Patterns of testing in the extensive Danish national SARS-CoV-2 test set-up

Comparative effectiveness of bivalent BA.4-5 or BA.1 mRNA booster vaccines among immunocompromised individuals across three Nordic countries: A nationwide cohort study

OBJECTIVES

To estimate the effectiveness and waning of the bivalent BA.4-5 or BA.1 mRNA booster vaccine against Covid-19-related hospitalization and death in immunocompromised individuals.

METHODS

Nationwide analyses across Nordic countries from 1 September 2022 to 31 October 2023 using a matched cohort design. Individuals boosted with a BA.4-5 or BA.1 vaccine were matched 1:1 with unboosted individuals. The outcomes of interest were country-combined vaccine effectiveness (VE) estimates against Covid-19-related hospitalization and death at day 270 of follow-up. Waning was assessed in 45-day intervals.

RESULTS

A total of 352,762 BA.4-5 and 191,070 BA.1 booster vaccine doses were included. At day 270, the comparative VE against Covid-19-related hospitalization was 34.2% (95% CI, 7.1% to 61.3%) for the bivalent BA.4-5 vaccine and 42.6% (95% CI, 31.3% to 53.9%) for the BA.1 vaccine compared with matched unboosted. The comparative VE against Covid-19-related death was 53.9% (95% CI, 38.6% to 69.3%) for the bivalent BA.4-5 vaccine and 57.9% (95% CI, 48.5% to 67.4%) for the BA.1 vaccine.

CONCLUSIONS

In immunocompromised individuals, vaccination with bivalent BA.4-5 or BA.1 booster lowered the risk of Covid-19-related hospitalization and death over a follow-up period of 9 months. The effectiveness was highest during the first months since vaccination with subsequent gradual waning.

Post-COVID-19 Condition Fatigue Outcomes Among Danish Residents

Importance

Fatigue remains one of the most common and debilitating symptoms of post-COVID-19 condition; however, existing studies are limited to select populations and often lack noninfected controls. It also remains unclear to what extent severity of infection and psychiatric conditions, which are often linked to chronic fatigue, modify the risk of post-COVID-19 condition fatigue symptoms.

Objective

To evaluate the impact of SARS-CoV-2 infection on self-reported fatigue and postexertional malaise over time and to explore possible risk factors, such as the impact of acute SARS-CoV-2 hospitalization and preexisting psychiatric conditions on postacute fatigue.

Design, Setting, and Participants

In this cohort study, Danish residents aged 15 years and older were invited to participate in the EFTER-COVID survey, which used repeated, self-reported online questionnaires that collected information on fatigue (Fatigue Assessment Scale) and postexertional malaise scores (DePaul Symptom Questionnaire) after individuals' index SARS-CoV-2 polymerase chain reaction test. Participants were included if they completed a baseline and at least 1 follow-up questionnaire 2 to 18 months after testing for SARS-CoV-2.

Exposure

Testing for SARS-CoV-2 infection.

Main Outcomes and Measures

The primary outcomes were fatigue and postexertional malaise 2 to 18 months after testing. Mixed-effects models were used to compare scores between SARS-CoV-2 test-positive and test-negative individuals (testing period April 2021 to February 2023).

Results

Of a total of 50 115 participants (median [IQR] age at test date, 57 [46-67] years; 29 774 female [59.4%]), 25 249 were test positive and 24 866 were test negative. Most participants were vaccinated with at least 2 doses (21 164 test-negative participants [85.1%] and 22 120 test-positive participants [87.6%]) before their SARS-CoV-2 index test and fatigue reporting. In the period 2 to 18 months after testing, SARS-CoV-2 infection was associated with a small but significant 3% increase in self-reported fatigue scores (score ratio [SR], 1.03; 95% CI, 1.03-1.04) and higher odds of self-reported postexertional malaise (odds ratio, 2.04; 95% CI, 1.81-2.30), compared with test-negative participants. In the same period, hospitalization with SARS-CoV-2 increased fatigue scores by 23% (SR, 1.23; 95% CI, 1.20-1.26) compared with test-negative participants. Preexisting psychiatric conditions did not significantly modify postacute fatigue scores.

Conclusions and Relevance

In this cohort study, SARS-CoV-2 infection was associated with a subtle increase in self-reported fatigue and postexertional malaise symptoms 2 to 18 months after mild infection. In contrast, individuals hospitalized with acute SARS-CoV-2 experienced a more substantial increase in postacute symptoms. Preexisting psychiatric conditions did not significantly modify the risk of postacute fatigue symptoms. The findings largely captured symptoms following first-time infections in a population where most had been vaccinated. Persons who experienced severe acute infection may benefit from clinical follow-up for fatigue.

Automated local lockdowns for SARS-CoV-2 epidemic control-assessment of effect by controlled interrupted time series analysis

Objectives

During the COVID-19 pandemic, broad non-pharmaceutical interventions such as national lockdowns were effective but had significant drawbacks, prompting targeted approaches, such as Denmark's localized lockdowns, based on specific epidemiological criteria. This study evaluates the effect of Denmark's automated local lockdown strategy on epidemic control to inform future response.

Methods

This was a register-based controlled interrupted time series analysis, examining SARS-CoV-2 infection rates in Danish parishes from March to September 2021. The matching of control parishes was based on location, time, and pre-lockdown infection trends, with the lockdown's start defined as the day after a parish exceeded the lockdown criteria. Follow-up included 3-week pre-lockdown and 2-week post-lockdown.

Results

A total of 30 parishes were mandated to lockdown, approximately 3.5% of the population of Denmark. A total of 94 control parishes were used as 109 controls. The decrease in the incidence during the 2-week follow-up period after the initiation of the lockdown was 13% points higher in case parishes: in case parishes, the incidence was reduced by 78% compared with 65% in control parishes.

Conclusions

Our findings demonstrate that local lockdowns did have a positive effect in mitigating the spread of the SARS-CoV-2 virus, making them valuable in the fight against the COVID-19 pandemic and an important alternative to national lockdowns.

High-resolution epidemiological landscape from ~290,000 SARS-CoV-2 genomes from Denmark

Vast amounts of pathogen genomic, demographic and spatial data are transforming our understanding of SARS-CoV-2 emergence and spread. We examined the drivers of molecular evolution and spread of 291,791 SARS-CoV-2 genomes from Denmark in 2021. With a sequencing rate consistently exceeding 60%, and up to 80% of PCR-positive samples between March and November, the viral genome set is broadly whole-epidemic representative. We identify a consistent rise in viral diversity over time, with notable spikes upon the importation of novel variants (e.g., Delta and Omicron). By linking genomic data with rich individual-level demographic data from national registers, we find that individuals aged  < 15 and  > 75 years had a lower contribution to molecular change (i.e., branch lengths) compared to other age groups, but similar molecular evolutionary rates, suggesting a lower likelihood of introducing novel variants. Similarly, we find greater molecular change among vaccinated individuals, suggestive of immune evasion. We also observe evidence of transmission in rural areas to follow predictable diffusion processes. Conversely, urban areas are expectedly more complex due to their high mobility, emphasising the role of population structure in driving virus spread. Our analyses highlight the added value of integrating genomic data with detailed demographic and spatial information, particularly in the absence of structured infection surveys.

Short, stringent lockdowns halted SARS-CoV-2 transmissions in Danish municipalities

In late 2020, the focus of the global effort against the COVID-19 pandemic centered around the development of a vaccine, when reports of a mutated SARS-CoV-2 virus variant in a population of 17 million farmed mink came from Denmark, threatening to jeopardize this effort. Spillover infections of the new variant between mink and humans were feared to threaten the efficacy of upcoming vaccines. In this study the ensuing short-lived yet stringent lockdowns imposed in 7 of the countries 98 municipalities are analysed for their effectiveness to reduce SARS-CoV-2 infections. Synthetic counterfactuals are created for each of these municipalities using a weighted average combination of the remaining municipalities not targeted by the stringent measures. This allows for a clear overview regarding the development of test-positivity rates, citizen mobility behaviours and lastly daily infection numbers in response to the restrictions. The findings show that these targeted, short-term lockdowns significantly curtailed further infections, demonstrating a marked decrease, first in citizens mobility and then in daily cases when compared to their synthetic counterfactuals. Overall, the estimates indicate average reductions to infection numbers to be around 31%. This study underscores the potential of strict, yet severe lockdowns in breaking ongoing infection dynamics, by utilising a rare quasi-experimental design case that avoids bias introduced through treatment selection.

Confounding and Negative Control Methods in Observational Study of SARS-CoV-2 Vaccine Effectiveness: A Nationwide, Population-Based Danish Health Registry Study

Background

Observational studies of SARS-CoV-2 vaccine effectiveness are prone to confounding, which can be illustrated using negative control methods.

Methods

Nationwide population-based cohort study including two cohorts of Danish residents 60-90 years of age matched 1:1 on age and sex: A vaccinated and a non-vaccinated cohort, including 61052 SARS-CoV-2 vaccinated individuals between 1 March and 1 July 2021 and 61052 individuals not vaccinated preceding 1 July 2021. From these two cohorts, we constructed negative control cohorts of individuals diagnosed with SARS-CoV-2 infection or acute myocardial infarction, stroke, cancer, low energy fracture, or head-trauma. Outcomes were SARS-CoV-2 infection, negative control outcomes (eg, mammography, prostate biopsy, operation for cataract, malignant melanoma, examination of eye and ear), and death. We used Cox regression to calculate adjusted incidence and mortality rate ratios (aIRR and aMRR).

Results

Risks of SARS-CoV2 infection and all negative control outcomes were elevated in the vaccinated population, ranging from an aIRR of 1.15 (95% CI: 1.09-1.21) for eye examinations to 3.05 (95% CI: 2.24-4.14) for malignant melanoma. Conversely, the risk of death in the SARS-CoV-2 infected cohort and in all negative control cohorts was lower in vaccinated individuals, ranging from an aMRR of 0.23 (95% CI: 0.19-0.26) after SARS-CoV-2 infection to 0.50 (95% CI: 0.37-0.67) after stroke.

Conclusion

Our findings indicate that observational studies of SARS-CoV-2 vaccine effectiveness may be subject to substantial confounding. Therefore, randomized trials are essential to establish vaccine efficacy after the emergence of new SARS-CoV-2 variants and the rollout of multiple booster vaccines.

Variations in the persistence of 5'-end genomic and subgenomic SARS-CoV-2 RNAs in wastewater from aircraft, airports and wastewater treatment plants

Wastewater sequencing has become a powerful supplement to clinical testing in monitoring SARS-CoV-2 infections in the post-COVID-19 pandemic era. While its applications in measuring the viral burden and main circulating lineages in the community have proved their efficacy, the variations in sequencing quality and coverage across the different regions of the SARS-CoV-2 genome are not well understood. Furthermore, it is unclear how different sample origins, viral extraction and concentration methods and environmental factors impact the reads sequenced from wastewater. Using high-coverage, amplicon-based, paired-end read sequencing of viral RNA extracted from wastewater collected directly from aircraft, pooled from different aircraft and airport buildings or from regular wastewater plants, we assessed the genome coverage across the sample groups with a focus on the 5'-end region covering the leader sequence and investigated whether it was possible to detect subgenomic RNA from viral material recovered from wastewater. We identified distinct patterns in the persistence of the different genomic regions across the different types of wastewaters and the existence of chimeric reads mapping to non-amplified regions. Our findings suggest that preservation of the 5'-end of the genome and the ability to detect subgenomic RNA reads, though highly susceptible to environment and sample processing conditions, may be indicative of the quality and amount of the viral RNA present in wastewater.

Cohort profile: EFTER-COVID - a Danish nationwide cohort for assessing the long-term health effects of the COVID-19 pandemic

PURPOSE

To follow SARS-CoV-2-infected persons up to 18 months after a positive test in order to assess the burden and nature of post acute symptoms and health problems.

PARTICIPANTS

Persons in Denmark above 15 years of age, who were tested positive for SARS-CoV-2 during 1 September 2020 to 21 February 2023 using a RT-PCR test. As a reference group, three test-negative individuals were selected for every two test-positive individuals by matching on test date.

FINDINGS TO DATE

In total, 2 427 913 invitations to baseline questionnaires have been sent out and 839 528 baseline questionnaires (34.5%) have been completed. Females, the age group 50-69 years, Danish-born and persons, who had received at least one SARS-CoV-2 vaccination booster dose were more likely to participate. Follow-up questionnaires were sent at 2, 4, 6, 9, 12 and 18 months after the test, with response rates at 42%-54%.

FUTURE PLANS

New participants have been recruited on a daily basis from 1 August 2021 to 23 March 2023. Data collection will continue until the last follow-up questionnaires (at 18 months after test) have been distributed in August 2024.

COVID-19 Rapid Antigen Tests With Self-Collected vs Health Care Worker-Collected Nasal and Throat Swab Specimens: A Randomized Clinical Trial

Importance

Self- or health care worker (HCW)-collected nasal swab specimens are the preferred sampling method to perform rapid antigen testing for COVID-19, but it is debated whether throat specimens can improve test sensitivity.

Objective

To compare the diagnostic accuracy of self- and HCW-collected nasal vs throat swab specimens for COVID-19 rapid antigen testing.

Design, Setting, and Participants

This per-protocol multicenter randomized clinical trial was conducted from February 15 through March 25, 2022. The participants, individuals aged 16 years or older requesting a COVID-19 test for diagnostic or screening purposes, had 4 specimens collected for individual testing at 1 of 2 urban COVID-19 outpatient test centers in Copenhagen, Denmark.

Interventions

Participants were randomized 1:1 to self-collected or HCW-collected nasal and throat swab specimens for rapid antigen testing. Additional HCW-collected nasal and throat swab specimens for reverse transcriptase-polymerase chain reaction (RT-PCR) were used as the reference standard.

Main Outcomes and Measures

The primary outcome was sensitivity to diagnose COVID-19 of a self- vs HCW-collected nasal and throat specimen for rapid antigen testing compared with RT-PCR.

Results

Of 2941 participants enrolled, 2674 (90.9%) had complete test results and were included in the final analysis (1535 [57.4%] women; median age, 40 years [IQR, 28-55 years]); 1074 (40.2%) had COVID-19 symptoms, and 827 (30.9%) were positive for SARS-CoV-2 by RT-PCR. Health care worker-collected throat specimens had higher mean sensitivity than HCW-collected nasal specimens for rapid antigen testing (69.4% [95% CI, 65.1%-73.6%] vs 60.0% [95% CI, 55.4%-64.5%]). However, a subgroup analysis of symptomatic participants found that self-collected nasal specimens were more sensitive than self-collected throat specimens for rapid antigen testing (mean sensitivity, 71.5% [95% CI, 65.3%-77.6%] vs 58.0% [95% CI, 51.2%-64.7%]; P < .001). Combining nasal and throat specimens increased sensitivity for HCW- and self-collected specimens by 21.4 and 15.5 percentage points, respectively, compared with a single nasal specimen (both P < .001).

Conclusions and Relevance

This randomized clinical trial found that a single HCW-collected throat specimen had higher sensitivity for rapid antigen testing for SARS-CoV-2 than a nasal specimen. In contrast, the self-collected nasal specimens had higher sensitivity than throat specimens for symptomatic participants. Adding a throat specimen to the standard practice of collecting a single nasal specimen could improve sensitivity for rapid antigen testing in health care and home-based settings.

Trial Registration

ClinicalTrials.gov Identifier: NCT05209178.

A hybrid register and questionnaire study of Covid-19 and post-acute sick leave in Denmark

Post-acute sick leave is an underexplored indicator of the societal burden of SARS-CoV-2. Here,  we report findings about self-reported sick leave and risk factors thereof from a hybrid survey and register study, which include 37,482 RT-PCR confirmed SARS-CoV-2 cases and 51,336 test-negative controls who were tested during the index- and alpha-dominant waves. We observe that an additional 33 individuals per 1000 took substantial sick leave following acute infection compared to persons with no known history of infection, where substantial sick leave is defined as >1 month of sick leave within the period 1-9 months after the RT-PCR test date. Being female, 50-65 years, or having certain pre-existing health conditions such as obesity, chronic lung diseases, and fibromyalgia each increase risk for taking substantial sick leave. Altogether, these results may help motivate improved diagnostic and treatment options for persons living with post-Covid conditions.

Surveillance of SARS-CoV-2 infection based on self-administered swabs, Denmark, May to July 2022: evaluation of a pilot study

BackgroundDuring the COVID-19 pandemic, the Danish National Institute for Infectious Disease, Statens Serum Institute (SSI) developed a home-based SARS-CoV-2 surveillance system.AimsWe wanted to determine whether a cohort of individuals performing self-administered swabs for PCR at home could support surveillance of SARS-CoV-2, including detection and assessment of new variants. We also aimed to evaluate the logistical setup.MethodsFrom May to July 2022, 10,000 blood donors were invited to participate, along with their household members. Participation required performing a self-swab for 4 consecutive weeks and answering symptom questionnaires via a web app. Swabs were sent by post to SSI for PCR analysis and whole genome sequencing. After study completion, participants were asked to complete a questionnaire concerning their experience.ResultsIn total, 2,186 individuals enrolled (47.4% blood donors), and 1,333 performed self-swabbing (53.0 blood donors), of whom 48 had at least one SARS-CoV-2-positive sample. Fourteen different Omicron subvariants, primarily BA.5 subvariants, were identified by whole genome sequencing (WGS). In total, 29 of the 63 SARS-CoV-2-positive samples were taken from individuals who were asymptomatic at the time of swabbing. Participants collected 2.9 swabs on average, with varying intervals between swabs. Transmission within households was observed in only three of 25 households.ConclusionParticipants successfully performed self-swabs and answered symptom questionnaires. Also, WGS analysis of samples was possible. The system can support surveillance of respiratory pathogens and also holds potential as a diagnostic tool, easing access to test for at-risk groups, while also reducing the burden on healthcare system resources.

Factors associated with the formation of SARS-CoV-2 case-clusters in Danish schools: a nationwide register-based observational study

A register-based retrospective observational study was conducted to describe SARS-CoV-2 cases and case-clusters in schoolchildren of Danish primary and lower secondary schools and identify which factors were associated with the occurrence of case-clusters in schools. The study period was the autumn school semester 2021. Clusters were defined as three or more cases in a school-class level within 14 days. Descriptive analysis was carried out and multivariable logistic regression analysis was performed to determine which factors were associated with case introductions (i.e., primary case) being linked to a cluster. More cases and clusters were identified in lower than in higher class levels. Out of 21,497 cases introduced into a school, 41.6% started a cluster. A higher assumed immunity level in a class level was significantly reducing the odds of a case introduction being linked to a cluster (e.g., assumed immunity of ≥80% vs <20%: OR: 0.28; 95%CI: 0.17-0.44). A previous infection (in the primary case) had a protective effect (OR: 0.58; 95%CI: 0.33-0.99). This study suggests that most cases appearing in schools did not induce clusters, but that once cluster occur sizes can be large. It further indicates that vaccination of children markedly reduces the risk of secondary infections.