Resurgence of influenza and respiratory syncytial virus in Egypt following two years of decline during the COVID-19 pandemic: outpatient clinic survey of infants and children, October 2022

Investigating DNA damage caused by COVID-19 and influenza in post COVID-19

The SARS-CoV-2 virus (termed COVID-19) was responsible for over 34 million global deaths. Although the COVID-19 pandemic has subsided, infection by emerging mutant variants of SARS-CoV-2 poses a continuing threat to public health. COVID-19 infection has been associated with the development of cytokine storm syndrome, hypercoagulability, immunological dysregulation and direct viral invasion of organs, and the long-term consequences for the health of COVID-19 survivors are currently unknown. Our research focuses on the possible mutagenic aspects of infection by COVID-19 and measures their harmful effects on DNA composition. DNA damage was investigated, using the comet assay method, during two periods: in the epidemic peak of COVID-19 and during the post-COVID-19 period, both in patients infected with COVID-19 and in those with influenza. During the epidemic peak, the levels of DNA damage ranged from the highest to the lowest levels in the following groups, respectively: intubated-ICU, non-intubated-ICU, non-ICU, and influenza, with a discernible increase in DNA damage in ICU-treated patients. The levels of DNA damage in the post-COVID-19 period were significantly lower compared to those in the epidemic peak period but there was still a discernible increase in DNA damage in the ICU group. Our results indicate that levels of DNA damage may be an effective indicator in prognostic decision-making and may therefore help to reduce mortality. Given that DNA damage and impaired repair processes can contribute to chronic diseases like diabetes, cancer, and neurodegenerative conditions, it will be crucial to investigate potential similar effects in patients with COVID-19.

Nonbacterial Respiratory Pathogens Following the Easing of COVID-19 Restrictive Measures

Nonbacterial respiratory pathogens are major acute respiratory infection (ARI) agents in children. We aimed to characterize the epidemiological changes in 11 common nonbacterial pathogens after easing COVID-19 restrictions in Zhejiang, China, to guide prevention and treatment. A retrospective study was conducted on children with ARIs at Children's Hospital, Zhejiang University School of Medicine in 2023, and epidemiological characteristics were analyzed for gender, age, month, sampling method, and immune status. In total, 59.48% of the children identified pathogens, and Mycoplasma pneumoniae ranked first. Various pathogens showed new features regarding detection rates, seasonal patterns, and susceptible populations. The host age, onset time, sampling method, and immunity status affected the mixed infection rate and unusual coinfection pairs emerged. The epidemiology of respiratory pathogens among children in Zhejiang has changed with local characteristics, and possible preventive actions are needed.

Changes in Respiratory Viruses' Activity in Children During the COVID-19 Pandemic: A Systematic Review

Background/Objectives: The impact of the coronavirus disease 2019 (COVID-19) pandemic on health was significant worldwide. The measures adopted to limit the spread of the virus had an indirect effect on the epidemiology of other infectious diseases with similar mechanisms of inter-human transmission. The present literature review analyzed the scenario of pediatric acute respiratory infections in the post-lockdown period compared to the pre-pandemic and lockdown periods. The different patterns of viruses' outbreaks were evaluated according to the type of local COVID-19 restrictive measures and to the type of pathogen. Methods: Relevant scientific literature published between March 2020 and November 2024 was identified by means of electronic keyword searches in the PubMed, Scopus, and Cochrane Library databases. Results: Worldwide implementation of non-pharmacological public health interventions aimed at limiting the COVID-19 pandemic resulted in a measurable effect on the circulation of other common respiratory viruses, significantly affecting their usual seasonality. Most viruses significantly reduced their activity during the lockdown period but returned to or exceeded historical levels after discontinuation of preventive non-pharmacological measures. For many respiratory viruses, particularly respiratory syncytial virus, an off-season increase was reported. Conclusions: The non-pharmacological interventions, which effectively helped limit the COVID-19 pandemic, resulted in relevant epidemiologic changes in most common respiratory viruses. Given the different seasonality and clinical severity observed for some pathogens after lockdown, possible future off-season or more severe epidemics should be expected.

Epidemiological characteristics of five non-COVID respiratory viruses among 37,139 all-age patients during 2018 - 2023 in Weifang, China: a cross-sectional study

BACKGROUND

Common non-COVID respiratory viruses, such as influenza virus (IFVA/IFVB), parainfluenza virus (PIV), respiratory syncytial virus (RSV), and adenovirus (ADV), often cause acute respiratory infections (ARIs). This study aimed to explore the epidemiological characteristics of these five viruses in patients with ARIs before, during, and after the COVID-19 pandemic from 2018 to 2023.

METHODS

A total of 37,139 serum specimens and epidemiological data from all-aged patients who presented with ARIs were collected from January 2018 to December 2023. The IgM antibodies of five non-COVID respiratory viruses were tested by an IgM kit with indirect immunofluorescent assay (lFA).

RESULTS

12,806 specimens were screened as positive for any one of the targeted viruses, with an overall positivity rate of 34.48%. Among all age groups, the most prevalent respiratory viruses were PIV (21.30%) and influenza virus (17.30% of IFVB and 9.91% of IFVA). Children aged 1-14 years were most vulnerable to lower respiratory viruses, and children aged 4-6 years have the highest prevalence no matter the positivity rate for overall viruses (53.06%) or for each virus. From 2018 to 2023, the annual percentage change (APC) revealed that the prevalence of total viruses have a 13.53% rise (p < 0.05), which increased with statistically significant for all age groups. In addition, both the infection rate and the number of samples detected have decreased significantly in the "first-level response" stage of the COVID-19 pandemic and in the "first three months" after fully lifted. Compared to those in the previous five years, the total infection rate (44.64%) and infection rate (26.93%) of the older adults (> 60 years) were all the highest in 2023, and the number of samples collected in 2023 sharply increased, increasing by 77.10% compared to the average of the number of detected in 2018-2022.

CONCLUSIONS

The data from this study indicate that the epidemiological characteristics of five non-COVID respiratory viruses are vulnerability to the environment, age, sex, and epidemics status among AIR patients, and that the detected number and positivity rate of these viruses have increased in the "post-pandemic era", which is critical for the late or retrospective diagnosis and can serve as a useful surveillance tool to inform local public policy in Weifang, China.

An Overview on Disease Burden and Management of Respiratory Syncytial Virus Infections in Older Adults in the Asia-Pacific Region

Respiratory syncytial virus (RSV) represents a significant burden on older adults (aged ≥ 50 years) globally and can lead to acute respiratory tract infections with substantial morbidity and mortality. However, there is a significant gap in knowledge regarding RSV infection in older adults, particularly in the Asia-Pacific region. This knowledge gap underscores the need for targeted and comprehensive studies to fully understand the nuanced epidemiology of RSV in ageing populations. This review synthesises data from various countries, emphasising the impact of RSV on older populations in the Asia-Pacific region. The overall proportions of RSV-related ARIs among older patients ranged from 0.2% to 5.6%. Among older adult patients with CAP, RSV accounted for 1.1%-10.3% of cases. However, it is crucial to note that the diversity in reported percentages highlights the influence of factors such as geographic location, health care settings and diagnostic practices. The most common symptoms observed in older adults with RSV infection were cough, sputum production and fever, followed by dyspnoea, sore throat and rhinorrhoea. Most of the old adults with RSV infection had underlying diseases, and RSV can cause significant morbidity and mortality in old adults. Treatment of RSV infections predominantly involve supportive care, with aerosolised ribavirin reserved for severe cases, especially immunocompromised patients. Emerging antiviral agents, including fusion and nucleoprotein inhibitors, offer promising avenues for future therapeutics. The recent approval of the bivalent RSV prefusion F protein-based vaccine for individuals aged 60 and older represents a milestone in preventive strategies. In conclusion, RSV infection remains a significant threat to older adults in the Asia-Pacific region, necessitating ongoing research and surveillance efforts. The recent vaccine approval marks a positive milestone, but further studies are crucial for refining prevention and treatment approaches.

Molecular Analysis of Coxsackievirus B2 Associated With Severe Symptoms of the Central Nervous System

Coxsackievirus B2 (CVB2) is a member of the enterovirus group known to induce a spectrum of illnesses, from mild to severe. In the summer of 2022, an unusual outbreak of enteroviral central nervous system (CNS) infections occurred that was attributed to CVB2. Cerebrospinal fluid (CSF) samples collected from patients in 2015-2022 were tested for enterovirus via RT-PCR, followed by Sanger sequencing for positive cases. CVB2 samples were further sequenced in the P1 region using NGS. A total of 30 CSF samples were identified as CVB2, with 60% of these cases occurring between June and August 2022. The 2022 CVB2 variants were associated with severe clinical symptoms, including encephalitis (50%) and ataxia (27.8%). Samples from 2015 to 2020 were also included due to the absence of these symptoms. Phylogenetic analysis revealed that CVB2 strains from 2019 to 2020 were also distinct from those obtained in 2022. Amino acid analysis of the capsid proteins VP1, VP2, and VP3 identified three unique substitutions with potential antigenic significance in the 2022 variant: S67A in VP2, and T93A and E274D in VP1. These substitutions were not present in earlier strains or reported in the literature, suggesting they may influence the virus's virulence. The clinical observations from this study highlight new patterns of CVB2 infection in the CNS that had not been previously observed. Additionally, it identifies unique genetic changes in the 2022 CVB2 variant that may account for the increased virulence seen in the 2022 outbreak. However, further analysis is required to validate this assumption.

Key Challenges to Understanding the Burden of Respiratory Syncytial Virus in Older Adults in Southeast Asia, the Middle East, and North Africa: An Expert Perspective

INTRODUCTION

Respiratory syncytial virus (RSV) is a common, highly contagious pathogen and a leading cause of serious illness among infants and older adults. While existing scientific evidence has predominantly focused on the epidemiology and disease burden of RSV in infants, data in older adults remain limited in some countries, including those in Southeast Asia (SEA) and the Middle East and North Africa (MENA) region. Here, we outline the key challenges for understanding the burden of RSV in older adults in SEA and the MENA region and we propose opportunities for improving understanding and eventually reducing the impact of RSV.

MAIN FINDINGS AND CONCLUSIONS

A key challenge identified by the expert group, particularly in older adults, is a lack of awareness (among healthcare professionals, policy makers, and the public) of RSV burden and the associated risks for severe outcomes. This is often confounded by the complexities of underdiagnosis, surveillance limitations, and comorbidities. To address these issues, we suggest medical education initiatives for physicians in SEA and the MENA region to better understand the need to protect older adults from RSV, and encourage more widespread routine testing to better understand the burden of RSV. We also recommend surveillance studies in these regions to provide comprehensive and accurate epidemiological data on RSV in older adults. Finally, in the absence of current surveillance data in these regions, we propose extrapolating existing global data and local pediatric data to inform the likely burden of RSV in older adults. A graphical abstract is available with this article.

Epidemiological characteristics of influenza outbreaks in schools in Jiangsu Province, China, 2020-2023 post-COVID-19 pandemic

BACKGROUND

This study aimed to analyze the epidemic characteristics and influencing factors of school influenza outbreaks in Jiangsu Province, China from 2020 to 2023,following the COVID-19 pandemic, to inform prevention and control strategies.

METHODS

Data on influenza-like illness(ILI) outbreaks from the Chinese Influenza Surveillance Information System and national-level influenza surveillance sentinel hospitals were analyzed. The temporal distribution, school type, virus strains, and outbreak scales were examined using descriptive statistics.

RESULTS

From 2020 to 2023, 1142 influenza outbreaks occurred in schools, with primary schools(ages 6 to 12) accounting for 71.80%. Most large outbreaks were caused by A(H1N1) and A(H3N2), responsible for 8.99% of total outbreaks. Outbreaks were predominantly reported in the pre-peak periods of B(Victoria) and A(H1N1) circulation, accounting for 86.31% and 92.32% of their respective total outbreaks. No concurrent influenza and COVID-19 outbreaks were observed during the study period.

CONCLUSION

Primary and secondary schools are high-risk settings for influenza outbreaks. A(H3N2) shows higher adaptability and is more likely to co-circulate with other subtypes/lineages, especially A(H1N1), leading to larger outbreaks. B(Victoria)-caused outbreaks are more frequent but smaller in scale. School influenza outbreaks are more likely to occur during the early stages of seasonal peaks, particularly for B(Victoria) and A(H1N1). This suggests that influenza outbreaks in schools may play a crucial role in seeding and accelerating the spread of the virus within the broader community.

Characteristics and outcomes of patients hospitalized for infection with Influenza A, SARS-CoV-2 or respiratory syncytial virus in the season 2023/2024 in a large German primary care centre

BACKGROUND

In addition to the persistence of SARS-CoV-2 infections, those with Influenza A/B and RSV have reappeared in 2022/23. To compare the development of prevalence, clinical outcomes and risk factors, we analysed data of the season 2023/24 from the same region/hospital as for 2022/23.

METHODS

Patients covering the whole age range with a positive polymerase chain reaction (PCR) test for SARS-CoV-2, Influenza A/B, RSV were included from the internal, neurological and paediatric units of the RoMed hospital Rosenheim, Germany/Bavaria, from August 1st 2023 to 29th February 2024.

RESULTS

Of 932 patients included, 912 showed single infections with SARS-CoV-2, Influenza A or RSV (47.9% female, median age 68.0 years; 52.9% SARS-CoV-2, 23.2% Influenza A, 21.8% RSV). Co-infections (2.0%) and Influenza B (0.1%) were negligible. In patients of age ≥ 18 years (n = 628, 68.5% SARS-CoV-2, 26.0% Influenza A, 5.6% RSV), patients with Influenza A were younger compared to SARS-CoV-2 (p < 0.001), with RSV similar to SARS-CoV-2. Heart failure and asthma were the most prevalent comorbidities for RSV, immunosuppression for Influenza A. Admission to Intensive Care Unit (ICU) occurred in 111 patients (17.0% of SARS-CoV-2, 17.2% Influenza A, 28.6% RSV), and 59 patients died (8.8% SARS-CoV-2, 8.6% Influenza A, 20.0% RSV). Low-flow oxygen supplementation and non-invasive ventilation (NIV) were most frequent for RSV (68.6% and 20.0%, respectively), oxygen demand upon admission for Influenza A (39.3%), without differences in high-flow oxygen supply or length of hospital stay. Among patients aged < 18 years (n = 284, 21.4% SARS-CoV-2, 18.0% Influenza A, 57.1% RSV), 15 were admitted to ICU (4.8% SARS-CoV-2, 3.8% Influenza A, 6.0% RSV); none of them died. Oxygen supply via high-flow, low-flow or upon admission was highest for RSV (23.8%, 70.2%, 21.4%, respectively), as well as the length of hospital stay.

CONCLUSION

Between 8/2023 to 2/2024, a large population of patients hospitalized due to respiratory tract infection, showed relative contributions of SARS-CoV-2, Influenza A or RSV similar to those in 2022/23. The findings underline that in both, adults and children, RSV posed a relatively higher clinical risk than Influenza A and SARS-CoV-2, though absolute numbers remained highest for SARS-CoV-2.

Investigating the relationship between lymphocyte cells apoptosis and DNA damage and oxidative stress and therapeutic and clinical outcomes of COVID-19 elderly patients

BACKGROUND

While COVID-19 has been controlled and deaths have decreased, the long-term consequences of COVID-19 remain a challenge we face today. This study was conducted to determine the relationship between the apoptosis of lymphocyte cells with DNA damage and oxidative stress and the therapeutic and clinical outcomes of elderly patients with COVID-19.

METHODS

This study was conducted from April 2020 to May 2021 (the period of severe attacks of the epidemic peak of COVID-19) and September 2022 (the post-COVID-19 period). The study groups included elderly patients with COVID-19 hospitalized in the ICU and normal wards of the hospital as well as elderly patients with influenza. A polymerase chain reaction was used to check the validity of the studied diseases. The Annexin V/Propidium Iodide method was used to evaluate the level of apoptosis. Genotoxic effects and DNA damage were assessed by the comet assay method. Total antioxidant status (TAS), total oxidant status (TOS), and myeloperoxidase activity (MPO) were measured by photometric methods.

RESULTS

The highest level of apoptosis in peripheral blood lymphocytes and the highest level of DNA damage were observed at both times in the intubated-ICU and non-intubated-ICU groups. In all groups, there was a significant increase in peripheral blood lymphocyte apoptosis levels and DNA damage levels compared to the healthy control group (p < 0.01). The level of apoptosis and DNA damage decreased significantly in the post-COVID-19 period (p < 0.01). In the investigation of oxidative stress biomarkers, the oxidative stress index, including TOS and MPO levels, increased in patients (p < 0.01), and the TAS level decreased (p < 0.01).

CONCLUSION

It shows that the apoptosis of lymphocyte cells, DNA damage, and oxidative stress can be effective in prognostic decisions and is a suitable predictor for diagnosing the condition of patients with viral infections such as COVID-19 and influenza.

Global, regional, and national incidence and mortality burden of non-COVID-19 lower respiratory infections and aetiologies, 1990-2021: a systematic analysis from the Global Burden of Disease Study 2021

BACKGROUND

Lower respiratory infections (LRIs) are a major global contributor to morbidity and mortality. In 2020-21, non-pharmaceutical interventions associated with the COVID-19 pandemic reduced not only the transmission of SARS-CoV-2, but also the transmission of other LRI pathogens. Tracking LRI incidence and mortality, as well as the pathogens responsible, can guide health-system responses and funding priorities to reduce future burden. We present estimates from the Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) 2021 of the burden of non-COVID-19 LRIs and corresponding aetiologies from 1990 to 2021, inclusive of pandemic effects on the incidence and mortality of select respiratory viruses, globally, regionally, and for 204 countries and territories.

METHODS

We estimated mortality, incidence, and aetiology attribution for LRI, defined by the GBD as pneumonia or bronchiolitis, not inclusive of COVID-19. We analysed 26 259 site-years of mortality data using the Cause of Death Ensemble model to estimate LRI mortality rates. We analysed all available age-specific and sex-specific data sources, including published literature identified by a systematic review, as well as household surveys, hospital admissions, health insurance claims, and LRI mortality estimates, to generate internally consistent estimates of incidence and prevalence using DisMod-MR 2.1. For aetiology estimation, we analysed multiple causes of death, vital registration, hospital discharge, microbial laboratory, and literature data using a network analysis model to produce the proportion of LRI deaths and episodes attributable to the following pathogens: Acinetobacter baumannii, Chlamydia spp, Enterobacter spp, Escherichia coli, fungi, group B streptococcus, Haemophilus influenzae, influenza viruses, Klebsiella pneumoniae, Legionella spp, Mycoplasma spp, polymicrobial infections, Pseudomonas aeruginosa, respiratory syncytial virus (RSV), Staphylococcus aureus, Streptococcus pneumoniae, and other viruses (ie, the aggregate of all viruses studied except influenza and RSV), as well as a residual category of other bacterial pathogens.

FINDINGS

Globally, in 2021, we estimated 344 million (95% uncertainty interval [UI] 325-364) incident episodes of LRI, or 4350 episodes (4120-4610) per 100 000 population, and 2·18 million deaths (1·98-2·36), or 27·7 deaths (25·1-29·9) per 100 000. 502 000 deaths (406 000-611 000) were in children younger than 5 years, among which 254 000 deaths (197 000-320 000) occurred in countries with a low Socio-demographic Index. Of the 18 modelled pathogen categories in 2021, S pneumoniae was responsible for the highest proportions of LRI episodes and deaths, with an estimated 97·9 million (92·1-104·0) episodes and 505 000 deaths (454 000-555 000) globally. The pathogens responsible for the second and third highest episode counts globally were other viral aetiologies (46·4 million [43·6-49·3] episodes) and Mycoplasma spp (25·3 million [23·5-27·2]), while those responsible for the second and third highest death counts were S aureus (424 000 [380 000-459 000]) and K pneumoniae (176 000 [158 000-194 000]). From 1990 to 2019, the global all-age non-COVID-19 LRI mortality rate declined by 41·7% (35·9-46·9), from 56·5 deaths (51·3-61·9) to 32·9 deaths (29·9-35·4) per 100 000. From 2019 to 2021, during the COVID-19 pandemic and implementation of associated non-pharmaceutical interventions, we estimated a 16·0% (13·1-18·6) decline in the global all-age non-COVID-19 LRI mortality rate, largely accounted for by a 71·8% (63·8-78·9) decline in the number of influenza deaths and a 66·7% (56·6-75·3) decline in the number of RSV deaths.

INTERPRETATION

Substantial progress has been made in reducing LRI mortality, but the burden remains high, especially in low-income and middle-income countries. During the COVID-19 pandemic, with its associated non-pharmaceutical interventions, global incident LRI cases and mortality attributable to influenza and RSV declined substantially. Expanding access to health-care services and vaccines, including S pneumoniae, H influenzae type B, and novel RSV vaccines, along with new low-cost interventions against S aureus, could mitigate the LRI burden and prevent transmission of LRI-causing pathogens.

FUNDING

Bill & Melinda Gates Foundation, Wellcome Trust, and Department of Health and Social Care (UK).

Influenza A, Influenza B, human respiratory syncytial virus and SARSCoV-2 molecular diagnostics and epidemiology in the post COVID-19 era

BACKGROUND

The concurrent circulation of SARS-CoV-2 with other respiratory viruses is unstoppable and represents a new diagnostic reality for clinicians and clinical microbiology laboratories. Multiplexed molecular testing on automated platforms that focus on the simultaneous detection of multiple respiratory viruses in a single tube is a useful approach for current and future diagnosis of respiratory infections in the clinical setting.

METHODS

Two time periods were included in the study: from February to April 2022, an early 2022 period, during the gradual lifting of COVID-19 prevention measures in the country, and from October 2022 to April 2023, the 2022/23 respiratory infections season. We analysed a total of 1,918 samples in the first period and 18,131 respiratory samples in the second period using a multiplex molecular assay for the simultaneous detection of Influenza A (Flu-A), Influenza B (Flu-B), Human Respiratory Syncytial Virus (HRSV) and SARS-CoV-2.

RESULTS

The results from early 2022 showed a strong dominance of SARS-CoV-2 infections with 1,267/1,918 (66.1%) cases. Flu-A was detected in 30/1,918 (1.6%) samples, HRSV in 14/1,918 (0.7%) samples, and Flu-B in 2/1,918 (0.1%) samples. Flu-A/SARS-CoV-2 co-detections were observed in 11/1,267 (0.9%) samples, and HRSV/SARS-CoV-2 co-detection in 5/1,267 (0.4%) samples. During the 2022/23 winter respiratory season, SARS-CoV-2 was detected in 1,738/18,131 (9.6%), Flu-A in 628/18,131 (3.5%), Flu-B in 106/18,131 (0.6%), and HRSV in 505/18,131 (2.8%) samples. Interestingly, co-detections were present to a similar extent as in early 2022.

CONCLUSION

The results show that the multiplex molecular approach is a valuable tool for the simultaneous laboratory diagnosis of SARS-CoV-2, Flu-A/B, and HRSV in hospitalized and outpatients. Infections with Flu-A/B, and HRSV occurred shortly after the COVID-19 control measures were lifted, so a strong reoccurrence of various respiratory infections and co-detections in the post COVID-19 period was to be expected.

Dynamic Patterns and Predominance of Respiratory Pathogens Post-COVID-19: Insights from a Two-Year Analysis

INTRODUCTION

Respiratory tract infections (RTIs) stand out as the most frequent causes leading to visits to the emergency department and hospitalizations. This study aims to assess the types and prevalence of respiratory infections across two years following the end of the COVID-19 pandemic.

METHODS

Patients presenting with an influenza-like illness (ILI) were tested using multiplex RT-PCR (QIAstat-Dx, Qiagen). The multiplexed RT- PCR test detects 21 respiratory viruses and bacteria.

RESULTS

During the study period, PCR test was done on a total of 1,790 samples were tested, and 712 (40%) were positive for a total of 796 pathogens. The mean age (± SD) of the participants was 20.1 ± 28.4 years in 2022 and 21.9 ± 27.6 years in 2023. Among the detected pathogens, the most prevalent were Rhinovirus/Enterovirus 222 (12.4%), followed by RSV A&B (103 cases, 5.7%), and H1N1 Influenza (77 cases, 4.3%). Additionally,  Influenza A/B constituted 172 (9.6%) while parainfluenza constituted (58, 3.2%). SARS-CoV-2 was identified in 3.97% of the samples. Over the two-year period, the monthly pattern of the identified pathogens exhibited fluctuations in the prevalence. Furthermore, variations were observed in the detected pathogens across different age groups.

CONCLUSION

In addition to adding significant knowledge to the field of respiratory viral infections, this study emphasizes the necessity of ongoing research and surveillance for the detection and characterization of respiratory viruses, particularly those with the potential for emergence. Such studies would also require setting up a strategy for genotyping and/or sequencing of viruses.

Molecular detection of SARS-CoV-2 and other respiratory viruses in saliva and classroom air: a two winters tale

OBJECTIVES

To compare the prevalence of SARS-CoV-2 and other respiratory viruses in saliva and bioaerosols between two winters and to model the probability of virus detection in classroom air for different viruses.

METHODS

We analysed saliva, air, and air cleaner filter samples from studies conducted in two Swiss secondary schools (students aged 14-17 years) over 7 weeks during the winters of 2021/22 and 2022/23. Two bioaerosol sampling devices and high efficiency particulate air (HEPA) filters from air cleaners were used to collect airborne virus particles in four classrooms. Daily bioaerosol samples were pooled for each sampling device before PCR analysis of a panel of 19 respiratory viruses and viral subtypes. The probability of detection of airborne viruses was modelled using an adjusted Bayesian logistic regression model.

RESULTS

Three classes (58 students) participated in 2021/22, and two classes (38 students) in 2022/23. During winter 2021/22, SARS-CoV-2 dominated in saliva (19 of 21 positive samples) and bioaerosols (9 of 10). One year later, there were 50 positive saliva samples, mostly influenza B, rhinovirus, and adenovirus, and two positive bioaerosol samples, one rhinovirus and one adenovirus. The weekly probability of airborne detection was 34% (95% credible interval [CrI] 22-47%) for SARS-CoV-2 and 10% (95% CrI 5-16%) for other respiratory viruses.

DISCUSSION

There was a distinct shift in the distribution of respiratory viruses from SARS-CoV-2 during the omicron wave to other respiratory viruses one year later. SARS-CoV-2 is more likely to be detected in the air than other endemic respiratory viruses, possibly reflecting differences in viral characteristics and the composition of virus-carrying particles that facilitate airborne long-range transmission.

Incidence of influenza virus-associated Severe Acute Respiratory Infections in three districts in 2018 at Gharbia governorate, Egypt

AIMS

Influenza remains a contributor to substantial global morbidity and mortality. There is very limited data on disease burden in Egypt. The purpose of this study was to estimate the incidence of influenza-associated Severe Acute Respiratory Illness (SARI) in three districts in Gharbia governorate in 2018.

METHODS

This study Followed the World Health Organization (WHO) manual for estimating disease burden associated with seasonal influenza. The hospital admission database was screened for SARI patients in three districts at Gharbia governorate in 2018. A hospital admission survey (HAS) was used to define the catchment population. The incidence rate estimation was computed as the number of influenza-positive SARI cases per 100,000 population.

RESULTS

A total of 180 SARI cases were identified in the catchment area. The median age was 23 years [IQR: 2-53], and 45% were males. Out of the total SARI cases, 33.3% influenza was confirmed by the laboratory test of RP-PCR. Influenza A(H3N2) virus predominated representing 55.0% of patients, thanA(H1N1) 26.7% and Flu-B virus 18.3%. Influenza prevailed in winter and spring; no deaths from influenza were reported. The annual incidence of influenza-associated SARIs found higher in <2 years (282 /100,000) and ≥65 years patients (215/100,000) at significant level p<0.001.

CONCLUSION

The WHO Manual for estimating disease burden associated with seasonal influenza was successfully operationalized in the three districts of Gharbia governorate. It can be used in other districts. A considerable burden was associated with influenza viruses requiring hospitalization, especially among the older adult group.

Improving croup management at a pediatric emergency department

OBJECTIVES

Over-testing and over-treatment are common in children with croup at pediatric emergency departments (PED). The objective of the study was to improve care for children with croup.

METHODS

In this quality improvement (QI) initiative, all pediatric residents starting their rotation in the PED attended an informative presentation about croup and were provided reminders throughout their rotation. The primary outcome of this QI initiative was to reduce nebulized epinephrine (NE) use among children with mild croup by 50% over 7 months. The secondary outcome was to reduce X-rays by 50% over 7 months. Other outcomes included the administration of dexamethasone to all children with croup, reduction of antibiotics, laboratory tests, and revisits, and shortening the duration between physical examination to dexamethasone and NE treatments, and the length of stay (LOS) at the PED.

RESULTS

NE administration to patients with mild croup decreased from 80.2% to 36.3% (p < 0.001). The proportion of children with X-rays decreased from 37.4% to 17.1% (p < 0.001). There was a significant increase in dexamethasone administration, and significant decreases in laboratory blood tests, expanded viral PCR panel tests, and antibiotic prescription among all croup cases (p < 0.001). Revisit rates were not significantly different (p > 0.05). Time to dexamethasone and LOS shortened significantly (p < 0.001).

CONCLUSION

With this QI intervention, decreases in the rate of administration of NE to mild croup cases, antibiotic prescription, X-ray, laboratory blood and respiratory PCR panel tests in all croup cases were achieved without an increase in revisits. However, unnecessary NE, antibiotic, and X-ray rates are still high.

JC Virus in Kidney Transplant Population: Are We Cautious Enough?

The John Cunningham virus (JCV) is a polyomavirus that usually infects people at a young age and does not cause any symptoms in immunocompetent individuals. However, in immunocompromised individuals, such as kidney transplant recipients, JCV can cause severe and potentially fatal disease. Unfortunately, JCV has not been researched as extensively as the BK virus and is not mentioned in relevant kidney transplant guidelines. This lack of attention to JCV can lead to less consideration in kidney transplant patients' care. Surveillance using locally available diagnostic methods is of the utmost importance. The presence of JCV can be diagnosed with urine decoy cells, viruria, or viremia verified by the PCR method. A low threshold for considering JCV as a possible cause of any neurological or renal dysfunction in kidney transplant recipients must be maintained. In such cases, kidney and brain biopsy are indicated. Maintaining the appropriate immunosuppression while avoiding over-immunosuppression to prevent JCV disease is crucial, and the approach should be individual, according to overall immunological risk. We hypothesize that the presence of the JCV can indicate overt immunosuppression and identify kidney transplant recipients more prone to opportunistic infections and diseases, including some malignancies. To explore that, future observational studies are needed.

Evaluation of disease severity and prediction of severe cases in children hospitalized with influenza A (H1N1) infection during the post-COVID-19 era: a multicenter retrospective study

BACKGROUND

The rebound of influenza A (H1N1) infection in post-COVID-19 era recently attracted enormous attention due the rapidly increased number of pediatric hospitalizations and the changed characteristics compared to classical H1N1 infection in pre-COVID-19 era. This study aimed to evaluate the clinical characteristics and severity of children hospitalized with H1N1 infection during post-COVID-19 period, and to construct a novel prediction model for severe H1N1 infection.

METHODS

A total of 757 pediatric H1N1 inpatients from nine tertiary public hospitals in Yunnan and Shanghai, China, were retrospectively included, of which 431 patients diagnosed between February 2023 and July 2023 were divided into post-COVID-19 group, while the remaining 326 patients diagnosed between November 2018 and April 2019 were divided into pre-COVID-19 group. A 1:1 propensity-score matching (PSM) was adopted to balance demographic differences between pre- and post-COVID-19 groups, and then compared the severity across these two groups based on clinical and laboratory indicators. Additionally, a subgroup analysis in the original post-COVID-19 group (without PSM) was performed to investigate the independent risk factors for severe H1N1 infection in post-COIVD-19 era. Specifically, Least Absolute Shrinkage and Selection Operator (LASSO) regression was applied to select candidate predictors, and logistic regression was used to further identify independent risk factors, thus establishing a prediction model. Receiver operating characteristic (ROC) curve and calibration curve were utilized to assess discriminative capability and accuracy of the model, while decision curve analysis (DCA) was used to determine the clinical usefulness of the model.

RESULTS

After PSM, the post-COVID-19 group showed longer fever duration, higher fever peak, more frequent cough and seizures, as well as higher levels of C-reactive protein (CRP), interleukin 6 (IL-6), IL-10, creatine kinase-MB (CK-MB) and fibrinogen, higher mechanical ventilation rate, longer length of hospital stay (LOS), as well as higher proportion of severe H1N1 infection (all P < 0.05), compared to the pre-COVID-19 group. Moreover, age, BMI, fever duration, leucocyte count, lymphocyte proportion, proportion of CD3+ T cells, tumor necrosis factor α (TNF-α), and IL-10 were confirmed to be independently associated with severe H1N1 infection in post-COVID-19 era. A prediction model integrating these above eight variables was established, and this model had good discrimination, accuracy, and clinical practicability.

CONCLUSIONS

Pediatric H1N1 infection during post-COVID-19 era showed a higher overall disease severity than the classical H1N1 infection in pre-COVID-19 period. Meanwhile, cough and seizures were more prominent in children with H1N1 infection during post-COVID-19 era. Clinicians should be aware of these changes in such patients in clinical work. Furthermore, a simple and practical prediction model was constructed and internally validated here, which showed a good performance for predicting severe H1N1 infection in post-COVID-19 era.

Effect of the COVID-19 pandemic on the pediatric infectious disease landscape

This narrative review aims to present an overview of the COVID-19 pandemic's effects on the landscape of pediatric infectious diseases. While COVID-19 generally results in mild symptoms and a favorable prognosis in children, the pandemic brought forth significant consequences. These included persistent symptoms among infected children ("long COVID"), a profound transformation in healthcare utilization (notably through the widespread adoption of telemedicine), and the implementation of optimization strategies within healthcare settings. Furthermore, the pandemic resulted in alterations in the circulation patterns of respiratory pathogens, including influenza, RSV, and Streptococcus pneumoniae. The possible reasons for those changes are discussed in this review. COVID-19 effect was not limited to respiratory infectious diseases, as other diseases, including urinary tract and gastrointestinal infections, have displayed decreased transmission rates, likely attributable to heightened hygiene measures and shifts in care-seeking behaviors. Finally, the disruption of routine childhood vaccination programs has resulted in reduced immunization coverage and an upsurge in vaccine hesitancy. In addition, the pandemic was associated with issues of antibiotic misuse and over-prescription.     Conclusion: In conclusion, the COVID-19 pandemic has left a profound and multifaceted impact on the landscape of pediatric infectious diseases, ranging from the emergence of "long COVID" in children to significant changes in healthcare delivery, altered circulation patterns of various pathogens, and concerning disruptions in vaccination programs and antibiotic usage. What is Known: • COVID-19 usually presents with mild symptoms in children, although severe and late manifestations are possible. • The pandemic resulted in a dramatically increased use of health care services, as well as alterations in the circulation patterns of respiratory pathogens, decreased rates of other, non-respiratory, infections, disruption of routine childhood vaccination programs, and antibiotic misuse. What is New: • Possible strategies to tackle future outbreaks are presented, including changes in health care services utilization, implementation of updated vaccine programs and antibiotic stewardship protocols. • The decline in RSV and influenza circulation during COVID-19 was probably not primarily related to NPI measures, and rather related to other, non-NPI measures implementation, including specific pathogen-host interactions on the level of the biological niche (the nasopharynx).

Impact of COVID‑19 pandemic restrictions and subsequent relaxation on the prevalence of respiratory virus hospitalizations in children

BACKGROUND

The COVID-19 pandemic and the consequently adopted worldwide control measures have resulted in global changes in the epidemiology and severity of other respiratory viruses. We compared the number and severity of viral acute lower respiratory tract infection (ALRTI) hospitalizations and determined changes in causative respiratory pathogens before, during, and after the pandemic among young children in Qatar.

METHODS

In this single-center retrospective study, we reviewed data of children ≤ 36 months old who were admitted to Sidra Medicine in Qatar with a viral ALRTI during winter seasons (September-April) between 2019 and 2023. The study period was divided into three distinct seasons based on the pandemic-imposed restrictions as follows: (1) the period between September 2019 and April 2020 was considered the pre-COVID-19 pandemic season; (2) the periods between September 2020 and April 2021, and the period between January and April 2022 were considered the COVID-19 pandemic seasons; and (3) the periods between September 2022 and April 2023 was considered the post-COVID-19 pandemic season.

RESULTS

During the COVID-19 season, 77 patients were admitted, compared with 153 patients during the pre-COVID-19 season and 230 patients during the post-COVID-19 season. RSV was the dominant virus during the pre-COVID-19 season, with a detection rate of 50.9%. RSV infection rate dropped significantly during the COVID-19 season to 10.4% and then increased again during the post-COVID-19 season to 29.1% (P < 0.001). Rhinovirus was the dominant virus during the COVID-19 (39.1%) and post-COVID-19 seasons (61%) compared to the pre-COVID-19 season (31.4%) (P < 0.001). The average length of hospital stay was significantly longer in the post-COVID-19 season than in the pre-COVID-19 and COVID-19 seasons (P < 0.001). No significant differences in the pediatric intensive care unit (PICU) admission rate (P = 0.22), PICU length of stay (p = 0.479), or respiratory support requirements were detected between the three seasons.

CONCLUSION

Our study showed reduced viral ALRTI hospitalizations in Qatar during the COVID-19 pandemic with reduced RSV detection. An increase in viral ALRTI hospitalizations accompanied by a resurgence of RSV circulation following the relaxation of COVID-19 restrictions was observed without changes in disease severity.

Adult vaccination against respiratory infections in Egypt: a review of expert opinions

INTRODUCTION

Lower respiratory tract infection is one of the leading causes of morbidity and mortality all over the world, with a substantial impact on healthcare costs. In Egypt, local consensus on its burden, diagnosis, and vaccination is scarce. This expert opinion is the first to address the local recommendations for vaccinating adults against respiratory infection. It sheds light on the growing need to understand the barriers and underpublicized concept of adult vaccination in Egypt.

AREAS COVERED

A collaborative multidisciplinary panel from Egypt developed an expert opinion-based suggestions/points, including epidemiology, microbiology, and highlights on vaccination in Egypt, as well as challenges and recommendations regarding adult vaccination.

EXPERT OPINION

Adult vaccinations against respiratory infections are now recommended for high-risk people by all healthcare regulatory bodies. However, it was acknowledged that there may be hesitancy and concerns among patients; in addition, healthcare professionals' awareness about vaccination guidelines and benefits needs improvement. There are several strategies that could be implemented to enhance vaccine adherence in Egypt. These approaches encompass conducting community education programs, addressing the concerns of patients, and enhancing awareness among healthcare professionals through education, policy changes, and periodical reminders in each healthcare setting.

Multicenter study to describe viral etiologies, clinical profiles, and outcomes of hospitalized children with severe acute respiratory infections, Egypt 2022

In late 2022, severe acute respiratory infections (SARI) surveillance reported an abrupt increase in non-COVID-19 infections among children after three years of drastic reductions. Signals of increased absenteeism due to respiratory symptoms among primary and preparatory school children were detected by Event-Based Surveillance. We conducted a hospital-based survey of children who were admitted with SARI to identify the causative pathogen(s) and estimate the burden of infection. A survey was conducted among children < 16 years in 21 referral hospitals in the three governorates with the highest SARI rates. Patients' demographics, clinical symptoms, and severity were collected from medical records using a line list. Patients were swabbed and tested for a panel of 33 respiratory pathogens by RT-PCR at the Central Laboratory in Cairo. Descriptive data analysis was performed for demographic data. Patients' characteristics were compared by causative agents' clinical picture and severity using Chi2 with a p < 0.05 significance. Overall, 317 patients were enrolled, 58.3% were ≤ 1 year of age, 61.5% were males. Of 229 (72.7%) of positively tested patients, viruses caused 92.1% including RSV 63.8%, Rhinovirus 10.0%, Influenza 9.2%, Adenovirus 5.2%, and 1.3% co-infected with two viruses. Bacteria caused 3.5% of cases and 4.4% had mixed viral-bacterial infections. Rhinovirus was the most common cause of death among children with SARI, followed by RSV (8.7% and 1.4%), whereas influenza and Adenovirus did not result in any deaths. Patients with viral-bacterial infections are more likely to be admitted to ICU and die at the hospital than bacterial or viral infections (60% and 20% vs. 31.8% and 1.9% vs. 12.5% and 12.5%, p < 0.001). Viruses particularly RSV are the leading cause of SARI causing significant health problem among children < 16 years in Egypt. Bacterial on top of viral infection can worsen disease courses and outcomes. Studies are required to estimate the SARI burden accurately among Egyptian children and a comprehensive approach tailored to Egypt is necessary to reduce its burden.

Unraveling the association between vaccine attitude, vaccine conspiracies and self-reported side effects following COVID-19 vaccination among nurses and physicians in Jordan

Background

The negative impact of vaccine conspiracies is linked with negative health behavior. The aim of the current study was to examine the association between attitudes toward booster COVID-19, influenza, and monkeypox (mpox) vaccinations with post-COVID-19 vaccine side effects, vaccine conspiracies, and attitude towards mandatory vaccination among nurses and physicians in Jordan.

Methods

A structured closed-ended questionnaire was used to collect data on demographics, COVID-19 history, COVID-19 vaccine type and doses received, self-reported side effects post-COVID-19 vaccination, acceptance of booster COVID-19, seasonal influenza, and mpox vaccinations, attitudes towards mandatory vaccination, and beliefs in vaccine conspiracies.

Results

The study sample comprised a total of 341 participants. Acceptance of yearly booster COVID-19 vaccination was expressed by 46.6% of the sample, while 73.3% accepted seasonal influenza vaccination, and only 37.0% accepted mpox vaccination. A higher frequency of self-reported side effects following the first COVID-19 vaccine dose was associated with embrace of vaccine conspiracies and vaccine type. For the second vaccine dose, a higher frequency of self-reported side effects was associated with the embrace of vaccine conspiracies, older age, and affiliation to private sector. In multinomial logistic regression analyses, the lower embrace of vaccine conspiracies was associated with lower odds of reporting side effects post-COVID-19 vaccination. The lower embrace of vaccine conspiracies and favorable attitude towards mandatory vaccination were associated with the willingness to get COVID-19, influenza, and mpox vaccinations.

Conclusion

The study findings highlighted the negative impact of embracing vaccine conspiracies on health-seeking behavior among nurses and physicians. The findings indicated that the willingness to get vaccinated was associated with lower endorsement of vaccine conspiracies. Additionally, the lower embrace of vaccine conspiracies was associated with a lower frequency of self-reported side effects following COVID-19 vaccination. These results emphasize the importance of addressing vaccine misinformation and promoting accurate information to ensure optimal vaccine uptake and public health outcomes.

Supervised Machine Learning Methods for Seasonal Influenza Diagnosis

Influenza has been a stationary disease in Mexico since 2009, and this causes a high cost for the national public health system, including its detection using RT-qPCR tests, treatments, and absenteeism in the workplace. Despite influenza's relevance, the main clinical features to detect the disease defined by international institutions like the World Health Organization (WHO) and the United States Centers for Disease Control and Prevention (CDC) do not follow the same pattern in all populations. The aim of this work is to find a machine learning method to facilitate decision making in the clinical differentiation between positive and negative influenza patients, based on their symptoms and demographic features. The research sample consisted of 15480 records, including clinical and demographic data of patients with a positive/negative RT-qPCR influenza tests, from 2010 to 2020 in the public healthcare institutions of Mexico City. The performance of the methods for classifying influenza cases were evaluated with indices like accuracy, specificity, sensitivity, precision, the f1-measure and the area under the curve (AUC). Results indicate that random forest and bagging classifiers were the best supervised methods; they showed promise in supporting clinical diagnosis, especially in places where performing molecular tests might be challenging or not feasible.

Comparative Analysis of Pediatric Hospitalizations during Two Consecutive Influenza and Respiratory Virus Seasons Post-Pandemic

BACKGROUND

The COVID-19 pandemic has had a significant impact on the epidemiology of respiratory viruses. Non-pharmaceutical interventions (NPIs) led to a dramatic reduction in respiratory infections. However, the long-term effects on respiratory virus epidemiology remain unclear.

MATERIALS AND METHODS

We conducted a comparative study on hospitalized pediatric patients with respiratory illness during two seasons: 1 October 2021 to 15 March 2022 and 1 October 2022 to 15 March 2023. We compared the type of virus, mean duration of hospitalization, and disease severity.

RESULTS

In the first season, 47.1% of patients (65/138) tested positive for at least one respiratory virus, with respiratory syncytial virus (RSV) being the most frequent (23.2%). In the second season, 82.9% of patients (102/123) tested positive, with RSV and Rhinovirus being the most prevalent (28.38% and 27.03%, respectively). Other viruses, such as Influenza A/B, Metapneumovirus, and Adenovirus, also showed increased prevalence. Disease severity and mean duration of hospitalization were similar between the two seasons.

CONCLUSIONS

Our study highlights increased prevalence in respiratory viruses, including RSV and Rhinovirus, following the easing of NPIs. The prevalence in respiratory viruses, including RSV and Rhinovirus, increased in the second season compared to the first one. Interestingly, RSV's peak incidence shifted from February to November. The emergence of rhinovirus as the most prevalent respiratory virus during certain months suggests viral competition and dynamic changes in viral circulation. The overall severity of respiratory infections remained relatively stable between the seasons.

Prospective Attitudes towards Respiratory Syncytial Virus (RSV) Vaccination: Validation of a Survey Instrument among Young Females in Jordan Pending Vaccine Authorization

In May 2023, the U.S. FDA advisors endorsed Pfizer's pregnancy-administered vaccine (branded ABRYSVO) to protect infants from respiratory syncytial virus (RSV) infection. Vaccination can reduce the burden of RSV-related respiratory disease, with previous studies showing its substantial medical and financial burden in Jordan. However, pregnant women may exhibit hesitancy to get vaccinated due to concerns about potential risks to themselves or their fetuses. This study aimed to assess the acceptance of the RSV vaccine among young females and identify the determinants influencing their decision using a newly constructed instrument. A survey instrument was developed and validated, comprising 26 items to measure RSV vaccine acceptance. A cross-sectional study design was employed, with data collection from a sample of females aged 18 to 45 residing in Jordan during 5-6 July 2023, using a convenient approach via an online distributed questionnaire. The final study sample comprised 315 respondents, with 67.6% who have heard of RSV before the study. If the vaccine was safe, effective, and provided freely, 70.2% showed willingness to get the RSV vaccine, 15.2% resisted, and 14.6% were hesitant. Principal component analysis identified six internally consistent sub-scales with the following suggested themes: Advice, Burden, Conspiracy, Dangers, Efficiency, and Fear, comprising 21 items collectively as assigned as the "ABCDEF" scale for RSV vaccine acceptance. RSV vaccine acceptance in this study was associated with the advice and fear constructs. The validated survey instrument successfully captured important determinants of RSV vaccine acceptance among young females. RSV vaccine promotion efforts should focus on the following: enhancing vaccine education, improving trust in healthcare institutions and providers, reducing burdens through resolving cost issues and focusing on the role of social support, addressing safety concerns, and tailoring communication strategies to effectively promote the benefits of the vaccine. These insights can inform public health policies and interventions aiming to promote RSV vaccination and mitigate the burden of RSV-related diseases among infants. Follow-up studies are recommended with pregnant women as the target group to assess their attitude towards RSV vaccination and to confirm the validity of the conceived ABCDEF survey instrument.