Comprehensive surveillance of acute respiratory infections during the COVID-19 pandemic: a methodological approach using sentinel networks, Castilla y León, Spain, January 2020 to May 2022.

BackgroundSince 1996, epidemiological surveillance of acute respiratory infections (ARI) in Spain has been limited to seasonal influenza, respiratory syncytial virus (RSV) and potential pandemic viruses. The COVID-19 pandemic provides opportunities to adapt existing systems for extended surveillance to capture a broader range of ARI.AimTo describe how the Influenza Sentinel Surveillance System of Castilla y León, Spain was rapidly adapted in 2020 to comprehensive sentinel surveillance for ARI, including influenza and COVID-19.MethodsUsing principles and methods of the health sentinel network, we integrated electronic medical record data from 68 basic surveillance units, covering 2.6% of the regional population between January 2020 to May 2022. We tested sentinel and non-sentinel samples sent weekly to the laboratory network for SARS-CoV-2, influenza viruses and other respiratory pathogens. The moving epidemic method (MEM) was used to calculate epidemic thresholds.ResultsARI incidence was estimated at 18,942 cases per 100,000 in 2020/21 and 45,223 in 2021/22, with similar seasonal fold increases by type of respiratory disease. Incidence of influenza-like illness was negligible in 2020/21 but a 5-week epidemic was detected by MEM in 2021/22. Epidemic thresholds for ARI and COVID-19 were estimated at 459.4 and 191.3 cases per 100,000 population, respectively. More than 5,000 samples were tested against a panel of respiratory viruses in 2021/22.ConclusionExtracting data from electronic medical records reported by trained professionals, combined with a standardised microbiological information system, is a feasible and useful method to adapt influenza sentinel reports to comprehensive ARI surveillance in the post-COVID-19 era.

The relationship between hand hygiene and rates of acute respiratory infections among Umrah pilgrims: A pilot randomised controlled trial.

BACKGROUND: There is a lack of randomised controlled trials (RCTs) investigating the role of hand hygiene in preventing and containing acute respiratory infections (ARIs) in mass gatherings. In this pilot RCT, we assessed the feasibility of establishing a large-scale trial to explore the relationship between practising hand hygiene and rates of ARI in Umrah pilgrimage amidst the COVID-19 pandemic. METHODS: A parallel RCT was conducted in hotels in Makkah, Saudi Arabia, between April and July 2021. Domestic adult pilgrims who consented to participate were randomised 1:1 to the intervention group who received alcohol-based hand rub (ABHR) and instructions, or to the control group who did not receive ABHR or instructions but were free to use their own supplies. Pilgrims in both groups were then followed up for seven days for ARI symptoms. The primary outcome was the difference in the proportions of syndromic ARIs among pilgrims between the randomised groups. RESULTS: A total of 507 (control: intervention = 267: 240) participants aged between 18 and 75 (median 34) years were randomised; 61 participants were lost to follow-up or withdrew leaving 446 participants (control: intervention = 237:209) for the primary outcome analysis; of whom 10 (2.2 %) had developed at least one respiratory symptom, three (0.7 %) had 'possible ILI' and two (0.4 %) had 'possible COVID-19'. The analysis of the primary outcome found no evidence of difference in the proportions of ARIs between the randomised groups (odds ratio 1.1 [0.3-4.0] for intervention relative to control). CONCLUSION: This pilot trial suggests that conducting a future definitive RCT to assess the role of hand hygiene in the prevention of ARIs is feasible in Umrah setting amidst such a pandemic; however, outcomes from this trial are inconclusive, and such a study would need to be very large given the low rates of outcomes observed here. TRIAL REGISTRATION: This trial was registered in the Australian New Zealand Clinical Trials Registry (ANZCTR) (ACTRN12622001287729), the full protocol can be accessed there.

Five-Year Community Surveillance Study for Acute Respiratory Infections Using Text Messaging: Findings From the MoSAIC Study.

BACKGROUND: Acute respiratory infections (ARI) are the most common infectious diseases globally. Community surveillance may provide a more comprehensive picture of disease burden than medically attended illness alone. METHODS: In this longitudinal study conducted from 2012 to 2017 in the Washington Heights/Inwood area of New York City, we enrolled 405 households with 1915 individuals. Households were sent research text messages twice weekly inquiring about ARI symptoms. Research staff confirmed symptoms by follow-up call. If ≥2 criteria for ARI were met (fever/feverish, cough, congestion, pharyngitis, myalgias), staff obtained a mid-turbinate nasal swab in participants' homes. Swabs were tested using the FilmArray reverse transcription polymerase chain reaction (RT-PCR) respiratory panel. RESULTS: Among participants, 43.9% were children, and 12.8% had a chronic respiratory condition. During the 5 years, 114 724 text messages were sent; the average response rate was 78.8% ± 6.8%. Swabs were collected for 91.4% (2756/3016) of confirmed ARI; 58.7% had a pathogen detected. Rhino/enteroviruses (51.9%), human coronaviruses (13.9%), and influenza (13.2%) were most commonly detected. The overall incidence was 0.62 ARI/person-year, highest (1.73) in <2 year-olds and lowest (0.46) in 18-49 year-olds. Approximately one-fourth of those with ARI sought healthcare; percents differed by pathogen, demographic factors, and presence of a chronic respiratory condition. CONCLUSIONS: Text messaging is a novel method for community-based surveillance that could be used both seasonally as well as during outbreaks, epidemics and pandemics. The importance of community surveillance to accurately estimate disease burden is underscored by the findings of low rates of care-seeking that varied by demographic factors and pathogens.

Role of vitamin D in modulating the immune response to SARS-CoV-2 and other coronavirus infections.

In recent years, new data have been obtained on the significant prevalence of vitamin D (VD) deficiency in the population, and knowledge about the role of vitamin D in the regulation of many physiological processes in the body, including the functioning of the immune system, has increased. The SARS-CoV-2 pandemic has further highlighted the issue of an adequate immune response in vitamin D deficiency. Objective of the review. To present and summarize the evidence on the role of VD in different parts of the immune response in COVID-19, to analyze available studies of the VD status effect on the course and outcome of COVID-19 in patients from different population groups. Material and methods. A search of domestic and foreign literature on the role of VD in the immune response in respiratory viral infections and SARS-CoV-2, as well as practical measures of VD-status correction in COVID-19, was performed. We used Scopus, Web of Science, PubMed, Google Scholar, eLibrary, and Cyberleninka databases. Results. Numerous clinical and observational studies have found an association between 25-hydroxyvitamin D levels, COVID-19 severity, and mortality. This association can be explained by the multifaceted role of vitamin D in the physiology of the human immune and endocrine systems. On the immunological side, the active form of VD promotes the secretion of antimicrobial peptides responsible for inhibiting viral replication and stimulates autophagy by increasing the level of Beclin1 protein and decreasing the level of mTOR protein regulating cellular homeostasis. It leads to the presentation of antigens followed by activation of the antiviral pathway of type I interferons. VD also stabilizes intercellular junctions, including those in the airway epithelium, reducing their permeability to pathogens, stimulates the activity of angiotensin-converting enzyme-2, whose receptors are a conduit for SARS-CoV-2 into cells, and several pathophysiological responses associated with the disease symptoms and acute lung injury. Adequate vitamin D status can provide significant benefits during the pandemic. Conclusion. To date, ideas about the role of vitamin D in regulating the immune response in respiratory infections have significantly expanded. However, its use in the complex preventive measures and adjuvant therapy of viral infections, including COVID-19, should be the subject of further scientific research.Copyright © 2023, Media Sphera Publishing Group. All rights reserved.

Acute respiratory infection emergency access in a tertiary care children hospital in Italy, prior and after the SARS-CoV-2 emergence.

Background: The COVID-19 pandemic has changed the epidemiology of acute respiratory infections (ARIs) in children. The aims of the present study were to describe the epidemiological trend of ARI emergency visits and virology results prior and after the SARS-CoV-2 emergence and to estimate the association of ARI emergency department (ED) visits with respiratory viruses. Methods: This study was conducted at the Bambino Gesù Children's Hospital, a tertiary care children's hospital in the Lazio Region, Italy. The demographic and clinical information of children who accessed the ED and were diagnosed with ARI from January 1, 2018 to June 30, 2022 was retrospectively extracted from the electronic health records. The observed temporal trends in viruses diagnosed from respiratory samples were compared with the number of ARI ED visits over the same period through a multivariable linear regression model. Results: During the study period, there were 72,959 ED admissions for ARIs and 33,355 respiratory samples resulted positive for viruses. Prior to the pandemic, respiratory syncytial virus (RSV) and influenza had a clear seasonal pattern, which was interrupted in 2020. In 2021-2022, RSV reached the highest peak observed during the study period, whereas influenza activity was minimal. The peaks of ARI ED visits corresponded to peaks of influenza, RSV, and rhinovirus in the 2018-2019 and 2019-2020 seasons, to SARS-CoV-2 and rhinovirus in 2020, and to RSV and parainfluenza in 2021-2022. Conclusions: ARI resulting in ED visits should be included in the ARI disease burden measurement for a more accurate measure of the impact of preventive measures.

Merging citizen science with epidemiology: design of a prospective feasibility study of health events and air pollution in Cologne, Germany.

BACKGROUND: Citizen science as an approach to merge society and science is not a new paradigm. Yet it is not common in public health, epidemiology, or medical sciences. SMARAGD (Sensors for Measuring Aerosols and ReActive Gases to Deduce health effects) assesses air pollution at participants' homes or workplaces in Cologne, Germany, as feasibility study with a citizen science approach. Personal exposure to air pollutants is difficult to study, because the distribution of pollutants is heterogeneous, especially in urban areas. Targeted data collection allows to establish connections between air pollutant concentration and the health of the study population. Air pollution is among the most urgent health risks worldwide. Yet links of individualized pollution levels and respiratory infections remain to be validated, which also applies for the feasibility of the citizen science approach for epidemiological studies. METHODS: We co-designed a prospective feasibility study with two groups of volunteers from Cologne, Germany. These citizen scientists and researchers determined that low-cost air-quality sensors (hereafter low-cost sensors) were to be mounted at participants' homes/workplaces to acquire stationary data. The advantage of deploying low-cost sensors is the achievable physical proximity to the participants providing health data. Recruitment started in March 2021 and is currently ongoing (as of 09/22). Sensor units specifically developed for this study using commercially available electronic sensor components will measure particulate matter and trace gases such as ozone, nitrogen oxides, and carbon monoxide. Health data are collected using the eResearch system "Prospective Management and Monitoring-App" (PIA). Due to the ongoing SARS-CoV-2 pandemic, we also focus on COVID-19 as respiratory infection. DISCUSSION: Citizen science offers many benefits for science in general but also for epidemiological studies. It provides scientific information to society, enables scientific thinking in critical discourses, can counter anti-scientific ideologies, and takes into account the interests of society. However, it poses many challenges, as it requires extensive resources from researchers and society and can raise concerns regarding data protection and methodological challenges such as selection bias.

Influence of COVID-19-Related Interventions on the Number of Inpatients with Acute Viral Respiratory Infections: Using Interrupted Time Series Analysis.

After the first COVID-19 patient was diagnosed, non-pharmaceutical interventions such as social distancing and behavior change campaigns were implemented in South Korea. The social distancing policy restricted unnecessary gatherings and activities to prevent local transmission. This study aims to evaluate the effect of social distancing, a strategy for COVID-19 prevention, on the number of acute respiratory infection inpatients. This study used the number of hospitalized patients with acute respiratory infection from the Infectious Disease Portal of the Korea Centers for Disease Control and Prevention (KCDC) between the first week of January 2018, to the last week of January 2021. Intervention 1t represents the first patient occurrence of COVID-19, Intervention 2t represents the relaxing of the social distancing policy. We used acute respiratory infection statistics from Korea and segmented regression analysis was used. The analysis showed that the trend of the number of acute respiratory infection inpatients decreased after the implementation of the first patient incidence of COVID-19 due to prevention activities. After the relaxing of the social distancing policy, the number of inpatients with acute respiratory infections significantly increased. This study verified the effect of social distancing on the reduction in hospital admissions for acute respiratory viral infections.

The dilemma of improving rational antibiotic use in pediatric community-acquired pneumonia.

Pneumonia is the number one cause of disease and deaths in children under five years old, outside the neonatal period, with the greatest number of cases reported from resource-limited settings. The etiology is variable, with not much information on the local etiology drug resistance profile in many countries. Recent studies suggest an increasing contribution from respiratory viruses, also in children with severe pneumonia, with an increased relative contribution in settings that have good vaccine coverage against common bacterial pathogens. Respiratory virus circulation was greatly reduced during highly restrictive measures to contain the spread of COVID-19 but rebounded once COVID-19 restrictions were relaxed. We conducted a comprehensive literature review of the disease burden, pathogens, case management and current available prevention of community acquired childhood pneumonia, with a focus on rational antibiotic use, since the treatment of respiratory infections is the leading cause of antibiotic use in children. Consistent application of revised World Health Organisation (WHO) guidance that children presenting with coryzal symptoms or wheeze can be managed without antibiotics in the absence of fever, will help to reduce unnecessary antibiotic use, as will increased availability and use of bedside inflammatory marker tests, such as C-reactive protein (CRP) in children with respiratory symptoms and fever.

Viral co-infection with human respiratory syncytial virus in suspected acute and severe respiratory tract infections during COVID-19 pandemic in Yaoundé, Cameroon, 2020-2021.

BACKGROUND: Acute lower respiratory tract infections (ALRIs) are one one of the leading causes of morbidity and mortality among people of all ages worldwide, particularly in low- and middle-income countries (LMICs). The purpose of this study was to determine epidemiological characteristics of respiratory viruses in acute respiratory infection (ARI) patients during the COVID-19 pandemic in Yaoundé, Cameroon. METHODS: Patients were monitored for respiratory symptoms as part of the surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and other respiratory viral infections. Patients of all ages with respiratory symptoms less than 5 days were considered. Sociodemographic and clinical data as well as nasopharyngeal samples was collected from patients. Nasopharyngeal samples were tested for SARS-CoV-2, influenza, and respiratory syncytial virus (RSV) using real-time reverse-transcription polymerase chain reaction methods. Virus distribution and demographic data were analyzed with R version 2.15.1. RESULTS: From July 2020 to October 2021, 1120 patients were included. The overall viral detection rate was 32.5%, including 9.5% for RSV, 12.6% for influenza virus and 12.8% for SARS-CoV-2. Co-infections were detected in 6.9% of positive cases. While RSV and influenza virus showed seasonal trends, SARS-CoV-2 was detected throughout the study period. CONCLUSION: We found that during COVID-19 pandemic, respiratory viruses play an important role in etiology of influenza-like illness in Cameroon, and this observation was true for patients of all ages.

Estimating the burden of influenza-attributable severe acute respiratory infections on the hospital system in Metropolitan France, 2012-2018.

BACKGROUND: To date, estimating the burden of seasonal influenza on the hospital system in France has been restricted to influenza diagnoses in patients (estimated hospitalization rate of 35/100,000 on average from 2012 to 2018). However, many hospitalizations for diagnosed respiratory infections (e.g. pneumonia, acute bronchitis) occur without concurrent screening for virological influenza, especially in the elderly. Specifically, we aimed to estimate the burden of influenza on the French hospital system by examining the proportion of severe acute respiratory infections (SARI) attributable to influenza. METHODS: Using French national hospital discharge data from 1/7/2012 to 30/6/2018, we extracted SARI hospitalizations with ICD-10 codes J09-J11 (influenza codes) in main or associated diagnoses, and J12-J20 (pneumonia and bronchitis codes) in main diagnoses. We estimated influenza-attributable SARI hospitalizations during influenza epidemics, as the number of influenza-coded hospitalizations plus the influenza-attributable number of pneumonia- and acute bronchitis-coded hospitalizations using periodic regression and generalized linear models. Additional analyses stratified by age group, diagnostic category (pneumonia and bronchitis), and region of hospitalization were performed using the periodic regression model only. RESULTS: The average estimated hospitalization rate of influenza-attributable SARI during the five annual influenza epidemics covered (2013-2014 to 2017-2018) was 60/100,000 with the periodic regression model, and 64/100,000 with the generalized linear model. Over the six epidemics (2012-2013 to 2017-2018), of the 533,456 SARI hospitalizations identified, an estimated 227,154 were influenza-attributable (43%). Fifty-six percent of cases were diagnosed with influenza, 33% pneumonia, and 11% bronchitis. Diagnoses varied between age groups: 11% of patients under 15 years old had pneumonia versus 41% of patients aged 65 and older. CONCLUSION: Compared to influenza surveillance in France to date, analyzing excess SARI hospitalizations provided a much larger estimate of the burden of influenza on the hospital system. This approach was more representative and allowed the burden to be assessed according to age group and region. The emergence of SARS-Cov-2 has led to a change in the dynamics of winter respiratory epidemics. The co-circulation of the three current major respiratory viruses (influenza, SARS-Cov-2, and RSV) and the evolution of diagnostic confirmation practices must now be taken into account when analyzing SARI.

Role of vitamin D in modulating the immune response to SARS-CoV-2 and other coronavirus infections

In recent years, new data have been obtained on the significant prevalence of vitamin D (VD) deficiency in the population, and knowledge about the role of vitamin D in the regulation of many physiological processes in the body, including the functioning of the immune system, has increased. The SARS-CoV-2 pandemic has further highlighted the issue of an adequate immune response in vitamin D deficiency. Objective of the review. To present and summarize the evidence on the role of VD in different parts of the immune response in COVID-19, to analyze available studies of the VD status effect on the course and outcome of COVID-19 in patients from different population groups. Material and methods. A search of domestic and foreign literature on the role of VD in the immune response in respiratory viral infections and SARS-CoV-2, as well as practical measures of VD-status correction in COVID-19, was performed. We used Scopus, Web of Science, PubMed, Google Scholar, eLibrary, and Cyberleninka databases. Results. Numerous clinical and observational studies have found an association between 25-hydroxyvitamin D levels, COVID-19 severity, and mortality. This association can be explained by the multifaceted role of vitamin D in the physiology of the human immune and endocrine systems. On the immunological side, the active form of VD promotes the secretion of antimicrobial peptides responsible for inhibiting viral replication and stimulates autophagy by increasing the level of Beclin1 protein and decreasing the level of mTOR protein regulating cellular homeostasis. It leads to the presentation of antigens followed by activation of the antiviral pathway of type I interferons. VD also stabilizes intercellular junctions, including those in the airway epithelium, reducing their permeability to pathogens, stimulates the activity of angiotensin-converting enzyme-2, whose receptors are a conduit for SARS-CoV-2 into cells, and several pathophysiological responses associated with the disease symptoms and acute lung injury. Adequate vitamin D status can provide significant benefits during the pandemic. Conclusion. To date, ideas about the role of vitamin D in regulating the immune response in respiratory infections have significantly expanded. However, its use in the complex preventive measures and adjuvant therapy of viral infections, including COVID-19, should be the subject of further scientific research. © 2023, Media Sphera Publishing Group. All rights reserved.

Effectiveness of vero cell inactivated vaccine against severe acute respiratory infections (SARI) in Sibu, Malaysia: A retrospective test-negative design.

The effectiveness of the vero cell inactivated vaccine (CoronaVac®) against severe acute respiratory infection ( SARI) caused by SARS-CoV-2 in the real world was assessed. A matched test-negative case-control design was employed using the web-based national information system, as well as the hospitalization dataset in Sibu Hospital. Vaccine effectiveness was measured by conditional logistic regression with adjustment for gender, underlying comorbidity, smoking status, and education level. Between 15 March and 30 September 2021, 838 eligible SARI patients were identified from the hospitalization records. Vaccine effectiveness was 42.4% (95% confidence interval [CI]: -28.3 to 74.1) for partial vaccination (after receiving the first dose to 14 days after receiving the second dose), and 76.5% (95% CI: 45.6 to 89.8) for complete vaccination (at 15 days or more after receiving the second dose). This analysis indicated that two doses of CoronaVac® vaccine provided efficacious protection against SARI caused by SARS-CoV-2 in the short term. However, the duration of protection, and performance against new variants need to be studied continuously.

Clinical and etiological characteristics of mixed infections in children in the Izhevsk hospital

Aim: to study the structure, features of the findings and treatment of mixed infections in children at the present stage. Materials and methods. 85 case histories of children aged 5 months to 17 years and 10 months were examined, the final diagnosis of which included 2 or more infections on the basis of the children's infectious diseases department City Clinical Hospital No. 7 of Izhevsk. Children with acute infectious pathology (acute intestinal infections, acute respiratory infections, herpes infections) are hospitalized in this hospital. Diagnostic methods: polymerase chain reaction, ELISA, bacteriological. Results. Mixed infections are equally common in both boys and girls, while there is a predominance of mixed infections in young children (up to 1 year and from 1 year to 3 years) 62.4%. The structure of infectious morbidity is consistently dominated by acute enteric infection - 83.5% cases and acute respiratory infections - 53.0% cases. The progression of SARS-CoV-2-associated and herpes-associated mixed infections is characterized by a pronounced polymorphism of clinical manifestations. The etiological factor for each nosology was deciphered only in 17.7%;in 43.5% of cases, only one etiological factor was verified in the laboratory;in 38.8% of cases, no etiological factor was confirmed in the laboratory. Copyright © The Author(s) 2022.

The Design and Implementation of the ECOVIR Project: A Primary Health Care Surveillance System to Strengthen Co-Detection of Respiratory Viruses in Normandy.

Acute respiratory infections (ARIs) need to be better understood and treated, as they are critical to public health, especially during crises such as the SARS-CoV2 pandemic. These are the most abundant infections in the general population and are seen primarily in primary care by general practitioners (GPs). Many different viruses are involved, according to epidemic variations. Viral co-detections account for a significant proportion of ARIs in hospital cohorts. The objective of the ECOVIR cohort was to study viral co-detections by setting up a biobank of respiratory tract samples from patients consulting their general practitioner for ARI symptoms. We report here on the course of the study: the design, the conduct, and the difficulties encountered. ECOVIR (Etude des CO-detections VIrales dans les prélèvements Respiratoires) was a prospective, multicenter cohort conducted in France during two epidemic seasons (2018-2019 and 2019-2020). We recruited GPs. Each GP investigator (GPI) saw patients weekly for examination, clinical data collection, and nasopharyngeal swabbing. Each sample was sent to the virology unit for biobanking and molecular analysis. Clinical and sociodemographic data were collected 7 days after inclusion. ECOVIR involved 36 GPIs. Patients with symptoms of an ARI were included (n = 685). The median number of inclusions was 16 patients per GPI over both seasons (IC25-75% [4.75; 27]). Patients aged 18 to 64 years were the most numerous (57%), followed by children (30%), and the elderly (13% over 65 years). This age distribution emphasizes the young adult and middle-aged population. Residents participated in the project and called patients on day 7 to obtain clinical and sociodemographic data. Our study triggered the creation of an original network, which plans to establish a functional link between research and primary health care. Primary care is unfortunately poorly represented in research protocols, particularly in respiratory infections, even though it is a cornerstone of our French health care system, as demonstrated every day in this period of crisis.

COVID-19 in the Emergency Department of the Primary Healthcare Centre Banja Luka

Background / Aim: COVID-19 is acute virus disease caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS–CoV-2). It was proclaimed as pandemic starting from March 2020 and is still ongoing. COVID-19 pandemic forced all segments of the society, particularly the health sector, to function in changed and aggravating circumstances and because of the transmission and new strains of the virus it resulted in the change of the number of infected people with peaks and oscillations. Aim of this study was to make analysis of the data related to COVID-19 positive/suspect patients examined in the Primary Healthcare Centre Banja Luka in the period 15 March 2020 – 15 March 2021, which refers to the incidence of the infected persons, sex and age representation, laboratory diag-nostics and clinical parameters, applied therapy, as well as the number of patients sent for the hospital treatment. Methods: Data for the analysis were obtained by the retrospective analysis of the statistical data from the electronic medical record of the examined COVID-19 positive/suspect patients in the Outpatient Clinic for Acute Respiratory Infections (ARI) and in the field. Pearson’s χ2 test of contingency was used for the comparison of differences of the observed characteristics of the examined groups. Results: Personnel of the Emergency Department (ED) of the Primary Health-care Centre Banja Luka, in the period 15 March 2020 – 15 March 2021, examined the total of 3,937 COVID-19 positive patients and patients suspect of COVID-19. Out of that number, 3,601 patients were examined in the ED – ARI and 336 patients were examined in the field. The biggest number of patients was registered in November 2020 (768). Male sex prevailed (55.50 %) and patients of 20-50 years of age were most represented. There were 3.10 % of those highly febrile patients and 2.5 % of those with low SpO2 of under 90 %. 14.90 % of patients had higher values of troponin T and 45.50 % of them had higher values of D-dimer. In the field, 69.60 % of patients had pathological changes on lungs and 33.30 % had pathological ECG report. The number of patients sent from the ARI for further diagnostic procedure or hospitalisation to the Clinic for Infectious Diseases of the University Clinical Centre of Banja Luka was 1,191 and 258 patients were sent from the field. Conclusion: For the purpose of preventing the spread of epidemics, the ED reor-ganised the existing space by introducing temporary clinics – containers for the patients with acute respiratory infections and febrile status, COVID-19 suspects. Clinical parameters changed depending on the new virus strains, as well as on age distribution and infection complications. © 2022 Banjac et al.

Next Generation Sequencing Approaches to Characterize the Respiratory Tract Virome.

The COVID-19 pandemic and heightened perception of the risk of emerging viral infections have boosted the efforts to better understand the virome or complete repertoire of viruses in health and disease, with a focus on infectious respiratory diseases. Next-generation sequencing (NGS) is widely used to study microorganisms, allowing the elucidation of bacteria and viruses inhabiting different body systems and identifying new pathogens. However, NGS studies suffer from a lack of standardization, in particular, due to various methodological approaches and no single format for processing the results. Here, we review the main methodological approaches and key stages for studies of the human virome, with an emphasis on virome changes during acute respiratory viral infection, with applications for clinical diagnostics and epidemiologic analyses.

Real-time surveillance of severe acute respiratory infections in Scottish hospitals: an electronic register-based approach, 2017-2022.

OBJECTIVES: The COVID-19 pandemic highlighted the importance of routine syndromic surveillance of respiratory infections, specifically new cases of severe acute respiratory infection (SARI). This surveillance often relies on questionnaires carried out by research nurses or transcriptions of doctor's notes, but existing, routinely collected electronic healthcare data sets are increasingly being used for such surveillance. We investigated how patient diagnosis codes, recorded within such data sets, could be used to capture SARI trends in Scotland. STUDY DESIGN: We conducted a retrospective observational study using electronic healthcare data sets between 2017 and 2022. METHODS: Sensitive, specific and timely case definition (CDs) based on patient diagnosis codes contained within national registers in Scotland were proposed to identify SARI cases. Representativeness and sensitivity analyses were performed to assess how well SARI cases captured by each definition matched trends in historic influenza and SARS-CoV-2 data. RESULTS: All CDs accurately captured the peaks seen in laboratory-confirmed positive influenza and SARS-CoV-2 data, although the completeness of patient diagnosis records was discovered to vary widely. The timely CD provided the earliest detection of changes in SARI activity, whilst the sensitive CD provided insight into the burden and severity of SARI infections. CONCLUSIONS: A universal SARI surveillance system has been developed and demonstrated to accurately capture seasonal SARI trends. It can be used as an indicator of emerging secondary care burden of emerging SARI outbreaks. The system further strengthens Scotland's existing strategies for respiratory surveillance, and the methods described here can be applied within any country with suitable electronic patient records.

SARS-CoV-2 Invasion: What Happens to Other Respiratory Viruses?

This letter briefly presents the relationships between respiratory viruses in the years prior to and during the COVID-19 pandemic. Viral common colds are self-limiting infections that typically resolve within a few days. However, when well-established epidemiological relationships are disrupted during a pandemic, they behave differently. For instance, during the 2009 influenza pandemic, while the majority of seasonal respiratory viruses lost ground under the pressure of a new pandemic strain, some others (for instance, human rhinoviruses) continued to circulate along with the pandemic pathogen and in some cases, even delayed its spread. With the arrival of the COVID-19 pandemic, the degree of circulation of many respiratory viruses has changed dramatically. Along with a significant reduction in the circulation of many seasonal respiratory pathogens, rhinoviruses, respiratory syncytial virus and non-COVID-19 coronaviruses—being the most frequently identified respiratory pathogens—have shown their unique capability to compete with SARS-CoV-2. © 2022 Kiseleva et al.

Epidemiologic and clinical characteristics of human bocavirus infection in children hospitalized for acute respiratory tract infection in Qingdao, China.

Persistent infection and prolonged shedding of human bocavirus 1 (HBoV1) in children have been reported, and the role of HBoV1 as a sole causative pathogen in acute respiratory infection (ARI) is yet to be established. While the reported prevalence of HBoV infection varies due to different detection methods and sampling criteria, determining the viral and bacterial etiology of HBoV infection using multiplex real-time PCR is yet to be reported. Herein, we aimed to further explore the pathogenicity of HBoV in patients with ARI by screening the viral and bacterial infections in children with ARI in Qingdao and comparing the epidemiological, clinical characteristics, and etiological results. Human bocavirus was identified in 28.1% of the samples, and further sequencing analysis of the detected HBoV confirmed 96.4% as HBoV1. The rate of HBoV as a single viral infection was 75%, and the rate of coinfection with bacteria was 66.1%, suggesting the need for continued monitoring of HBoV in children with ARIs. Clinical characterization suggested that HBoV infection may affect the function of organs, such as the liver, kidney, and heart, and the blood acid-base balance. Additionally, it is essential to promote awareness about the importance of disinfection and sterilization of the hospital environment and standardizing operations. The interactions between HBoV and other pathogens remain to be investigated in further detail in the future.

Pathogen Profile of Children Hospitalised with Severe Acute Respiratory Infections during COVID-19 Pandemic in the Free State Province, South Africa.

Severe acute respiratory infections (SARI) contribute to mortality in children ≤5 years. Their microbiological aetiologies are often unknown and may be exacerbated in light of coronavirus disease 19 (COVID-19). This study reports on respiratory pathogens in children ≤5 years (n = 84) admitted with SARI during and between the second and third waves of COVID-19 infection in South Africa. Nasopharyngeal/oropharyngeal swabs collected were subjected to viral detection using QIAstat-Dx® Respiratory SARS-CoV-2 Panel. The results revealed viral positivity and negativity detection rates of 88% (74/84) and 12% (10/84), respectively. Of the 21 targeted pathogens, human rhinovirus/enterovirus (30%), respiratory syncytial virus (RSV; 26%), and severe acute respiratory syndrome coronavirus 2 (24%) were mostly detected, with other viruses being 20% and a co-infection rate of 64.2% (54/84). Generally, RSV-positive samples had lower Ct values, and fewer viruses were detected during the third wave. Changes in the circulation patterns of respiratory viruses with total absence of influenza virus could be attributed to measures against COVID-19 transmission, which may result in waned immunity, thereby increasing susceptibility to severe infections in the following season. High viral co-infection rate, as detected, may complicate diagnosis. Nonetheless, accurate identification of the pathogens may guide treatment decisions and infection control.