Transmissibility, hospitalization, and intensive care admissions due to omicron compared to delta variants of SARS-CoV-2 in Catalonia: A cohort study and ecological analysis

COVID-19; Cohorts; SeverityCOVID-19; Cohorts; GravetatCOVID-19; Cohortes; GravedadPurpose: We aim to compare the severity of infections between omicron and delta variants in 609,352 SARS-CoV-2 positive cases using local hospitalization, vaccination, and variants data from the Catalan Health Care System (which covers around 7. 8 million people). Methods: We performed a substitution model to establish the increase in transmissibility of omicron using variant screening data from primary care practices (PCP) and hospital admissions. In addition, we used this data from PCP to establish the two periods when delta and omicron were, respectively, dominant (above 95% of cases). After that, we performed a population-based cohort analysis to calculate the rates of hospital and intensive care unit (ICU) admissions for both periods and to estimate reduction in severity. Rate ratios (RR) and 95% confidence intervals (95% CI) were calculated and stratified by age and vaccination status. In a second analysis, the differential substitution model in primary care vs. hospitals allowed us to obtain a population-level average change in severity. Results: We have included 48,874 cases during the delta period and 560,658 during the omicron period. During the delta period, on average, 3.8% of the detected cases required hospitalization for COVID-19. This percentage dropped to 0.9% with omicron [RR of 0.46 (95% CI: 0.43 to 0.49)]. For ICU admissions, it dropped from 0.8 to 0.1% [RR 0.25 (95% CI: 0.21 to 0.28)]. The proportion of cases hospitalized or admitted to ICU was lower in the vaccinated groups, independently of the variant. Omicron was associated with a reduction in risk of admission to hospital and ICU in all age and vaccination status strata. The differential substitution models showed an average RR between 0.19 and 0.50. Conclusion: Both independent methods consistently show an important decrease in severity for omicron relative to delta. The systematic reduction happens regardless of age. The severity is also reduced for non-vaccinated and vaccinated groups, but it remains always higher in the non-vaccinated population. This suggests an overall reduction in severity, which could be intrinsic to the omicron variant. The fact is that the RR in ICU admission is systematically smaller than in hospitalization points in the same direction.MC received funding from la Caixa Foundation ID 100010434, under agreement LCF/PR/GN17/50300003. MC, CP, and SA received funding from Ministerio de Ciencia, Innovación y Universidades and FEDER, with the project PGC2018-095456-B-I00

Variability of the prevalence of depression in function of sociodemographic and environmental factors: ecological model

Major depression etiopathogenesis is related to a wide variety of genetics, demographic and psychosocial factors, as well as to environmental factors. The objective of this study is to analyze sociodemographic and environmental variables that are related to the prevalence of depression through correlation analysis and to develop a regression model that explains the behavior of this disease from an ecological perspective. This is an ecological, retrospective, cross-sectional study. The target population was 1,148,430 individuals over the age of 16 who were registered in Aragon (Spain) during 2010, with electronic medical records in the community’s primary health care centers. The spatial unit was the Basic Health Area (BHA). The dependent variable was the diagnosis of Depression and the ecological independent variables were: Demographic variables (gender and age), population distribution, typology of the entity, population structure by sex and age, by nationality, by education, by work, by salary, by marital status, structure of the household by number of members, and state of the buildings. The results show moderate and positive correlations with higher rates of depression in areas having a higher femininity index, higher population density, areas with a higher unemployment rate and higher average salary. The results of the linear regression show that aging +75 and rural entities act as protective factors for depression, while urban areas and deficient buildings act as risk factors. In conclusion, the ecological methodology may be a useful tool which, together with the statistical epidemiological analysis, can help in the political decision making process

Monitoring of SARS-CoV-2 seroprevalence among primary healthcare patients in the Barcelona Metropolitan Area: the SeroCAP sentinel network protocol

COVID-19; Epidemiology; Primary careCOVID-19; Epidemiología; Atención primariaCOVID-19; Epidemiologia; Atenció primàriaIntroduction SARS-CoV-2 seroprevalence studies are currently being recommended and implemented in many countries. Forming part of the COVID-19 monitoring and evaluation plan of the Catalan Government Health Department, our network aims to initiate a primary healthcare sentinel monitoring system as a surrogate of SARS-CoV-2 exposure in the Barcelona Metropolitan Area. Methods and analysis The seroCAP is a serial cross-sectional study, which will be performed in the Barcelona Metropolitan Area to estimate antibodies against SARS-CoV-2. From February 2021 to March 2022, the detection of serum IgG antibodies against SARS-CoV-2 trimeric spike protein will be performed on a monthly basis in blood samples collected for diverse clinical purposes in three reference hospitals from the three Barcelona healthcare areas (BCN areas). The samples (n=2588/month) will be from patients attended by 30 primary healthcare teams at 30 basic healthcare areas (BHA). A lab software algorithm will systematically select the samples by age and sex. Seroprevalence will be estimated and monitored by age, sex, BCN area and BHA. Descriptive and cluster analysis of the characteristics and distribution of SARS-CoV-2 infections will be performed. Sociodemographic, socioeconomic and morbidity-associated factors will be determined using logistic regression. We will explore the association between seroprevalence, SARS-CoV-2 confirmed cases and the implemented measures using interrupted time series analysis. Ethics and dissemination Ethical approval was obtained from the University Institute Foundation for Primary Health Care Research Jordi Gol i Gurina ethics committee. An informed consent is not required regarding the approval of the secondary use of biological samples within the framework of the COVID-19 pandemic. A report will be generated quarterly. The final analysis, conclusions and recommendations will be shared with the stakeholders and communicated to the general public. Manuscripts resulting from the network will be submitted for publication in peer-reviewed journals.This work will be supported by the Health Department of the Government of Catalunya (No grant number)

Integrated genomic surveillance enables tracing of person-to-person SARS-CoV-2 transmission chains during community transmission and reveals extensive onward transmission of travel-imported infections, Germany, June to July 2021

Genomic surveillance; Next generation sequencing; Contact tracingVigilancia genómica; Secuenciación de última generación; Rastreo de contactosVigilància genòmica; Seqüenciació de nova generació; Seguiment de contactesBackgroundTracking person-to-person SARS-CoV-2 transmission in the population is important to understand the epidemiology of community transmission and may contribute to the containment of SARS-CoV-2. Neither contact tracing nor genomic surveillance alone, however, are typically sufficient to achieve this objective.AimWe demonstrate the successful application of the integrated genomic surveillance (IGS) system of the German city of Düsseldorf for tracing SARS-CoV-2 transmission chains in the population as well as detecting and investigating travel-associated SARS-CoV-2 infection clusters.MethodsGenomic surveillance, phylogenetic analysis, and structured case interviews were integrated to elucidate two genetically defined clusters of SARS-CoV-2 isolates detected by IGS in Düsseldorf in July 2021.ResultsCluster 1 (n = 67 Düsseldorf cases) and Cluster 2 (n = 36) were detected in a surveillance dataset of 518 high-quality SARS-CoV-2 genomes from Düsseldorf (53% of total cases, sampled mid-June to July 2021). Cluster 1 could be traced back to a complex pattern of transmission in nightlife venues following a putative importation by a SARS-CoV-2-infected return traveller (IP) in late June; 28 SARS-CoV-2 cases could be epidemiologically directly linked to IP. Supported by viral genome data from Spain, Cluster 2 was shown to represent multiple independent introduction events of a viral strain circulating in Catalonia and other European countries, followed by diffuse community transmission in Düsseldorf.ConclusionIGS enabled high-resolution tracing of SARS-CoV-2 transmission in an internationally connected city during community transmission and provided infection chain-level evidence of the downstream propagation of travel-imported SARS-CoV-2 cases.This work was supported by the Ministry for Work, Health and Social Affairs of the State of North Rhine-Westphalia (“24.04.01 Gen. u. IKA” and CPS-1-1A); the Jürgen Manchot Foundation; the German Federal Ministry of Education and Research (Bundesministerium für Bildung und Forschung; award numbers 031L0184B and 01KX2021); the German Research Foundation (award 428994620)

Re-emergence of enterovirus D68 in Europe after easing the COVID-19 lockdown, September 2021

Acute flaccid myelitis; Enterovirus D68; SurveillanceMielitis flàcida aguda; Enterovirus D68; VigilànciaMielitis flácida aguda; Enterovirus D68; VigilanciaWe report a rapid increase in enterovirus D68 (EV-D68) infections, with 139 cases reported from eight European countries between 31 July and 14 October 2021. This upsurge is in line with the seasonality of EV-D68 and was presumably stimulated by the widespread reopening after COVID-19 lockdown. Most cases were identified in September, but more are to be expected in the coming months. Reinforcement of clinical awareness, diagnostic capacities and surveillance of EV-D68 is urgently needed in Europe

Evolution, geographic spreading, and demographic distribution of Enterovirus D68

Viral evolution; Age distribution; Molecular evolutionEvolución viral; Distribución de edad; Evolución molecularEvolució viral; Distribució per edats; Evolució molecularWorldwide outbreaks of enterovirus D68 (EV-D68) in 2014 and 2016 have caused serious respiratory and neurological disease. We collected samples from several European countries during the 2018 outbreak and determined 53 near full-length genome (‘whole genome’) sequences. These sequences were combined with 718 whole genome and 1,987 VP1-gene publicly available sequences. In 2018, circulating strains clustered into multiple subgroups in the B3 and A2 subclades, with different phylogenetic origins. Clusters in subclade B3 emerged from strains circulating primarily in the US and Europe in 2016, though some had deeper roots linking to Asian strains, while clusters in A2 traced back to strains detected in East Asia in 2015-2016. In 2018, all sequences from the USA formed a distinct subgroup, containing only three non-US samples. Alongside the varied origins of seasonal strains, we found that diversification of these variants begins up to 18 months prior to the first diagnostic detection during a EV-D68 season. EV-D68 displays strong signs of continuous antigenic evolution and all 2018 A2 strains had novel patterns in the putative neutralizing epitopes in the BC- and DE-loops. The pattern in the BC-loop of the USA B3 subgroup had not been detected on that continent before. Patients with EV-D68 in subclade A2 were significantly older than patients with a B3 subclade virus. In contrast to other subclades, the age distribution of A2 is distinctly bimodal and was found primarily among children and in the elderly. We hypothesize that EV-D68’s rapid evolution of surface proteins, extensive diversity, and high rate of geographic mixing could be explained by substantial reinfection of adults. Better understanding of evolution and immunity across diverse viral pathogens, including EV-D68 and SARS-CoV-2, is critical to pandemic preparedness in the future

Molecular epidemiology of an enterovirus A71 outbreak associated with severe neurological disease, Spain, 2016

Encephalitis; Enterovirus; OutbreaksEncefalitis; Enterovirus; Brot epidèmicEncefalitis; Enterovirus; Brote epidémicoIntroductionEnterovirus A71 (EV-A71) is an emerging pathogen that causes a wide range of disorders including severe neurological manifestations. In the past 20 years, this virus has been associated with large outbreaks of hand, foot and mouth disease with neurological complications in the Asia-Pacific region, while in Europe mainly sporadic cases have been reported. In spring 2016, however, an EV-A71 outbreak associated with severe neurological cases was reported in Catalonia and spread further to other Spanish regions.AimOur objective was to investigate the epidemiology and clinical characteristics of the outbreak.MethodsWe carried out a retrospective study which included 233 EV-A71-positive samples collected during 2016 from hospitalised patients. We analysed the clinical manifestations associated with EV-A71 infections and performed phylogenetic analyses of the 3'-VP1 and 3Dpol regions from all Spanish strains and a set of EV-A71 from other countries.ResultsMost EV-A71 infections were reported in children (mean age: 2.6 years) and the highest incidence was between May and July 2016 (83%). Most isolates (218/233) were classified as subgenogroup C1 and 217 of them were grouped in one cluster phylogenetically related to a new recombinant variant strain associated with severe neurological diseases in Germany and France in 2015 and 2016. Moreover, we found a clear association of EV-A71-C1 infection with severe neurological disorders, brainstem encephalitis being the most commonly reported.ConclusionAn emerging recombinant variant of EV-A71-C1 was responsible for the large outbreak in 2016 in Spain that was associated with many severe neurological cases

Schools as a Framework for COVID-19 Epidemiological Surveillance of Children in Catalonia, Spain: A Population-Based Study

COVID-19; Niño; EscuelasCOVID-19; Nen; EscolesCOVID-19; Child; SchoolsObjective: We describe and analyze the childhood (<18 years) COVID-19 incidence in Catalonia, Spain, during the first 36 weeks of the 2020-2021 school-year and to compare it with the incidence in adults. Methods: Data on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) tests were obtained from the Catalan Agency for Quality and Health Assessment. Overall, 7,203,663 SARS-CoV-2 tests were performed, of which 491,819 were positive (6.8%). We collected epidemiological data including age-group incidence, diagnostic effort, and positivity rate per 100,000 population to analyze the relative results for these epidemiological characteristics. Results: Despite a great diagnostic effort among children, with a difference of 1,154 tests per 100,000 population in relation to adults, the relative incidence of SARS-CoV-2 for <18 years was slightly lower than for the general population, and it increased with the age of the children. Additionally, positivity of SARS-CoV-2 in children (5.7%) was lower than in adults (7.2%), especially outside vacation periods, when children were attending school (4.9%). Conclusions: A great diagnostic effort, including mass screening and systematic whole-group contact tracing when a positive was detected in the class group, was associated with childhood SARS-CoV-2 incidence and lower positivity rate in the 2020-2021 school year. Schools have been a key tool in epidemiological surveillance rather than being drivers of SARS-CoV-2 incidence in Catalonia, Spain.This study was partially supported by the Direcció General de Recerca i Innovació en Salut (DGRIS), Catalan Health Ministry, Generalitat de Catalunya through Vall d'Hebron Research Institute (VHIR)

Exploring the diversity of coronavirus in sewage during COVID-19 pandemic: Don't miss the forest for the trees

Coronavirus; Secuenciación de nueva generación; Viroma de aguas residualesCoronavirus; Seqüenciació de nova generació; Viroma d'aigües residualsCoronavirus; Next generation sequencing; Sewage viromeIn the wake of the COVID-19 pandemic, the use of next generation sequencing (NGS) has proved to be an important tool for the genetic characterization of SARS-CoV-2 from clinical samples. The use of different available NGS tools applied to wastewater samples could be the key for an in-depth study of the excreted virome, not only focusing on SARS-CoV-2 circulation and typing, but also to detect other potentially pandemic viruses within the same family. With this aim, 24-hours composite wastewater samples from March and July 2020 were sequenced by applying specific viral NGS as well as target enrichment NGS. The full virome of the analyzed samples was obtained, with human Coronaviridae members (CoV) present in one of those samples after applying the enrichment. One contig was identified as HCoV-OC43 and 8 contigs as SARS-CoV-2. CoVs from other animal hosts were also detected when applying this technique. These contigs were compared with those obtained from contemporary clinical specimens by applying the same target enrichment approach. The results showed that there is a co-circulation in urban areas of human and animal coronaviruses infecting domestic animals and rodents. NGS enrichment-based protocols might be crucial to describe the occurrence and genetic characteristics of SARS-CoV-2 and other Coronaviridae family members within the excreted virome present in wastewater.This study was partially supported by the Ministry of Science, Innovation and Universities (AGL2017-86797-C2-1-R) through the University of Barcelona and the Direcció General de Recerca i Innovació en Salut (DGRIS) Catalan Health Ministry Generalitat de Catalunya through Vall d'Hebron Research Institute (VHIR). Sílvia Bofill-Mas is a Serra-Hunter fellow at the University of Barcelona