Nationwide study on SARS-CoV-2 transmission within households from lockdown to reopening, Denmark, 27 February 2020 to 1 August 2020

BACKGROUND: The 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. AIM: The objective of this observational study was to investigate SARS-CoV-2 transmission in Danish households during the early stages of the COVID-19 pandemic. METHODS: We 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. RESULTS: We 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). CONCLUSIONS: Although 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

A common framework for using and reporting consumer purchase data (CPD) in foodborne outbreak investigations in Europe

Publisher Copyright: © 2021 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.Consumer purchase data (CPD) can be a powerful tool in the investigation of foodborne outbreaks through analyses of electronic records of food that individuals buy. The objective of this study was to develop a common framework for use of CPD in foodborne outbreak investigations using the expertise of European public health professionals from 11 European countries. We also aimed to describe barriers and limitations preventing CPD utilization. CPD are mainly gathered from supermarket loyalty programmes, smaller consortia, and independent supermarkets. Privacy legislation governing CPD was perceived as the most crucial barrier for CPD usage, but still resolvable. The main practical challenges were obtaining consumer consent for CPD usage, the associated workload, data access, format, and analysis. Harmonising methods and reporting across countries, standardised consent forms and electronic consent methods were identified as solutions. This guideline was developed to support outbreak investigators in overcoming barriers in using CPD, thereby increasing public health professionals’ application and value of this powerful investigation tool. In addition, we hope this framework will lead to more public health institutions, in collaboration with food safety authorities, making use of CPD in outbreak investigations in the future.Peer reviewe

Observed protection against SARS-CoV-2 reinfection following a primary infection: A Danish cohort study among unvaccinated using two years of nationwide PCR-test data.

Background: The level of protection after a SARS-CoV-2 infection against reinfection and COVID-19 disease remains important with much of the world still unvaccinated. Methods: Analysing nationwide, individually referable, Danish register data including RT-PCR-test results, we conducted a cohort study using Cox regression to compare SARS-CoV-2 infection rates before and after a primary infection among still unvaccinated individuals, adjusting for sex, age, comorbidity and residency region. Estimates of protection against infection were calculated as 1 minus the hazard ratio. Estimates of protection against symptomatic infections and infections leading to hospitalisation were also calculated. The prevalence of infections classified as symptomatic or asymptomatic was compared for primary infections and reinfections. The study also assessed protection against each of the main viral variants after a primary infection with an earlier variant by restricting follow-up time to distinct, mutually exclusive periods during which each variant dominated. Findings: Until 1 July 2021 the estimated protection against reinfection was 83.4% (95%CI: 82.2-84.6%); but lower for the 65+ year-olds (72.2%; 95%CI: 53.2-81.0%). Moderately higher estimates were found for protection against symptomatic disease, 88.3% overall (95%CI: 85.9-90.3%). First-time cases who reported no symptoms were more likely to experience a reinfection (odds ratio: 1.48; 95%CI: 1.35-1.62). By autumn 2021, when infections were almost exclusively caused by the Delta variant, the estimated protection following a recent first infection was 91.3% (95%CI: 89.7-92.7%) compared to 71.4% (95%CI: 66.9-75.3%) after a first infection over a year earlier. With Omicron, a first infection with an earlier variant in the past 3-6 months gave an estimated 51.0% (95%CI: 50.1-52.0%) protection, whereas a first infection longer than 12 months earlier provided only 19.0% (95%CI: 17.2-20.5%) protection. Protection by an earlier variant-infection against hospitalisation due to a new infection was estimated at: 86.6% (95%CI: 46.3-96.7%) for Alpha, 97.2% (95%CI: 89.0-99.3%) for Delta, and 69.8% (95%CI: 51.5-81.2%) for the Omicron variant. Interpretation: SARS-CoV-2 infection offered a high level of sustained protection against reinfection, comparable with that offered by vaccines, but decreased with the introduction of new main virus variants; dramatically so when Omicron appeared. Protection was lower among the elderly but appeared more pronounced following symptomatic compared to asymptomatic infections. The level of estimated protection against serious disease was somewhat higher than that against infection and possibly longer lasting. Decreases in protection against reinfection, seemed primarily to be driven by viral evolution. Funding: None

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 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

Simulation and identification of foodborne outbreaks in a large supermarket consumer purchase dataset

Foodborne outbreaks represent a significant public health burden. Outbreak investigations are often challenging and time-consuming, and most outbreak vehicles remain unidentified. The development of alternative investigative strategies is therefore needed. Automated analysis of Consumer Purchase Data (CPD) gathered by retailers represents one such alternative strategy. CPD-aided investigations do not require trawling questionnaires to create a hypothesis and can provide analytical measures of association by direct data analysis. Here, we used anonymized CPD from 920,384 customers enrolled in Norway’s largest supermarket loyalty program to simulate foodborne outbreaks across a range of different parameters and scenarios. We then applied a logistic regression model to calculate an odds ratio for each of the different possible food vehicles. By this method, we were able to identify outbreak vehicles with a 90% accuracy within a median of 6 recorded case-patients. The outbreak vehicle identification rate declined significantly when using data from only one of two retailers involved in a simulated outbreak. Performance was also reduced in simulations that restricted analysis from product ID to the product group levels accessible by trawling questionnaires. Our results show that—assuming agreements are in place with major retailers—CPD collection and analysis can solve foodborne outbreaks originating from supermarkets both more rapidly and accurately than than questionnaire-based methods and might provide a significant enhancement to current outbreak investigation methods

Overweight in childhood and consumer purchases in a Danish cohort

BACKGROUND: Prevention and management of childhood overweight involves the entire family. We aimed to investigate purchase patterns in households with at least one member with overweight in childhood by describing expenditure on different food groups.METHODS: This Danish register-based cohort study included households where at least one member donated receipts concerning consumers purchases in 2019-2021 and at least one member had their Body mass index (BMI) measured in childhood within ten years prior to first purchase. A probability index model was used to evaluate differences in proportion expenditure spent on specific food groups.RESULTS: We identified 737 households that included a member who had a BMI measurement in childhood, 220 with overweight and 517 with underweight or normal weight (reference households). Adjusting for education, income, family type, and urbanization, households with a member who had a BMI classified as overweight in childhood had statistically significant higher probability of spending a larger proportion of expenditure on ready meals 56.29% (95% CI: 51.70;60.78) and sugary drinks 55.98% (95% CI: 51.63;60.23). Conversely, they had a statistically significant lower probability of spending a larger proportion expenditure on vegetables 38.44% (95% CI: 34.09;42.99), compared to the reference households.CONCLUSION: Households with a member with BMI classified as overweight in childhood spent more on unhealthy foods and less on vegetables, compared to the reference households. This study highlights the need for household/family-oriented nutrition education and intervention.</p