Comparing COVID-19 severity in patients hospitalized for community-associated Delta, BA.1 and BA.4/5 variant infection.

Background: Despite decreasing COVID-19 disease severity during the Omicron waves, a proportion of patients still require hospitalization and intensive care. Objective: To compare demographic characteristics, comorbidities, vaccination status, and previous infections in patients hospitalized for community-associated COVID-19 (CAC) in predominantly Delta, Omicron BA.1 and BA.4/5 SARS-CoV-2 waves. Methods: Data were extracted from three national databases-the National COVID-19 Database, National Vaccination Registry and National Registry of Hospitalizations. Results: Among the hospitalized CAC patients analyzed in this study, 5,512 were infected with Delta, 1,120 with Omicron BA.1, and 1,143 with the Omicron BA.4/5 variant. The age and sex structure changed from Delta to BA.4/5, with the proportion of women (9.5% increase), children and adolescents (10.4% increase), and octa- and nonagenarians increasing significantly (24.5% increase). Significantly more patients had comorbidities (measured by the Charlson Comorbidity Index), 30.3% in Delta and 43% in BA.4/5 period. The need for non-invasive ventilatory support (NiVS), ICU admission, mechanical ventilation (MV), and in-hospital mortality (IHM) decreased from Delta to Omicron BA.4/5 period for 12.6, 13.5, 11.5, and 6.3%, respectively. Multivariate analysis revealed significantly lower odds for ICU admission (OR 0.68, CI 0.54-0.84, p < 0.001) and IHM (OR 0.74, CI 0.58-0.93, p = 0.011) during the Delta period in patients who had been fully vaccinated or boosted with a COVID-19 vaccine within the previous 6 months. In the BA.1 variant period, patients who had less than 6 months elapsed between the last vaccine dose and SARS-CoV-2 positivity had lower odds for MV (OR 0.38, CI 0.18-0.72, p = 0.005) and IHM (OR 0.56, CI 0.37- 0.83, p = 0.005), but not for NIVS or ICU admission. Conclusion: The likelihood of developing severe CAC in hospitalized patients was higher in those with the Delta and Omicron BA.1 variant compared to BA.4/5.

Seasonal and inter-seasonal RSV activity in the European Region during the COVID-19 pandemic from autumn 2020 to summer 2022.

Background: The emergence of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in early 2020 and subsequent implementation of public health and social measures (PHSM) disrupted the epidemiology of respiratory viruses. This work describes the epidemiology of respiratory syncytial virus (RSV) observed during two winter seasons (weeks 40-20) and inter-seasonal periods (weeks 21-39) during the pandemic between October 2020 and September 2022. Methods: Using data submitted to The European Surveillance System (TESSy) by countries or territories in the World Health Organization (WHO) European Region between weeks 40/2020 and 39/2022, we aggregated country-specific weekly RSV counts of sentinel, non-sentinel and Severe Acute Respiratory Infection (SARI) surveillance specimens and calculated percentage positivity. Results for both 2020/21 and 2021/22 seasons and inter-seasons were compared with pre-pandemic 2016/17 to 2019/20 seasons and inter-seasons. Results: Although more specimens were tested than in pre-COVID-19 pandemic seasons, very few RSV detections were reported during the 2020/21 season in all surveillance systems. During the 2021 inter-season, a gradual increase in detections was observed in all systems. In 2021/22, all systems saw early peaks of RSV infection, and during the 2022 inter-seasonal period, patterns of detections were closer to those seen before the COVID-19 pandemic. Conclusion: RSV surveillance continued throughout the COVID-19 pandemic, with an initial reduction in transmission, followed by very high and out-of-season RSV circulation (summer 2021) and then an early start of the 2021/22 season. As of the 2022/23 season, RSV circulation had not yet normalised.

Seroprevalence of Anti-SARS-CoV-2 Antibodies Following the Omicron BA.1 Wave.

We conducted a seroprevalence study using convenient residual sera samples from the Slovenian population collected after the end of the Omicron BA.1 pandemic wave. Serum samples were tested for spike glycoprotein (anti-S) and nucleocapsid protein (anti-N) antibodies. Participants' data regarding confirmed infection and vaccination was obtained from national registries. Anti-S antibodies were detected in 2439 (84.1%) of 2899 sera from persons aged 0-90 years, with the lowest prevalence in the 0-17 age group. The proportion of anti-N positives was the lowest in the ≥70 age group. The proportion of anti-N positives was significantly higher among participants with confirmed past infection and among those who had never been vaccinated. In participants who had not been notified as infected and who had never been vaccinated, the seroprevalence of anti-S and anti-N antibodies was 53% and 35.5%, respectively. From the time of serum collection to mid-November 2022, 445 participants (15.3%) tested positive for SARS-CoV-2, with higher odds in seronegative participants, participants in the 40-59 age group, and those without notified previous infection. Vaccination status and gender had no significant effects on infection risk. This study underlines the importance of serosurveys in understanding the development of the pandemic.

Milder outcomes of SARS-CoV-2 genetically confirmed reinfections compared to primary infections with the delta variant: A retrospective case-control study.

Background: SARS-CoV-2 infection does not confer long immunity. However, studies suggest that prior infection is associated with lower risk of reinfection and milder outcomes of recurrent infections. The aims of this retrospective observational case-control study were to describe the clinical and molecular characteristics of genetically confirmed Delta reinfection cases and to assess the potential protective role of preceding infection on the severity of reinfection. Methods: We used next generation sequencing (NGS) to explore if cases with two positive real time RT-PCR tests > 90 days apart were infected with a different SARS-CoV-2 variant. Cases with confirmed reinfection between August 1st and October 31st, 2021 (the Delta wave) in Slovenia were matched 1:4 by age, sex and timeframe (week of positive test) with individuals with primary infection. Sociodemographic and epidemiologic data, vaccination status, and data on hospitalization and outcome of infection were retrieved from several centralized and standardized national databases. Additional epidemiologic surveys were performed on a limited number of cases and controls. Results: We identified 628 cases of genetically confirmed reinfection during the study period and matched them with 2,512 control subjects with Delta primary infection. Primary infections in individuals with reinfection were mainly caused by B.1.258.17 (51.1%), followed by B.1.1.7 (15.1%) and reinfection was detected on average 271 days after primary infection (range 101-477 days). Our results show a substantially lower probability of hospitalization in cases with reinfection compared with controls (OR: 0.21, p = 0.017), but no significant difference was observed in intensive care unit admission and deaths. We observed a significantly lower proportion of vaccinated individuals among cases compared to controls (4.5% vs. 28.2%), suggesting that hybrid immunity leads to lower probability of reinfection. Detailed analysis of the temporal distribution of variants, responsible for reinfections, showed no significant differences in reinfection potential. Conclusion: Reinfection with the SARS-CoV-2 Delta variant resulted in fewer hospitalizations compared to the primary Delta infection, suggesting that primary infection may, to some extent, produce at least short lasting protective immunity. This study provides additional insight into the reinfection dynamics that may allow appropriate public health measures to be taken in subsequent waves of the COVID-19 pandemic.

Determinants of seropositivity for SARS-CoV-2 in hospital staff in the second wave of the pandemic in Slovenia.

OBJECTIVES: The pandemic caused by the novel coronavirus (SARS-CoV-2) affected a disproportionately high percentage of healthcare workers (HCWs). The aim of the study was to assess the seroprevalence of SARS-CoV-2-specific IgG antibodies in nurses and clinicians working in 2 Slovenian regional hospitals, and to identify the factors associated with seropositivity. MATERIAL AND METHODS: The study was designed as a crosssectional study. Clinicians and nurses were invited to participate in November-December 2020. The respondents (813, 65.8%) completed a questionnaire and consented to provide 10 ml of blood for determining the presence of SARS-CoV-2 IgG antibodies. RESULTS: The authors observed a seroprevalence rate of 20.4%. The results of the univariate analysis proved that the age of a nurse or clinician was the factor most strongly associated with seropositivity - in fact, the youngest nurses and clinicians were 8.33 times more likely to be seropositive than those in the oldest age group (p = 0.041). Being in contact with a family/household member who was SARS-CoV-2-positive was also a very important factor. In the work-related factors group, being in the contact with a SARS-CoV-2-positive colleague (OR = 2.35, p = 0.026) or being in contact with a COVID-19 patient (OR = 1.96, p = 0.004) correlated with seropositivity. In the primary work location/department group, the only significant association appeared among those working in surgical, ENT or ophthalmology departments. The results of the multivariate analysis further supported the thesis that the age of nurses and clinicians was the factor most strongly associated with seropositivity. The youngest nurses and clinicians were 12.5 times more likely to be seropositive than those in the oldest age group (p = 0.024). Being in contact with a SARS-CoV-2-positive family/household member remained the second most important factor. CONCLUSIONS: A significant number of clinicians and nurses working in secondary healthcare were infected in the first 9 months of the pandemic. Int J Occup Med Environ Health. 2022;35(5):571-84.

Detection of SARS-CoV-2 RNA in hospital wastewater from a low COVID-19 disease prevalence area.

Previous studies on SARS-CoV and MERS-CoV reported the detection of viral RNA in the stool of both symptomatic and asymptomatic individuals. These clinical observations suggest that municipal and hospital wastewater from affected communities may contain SARS-CoV-2 RNA. Recent studies have also reported the presence of SARS-CoV-2 RNA in human feces. Wastewater-based epidemiology (WBE) is a promising approach to understand the prevalence of viruses in a given catchment population, as wastewater contains viruses from symptomatic and asymptomatic individuals. The current study reports the first detection of SARS-CoV-2 RNA in untreated wastewater in Slovenia. Two sizes of centrifugal filters were tested: 30 kDa and 10 kDA AMICON® Ultra-15 Centrifugal Filters, where 10 kDA resulted in a higher concentration factor and higher recovery efficiency. The results in hospital wastewater show that WBE can be used for monitoring COVID -19 and could be applied in municipal wastewater treatment plants as a potential complementary tool for public health monitoring at population level.

Virological surveillance of influenza viruses in the WHO European Region in 2019/20 - impact of the COVID-19 pandemic.

The COVID-19 pandemic negatively impacted the 2019/20 WHO European Region influenza surveillance. Compared with previous 4-year averages, antigenic and genetic characterisations decreased by 17% (3,140 vs 2,601) and 24% (4,474 vs 3,403). Of subtyped influenza A viruses, 56% (26,477/47,357) were A(H1)pdm09, 44% (20,880/47,357) A(H3). Of characterised B viruses, 98% (4,585/4,679) were B/Victoria. Considerable numbers of viruses antigenically differed from northern hemisphere vaccine components. In 2020/21, maintaining influenza virological surveillance, while supporting SARS-CoV-2 surveillance is crucial.

Improving influenza virological surveillance in Europe: strain-based reporting of antigenic and genetic characterisation data, 11 European countries, influenza season 2013/14.

Influenza antigenic and genetic characterisation data are crucial for influenza vaccine composition decision making. Previously, aggregate data were reported to the European Centre for Disease Prevention and Control by European Union/European Economic Area (EU/EEA) countries. A system for collecting case-specific influenza antigenic and genetic characterisation data was established for the 2013/14 influenza season. In a pilot study, 11 EU/EEA countries reported through the new mechanism. We demonstrated feasibility of reporting strain-based antigenic and genetic data and ca 10% of influenza virus-positive specimens were selected for further characterisation. Proportions of characterised virus (sub)types were similar to influenza virus circulation levels. The main genetic clades were represented by A/StPetersburg/27/2011(H1N1)pdm09 and A/Texas/50/2012(H3N2). A(H1N1)pdm09 viruses were more prevalent in age groups (by years) < 1 (65%; p = 0.0111), 20-39 (50%; p = 0.0046) and 40-64 (55%; p = 0.00001) while A(H3N2) viruses were most prevalent in those ≥ 65 years (62%*; p = 0.0012). Hospitalised patients in the age groups 6-19 years (67%; p = 0.0494) and ≥ 65 years (52%; p = 0.0005) were more frequently infected by A/Texas/50/2012 A(H3N2)-like viruses compared with hospitalised cases in other age groups. Strain-based reporting enabled deeper understanding of influenza virus circulation among hospitalised patients and substantially improved the reporting of virus characterisation data. Therefore, strain-based reporting of readily available data is recommended to all reporting countries within the EU/EEA.

Predominance of influenza A(H1N1)pdm09 virus genetic subclade 6B.1 and influenza B/Victoria lineage viruses at the start of the 2015/16 influenza season in Europe.

Influenza A(H1N1)pdm09 viruses predominated in the European influenza 2015/16 season. Most analysed viruses clustered in a new genetic subclade 6B.1, antigenically similar to the northern hemisphere vaccine component A/California/7/2009. The predominant influenza B lineage was Victoria compared with Yamagata in the previous season. It remains to be evaluated at the end of the season if these changes affected the effectiveness of the vaccine for the 2015/16 season.

Associations between Meteorological Parameters and Influenza Activity in Berlin (Germany), Ljubljana (Slovenia), Castile and León (Spain) and Israeli Districts.

BACKGROUND: Studies in the literature have indicated that the timing of seasonal influenza epidemic varies across latitude, suggesting the involvement of meteorological and environmental conditions in the transmission of influenza. In this study, we investigated the link between meteorological parameters and influenza activity in 9 sub-national areas with temperate and subtropical climates: Berlin (Germany), Ljubljana (Slovenia), Castile and León (Spain) and all 6 districts in Israel. METHODS: We estimated weekly influenza-associated influenza-like-illness (ILI) or Acute Respiratory Infection (ARI) incidence to represent influenza activity using data from each country's sentinel surveillance during 2000-2011 (Spain) and 2006-2011 (all others). Meteorological data was obtained from ground stations, satellite and assimilated data. Two generalized additive models (GAM) were developed, with one using specific humidity as a covariate and another using minimum temperature. Precipitation and solar radiation were included as additional covariates in both models. The models were adjusted for previous weeks' influenza activity, and were trained separately for each study location. RESULTS: Influenza activity was inversely associated (p<0.05) with specific humidity in all locations. Minimum temperature was inversely associated with influenza in all 3 temperate locations, but not in all subtropical locations. Inverse associations between influenza and solar radiation were found in most locations. Associations with precipitation were location-dependent and inconclusive. We used the models to estimate influenza activity a week ahead for the 2010/2011 period which was not used in training the models. With exception of Ljubljana and Israel's Haifa District, the models could closely follow the observed data especially during the start and the end of epidemic period. In these locations, correlation coefficients between the observed and estimated ranged between 0.55 to 0.91and the model-estimated influenza peaks were within 3 weeks from the observations. CONCLUSION: Our study demonstrated the significant link between specific humidity and influenza activity across temperate and subtropical climates, and that inclusion of meteorological parameters in the surveillance system may further our understanding of influenza transmission patterns.

A comparison of the demographic and clinical characteristics of laboratory-confirmed influenza B Yamagata and Victoria lineage infection.

BACKGROUND: The evolution of influenza viruses is characterized by the co-circulation of two antigenically and genetically distinct lineages B/Victoria/2/87-like viruses (Victoria) and B/Yamagata/16/88-like viruses (Yamagata). To date, there is not much data associating lineages variation with demographic and clinical data. OBJECTIVES: We compared the demographic and clinical characteristics of patients with laboratory-confirmed influenza B Victoria or Yamagata lineage infection. STUDY DESIGN: We retrospectively analyzed data from 6811 patients aged from <1 through 99 years with influenza like-illness who consulted the sentinel site or sentinel hospital in the seasons 2010/2011, 2011/2012 and 2012/2013. There were 662 patients positive for influenza B virus by multiplex real-time RT-PCR. Six hundred thirty-seven (96.8%) were successfully subtyped for Victoria or Yamagata lineage infection. The available demographic and clinical data was compared. RESULTS: Patients with the Victoria lineage were significantly younger compared to patients infected with the Yamagata lineage. The Victoria lineage was the predominant strain in the 15-34 age groups in patients consulting at primary care level and in hospitalized patients. In the youngest age group (0-4 years) approximately half of the confirmed influenza B cases belonged to the Victoria (55%) and the rest to the Yamagata lineage (45%). Aside from age, there was no statistically significant difference found in gender distribution, vaccination history, clinical presentation or risk factors for severe influenza infection in hospitalized patients after adjustment for the age. CONCLUSIONS: The frequency of influenza B Victoria and Yamagata infection is age dependent with no significant differences detected in clinical presentation comparing both lineages.

Seroprevalence study of antibodies against influenza A(H1N1) 2009 virus after the second pandemic wave in Slovenia.

OBJECTIVE: The pandemic influenza (H1N1) 2009 virus, which combined genes from swine, human and avian influenza viruses, emerged in April 2009 and spread globally within the next month. The post-pandemic serological response to the influenza A(H1N1) 2009 virus in non-vaccinated individuals from the central part of Slovenia was studied. METHODS: After the second pandemic wave, 226 serum samples from healthy preschool children, students, health care workers and blood donors not previously vaccinated with pandemic vaccine were investigated by use of microneutralization assays (MN). Data on previous vaccinations with seasonal influenza vaccine and recent acute respiratory infections were collected. RESULTS: The overall rate of seropositivity to the pandemic influenza virus was high: 76.9% of the participants had antibody titres of ≥20. A titre of ≥40 was detected in 54% of the serum samples tested, the highest prevalence being in the 15-17 age group. There was no statistically significant difference in MN titres between individuals who had never been vaccinated with influenza vaccine and those vaccinated at least once. History of ARI was not more frequent in subjects with MN titres ≥20, ≥40 or ≥80 (p-value 0.654, p-value 0.755 and p-value 1, respectively). CONCLUSIONS: High seroprevalence to pandemic influenza has been found in all age groups regardless of the absence of clinical picture compatible with acute respiratory infection. Previous vaccinations with seasonal influenza vaccines had no impact on serological response to the influenza A(H1N1) 2009 virus.

European Sero-Epidemiology Network 2: standardisation of immunoassay results for pertussis requires homogeneity in the antigenic preparations.

A standardisation process, already developed during the earlier European Sero-Epidemiology Network (ESEN) project, was employed with a more robust algorithm to harmonise results of pertussis serological assays performed in 12 European and non-European countries. Initially, results from each country's own assay were compared with those obtained at the reference laboratory by means of an in-house pertussis toxin (PT)-based ELISA: seven countries used in-house or commercial PT-ELISAs; the other countries used assays based on Bordetella pertussis whole cell extracts (WCE) (three countries) or on combined PT-FHA (filamentous haemagglutinin) antigenic preparations (two countries). The WCE assays, although admitted for diagnostic purposes, confirmed their low correlation with the PT-ELISAs and their results could not be used for standardisation; the PT-FHA ELISAs gave results that were suitable for standardisation in one country but unsatisfactory in the other; the use of purified PT in serological assays confirmed its better reliability than other preparations and all PT-ELISAs results could be calibrated against those of the reference centre. In the standardisation process two high-titre cut-offs indicative of likelihood of recent infection (from within 4 weeks of disease onset up to 1 year after) were included for evaluations as they are suggested to be more useful, for the sero-epidemiological assays of immunity to pertussis, than the cut-off of protection, commonly employed, but still not defined for pertussis. Providing PT-ELISAs are used, standardisation of pertussis assay results is always possible and, when standardisation is performed, evaluation and comparison of the impact of different interventions can be also allowed, by measuring at the distribution of high antibody titres in the populations.

Towards elimination: measles susceptibility in Australia and 17 European countries.

OBJECTIVE: To evaluate age-specific measles susceptibility in Australia and 17 European countries. METHODS: As part of the European Sero-Epidemiology Network 2 (ESEN2), 18 countries collected large national serum banks between 1996 and 2004. These banks were tested for measles IgG and the results converted to a common unitage to enable valid intercountry comparisons. Historical vaccination and disease incidence data were also collected. Age-stratified population susceptibility levels were compared to WHO European Region targets for measles elimination of < 15% in those aged 2-4 years, < 10% in 5-9-year-olds and < 5% in older age groups. FINDINGS: Seven countries (Czech Republic, Hungary, Luxembourg, Spain, Slovakia, Slovenia and Sweden) met or came very close to the elimination targets. Four countries (Australia, Israel, Lithuania and Malta) had susceptibility levels above WHO targets in some older age groups indicating possible gaps in protection. Seven countries (Belgium, Bulgaria, Cyprus, England and Wales, Ireland, Latvia and Romania) were deemed to be at risk of epidemics as a result of high susceptibility in children and also, in some cases, adults. CONCLUSION: Although all countries now implement a two-dose measles vaccination schedule, if the WHO European Region target of measles elimination by 2010 is to be achieved higher routine coverage as well as vaccination campaigns in some older age cohorts are needed in some countries. Without these improvements, continued measles transmission and outbreaks are expected in Europe.

Comparison of rubella seroepidemiology in 17 countries: progress towards international disease control targets.

OBJECTIVE: To standardize serological surveillance to compare rubella susceptibility in Australia and 16 European countries, and measure progress towards international disease-control targets. METHODS: Between 1996 and 2004, representative serum banks were established in 17 countries by collecting residual sera or community sampling. Serum banks were tested in each country and assay results were standardized. With a questionnaire, we collected information on current and past rubella vaccination programmes in each country. The percentage of seronegative (< 4 IU/ml) children (2-14 years of age) was used to evaluate rubella susceptibility, and countries were classified by seronegativity as group I (< 5%), group II (5-10%) or group III (> 10%). The proportion of women of childbearing age without rubella protection (< or = 10 IU/ml) was calculated and compared with WHO targets of < 5%. FINDINGS: Only Romania had no rubella immunization programme at the time of the survey; the remaining countries had a two-dose childhood schedule using the measles, mumps and rubella (MMR) vaccine. The percentage of susceptible children defined five countries as group I, seven as group II and four as group III. Women of childbearing age without rubella protection were < 5% in only five countries. CONCLUSION: Despite the low reported incidence in many countries, strengthening the coverage of the routine two-dose of MMR vaccine among children is needed, especially in group III countries. Catch-up campaigns in older age groups and selective targeting of older females are needed in many countries to ensure necessary levels of protective immunity among women of childbearing age.

Seroprevalence of IgG antibodies to pertussis toxin in the Slovene population.

BACKGROUND: The use of pertussis vaccines has reduced the morbidity and mortality of whooping cough. Immunity following the natural disease or vaccination is not life-long and reinfections causing an increase of pertussis antibodies can occur. In this study, the distribution of IgG antibodies to pertussis toxin (anti-PT IgG) among different age groups in Slovenia was determined. METHODS: The seroprevalence of anti-PT IgG antibodies to Bordetella pertussis was investigated in 3418 persons (49.1% males). The population under study was stratified into 27 age groups. The serological results were assigned to five groups, according to their titer levels. The geometric mean titers (GMT) were calculated. RESULTS: In 11.5% sera tested, no IgG antibodies to pertussis toxin were detected. High titers (> or =125 U/ml) were confirmed in 2.3% sera. There were no statistically significant differences between age groups in the proportion of antibody levels. Pre-school children from three to five years of age had the lowest anti-PT IgG GMTs (9.6-10.7 U/ml). Vaccinated children (aged from one to two years) and adolescents from 17-18 years of age had the highest GMTs (>20 U/ml). GMTs were not statistically significantly different between males and females. CONCLUSIONS: The study demonstrated an early decline of anti-PT IgG after vaccination. According to the serological profile, school-age children and adolescents have the highest rate of infection. The large proportion of seropositive adults indicates that reinfection with B. pertussis is relatively common.