Indirect effectiveness of COVID-19 vaccines in the pre-omicron and omicron periods: a nation-wide test-negative case-control study in Brazil.

BACKGROUND: Mass COVID-19 immunisation campaigns altered the pandemic's progress by protecting the vaccine recipient and reducing transmission. However, evidence for indirect vaccine effectiveness (IVE) is limited due to the difficulties of ascertaining this type of protection. METHODS: Using linked national Brazilian databases, we adapted the test-negative design to evaluate the IVE against symptomatic infection. We analysed data from January 1-December 1, 2021 (Pre-Omicron) and January 1-April 30, 2022 (Omicron BA.1 and BA.2). We compared the probability of testing positive across various levels of second ancestral-strain monovalent COVID-19 vaccine dose coverage, including only unvaccinated individuals in the main analysis and both vaccinated and unvaccinated individuals in additional analyses. Sensitivity analysis focused on children under 12, who did not have access to COVID-19 vaccines during the pre-omicron-period. FINDINGS: We included 11,039,315 unvaccinated individuals tested during the pre-omicron study period. IVE was minimal until 30% vaccination coverage (<10%), then it follows a dose-dependent pattern, peaking at 37.7(95%CI:32-42.8) at 70% coverage. For children under 12, IVE peaked at 59.8%(95%CI:52.7-65.9) at 70% coverage. During Omicron-period, IVE remained constant at about 5% across all comparisons. INTERPRETATION: Our findings confirm that high vaccination coverage using vaccines that prevent infection indirectly protects the community. However, IVE was substantially higher during the pre-Omicron period.

Scientific Committee guidance on appraising and integrating evidence from epidemiological studies for use in EFSA's scientific assessments.

EFSA requested its Scientific Committee to prepare a guidance document on appraising and integrating evidence from epidemiological studies for use in EFSA's scientific assessments. The guidance document provides an introduction to epidemiological studies and illustrates the typical biases, which may be present in different epidemiological study designs. It then describes key epidemiological concepts relevant for evidence appraisal. This includes brief explanations for measures of association, exposure assessment, statistical inference, systematic error and effect modification. The guidance then describes the concept of external validity and the principles of appraising epidemiological studies. The customisation of the study appraisal process is explained including tailoring of tools for assessing the risk of bias (RoB). Several examples of appraising experimental and observational studies using a RoB tool are annexed to the document to illustrate the application of the approach. The latter part of this guidance focuses on different steps of evidence integration, first within and then across different streams of evidence. With respect to risk characterisation, the guidance considers how evidence from human epidemiological studies can be used in dose-response modelling with several different options being presented. Finally, the guidance addresses the application of uncertainty factors in risk characterisation when using evidence from human epidemiological studies.

Potential asthma risk factors do not account for global asthma symptom prevalence patterns and time trends in children and adolescents.

Background: The International Study of Asthma and Allergies in Childhood (ISAAC) and the Global Asthma Network (GAN) conducted a series of global asthma prevalence surveys, between 1990 and 2020, in adolescents aged 13-14 and children aged 6-7 years. We used them to assess whether potential asthma risk factors explain global asthma symptom prevalence trends over this period. Method: We fitted mixed-effects linear regression models to estimate associations between centre-level risk factor prevalence and both the mid-point asthma symptom prevalence and the change per decade. We also estimated the 2019 asthma symptom prevalence across all included centres. Results: For adolescents, across 50 centres in 26 countries there was weak evidence that decreasing asthma prevalence over time was associated with regular fast-food consumption and frequent television viewing. However, frequent television viewing, along with heavy truck traffic, were associated with higher prevalence of asthma symptoms at the study mid-point. For children, across 41 centres in 21 countries, no risk factors were associated with time trends in asthma symptom prevalence, but truck traffic and paracetamol in the first year of life were associated with higher mid-point prevalence.We estimated the 2019 asthma symptom prevalence, across a total of 124 centres, to be 12.8% (11.4%, 14.2%) with little evidence of a difference by age. Low-income countries had lower prevalence (children 5.2% [2.5%, 7.8%], adolescents 5.3% [2.8%, 7.8%]), than lower-middle-, upper-middle- and high-income countries (all approximately 14-15%). Including risk factors in the models did not change the estimates. Conclusion: Potential asthma risk factors do not seem to explain the global prevalence patterns or time trends. Country income accounts for some of the differences, but the unexplained variation is very high.

A UK framework for the assessment and integration of different scientific evidence streams in chemical risk assessment.

BACKGROUND: Few methods are available for transparently combining different evidence streams for chemical risk assessment to reach an integrated conclusion on the probability of causation. Hence, the UK Committees on Toxicity (COT) and on Carcinogenicity (COC) have reviewed current practice and developed guidance on how to achieve this in a transparent manner, using graphical visualisation. METHODS/APPROACH: All lines of evidence, including toxicological, epidemiological, new approach methodologies, and mode of action should be considered, taking account of their strengths/weaknesses in their relative weighting towards a conclusion on the probability of causation. A qualitative estimate of the probability of causation is plotted for each line of evidence and a combined estimate provided. DISCUSSION/CONCLUSIONS: Guidance is provided on integration of multiple lines of evidence for causation, based on current best practice. Qualitative estimates of probability for each line of evidence are plotted graphically. This ensures a deliberative, consensus conclusion on likelihood of causation is reached. It also ensures clear communication of the influence of the different lines of evidence on the overall conclusion on causality. Issues on which advice from the respective Committees is sought varies considerably, hence the guidance is designed to be sufficiently flexible to meet this need.

A SARS-CoV-2 outbreak in a public order and safety training facility in England, June 2021.

BACKGROUND: The public order and safety (POS) sector remains susceptible to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreaks, as workplace attendance is typically compulsory and close physical contact is often needed. Here, we report on a SARS-CoV-2 outbreak with an attack rate of 39% (9/23), which occurred between 19 and 29 June 2021 among a cohort of new POS recruits participating in a mandatory 18-week training programme in England. METHODS: The COVID-OUT (COVID-19 Outbreak investigation to Understand Transmission) study team undertook a multidisciplinary outbreak investigation, including viral surface sampling, workplace environmental assessment, participant viral and antibody testing, and questionnaires, at the two associated training facilities between 5 July and 24 August 2021. RESULTS: Environmental factors, such as ventilation, were deemed inadequate in some areas of the workplace, with carbon dioxide (CO2) levels exceeding 1,500 ppm on multiple occasions within naturally ventilated classrooms. Activities during safety training required close contact, with some necessitating physical contact, physical exertion, and shouting. Furthermore, most participants reported having physical contact with colleagues (67%) and more than one close work contact daily (97%). CONCLUSIONS: Our investigation suggests that site- and activity-specific factors likely contributed to the transmission risks within the POS trainee cohort. Potential interventions for mitigating SARS-CoV-2 transmission in this POS training context could include implementing regular rapid lateral flow testing, optimizing natural ventilation, using portable air cleaning devices in classrooms, and expanding use of well-fitted FFP2/FFP3 respirators during activities where prolonged close physical contact is required.

Disagreement concerning atopic dermatitis subtypes between an English prospective cohort (ALSPAC) and linked electronic health records.

BACKGROUND: Subtypes of atopic dermatitis (AD) have been derived from the Avon Longitudinal Study of Parents and Children (ALSPAC) based on presence and severity of symptoms reported in questionnaires (Severe-Frequent, Moderate-Frequent, Moderate-Declining, Mild-Intermittent, Unaffected/Rare). Good agreement between ALSPAC and linked electronic health records (EHRs) would increase trust in the clinical validity of these subtypes and allow inferring subtypes from EHRs alone, which would enable their study in large primary care databases. OBJECTIVES: 1. Explore if presence and number of AD records in EHRs agrees with AD symptom and severity reports from ALSPAC; 2. Explore if EHRs agree with ALSPAC-derived AD subtypes; 3. Construct models to classify ALSPAC-derived AD subtype using EHRs. METHODS: We used data from the ALSPAC prospective cohort study from 11 timepoints until age 14 years (1991-2008), linked to local general practice EHRs. We assessed how far ALSPAC questionnaire responses and derived subtypes agreed with AD as established in EHRs using different AD definitions (e.g., diagnosis and/or prescription) and other AD-related records. We classified AD subtypes using EHRs, fitting multinomial logistic regression models tuning hyperparameters and evaluating performance in the testing set (ROC AUC, accuracy, sensitivity, and specificity). RESULTS: 8,828 individuals out of a total 13,898 had both been assigned an AD subtype and had linked EHRs. The number of AD-related codes in EHRs generally increased with severity of AD subtype, however not all with the Severe-Frequent subtypes had AD in EHRs, and many with the Unaffected/Rare subtype did have AD in EHRs. When predicting ALSPAC AD subtype using EHRs, the best tuned model had ROC AUC of 0.65, sensitivity of 0.29 and specificity of 0.83 (both macro averaged); when different sets of predictors were used, individuals with missing EHR coverage excluded, and subtypes combined, sensitivity was not considerably improved. CONCLUSIONS: ALSPAC and EHRs disagreed not just on AD subtypes, but also on whether children had AD or not. Researchers should be aware that individuals considered as having AD in one source may not be considered as having AD in another.

Gut microbiome signature and nasal lavage inflammatory markers in young people with asthma.

Background: Asthma is a complex disease and a severe global public health problem resulting from interactions between genetic background and environmental exposures. It has been suggested that gut microbiota may be related to asthma development; however, such relationships needs further investigation. Objective: This study aimed to characterize the gut microbiota as well as the nasal lavage cytokine profile of asthmatic and nonasthmatic individuals. Methods: Stool and nasal lavage samples were collected from 29 children and adolescents with type 2 asthma and 28 children without asthma in Brazil. Amplicon sequencing of the stool bacterial V4 region of the 16S rRNA gene was performed using Illumina MiSeq. Microbiota analysis was performed by QIIME 2 and PICRUSt2. Type 2 asthma phenotype was characterized by high sputum eosinophil counts and positive skin prick tests for house dust mite, cockroach, and/or cat or dog dander. The nasal immune marker profile was assessed using a customized multiplex panel. Results: Stool microbiota differed significantly between asthmatic and nonasthmatic participants (P = .001). Bacteroides was more abundant in participants with asthma (P < .05), while Prevotella was more abundant in nonasthmatic individuals (P < .05). In people with asthma, the relative abundance of Bacteroides correlated with IL-4 concentration in nasal lavage samples. Inference of microbiota functional capacity identified differential fatty acid biosynthesis in asthmatic compared to nonasthmatic subjects. Conclusion: The stool microbiota differed between asthmatic and nonasthmatic young people in Brazil. Asthma was associated with higher Bacteroides levels, which correlated with nasal IL-4 concentration.

A SARS-CoV-2 outbreak investigation at a storage and distribution centre in England: an assessment of worker- and workplace-related risk factors.

An outbreak of SARS-CoV-2 (1 March to 10 May 2021) with an attack rate of 26.5% among approximately 1150 workers at a storage and distribution centre in England prompted a multidisciplinary outbreak investigation (5 May to 6 August 2021), with the aim of better understanding worker- and workplace-related risk factors for viral transmission in the warehousing sector. Overall, environmental factors (e.g., ventilation, humidity and temperature) were assessed to be appropriate at the facility. Nevertheless, 39 (51.3%) surface samples from across the site tested positive for low/ very low levels of SARS-CoV-2 RNA (Ct value ≥ 32.0 for all). Among the study participants, of whom 35.6% were confirmed or suspected cases, 95.5% reported having received COVID-19 prevention training, 100.0% reported handwashing, and 80.0% reported use of face coverings at work. Notably, 43.9% and 19.0% reported working with a symptomatic and a positive contact respectively. Furthermore, 80.5% and 46.3% had concerns regarding reduction in their income and future unemployment, respectively, due to self-isolation. The findings of this study suggest that, in addition to targeted workplace infection control measures and tailored work area specific risk assessments, an enhanced and equitable sick leave policy may help limit presenteeism and viral transmission in large workplaces.

Rescue from complications after pancreaticoduodenectomies at a low-volume Caribbean center: Value of tailored peri-pancreatectomy protocols.

BACKGROUND: Pancreaticoduodenectomy (PD) is a technically complex operation, with a relatively high risk for complications. The ability to rescue patients from post-PD complications is as a recognized quality measure. Tailored protocols were instituted at our low volume facility in the year 2013. AIM: To document the rate of rescue from post-PD complications with tailored protocols in place as a measure of quality. METHODS: A retrospective audit was performed to collect data from patients who experienced major post-PD complications at a low volume pancreatic surgery unit in Trinidad and Tobago between January 1, 2013 and June 30, 2023. Standardized definitions from the International Study Group of Pancreatic Surgery were used to define post-PD complications, and the modified Clavien-Dindo classification was used to classify post-PD complications. RESULTS: Over the study period, 113 patients at a mean age of 57.5 years (standard deviation [SD] ± 9.23; range: 30-90; median: 56) underwent PDs at this facility. Major complications were recorded in 33 (29.2%) patients at a mean age of 53.8 years (SD: ± 7.9). Twenty-nine (87.9%) patients who experienced major morbidity were salvaged after aggressive treatment of their complication. Four (3.5%) died from bleeding pseudoaneurysm (1), septic shock secondary to a bile leak (1), anastomotic leak (1), and myocardial infarction (1). There was a significantly greater salvage rate in patients with American Society of Anesthesiologists scores ≤ 2 (93.3% vs 25%; P = 0.0024). CONCLUSION: This paper adds to the growing body of evidence that volume alone should not be used as a marker of quality for patients requiring PD. Despite low volumes at our facility, we demonstrated that 87.9% of patients were rescued from major complications. We attributed this to several factors including development of rescue protocols, the competence of the pancreatic surgery teams and continuous, and adaptive learning by the entire institution, culminating in the development of tailored peri-pancreatectomy protocols.

Risk factors for SARS-CoV-2 infection at a UK electricity-generating company: a test-negative design case-control study.

OBJECTIVES: Identify workplace risk factors for SARS-CoV-2 infection, using data collected by a UK electricity-generating company. METHODS: Using a test-negative design case-control study, we estimated the OR of infection by job category, site, test reason, sex, vaccination status, vulnerability, site outage and site COVID-19 weekly risk rating, adjusting for age, test date and test type. RESULTS: From an original 80 077 COVID-19 tests, there were 70 646 included in the final analysis. Most exclusions were due to being visitor tests (5030) or tests after an individual first tested positive (2968).Women were less likely to test positive than men (OR=0.71; 95% CI 0.58 to 0.86). Test reason was strongly associated with positivity and although not a cause of infection itself, due to differing test regimes by area, it was a strong confounder for other variables. Compared with routine tests, tests due to symptoms were highest risk (94.99; 78.29 to 115.24), followed by close contact (16.73; 13.80 to 20.29) and broader-defined work contact 2.66 (1.99 to 3.56). After adjustment, we found little difference in risk by job category, but some differences by site with three sites showing substantially lower risks, and one site showing higher risks in the final model. CONCLUSIONS: In general, infection risk was not associated with job category. Vulnerable individuals were at slightly lower risk, tests during outages were higher risk, vaccination showed no evidence of an effect on testing positive, and site COVID-19 risk rating did not show an ordered trend in positivity rates.

Excess Mortality Calculations to Assess the Impact of the COVID-19 Pandemic: Concepts and Methodological Issues.

We discuss some intriguing methodological aspects of excess mortality analyses, which have been widely used to describe the impact of the COVID-19 pandemic. We describe the main ways of presenting excess mortality: as a mortality rate (incidence rate) or as a percentage increase (relative risk or rate ratio). We discuss what should be regarded as the null value of excess mortality (i.e., when countries or regions can be judged as having fared equally well) and when age and sex standardization, adjustment for other determinants of the spread of a pandemic, or both is necessary. We discuss the level of detail by time and place and person that may be necessary. We note that an excess mortality comparison is essentially a difference-in-differences analysis. We conclude that, although one cannot rule out using excess mortality analyses for causal effect estimates, such analyses will remain most fruitful for generating hypotheses about both the efficiency of measures to curtail the pandemic and factors that cannot be influenced. Nevertheless, a judicious use of arguments and counterarguments can then lead to identifying best practices for various situations. (Am J Public Health. 2024;114(6):593-598. https://doi.org/10.2105/AJPH.2024.307572).

Risk factors for SARS-CoV-2 infection: a test-negative case-control study with additional population controls in Norway.

OBJECTIVES: This study aims to assess risk factors for SARS-CoV-2 infection by combined design; first comparing positive cases to negative controls as determined by PCR testing and then comparing these two groups to an additional prepandemic population control group. DESIGN AND SETTING: Test-negative design (TND), multicentre case-control study with additional population controls in South-Eastern Norway. PARTICIPANTS: Adults who underwent SARS-CoV-2 PCR testing between February and December 2020. PCR-positive cases, PCR-negative controls and additional age-matched population controls. PRIMARY OUTCOME MEASURES: The associations between various risk factors based on self- reported questionnaire and SARS-CoV-2 infection comparing PCR-positive cases and PCR-negative controls. Using subgroup analysis, the risk factors for both PCR-positive and PCR-negative participants were compared with a population control group. RESULTS: In total, 400 PCR-positive cases, 719 PCR-negative controls and 14 509 population controls were included. Male sex was associated with the risk of SARS-CoV-2 infection only in the TND study (OR 1.9, 95% CI 1.4 to 2.6), but not when PCR-positive cases were compared with population controls (OR 1.2, 95% CI 0.9. to 1.5). Some factors were positively (asthma, wood heating) or negatively (hypertension) associated with SARS-CoV-2 infection when PCR-positive cases were compared with population controls, but lacked convincing association in the TND study. Smoking was negatively associated with the risk of SARS-CoV-2 infection in both analyses (OR 0.5, 95% CI 0.3 to 0.8 and OR 0.6, 95% CI 0.4 to 0.8). CONCLUSIONS: Male sex was a possible risk factor for SARS-CoV-2 infection only in the TND study, whereas smoking was negatively associated with SARS-CoV-2 infection in both the TND study and when using population controls. Several factors were associated with SARS-CoV-2 infection when PCR-positive cases were compared with population controls, but not in the TND study, highlighting the strength of combining case-control study designs during the pandemic.

Prevalent occupational exposures and risk of lung cancer among women: Results from the application of the Canadian Job-Exposure Matrix (CANJEM) to a combined set of ten case-control studies.

BACKGROUND: Worldwide, lung cancer is the second leading cause of cancer death in women. The present study explored associations between occupational exposures that are prevalent among women, and lung cancer. METHODS: Data from 10 case-control studies of lung cancer from Europe, Canada, and New Zealand conducted between 1988 and 2008 were combined. Lifetime occupational history and information on nonoccupational factors including smoking were available for 3040 incident lung cancer cases and 4187 controls. We linked each reported job to the Canadian Job-Exposure Matrix (CANJEM), which provided estimates of probability, intensity, and frequency of exposure to each selected agent in each job. For this analysis, we selected 15 agents (cleaning agents, biocides, cotton dust, synthetic fibers, formaldehyde, cooking fumes, organic solvents, cellulose, polycyclic aromatic hydrocarbons from petroleum, ammonia, metallic dust, alkanes C18+, iron compounds, isopropanol, and calcium carbonate) that had lifetime exposure prevalence of at least 5% in the combined study population. For each agent, we estimated lung cancer risk in each study center for ever-exposure, by duration of exposure, and by cumulative exposure, using separate logistic regression models adjusted for smoking and other covariates. We then estimated the meta-odds ratios using random-effects meta-analysis. RESULTS AND CONCLUSIONS: None of the agents assessed showed consistent and compelling associations with lung cancer among women. The following agents showed elevated odds ratio in some analyses: metallic dust, iron compounds, isopropanol, and organic solvents. Future research into occupational lung cancer risk factors among women should prioritize these agents.

Population-level detection of early loss of kidney function: 7-year follow-up of a young adult cohort at risk of Mesoamerican nephropathy.

BACKGROUND: Mesoamerican nephropathy is a leading contributor to premature mortality in Central America. Efforts to identify the cause are hampered by difficulties in distinguishing associations with potential initiating factors from common exposures thought to exacerbate the progression of all forms of established chronic kidney disease (CKD). We explored evidence of disease onset or departure from the healthy estimated glomerular filtration rate distribution [departure from ∼eGFR(healthy)] in an at-risk population. METHODS: Two community-based cohorts (adults aged 18-30 years, n = 351 and 420) from 11 rural communities in Northwest Nicaragua were followed up over 7 and 3 years respectively. We examined associations with both (i) incident CKD and (ii) the time point of departure from ∼eGFR(healthy), using a hidden Markov model. RESULTS: CKD occurred in men only (male incidence rate: 0.7%/year). Fifty-three (out of 1878 visits, 2.7%) and 8 (out of 1067 visits, 0.8%) episodes of probable departure from ∼eGFR(healthy) occurred in men and women, respectively. Cumulative time in sugarcane work and symptoms of excess occupational sun exposure were associated with incident CKD. The same exposures were associated with probability of departure from ∼eGFR(healthy) in time-updated analyses along with measured and self-reported weight loss, nausea, vomiting and cramps, as well as non-steroidal anti-inflammatory drug use. CONCLUSIONS: CKD burden in this population is high and risk factors for established disease are occupational. Additionally, a syndrome suggesting an alternative exposure is associated with evidence of disease onset supporting a possible separate unknown initiating factor for which further investigation is needed. Interventions to reduce the impact of occupational risks should be pursued meanwhile.

Potential contribution of vaccination uptake to occupational differences in risk of SARS-CoV-2: analysis of the ONS COVID-19 Infection Survey.

OBJECTIVES: To assess variation in vaccination uptake across occupational groups as a potential explanation for variation in risk of SARS-CoV-2 infection. DESIGN: We analysed data from the UK Office of National Statistics COVID-19 Infection Survey linked to vaccination data from the National Immunisation Management System in England from 1 December 2020 to 11 May 2022. We analysed vaccination uptake and SARS-CoV-2 infection risk by occupational group and assessed whether adjustment for vaccination reduced the variation in risk between occupational groups. RESULTS: Estimated rates of triple vaccination were high across all occupational groups (80% or above), but were lowest for food processing (80%), personal care (82%), hospitality (83%), manual occupations (84%) and retail (85%). High rates were observed for individuals working in health (95% for office based, 92% for those in patient-facing roles) and education (91%) and office-based workers not included in other categories (90%). The impact of adjusting for vaccination when estimating relative risks of infection was generally modest (ratio of hazard ratios across all occupational groups reduced from 1.37 to 1.32), but was consistent with the hypothesis that low vaccination rates contribute to elevated risk in some groups. CONCLUSIONS: Variation in vaccination coverage might account for a modest proportion of occupational differences in infection risk. Vaccination rates were uniformly very high in this cohort, which may suggest that the participants are not representative of the general population. Accordingly, these results should be considered tentative pending the accumulation of additional evidence.