. Note – negative tests for replication potential indicate that wastewater might be no major route for transmission to humans.
Graham NSN, Junghans C, McLaren R, et al. High rates of SARS-CoV-2 seropositivity in nursing home residents. J Infection August 26, 2020. Full-text: https://doi.org/10.1016/j.jinf.2020.08.040
What incredibly high infection rates in nursing homes! During March – April 2020 the authors investigated outbreaks in four UK nursing homes where 40% of 394 residents tested positive on RT-PCR. Now they demonstrate that COVID-19 infection was considerably more widespread. Seventy-two percent of nursing home residents (95% CI 66 – 77) were anti-SARS-CoV-2 IgG antibody positive, representing 173 of 241 residents available and consenting to testing. This included 93% of those tested who were previously RT-PCR positive and 59% of those who were previously RT-PCR negative. Seropositivity was not associated with the presence of comorbidities.
Fouillet A, Pontais I, Caserio-Schönemann C. Excess all-cause mortality during the first wave of the COVID-19 epidemic in France, March to May 2020. Eurosurveillance 2020;25(34. Full-text: https://doi.org/10.2807/1560-7917.ES.2020.25.34.2001485
Through a weekly all-cause mortality surveillance system in France, the authors observed a major all-cause excess mortality from March to May 2020 (25,030 deaths, mainly among elderly people). Five metropolitan regions were the most affected, particularly the Île-de-France and the Grand-Est regions. However, assessing the excess mortality related to COVID-19 is complex because of the potential protective effect of the lockdown period on other causes of mortality.
Virology
O’Leary VB, Ovsepian SV. Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Trends in Genetics. Published August 26, 2020. Full-text: https://doi.org/10.1016/j.tig.2020.08.014
Brief review of the genome of SARS-CoV-2. Valerie Bríd O’Leary and Saak Victor Ovsepian also provide a fun fact you should know before you die: The SARS-CoV-2 non-structural protein 3 has a 46% similarity to a protein also found in a ray-finned fish Labrus bergylta (Ballan wrasse), a protogynous hermaphrodite, that begins life as a female yet with territorial dominance becomes male. If you are tempted to try CoV-2-protein: wrasses have firm meat and taste excellent.
Sardar R, Satish D, Birla S. Integrative analyses of SARS-CoV-2 genomes from different geographical locations reveal unique features potentially consequential to host-virus interaction, pathogenesis and clues for novel therapies. Heliyon August 20, 2020. Full-text: https://doi.org/10.1016/j.heliyon.2020.e04658
Integrative analysis of SARS-CoV-2 genome sequences from different countries, confirming unique features absent in other evolutionarily related coronavirus family genomes, which presumably confer unique infection, transmission and virulence capabilities to the virus. This work explores the functional impact of the virus mutations on its proteins and interaction of its genes with host antiviral mechanisms.
Prevention
Sauceda JA, Neilands TB, Lightfoot M, Saberi P. Findings from a probability-based survey of U.S. households about prevention measures based on race, ethnicity, and age in response to SARS-CoV-2. J Infect Dis. 2020 Aug 29:jiaa554. PubMed: https://pubmed.gov/32860499. Full-text: https://doi.org/10.1093/infdis/jiaa554
This survey in a “nationally-representative” sample of 2,029 US adults revealed that all groups engaged in the same prevention behaviors, but Whites reported being more likely to use digital tools to report/act on symptoms and seek testing, versus African Americans and Latinos. Individual behaviors may not explain COVID-19 case disparities, and digital tools for tracking should be focus on uptake among racial/ethnic minorities.
Diagnostics
Weiss S, Klingler J, Hioe C, et al. A High Through-Put Assay For Circulating Antibodies Directed Against The S Protein Of Severe Acute Respiratory Syndrome Coronavirus 2 (Sars-Cov-2). J Infect Dis. 2020 Aug 29:jiaa531. PubMed: https://pubmed.gov/32860510. Full-text: https://doi.org/10.1093/infdis/jiaa531
Svenja Weiss and colleagues developed a Luminex binding assay to assess simultaneously the presence of COVID-19-specific antibodies in human serum and plasma. Clear differentiation was achieved between specimens from infected and uninfected subjects, and a wide range of serum/plasma antibody levels were delineated in infected subjects. Since the Luminex Ab assay can simultaneously test qualitatively and quantitatively for RBD and S protein Abs and can be performed in < 2.5 hours with 5 – 10 ng of antigen per test, it provides a platform that will result in cost savings and the processing of large numbers of samples per day.
Clinical
Boulle A, Davies MA, Hussey H, et al. Risk factors for COVID-19 death in a population cohort study from the Western Cape Province, South Africa. Clin Infect Dis. 2020 Aug 29:ciaa1198. PubMed: https://pubmed.gov/32860699. Full-text: https://doi.org/10.1093/cid/ciaa1198
The by far longest co-author list of the day. Around 300 researchers were needed to evaluate risk factors among 3,460,932 patients (16% HIV+) in South Africa. In total, 22,308 were diagnosed with COVID-19, of whom 625 died. COVID-19 death was associated with male sex, increasing age, diabetes, hypertension and chronic kidney disease. HIV and current tuberculosis were independently associated with increased COVID-19 mortality. Adjusted hazard ratio for mortality was 2.14 for HIV (95% CI 1.70-2.70), with similar risks across strata of viral load and immunosuppression. Current and previous tuberculosis were also associated with COVID-19 death (aHRs 2.70 and 1.51).
White PL, Dhillon R, Cordey A, et al. A national strategy to diagnose COVID-19 associated invasive fungal disease in the ICU. Clin Infect Dis. 2020 Aug 29:ciaa1298. PubMed: https://pubmed.gov/32860682. Full-text: https://doi.org/10.1093/cid/ciaa1298
P Lewis White and colleagues from Wales have screened 135 patients admitted to Welsh ICUs with COVID-19 infection for invasive fungal co-infection. The incidence was 26.7% (14.1% aspergillosis, 12.6% yeast infections). The overall mortality rate was 53% and 31% in patients with and without fungal disease, respectively. The use of corticosteroids and history of chronic respiratory disease increased the likelihood of aspergillosis. The authors conclude that screening using a strategic diagnostic approach and antifungal prophylaxis of patients with risk factors will likely enhance the management of COVID-19 patients.
Comorbidities
Piñana JL, Xhaard A, Tridello G, et al. Seasonal human coronaviruses respiratory tract infection in recipients of allogeneic hematopoietic stem cell transplantation. J Infect Dis. 2020 Aug 29:jiaa553. PubMed: https://pubmed.gov/32860509. Full-text: https://doi.org/10.1093/infdis/jiaa553
In this retrospective multicenter study, which included 402 allo-HCT recipients (adults and children) with upper and/or lower respiratory tract disease (RTD) caused by seasonal HCoV diagnosed through multiplex PCR assays 2012-2019, a significant morbidity was found. HCoV infection frequently required hospitalization (18%), oxygen administration (13%) and ICU admission (3%). Three-month overall mortality after HCoV detection was 7% in the full cohort and 16% in those with lower RTD. Three conditions were identified with higher mortality in recipients with lower RTD: low absolute lymphocyte counts, corticosteroids and, not suprisingly, ICU admission.