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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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Seroprevalence of IgG antibodies against SARS-CoV-2 – a serial prospective cross-sectional nationwide study of residual samples, Belgium, March to October 2020
BackgroundTo control epidemic waves, it is important to know the susceptibility to SARS-CoV-2 and its evolution over time in relation to the control measures taken.
AimTo assess the evolving SARS-CoV-2 seroprevalence and seroincidence related to the first national lockdown in Belgium, we performed a nationwide seroprevalence study, stratified by age, sex and region using 3,000–4,000 residual samples during seven periods between 30 March and 17 October 2020.
MethodsWe analysed residual sera from ambulatory patients for IgG antibodies against the SARS-CoV-2 S1 protein with a semiquantitative commercial ELISA. Weighted seroprevalence (overall and by age category and sex) and seroincidence during seven consecutive periods were estimated for the Belgian population while accommodating test-specific sensitivity and specificity.
ResultsThe weighted overall seroprevalence initially increased from 1.8% (95% credible interval (CrI): 1.0–2.6) to 5.3% (95% CrI: 4.2–6.4), implying a seroincidence of 3.4% (95% CrI: 2.4–4.6) between the first and second collection period over a period of 3 weeks during lockdown (start lockdown mid-March 2020). Thereafter, seroprevalence stabilised, however, significant decreases were observed when comparing the third with the fifth, sixth and seventh period, resulting in negative seroincidence estimates after lockdown was lifted. We estimated for the last collection period mid-October 2020 a weighted overall seroprevalence of 4.2% (95% CrI: 3.1–5.2).
ConclusionDuring lockdown, an initially small but increasing fraction of the Belgian population showed serologically detectable signs of exposure to SARS-CoV-2, which did not further increase when confinement measures eased and full lockdown was lifted.
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From more testing to smart testing: data-guided SARS-CoV-2 testing choices, the Netherlands, May to September 2020
BackgroundSARS-CoV-2 RT-PCR assays are more sensitive than rapid antigen detection assays (RDT) and can detect viral RNA even after an individual is no longer infectious. RDT can reduce the time to test and the results might better correlate with infectiousness.
AimWe assessed the ability of five RDT to identify infectious COVID-19 cases and systematically recorded the turnaround time of RT-PCR testing.
MethodsSensitivity of RDT was determined using a serially diluted SARS-CoV-2 stock with known viral RNA concentration. The probability of detecting infectious virus at a given viral load was calculated using logistic regression of viral RNA concentration and matched culture results of 78 specimens from randomly selected non-hospitalised cases. The probability of each RDT to detect infectious cases was calculated as the sum of the projected probabilities for viral isolation success for every viral RNA load found at the time of diagnosis in 1,739 confirmed non-hospitalised COVID-19 cases.
ResultsThe distribution of quantification cycle values and estimated RNA loads for patients reporting to drive-through testing was skewed to high RNA loads. With the most sensitive RDT (Abbott and SD Biosensor), 97.30% (range: 88.65–99.77) of infectious individuals would be detected. This decreased to 92.73% (range: 60.30–99.77) for Coris BioConcept and GenBody, and 75.53% (range: 17.55–99.77) for RapiGEN. Only 32.9% of RT-PCR results were available on the same day as specimen collection.
ConclusionThe most sensitive RDT detected infectious COVID-19 cases with high sensitivity and may considerably improve containment through more rapid isolation and contact tracing.
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COVID-19 mortality, excess mortality, deaths per million and infection fatality ratio, Belgium, 9 March 2020 to 28 June 2020
Geert Molenberghs , Christel Faes , Johan Verbeeck , Patrick Deboosere , Steven Abrams , Lander Willem , Jan Aerts , Heidi Theeten , Brecht Devleesschauwer , Natalia Bustos Sierra , Françoise Renard , Sereina Herzog , Patrick Lusyne , Johan Van der Heyden , Herman Van Oyen , Pierre Van Damme and Niel HensBackgroundCOVID-19 mortality, excess mortality, deaths per million population (DPM), infection fatality ratio (IFR) and case fatality ratio (CFR) are reported and compared for many countries globally. These measures may appear objective, however, they should be interpreted with caution.
AimWe examined reported COVID-19-related mortality in Belgium from 9 March 2020 to 28 June 2020, placing it against the background of excess mortality and compared the DPM and IFR between countries and within subgroups.
MethodsThe relation between COVID-19-related mortality and excess mortality was evaluated by comparing COVID-19 mortality and the difference between observed and weekly average predictions of all-cause mortality. DPM were evaluated using demographic data of the Belgian population. The number of infections was estimated by a stochastic compartmental model. The IFR was estimated using a delay distribution between infection and death.
ResultsIn the study period, 9,621 COVID-19-related deaths were reported, which is close to the excess mortality estimated using weekly averages (8,985 deaths). This translates to 837 DPM and an IFR of 1.5% in the general population. Both DPM and IFR increase with age and are substantially larger in the nursing home population.
DiscussionDuring the first pandemic wave, Belgium had no discrepancy between COVID-19-related mortality and excess mortality. In light of this close agreement, it is useful to consider the DPM and IFR, which are both age, sex, and nursing home population-dependent. Comparison of COVID-19 mortality between countries should rather be based on excess mortality than on COVID-19-related mortality.
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Risk reduction of severe outcomes in vaccinated COVID-19 cases: an analysis of surveillance data from Estonia, Ireland, Luxembourg and Slovakia, January to November 2021
Despite high COVID-19 vaccine coverage in the EU/EEA, there are increasing reports of SARS-CoV-2 infections and hospitalisations in vaccinated individuals. Using surveillance data from Estonia, Ireland, Luxembourg and Slovakia (January–November 2021), we estimated risk reduction of severe outcomes in vaccinated cases. Increasing age remains the most important driver of severity, and vaccination significantly reduces risk in all ages for hospitalisation (adjusted relative risk (aRR): 0.32; 95% confidence interval (CI): 0.26–0.39) and death (aRR: 0.20; 95% CI: 0.13–0.29).
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SARS-CoV-2 testing in patients with low COVID-19 suspicion at admission to a tertiary care hospital, Stockholm, Sweden, March to September 2020
BackgroundUniversal SARS-CoV-2 testing at hospital admission has been proposed to prevent nosocomial transmission.
AimTo investigate SARS-CoV-2 positivity in patients tested with low clinical COVID-19 suspicion at hospital admission.
MethodsWe characterised a retrospective cohort of patients admitted to Karolinska University Hospital tested for SARS-CoV-2 by PCR from March to September 2020, supplemented with an in-depth chart review (16 March–12 April). We compared positivity rates in patients with and without clinical COVID-19 suspicion with Spearman’s rank correlation coefficient. We used multivariable logistic regression to identify factors associated with test positivity.
ResultsFrom March to September 2020, 66.9% (24,245/36,249) admitted patient episodes were tested; of those, 61.2% (14,830/24,245) showed no clinical COVID-19 suspicion, and the positivity rate was 3.2% (469/14,830). There was a strong correlation of SARS-CoV-2 positivity in patients with low vs high COVID-19 suspicion (rho = 0.92; p < 0.001).
From 16 March to 12 April, the positivity rate was 3.9% (58/1,482) in individuals with low COVID-19 suspicion, and 3.1% (35/1,114) in asymptomatic patients. Rates were higher in women (5.0%; 45/893) vs men (2.0%; 12/589; p = 0.003), but not significantly different if pregnant women were excluded (3.7% (21/566) vs 2.2% (12/589); p = 0.09). Factors associated with SARS-CoV-2 positivity were testing of pregnant women before delivery (odds ratio (OR): 2.6; 95% confidence interval (CI): 1.3–5.4) and isolated symptoms in adults (OR: 3.3; 95% CI: 1.8–6.3).
ConclusionsThis study shows a relatively high SARS-CoV-2 positivity rate in patients with low COVID-19 suspicion upon hospital admission. Universal SARS-CoV-2 testing of pregnant women before delivery should be considered.
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Early chains of transmission of COVID-19 in France, January to March 2020
IntroductionSARS-CoV-2, the virus that causes COVID-19, has spread rapidly worldwide. In January 2020, a surveillance system was implemented in France for early detection of cases and their contacts to help limit secondary transmissions.
AimTo use contact-tracing data collected during the initial phase of the COVID-19 pandemic to better characterise SARS-CoV-2 transmission.
MethodsWe analysed data collected during contact tracing and retrospective epidemiological investigations in France from 24 January to 30 March 2020. We assessed the secondary clinical attack rate and characterised the risk of a contact becoming a case. We described chains of transmission and estimated key parameters of spread.
ResultsDuring the study period, 6,082 contacts of 735 confirmed cases were traced. The overall secondary clinical attack rate was 4.1% (95% confidence interval (CI): 3.6–4.6), increasing with age of index case and contact. Compared with co-workers/friends, family contacts were at higher risk of becoming cases (adjusted odds ratio (AOR): 2.1, 95% CI: 1.4–3.0) and nosocomial contacts were at lower risk (AOR: 0.3, 95% CI: 0.1–0.7). Of 328 infector/infectee pairs, 49% were family members. The distribution of secondary cases was highly over-dispersed: 80% of secondary cases were caused by 10% of cases. The mean serial interval was 5.1 days (interquartile range (IQR): 2–8 days) in contact tracing pairs, where late transmission events may be censored, and 6.8 (3–8) days in pairs investigated retrospectively.
ConclusionThis study increases knowledge of SARS-CoV-2 transmission, including the importance of superspreading events during the onset of the pandemic.
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Epidemiological and clinical insights from SARS-CoV-2 RT-PCR crossing threshold values, France, January to November 2020
Samuel Alizon , Christian Selinger , Mircea T Sofonea , Stéphanie Haim-Boukobza , Jean-Marc Giannoli , Laetitia Ninove , Sylvie Pillet , Vincent Thibault , Alexis de Rougemont , Camille Tumiotto , Morgane Solis , Robin Stephan , Céline Bressollette-Bodin , Maud Salmona , Anne-Sophie L’Honneur , Sylvie Behillil , Caroline Lefeuvre , Julia Dina , Sébastien Hantz , Cédric Hartard , David Veyer , Héloïse M Delagrèverie , Slim Fourati , Benoît Visseaux , Cécile Henquell , Bruno Lina , Vincent Foulongne , Sonia Burrel and on behalf of the SFM COVID-19 study groupBackgroundThe COVID-19 pandemic has led to an unprecedented daily use of RT-PCR tests. These tests are interpreted qualitatively for diagnosis, and the relevance of the test result intensity, i.e. the number of quantification cycles (Cq), is debated because of strong potential biases.
AimWe explored the possibility to use Cq values from SARS-CoV-2 screening tests to better understand the spread of an epidemic and to better understand the biology of the infection.
MethodsWe used linear regression models to analyse a large database of 793,479 Cq values from tests performed on more than 2 million samples between 21 January and 30 November 2020, i.e. the first two pandemic waves. We performed time series analysis using autoregressive integrated moving average (ARIMA) models to estimate whether Cq data information improves short-term predictions of epidemiological dynamics.
ResultsAlthough we found that the Cq values varied depending on the testing laboratory or the assay used, we detected strong significant trends associated with patient age, number of days after symptoms onset or the state of the epidemic (the temporal reproduction number) at the time of the test. Furthermore, knowing the quartiles of the Cq distribution greatly reduced the error in predicting the temporal reproduction number of the COVID-19 epidemic.
ConclusionOur results suggest that Cq values of screening tests performed in the general population generate testable hypotheses and help improve short-term predictions for epidemic surveillance.
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Investigation of outbreak cases infected with the SARS-CoV-2 B.1.640 variant in a fully vaccinated elderly population, Normandy, France, November to December 2021
Three confirmed infections with the SARS-CoV-2 B.1.640 variant under monitoring were reported in Normandy, north-western France in late November 2021. Investigations led to the identification of two events linked to the same cluster. A total of 75 confirmed and probable B.1.640 cases were reported. All had completed the primary vaccination series. Sixty-two cases were older than 65 years. Fifty-six cases had symptoms and four were hospitalised. This investigation provides preliminary results concerning a variant with limited information currently available.
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Nationwide study on SARS-CoV-2 transmission within households from lockdown to reopening, Denmark, 27 February 2020 to 1 August 2020
BackgroundThe COVID-19 pandemic is one of the most serious global public health threats of recent times. Understanding SARS-CoV-2 transmission is key for outbreak response and to take action against the spread of disease. Transmission within the household is a concern, especially because infection control is difficult to apply within this setting.
AimThe objective of this observational study was to investigate SARS-CoV-2 transmission in Danish households during the early stages of the COVID-19 pandemic.
MethodsWe used comprehensive administrative register data from Denmark, comprising the full population and all COVID-19 tests from 27 February 2020 to 1 August 2020, to estimate household transmission risk and attack rate.
ResultsWe found that the day after receiving a positive test result within the household, 35% (788/2,226) of potential secondary cases were tested and 13% (98/779) of these were positive. In 6,782 households, we found that 82% (1,827/2,226) of potential secondary cases were tested within 14 days and 17% (371/2,226) tested positive as secondary cases, implying an attack rate of 17%. We found an approximate linear increasing relationship between age and attack rate. We investigated the transmission risk from primary cases by age, and found an increasing risk with age of primary cases for adults (aged ≥ 15 years), while the risk seems to decrease with age for children (aged < 15 years).
ConclusionsAlthough there is an increasing attack rate and transmission risk of SARS-CoV-2 with age, children are also able to transmit SARS-CoV-2 within the household.
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