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Real-time monitoring shows substantial excess all-cause mortality during second wave of COVID-19 in Europe, October to December 2020
Sarah K. Nørgaard , Lasse S. Vestergaard , Jens Nielsen , Lukas Richter , Daniela Schmid , Natalia Bustos , Toon Braye , Maria Athanasiadou , Theodore Lytras , Gleb Denissov , Tatjana Veideman , Oskari Luomala , Teemu Möttönen , Anne Fouillet , Céline Caserio-Schönemann , Matthias an der Heiden , Helmut Uphoff , Kassiani Gkolfinopoulou , Janos Bobvos , Anna Paldy , Naama Rotem , Irene Kornilenko , Lisa Domegan , Joan O’Donnell , Francesca De Donato , Matteo Scortichini , Patrick Hoffmann , Telma Velez , Kathleen England , Neville Calleja , Liselotte van Asten , Lenny Stoeldraijer , Richard A White , Trine H Paulsen , Susana P da Silva , Ana P Rodrigues , Petra Klepac , Metka Zaletel , Mario Fafangel , Amparo Larrauri , Inmaculada León , Ahmed Farah , Ilias Galanis , Christoph Junker , Damir Perisa , Mary Sinnathamby , Nick Andrews , Mark G O'Doherty , David Irwin , Sharon Kennedy , Jim McMenamin , Cornelia Adlhoch , Nick Bundle , Pasi Penttinen , Jukka Pukkila , Richard Pebody , Tyra G Krause and Kåre MølbakThe European monitoring of excess mortality for public health action (EuroMOMO) network monitors weekly excess all-cause mortality in 27 European countries or subnational areas. During the first wave of the coronavirus disease (COVID-19) pandemic in Europe in spring 2020, several countries experienced extraordinarily high levels of excess mortality. Europe is currently seeing another upsurge in COVID-19 cases, and EuroMOMO is again witnessing a substantial excess all-cause mortality attributable to COVID-19.
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Control of a COVID-19 outbreak in a nursing home by general screening and cohort isolation in Germany, March to May 2020
More LessElderly care facilities have become a major focus of coronavirus disease (COVID-19) control. Here, we describe an outbreak of COVID-19 in a nursing home in Germany from 8 March to 4 May 2020 (58 days), and the effect of an intervention of general screening and cohort isolation. COVID-19 cases among residents and staff were recorded on a daily basis from the first positive SARS-CoV-2 test from a resident on 8 March 2020, until 4 May 2020 when the last staff member was classified COVID-19 negative. Eighty of 160 residents (50%) and 37 of 135 staff members (27%) tested positive for SARS-CoV-2. Twenty-seven of the 80 residents were asymptomatic but tested positive during the first general screening. Cohort isolation of SARS-CoV-2 positive residents by reorganising the facility proved to be a major effort. After the intervention, four further asymptomatic residents tested positive in follow-up screenings within a period of 6 days, and were possibly infected prior to the intervention. Thereafter, no further infections were recorded among residents. The described outbreak was controlled by implementing general screening and rigorous cohort isolation, providing a blueprint for similar facilities.
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Early transmissibility assessment of the N501Y mutant strains of SARS-CoV-2 in the United Kingdom, October to November 2020
More LessTwo new SARS-CoV-2 lineages with the N501Y mutation in the receptor-binding domain of the spike protein spread rapidly in the United Kingdom. We estimated that the earlier 501Y lineage without amino acid deletion Δ69/Δ70, circulating mainly between early September and mid-November, was 10% (6–13%) more transmissible than the 501N lineage, and the 501Y lineage with amino acid deletion Δ69/Δ70, circulating since late September, was 75% (70–80%) more transmissible than the 501N lineage.
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Impact of mass testing during an epidemic rebound of SARS-CoV-2: a modelling study using the example of France
We used a mathematical model to evaluate the impact of mass testing in the control of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Under optimistic assumptions, one round of mass testing may reduce daily infections by up to 20–30%. Consequently, very frequent testing would be required to control a quickly growing epidemic if other control measures were to be relaxed. Mass testing is most relevant when epidemic growth remains limited through a combination of interventions.
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Minimal transmission of SARS-CoV-2 from paediatric COVID-19 cases in primary schools, Norway, August to November 2020
An intense debate on school closures to control the COVID-19 pandemic is ongoing in Europe. We prospectively examined transmission of SARS-CoV-2 from confirmed paediatric cases in Norwegian primary schools between August and November 2020. All in-school contacts were systematically tested twice during their quarantine period. With preventive measures implemented in schools, we found minimal child-to-child (0.9%, 2/234) and child-to-adult (1.7%, 1/58) transmission, supporting that under 14 year olds are not the drivers of SARS-CoV-2 transmission.
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Early assessment of the impact of mitigation measures to control COVID-19 in 22 French metropolitan areas, October to November 2020
Guillaume Spaccaferri , Sophie Larrieu , Jérôme Pouey , Clémentine Calba , Thomas Benet , Cécile Sommen , Daniel Lévy-Bruhl , Sabira Smaili , Didier Che , Laurent Filleul , Céline Caserio-Schönemann , Fatima Ait-El-Belghiti , Sylvie Haeghebaert , Jean-Claude Desenclos , Laëtitia Huiart , Anne Laporte and Patrick RollandIn France, measures including curfew and lockdown were implemented to control the COVID-19 pandemic second wave in 2020. This study descriptively assesses their possible effects, also relative to their timing. A considerable decrease in incidence of COVID-19 cases and hospital admissions was observed 7 to 10 days after mitigation measures were put in place, occurring earlier in metropolitan areas which had implemented these first. This temporal coincidence suggests the measures’ positive impact, consistent with international experiences.
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Estimating the false-negative test probability of SARS-CoV-2 by RT-PCR
More LessBackgroundReverse-transcription PCR (RT-PCR) assays are used to test for infection with the SARS-CoV-2 virus. RT-PCR tests are highly specific and the probability of false positives is low, but false negatives are possible depending on swab type and time since symptom onset.
AimTo determine how the probability of obtaining a false-negative test in infected patients is affected by time since symptom onset and swab type.
MethodsWe used generalised additive mixed models to analyse publicly available data from patients who received multiple RT-PCR tests and were identified as SARS-CoV-2 positive at least once.
ResultsThe probability of a positive test decreased with time since symptom onset, with oropharyngeal (OP) samples less likely to yield a positive result than nasopharyngeal (NP) samples. The probability of incorrectly identifying an uninfected individual due to a false-negative test was considerably reduced if negative tests were repeated 24 hours later. For a small false-positive test probability (<0.5%), the true number of infected individuals was larger than the number of positive tests. For a higher false-positive test probability, the true number of infected individuals was smaller than the number of positive tests.
ConclusionNP samples are more sensitive than OP samples. The later an infected individual is tested after symptom onset, the less likely they are to test positive. This has implications for identifying infected patients, contact tracing and discharging convalescing patients who are potentially still infectious.
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Evaluation of lockdown effect on SARS-CoV-2 dynamics through viral genome quantification in waste water, Greater Paris, France, 5 March to 23 April 2020
S Wurtzer , V Marechal , JM Mouchel , Y Maday , R Teyssou , E Richard , JL Almayrac and L MoulinIntroductionSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiological agent of coronavirus disease (COVID-19). People infected with SARS-CoV-2 may exhibit no or mild non-specific symptoms; thus, they may contribute to silent circulation of the virus among humans. Since SARS-CoV-2 RNA can be detected in stool samples, monitoring SARS-CoV-2 RNA in waste water (WW) has been proposed as a complementary tool to investigate virus circulation in human populations.
AimTo test if the quantification of SARS-CoV-2 genomes in WW correlates with the number of symptomatic or non-symptomatic carriers.
MethodWe performed a time-course quantitative analysis of SARS-CoV-2 by RT-qPCR in raw WW samples collected from several major WW treatment plants in Greater Paris. The study period was 5 March to 23 April 2020, including the lockdown period in France (from 17 March).
ResultsWe showed that the increase of genome units in raw WW accurately followed the increase of human COVID-19 cases observed at the regional level. Of note, the viral genome could be detected before the epidemic grew massively (around 8 March). Equally importantly, a marked decrease in the quantities of genome units was observed concomitantly with the reduction in the number of new COVID-19 cases, 29 days following the lockdown.
ConclusionThis work suggests that a quantitative monitoring of SARS-CoV-2 genomes in WW could generate important additional information for improved monitoring of SARS-CoV-2 circulation at local or regional levels and emphasises the role of WW-based epidemiology.
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Occupation- and age-associated risk of SARS-CoV-2 test positivity, the Netherlands, June to October 2020
High coronavirus incidence has prompted the Netherlands to implement a second lockdown. To elucidate the epidemic’s development preceding this second wave, we analysed weekly test positivity in public test locations by population subgroup between 1 June and 17 October 2020. Hospitality and public transport workers, driving instructors, hairdressers and aestheticians had higher test positivity compared with a reference group of individuals without a close-contact occupation. Workers in childcare, education and healthcare showed lower test positivity.
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The first wave of the COVID-19 pandemic in Spain: characterisation of cases and risk factors for severe outcomes, as at 27 April 2020
More LessBackgroundThe first wave of the coronavirus disease (COVID-19) pandemic spread rapidly in Spain, one of Europe’s most affected countries. A national lockdown was implemented on 15 March 2020.
AimTo describe reported cases and the impact of national lockdown, and to identify disease severity risk factors.
MethodsNational surveillance data were used to describe PCR-confirmed cases as at 27 April 2020. We compared case characteristics by severity categories (hospitalisation, admission to intensive care unit (ICU), death) and identified severity risk factors using multivariable regression.
ResultsThe epidemic peaked on 20 March. Of 218,652 COVID-19 cases, 45.4% were hospitalised, 4.6% were admitted to ICU and 11.9% died. Among those who died, 94.8% had at least one underlying disease. Healthcare workers (HCWs) represented 22.9% of cases. Males were more likely to have severe outcomes than females. Cardiovascular disease was a consistent risk factor. Patients with pneumonia had higher odds of hospitalisation (odds ratio (OR): 26.63; 95% confidence interval (CI): 25.03–28.33). The strongest predictor of death was age ≥ 80 years (OR: 28.4; 95% CI: 19.85–40.78). Among underlying diseases, chronic renal disease had highest odds of death (OR: 1.47; 95% CI: 1.29–1.68).
ConclusionsCOVID-19 case numbers began declining 6 days after the national lockdown. The first wave of the COVID-19 pandemic in Spain had a severe impact on elderly people. Patients with cardiovascular or renal conditions were at higher risk for severe outcomes. A high proportion of cases were HCWs. Enhanced surveillance and control measures in these subgroups are crucial during future COVID-19 waves.
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Community use of face masks and similar barriers to prevent respiratory illness such as COVID-19: a rapid scoping review
More LessBackgroundEvidence for face-mask wearing in the community to protect against respiratory disease is unclear.
AimTo assess effectiveness of wearing face masks in the community to prevent respiratory disease, and recommend improvements to this evidence base.
MethodsWe systematically searched Scopus, Embase and MEDLINE for studies evaluating respiratory disease incidence after face-mask wearing (or not). Narrative synthesis and random-effects meta-analysis of attack rates for primary and secondary prevention were performed, subgrouped by design, setting, face barrier type, and who wore the mask. Preferred outcome was influenza-like illness. Grading of Recommendations, Assessment, Development and Evaluations (GRADE) quality assessment was undertaken and evidence base deficits described.
Results33 studies (12 randomised control trials (RCTs)) were included. Mask wearing reduced primary infection by 6% (odds ratio (OR): 0.94; 95% CI: 0.75–1.19 for RCTs) to 61% (OR: 0.85; 95% CI: 0.32–2.27; OR: 0.39; 95% CI: 0.18–0.84 and OR: 0.61; 95% CI: 0.45–0.85 for cohort, case–control and cross-sectional studies respectively). RCTs suggested lowest secondary attack rates when both well and ill household members wore masks (OR: 0.81; 95% CI: 0.48–1.37). While RCTs might underestimate effects due to poor compliance and controls wearing masks, observational studies likely overestimate effects, as mask wearing might be associated with other risk-averse behaviours. GRADE was low or very low quality.
ConclusionWearing face masks may reduce primary respiratory infection risk, probably by 6–15%. It is important to balance evidence from RCTs and observational studies when their conclusions widely differ and both are at risk of significant bias. COVID-19-specific studies are required.
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Epidemiological characteristics of COVID-19 cases and estimates of the reproductive numbers 1 month into the epidemic, Italy, 28 January to 31 March 2020
Flavia Riccardo , Marco Ajelli , Xanthi D Andrianou , Antonino Bella , Martina Del Manso , Massimo Fabiani , Stefania Bellino , Stefano Boros , Alberto Mateo Urdiales , Valentina Marziano , Maria Cristina Rota , Antonietta Filia , Fortunato D'Ancona , Andrea Siddu , Ornella Punzo , Filippo Trentini , Giorgio Guzzetta , Piero Poletti , Paola Stefanelli , Maria Rita Castrucci , Alessandra Ciervo , Corrado Di Benedetto , Marco Tallon , Andrea Piccioli , Silvio Brusaferro , Giovanni Rezza , Stefano Merler , Patrizio Pezzotti and the COVID-19 working groupBackgroundOn 20 February 2020, a locally acquired coronavirus disease (COVID-19) case was detected in Lombardy, Italy. This was the first signal of ongoing transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the country. The number of cases in Italy increased rapidly and the country became the first in Europe to experience a SARS-CoV-2 outbreak.
AimOur aim was to describe the epidemiology and transmission dynamics of the first COVID-19 cases in Italy amid ongoing control measures.
MethodsWe analysed all RT-PCR-confirmed COVID-19 cases reported to the national integrated surveillance system until 31 March 2020. We provide a descriptive epidemiological summary and estimate the basic and net reproductive numbers by region.
ResultsOf the 98,716 cases of COVID-19 analysed, 9,512 were healthcare workers. Of the 10,943 reported COVID-19-associated deaths (crude case fatality ratio: 11.1%) 49.5% occurred in cases older than 80 years. Male sex and age were independent risk factors for COVID-19 death. Estimates of R0 varied between 2.50 (95% confidence interval (CI): 2.18–2.83) in Tuscany and 3.00 (95% CI: 2.68–3.33) in Lazio. The net reproduction number Rt in northern regions started decreasing immediately after the first detection.
ConclusionThe COVID-19 outbreak in Italy showed a clustering onset similar to the one in Wuhan, China. R0 at 2.96 in Lombardy combined with delayed detection explains the high case load and rapid geographical spread. Overall, Rt in Italian regions showed early signs of decrease, with large diversity in incidence, supporting the importance of combined non-pharmacological control measures.
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Clinical characteristics and risk factors associated with severe COVID-19: prospective analysis of 1,045 hospitalised cases in North-Eastern France, March 2020
Charlotte Kaeuffer , Coralie Le Hyaric , Thibaut Fabacher , Joy Mootien , Benjamin Dervieux , Yvon Ruch , Antonin Hugerot , Yves-Jean Zhu , Valentin Pointurier , Raphael Clere-Jehl , Valentin Greigert , Loic Kassegne , Nicolas Lefebvre , Floriane Gallais , Covid Alsace Study Group , Nicolas Meyer , Yves Hansmann , Olivier Hinschberger and François DanionBackgroundIn March 2020, the COVID-19 outbreak was declared a pandemic by the World Health Organization.
AimOur objective was to identify risk factors predictive of severe disease and death in France.
MethodsIn this prospective cohort study, we included patients ≥ 18 years old with confirmed COVID-19, hospitalised in Strasbourg and Mulhouse hospitals (France), in March 2020. We respectively compared patients who developed severe disease (admission to an intensive care unit (ICU) or death) and patients who died, to those who did not, by day 7 after hospitalisation.
ResultsAmong 1,045 patients, 424 (41%) had severe disease, including 335 (32%) who were admitted to ICU, and 115 (11%) who died. Mean age was 66 years (range: 20–100), and 612 (59%) were men. Almost 75% of patients with body mass index (BMI) data (n = 897) had a BMI ≥ 25 kg/m2 (n = 661). Independent risk factors associated with severe disease were advanced age (odds ratio (OR): 1.1 per 10-year increase; 95% CrI (credible interval): 1.0–1.2), male sex (OR: 2.1; 95% CrI: 1.5–2.8), BMI of 25–29.9 kg/m2 (OR: 1.8; 95% CrI: 1.2–2.7) or ≥ 30 (OR: 2.2; 95% CrI: 1.5–3.3), dyspnoea (OR: 2.5; 95% CrI: 1.8–3.4) and inflammatory parameters (elevated C-reactive protein and neutrophil count, low lymphocyte count). Risk factors associated with death were advanced age (OR: 2.7 per 10-year increase; 95% CrI: 2.1–3.4), male sex (OR: 1.7; 95% CrI: 1.1–2.7), immunosuppression (OR: 3.8; 95% CrI: 1.6–7.7), diabetes (OR: 1.7; 95% CrI: 1.0–2.7), chronic kidney disease (OR: 2.3; 95% CrI: 1.3–3.9), dyspnoea (OR: 2.1; 95% CrI: 1.2–3.4) and inflammatory parameters.
ConclusionsOverweightedness, obesity, advanced age, male sex, comorbidities, dyspnoea and inflammation are risk factors for severe COVID-19 or death in hospitalised patients. Identifying these features among patients in routine clinical practice might improve COVID-19 management.
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Epidemiology and public health response in early phase of COVID-19 pandemic, Veneto Region, Italy, 21 February to 2 April 2020
BackgroundVeneto was one of the Italian regions hit hardest by the early phase of the coronavirus disease (COVID-19) pandemic.
AimThis paper describes the public health response and epidemiology of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections in the Veneto Region from 21 February to 2 April 2020.
MethodsInformation on the public health response was collected from regional health authorities’ official sources. Epidemiological data were extracted from a web-based regional surveillance system. The epidemic curve was represented by date of testing. Characteristics of hospitalised COVID-19 cases were described and compared to those never admitted to hospital. Age- and sex-stratified case-fatality ratios (CFRs) were calculated.
ResultsKey elements of the regional public health response were thorough case-finding and contact tracing, home care for non-severe cases, creation of dedicated COVID-19 healthcare facilities and activation of sub-intensive care units for non-invasive ventilation. As at 2 April 2020, 91,345 individuals were tested for SARS-CoV-2 and 10,457 (11.4%) were positive. Testing and attack rates were 18.6 per 1,000 and 213.2 per 100,000 population, respectively. The epidemic peaked around 20 to 24 March, with case numbers declining thereafter. Hospitalised cases (n = 3,623; 34.6%) were older and more frequently male compared with never-hospitalised cases. The CFR was 5.6% overall, and was higher among males and people > 60 years of age.
ConclusionIn the Veneto Region, the strict social distancing measures imposed by the Italian government were supported by thorough case finding and contact tracing, as well as well-defined roles for different levels of care.
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Impact of the COVID-19 pandemic on testing services for HIV, viral hepatitis and sexually transmitted infections in the WHO European Region, March to August 2020
We present preliminary results of a coronavirus disease (COVID-19) impact assessment on testing for HIV, viral hepatitis and sexually transmitted infections in the WHO European Region. We analyse 98 responses from secondary care (n = 36), community testing sites (n = 52) and national level (n = 10). Compared to pre-COVID-19, 95% of respondents report decreased testing volumes during March–May and 58% during June–August 2020. Reasons for decreases and mitigation measures were analysed.
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Serology- and PCR-based cumulative incidence of SARS-CoV-2 infection in adults in a successfully contained early hotspot (CoMoLo study), Germany, May to June 2020
Claudia Santos-Hövener , Hannelore K Neuhauser , Angelika Schaffrath Rosario , Markus Busch , Martin Schlaud , Robert Hoffmann , Antje Gößwald , Carmen Koschollek , Jens Hoebel , Jennifer Allen , Antje Haack-Erdmann , Stefan Brockmann , Thomas Ziese , Andreas Nitsche , Janine Michel , Sebastian Haller , Hendrik Wilking , Osamah Hamouda , Victor M Corman , Christian Drosten , Lars Schaade , Lothar H Wieler , CoMoLo Study Group and Thomas LampertThree months after a coronavirus disease (COVID-19) outbreak in Kupferzell, Germany, a population-based study (n = 2,203) found no RT-PCR-positives. IgG-ELISA seropositivity with positive virus neutralisation tests was 7.7% (95% confidence interval (CI): 6.5–9.1) and 4.3% with negative neutralisation tests. We estimate 12.0% (95% CI: 10.4–14.0%) infected adults (24.5% asymptomatic), six times more than notified. Full hotspot containment confirms the effectiveness of prompt protection measures. However, 88% naïve adults are still at high COVID-19 risk.
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Where has all the influenza gone? The impact of COVID-19 on the circulation of influenza and other respiratory viruses, Australia, March to September 2020
The coronavirus disease pandemic was declared in March 2020, as the southern hemisphere’s winter approached. Australia expected co-circulation of severe acute respiratory syndrome coronavirus 2, influenza and other seasonal respiratory viruses. However, influenza notifications were 7,029 (March–September) compared with an average 149,832 for the same period in 2015–2109, despite substantial testing. Restrictions on movement within and into Australia may have temporarily eliminated influenza. Other respiratory pathogens also showed remarkably changed activity in 2020.
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Virological surveillance of influenza viruses in the WHO European Region in 2019/20 – impact of the COVID-19 pandemic
The COVID-19 pandemic negatively impacted the 2019/20 WHO European Region influenza surveillance. Compared with previous 4-year averages, antigenic and genetic characterisations decreased by 17% (3,140 vs 2,601) and 24% (4,474 vs 3,403). Of subtyped influenza A viruses, 56% (26,477/47,357) were A(H1)pdm09, 44% (20,880/47,357) A(H3). Of characterised B viruses, 98% (4,585/4,679) were B/Victoria. Considerable numbers of viruses antigenically differed from northern hemisphere vaccine components. In 2020/21, maintaining influenza virological surveillance, while supporting SARS-CoV-2 surveillance is crucial.
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Convalescent plasma for COVID-19: male gender, older age and hospitalisation associated with high neutralising antibody levels, England, 22 April to 12 May 2020
More LessWe analysed factors associated with neutralising antibody levels in 330 convalescent plasma donors. Women and younger donors were more likely not to have measurable neutralising antibodies, while higher antibody levels were observed in men, in older donors and in those who had been hospitalised. These data will be of value in the timely recruitment of convalescent plasma donors most likely to have high levels of neutralising antibodies for ongoing studies investigating its effectiveness.
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Epidemiological parameters of COVID-19 and its implication for infectivity among patients in China, 1 January to 11 February 2020
Qing-Bin Lu , Yong Zhang , Ming-Jin Liu , Hai-Yang Zhang , Neda Jalali , An-Ran Zhang , Jia-Chen Li , Han Zhao , Qian-Qian Song , Tian-Shuo Zhao , Jing Zhao , Han-Yu Liu , Juan Du , Ai-Ying Teng , Zi-Wei Zhou , Shi-Xia Zhou , Tian-Le Che , Tao Wang , Tong Yang , Xiu-Gang Guan , Xue-Fang Peng , Yu-Na Wang , Yuan-Yuan Zhang , Shou-Ming Lv , Bao-Cheng Liu , Wen-Qiang Shi , Xiao-Ai Zhang , Xiao-Gang Duan , Wei Liu , Yang Yang and Li-Qun FangBackgroundThe natural history of disease in patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) remained obscure during the early pandemic.
AimOur objective was to estimate epidemiological parameters of coronavirus disease (COVID-19) and assess the relative infectivity of the incubation period.
MethodsWe estimated the distributions of four epidemiological parameters of SARS-CoV-2 transmission using a large database of COVID-19 cases and potential transmission pairs of cases, and assessed their heterogeneity by demographics, epidemic phase and geographical region. We further calculated the time of peak infectivity and quantified the proportion of secondary infections during the incubation period.
ResultsThe median incubation period was 7.2 (95% confidence interval (CI): 6.9‒7.5) days. The median serial and generation intervals were similar, 4.7 (95% CI: 4.2‒5.3) and 4.6 (95% CI: 4.2‒5.1) days, respectively. Paediatric cases < 18 years had a longer incubation period than adult age groups (p = 0.007). The median incubation period increased from 4.4 days before 25 January to 11.5 days after 31 January (p < 0.001), whereas the median serial (generation) interval contracted from 5.9 (4.8) days before 25 January to 3.4 (3.7) days after. The median time from symptom onset to discharge was also shortened from 18.3 before 22 January to 14.1 days after. Peak infectivity occurred 1 day before symptom onset on average, and the incubation period accounted for 70% of transmission.
ConclusionThe high infectivity during the incubation period led to short generation and serial intervals, necessitating aggressive control measures such as early case finding and quarantine of close contacts.
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SARS-CoV-2 samples may escape detection because of a single point mutation in the N gene
We found that a single nucleotide polymorphism (SNP) in the nucleoprotein gene of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from a patient interfered with detection in a widely used commercial assay. Some 0.2% of the isolates in the EpiCoV database contain this SNP. Although SARS-CoV-2 was still detected by the other probe in the assay, this underlines the necessity of targeting two independent essential regions of a pathogen for reliable detection.
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Surveillance of COVID-19 school outbreaks, Germany, March to August 2020
More LessMitigation of the coronavirus disease (COVID-19) pandemic in Germany included school closures in early March 2020. After reopening in April, preventive measures were taken in schools. We analysed national surveillance system data on COVID-19 school outbreaks during different time periods. After reopening, smaller outbreaks (average: 2.2/week) occurred despite low incidence in the general population. School closures might have a detrimental effect on children and should be applied only cautiously and in combination with other measures.
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Poor self-reported adherence to COVID-19-related quarantine/isolation requests, Norway, April to July 2020
To limit SARS-CoV-2 spread, quarantine and isolation are obligatory in several situations in Norway. We found low self-reported adherence to requested measures among 1,704 individuals (42%; 95% confidence interval: 37–48). Adherence was lower in May–June–July (33–38%) compared with April (66%), and higher among those experiencing COVID-19-compatible symptoms (71%) compared with those without (28%). These findings suggest that consideration is required of strategies to improve people’s adherence to quarantine and isolation.
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Reduced maximal aerobic capacity after COVID-19 in young adult recruits, Switzerland, May 2020
In March 2020, we observed an outbreak of COVID-19 among a relatively homogenous group of 199 young (median age 21 years; 87% men) Swiss recruits. By comparing physical endurance before and in median 45 days after the outbreak, we found a significant decrease in predicted maximal aerobic capacity in COVID-19 convalescent but not in asymptomatically infected and SARS-CoV-2 naive recruits. This finding might be indicative of lung injury after apparently mild COVID-19 in young adults.
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Transmission of SARS-CoV-2 in children aged 0 to 19 years in childcare facilities and schools after their reopening in May 2020, Baden-Württemberg, Germany
J Ehrhardt , A Ekinci , H Krehl , M Meincke , I Finci , J Klein , B Geisel , C Wagner-Wiening , M Eichner and SO BrockmannWe investigated data from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infected 0–19 year olds, who attended schools/childcare facilities, to assess their role in SARS-CoV-2 transmission after these establishments’ reopening in May 2020 in Baden-Württemberg, Germany. Child-to-child transmission in schools/childcare facilities appeared very uncommon. We anticipate that, with face mask use and frequent ventilation of rooms, transmission rates in schools/childcare facilities would remain low in the next term, even if classes’ group sizes were increased.
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COVID-19 outbreaks in a transmission control scenario: challenges posed by social and leisure activities, and for workers in vulnerable conditions, Spain, early summer 2020
More LessSevere acute respiratory syndrome coronavirus 2 community-wide transmission declined in Spain by early May 2020, being replaced by outbreaks and sporadic cases. From mid-June to 2 August, excluding single household outbreaks, 673 outbreaks were notified nationally, 551 active (>6,200 cases) at the time. More than half of these outbreaks and cases coincided with: (i) social (family/friends’ gatherings or leisure venues) and (ii) occupational (mainly involving workers in vulnerable conditions) settings. Control measures were accordingly applied.
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Excess all-cause mortality during the first wave of the COVID-19 epidemic in France, March to May 2020
More LessThrough a weekly all-cause mortality surveillance system, we observed in France a major all-cause excess mortality from March to May 2020, concomitant with the coronavirus disease (COVID-19) epidemic. The excess mortality was 25,030 deaths, mainly among elderly people. Five metropolitan regions were the most affected, particularly Île-de-France and the Grand-Est regions. 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.
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Three infection clusters related with potential pre-symptomatic transmission of coronavirus disease (COVID-19), Shanghai, China, January to February 2020
Xiaohuan Gong , Wenjia Xiao , Yan Cui , Yuanping Wang , Dechuan Kong , Shenghua Mao , Yaxu Zheng , Lunhui Xiang , Lu Lu , Chenyan Jiang , Xiao Yu , Yiyi Zhu , Qiwen Fang , Hao Pan and Huanyu WuWe report three clusters related with potential pre-symptomatic transmission of coronavirus disease (COVID-19) between January and February 2020 in Shanghai, China. Investigators interviewed suspected COVID-19 cases to collect epidemiological information, including demographic characteristics, illness onset, hospital visits, close contacts, activities’ trajectories between 14 days before illness onset and isolation, and exposure histories. Respiratory specimens of suspected cases were collected and tested for SARS-CoV-2 by real-time reverse-transcriptase polymerase chain reaction (rRT-PCR) assay. The interval between the onset of illness in the primary case and the last contact of the secondary case with the primary case in our report was 1 to 7 days. In Cluster 1 (five cases), illness onset in the five secondary cases was 2 to 5 days after the last contact with the primary case. In Cluster 2 (five cases) and Cluster 3 (four cases), the illness onset in secondary cases occurred prior to or on the same day as the onset in the primary cases. The study provides empirical evidence for transmission of COVID-19 during the incubation period and indicates that pre-symptomatic person-to-person transmission can occur following sufficient exposure to confirmed COVID-19 cases. The potential pre-symptomatic person-to-person transmission puts forward higher requirements for prevention and control measures.
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Duration of infectiousness and correlation with RT-PCR cycle threshold values in cases of COVID-19, England, January to May 2020
Severe acute respiratory syndrome coronavirus 2 viral load in the upper respiratory tract peaks around symptom onset and infectious virus persists for 10 days in mild-to-moderate coronavirus disease (n = 324 samples analysed). RT-PCR cycle threshold (Ct) values correlate strongly with cultivable virus. Probability of culturing virus declines to 8% in samples with Ct > 35 and to 6% 10 days after onset; it is similar in asymptomatic and symptomatic persons. Asymptomatic persons represent a source of transmissible virus.
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Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020
We show the distribution of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) genetic clades over time and between countries and outline potential genomic surveillance objectives. We applied three genomic nomenclature systems to all sequence data from the World Health Organization European Region available until 10 July 2020. We highlight the importance of real-time sequencing and data dissemination in a pandemic situation, compare the nomenclatures and lay a foundation for future European genomic surveillance of SARS-CoV-2.
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Age-specific SARS-CoV-2 infection fatality ratio and associated risk factors, Italy, February to April 2020
We analysed 5,484 close contacts of coronavirus disease (COVID-19) cases in Italy, all tested for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Infection fatality ratio was 0.43% (95% confidence interval (CI): 0.21–0.79) for individuals younger than 70 years and 10.5% (95% CI: 8.0–13.6) for older individuals. Risk of death after infection was 62% lower (95% CI: 31–80) in clusters identified after 16 March 2020 and 1.8-fold higher for males (95% CI: 1.03–3.16).
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Epidemiology of measles during the COVID-19 pandemic, a description of the surveillance data, 29 EU/EEA countries and the United Kingdom, January to May 2020
The number of measles cases declined in European Union/European Economic Area countries and the United Kingdom in 2020. Reported cases to The European Centre for Disease Prevention and Control decreased from 710 to 54 between January and May. Epidemic intelligence screening observed a similar trend. Under-diagnoses and under-reporting during the coronavirus disease (COVID-19) pandemic should be ruled out before concluding reduced measles circulation is because of social distancing and any community control measures taken to control COVID-19.
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Repeated leftover serosurvey of SARS-CoV-2 IgG antibodies, Greece, March and April 2020
Zacharoula Bogogiannidou , Alexandros Vontas , Katerina Dadouli , Maria A Kyritsi , Soteris Soteriades , Dimitrios J Nikoulis , Varvara Α Mouchtouri , Michalis Koureas , Evangelos I Kazakos , Emmanouil G Spanos , Georgia Gioula , Evangelia E Ntzani , Alexandros A Eleftheriou , Alkiviadis Vatopoulos , Efthimia Petinaki , Vassiliki Papaevangelou , Matthaios Speletas , Sotirios Tsiodras and Christos HadjichristodoulouA serosurvey of IgG antibodies against severe acute respiratory coronavirus 2 (SARS-CoV-2) was performed during March and April 2020. Among 6,586 leftover sera, 24 (0.36%) were positive, with higher prevalence in females, older individuals and residents of large urban areas. Seroprevalence was estimated at 0.02% and 0.25%, respectively, in March and April, infection fatality rate at 2.66% and 0.54%. Our findings confirm low COVID-19 incidence in Greece and possibly the effectiveness of early measures.
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Duration of SARS-CoV-2 RNA detection in COVID-19 patients in home isolation, Rhineland-Palatinate, Germany, 2020 – an interval-censored survival analysis
Sarah Omar , Christoph Bartz , Sabine Becker , Silke Basenach , Sandra Pfeifer , Corinna Trapp , Hildegard Hamm , Hans Christoph Schlichting , Magdalena Friederichs , Ulrich Koch , Christian Jestrabek , Ernst Hilger , Manfred Vogt , Klaus Jahn , Simiao Chen , Till Bärnighausen , Philipp Zanger and on behalf of the Palatina Public Health Study GroupWe analysed consecutive RT-qPCR results of 537 symptomatic coronavirus disease (COVID-19) patients in home quarantine. Respectively 2, 3, and 4 weeks after symptom onset, 50%, 25% and 10% of patients had detectable RNA from severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). In patients with mild COVID-19, RNA detection is likely to outlast currently known periods of infectiousness by far and fixed time periods seem more appropriate in determining the length of home isolation than laboratory-based approaches.
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Legionella pneumonia: increased risk after COVID-19 lockdown? Italy, May to June 2020
We report a case of Legionella pneumonia in a dishwasher of a restaurant in Rome, Italy, just after the end of the lockdown that was in place to control the SARS-CoV-2 epidemic. The case highlights the importance of strict monitoring of water and air systems immediately before reopening business or public sector buildings, and the need to consider Legionella infections among the differential diagnosis of respiratory infections after lockdown due to the ongoing COVID-19 pandemic.
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A large COVID-19 outbreak in a high school 10 days after schools’ reopening, Israel, May 2020
On 13 March 2020, Israel’s government declared closure of all schools. Schools fully reopened on 17 May 2020. Ten days later, a major outbreak of coronavirus disease (COVID-19) occurred in a high school. The first case was registered on 26 May, the second on 27 May. They were not epidemiologically linked. Testing of the complete school community revealed 153 students (attack rate: 13.2%) and 25 staff members (attack rate: 16.6%) who were COVID-19 positive.
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All-cause excess mortality observed by age group and regions in the first wave of the COVID-19 pandemic in England
England has experienced one of the highest excess in all-cause mortality in Europe during the current COVID-19 pandemic. As COVID-19 emerged, the excess in all-cause mortality rapidly increased, starting in March 2020. The excess observed during the pandemic was higher than excesses noted in the past 5 years. It concerned all regions and all age groups, except the 0–14 year olds, but was more pronounced in the London region and in those aged ≥ 85 years.
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Convalescent plasma treatment for SARS-CoV-2 infection: analysis of the first 436 donors in England, 22 April to 12 May 2020
Serological reactivity was analysed in plasma from 436 individuals with a history of disease compatible with COVID-19, including 256 who had been laboratory-confirmed with SARS-CoV-2 infection. Over 99% of laboratory-confirmed cases developed a measurable antibody response (254/256) and 88% harboured neutralising antibodies (226/256). Antibody levels declined over 3 months following diagnosis, emphasising the importance of the timing of convalescent plasma collections. Binding antibody measurements can inform selection of convalescent plasma donors with high neutralising antibody levels.
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Monoclonal antibodies for the S2 subunit of spike of SARS-CoV-1 cross-react with the newly-emerged SARS-CoV-2
BackgroundA novel coronavirus, SARS-CoV-2, which emerged at the end of 2019 and causes COVID-19, has resulted in worldwide human infections. While genetically distinct, SARS-CoV-1, the aetiological agent responsible for an outbreak of severe acute respiratory syndrome (SARS) in 2002–2003, utilises the same host cell receptor as SARS-CoV-2 for entry: angiotensin-converting enzyme 2 (ACE2). Parts of the SARS-CoV-1 spike glycoprotein (S protein), which interacts with ACE2, appear conserved in SARS-CoV-2.
AimThe cross-reactivity with SARS-CoV-2 of monoclonal antibodies (mAbs) previously generated against the S protein of SARS-CoV-1 was assessed.
MethodsThe SARS-CoV-2 S protein sequence was aligned to those of SARS-CoV-1, Middle East respiratory syndrome (MERS) and common-cold coronaviruses. Abilities of mAbs generated against SARS-CoV-1 S protein to bind SARS-CoV-2 or its S protein were tested with SARS-CoV-2 infected cells as well as cells expressing either the full length protein or a fragment of its S2 subunit. Quantitative ELISA was also performed to compare binding of mAbs to recombinant S protein.
ResultsAn immunogenic domain in the S2 subunit of SARS-CoV-1 S protein is highly conserved in SARS-CoV-2 but not in MERS and human common-cold coronaviruses. Four murine mAbs raised against this immunogenic fragment could recognise SARS-CoV-2 S protein expressed in mammalian cell lines. In particular, mAb 1A9 was demonstrated to detect S protein in SARS-CoV-2-infected cells and is suitable for use in a sandwich ELISA format.
ConclusionThe cross-reactive mAbs may serve as useful tools for SARS-CoV-2 research and for the development of diagnostic assays for COVID-19.
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