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Minimising school disruption under high incidence conditions due to the Omicron variant in France, Switzerland, Italy, in January 2022
BackgroundAs record cases of Omicron variant were registered in Europe in early 2022, schools remained a vulnerable setting undergoing large disruption.
AimThrough mathematical modelling, we compared school protocols of reactive screening, regular screening, and reactive class closure implemented in France, in Baselland (Switzerland), and in Italy, respectively, and assessed them in terms of case prevention, testing resource demand, and schooldays lost.
MethodsWe used a stochastic agent-based model of SARS-CoV-2 transmission in schools accounting for within- and across-class contacts from empirical contact data. We parameterised it to the Omicron BA.1 variant to reproduce the French Omicron wave in January 2022. We simulated the three protocols to assess their costs and effectiveness for varying peak incidence rates in the range experienced by European countries.
ResultsWe estimated that at the high incidence rates registered in France during the Omicron BA.1 wave in January 2022, the reactive screening protocol applied in France required higher test resources compared with the weekly screening applied in Baselland (0.50 vs 0.45 tests per student-week), but achieved considerably lower control (8% vs 21% reduction of peak incidence). The reactive class closure implemented in Italy was predicted to be very costly, leading to > 20% student-days lost.
ConclusionsAt high incidence conditions, reactive screening protocols generate a large and unplanned demand in testing resources, for marginal control of school transmissions. Comparable or lower resources could be more efficiently used through weekly screening. Our findings can help define incidence levels triggering school protocols and optimise their cost-effectiveness.
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Risk reduction of hospitalisation and severe disease in vaccinated COVID-19 cases during the SARS-CoV-2 variant Omicron BA.1-predominant period, Navarre, Spain, January to March 2022
BackgroundAs COVID-19 vaccine effectiveness against SARS-CoV-2 infection was lower for cases of the Omicron vs the Delta variant, understanding the effect of vaccination in reducing risk of hospitalisation and severe disease among COVID-19 cases is crucial.
AimTo evaluate risk reduction of hospitalisation and severe disease in vaccinated COVID-19 cases during the Omicron BA.1-predominant period in Navarre, Spain.
MethodsA case-to-case comparison included COVID-19 epidemiological surveillance data in adults ≥ 18 years from 3 January–20 March 2022. COVID-19 vaccination status was compared between hospitalised and non-hospitalised cases, and between severe (intensive care unit admission or death) and non-severe cases using logistic regression models.
ResultsAmong 58,952 COVID-19 cases, 565 (1.0%) were hospitalised and 156 (0.3%) were severe. The risk of hospitalisation was reduced within the first 6 months after full COVID-19 vaccination (complete primary series) (adjusted odds ratio (aOR): 0.06; 95% CI: 0.04–0.09) and after 6 months (aOR: 0.16; 95% CI: 0.12–0.21; pcomparison < 0.001), as well as after a booster dose (aOR: 0.06: 95% CI: 0.04–0.07). Similarly, the risk of severe disease was reduced (aOR: 0.13, 0.18, and 0.06, respectively). Compared with cases fully vaccinated 6 months or more before a positive test, those who had received a booster dose had lower risk of hospitalisation (aOR: 0.38; 95% CI: 0.28–0.52) and severe disease (aOR: 0.38; 95% CI: 0.21–0.68).
ConclusionsFull COVID-19 vaccination greatly reduced the risk of hospitalisation and severe outcomes in COVID-19 cases with the Omicron variant, and a booster dose improved this effect in people aged over 65 years.
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Association of SARS-CoV-2 viral load distributions with individual demographics and suspected variant type: results from the Liverpool community testing pilot, England, 6 November 2020 to 8 September 2021
BackgroundThe PCR quantification cycle (Cq) is a proxy measure of the viral load of a SARS-CoV-2-infected individual.
AimTo investigate if Cq values vary according to different population characteristics, in particular demographic ones, and within the COVID-19 pandemic context, notably the SARS-CoV-2 type/variant individuals get infected with.
MethodsWe considered all positive PCR results from Cheshire and Merseyside, England, between 6 November 2020 and 8 September 2021. Cq distributions were inspected with Kernel density estimates. Multivariable quantile regression models assessed associations between people’s features and Cq.
ResultsWe report Cq values for 188,821 SARS-CoV-2 positive individuals. Median Cqs increased with decreasing age for suspected wild-type virus and Alpha variant infections, but less so, if not, for Delta. For example, compared to 30–39-year-olds (median age group), 5–11-year-olds exhibited 1.8 (95% CI: 1.5 to 2.1), 2.2 (95% CI: 1.8 to 2.6) and 0.8 (95% CI: 0.6 to 0.9) higher median Cqs for suspected wild-type, Alpha and Delta positives, respectively, in multivariable analysis. 12–18-year-olds also had higher Cqs for wild-type and Alpha positives, however, not for Delta. Overall, in univariable analysis, suspected Delta positives reported 2.8 lower median Cqs than wild-type positives (95% CI: 2.7 to 2.8; p < 0.001). Suspected Alpha positives had 1.5 (95% CI: 1.4 to 1.5; p < 0.001) lower median Cqs than wild type.
ConclusionsWild-type- or Alpha-infected school-aged children (5–11-year-olds) might transmit less than adults (> 18 years old), but have greater mixing exposures. Smaller differences in viral loads with age occurred in suspected Delta infections. Suspected-Alpha- or Delta-infections involved higher viral loads than wild type, suggesting increased transmission risk. COVID-19 control strategies should consider age and dominant variant.
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Low SARS-CoV-2 Cq values in healthcare workers with symptomatic COVID-19 infections, regardless of symptom severity, The Netherlands, January to August 2022
We analysed SARS-CoV-2 PCR Cq values from 3,183 healthcare workers who tested positive between January and August 2022. Median Cq values were lower in symptomatic than in asymptomatic HCW. The difference in Cq values between HCW with mild vs moderate/severe symptoms was statistically significant but negligibly small. To prevent nosocomial infections, all symptomatic HCW should be tested irrespective of symptom severity. This information can support decisions on testing and isolation, in the context of ongoing pressure on healthcare systems.
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Adverse events following first and second dose COVID-19 vaccination in England, October 2020 to September 2021: a national vaccine surveillance platform self-controlled case series study
Ruby SM Tsang , Mark Joy , Rachel Byford , Chris Robertson , Sneha N Anand , William Hinton , Nikhil Mayor , Debasish Kar , John Williams , William Victor , Ashley Akbari , Declan T Bradley , Siobhan Murphy , Dermot O’Reilly , Rhiannon K Owen , Antony Chuter , Jillian Beggs , Gary Howsam , Aziz Sheikh , FD Richard Hobbs and Simon de LusignanBackgroundPost-authorisation vaccine safety surveillance is well established for reporting common adverse events of interest (AEIs) following influenza vaccines, but not for COVID-19 vaccines.
AimTo estimate the incidence of AEIs presenting to primary care following COVID-19 vaccination in England, and report safety profile differences between vaccine brands.
MethodsWe used a self-controlled case series design to estimate relative incidence (RI) of AEIs reported to the national sentinel network, the Oxford-Royal College of General Practitioners Clinical Informatics Digital Hub. We compared AEIs (overall and by clinical category) 7 days pre- and post-vaccination to background levels between 1 October 2020 and 12 September 2021.
ResultsWithin 7,952,861 records, 781,200 individuals (9.82%) presented to general practice with 1,482,273 AEIs, 4.85% within 7 days post-vaccination. Overall, medically attended AEIs decreased post-vaccination against background levels. There was a 3–7% decrease in incidence within 7 days after both doses of Comirnaty (RI: 0.93; 95% CI: 0.91–0.94 and RI: 0.96; 95% CI: 0.94–0.98, respectively) and Vaxzevria (RI: 0.97; 95% CI: 0.95–0.98). A 20% increase was observed after one dose of Spikevax (RI: 1.20; 95% CI: 1.00–1.44). Fewer AEIs were reported as age increased. Types of AEIs, e.g. increased neurological and psychiatric conditions, varied between brands following two doses of Comirnaty (RI: 1.41; 95% CI: 1.28–1.56) and Vaxzevria (RI: 1.07; 95% CI: 0.97–1.78).
ConclusionCOVID-19 vaccines are associated with a small decrease in medically attended AEI incidence. Sentinel networks could routinely report common AEI rates, contributing to reporting vaccine safety.
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COVID-19 mortality attenuated during widespread Omicron transmission, Denmark, 2020 to 2022
BackgroundIt sparked considerable attention from international media when Denmark lifted restrictions against COVID-19 in February 2022 amidst widespread transmission of the new SARS-CoV-2 Omicron variant and a steep rise in reported COVID-19 mortality based on the 30-day COVID-19 death count.
AimOur aim was to investigate how coincidental infections affected COVID-19 mortality estimates following the introduction of the Omicron variant in late 2021.
MethodsWe compared the 30-day COVID-19 death count with the observed mortality using three alternative mortality estimation methods; (i) a mathematical model to correct the 30-day COVID-19 death count for coincidental deaths, (ii) the Causes of Death Registry (CDR) and (iii) all-cause excess mortality.
ResultsThere was a substantial peak in the 30-day COVID-19 death count following the emergence of the Omicron variant in late 2021. However, there was also a substantial change in the proportion of coincidental deaths, increasing from 10–20% to around 40% of the recorded COVID-19 deaths. The high number of 30-day COVID-19 deaths was not reflected in the number of COVID-19 deaths in the CDR and the all-cause excess mortality surveillance.
ConclusionOur analysis showed a distinct change in the mortality pattern following the introduction of Omicron in late 2021 with a markedly higher proportion of people estimated to have died with, rather than of, COVID-19 compared with mortality patterns observed earlier in the COVID-19 pandemic. Our findings highlight the importance of incorporating alternative mortality surveillance methods to more correctly estimate the burden of COVID-19 as the pandemic continues to evolve.
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Genomic surveillance of SARS-CoV-2 positive passengers on flights from China to Italy, December 2022
Federica Novazzi , Emanuela Giombini , Martina Rueca , Andreina Baj , Lavinia Fabeni , Angelo Genoni , Francesca Drago Ferrante , Giulia Gramigna , Cesare Ernesto Maria Gruber , Sara Boutahar , Claudia Minosse , Ornella Butera , Renee Pasciuta , Daniele Focosi , Alberto Colombo , Andrea Antinori , Enrico Girardi , Francesco Vaia and Fabrizio MaggiWith numbers of COVID-19 cases having substantially increased at the end of 2022 in China, some countries have started or expanded testing and genomic surveillance of travellers. We report screening results in Italy in late December 2022 of 556 flight passengers in provenance from two Chinese provinces. Among these passengers, 126 (22.7%) tested SARS-CoV-2 positive. Whole genome sequencing of 61 passengers’ positive samples revealed Omicron variants, notably sub-lineages BA.5.2.48, BF.7.14 and BQ.1.1, in line with data released from China.
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Detecting early signals of COVID-19 outbreaks in 2020 in small areas by monitoring healthcare utilisation databases: first lessons learned from the Italian Alert_CoV project
Ivan Merlo , Mariano Crea , Paolo Berta , Francesca Ieva , Flavia Carle , Federico Rea , Gloria Porcu , Laura Savaré , Raul De Maio , Marco Villa , Danilo Cereda , Olivia Leoni , Francesco Bortolan , Giuseppe Maria Sechi , Antonino Bella , Patrizio Pezzotti , Silvio Brusaferro , Gian Carlo Blangiardo , Massimo Fedeli , Giovanni Corrao and on behalf of the Italian Alert_CoV Project groupBackgroundDuring the COVID-19 pandemic, large-scale diagnostic testing and contact tracing have proven insufficient to promptly monitor the spread of infections.
AimTo develop and retrospectively evaluate a system identifying aberrations in the use of selected healthcare services to timely detect COVID-19 outbreaks in small areas.
MethodsData were retrieved from the healthcare utilisation (HCU) databases of the Lombardy Region, Italy. We identified eight services suggesting a respiratory infection (syndromic proxies). Count time series reporting the weekly occurrence of each proxy from 2015 to 2020 were generated considering small administrative areas (i.e. census units of Cremona and Mantua provinces). The ability to uncover aberrations during 2020 was tested for two algorithms: the improved Farrington algorithm and the generalised likelihood ratio-based procedure for negative binomial counts. To evaluate these algorithms’ performance in detecting outbreaks earlier than the standard surveillance, confirmed outbreaks, defined according to the weekly number of confirmed COVID-19 cases, were used as reference. Performances were assessed separately for the first and second semester of the year. Proxies positively impacting performance were identified.
ResultsWe estimated that 70% of outbreaks could be detected early using the proposed approach, with a corresponding false positive rate of ca 20%. Performance did not substantially differ either between algorithms or semesters. The best proxies included emergency calls for respiratory or infectious disease causes and emergency room visits.
ConclusionImplementing HCU-based monitoring systems in small areas deserves further investigations as it could facilitate the containment of COVID-19 and other unknown infectious diseases in the future.
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COVID-19 vaccine effectiveness against SARS-CoV-2 infection during the Delta period, a nationwide study adjusting for chance of exposure, the Netherlands, July to December 2021
BackgroundDifferential SARS-CoV-2 exposure between vaccinated and unvaccinated individuals may confound vaccine effectiveness (VE) estimates.
AimWe conducted a test-negative case–control study to determine VE against SARS-CoV-2 infection and the presence of confounding by SARS-CoV-2 exposure.
MethodsWe included adults tested for SARS-CoV-2 at community facilities between 4 July and 8 December 2021 (circulation period of the Delta variant). The VE against SARS-CoV-2 infection after primary vaccination with an mRNA (Comirnaty or Spikevax) or vector-based vaccine (Vaxzevria or Janssen) was calculated using logistic regression adjusting for age, sex and calendar week (Model 1). We additionally adjusted for comorbidity and education level (Model 2) and SARS-CoV-2 exposure (number of close contacts, visiting busy locations, household size, face mask wearing, contact with SARS-CoV-2 case; Model 3). We stratified by age, vaccine type and time since vaccination.
ResultsVE against infection (Model 3) was 64% (95% CI: 50–73), only slightly lower than in Models 1 (68%; 95% CI: 58–76) and 2 (67%; 95% CI: 56–75). Estimates stratified by age group, vaccine and time since vaccination remained similar: mRNA VE (Model 3) among people ≥ 50 years decreased significantly (p = 0.01) from 81% (95% CI: 66–91) at < 120 days to 61% (95% CI: 22–80) at ≥ 120 days after vaccination. It decreased from 83% to 59% in Model 1 and from 81% to 56% in Model 2.
ConclusionSARS-CoV-2 exposure did not majorly confound the estimated COVID-19 VE against infection, suggesting that VE can be estimated accurately using routinely collected data without exposure information.
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Tracking the progressive spread of the SARS-CoV-2 Omicron variant in Italy, December 2021 to January 2022
Paola Stefanelli , Filippo Trentini , Daniele Petrone , Alessia Mammone , Luigina Ambrosio , Mattia Manica , Giorgio Guzzetta , Valeria d'Andrea , Valentina Marziano , Agnese Zardini , Carla Molina Grane’ , Marco Ajelli , Angela Di Martino , Flavia Riccardo , Antonino Bella , Monica Sane Schepisi , Francesco Maraglino , Piero Poletti , Anna Teresa Palamara , Silvio Brusaferro , Giovanni Rezza , Patrizio Pezzotti , Stefano Merler , the Genomic SARS–CoV–2 National Surveillance Working Group and the Italian Integrated Surveillance of COVID–19 Study GroupBackgroundThe SARS-CoV-2 variant of concern Omicron was first detected in Italy in November 2021.
AimTo comprehensively describe Omicron spread in Italy in the 2 subsequent months and its impact on the overall SARS-CoV-2 circulation at population level.
MethodsWe analyse data from four genomic surveys conducted across the country between December 2021 and January 2022. Combining genomic sequencing results with epidemiological records collated by the National Integrated Surveillance System, the Omicron reproductive number and exponential growth rate are estimated, as well as SARS-CoV-2 transmissibility.
ResultsOmicron became dominant in Italy less than 1 month after its first detection, representing on 3 January 76.9–80.2% of notified SARS-CoV-2 infections, with a doubling time of 2.7–3.3 days. As of 17 January 2022, Delta variant represented < 6% of cases. During the Omicron expansion in December 2021, the estimated mean net reproduction numbers respectively rose from 1.15 to a maximum of 1.83 for symptomatic cases and from 1.14 to 1.36 for hospitalised cases, while remaining relatively stable, between 0.93 and 1.21, for cases needing intensive care. Despite a reduction in relative proportion, Delta infections increased in absolute terms throughout December contributing to an increase in hospitalisations. A significant reproduction numbers’ decline was found after mid-January, with average estimates dropping below 1 between 10 and 16 January 2022.
ConclusionEstimates suggest a marked growth advantage of Omicron compared with Delta variant, but lower disease severity at population level possibly due to residual immunity against severe outcomes acquired from vaccination and prior infection.
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A scenario modelling analysis to anticipate the impact of COVID-19 vaccination in adolescents and children on disease outcomes in the Netherlands, summer 2021
BackgroundSince the roll-out of COVID-19 vaccines in late 2020 and throughout 2021, European governments have relied on mathematical modelling to inform policy decisions about COVID-19 vaccination.
AimWe present a scenario-based modelling analysis in the Netherlands during summer 2021, to inform whether to extend vaccination to adolescents (12–17-year-olds) and children (5–11-year-olds).
MethodsWe developed a deterministic, age-structured susceptible-exposed-infectious-recovered (SEIR) model and compared modelled incidences of infections, hospital and intensive care admissions, and deaths per 100,000 people across vaccination scenarios, before the emergence of the Omicron variant.
ResultsOur model projections showed that, on average, upon the release of all non-pharmaceutical control measures on 1 November 2021, a large COVID-19 wave may occur in winter 2021/22, followed by a smaller, second wave in spring 2022, regardless of the vaccination scenario. The model projected reductions in infections/severe disease outcomes when vaccination was extended to adolescents and further reductions when vaccination was extended to all people over 5 years-old. When examining projected disease outcomes by age group, individuals benefitting most from extending vaccination were adolescents and children themselves. We also observed reductions in disease outcomes in older age groups, particularly of parent age (30–49 years), when children and adolescents were vaccinated, suggesting some prevention of onward transmission from younger to older age groups.
ConclusionsWhile our scenarios could not anticipate the emergence/consequences of SARS-CoV-2 Omicron variant, we illustrate how our approach can assist decision making. This could be useful when considering to provide booster doses or intervening against future infection waves.
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Omicron BA.2.75 variant is efficiently neutralised following BA.1 and BA.5 breakthrough infection in vaccinated individuals, Israel, June to September 2022
We evaluated neutralising antibody titres against wild type (WT) SARS-CoV-2 and four Omicron variants (BA.1, BA.2, BA.5 and BA.2.75) in fully vaccinated (three doses of Comirnaty vaccine) healthcare workers (HCW) in Israel who had breakthrough BA.1/BA5 infections. Omicron breakthrough infections in vaccinated individuals resulted in increased neutralising antibodies against the WT and Omicron variants compared with vaccinated uninfected HCW. HCW who recovered from BA.1 or BA.5 infections showed similar neutralising antibodies levels against BA.2.75.
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External quality assessment of SARS-CoV-2 serology in European expert laboratories, April 2021
Ramona Mögling , Francesca Colavita , Johan Reimerink , Angeliki Melidou , Katrin Leitmeyer , Maria Keramarou , Daniele Lapa , Massimo Francalancia , Jean-Luc Murk , Ann Vossen , Fabrizio Carletti , Boris Hogema , Adam Meijer , Liesbet Deprez , Antonino di Caro , Concetta Castilletti and Chantal BEM ReuskenBackgroundCountries worldwide are focusing to mitigate the ongoing SARS-CoV-2 pandemic by employing public health measures. Laboratories have a key role in the control of SARS-CoV-2 transmission. Serology for SARS-CoV-2 is of critical importance to support diagnosis, define the epidemiological framework and evaluate immune responses to natural infection and vaccine administration.
AimThe aim of this study was the assessment of the actual capability among laboratories involved in sero-epidemiological studies on COVID-19 in EU/EEA and EU enlargement countries to detect SARS-CoV-2 antibodies through an external quality assessment (EQA) based on proficiency testing.
MethodsThe EQA panels were composed of eight different, pooled human serum samples (all collected in 2020 before the vaccine roll-out), addressing sensitivity and specificity of detection. The panels and two EU human SARS-CoV-2 serological standards were sent to 56 laboratories in 30 countries.
ResultsThe overall performance of laboratories within this EQA indicated a robust ability to establish past SARS-CoV-2 infections via detection of anti-SARS-CoV-2 antibodies, with 53 of 55 laboratories using at least one test that characterised all EQA samples correctly. IgM-specific test methods provided most incorrect sample characterisations (24/208), while test methods detecting total immunoglobulin (0/119) and neutralising antibodies (2/230) performed the best. The semiquantitative assays used by the EQA participants also showed a robust performance in relation to the standards.
ConclusionOur EQA showed a high capability across European reference laboratories for reliable diagnostics for SARS-CoV-2 antibody responses. Serological tests that provide robust and reliable detection of anti-SARS-CoV-2 antibodies are available.
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Public health measures during the COVID-19 pandemic through the lens of community organisations and networks in the Netherlands (2020–2021): five lessons for pandemic decision-making
BackgroundDuring the coronavirus disease (COVID-19) pandemic, key persons who were formally or informally active in community organisations and networks, such as sports clubs or cultural, educational, day care and healthcare facilities, occupied a key position between governments and citizens. However, their experiences, the dilemmas they faced and the solutions they generated when implementing COVID-19 measures in their respective settings are understudied.
AimWe aimed to understand how key persons in different community organisations and networks experienced and responded to the COVID-19 measures in the Netherlands.
MethodsBetween October 2020 and December 2021, the Corona Behavioural Unit at the Dutch national public health institute, conducted qualitative research based on narratives derived from 65 in-depth interviews with 95 key persons from 32 organisations and networks in eight different sectors.
ResultsFirstly, key persons enhanced adherence and supported the resilience and well-being of people involved in their settings. Secondly, adherence was negatively affected where COVID-19 measures conflicted with important organisational goals and values. Thirdly, small changes and ambiguities in COVID-19 policy had substantial consequences, depending on the context. Fourthly, problem-solving was achieved through trial-and-error, peer support, co-creation and transparent communication. Lastly, the COVID-19 pandemic and measures highlighted inequalities in access to resources.
ConclusionPandemic preparedness requires organisational and community preparedness and a multidisciplinary public health approach. Structural engagement of governments with key persons in community organisations and networks is key to enhance public trust and adherence to pandemic measures and contributes to health equity and the well-being of the people involved.
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Non-pharmaceutical interventions in response to the COVID-19 pandemic in 30 European countries: the ECDC–JRC Response Measures Database
In response to the COVID-19 pandemic, the European Union/European Economic Area (EU/EEA) countries implemented a wide set of non-pharmaceutical interventions (NPIs), sometimes with limited knowledge on their effect and impact on population. The European Centre for Disease Prevention and Control (ECDC) and the European Commission’s Joint Research Centre (JRC) developed a Response Measures Database (ECDC–JRC RMD) to archive NPIs in 30 EU/EEA countries from 1 January 2020 to 30 September 2022. We aimed to introduce a tool for the wider scientific community to assess COVID-19 NPIs effect and impact in the EU/EEA. We give an overview of the ECDC–JRC RMD rationale and structure, including a brief analysis of the main NPIs applied in 2020, before the roll-out of the COVID-19 vaccination campaigns. The ECDC–JRC RMD organises NPIs through a three-level hierarchical structure and uses four additional parameters (‘status’, ‘implementation’, ‘target group’ and ‘geographical representation’) to provide further information on the implementation of each measure. Features including the ready-for-analysis, downloadable format and its agile taxonomy and structure highlight the potential of the ECDC–JRC RMD to facilitate further NPI analysis and optimise decision making on public health response policies.
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Exploring behavioural factors influencing COVID-19-specific infection prevention and control measures in Finland: a mixed-methods study, December 2020 to March 2021
More LessBackgroundCompliance with infection prevention and control (IPC) measures is critical to preventing COVID-19 transmission in healthcare settings.
AimTo identify and explain factors influencing compliance with COVID-19-specific IPC measures among healthcare workers (HCWs) in long-term care facilities (LTCF) in Finland.
MethodsThe study included a web-based survey and qualitative study based on the Theoretical Domains Framework (TDF). The link to the anonymous survey was distributed via email to LTCFs through regional IPC experts in December 2020. Outcome was modelled using ordinary logistic regression and penalised ridge logistic regression using regrouped explanatory variables and an original, more correlated set of explanatory variables, respectively. In-depth interviews were conducted among survey participants who volunteered during January–March 2021. Data were analysed thematically using qualitative data analysis software (NVIVO12).
ResultsA total of 422 HCWs from 17/20 regions responded to the survey. Three TDF domains were identified that negatively influenced IPC compliance: environmental context and resources, reinforcement and beliefs about capabilities. Twenty HCWs participated in interviews, which resulted in identification of several themes: changes in professional duties and lack of staff planning for emergencies (domain: environmental context and resources); management culture and physical absence of management (domain: reinforcement), knowledge of applying IPC measures, nature of tasks and infrastructure that supports implementation (domain: beliefs about capabilities), that explained how the domains negatively influenced their IPC behaviour.
ConclusionsThis study provides insights into behavioural domains that can be used in developing evidence-based behaviour change interventions to support HCW compliance with pandemic-specific IPC measures in LTCFs.
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Age-specific associations between underlying health conditions and hospitalisation, death and in-hospital death among confirmed COVID-19 cases: a multi-country study based on surveillance data, June to December 2020
Tjede Funk , Francesco Innocenti , Joana Gomes Dias , Lina Nerlander , Tanya Melillo , Charmaine Gauci , Jackie M Melillo , Patrik Lenz , Helena Sebestova , Pavel Slezak , Iva Vlckova , Jacob Dag Berild , Camilla Mauroy , Elina Seppälä , Ragnhild Tønnessen , Anne Vergison , Joël Mossong , Silvana Masi , Laetitia Huiart , Gillian Cullen , Niamh Murphy , Lois O’Connor , Joan O’Donnell , Piers Mook , Richard G Pebody and Nick BundleBackgroundUnderlying conditions are risk factors for severe COVID-19 outcomes but evidence is limited about how risks differ with age.
AimWe sought to estimate age-specific associations between underlying conditions and hospitalisation, death and in-hospital death among COVID-19 cases.
MethodsWe analysed case-based COVID-19 data submitted to The European Surveillance System between 2 June and 13 December 2020 by nine European countries. Eleven underlying conditions among cases with only one condition and the number of underlying conditions among multimorbid cases were used as exposures. Adjusted odds ratios (aOR) were estimated using 39 different age-adjusted and age-interaction multivariable logistic regression models, with marginal means from the latter used to estimate probabilities of severe outcome for each condition–age group combination.
ResultsCancer, cardiac disorder, diabetes, immunodeficiency, kidney, liver and lung disease, neurological disorders and obesity were associated with elevated risk (aOR: 1.5–5.6) of hospitalisation and death, after controlling for age, sex, reporting period and country. As age increased, age-specific aOR were lower and predicted probabilities higher. However, for some conditions, predicted probabilities were at least as high in younger individuals with the condition as in older cases without it. In multimorbid patients, the aOR for severe disease increased with number of conditions for all outcomes and in all age groups.
ConclusionWhile supporting age-based vaccine roll-out, our findings could inform a more nuanced, age- and condition-specific approach to vaccine prioritisation. This is relevant as countries consider vaccination of younger people, boosters and dosing intervals in response to vaccine escape variants.
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Epidemiological profile of COVID-19 in the French overseas department Mayotte, 2020 to 2021
Marion Subiros , Charlotte Robert De Latour , Fanny Parenton , Ibtissame Soulaimana , Youssouf Hassani , Renaud Blondé , François Pousset , Yvonnick Boué , Camille Estagnasie , Gonzague Martin-Lecamp , Abdoulahy Diallo , Lucas Balloy , Mohamadou Niang , Christophe Caralp , Aurélie Cann , Abdourahim Chamouine , Alice Miquel , Geneviève Dennetière , Julie Durand , Maxime Jean , Sophie Olivier , Louis Collet , Nicole Tayeb and Patrice CombeBackgroundDuring the COVID-19 pandemic, national and local measures were implemented on the island of Mayotte, a French overseas department in the Indian Ocean with critical socioeconomic and health indicators.
AimWe aimed to describe the COVID-19 outbreak in Mayotte from March 2020 to March 2021, with two waves from 9 March to 31 December 2020 and from 1 January to 14 March 2021, linked to Beta (20H/501Y.V2) variant.
MethodsTo understand and assess the dynamic and the severity of the COVID-19 outbreak in Mayotte, surveillance and investigation/contact tracing systems were set up including virological, epidemiological, hospitalisation and mortality indicators.
ResultsIn total, 18,131 cases were laboratory confirmed, with PCR or RAT. During the first wave, incidence rate (IR) peaked in week 19 2020 (133/100,000). New hospitalisations peaked in week 20 (54 patients, including seven to ICU). Testing rate increased tenfold during the second wave. Between mid-December 2020 and mid-January 2021, IR doubled (851/100,000 in week 5 2021) and positivity rate tripled (28% in week 6 2021). SARS-CoV-2 Beta variant (Pangolin B.1.351) was detected in more than 80% of positive samples. Hospital admissions peaked in week 6 2021 with 225 patients, including 30 to ICU.
ConclusionThis massive second wave could be linked to the high transmissibility of the Beta variant. The increase in the number of cases has naturally led to a higher number of severe cases and an overburdening of the hospital. This study shows the value of a real-time epidemiological surveillance for better understanding crisis situations.
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Role of population and test characteristics in antigen-based SARS-CoV-2 diagnosis, Czechia, August to November 2021
More LessBackgroundAnalyses of diagnostic performance of SARS-CoV-2 antigen rapid diagnostic tests (AG-RDTs) based on long-term data, population subgroups and many AG-RDT types are scarce.
AimWe aimed to analyse sensitivity and specificity of AG-RDTs for subgroups based on age, incidence, sample type, reason for test, symptoms, vaccination status and the AG-RDT’s presence on approved lists.
MethodsWe included AG-RDT results registered in Czechia’s Information System for Infectious Diseases between August and November 2021. Subpopulations were analysed based on 346,000 test results for which a confirmatory PCR test was recorded ≤ 3 days after the AG-RDT; 38 AG-RDTs with more than 100 PCR-positive and 300 PCR-negative samples were individually evaluated.
ResultsAverage sensitivity and specificity were 72.4% and 96.7%, respectively. We recorded lower sensitivity for age groups 0–12 (65.5%) and 13–18 years (65.3%). The sensitivity level rose with increasing SARS-CoV-2 incidence from 66.0% to 76.7%. Nasopharyngeal samples had the highest sensitivity and saliva the lowest. Sensitivity for preventive reasons was 63.6% vs 86.1% when testing for suspected infection. Sensitivity was 84.8% when one or more symptoms were reported compared with 57.1% for no symptoms. Vaccination was associated with a 4.2% higher sensitivity. Significantly higher sensitivity levels pertained to AG-RDTs on the World Health Organization Emergency Use List (WHO EUL), European Union Common List and the list of the United Kingdom’s Department of Health and Social Care.
ConclusionAG-RDTs from approved lists should be considered, especially in situations associated with lower viral load. Results are limited to SARS-CoV-2 delta variant.
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Seroprevalence of antibodies against SARS-CoV-2 and risk of COVID-19 in Navarre, Spain, May to July 2022
In Navarre, Spain, in May 2022, the seroprevalence of anti-nucleocapsid (N) and anti-spike (S) antibodies of SARS-CoV-2 was 58.9% and 92.7%, respectively. The incidence of confirmed COVID-19 thereafter through July was lower in people with anti-N antibodies (adjusted odds ratio (aOR) = 0.08; 95% confidence interval (CI): 0.05–0.13) but not with anti-S antibodies (aOR = 1.06; 95% CI: 0.47–2.38). Hybrid immunity, including anti-N antibodies induced by natural exposure to SARS-CoV-2, seems essential in preventing Omicron COVID-19 cases.
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SARS-CoV-2 infection in households with and without young children: Nationwide cohort study, Denmark, 27 February 2020 to 26 February 2021
More LessBackgroundInfections with seasonally spreading coronaviruses are common among young children during winter months in the northern hemisphere; the immunological response lasts around a year. However, it is not clear if living with young children changes the risk of SARS-CoV-2 infection among adults.
AimOur aim was to investigate the association between living in a household with younger children and the risk of SARS-CoV-2 infections and hospitalisation.
MethodsIn a nationwide cohort study, we followed all adults in Denmark aged 18 to 60 years from 27 February 2020 to 26 February 2021. Hazard ratios of SARS-CoV-2 infection by number of 10 months to 5 year-old children in the household were estimated using Cox regression adjusted for adult age, sex and other potential confounders. In a sensitivity analysis, we investigated the effect of the children's age.
ResultsAmong 450,007 adults living in households with young children, 19,555 were tested positive for SARS-CoV-2, while among 2,628,500 adults without young children in their household, 110,069 were tested positive for SARS-CoV-2 (adjusted hazard ratio (aHR) = 1.10; 95% confidence interval (CI): 1.08–1.12). Among adults with young children, 620 were hospitalised with SARS-CoV-2, while 4,002 adults without children were hospitalised with SARS-CoV-2 (aHR = 0.97; 95% CI: 0.88–1.08). Sensitivity analyses found that an increasing number of younger children substantially increased the risk of SARS-CoV-2 infection but not hospitalisation.
ConclusionLiving in a household with young children was associated with a small increased risk of SARS-CoV-2 infection.
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Impact of stringent non-pharmaceutical interventions applied during the second and third COVID-19 epidemic waves in Portugal, 9 November 2020 to 10 February 2021: an ecological study
BackgroundNon-pharmaceutical interventions (NPIs) were implemented worldwide to control the spread of SARS-CoV-2.
AimTo evaluate the impact of tiered NPIs and a nationwide lockdown on reduction of COVID-19 incidence during the second and third epidemic waves in Portugal.
MethodsSurveillance data on laboratory-confirmed COVID-19 cases were used to conduct an interrupted time series analysis to estimate changes in daily incidence during a second wave tiered NPI period (9 November–18 December 2020), and a third wave lockdown period without (15–21 January 2021) and with school closure (22 January–10 February 2021).
ResultsSignificant changes in trends were observed for the overall incidence rate; declining trends were observed for tiered NPIs (−1.9% per day; incidence rate ratio (IRR): 0.981; 95% confidence interval (CI): 0.973–0.989) and a lockdown period without (−3.4% per day; IRR: 0.966; 95% CI: 0.935–0.998) and with school closure (−10.3% per day, IRR: 0.897; 95% CI: 0.846–0.951). Absolute effects associated with tiered NPIs and a lockdown on a subsequent 14-day period yielded 137 cases and 437 cases per 100,000 population potentially averted, respectively.
ConclusionOur results indicate that tiered NPIs implemented during the second wave caused a decline in COVID-19 incidence, although modest. Moreover, a third wave lockdown without school closure was effective in reducing COVID-19 incidence, but the addition of school closure provided the strongest effect. These findings emphasise the importance of early and assertive decision-making to control the pandemic.
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SARS-CoV-2 Omicron variants BA.1 and BA.2 both show similarly reduced disease severity of COVID-19 compared to Delta, Germany, 2021 to 2022
German national surveillance data analysis shows that hospitalisation odds associated with Omicron lineage BA.1 or BA.2 infections are up to 80% lower than with Delta infection, primarily in ≥ 35-year-olds. Hospitalised vaccinated Omicron cases’ proportions (2.3% for both lineages) seemed lower than those of the unvaccinated (4.4% for both lineages). Independent of vaccination status, the hospitalisation frequency among cases with Delta seemed nearly threefold higher (8.3%) than with Omicron (3.0% for both lineages), suggesting that Omicron inherently causes less severe disease.
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Detection of SARS-CoV-2 in young children attending day-care centres in Belgium, May 2020 to February 2022
Liesbet Van Heirstraeten , Esra Ekinci , Mathias Smet , Matilda Berkell , Laura Willen , Jasmine Coppens , An Spiessens , Basil Britto Xavier , Christine Lammens , Jan Verhaegen , Pierre Van Damme , Herman Goossens , Philippe Beutels , Veerle Matheeussen , Stefanie Desmet , Heidi Theeten and Surbhi Malhotra-KumarPresence of SARS-CoV-2 was monitored in nasopharyngeal samples from young children aged 6−30 months attending day-care centres (DCCs) in Belgium from May 2020−February 2022. SARS-CoV-2 carriage among DCC children was only detected from November 2021, after emergence of Delta and Omicron variants, in 9 of the 42 DCCs screened. In only one DCC, two children tested positive for SARS-CoV-2 at the same sampling time point, suggesting limited transmission of SARS-CoV-2 in Belgian DCCs among young children during the studied period.
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Investigation of a COVID-19 outbreak on the Charles de Gaulle aircraft carrier, March to April 2020: a retrospective cohort study
Franck de Laval , Hervé Chaudet , Olivier Gorgé , Joffrey Marchi , Constance Lacrosse , Aissata Dia , Vanessa Marbac , Bakridine Mmadi Mrenda , Gaëtan Texier , Flavie Letois , Charles Chapus , Véronique Sarilar , Jean-Nicolas Tournier , Anthony Levasseur , Jacques Cobola , Flora Nolent , Fabien Dutasta , Frédéric Janvier , PA-CDG COVID-19 investigation group , Jean-Baptiste Meynard and Vincent Pommier de SantiBackgroundSARS-CoV-2 emergence was a threat for armed forces. A COVID-19 outbreak occurred on the French aircraft carrier Charles de Gaulle from mid-March to mid-April 2020.
AimTo understand how the virus was introduced, circulated then stopped circulation, risk factors for infection and severity, and effectiveness of preventive measures.
MethodsWe considered the entire crew as a cohort and collected personal, clinical, biological, and epidemiological data. We performed viral genome sequencing and searched for SARS-CoV-2 in the environment.
ResultsThe attack rate was 65% (1,148/1,767); 1,568 (89%) were included. The male:female ratio was 6.9, and median age was 29 years (IQR: 24–36). We examined four clinical profiles: asymptomatic (13.0%), non-specific symptomatic (8.1%), specific symptomatic (76.3%), and severe (i.e. requiring oxygen therapy, 2.6%). Active smoking was not associated with severe COVID-19; age and obesity were risk factors. The instantaneous reproduction rate (Rt) and viral sequencing suggested several introductions of the virus with 4 of 5 introduced strains from within France, with an acceleration of Rt when lifting preventive measures. Physical distancing prevented infection (adjusted OR: 0.55; 95% CI: 0.40–0.76). Transmission may have stopped when the proportion of infected personnel was large enough to prevent circulation (65%; 95% CI: 62–68).
ConclusionNon-specific clinical pictures of COVID-19 delayed detection of the outbreak. The lack of an isolation ward made it difficult to manage transmission; the outbreak spread until a protective threshold was reached. Physical distancing was effective when applied. Early surveillance with adapted prevention measures should prevent such an outbreak.
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Assessment of mortality and hospital admissions associated with confirmed infection with SARS-CoV-2 Alpha variant: a matched cohort and time-to-event analysis, England, October to December 2020
Gavin Dabrera , Hester Allen , Asad Zaidi , Joe Flannagan , Katherine Twohig , Simon Thelwall , Elizabeth Marchant , Nurin Abdul Aziz , Theresa Lamagni , Richard Myers , André Charlett , Fernando Capelastegui , Dimple Chudasama , Tom Clare , Flavien Coukan , Mary Sinnathamby , Neil Ferguson , Susan Hopkins , Meera Chand , Russell Hope , Meaghan Kall and on behalf of the COG-UK ConsortiumBackgroundThe emergence of the SARS-CoV-2 Alpha variant in England coincided with a rapid increase in the number of PCR-confirmed COVID-19 cases in areas where the variant was concentrated.
AimOur aim was to assess whether infection with Alpha was associated with more severe clinical outcomes than the wild type.
MethodsLaboratory-confirmed infections with genomically sequenced SARS-CoV-2 Alpha and wild type between October and December 2020 were linked to routine healthcare and surveillance datasets. We conducted two statistical analyses to compare the risk of hospital admission and death within 28 days of testing between Alpha and wild-type infections: a matched cohort study and an adjusted Cox proportional hazards model. We assessed differences in disease severity by comparing hospital admission and mortality, including length of hospitalisation and time to death.
ResultsOf 63,609 COVID-19 cases sequenced in England between October and December 2020, 6,038 had the Alpha variant. In the matched cohort analysis, we matched 2,821 cases with Alpha to 2,821 to cases with wild type. In the time-to-event analysis, we observed a 34% increased risk in hospitalisation associated with Alpha compared with wild type, but no significant difference in the risk of mortality.
ConclusionWe found evidence of increased risk of hospitalisation after adjusting for key confounders, suggesting increased infection severity associated with the Alpha variant. Rapid assessments of the relative morbidity in terms of clinical outcomes and mortality associated with emerging SARS-CoV-2 variants compared with dominant variants are required to assess overall impact of SARS-CoV-2 mutations.
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Hospitalised patients with breakthrough COVID-19 following vaccination during two distinct waves in Israel, January to August 2021: a multicentre comparative cohort study
Tal Brosh-Nissimov , Yasmin Maor , Meital Elbaz , Shelly Lipman-Arens , Yonit Wiener-Well , Khetam Hussein , Efrat Orenbuch-Harroch , Regev Cohen , Oren Zimhony , Bibiana Chazan , Lior Nesher , Galia Rahav , Hiba Zayyad , Mirit Hershman-Sarafov , Miriam Weinberger , Ronza Najjar-Debbiny and Michal ChowersBackgroundChanging patterns of vaccine breakthrough can clarify vaccine effectiveness.
AimTo compare breakthrough infections during a SARS-CoV-2 Delta wave vs unvaccinated inpatients, and an earlier Alpha wave.
MethodsIn an observational multicentre cohort study in Israel, hospitalised COVID-19 patients were divided into three cohorts: breakthrough infections in Comirnaty-vaccinated patients (VD; Jun–Aug 2021) and unvaccinated cases during the Delta wave (ND) and breakthrough infections during an earlier Alpha wave (VA; Jan–Apr 2021). Primary outcome was death or ventilation.
ResultsWe included 343 VD, 162 ND and 172 VA patients. VD were more likely older (OR: 1.06; 95% CI: 1.05–1.08), men (OR: 1.6; 95% CI: 1.0–2.5) and immunosuppressed (OR: 2.5; 95% CI: 1.1–5.5) vs ND. Median time between second vaccine dose and admission was 179 days (IQR: 166–187) in VD vs 41 days (IQR: 28–57.5) in VA. VD patients were less likely to be men (OR: 0.6; 95% CI: 0.4–0.9), immunosuppressed (OR: 0.3; 95% CI: 0.2–0.5) or have congestive heart failure (OR: 0.6; 95% CI: 0.3–0.9) vs VA. The outcome was similar between all cohorts and affected by age and immunosuppression and not by vaccination, variant or time from vaccination.
ConclusionsVaccination was protective during the Delta variant wave, as suggested by older age and greater immunosuppression in vaccinated breakthrough vs unvaccinated inpatients. Nevertheless, compared with an earlier post-vaccination period, breakthrough infections 6 months post-vaccination occurred in healthier patients. Thus, waning immunity increased vulnerability during the Delta wave, which suggests boosters as a countermeasure.
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Risk and protective factors for SARS-CoV-2 reinfections, surveillance data, Italy, August 2021 to March 2022
We explored the risk factors associated with SARS-CoV-2 reinfections in Italy between August 2021 and March 2022. Regardless of the prevalent virus variant, being unvaccinated was the most relevant risk factor for reinfection. The risk of reinfection increased almost 18-fold following emergence of the Omicron variant compared with Delta. A severe first SARS-CoV-2 infection and age over 60 years were significant risk factors for severe reinfection.
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Assessing the effect of non-pharmaceutical interventions on COVID-19 transmission in Spain, 30 August 2020 to 31 January 2021
BackgroundAfter a national lockdown during the first wave of the COVID-19 pandemic in Spain, regional governments implemented different non-pharmaceutical interventions (NPIs) during the second wave.
AimTo analyse which implemented NPIs significantly impacted effective reproduction number (Rt) in seven Spanish provinces during 30 August 2020–31 January 2021.
MethodsWe coded each NPI and levels of stringency with a ‘severity index’ (SI) and computed a global SI (mean of SIs per six included interventions). We performed a Bayesian change point analysis on the Rt curve of each province to identify possible associations with global SI variations. We fitted and compared several generalised additive models using multimodel inference, to quantify the statistical effect on Rt of the global SI (stringency) and the individual SIs (separate effect of NPIs).
ResultsThe global SI had a significant lowering effect on the Rt (mean: 0.16 ± 0.05 units for full stringency). Mandatory closing times for non-essential businesses, limited gatherings, and restricted outdoors seating capacities (negative) as well as curfews (positive) were the only NPIs with a significant effect. Regional mobility restrictions and limited indoors seating capacity showed no effect. Our results were consistent with a 1- to 3-week-delayed Rt as a response variable.
ConclusionWhile response measures implemented during the second COVID-19 wave contributed substantially to a decreased reproduction number, the effectiveness of measures varied considerably. Our findings should be considered for future interventions, as social and economic consequences could be minimised by considering only measures proven effective.
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Mycoplasma pneumoniae detections before and during the COVID-19 pandemic: results of a global survey, 2017 to 2021
BackgroundMycoplasma pneumoniae respiratory infections are transmitted by aerosol and droplets in close contact.
AimWe investigated global M. pneumoniae incidence after implementation of non-pharmaceutical interventions (NPIs) against COVID-19 in March 2020.
MethodsWe surveyed M. pneumoniae detections from laboratories and surveillance systems (national or regional) across the world from 1 April 2020 to 31 March 2021 and compared them with cases from corresponding months between 2017 and 2020. Macrolide-resistant M. pneumoniae (MRMp) data were collected from 1 April 2017 to 31 March 2021.
ResultsThirty-seven sites from 21 countries in Europe, Asia, America and Oceania submitted valid datasets (631,104 tests). Among the 30,617 M. pneumoniae detections, 62.39% were based on direct test methods (predominantly PCR), 34.24% on a combination of PCR and serology (no distinction between methods) and 3.37% on serology alone (only IgM considered). In all countries, M. pneumoniae incidence by direct test methods declined significantly after implementation of NPIs with a mean of 1.69% (SD ± 3.30) compared with 8.61% (SD ± 10.62) in previous years (p < 0.01). Detection rates decreased with direct but not with indirect test methods (serology) (–93.51% vs + 18.08%; p < 0.01). Direct detections remained low worldwide throughout April 2020 to March 2021 despite widely differing lockdown or school closure periods. Seven sites (Europe, Asia and America) reported MRMp detections in one of 22 investigated cases in April 2020 to March 2021 and 176 of 762 (23.10%) in previous years (p = 0.04).
ConclusionsThis comprehensive collection of M. pneumoniae detections worldwide shows correlation between COVID-19 NPIs and significantly reduced detection numbers.
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Behavioural insights and the evolving COVID-19 pandemic
Behavioural sciences have complemented medical and epidemiological sciences in the response to the SARS-CoV-2 pandemic. As vaccination uptake continues to increase across the EU/EEA – including booster vaccinations – behavioural science research remains important for both pandemic policy, planning of services and communication. From a behavioural perspective, the following three areas are key as the pandemic progresses: (i) attaining and maintaining high levels of vaccination including booster doses across all groups in society, including socially vulnerable populations, (ii) informing sustainable pandemic policies and ensuring adherence to basic prevention measures to protect the most vulnerable population, and (iii) facilitating population preparedness and willingness to support and adhere to the reimposition of restrictions locally or regionally whenever outbreaks may occur. Based on mixed-methods research, expert consultations, and engagement with communities, behavioural data and interventions can thus be important to prevent and effectively respond to local or regional outbreaks, and to minimise socioeconomic and health disparities. In this Perspective, we briefly outline these topics from a European viewpoint, while recognising the importance of considering the specific context in individual countries.
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Public health considerations for transitioning beyond the acute phase of the COVID-19 pandemic in the EU/EEA
Many countries, including some within the EU/EEA, are in the process of transitioning from the acute pandemic phase. During this transition, it is crucial that countries’ strategies and activities remain guided by clear COVID-19 control objectives, which increasingly will focus on preventing and managing severe outcomes. Therefore, attention must be given to the groups that are particularly vulnerable to severe outcomes of SARS-CoV-2 infection, including individuals in congregate and healthcare settings. In this phase of pandemic management, a strong focus must remain on transitioning testing approaches and systems for targeted surveillance of COVID-19, capitalising on and strengthening existing systems for respiratory virus surveillance. Furthermore, it will be crucial to focus on lessons learned from the pandemic to enhance preparedness and to enact robust systems for the preparedness, detection, rapid investigation and assessment of new and emerging SARS-CoV-2 variants. Filling existing knowledge gaps, including behavioural insights, can help guide the response to future resurgences of SARS-CoV-2 and/or the emergence of other pandemics. Finally, ‘vaccine agility’ will be needed to respond to changes in people’s behaviours, changes in the virus, and changes in population immunity, all the while addressing issues of global health equity.
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Genomic and epidemiological report of the recombinant XJ lineage SARS-CoV-2 variant, detected in northern Finland, January 2022
Recombinant sequences of the SARS-CoV-2 Omicron variant were detected in surveillance samples collected in north-western Finland in January 2022. We detected 191 samples with an identical genome arrangement in weeks 3 to 11, indicating sustained community transmission. The recombinant lineage has a 5’-end of BA.1, a recombination breakpoint between orf1a and orf1b (nucleotide position 13,296–15,240) and a 3’-end of BA.2 including the S gene. We describe the available genomic and epidemiological data about this currently circulating recombinant XJ lineage.
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The impact of SARS-CoV-2 on respiratory syndromic and sentinel surveillance in Israel, 2020: a new perspective on established systems
Aharona Glatman-Freedman , Lea Gur-Arie , Hanna Sefty , Zalman Kaufman , Michal Bromberg , Rita Dichtiar , Alina Rosenberg , Rakefet Pando , Ital Nemet , Limor Kliker2, , Ella Mendelson , Lital Keinan-Boker , Neta S Zuckerman , Michal Mandelboim and on behalf of The Israeli Respiratory Viruses Surveillance Network (IRVSN)BackgroundThe COVID-19 pandemic presented new challenges for the existing respiratory surveillance systems, and adaptations were implemented. Systematic assessment of the syndromic and sentinel surveillance platforms during the pandemic is essential for understanding the value of each platform in the context of an emerging pathogen with rapid global spread.
AimWe aimed to evaluate systematically the performance of various respiratory syndromic surveillance platforms and the sentinel surveillance system in Israel from 1 January to 31 December 2020.
MethodsWe compared the 2020 syndromic surveillance trends to those of the previous 3 years, using Poisson regression adjusted for overdispersion. To assess the performance of the sentinel clinic system as compared with the national SARS-CoV-2 repository, a cubic spline with 7 knots and 95% confidence intervals were applied to the sentinel network's weekly percentage of positive SARS-CoV-2 cases.
ResultsSyndromic surveillance trends changed substantially during 2020, with a statistically significant reduction in the rates of visits to physicians and emergency departments to below previous years' levels. Morbidity patterns of the syndromic surveillance platforms were inconsistent with the progress of the pandemic, while the sentinel surveillance platform was found to reflect the national circulation of SARS-CoV-2 in the population.
ConclusionOur findings reveal the robustness of the sentinel clinics platform for the surveillance of the main respiratory viruses during the pandemic and possibly beyond. The robustness of the sentinel clinics platform during 2020 supports its use in locations with insufficient resources for widespread testing of respiratory viruses.
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Vaccine-induced and naturally-acquired protection against Omicron and Delta symptomatic infection and severe COVID-19 outcomes, France, December 2021 to January 2022
More LessWe assessed the protection conferred by naturally-acquired, vaccine-induced and hybrid immunity during the concomitant Omicron and Delta epidemic waves in France on symptomatic infection and severe COVID-19. The greatest levels of protection against both variants were provided by hybrid immunity. Protection against Omicron symptomatic infections was systematically lower and waned at higher speed than against Delta in those vaccinated. In contrast, there were little differences in variant-specific protection against severe inpatient outcomes in symptomatic individuals.
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Transmission dynamics of COVID-19 in household and community settings in the United Kingdom, January to March 2020
Jamie Lopez Bernal , Nikolaos Panagiotopoulos , Chloe Byers , Tatiana Garcia Vilaplana , Nicki Boddington , Xu-Sheng Zhang , Andre Charlett , Suzanne Elgohari , Laura Coughlan , Rosie Whillock , Sophie Logan , Hikaru Bolt , Mary Sinnathamby , Louise Letley , Pauline MacDonald , Roberto Vivancos , Obaghe Edeghere , Charlotte Anderson , Karthik Paranthaman , Simon Cottrell , Jim McMenamin , Maria Zambon , Gavin Dabrera , Mary Ramsay and Vanessa SalibaBackgroundHouseholds appear to be the highest risk setting for COVID-19 transmission. Large household transmission studies in the early stages of the pandemic in Asia reported secondary attack rates ranging from 5 to 30%.
AimWe aimed to investigate the transmission dynamics of COVID-19 in household and community settings in the UK.
MethodsA prospective case-ascertained study design based on the World Health Organization FFX protocol was undertaken in the UK following the detection of the first case in late January 2020. Household contacts of cases were followed using enhanced surveillance forms to establish whether they developed symptoms of COVID-19, became confirmed cases and their outcomes. We estimated household secondary attack rates (SAR), serial intervals and individual and household basic reproduction numbers. The incubation period was estimated using known point source exposures that resulted in secondary cases.
ResultsWe included 233 households with two or more people with 472 contacts. The overall household SAR was 37% (95% CI: 31–43%) with a mean serial interval of 4.67 days, an R0 of 1.85 and a household reproduction number of 2.33. SAR were lower in larger households and highest when the primary case was younger than 18 years. We estimated a mean incubation period of around 4.5 days.
ConclusionsRates of COVID-19 household transmission were high in the UK for ages above and under 18 years, emphasising the need for preventative measures in this setting. This study highlights the importance of the FFX protocol in providing early insights on transmission dynamics.
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Impact of the Omicron variant on SARS-CoV-2 reinfections in France, March 2021 to February 2022
Since the first reports in summer 2020, SARS-CoV-2 reinfections have raised concerns about the immunogenicity of the virus, which will affect SARS-CoV-2 epidemiology and possibly the burden of COVID-19 on our societies in the future. This study provides data on the frequency and characteristics of possible reinfections, using the French national COVID-19 testing database. The Omicron variant had a large impact on the frequency of possible reinfections in France, which represented 3.8% of all confirmed COVID-19 cases since December 2021.
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Risk factors associated with an outbreak of COVID-19 in a meat processing plant in southern Germany, April to June 2020
Meat processing plants have been prominent hotspots for coronavirus disease (COVID-19) outbreaks around the world. We describe infection prevention measures and risk factors for infection spread at a meat processing plant in Germany with a COVID-19 outbreak from April to June 2020. We analysed a cohort of all employees and defined cases as employees with either a PCR or ELISA positive result. Of 1,270 employees, 453 (36%) had evidence of SARS-CoV-2 infection. The highest attack rates were observed in meat processing and slaughtering areas. Multivariable analysis revealed that being a subcontracted employee (adjusted risk ratio (aRR)): 1.43, 95% CI: 1.06–1.96), working in the meat cutting area (aRR: 2.44, 95% CI: 1.45–4.48), working in the slaughtering area (aRR: 2.35, 95% CI: 1.32–4.45) and being a veterinary inspector (aRR: 4.77, 95% CI: 1.16–23.68) increased infection risk. Sharing accommodation or transportation were not identified as risk factors for infection. Our results suggest that workplace was the main risk factor for infection spread. These results highlight the importance of implementing preventive measures targeting meat processing plants. Face masks, distancing, staggering breaks, increased hygiene and regular testing for SARS-CoV2 helped limit this outbreak, as the plant remained open throughout the outbreak.
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Seroprevalence of antibodies against SARS-CoV-2 in the adult population during the pre-vaccination period, Norway, winter 2020/21
BackgroundSince March 2020, 440 million people worldwide have been diagnosed with COVID-19, but the true number of infections with SARS-CoV-2 is higher. SARS-CoV-2 antibody seroprevalence can add crucial epidemiological information about population infection dynamics.
AimTo provide a large population-based SARS-CoV-2 seroprevalence survey from Norway; we estimated SARS-CoV-2 seroprevalence before introduction of vaccines and described its distribution across demographic groups.
MethodsIn this population-based cross-sectional study, a total of 110,000 people aged 16 years or older were randomly selected during November–December 2020 and invited to complete a questionnaire and provide a dried blood spot (DBS) sample.
ResultsThe response rate was 30% (31,458/104,637); compliance rate for return of DBS samples was 88% (27,700/31,458). National weighted and adjusted seroprevalence was 0.9% (95% CI (confidence interval): 0.7–1.0). Seroprevalence was highest among those aged 16–19 years (1.9%; 95% CI: 0.9–2.9), those born outside the Nordic countries 1.4% (95% CI: 1.0–1.9), and in the counties of Oslo 1.7% (95% CI: 1.2–2.2) and Vestland 1.4% (95% CI: 0.9–1.8). The ratio of SARS-CoV-2 seroprevalence (0.9%) to cumulative incidence of virologically detected cases by mid-December 2020 (0.8%) was slightly above one. SARS-CoV-2 seroprevalence was low before introduction of vaccines in Norway and was comparable to virologically detected cases, indicating that most cases in the first 10 months of the pandemic were detected.
ConclusionFindings suggest that preventive measures including contact tracing have been effective, people complied with physical distancing recommendations, and local efforts to contain outbreaks have been essential.
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Enhancing epidemiological surveillance of the emergence of the SARS-CoV-2 Omicron variant using spike gene target failure data, England, 15 November to 31 December 2021
Paula B Blomquist , Jessica Bridgen , Neil Bray , Anne Marie O’Connell , Daniel West , Natalie Groves , Eileen Gallagher , Lara Utsi , Christopher I Jarvis , Jo L Hardstaff , Chloe Byers , Soeren Metelmann , David Simons , Asad Zaidi , Katherine A Twohig , Bethan Savagar , Alessandra Løchen , Cian Ryan , Katie Wrenn , María Saavedra-Campos , Zahidul Abedin , Isaac Florence , Paul Cleary , Richard Elson , Roberto Vivancos and Iain R LakeWhen SARS-CoV-2 Omicron emerged in 2021, S gene target failure enabled differentiation between Omicron and the dominant Delta variant. In England, where S gene target surveillance (SGTS) was already established, this led to rapid identification (within ca 3 days of sample collection) of possible Omicron cases, alongside real-time surveillance and modelling of Omicron growth. SGTS was key to public health action (including case identification and incident management), and we share applied insights on how and when to use SGTS.
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Large-scale decontamination of disposable FFP2 and FFP3 respirators by hydrogen peroxide vapour, Finland, April to June 2020
Katri Laatikainen , Markku Mesilaakso , Ilpo Kulmala , Erja Mäkelä , Petri Ruutu , Outi Lyytikäinen , Susanna Tella , Tarmo Humppi , Satu Salo , Tuuli Haataja , Kristiina Helminen , Henri Karppinen , Heli Kähkönen , Tarja Vainiola , Kirsimarja Blomqvist , Sirpa Laitinen , Kati Peltonen , Marko Laaksonen , Timo Ristimäki and Jouni KoivistoBackgroundThe shortage of FFP2 and FFP3 respirators posed a serious threat to the operation of the healthcare system at the onset of the COVID-19 pandemic.
AimOur aim was to develop and validate a large-scale facility that uses hydrogen peroxide vapour for the decontamination of used respirators.
MethodsA multidisciplinary and multisectoral ad hoc group of experts representing various organisations was assembled to implement the collection and transport of used FFP2 and FFP3 respirators from hospitals covering 86% of the Finnish population. A large-scale decontamination facility using hydrogen peroxide vapour was designed and constructed. Microbiological tests were used to confirm efficacy of hydrogen peroxide vapour decontamination together with a test to assess the effect of decontamination on the filtering efficacy and fit of respirators. Bacterial and fungal growth in stored respirators was determined by standard methods.
ResultsLarge-scale hydrogen peroxide vapour decontamination of a range of FFP2 and FFP3 respirator models effectively reduced the recovery of biological indicators: Geobacillus stearothermophilus and Bacillus atrophaeus spores, as well as model virus bacteriophage MS2. The filtering efficacy and facial fit after hydrogen peroxide vapour decontamination were not affected by the process. Microbial growth in the hydrogen peroxide vapour-treated respirators indicated appropriate microbial cleanliness.
ConclusionsLarge-scale hydrogen peroxide vapour decontamination was validated. After effective decontamination, no significant changes in the key properties of the respirators were detected. European Union regulations should incorporate a facilitated pathway to allow reuse of appropriately decontaminated respirators in a severe pandemic when unused respirators are not available.
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SARS-CoV-2 infection among educational staff in Berlin, Germany, June to December 2020
BackgroundSARS-CoV-2 infections in preschool and school settings potentially bear occupational risks to educational staff.
AimWe aimed to assess the prevalence of SARS-CoV-2 infection in teachers and preschool educators and at identifying factors associated with infection.
MethodsWe analysed cross-sectional data derived from 17,448 voluntary, PCR-based screening tests of asymptomatic educational staff in Berlin, Germany, between June and December 2020 using descriptive statistics and a logistic regression model.
ResultsParticipants were largely female (73.0%), and median age was 41 years (range: 18-78). Overall, SARS-CoV-2 infection proportion was 1.2% (95% CI: 1.0–1.4). Proportion of positive tests in educational staff largely followed community incidence until the start of the second pandemic wave, when an unsteady plateau was reached. Then, the proportion of positive tests in a (concurrent) population survey was 0.9% (95% CI: 0.6–1.4), 1.2% (95% CI: 0.8–1.8) in teachers and 2.6% (95% CI: 1.6–4.0) in preschool educators. Compared with teachers, increased odds of infection were conferred by being a preschool educator (adjusted odds ratio (aOR): 1.6; 95% CI: 1.3–2.0) and by contact with a SARS-CoV-2 infected individual outside of work (aOR: 3.0; 95% CI: 1.5–5.5). In a step-wise backward selection, the best set of associated factors with SARS-CoV-2 infection involved age, occupation, and calendar week.
ConclusionsThese results indicate that preschool educators bear increased odds of SARS-CoV-2 infection compared with teachers. At the same time, the private environment appeared to be a relevant source of SARS-CoV-2 infection for educational staff in 2020.
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Surveillance and return to work of healthcare workers following SARS-CoV-2 Omicron variant infection, Sheffield, England, 17 January to 7 February 2022
More LessThe SARS-CoV-2 Omicron variant has challenged demands to minimise workplace transmission in healthcare settings while maintaining adequate staffing. Policymakers have shortened COVID-19 isolation periods, although little real-world data have evaluated the utility. Our findings from surveillance of 240 healthcare workers from Sheffield Teaching Hospitals, England, show that 55% of affected staff could return before day 10 of isolation with over 25% eligible on day 6, pending two successive negative antigen tests. This outcome is favourable for continuity of healthcare services.
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Estimating the effect of mobility on SARS-CoV-2 transmission during the first and second wave of the COVID-19 epidemic, Switzerland, March to December 2020
More LessIntroductionHuman mobility was considerably reduced during the COVID-19 pandemic. To support disease surveillance, it is important to understand the effect of mobility on transmission.
AimWe compared the role of mobility during the first and second COVID-19 wave in Switzerland by studying the link between daily travel distances and the effective reproduction number (Rt) of SARS-CoV-2.
MethodsWe used aggregated mobile phone data from a representative panel survey of the Swiss population to measure human mobility. We estimated the effects of reductions in daily travel distance on Rt via a regression model. We compared mobility effects between the first (2 March–7 April 2020) and second wave (1 October–10 December 2020).
ResultsDaily travel distances decreased by 73% in the first and by 44% in the second wave (relative to February 2020). For a 1% reduction in average daily travel distance, Rt was estimated to decline by 0.73% (95% credible interval (CrI): 0.34–1.03) in the first wave and by 1.04% (95% CrI: 0.66–1.42) in the second wave. The estimated mobility effects were similar in both waves for all modes of transport, travel purposes and sociodemographic subgroups but differed for movement radius.
ConclusionMobility was associated with SARS-CoV-2 Rt during the first two epidemic waves in Switzerland. The relative effect of mobility was similar in both waves, but smaller mobility reductions in the second wave corresponded to smaller overall reductions in Rt. Mobility data from mobile phones have a continued potential to support real-time surveillance of COVID-19.
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Inferring transmission fitness advantage of SARS-CoV-2 variants of concern from wastewater samples using digital PCR, Switzerland, December 2020 through March 2021
BackgroundThroughout the COVID-19 pandemic, SARS-CoV-2 genetic variants of concern (VOCs) have repeatedly and independently arisen. VOCs are characterised by increased transmissibility, increased virulence or reduced neutralisation by antibodies obtained from prior infection or vaccination. Tracking the introduction and transmission of VOCs relies on sequencing, typically whole genome sequencing of clinical samples. Wastewater surveillance is increasingly used to track the introduction and spread of SARS-CoV-2 variants through sequencing approaches.
AimHere, we adapt and apply a rapid, high-throughput method for detection and quantification of the relative frequency of two deletions characteristic of the Alpha, Beta, and Gamma VOCs in wastewater.
MethodsWe developed drop-off RT-dPCR assays and an associated statistical approach implemented in the R package WWdPCR to analyse temporal dynamics of SARS-CoV-2 signature mutations (spike Δ69–70 and ORF1a Δ3675–3677) in wastewater and quantify transmission fitness advantage of the Alpha VOC.
ResultsBased on analysis of Zurich wastewater samples, the estimated transmission fitness advantage of SARS-CoV-2 Alpha based on the spike Δ69–70 was 0.34 (95% confidence interval (CI): 0.30–0.39) and based on ORF1a Δ3675–3677 was 0.53 (95% CI: 0.49–0.57), aligning with the transmission fitness advantage of Alpha estimated by clinical sample sequencing in the surrounding canton of 0.49 (95% CI: 0.38–0.61).
ConclusionDigital PCR assays targeting signature mutations in wastewater offer near real-time monitoring of SARS-CoV-2 VOCs and potentially earlier detection and inference on transmission fitness advantage than clinical sequencing.
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Molecular epidemiology of the SARS-CoV-2 variant Omicron BA.2 sub-lineage in Denmark, 29 November 2021 to 2 January 2022
Jannik Fonager , Marc Bennedbæk , Peter Bager , Jan Wohlfahrt , Kirsten Maren Ellegaard , Anna Cäcilia Ingham , Sofie Marie Edslev , Marc Stegger , Raphael Niklaus Sieber , Ria Lassauniere , Anders Fomsgaard , Troels Lillebaek , Christina Wiid Svarrer , Frederik Trier Møller , Camilla Holten Møller , Rebecca Legarth , Thomas Vognbjerg Sydenham , Kat Steinke , Sarah Juel Paulsen , José Alfredo Samaniego Castruita , Uffe Vest Schneider , Christian Højte Schouw , Xiaohui Chen Nielsen , Maria Overvad , Rikke Thoft Nielsen , Rasmus L Marvig , Martin Schou Pedersen , Lene Nielsen , Line Lynge Nilsson , Jonas Bybjerg-Grauholm , Irene Harder Tarpgaard , Tine Snejbjerg Ebsen , Janni Uyen Hoa Lam , Vithiagaran Gunalan and Morten RasmussenFollowing emergence of the SARS-CoV-2 variant Omicron in November 2021, the dominant BA.1 sub-lineage was replaced by the BA.2 sub-lineage in Denmark. We analysed the first 2,623 BA.2 cases from 29 November 2021 to 2 January 2022. No epidemiological or clinical differences were found between individuals infected with BA.1 versus BA.2. Phylogenetic analyses showed a geographic east-to-west transmission of BA.2 from the Capital Region with clusters expanding after the Christmas holidays. Mutational analysis shows distinct differences between BA.1 and BA.2.
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Transmission dynamics and epidemiological characteristics of SARS-CoV-2 Delta variant infections in Guangdong, China, May to June 2021
Min Kang , Hualei Xin , Jun Yuan , Sheikh Taslim Ali , Zimian Liang , Jiayi Zhang , Ting Hu , Eric HY Lau , Yingtao Zhang , Meng Zhang , Benjamin J Cowling , Yan Li and Peng WuBackgroundThe Delta variant of SARS-CoV-2 had become predominant globally by November 2021.
AimWe evaluated transmission dynamics and epidemiological characteristics of the Delta variant in an outbreak in southern China.
MethodsData on confirmed COVID-19 cases and their close contacts were retrospectively collected from the outbreak that occurred in Guangdong, China in May and June 2021. Key epidemiological parameters, temporal trend of viral loads and secondary attack rates were estimated. We also evaluated the association of vaccination with viral load and transmission.
ResultsWe identified 167 patients infected with the Delta variant in the Guangdong outbreak. Mean estimates of latent and incubation period were 3.9 days and 5.8 days, respectively. Relatively higher viral load was observed in infections with Delta than in infections with wild-type SARS-CoV-2. Secondary attack rate among close contacts of cases with Delta was 1.4%, and 73.1% (95% credible interval (CrI): 32.9–91.4) of the transmissions occurred before onset. Index cases without vaccination (adjusted odds ratio (aOR): 2.84; 95% CI: 1.19–8.45) or with an incomplete vaccination series (aOR: 6.02; 95% CI: 2.45–18.16) were more likely to transmit infection to their contacts than those who had received the complete primary vaccination series.
DiscussionPatients infected with the Delta variant had more rapid symptom onset compared with the wild type. The time-varying serial interval should be accounted for in estimation of reproduction numbers. The higher viral load and higher risk of pre-symptomatic transmission indicated the challenges in control of infections with the Delta variant.
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Risk of severe COVID-19 from the Delta and Omicron variants in relation to vaccination status, sex, age and comorbidities – surveillance results from southern Sweden, July 2021 to January 2022
We compared the risk of severe COVID-19 during two periods 2021 and 2022 when Delta and Omicron, respectively, were the dominating virus variants in Scania county, Sweden. We adjusted for differences in sex, age, comorbidities, prior infection and vaccination. Risk of severe disease from Omicron was markedly lower among vaccinated cases. It was also lower among the unvaccinated but remained high (> 5%) for older people and middle-aged men with two or more comorbidities. Efforts to increase vaccination uptake should continue.
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