Synthesis of evidence from the PROTECT UK national core study: exploring occupational risks of SARS-CoV-2 infection and COVID-19 mortality

IntroductionThe PROTECT National Core Study was funded by the UK Health and Safety Executive (HSE) to investigate how SARS-CoV-2 is transmitted from person to person, and how this varies in different settings.One area of research aimed to compare relative differences between occupational groups and sectors in SARS-CoV-2 infection and COVID-19 mortality over time and explore the likely reasons.MethodsWe brought together evidence from nine published epidemiological studies supported by PROTECT relating to four data sets, plus new analyses relating to the Omicron period. We organised these studies into the following categories: those that specifically compared risks of infection mortality;and those that looked at risk factors for SARS-CoV-2 infection and/or COVID-19 mortality. We extracted descriptive study level data and results. We investigated risk across four pandemic waves using forest plots for key occupational groups by time. A workshop was organised in Oct 2022 with authors from each study to discuss and document key strengths and expected biases.ResultsHealthcare and social care sectors saw elevated risks of SARS-CoV-2 infection and COVID-19 mortality early in the pandemic but thereafter these declined and varied by specific occupational subgroup. The education sector saw sustained elevated risks of infection after the initial lockdown period with little evidence of elevated mortality. Results were largely consistent across different studies with differing expected biases, although unmeasured confounding cannot be ruled out.ConclusionDifferences between occupations and sectors in the UK in terms of COVID-19 risks that were observed in the early stages of the pandemic largely dissipated over time. Studies investigating risk factors suggest that reasons could include vaccination roll out, introduction of risk mitigation within high risk sectors, changes in patterns of home-working and lifting of restriction on social mixing (thereby reducing the relative effect of work).

Surveillance of respiratory viruses infections in sentinel hospitals of Guangming district, Shenzhen, between 2018 and 2021

OBJECTIVE: To investigate the prevalence of respiratory tract viruses infections in sentinel hospitals of Guangming District, Shenzhen, from 2018 to 2021. METHODS: A total of 1 183 influenza-like patients who were treated in University of Chinese Academy of Sciences Shenzhen Hospital(Guangming District) from Jan 2018 to Dec 2021 were recruited as the research subjects. The respiratory viruses that were isolated from throat swab specimens were detected by real-time fluorescent quantitative PCR, and the prevalence of the infections was observed. RESULTS: Among the throat swab specimens that were collected from the 1 183 influenza-like patients, 45.48%(538/1183) were tested positive for respiratory viruses. Among the 538 positive samples, 533 were single infection, and 5 were mixed infection;the patients with influenza virus infection accounted for 77.51%(417 cases), higher than the patients with infections of other viruses [adenovirus infection(6.51%), respiratory syncytial virus infection(1.30%), human metapneumovirus infection(1.67%), rhinovirus infection(6.88%), coronavirus infection(1.86%), parainfluenza virus infection(3.16%), boca virus infection(0.19%), P<0.05]. The incidence of respiratory viruses infections was higher in winter than in spring, summer and autumn(P<0.05), the proportion of the influenza virus was higher than that of other viruses in winter(P<0.05). The population aged between 26 and 40 years old was dominant among the patients with influenza virus infection, and the infection rate of the age group was higher than that of other age groups(P<0.05). The population aged between 26 and 40 years old was dominant among the patients with coronavirus infection, while the population aged less than 15 years old was dominant among the patients with infections of other respiratory viruses;the patients aged less than 15 years accounted for 59.46%(22 cases) among the patients with rhinovirus infection;the patients aged less than 5 years old accounted for 42.86%(15 cases) among the patients with adenovirus infection. There was no significant difference in the proportion of the patients with respiratory viruses infection between genders. CONCLUSION: The influenza virus is dominant among the viruses causing the respiratory tract infection, which is prevalent in winter. The incidence of respiratory tract infections is relatively high among the patients aged between 26 and 40 years old but is not associated with the gender.

Resurgence of Respiratory Syncytial Virus in Children: An Out-of-Season Epidemic in Portugal.

INTRODUCTION: An out-of-season increase in respiratory syncytial virus (RSV) incidence was observed in Portugal from June 2021 onwards, revealing a continuing surge in cases throughout 2021/2022 autumn/winter. We aimed to describe this out-of-season epidemic and define its epidemic period, by analysing RSV incidence from week 40 of 2020 (2020-W40) to week 18 of 2022 (2022-W18). MATERIAL AND METHODS: Surveillance data on weekly RSV laboratory confirmed cases, in Portugal, was used to monitor RSV incidence using CUSUM test methodology for count data. RESULTS: In 2021-W23, the CUSUM score identified a significant increase in the risk of RSV. By that time, the percentage of RSV positive tests rose from 1% in 2021-W22 (3/265) to 6% in 2021-W23 (18/298). Despite a sharp decrease in RSV incidence on 2021-W33 and on 2022-W02, the CUSUM score stayed over the limit up to 2022-W07, indicating that the RSV activity remained at an epidemic level. Distinct peaks of RSV cases were observed between 2021-W30 and 2021-W32 (average of 77 RSV cases per week) and between 2021-W39 and 2021-W41 (average of 79 RSV cases per week) with positivity rates around 60%. CONCLUSION: An out-of-season RSV epidemic was identified, with a longer epidemic period compared with previous seasons. Possible reasons include relaxation of COVID-19 physical distancing measures and a greater proportion of population susceptible to disease. As several factors may change the pattern of RSV activity, countries should implement year-round surveillance RSV surveillance systems. These findings might have an impact on public health planning regarding future RSV surges, namely, on the palivizumab prophylaxis period for high-risk infants.

The Road to SARS-CoV-2 Seasonality: A Vision of the Post-Pandemic Era

The end of the pandemic could be marked, not by the total eradication of the virus but by a decrease in cases and seasonal peaks in the frequency of SARSCoV-2. Although this has already happened with the influenza A (H1N1) pdm09 virus responsible for the 2009 pandemic, unlike on that occasion, many of the countries that have widely covered their population with the vaccination scheme, still receive the onslaught of COVID-19 and have resumed containment measures due to the appearance, above all, of new variants. The latter suggests that the path to SARS-CoV-2 seasonality may not be as benevolent as the 2009 influenza virus was. Therefore, it is necessary to study the characteristics by which this new virus can acquire seasonality. to consider this scenario and take the necessary measures to face it from a different perspective. © 2022 Academia Nacional de Medicina. All rights reserved.

Diagnostic accuracy of SARS-CoV-2 saliva antigen testing in a real-life clinical setting.

BACKGROUND: SARS-CoV-2 antigen tests with saliva facilitate examination in settings that lack trained personnel. However, little is known about the diagnostic accuracy in real-life clinical settings. Therefore, we studied the diagnostic accuracy of a saliva antigen test in diagnosing SARS-CoV-2 infection in a primary/secondary care testing facility. METHODS: Individuals who presented at a COVID-19 testing facility affiliated with a Swiss university hospital were prospectively recruited (n=377). Saliva specimen was obtained, and the PCL Inc. COVID19 Gold antigen test was conducted in parallel with 2 real-time polymerase chain reaction (RT-PCR) assays from a nasopharyngeal swab. RESULTS: RT-PCR results were positive in 53 individuals, corresponding to a prevalence of 14.1% (missing material in 1 individual). The PCL saliva antigen test was positive in 22 individuals (5.8%) and negative in 354 (93.9%). The sensitivity of the saliva antigen test was 30.2% (95% confidence interval 18.3, 44.3), both overall and in symptomatic individuals. The specificity was 98.1% (96.0, 99.3). CONCLUSIONS: The diagnostic accuracy of a SARS-CoV-2 saliva antigen test in a primary/secondary care testing facility was remarkably lower than that reported in the manufacturer's specifications.

COVID-19 in Jundiai/SP: temporal dynamics of notifications and spatial analysis of seroepidemiological prevalence

Background and Objectives: The COVID-19 pandemic brought a challenging scenario for public health worldwide, due to little knowledge about the infection and the exponential increase in new cases. This study aims to analyze the temporal trend and the spatial distribution of the positive cases for COVID-19 in the city of Jundiai/SP, Brazil, as well as its correlation with the income and population density of the neighborhoods. Methods: Cross-sectional study, conducted from February to June 2020. Data were obtained from cases confirmed by the Epidemiological Surveillance and by a seroepidemiological survey carried out in two stages: 1) with symptomatic users for Severe Acute Respiratory Syndrome who sought care in Basic Health Units;2) probabilistic sampling of households. An analysis of the time series of the cases confirmed by the Epidemiological Surveillance was carried out and maps with Kernel density and Local Moran Index (p <0.05) of the cases diagnosed in the seroepidemiological survey were prepared. Results: There was an increase in the number of cases in the period studied (2.35%), as well as the heterogeneous distribution in the territory, with a concentration in peripheral areas of the city. There was weak spatial autocorrelation between average per capita income (I = 0.11;p value <0.001) and population density by neighborhood (I = 0.05;p value = 0.03). Conclusion: The analysis of infection behavior in time and space can contribute to coping actions based on local needs.

COVID-19 and risk assessment room for public health in four Colombian cross-border territories

Introduction: Public health risk management in Colombia is led by the National Institute of Health. In the face of the COVID-19 emergency, response actions were carried out through the implementation of Risk Analysis Rooms, strengthening surveillance at points of entry into the country. Objective: To carry out an analysis of the implementation and maintenance phases of the COVID-19 Risk Analysis Rooms in four border departments of Colombia. Materials and methods: A qualitative study was carried of Risk Analysis Rooms in public health for COVID-19. The documentation and data generated in the period from March to June 2020 in Amazonas, Vichada, Guainia and Putumayo were reviewed. Semi-structured interviews were conducted with key actors. The analysis was performed with the NVivo plus version 11 application, in three cycles: open coding;identification of emerging categories and modeling by analyzing the identified strengths and weaknesses. Results: The components of the incident command structure and the relationships between the public health areas were identified. Strengths were found in the integration of the areas;management of information in real time, border surveillance and strengthening of immediate response teams. The weaknesses identified were established in the planning, community surveillance and risk communication processes. Conclusions: The Risk Analysis Rooms constitute a joint effort of the national and local level where the articulated participation of the actors is promoted to analyze information and optimize the organized response during the COVID-19 pandemic.

Serological testing for SARS-CoV-2 antibodies in clinical practice: A comparative diagnostic accuracy study.

BACKGROUND: Serological tests are a powerful tool in the monitoring of infectious diseases and the detection of host immunity. However, manufacturers often provide diagnostic accuracy data generated through biased studies, and the performance in clinical practice is essentially unclear. OBJECTIVES: We aimed to determine the diagnostic accuracy of various serological testing strategies for (a) identification of patients with previous coronavirus disease-2019 (COVID-19) and (b) prediction of neutralizing antibodies against SARS-CoV-2 in real-life clinical settings. METHODS: We prospectively included 2573 consecutive health-care workers and 1085 inpatients with suspected or possible previous COVID-19 at a Swiss University Hospital. Various serological immunoassays based on different analytical techniques (enzyme-linked immunosorbent assays, ELISA; chemiluminescence immunoassay, CLIA; electrochemiluminescence immunoassay, ECLIA; and lateral flow immunoassay, LFI), epitopes of SARS-CoV-2 (nucleocapsid, N; receptor-binding domain, RBD; extended RBD, RBD+; S1 or S2 domain of the spike [S] protein, S1/S2), and antibody subtypes (IgG, pan-Ig) were conducted. A positive real-time PCR test from a nasopharyngeal swab was defined as previous COVID-19. Neutralization assays with live SARS-CoV-2 were performed in a subgroup of patients to assess neutralization activity (n = 201). RESULTS: The sensitivity to detect patients with previous COVID-19 was ≥85% in anti-N ECLIA (86.8%) and anti-S1 ELISA (86.2%). Sensitivity was 84.7% in anti-S1/S2 CLIA, 84.0% in anti-RBD+LFI, 81.0% in anti-N CLIA, 79.2% in anti-RBD ELISA, and 65.6% in anti-N ELISA. The specificity was 98.4% in anti-N ECLIA, 98.3% in anti-N CLIA, 98.2% in anti-S1 ELISA, 97.7% in anti-N ELISA, 97.6% in anti-S1/S2 CLIA, 97.2% in anti-RBD ELISA, and 96.1% in anti-RBD+LFI. The sensitivity to detect neutralizing antibodies was ≥85% in anti-S1 ELISA (92.7%), anti-N ECLIA (91.7%), anti-S1/S2 CLIA (90.3%), anti-RBD+LFI (87.9%), and anti-RBD ELISA (85.8%). Sensitivity was 84.1% in anti-N CLIA and 66.2% in anti-N ELISA. The specificity was ≥97% in anti-N CLIA (100%), anti-S1/S2 CLIA (97.7%), and anti-RBD+LFI (97.9%). Specificity was 95.9% in anti-RBD ELISA, 93.0% in anti-N ECLIA, 92% in anti-S1 ELISA, and 65.3% in anti-N ELISA. Diagnostic accuracy measures were consistent among subgroups. CONCLUSIONS: The diagnostic accuracy of serological tests for SARS-CoV-2 antibodies varied remarkably in clinical practice, and the sensitivity to identify patients with previous COVID-19 deviated substantially from the manufacturer's specifications. The data presented here should be considered when using such tests to estimate the infection burden within a specific population and determine the likelihood of protection against re-infection.

A new SARS-CoV-2 variant with high lethality poorly detected by RT-PCR on nasopharyngeal samples: an observational study.

OBJECTIVES: In early January 2021 an outbreak of nosocomial cases of coronavirus disease 2019 (COVID-19) emerged in Western France; RT-PCR tests were repeatedly negative on nasopharyngeal samples but positive on lower respiratory tract samples. Whole-genome sequencing (WGS) revealed a new variant, currently defining a novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineage B.1.616. In March, the WHO classified this as a 'variant under investigation' (VUI). We analysed the characteristics and outcomes of COVID-19 cases related to this new variant. METHODS: Clinical, virological, and radiological data were retrospectively collected from medical charts in the two hospitals involved. We enrolled those inpatients with: (a) positive SARS-CoV-2 RT-PCR on a respiratory sample, (b) seroconversion with anti-SARS-CoV-2 IgG/IgM, or (c) suggestive symptoms and typical features of COVID-19 on a chest CT scan. Cases were categorized as B.1.616, a variant of concern (VOC), or unknown. RESULTS: From 1st January to 24th March 2021, 114 patients fulfilled the inclusion criteria: B.1.616 (n = 39), VOC (n = 32), and unknown (n = 43). B.1.616-related cases were older than VOC-related cases (81 years, interquartile range (IQR) 73-88 versus 73 years, IQR 67-82, p < 0.05) and their first RT-PCR tests were rarely positive (6/39, 15% versus 31/32, 97%, p < 0.05). The B.1.616 variant was independently associated with severe disease (multivariable Cox model HR 4.0, 95%CI 1.5-10.9) and increased lethality (28-day mortality 18/39 (46%) for B.1.616 versus 5/32 (16%) for VOC, p = 0.006). CONCLUSION: We report a nosocomial outbreak of COVID-19 cases related to a new variant, B.1.616, which is poorly detected by RT-PCR on nasopharyngeal samples and is associated with high lethality.

The Clinical Course of COVID-19 in the Outpatient Setting: A Prospective Cohort Study.

BACKGROUND: Outpatient coronavirus disease 2019 (COVID-19) has been insufficiently characterized. To determine the progression of disease and determinants of hospitalization, we conducted a prospective cohort study. METHODS: Outpatient adults with positive reverse transcription polymerase chain reaction results for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) were recruited by phone between April 21 and July 23, 2020, after receiving outpatient or emergency department testing within a large health network in Maryland, United States. Symptoms were collected by participants on days 0, 3, 7, 14, 21, and 28, and portable pulse oximeter oxygen saturation (SaO2), heart rate, and temperature were collected for 15 consecutive days. Baseline demographics, comorbid conditions, and vital signs were evaluated for risk of subsequent hospitalization using negative binomial and logistic regression. RESULTS: Among 118 SARS-CoV-2-infected outpatients, the median age (interquartile range [IQR]) was 56.0 (50.0-63.0) years, and 50 (42.4%) were male. Among individuals in the first week of illness (n = 61), the most common symptoms included weakness/fatigue (65.7%), cough (58.8%), headache (45.6%), chills (38.2%), and anosmia (27.9%). Participants returned to their usual health a median (IQR) of 20 (13-38) days from symptom onset, and 66.0% of respondents were at their usual health during the fourth week of illness. Over 28 days, 10.9% presented to the emergency department and 7.6% required hospitalization. The area under the receiver operating characteristics curve for the initial home SaO2 for predicting subsequent hospitalization was 0.86 (95% CI, 0.73-0.99). CONCLUSIONS: Symptoms often persisted but uncommonly progressed to hospitalization among outpatients with COVID-19. Home SaO2 may be a helpful tool to stratify risk of hospitalization.

A Risk-Based Approach to the COVID-19 Pandemic: The Experience in National Dental Centre Singapore.

The emergence of a highly infectious coronavirus strain, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has led to a major global public health emergency. The increasing number of infected cases and fatalities worldwide forced several countries into lockdown in a bid to control virus transmission. The practice of dentistry is considered high-risk due to the generation of aerosols associated with most dental procedures, and healthcare professionals must take appropriate precautions whilst working in this challenging environment. This review aims to provide an overview on transmission routes and shares a risk-based approach to coronavirus disease 2019 (COVID-19) in a specialty tertiary center. Risk assessment and mitigation focussed on staff and patient safety, adopting a wide safety margin, and responding dynamically to the level of risk at the workplace. As the severity of the pandemic depends on many still-unknown factors and shows little sign of abating, the routine practice of dentistry will continue to be disrupted in the near future. We describe a color-coded framework to maximize safety and to minimize disease spread. Areas covered include healthcare team management, personal protective equipment, clinical work, and dental education. Guidelines in each category change with the corresponding severity of the situation, and we believe it will be useful for the safer practice of dentistry in this current climate and can be modified for future similar disease outbreaks.

Population-based Estimates for High Risk of Severe COVID-19 Disease due to Age and Underlying Health Conditions.

INTRODUCTION: COVID-19 is a viral respiratory disease, which became a global threat to public health. Specific subsets of the population are more vulnerable, namely those with chronic diseases. We aimed to estimate the share of the Portuguese population at the highest risk for complications following COVID-19 infection due to both old age and specific comorbidities. MATERIAL AND METHODS: Our sample included all people aged 65 years and above (2215 men and 3486 women) who participated in the fifth Portuguese National Health Interview Survey, conducted in 2014. In order to project the potential population at highest risk for COVID-19, we used the latest available official demographic estimates from the National Institute of Statistics - INE 2018. We used a more restrictive definition of risk combining old age criteria and the following chronic conditions as potential risk factors for COVID-19 according to the available literature: hypertension, diabetes, chronic obstructive pulmonary disease, cardio- and cerebrovascular disease. RESULTS: We estimated that 15.5% (n = 1 560 667) of the Portuguese population might be at increased risk for complications from COVID-19 because of old age and existing chronic conditions. Such estimates vary across the country (from 1.7% in Azores to 33.7% in Northern Portugal). Northern Portugal not only has the highest prevalence of selected morbidity (72.8%) within mainland Portugal, but also has the largest population at risk for COVID-19 (n = 526 607). This was followed by the Lisbon and Tagus Valley region (n = 408 564) and Central Portugal (n = 388 867). DISCUSSION: Our results should encourage authorities to continue protecting those more vulnerable to the pandemic threat, particularly on those areas of the country which are more likely to be further affected. CONCLUSION: We projected a considerable number of Portuguese people at the highest risk for severe COVID-19 disease due to both old age and pre-existing chronic conditions. Such estimates vary across the country.

Protocol of a population-based prospective COVID-19 cohort study Munich, Germany (KoCo19).

BACKGROUND: Due to the SARS-CoV-2 pandemic, public health interventions have been introduced globally in order to prevent the spread of the virus and avoid the overload of health care systems, especially for the most severely affected patients. Scientific studies to date have focused primarily on describing the clinical course of patients, identifying treatment options and developing vaccines. In Germany, as in many other regions, current tests for SARS-CoV2 are not conducted on a representative basis and in a longitudinal design. Furthermore, knowledge about the immune status of the population is lacking. Nonetheless, these data are needed to understand the dynamics of the pandemic and hence to appropriately design and evaluate interventions. For this purpose, we recently started a prospective population-based cohort in Munich, Germany, with the aim to develop a better understanding of the state and dynamics of the pandemic. METHODS: In 100 out of 755 randomly selected constituencies, 3000 Munich households are identified via random route and offered enrollment into the study. All household members are asked to complete a baseline questionnaire and subjects ≥14 years of age are asked to provide a venous blood sample of ≤3 ml for the determination of SARS-CoV-2 IgG/IgA status. The residual plasma and the blood pellet are preserved for later genetic and molecular biological investigations. For twelve months, each household member is asked to keep a diary of daily symptoms, whereabouts and contacts via WebApp. If symptoms suggestive for COVID-19 are reported, family members, including children < 14 years, are offered a pharyngeal swab taken at the Division of Infectious Diseases and Tropical Medicine, LMU University Hospital Munich, for molecular testing for SARS-CoV-2. In case of severe symptoms, participants will be transferred to a Munich hospital. For one year, the study teams re-visits the households for blood sampling every six weeks. DISCUSSION: With the planned study we will establish a reliable epidemiological tool to improve the understanding of the spread of SARS-CoV-2 and to better assess the effectiveness of public health measures as well as their socio-economic effects. This will support policy makers in managing the epidemic based on scientific evidence.