Corona peer reviewed artikelen +datavisualisatie & statistieken topic

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The temporal association of introducing and lifting non-pharmaceutical interventions with the time-varying reproduction number (R) of SARS-CoV-2: a modelling study across 131 countries

Research in context
Evidence before this study
The time-varying reproduction number (R; also known as Rt), defined by the expected number of secondary cases arising from a primary case infected at time t, is a metric that describes viral transmission at the population level. An R value above 1 indicates a growing outbreak, and an R value below 1 indicates a shrinking outbreak. We searched PubMed, medRxiv, and bioRxiv for studies that reported the effects of introducing and lifting non-pharmaceutical interventions (NPIs) on R of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) published between Jan 1 and Aug 5, 2020, using the keywords “COVID-19”, “SARS-CoV-2”, “intervention”, and “transmission”. No language restriction was applied. Studies in China, Hong Kong, South Korea, Singapore, and many European countries showed that several NPIs, including school closure, physical distancing, and lockdown, could reduce R substantially to near or below 1. However, little is known about the effects on R following the relaxation of these NPIs.
Added value of this study
To the best of our knowledge, this study is the first to explicitly quantify the effects of both introducing and lifting individual NPIs on R over time. By linking a global dataset of country-level daily R values with a global dataset of country-level policies on NPIs, we modelled the change in R values (as R ratio) from day 1 to day 28 following the introduction and relaxation of eight individual NPIs among 131 countries. We found that reopening schools, lifting bans on public events, lifting bans on public gatherings of more than ten people, lifting requirements to stay at home, and lifting internal movement limits were associated with an increase in R of 11–25% on day 28 following the relaxation. However, the effects of introducing and lifting NPIs were not immediate; it took a median of 8 days (IQR 6–9) following the introduction of NPIs to observe 60% of their maximum reduction in R and even longer (17 days [14–20]) following the relaxation to observe 60% of the maximum increase in R. A similar delay in response to the introduction and relaxation of NPIs was also identified using Google mobility data. We compared four different candidates of composite NPIs that countries might consider in response to a possible resurgence of COVID-19.
Implications of all the available evidence
We quantified the change in transmission of SARS-CoV-2, as measured by R, following the introduction and relaxation of individual NPIs, and found a delay of 1–3 weeks in observing the effects of introducing and lifting these NPIs. These findings provide additional evidence that can inform policy-maker decisions on which NPIs to introduce or lift and when to expect a notable effect following the introduction or the relaxation.

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Genomic evidence for reinfection with SARS-CoV-2: a case study
Summary
Background
The degree of protective immunity conferred by infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is currently unknown. As such, the possibility of reinfection with SARS-CoV-2 is not well understood. We describe an investigation of two instances of SARS-CoV-2 infection in the same individual.
Methods
A 25-year-old man who was a resident of Washoe County in the US state of Nevada presented to health authorities on two occasions with symptoms of viral infection, once at a community testing event in April, 2020, and a second time to primary care then hospital at the end of May and beginning of June, 2020. Nasopharyngeal swabs were obtained from the patient at each presentation and twice during follow-up. Nucleic acid amplification testing was done to confirm SARS-CoV-2 infection. We did next-generation sequencing of SARS-CoV-2 extracted from nasopharyngeal swabs. Sequence data were assessed by two different bioinformatic methodologies. A short tandem repeat marker was used for fragment analysis to confirm that samples from both infections came from the same individual.
Findings
The patient had two positive tests for SARS-CoV-2, the first on April 18, 2020, and the second on June 5, 2020, separated by two negative tests done during follow-up in May, 2020. Genomic analysis of SARS-CoV-2 showed genetically significant differences between each variant associated with each instance of infection. The second infection was symptomatically more severe than the first.
Interpretation
Genetic discordance of the two SARS-CoV-2 specimens was greater than could be accounted for by short-term in vivo evolution. These findings suggest that the patient was infected by SARS-CoV-2 on two separate occasions by a genetically distinct virus. Thus, previous exposure to SARS-CoV-2 might not guarantee total immunity in all cases. All individuals, whether previously diagnosed with COVID-19 or not, should take identical precautions to avoid infection with SARS-CoV-2. The implications of reinfections could be relevant for vaccine development and application.

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The major genetic risk factor for severe COVID-19 is inherited from Neanderthals

Abstract

A recent genetic association study1 identified a gene cluster on chromosome 3 as a risk locus for respiratory failure after infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). A separate study (COVID-19 Host Genetics Initiative)2 comprising 3,199 hospitalized patients with coronavirus disease 2019 (COVID-19) and control individuals showed that this cluster is the major genetic risk factor for severe symptoms after SARS-CoV-2 infection and hospitalization. Here we show that the risk is conferred by a genomic segment of around 50 kilobases in size that is inherited from Neanderthals and is carried by around 50% of people in south Asia and around 16% of people in Europe.

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Dexamethasone in hospitalised patients with COVID-19: addressing uncertainties

The impressive results of the RECOVERY trial established that a moderate dose of dexamethasone (6 mg daily for 10 days) reduced mortality in hospitalised patients with COVID-19 and respiratory failure who required therapy with supplemental oxygen or mechanical ventilation.
The data also indicated that dexamethasone might increase mortality in hospitalised patients who were not receiving oxygen. This landmark trial and the subsequent practice guidelines from several academic and health organisations recommending dexamethasone use in patients with severe COVID-19 have changed clinical practice for hospitalised patients on supplemental oxygen or mechanical ventilation
These favourable findings are supported by three other trialsof glucocorticoids for COVID-19, which stopped enrolment in early June, 2020, when the RECOVERY trial results were released. Each of these trials showed some evidence of benefit, although none had completed enrolment. A prospective meta-analysis of these and other trials, totalling 1703 participants (1007 [59%] from the RECOVERY trial), confirmed a reduction in 28-day mortality (summary odds ratio [OR] 0·66, 95% CI 0·53–0·82; p<0·001), with minimal heterogeneity across studies.6
While confirming beneficial effects of corticosteroids for critically ill hospitalised patients with COVID-19, some unanswered questions and issues remain that deserve discussion and should be addressed in future research.

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Early Hydroxychloroquine but not Chloroquine use reduces ICU admission in COVID-19 patients

Highlights

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After the global push for the use of Hydroxychloroquine and Chloroquine there is ongoing discussion about the effectivity of these drugs.
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Findings of this observational study provide crucial data on a potential protective effect of Hydroxychloroquine in non-ICU, hospitalized COVID-19 patients.
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Early treatment with HCQ on the first day of admission is associated with a reduced risk of 53% in transfer to the ICU for mechanical ventilation.
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This protective effect was not observed for Chloroquine, therefore these drugs cannot be regarded as interchangeable.

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Op maandag 2 november 2020 20:05 schreef Discombobulate het volgende:

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Nou, dat werd tijd na die hele media hetze tegen hydroxychloroquine. Het ging velen die voor HCQ waren namelijk om het zo vroeg mogelijk toedienen ervan, maar daar was tot voor kort weinig onderzoek naar gedaan.

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Race, Ethnicity, and Age Trends in Persons Who Died from COVID-19 — United States, May–August 2020

Summary

What is already known about this topic?

Persons aged ≥65 years and members of minority racial and ethnic groups are disproportionately represented among COVID-19–associated deaths.

What is added by this report?

Analysis of 114,411 COVID-19–associated deaths reported to National Vital Statistics System during May–August 2020, found that 51.3% of decedents were non-Hispanic White, 24.2% were Hispanic or Latino (Hispanic), and 18.7% were non-Hispanic Black. The percentage of Hispanic decedents increased from 16.3% in May to 26.4% in August.

What are the implications for public health practice?

These results can inform public health messaging and mitigation efforts focused on prevention and early detection of infection among disproportionately affected groups so as to minimize subsequent mortality.

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Physical distancing, face masks, and eye protection to prevent person-to-person transmission of SARS-CoV-2 and COVID-19: a systematic review and meta-analysis

Background

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes COVID-19 and is spread person-to-person through close contact. We aimed to investigate the effects of physical distance, face masks, and eye protection on virus transmission in health-care and non-health-care (eg, community) settings.
Methods

We did a systematic review and meta-analysis to investigate the optimum distance for avoiding person-to-person virus transmission and to assess the use of face masks and eye protection to prevent transmission of viruses. We obtained data for SARS-CoV-2 and the betacoronaviruses that cause severe acute respiratory syndrome, and Middle East respiratory syndrome from 21 standard WHO-specific and COVID-19-specific sources. We searched these data sources from database inception to May 3, 2020, with no restriction by language, for comparative studies and for contextual factors of acceptability, feasibility, resource use, and equity. We screened records, extracted data, and assessed risk of bias in duplicate. We did frequentist and Bayesian meta-analyses and random-effects meta-regressions. We rated the certainty of evidence according to Cochrane methods and the GRADE approach. This study is registered with PROSPERO, CRD42020177047.

Findings

Our search identified 172 observational studies across 16 countries and six continents, with no randomised controlled trials and 44 relevant comparative studies in health-care and non-health-care settings (n=25 697 patients). Transmission of viruses was lower with physical distancing of 1 m or more, compared with a distance of less than 1 m (n=10 736, pooled adjusted odds ratio [aOR] 0·18, 95% CI 0·09 to 0·38; risk difference [RD] −10·2%, 95% CI −11·5 to −7·5; moderate certainty); protection was increased as distance was lengthened (change in relative risk [RR] 2·02 per m; pinteraction=0·041; moderate certainty). Face mask use could result in a large reduction in risk of infection (n=2647; aOR 0·15, 95% CI 0·07 to 0·34, RD −14·3%, −15·9 to −10·7; low certainty), with stronger associations with N95 or similar respirators compared with disposable surgical masks or similar (eg, reusable 12–16-layer cotton masks; pinteraction=0·090; posterior probability >95%, low certainty). Eye protection also was associated with less infection (n=3713; aOR 0·22, 95% CI 0·12 to 0·39, RD −10·6%, 95% CI −12·5 to −7·7; low certainty). Unadjusted studies and subgroup and sensitivity analyses showed similar findings.

Interpretation

The findings of this systematic review and meta-analysis support physical distancing of 1 m or more and provide quantitative estimates for models and contact tracing to inform policy. Optimum use of face masks, respirators, and eye protection in public and health-care settings should be informed by these findings and contextual factors. Robust randomised trials are needed to better inform the evidence for these interventions, but this systematic appraisal of currently best available evidence might inform interim guidance.

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Bidirectional associations between COVID-19 and psychiatric disorder: retrospective cohort studies of 62 354 COVID-19 cases in the USA

Background
Adverse mental health consequences of COVID-19, including anxiety and depression, have been widely predicted but not yet accurately measured. There are a range of physical health risk factors for COVID-19, but it is not known if there are also psychiatric risk factors. In this electronic health record network cohort study using data from 69 million individuals, 62 354 of whom had a diagnosis of COVID-19, we assessed whether a diagnosis of COVID-19 (compared with other health events) was associated with increased rates of subsequent psychiatric diagnoses, and whether patients with a history of psychiatric illness are at a higher risk of being diagnosed with COVID-19.

Methods
We used the TriNetX Analytics Network, a global federated network that captures anonymised data from electronic health records in 54 health-care organisations in the USA, totalling 69·8 million patients. TriNetX included 62 354 patients diagnosed with COVID-19 between Jan 20, and Aug 1, 2020. We created cohorts of patients who had been diagnosed with COVID-19 or a range of other health events. We used propensity score matching to control for confounding by risk factors for COVID-19 and for severity of illness. We measured the incidence of and hazard ratios (HRs) for psychiatric disorders, dementia, and insomnia, during the first 14 to 90 days after a diagnosis of COVID-19.

Findings
In patients with no previous psychiatric history, a diagnosis of COVID-19 was associated with increased incidence of a first psychiatric diagnosis in the following 14 to 90 days compared with six other health events (HR 2·1, 95% CI 1·8–2·5 vs influenza; 1·7, 1·5–1·9 vs other respiratory tract infections; 1·6, 1·4–1·9 vs skin infection; 1·6, 1·3–1·9 vs cholelithiasis; 2·2, 1·9–2·6 vs urolithiasis, and 2·1, 1·9–2·5 vs fracture of a large bone; all p<0·0001). The HR was greatest for anxiety disorders, insomnia, and dementia. We observed similar findings, although with smaller HRs, when relapses and new diagnoses were measured. The incidence of any psychiatric diagnosis in the 14 to 90 days after COVID-19 diagnosis was 18·1% (95% CI 17·6–18·6), including 5·8% (5·2–6·4) that were a first diagnosis. The incidence of a first diagnosis of dementia in the 14 to 90 days after COVID-19 diagnosis was 1·6% (95% CI 1·2–2·1) in people older than 65 years. A psychiatric diagnosis in the previous year was associated with a higher incidence of COVID-19 diagnosis (relative risk 1·65, 95% CI 1·59–1·71; p<0·0001). This risk was independent of known physical health risk factors for COVID-19, but we cannot exclude possible residual confounding by socioeconomic factors.
Interpretation
Survivors of COVID-19 appear to be at increased risk of psychiatric sequelae, and a psychiatric diagnosis might be an independent risk factor for COVID-19. Although preliminary, our findings have implications for clinical services, and prospective cohort studies are warranted.

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Age-specific mortality and immunity patterns of SARS-CoV-2

Estimating the size and infection severity of the SARS-CoV-2 epidemic is made challenging by inconsistencies in available data. The number of COVID-19 deaths is often used as a key indicator for the epidemic size, but observed deaths represent only a minority of all infections1,2. Additionally, the heterogeneous burden in nursing homes and variable reporting of deaths in elderly individuals can hamper direct comparisons across countries of the underlying level of transmission and mortality rates3. Here we use age-specific COVID-19 death data from 45 countries and the results of 22 seroprevalence studies to investigate the consistency of infection and fatality patterns across multiple countries. We find that the age distribution of deaths in younger age groups (<65 years) is very consistent across different settings and demonstrate how this data can provide robust estimates of the share of the population that has been infected. We estimate that the infection-to-fatality ratio (IFR) is lowest among 5-9 years old, with a log-linear increase by age among individuals older than 30 years. Population age-structures and heterogeneous burdens in nursing homes explain some but not all of the heterogeneity between countries in infection-fatality ratios. Among the 45 countries included in our analysis, we estimate approximately 5% of these populations had been infected by the 1st of September 2020, with much higher transmission likely to have occurred in a number of Latin American countries. This simple modelling framework can help countries assess the progression of the pandemic and can be applied wherever reliable age-specific death data exists.

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Mobility network models of COVID-19 explain inequities and inform reopening

The COVID-19 pandemic dramatically changed human mobility patterns, necessitating epidemiological models which capture the effects of changes in mobility on virus spread1. We introduce a metapopulation SEIR model that integrates fine-grained, dynamic mobility networks to simulate the spread of SARS-CoV-2 in 10 of the largest US metropolitan statistical areas. Derived from cell phone data, our mobility networks map the hourly movements of 98 million people from neighborhoods (census block groups, or CBGs) to points of interest (POIs) such as restaurants and religious establishments, connecting 57k CBGs to 553k POIs with 5.4 billion hourly edges. We show that by integrating these networks, a relatively simple SEIR model can accurately fit the real case trajectory, despite substantial changes in population behavior over time. Our model predicts that a small minority of “superspreader” POIs account for a large majority of infections and that restricting maximum occupancy at each POI is more effective than uniformly reducing mobility. Our model also correctly predicts higher infection rates among disadvantaged racial and socioeconomic groups2–8 solely from differences in mobility: we find that disadvantaged groups have not been able to reduce mobility as sharply, and that the POIs they visit are more crowded and therefore higher-risk. By capturing who is infected at which locations, our model supports detailed analyses that can inform more effective and equitable policy responses to COVID-19.

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The 40 health systems, COVID-19 (40HS, C-19) study

Background

The health, social and economic consequences of the severe acute respiratory syndrome coronavirus (SARS-CoV-2, henceforth COVID-19) pandemic have loomed large as every national government made decisions about how to respond. The 40 Health Systems, COVID-19 (40HS, C-19) study aimed to investigate relationships between governments’ capacity to respond (CTR), their response stringency, scope of COVID-19 testing and COVID-19 outcomes.

Methods

Data over March and April 2020 were extracted for 40 national health systems on prepandemic government CTR (Global Competitiveness Index), stringency measures (Oxford COVID-19 Government Response Tracker Stringency Index), approach to COVID-19 testing and COVID-19 cases and deaths (Our-World-in-Data). Multidimensional scaling (MDS) and cluster analysis were applied to examine latent dimensions and visualize country similarities and dissimilarities. Outcomes were tested using multivariate and one-way analyses of variances and Kruskal–Wallis H tests.

Results

The MDS model found three dimensions explaining 91% of the variance and cluster analysis identified five national groupings. There was no association between national governments’ prepandemic CTR and the adoption of early stringent public health measures or approach to COVID-19 testing. Two national clusters applied early stringency measures and reported significantly lower cumulative deaths. The best performing national cluster (comprising Australia, South Korea, Iceland and Taiwan) adopted relatively early stringency measures but broader testing earlier than others, which was associated with a change in disease trajectory and the lowest COVID-19 death rates. Two clusters (one with high CTR and one low) both adopted late stringency measures and narrow testing and performed least well in COVID-19 outcomes.

Conclusion

Early stringency measures and intrinsic national capacities to deal with a pandemic are insufficient. Extended stringency measures, important in the short term, are not economically sustainable. Broad-based testing is key to managing COVID-19.

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Transmission of SARS-CoV-2 on mink farms between humans and mink and back to humans

Abstract

Animal experiments have shown that non-human primates, cats, ferrets, hamsters, rabbits and bats can be infected by SARS-CoV-2. In addition, SARS-CoV-2 RNA has been detected in felids, mink and dogs in the field. Here, we describe an in-depth investigation using whole genome sequencing of outbreaks on 16 mink farms and the humans living or working on these farms. We conclude that the virus was initially introduced from humans and has since evolved, most likely reflecting widespread circulation among mink in the beginning of the infection period several weeks prior to detection. Despite enhanced biosecurity, early warning surveillance and immediate culling of infected farms, transmission occurred between mink farms in three big transmission clusters with unknown modes of transmission. Sixty-eight percent (68%) of the tested mink farm residents, employees and/or contacts had evidence of SARS-CoV-2 infection. Where whole genomes were available, these persons were infected with strains with an animal sequence signature, providing evidence of animal to human transmission of SARS-CoV-2 within mink farms.

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Persistence and Evolution of SARS-CoV-2 in an Immunocompromised Host

The coronavirus can mutate swiftly in one person’s body

The new coronavirus resurged again and again in the body of an infected man, eventually killing him while showing evidence of fast-paced evolution.

Manuela Cernadas and Jonathan Li at Brigham and Women’s Hospital in Boston, Massachusetts, and their colleagues followed the course of COVID-19 in a 45-year-old man with a long-standing autoimmune disorder, who was on a medication regimen that included powerful immunosuppressants (B. Choi et al. N. Engl. J. Med. https://doi.org/fhv8; 2020). Roughly 40 days after the man first tested positive for SARS-CoV-2, follow-up tests indicated that the virus was dwindling — but it surged back, despite antiviral treatment.

The man’s infection subsided and then returned twice more before he died, five months after his first COVID-19 diagnosis. Genomic analysis showed that the man had not been infected multiple times. Instead, the virus had lingered and quickly mutated in his body.

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Ranking the effectiveness of worldwide COVID-19 government interventions

Assessing the effectiveness of non-pharmaceutical interventions (NPIs) to mitigate the spread of SARS-CoV-2 is critical to inform future preparedness response plans. Here we quantify the impact of 6,068 hierarchically coded NPIs implemented in 79 territories on the effective reproduction number, Rt, of COVID-19. We propose a modelling approach that combines four computational techniques merging statistical, inference and artificial intelligence tools. We validate our findings with two external datasets recording 42,151 additional NPIs from 226 countries. Our results indicate that a suitable combination of NPIs is necessary to curb the spread of the virus. Less disruptive and costly NPIs can be as effective as more intrusive, drastic, ones (for example, a national lockdown). Using country-specific ‘what-if’ scenarios, we assess how the effectiveness of NPIs depends on the local context such as timing of their adoption, opening the way for forecasting the effectiveness of future interventions

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Immunological memory to SARS-CoV-2 assessed for greater than six months after infection

Abstract

Understanding immune memory to SARS-CoV-2 is critical for improving diagnostics and vaccines, and for assessing the likely future course of the pandemic. We analyzed multiple compartments of circulating immune memory to SARS-CoV-2 in 185 COVID-19 cases, including 41 cases at > 6 months post-infection. Spike IgG was relatively stable over 6+ months. Spike-specific memory B cells were more abundant at 6 months than at 1 month. SARS-CoV-2-specific CD4+ T cells and CD8+ T cells declined with a half-life of 3-5 months. By studying antibody, memory B cell, CD4+ T cell, and CD8+ T cell memory to SARS-CoV-2 in an integrated manner, we observed that each component of SARS-CoV-2 immune memory exhibited distinct kinetics.
Competing Interest Statement

A.S. is a consultant for Gritstone, Flow Pharma, Merck, Epitogenesis, Gilead and Avalia. S.C. is a consultant for Avalia. LJI has filed for patent protection for various aspects of T cell epitope and vaccine design work. Mount Sinai has licensed serological assays to commercial entities and has filed for patent protection for serological assays. D.S., F.A., V.S. and F.K. are listed as inventors on the pending patent application (F.K., V.S.), and Newcastle disease virus (NDV)-based SARS-CoV-2 vaccines that name F.K. as inventor. All other authors declare no conflict of interest.

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Op donderdag 19 november 2020 10:53 schreef George_of_the_Jungle het volgende:
https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(20)32466-1/fulltext
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En een press release over dezelfde studie: https://covid19vaccinetrial.co.uk/phase-ii-trial-publication

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Antibodies to SARS-CoV-2 are associated with protection against reinfection

Background It is critical to understand whether infection with Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) protects from subsequent reinfection. Methods We investigated the incidence of SARS-CoV-2 PCR-positive results in seropositive and seronegative healthcare workers (HCWs) attending asymptomatic and symptomatic staff testing at Oxford University Hospitals, UK. Baseline antibody status was determined using anti-spike and/or anti-nucleocapsid IgG assays and staff followed for up to 30 weeks. We used Poisson regression to estimate the relative incidence of PCR-positive results and new symptomatic infection by antibody status, accounting for age, gender and changes in incidence over time. Results A total of 12219 HCWs participated and had anti-spike IgG measured, 11052 were followed up after negative and 1246 after positive antibody results including 79 who seroconverted during follow up. 89 PCR-confirmed symptomatic infections occurred in seronegative individuals (0.46 cases per 10,000 days at risk) and no symptomatic infections in those with anti-spike antibodies. Additionally, 76 (0.40/10,000 days at risk) anti-spike IgG seronegative individuals had PCR-positive tests in asymptomatic screening, compared to 3 (0.21/10,000 days at risk) seropositive individuals. Overall, positive baseline anti-spike antibodies were associated with lower rates of PCR-positivity (with or without symptoms) (adjusted rate ratio 0.24 [95%CI 0.08-0.76, p=0.015]). Rate ratios were similar using anti-nucleocapsid IgG alone or combined with anti-spike IgG to determine baseline status. Conclusions Prior SARS-CoV-2 infection that generated antibody responses offered protection from reinfection for most people in the six months following infection. Further work is required to determine the long-term duration and correlates of post-infection immunity.

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The effect of temperature and humidity on the stability of SARS-CoV-2 and other enveloped viruses

Abstract

Understanding the impact of environmental conditions on virus viability and transmission potential is crucial to anticipating epidemic dynamics and designing mitigation strategies. Ambient temperature and humidity are known to have strong effects on the environmental stability of viruses, but a general quantitative understanding of how temperature and humidity affect virus stability has remained elusive. We characterize the stability of SARS-CoV-2 on an inert surface at a variety of temperature and humidity conditions, and introduce a mechanistic model that enables accurate prediction of virus stability in unobserved conditions. We find that SARS-CoV-2 survives better at low temperatures and extreme relative humidities; median estimated virus half-life was more than 24 hours at 10 °C and 40 % RH, but approximately an hour and a half at 27 °C and 65 % RH. Moreover, our model predicts observations from other human coronaviruses and other studies of SARS-CoV-2, suggesting the existence of shared mechanisms that determine environmental stability across a number of enveloped viruses. Our results highlight scenarios of particular transmission risk and point to broad strategies for pandemic mitigation, while opening new frontiers for the mechanistic study of viral transmission.

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No evidence for increased transmissibility from recurrent mutations in SARS-CoV-2

COVID-19 is caused by the coronavirus SARS-CoV-2, which jumped into the human population in late 2019 from a currently uncharacterised animal reservoir. Due to this recent association with humans, SARS-CoV-2 may not yet be fully adapted to its human host. This has led to speculations that SARS-CoV-2 may be evolving towards higher transmissibility. The most plausible mutations under putative natural selection are those which have emerged repeatedly and independently (homoplasies). Here, we formally test whether any homoplasies observed in SARS-CoV-2 to date are significantly associated with increased viral transmission. To do so, we develop a phylogenetic index to quantify the relative number of descendants in sister clades with and without a specific allele. We apply this index to a curated set of recurrent mutations identified within a dataset of 46,723 SARS-CoV-2 genomes isolated from patients worldwide. We do not identify a single recurrent mutation in this set convincingly associated with increased viral transmission. Instead, recurrent mutations currently in circulation appear to be evolutionary neutral and primarily induced by the human immune system via RNA editing, rather than being signatures of adaptation. At this stage we find no evidence for significantly more transmissible lineages of SARS-CoV-2 due to recurrent mutations.

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Effectiveness of face masks for the population

Background: Health authorities and organizations consider non-medical face masks as an additional passive means to prevent virus diffusion. Communication strategies disseminate information among the population that such masks are essential for mitigating virus diffusion. However, scientific studies are not conclusive in showing the undisputed filtration efficiency of fabric/cloth facial masks (both commercial and homemade).

Objectives: This study examines scientific data about the effectiveness of face masks before and during the COVID-19 emergency. Present trends in the making of commercial and homemade fabric/cloth face masks are also examined.

Methods: Statistical data of published studies are analyzed and compared. Main considerations and suggestions are also extracted and discussed. Current approaches are examined for assessing the characteristics and effectiveness of fabric/cloth commercial and homemade face masks intended for the population.

Result: Conflicting data exist as to whether non-medical masks have a protective effect from the spread of respiratory viruses. Both medical masks (MDs) and respiratory personal protection equipment (PPE) show a given effectiveness value.

Conclusion: Concerning commercial and homemade fabric/cloth masks, giving general indications on the choice of materials and their assemblage is difficult as it is not possible to assess the effectiveness of the filter media with respect to the kind of multiphase fluid that may be emitted upon breathing, sneezing, or coughing under different environmental conditions. This is particularly important because airflow rate, temperature, humidity, and duration of use will affect the performance of filter media. Moreover, while a mask may have excellent filter media, droplets may leak into the face-piece unless there is an adequate facial seal. In the presence of leaks, any type of mask may actually offer less protection independently of its nominal filtering effìciency.

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Model-based evaluation of school- and non-school-related measures to control the COVID-19 pandemic


Background In autumn 2020, many countries, including the Netherlands, are experiencing a second wave of the COVID-19 pandemic. Health policymakers are struggling with choosing the right mix of measures to keep the COVID-19 case numbers under control, but still allow a minimum of social and economic activity. The priority to keep schools open is high, but the role of school-based contacts in the epidemiology of SARS-CoV-2 is incompletely understood. We used a transmission model to estimate the impact of school contacts on transmission of SARS-CoV-2 and to assess the effects of school-based measures, including school closure, on controlling the pandemic at different time points during the pandemic.

Methods and Findings The age-structured model was fitted to age-specific seroprevalence and hospital admission data from the Netherlands during spring 2020. Compared to adults older than 60 years, the estimated susceptibility was 23% (95%CrI 20—28%) for children aged 0 to 20 years and 61% (95%CrI 50%—72%) for the age group of 20 to 60 years. The time points considered in the analyses were August 2020 when the effective reproduction number (Re) was estimated to be 1.31 (95%CrI 1.15—2.07), schools just opened after the summer holidays and measures were reinforced with the aim to reduce Re to a value below 1, and (ii) November 2020 when measures had reduced Re to 1.00 (95%CrI 0.94—1.33). In this period schools remained open. Our model predicts that keeping schools closed after the summer holidays, in the absence of other measures, would have reduced Re by 10% (from 1.31 to 1.18 (95%CrI 1.04—1.83)) and thus would not have prevented the second wave in autumn 2020. Reducing non-school-based contacts in August 2020 to the level observed during the first wave of the pandemic would have reduced Re to 0.83 (95%CrI 0.75—1.10). Yet, this reduction was not achieved and the observed Re in November was 1.00. Our model predicts that closing schools in November 2020 could reduce Re from the observed value of 1.00 to 0.84 (95%CrI 0.81—0.90), with unchanged non-school based contacts. Reductions in Re due to closing schools in November 2020 were 8% for 10 to 20 years old children, 5% for 5 to 10 years old children and negligible for 0 to 5 years old children.

Conclusions The impact of measures reducing school-based contacts, including school closure, depends on the remaining opportunities to reduce non-school-based contacts. If opportunities to reduce Re with non-school-based measures are exhausted or undesired and Re is still close to 1, the additional benefit of school-based measures may be considerable, particularly among the older school children

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Exclusive: Kids catch and spread coronavirus half as much as adults, Iceland study confirms

Big decisions around COVID-19 and children have been heavy on politics and short on science. New large-scale studies are changing that.

“They can and do get infected and transmit to others, but they do both less frequently than adults,” says Kári Stefánsson, the chief executive of deCODE.

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Evidence of Long-Distance Droplet Transmission of SARS-CoV-2 by Direct Air Flow in a Restaurant in Korea

Abstract

Background

The transmission mode of severe acute respiratory syndrome coronavirus 2 is primarily known as droplet transmission. However, a recent argument has emerged about the possibility of airborne transmission. On June 17, there was a coronavirus disease 2019 (COVID-19) outbreak in Korea associated with long distance droplet transmission.

Methods

The epidemiological investigation was implemented based on personal interviews and data collection on closed-circuit television images, and cell phone location data. The epidemic investigation support system developed by the Korea Disease Control and Prevention Agency was used for contact tracing. At the restaurant considered the site of exposure, air flow direction and velocity, distances between cases, and movement of visitors were investigated.

Results

A total of 3 cases were identified in this outbreak, and maximum air flow velocity of 1.2 m/s was measured between the infector and infectee in a restaurant equipped with ceiling-type air conditioners. The index case was infected at a 6.5 m away from the infector and 5 minutes exposure without any direct or indirect contact.

Conclusion

Droplet transmission can occur at a distance greater than 2 m if there is direct air flow from an infected person. Therefore, updated guidelines involving prevention, contact tracing, and quarantine for COVID-19 are required for control of this highly contagious disease.

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Inferring the effectiveness of government interventions against COVID-19

Abstract

Governments are attempting to control the COVID-19 pandemic with nonpharmaceutical interventions (NPIs). However, the effectiveness of different NPIs at reducing transmission is poorly understood. We gathered chronological data on the implementation of NPIs for several European, and other, countries between January and the end of May 2020. We estimate the effectiveness of NPIs, ranging from limiting gathering sizes, business closures, and closure of educational institutions to stay-at-home orders. To do so, we used a Bayesian hierarchical model that links NPI implementation dates to national case and death counts and supported the results with extensive empirical validation. Closing all educational institutions, limiting gatherings to 10 people or less, and closing face-to-face businesses each reduced transmission considerably. The additional effect of stay-at-home orders was comparatively small.

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Infectivity of asymptomatic versus symptomatic COVID-19

Negative 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% CI2·06–7·19; p<0·0001; appendix).

Our findings suggest that people with asymptomatic COVID-19 are infectious but might be less infectious than symptomatic cases. We also identified that the proportion of close contacts who became infected did not depend on the serology status of the index case. One reason for this observation could be that close contacts tend to live or work with the index case and are exposed because of their regular contact with a person who was infectious before turning seropositive.

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High rate of persistent symptoms up to 4 months after community and hospital-managed SARS-CoV-2 infection

Recovery after severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection remains uncertain. A considerable proportion of patients experience persistent symptoms after SARS-CoV-2 infection which impacts health-related quality of life and physical function. Multi-disciplinary follow-up is recommended for patients with post-COVID illness and to assess health-related quality of life and physical function.

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Antibody Status and Incidence of SARS-CoV-2 Infection in Health Care Workers

Background

The relationship between the presence of antibodies to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the risk of subsequent reinfection remains unclear.

Methods

We investigated the incidence of SARS-CoV-2 infection confirmed by polymerase chain reaction (PCR) in seropositive and seronegative health care workers attending testing of asymptomatic and symptomatic staff at Oxford University Hospitals in the United Kingdom. Baseline antibody status was determined by anti-spike (primary analysis) and anti-nucleocapsid IgG assays, and staff members were followed for up to 31 weeks. We estimated the relative incidence of PCR-positive test results and new symptomatic infection according to antibody status, adjusting for age, participant-reported gender, and changes in incidence over time.

Results

A total of 12,541 health care workers participated and had anti-spike IgG measured; 11,364 were followed up after negative antibody results and 1265 after positive results, including 88 in whom seroconversion occurred during follow-up. A total of 223 anti-spike–seronegative health care workers had a positive PCR test (1.09 per 10,000 days at risk), 100 during screening while they were asymptomatic and 123 while symptomatic, whereas 2 anti-spike–seropositive health care workers had a positive PCR test (0.13 per 10,000 days at risk), and both workers were asymptomatic when tested (adjusted incidence rate ratio, 0.11; 95% confidence interval, 0.03 to 0.44; P=0.002). There were no symptomatic infections in workers with anti-spike antibodies. Rate ratios were similar when the anti-nucleocapsid IgG assay was used alone or in combination with the anti-spike IgG assay to determine baseline status.

Conclusions

The presence of anti-spike or anti-nucleocapsid IgG antibodies was associated with a substantially reduced risk of SARS-CoV-2 reinfection in the ensuing 6 months. (Funded by the U.K. Government Department of Health and Social Care and others.)