Interference between rhinovirus and influenza A virus: a clinical data analysis and experimental infection study

Prospective cohort study of patient demographics, viral agents, seasonality, and outcomes of influenza-like illness in Mexico in the late H1N1-pandemic and post-pandemic years (2010-2014)

Objectives

Influenza-like illness (ILI) caused by respiratory viruses results in various respiratory clinical manifestations. The ILI002 prospective observational cohort study aimed to describe viral agents, seasonality, and outcomes of patients with ILI during four seasons in the influenza H1N1-pandemic and post-pandemic years (2010-2014).

Methods

Patients from six Mexican hospitals were enrolled from April 2010 to March 2014. Clinical data and nasopharyngeal swabs were obtained and tested for viral respiratory pathogens by real-time reverse-transcription polymerase chain reaction.

Results

Of the 5662 enrolled participants, 64.9% were adults and 35.1% were children. Among the 5629 participants with single-pathogen detection, rhinovirus (20.2%), influenza virus (11.2%), respiratory syncytial virus (RSV) (7.2%), and coronavirus (6.8%) were the most frequent pathogens. Co-infection occurred in 14.5% of cases; 49.3% of participants required hospitalization, particularly in RSV cases (42.9% adults, 89.6% children). The mortality rate was 2.8% higher among older adult participants and those with comorbidities. Influenza H1N1 had the highest mortality rate, yet almost half of the deceased had no pathogen. Rhinovirus persisted year-round, while influenza, coronavirus, and RSV peaked during cooler months.

Conclusions

Analyses showed that some viruses causing ILI may lead to severe disease and hospitalization irrespective of comorbidities. These findings may help in decision-making about public health policies on prevention measures, vaccination, treatment, and administration of health care.

Digital epidemiology: harnessing big data for early detection and monitoring of viral outbreaks

Digital epidemiology is the process of investigating the dynamics of disease-related patterns, both social and clinical, as well as the causes of these trends in epidemiology. Digital epidemiology, utilising big data from a variety of digital sources, has emerged as a viable method for early detection and monitoring of viral outbreaks. The present review gives an overview of digital epidemiology, emphasising its importance in the timely detection of infectious disease outbreaks. Researchers may discover and track outbreaks in real time using digital data sources such as search engine queries, social media trends, and digital health records. However, data quality, concerns about privacy, and data interoperability must be addressed to maximise the effectiveness of digital epidemiology. As the global landscape of infectious diseases evolves, integrating digital epidemiology becomes critical to improving pandemic preparedness and response efforts. Integrating digital epidemiology into routine monitoring systems has the potential to improve global health outcomes and save lives in the event of viral outbreaks.

Unraveling the Role of Viral Interference in Disrupting Biennial RSV Epidemics in Northern Stockholm

Respiratory syncytial virus (RSV) primarily impacts infants and older adults, with seasonal winter outbreaks in temperate countries. Biennial cycles of RSV activity have also been identified in Northern Europe and some states in the United States. Delayed RSV activity was reported worldwide during the 2009 influenza pandemic, and a disrupted biennial pattern of RSV activity was observed in northern Stockholm following the pandemic. Biennial patterns shifted to early/large outbreaks in even-numbered years and late/small outbreaks in odd-numbered years. However, the mechanisms underpinning this change in pattern remain unknown. In this work, we constructed an age-stratified mechanistic model to explicitly test three factors that could lead to the change in RSV transmission dynamics: 1) birth rates, 2) temperatures, and 3) viral interference. By fitting the model to weekly RSV admission data over a 20-year period and comparing different models, we found that viral interference from influenza was the only mechanism that explained the shifted biennial pattern. Our work demonstrates the complex interplay between different respiratory viruses, providing evidence that supports the presence of interactions between the H1N1 pandemic influenza virus and RSV at the population level, with implications for future public health interventions.

Molecular surveillance of influenza A virus in Saudi Arabia: whole-genome sequencing and metagenomic approaches

Outbreaks of influenza A viruses are generally seasonal and cause annual epidemics worldwide. Due to their frequent reassortment and evolution, annual surveillance is of paramount importance to guide vaccine strategies. The aim of this study was to explore the molecular epidemiology of influenza A virus and nasopharyngeal microbiota composition in infected patients in Saudi Arabia. A total of 103 nasopharyngeal samples from 2015 and 12 samples from 2022 were collected from patients positive for influenza A. Sequencing of influenza A as well as metatranscriptomic analysis of the nasopharyngeal microbiota was conducted using Oxford Nanopore sequencing. Phylogenetic analysis of hemagglutinin, neuraminidase segments, and concatenated influenza A genomes was performed using MEGA7. Whole-genome sequencing analysis revealed changing clades of influenza A virus: from 6B.1 in 2015 to 5a.2a in 2022. One sample containing the antiviral resistance-mediating mutation S247N toward oseltamivir and zanamivir was found. Phylogenetic analysis showed the clustering of influenza A strains with the corresponding vaccine strains in each period, thus suggesting vaccine effectiveness. Principal component analysis and alpha diversity revealed the absence of a relationship between hospital admission status, age, or gender of infected patients and the nasopharyngeal microbial composition, except for the infecting clade 5a.2a. The opportunistic pathogens Staphylococcus aureus, Streptococcus pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis were the most common species detected. The molecular epidemiology appears to be changing in Saudi Arabia after the COVID-19 pandemic. Antiviral resistance should be carefully monitored in future studies. In addition, the disease severity of patients as well as the composition of the nasopharyngeal microbiota in patients infected with different clades should also be assessed.IMPORTANCEIn this work, we have found that the clade of influenza A virus circulating in Riyadh, KSA, has changed over the last few years from 6B.1 to 5a.2a. Influenza strains clustered with the corresponding vaccine strains in our population, thus emphasizing vaccine effectiveness. Metatranscriptomic analysis showed no correlation between the nasopharyngeal microbiome and the clinical and/or demographic characteristics of infected patients. This is except for the 5a.2a strains isolated post-COVID-19 pandemic. The influenza virus is among the continuously evolving viruses that can cause severe respiratory infections. Continuous surveillance of its molecular diversity and the monitoring of anti-viral-resistant strains are thus of vital importance. Furthermore, exploring potential microbial markers and/or dysbiosis of the nasopharyngeal microbiota during infection could assist in the better management of patients in severe cases.

SARS-CoV-2 co-detection with other respiratory pathogens-descriptive epidemiological study

BACKGROUND

Co-detection of respiratory pathogens with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is poorly understood. This descriptive epidemiological study aimed to determine the effect of the interaction of different respiratory pathogens on clinical variables.

METHODS

We retrospectively reviewed the results of comprehensive multiplex polymerase chain reaction (PCR) testing from November 2020 to March 2023 to estimate respiratory pathogen co-detection rates in Shinjuku, Tokyo. We evaluated the interactions of respiratory pathogens, particularly SARS-CoV-2, between observed and expected co-detection. We estimated the trend of co-detection with SARS-CoV-2 in terms of age and sex and applied a multiple logistic regression model adjusted for age, testing period, and sex to identify influencing factors between co-detection and single detection for each pathogen.

RESULTS

Among 57,746 patients who underwent multiplex PCR testing, 10,516 (18.2%) had positive for at least one of the 22 pathogens. Additionally, 881 (1.5%) patients were confirmed to have a co-detection. SARS-CoV-2 exhibited negative interactions with adenovirus, coronavirus, human metapneumovirus, parainfluenza virus, respiratory syncytial virus, and rhino/enterovirus. SARS-CoV-2 co-detection with other pathogens occurred most frequently in patients of the youngest age group (0-4 years). A multiple logistic regression model indicated that younger age was the most influential factor for SARS-CoV-2 co-detection with other respiratory pathogens.

CONCLUSION

The study highlights the prevalence of SARS-CoV-2 co-detection with other respiratory pathogens in younger age groups, necessitating further exploration of the clinical implications and severity of SARS-CoV-2 co-detection.

Considerations for viral co-infection studies in human populations

When respiratory viruses co-circulate in a population, individuals may be infected with multiple pathogens and experience possible virus-virus interactions, where concurrent or recent prior infection with one virus affects the infection process of another virus. While experimental studies have provided convincing evidence for within-host mechanisms of virus-virus interactions, evaluating evidence for viral interference or potentiation using population-level data has proven more difficult. Recent studies have quantified the prevalence of co-detections using populations drawn from clinical settings. Here, we focus on selection bias issues associated with this study design. We provide a quantitative account of the conditions under which selection bias arises in these studies, review previous attempts to address this bias, and propose unbiased study designs with sample size estimates needed to ascertain viral interference. We show that selection bias is expected in cross-sectional co-detection prevalence studies conducted in clinical settings, except under a strict set of assumptions regarding the relative probabilities of being included in a study limited to individuals with clinical disease under different viral states. Population-wide studies that collect samples from participants irrespective of their clinical status would meanwhile require large sample sizes to be sufficiently powered to detect viral interference, suggesting that a study's timing, inclusion criteria, and the expected magnitude of interference are instrumental in determining feasibility.

Viral interference between severe acute respiratory syndrome coronavirus 2 and influenza A viruses

Some respiratory viruses can cause a viral interference through the activation of the interferon (IFN) pathway that reduces the replication of another virus. Epidemiological studies of coinfections between SARS-CoV-2 and other respiratory viruses have been hampered by non-pharmacological measures applied to mitigate the spread of SARS-CoV-2 during the COVID-19 pandemic. With the ease of these interventions, SARS-CoV-2 and influenza A viruses can now co-circulate. It is thus of prime importance to characterize their interactions. In this work, we investigated viral interference effects between an Omicron variant and a contemporary influenza A/H3N2 strain, in comparison with an ancestral SARS-CoV-2 strain and the 2009 pandemic influenza A/H1N1 virus. We infected nasal human airway epitheliums with SARS-CoV-2 and influenza, either simultaneously or 24 h apart. Viral load was measured by RT-qPCR and IFN-α/β/λ1/λ2 proteins were quantified by immunoassay. Expression of four interferon-stimulated genes (ISGs; OAS1/IFITM3/ISG15/MxA) was also measured by RT-droplet digital PCR. Additionally, susceptibility of each virus to IFN-α/β/λ2 recombinant proteins was determined. Our results showed that influenza A, and especially A/H3N2, interfered with both SARS-CoV-2 viruses, but that SARS-CoV-2 did not significantly interfere with A/H3N2 or A/H1N1. Consistently with these results, influenza, and particularly the A/H3N2 strain, caused a higher production of IFN proteins and expression of ISGs than SARS-CoV-2. SARS-CoV-2 induced a marginal IFN production and reduced the IFN response during coinfections with influenza. All viruses were susceptible to exogenous IFNs, with the ancestral SARS-CoV-2 and Omicron being less susceptible to type I and type III IFNs, respectively. Thus, influenza A causes a viral interference towards SARS-CoV-2 most likely through an IFN response. The opposite is not necessarily true, and a concurrent infection with both viruses leads to a lower IFN response. Taken together, these results help us to understand how SARS-CoV-2 interacts with another major respiratory pathogen.

Influence of non-pharmaceutical interventions during the COVID-19 pandemic on respiratory viral infections - a prospective population-based cohort study

Non-pharmaceutical interventions (NPI) have been proven successful in a population-based approach to protect from SARS-CoV-2 transmission during the COVID-19 pandemic. As a consequential-effect, a reduction in the spread of all respiratory viruses has been observed, but the primary factors behind this phenomenon have yet to be identified. We conducted a subgroup analysis of participants from the ELISA study, a prospective longitudinal cohort study on SARS-CoV-2 transmission, at four timepoints from November 2020 - September 2022. The aim was to provide a detailed overview of the circulation of respiratory viruses over 2 years and to identify potential personal risk factors of virus distribution. All participants were screened using qPCR for respiratory viral infections from nasopharyngeal swabs and answered a questionnaire regarding behavioral factors. Several categories of risk factors for the transmission of respiratory viruses were evaluated using a scoring system. In total, 1,124 participants were included in the study, showing high adherence to governmental-introduced NPI. The overall number of respiratory virus infections was low (0-4.9% of participants), with adenovirus (1.7%), rhino-/enterovirus (3.2%) and SARS-CoV-2 (1.2%) being the most abundant. We detected an inverse correlation between the number and intensity of NPI and the number of detected respiratory viruses. More precisely, the attendance of social events and household size was associated with rhino-/enterovirus infection while social contacts were associated with being positive for any virus. NPI introduced during the COVID-19 pandemic reduced the occurrence of seasonal respiratory viruses in our study, showing different risk-factors for enhanced transmission between viruses.

Trial registration

DRKS.de, German Clinical Trials Register (DRKS), Identifier: DRKS00023418, Registered on 28 October 2020.

Viral Interference During Influenza A-SARS-CoV-2 Coinfection of the Human Airway Epithelium and Reversal by Oseltamivir

To gain insight into interactions among respiratory viruses, we modeled influenza A virus (IAV)-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) coinfections using differentiated human airway epithelial cultures. Replicating IAV induced a more robust interferon response than SARS-CoV-2 and suppressed SARS-CoV-2 replication in both sequential and simultaneous infections, whereas SARS-CoV-2 did not enhance host cell defense during influenza infection or suppress IAV replication. Oseltamivir, an antiviral targeting influenza, reduced IAV replication during coinfection but also reduced the host antiviral response and restored SARS-CoV-2 replication. These results demonstrate how perturbations in one viral infection can impact its effect on a coinfecting virus.

Presence and Significance of Multiple Respiratory Viral Infections in Children Admitted to a Tertiary Pediatric Hospital in Italy

Viral co-infections are frequently observed among children, but whether specific viral interactions enhance or diminish the severity of respiratory disease is still controversial. This study aimed to investigate the type of viral mono- and co-infections by also evaluating viral correlations in 3525 respiratory samples from 3525 pediatric in/outpatients screened by the Allplex Respiratory Panel Assays and with a Severe Acute Respiratory Syndrome-COronaVirus 2 (SARS-CoV-2) test available. Overall, viral co-infections were detected in 37.8% of patients and were more frequently observed in specimens from children with lower respiratory tract infections compared to those with upper respiratory tract infections (47.1% vs. 36.0%, p = 0.003). SARS-CoV-2 and influenza A were more commonly detected in mono-infections, whereas human bocavirus showed the highest co-infection rate (87.8% in co-infection). After analyzing viral pairings using Spearman's correlation test, it was noted that SARS-CoV-2 was negatively associated with all other respiratory viruses, whereas a markedly significant positive correlation (p < 0.001) was observed for five viral pairings (involving adenovirus/human bocavirus/human enterovirus/metapneumoviruses/rhinovirus). The correlation between co-infection and clinical outcome may be linked to the type of virus(es) involved in the co-infection rather than simple co-presence. Further studies dedicated to this important point are needed, since it has obvious implications from a diagnostic and clinical point of view.

Hepatocyte Intrinsic Innate Antiviral Immunity against Hepatitis Delta Virus Infection: The Voices of Bona Fide Human Hepatocytes

The pathogenesis of viral infection is attributed to two folds: intrinsic cell death pathway activation due to the viral cytopathic effect, and immune-mediated extrinsic cellular injuries. The immune system, encompassing both innate and adaptive immunity, therefore acts as a double-edged sword in viral infection. Insufficient potency permits pathogens to establish lifelong persistent infection and its consequences, while excessive activation leads to organ damage beyond its mission to control viral pathogens. The innate immune response serves as the front line of defense against viral infection, which is triggered through the recognition of viral products, referred to as pathogen-associated molecular patterns (PAMPs), by host cell pattern recognition receptors (PRRs). The PRRs-PAMPs interaction results in the induction of interferon-stimulated genes (ISGs) in infected cells, as well as the secretion of interferons (IFNs), to establish a tissue-wide antiviral state in an autocrine and paracrine manner. Cumulative evidence suggests significant variability in the expression patterns of PRRs, the induction potency of ISGs and IFNs, and the IFN response across different cell types and species. Hence, in our understanding of viral hepatitis pathogenesis, insights gained through hepatoma cell lines or murine-based experimental systems are uncertain in precisely recapitulating the innate antiviral response of genuine human hepatocytes. Accordingly, this review article aims to extract and summarize evidence made possible with bona fide human hepatocytes-based study tools, along with their clinical relevance and implications, as well as to identify the remaining gaps in knowledge for future investigations.

Mutations at the conserved N-Terminal of the human Rhinovirus capsid gene VP4, and their impact on the immune response

Rhinoviruses (RV) are the major cause of chronic obstructive pulmonary disease and are associated with exacerbation development as well as community-acquired pneumonia in children, leading to substantial morbidity, mortality, and hospital admission. Here we have examined how changes at the amino terminal of the conserved VP4 epitope of different RV serotypes may affect pulmonary cytokine and chemokine responses and disease severity. Samples positive for rhinovirus were used for genetic characterization, followed by profiling gene expression of pulmonary Th1 and Th2 cytokines/chemokines by RT-PCR arrays. Genetic sequencing and homology 3D modeling revealed changes at the amino terminal of the conserved viral protein 4 (VP4) epitope in the RV-A101 serotype, especially serine at several positions that are important for interactive binding with the host immune cells. We found dysregulation of pulmonary gene expression of Th1- and Th2-related cytokines and chemokines in RV-A 101 and RV-C 8 pneumonia patients. These findings might contribute to a better understanding of RV immunity and the potential mechanisms underlying the pathogenesis of severe RV infections, but further functional studies are needed to confirm the causal relationship.

Respiratory Viral Coinfections: Insights into Epidemiology, Immune Response, Pathology, and Clinical Outcomes

Respiratory viral coinfections are a global public health threat that poses an economic burden on individuals, families, and healthcare infrastructure. Viruses may coinfect and interact synergistically or antagonistically, or their coinfection may not affect their replication rate. These interactions are specific to different virus combinations, which underlines the importance of understanding the mechanisms behind these differential viral interactions and the need for novel diagnostic methods to accurately identify multiple viruses causing a disease in a patient to avoid misdiagnosis. This review examines epidemiological patterns, pathology manifestations, and the immune response modulation of different respiratory viral combinations that occur during coinfections using different experimental models to better understand the dynamics respiratory viral coinfection takes in driving disease outcomes and severity, which is crucial to guide the development of prevention and treatment strategies.

Prevalence and genetic diversity of human rhinovirus among patients with acute respiratory infections in China, 2012-2021

To understand the prevalence of rhinovirus (RV) among acute respiratory infection (ARI) patients, 10-year ARI surveillance in multiple provinces of China were conducted during 2012-2021. Of 15 645 ARI patients, 1180 (7.54%) were confirmed to have RV infection and 820 (69.49%) were children under 5 years of age. RV typing was performed on the 527 VP1 gene sequences, and species A, B, and C accounted for 73.24%, 4.93%, and 21.82%, respectively. Although no significant difference in the proportions of age groups or disease severity was found between RV species, RV-C was more frequently detected in children under 5 years of age, RV-A was more frequently detected in elderly individuals (≥60), and the proportions of pneumonia in RV-A and RV-C patients were higher than those in RV-B patients. The epidemic peak of RV-A was earlier than that of RV-C. A total of 57 types of RV-A, 13 types of RV-B, and 35 types of RV-C were identified in RV-infected patients, and two uncertain RV types were also detected. The findings showed a few differences in epidemiological and clinical features between RV species in ARI patients, and RV-A and RV-C were more prevalent than RV-B.

The role of viral interference in shaping RSV epidemics following the 2009 H1N1 influenza pandemic

Respiratory syncytial virus (RSV) primarily affects infants, young children, and older adults, with seasonal outbreaks in the United States (US) peaking around December or January. Despite the limited implementation of non-pharmaceutical interventions, disrupted RSV activity was observed in different countries following the 2009 influenza pandemic, suggesting possible viral interference from influenza. Although interactions between the influenza A/H1N1 pandemic virus and RSV have been demonstrated at an individual level, it remains unclear whether the disruption of RSV activity at the population level can be attributed to viral interference. In this work, we first evaluated changes in the timing and intensity of RSV activity across 10 regions of the US in the years following the 2009 influenza pandemic using dynamic time warping. We observed a reduction in RSV activity following the pandemic, which was associated with intensity of influenza activity in the region. We then developed an age-stratified, two-pathogen model to examine various hypotheses regarding viral interference mechanisms. Based on our model estimates, we identified three mechanisms through which influenza infections could interfere with RSV: 1) reducing susceptibility to RSV coinfection; 2) shortening the RSV infectious period in coinfected individuals; and 3) reducing RSV infectivity in coinfection. Our study offers statistical support for the occurrence of atypical RSV seasons following the 2009 influenza pandemic. Our work also offers new insights into the mechanisms of viral interference that contribute to disruptions in RSV epidemics and provides a model-fitting framework that enables the analysis of new surveillance data for studying viral interference at the population level.

Risk of Subsequent Respiratory Virus Detection After Primary Virus Detection in a Community Household Study-King County, Washington, 2019-2021

BACKGROUND

The epidemiology of respiratory viral infections is complex. How infection with one respiratory virus affects risk of subsequent infection with the same or another respiratory virus is not well described.

METHODS

From October 2019 to June 2021, enrolled households completed active surveillance for acute respiratory illness (ARI), and participants with ARI self-collected nasal swab specimens; after April 2020, participants with ARI or laboratory-confirmed severe acute respiratory syndrome coronavirus 2 and their household members self-collected nasal swab specimens. Specimens were tested using multiplex reverse-transcription polymerase chain reaction for respiratory viruses. A Cox regression model with a time-dependent covariate examined risk of subsequent detections following a specific primary viral detection.

RESULTS

Rhinovirus was the most frequently detected pathogen in study specimens (406 [9.5%]). Among 51 participants with multiple viral detections, rhinovirus to seasonal coronavirus (8 [14.8%]) was the most common viral detection pairing. Relative to no primary detection, there was a 1.03-2.06-fold increase in risk of subsequent virus detection in the 90 days after primary detection; risk varied by primary virus: human parainfluenza virus, rhinovirus, and respiratory syncytial virus were statistically significant.

CONCLUSIONS

Primary virus detection was associated with higher risk of subsequent virus detection within the first 90 days after primary detection.

Investigating epidemiological distribution (temporality and intensity) of respiratory pathogens following COVID-19 de-escalation process in Catalonia, September 2016-June 2021: Analysis of regional surveillance data

BACKGROUND

Following the low incidence rates of non-SARS-CoV-2 respiratory viruses registered during the strict lockdown enforced in the pandemic, a resurgence of several endemic viruses in Catalonia (Spain) was noted during the early summer of 2021.

OBJECTIVES

In this study, we investigated whether the circulation of non-SARS-CoV-2 respiratory viruses in Catalonia, assessed by Microbiological Reporting System of Catalonia (MRSC) and the Epidemiological Surveillance Network of Catalonia, was affected by the strict lockdown measures, as well as, the implication of the Coronavirus Disease 19 (COVID-19) de-escalation process in the late season outbreaks registered during the 2020-2021 season.

STUDY DESIGN

A retrospective comparison of epidemic patterns in the respiratory viruses' incidence, using regional public health surveillance data from MRSC, was performed between weeks 26/2016 to week 27/2021. Data were expressed as the weekly total number of test positivity for individual viruses. A segmented negative binomial regression model was conducted, with two parameters included (level and trend) for each segment of the time series (2020 pre-lockdown, 2020 post-lockdown and 2021). Results were reported as a unit changed in the strict lockdown.

RESULTS

A total of 51588 confirmed cases of the different respiratory viruses were included in the analysis, the majority were influenza cases (63.7%). An immediate reduction in the weekly number of cases was observed in 2020 after the COVID-19 outbreak for human adenovirus virus (HAdV) (β2 = -2.606; P <0.01), human parainfluenza virus (HPIV) (β2 = -3.023; P <0.01), influenza virus (IFV) (β2 = -1.259; P <0.01), but not for respiratory syncytial virus (RSV), where the number of cases remained unchanged. During 2020, a significant negative trend was found for RSV (β3 = -0.170, P <0.01), and a positive trend for HAdV (β3 = 0.075, P <0.01). During 2021, a significant reduction in the weekly number of cases was also observed for all respiratory viruses, and a borderline non-significant reduction for HPIV (β3 = -0.027; P = 0.086). Moreover, significant positive trends were found for each viral pathogen, except for influenza during 2020-2021 season, where cases remained close to zero. The respiratory viruses increased activity and their late season epidemic start particularly affected children under 6 years old.

CONCLUSIONS

Our data not only provides evidence that occurrence of different respiratory virus infections was affected by the strict lockdown taken against SARS-CoV-2 but it also shows a late resurgence of seasonal respiratory viruses' cases during the 2020-2021 season following the relaxation of COVID-19-targeted non-pharmaceutical interventions.

Prevalence of human respiratory pathogens and associated mucosal cytokine levels in young children and adults: a cross-sectional observational study in the Netherlands during the winter of 2012/2013

Respiratory pathogens can cause severe disease and even death, especially in the very young and very old. Studies investigating their prevalence often focus on individuals presenting to healthcare providers with symptoms. However, the design of prevention strategies, e.g. which target groups to vaccinate, will benefit from knowledge on the prevalence of, risk factors for and host response to these pathogens in the general population. In this study, upper respiratory samples (n = 1311) were collected cross-sectionally during winter from 11- and 24-month old children, their parents, and adults ≥60 years of age that were recruited irrespective of seeking medical care. Almost all children, approximately two-thirds of parents and a quarter of older adults tested positive for at least one pathogen, often in the absence of symptoms. Viral interference was evident for the combination of rhinovirus and respiratory syncytial virus. Attending childcare facilities and having siblings associated with increased pathogen counts in children. On average, children showed increased levels of mucosal cytokines compared to parents and especially proinflammatory molecules associated with the presence of symptoms. These findings may guide further research into transmission patterns of respiratory pathogens and assist in determining the most appropriate strategies for the prediction and prevention of disease.

Use of immunology in news and YouTube videos in the context of COVID-19: politicisation and information bubbles

Background

The COVID-19 pandemic propelled immunology into global news and social media, resulting in the potential for misinterpreting and misusing complex scientific concepts.

Objective

To study the extent to which immunology is discussed in news articles and YouTube videos in English and Italian, and if related scientific concepts are used to support specific political or ideological narratives in the context of COVID-19.

Methods

In English and Italian we searched the period 11/09/2019 to 11/09/2022 on YouTube, using the software Mozdeh, for videos mentioning COVID-19 and one of nine immunological concepts: antibody-dependent enhancement, anergy, cytokine storm, herd immunity, hygiene hypothesis, immunity debt, original antigenic sin, oxidative stress and viral interference. We repeated this using MediaCloud for news articles.Four samples of 200 articles/videos were obtained from the randomised data gathered and analysed for mentions of concepts, stance on vaccines, masks, lockdown, social distancing, and political signifiers.

Results

Vaccine-negative information was higher in videos than news (8-fold in English, 6-fold in Italian) and higher in Italian than English (4-fold in news, 3-fold in videos). We also observed the existence of information bubbles, where a negative stance towards one intervention was associated with a negative stance to other linked ideas. Some immunological concepts (immunity debt, viral interference, anergy and original antigenic sin) were associated with anti-vaccine or anti-NPI (non-pharmacological intervention) views. Videos in English mentioned politics more frequently than those in Italian and, in all media and languages, politics was more frequently mentioned in anti-guidelines and anti-vaccine media by a factor of 3 in video and of 3-5 in news.

Conclusion

There is evidence that some immunological concepts are used to provide credibility to specific narratives and ideological views. The existence of information bubbles supports the concept of the "rabbit hole" effect, where interest in unconventional views/media leads to ever more extreme algorithmic recommendations.

Prevalence of respiratory viruses among hospitalized children with lower respiratory tract infections during the COVID-19 pandemic in Wuhan, China

OBJECTIVES

We aimed to investigate the continuous changes in respiratory virus epidemics in hospitalized children with lower respiratory tract infections (LRTIs) persisting from January 2019 to December 2022 in Wuhan, China.

METHODS

We retrospectively enrolled children with LRTIs admitted to the Wuhan Children's Hospital. Specimens were nasopharyngeal aspirates which had been collected and detected the following microorganisms with direct immunofluorescence: influenza virus types A and B, respiratory syncytial virus, parainfluenza virus types 1-3, and adenovirus. We also analyzed demographic data and laboratory test results.

RESULTS

A total of 22,660 patients were enrolled. The total virus detection rate in 2019, 2021, and 2022 significantly declined gradually (36.96% vs 29.47% vs 22.62%, P value < 0.001). All the detected viruses did not follow previously observed seasonal patterns during the COVID-19 pandemic. Children hospitalized for LRTIs were older during the COVID-19 pandemic in contrast to the pre-period, particularly notable in cases attributed to respiratory syncytial virus and parainfluenza virus type 3 infections.

CONCLUSIONS

This work adds to our knowledge of the epidemiology characteristics of respiratory viruses spanning the COVID-19 pandemic among children with LRTIs. The circulation of respiratory viruses changed consistently, and active LRTI surveillance in children remains critical for defining the healthcare burden of respiratory viruses.

Prevalence of Endemic Respiratory Viruses During the COVID-19 Pandemic in Urban and Rural Malawi

Background

We investigated endemic respiratory virus circulation patterns in Malawi, where no lockdown was imposed, during the COVID-19 pandemic.

Methods

Within a prospective household cohort in urban and rural Malawi, adult participants provided upper respiratory tract (URT) samples at 4 time points between February 2021 and April 2022. Polymerase chain reaction (PCR) was performed for SARS-CoV-2, influenza, and other endemic respiratory viruses.

Results

1626 URT samples from 945 participants in 542 households were included. Overall, 7.6% (n = 123) samples were PCR- positive for >1 respiratory virus; SARS-CoV-2 (4.4%) and rhinovirus (2.0%) were most common. No influenza A virus was detected. Influenza B and respiratory syncytial virus (RSV) were rare. Higher virus positivity were detected in the rural setting and at earlier time points. Coinfections were infrequent.

Conclusions

Endemic respiratory viruses circulated in the community in Malawi during the pandemic, though influenza and RSV were rarely detected. Distinct differences in virus positivity and demographics were observed between urban and rural cohorts.

Assessing the impact of COVID-19 on epidemiological changes of severe pediatric respiratory syncytial virus infections in Malaysia

Introduction

Respiratory syncytial virus (RSV) is one of the leading causes of hospitalization and mortality among children with respiratory tract infections. The non-pharmaceutical preventive measures against severe acute respiratory syndrome coronavirus (COVID-19) may have reduced the transmission of RSV, altering its tropical epidemiological seasonality. Thus, this study represents the first attempt to evaluate changes in RSV epidemiology in the context of COVID-19 pandemic in Malaysia.

Methods

Conducted at a tertiary hospital in Kuala Lumpur, Malaysia, this retrospective study analyzed collated data of children aged <12 years who were admitted for severe respiratory infections from 2017 to 2022. Time series models were used to predict the differences between actual and forecasted RSV cases, while logistic regression assessed the statistical association between RSV and COVID-19.

Results

Among the 4,084 children analyzed, we reported a significant inverse relationship between RSV and COVID-19 infections during the pandemic (2020-2021) (p < 0.05). In 2020, the RSV positivity rate sharply declined to 8.3 and 5.9%, respectively, in the two prominent seasons. Time series analysis showed a tremendous decrease in cases compared to the expected values, with reductions of 98.3% in the first season and 95.7% in the second season. However, following the lifting of the restriction order in 2022, RSV infections rose sharply with a positivity rate of 36.3%, higher than pre-COVID-19 pandemic levels.

Conclusion

This study provides evidence of increasing RSV cases post-COVID-19 pandemic, due to immunity debt. Hence, the healthcare system must be prepared to address future RSV outbreaks with the appropriate implementation of prophylaxis and public health measures.

Evidence of the simultaneous replications of active viruses in specimens positive for multiple respiratory viruses

IMPORTANCE

Since the pandemic of coronavirus diseases 2019, the use of real-time PCR assay has become widespread among people who were not familiar with it in virus detection. As a result, whether a high real-time PCR value in one time test indicates virus transmissibly became a complicated social problem, regardless of the difference in assays and/or amplification conditions, the time and number of diagnostic test during the time course of infection. In addition, the multiple positives in the test of respiratory viruses further add to the confusion in the interpretation of the infection. To address this issue, we performed virus isolation using pediatric SARI (severe acute respiratory infections) specimens on air-liquid interface culture of human bronchial/tracheal epithelial cell culture. The result of this study can be a strong evidence that the specimens showing positivity for multiple agents in real-time PCR tests possibly contain infectious viruses.

Differences in the Clinical Manifestations and Host Immune Responses to SARS-CoV-2 Variants in Children Compared to Adults

The COVID-19 pandemic challenged the medical field to rapidly identify and implement new approaches to the diagnosis, treatment and prevention of SARS-CoV-2 infections. The scientific community also needed to rapidly initiate basic, translational, clinical and epidemiological studies to understand the pathophysiology of this new family of viruses, which continues to evolve with the emergence of new genetic variants. One of the earliest clinical observations that provided a framework for the research was the finding that, in contrast to most other respiratory viruses, children developed less severe acute and post-acute disease compared to adults. Although the clinical manifestations of SARS-CoV-2 infection changed with each new wave of the pandemic, which was dominated by evolving viral variants, the differences in severity between children and adults persisted. Comparative immunologic studies have shown that children mount a more vigorous local innate response characterized by the activation of interferon pathways and recruitment of innate cells to the mucosa, which may mitigate against the hyperinflammatory adaptive response and systemic cytokine release that likely contributed to more severe outcomes including acute respiratory distress syndrome in adults. In this review, the clinical manifestations and immunologic responses in children during the different waves of COVID-19 are discussed.

An overview on viral interference during SARS-CoV-2 pandemic

Respiratory viruses represent the most frequent cause of mortality, morbidity and high healthcare costs for emergency visits and hospitalization in the pediatric age. Respiratory viruses can circulate simultaneously and can potentially infect the same host, determining different types of interactions, the so-called viral interference. The role of viral interference has assumed great importance since December 2019, when the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) came on the scene. The aim of this narrative review is to present our perspective regarding research in respiratory virus interference and discuss recent advances on the topic because, following SARS-CoV-2 restrictions mitigation, we are experimenting the co-circulation of respiratory viruses along with SARS-CoV-2. This scenario is raising many concerns about possible virus-virus interactions, both positive and negative, and the clinical, diagnostic and therapeutic management of these coinfections. Moreover, we cannot rule out that also climatic conditions and social behaviours are involved. Thus, this situation can lead to different population epidemic dynamics, including changes in the age of the targeted population, disease course and severity, highlighting the need for prospective epidemiologic studies and mathematical modelling able to predict the timing and magnitude of epidemics caused by SARS-CoV-2/seasonal respiratory virus interactions in order to adjust better public health interventions.

Use of Epic Electronic Health Record System for Health Care Research: Scoping Review

BACKGROUND

Electronic health records (EHRs) enable health data exchange across interconnected systems from varied settings. Epic is among the 5 leading EHR providers and is the most adopted EHR system across the globe. Despite its global reach, there is a gap in the literature detailing how EHR systems such as Epic have been used for health care research.

OBJECTIVE

The objective of this scoping review is to synthesize the available literature on use cases of the Epic EHR for research in various areas of clinical and health sciences.

METHODS

We used established scoping review methods and searched 9 major information repositories, including databases and gray literature sources. To categorize the research data, we developed detailed criteria for 5 major research domains to present the results.

RESULTS

We present a comprehensive picture of the method types in 5 research domains. A total of 4669 articles were screened by 2 independent reviewers at each stage, while 206 articles were abstracted. Most studies were from the United States, with a sharp increase in volume from the year 2015 onwards. Most articles focused on clinical care, health services research and clinical decision support. Among research designs, most studies used longitudinal designs, followed by interventional studies implemented at single sites in adult populations. Important facilitators and barriers to the use of Epic and EHRs in general were identified. Important lessons to the use of Epic and other EHRs for research purposes were also synthesized.

CONCLUSIONS

The Epic EHR provides a wide variety of functions that are helpful toward research in several domains, including clinical and population health, quality improvement, and the development of clinical decision support tools. As Epic is reported to be the most globally adopted EHR, researchers can take advantage of its various system features, including pooled data, integration of modules and developing decision support tools. Such research opportunities afforded by the system can contribute to improving quality of care, building health system efficiencies, and conducting population-level studies. Although this review is limited to the Epic EHR system, the larger lessons are generalizable to other EHRs.

Development of Human Rhinovirus RNA Reference Material Using Digital PCR

The human rhinovirus (RV) is a positive-stranded RNA virus that causes respiratory tract diseases affecting both the upper and lower halves of the respiratory system. RV enhances its replication by concentrating RNA synthesis within a modified host membrane in an intracellular compartment. RV infections often occur alongside infections caused by other respiratory viruses, and the RV virus may remain asymptomatic for extended periods. Alongside qualitative detection, it is essential to accurately quantify RV RNA from clinical samples to explore the relationships between RV viral load, infections caused by the virus, and the resulting symptoms observed in patients. A reference material (RM) is required for quality evaluation, the performance evaluation of molecular diagnostic products, and evaluation of antiviral agents in the laboratory. The preparation process for the RM involves creating an RV RNA mixture by combining RV viral RNA with RNA storage solution and matrix. The resulting RV RNA mixture is scaled up to a volume of 25 mL, then dispensed at 100 µL per vial and stored at -80 °C. The process of measuring the stability and homogeneity of RV RMs was conducted by employing reverse transcription droplet digital polymerase chain reaction (RT-ddPCR). Digital PCR is useful for the analysis of standards and can help to improve measurement compatibility: it represents the equivalence of a series of outcomes for reference materials and samples being analyzed when a few measurement procedures are employed, enabling objective comparisons between quantitative findings obtained through various experiments. The number of copies value represents a measured result of approximately 1.6 × 105 copies/μL. The RM has about an 11% bottle-to-bottle homogeneity and shows stable results for 1 week at temperatures of 4 °C and -20 °C and for 12 months at a temperature of -80 °C. The developed RM can enhance the dependability of RV molecular tests by providing a precise reference value for the absolute copy number of a viral target gene. Additionally, it can serve as a reference for diverse studies.

Mathematical Modeling of the Lethal Synergism of Coinfecting Pathogens in Respiratory Viral Infections: A Review

Influenza A virus (IAV) infections represent a substantial global health challenge and are often accompanied by coinfections involving secondary viruses or bacteria, resulting in increased morbidity and mortality. The clinical impact of coinfections remains poorly understood, with conflicting findings regarding fatality. Isolating the impact of each pathogen and mechanisms of pathogen synergy during coinfections is challenging and further complicated by host and pathogen variability and experimental conditions. Factors such as cytokine dysregulation, immune cell function alterations, mucociliary dysfunction, and changes to the respiratory tract epithelium have been identified as contributors to increased lethality. The relative significance of these factors depends on variables such as pathogen types, infection timing, sequence, and inoculum size. Mathematical biological modeling can play a pivotal role in shedding light on the mechanisms of coinfections. Mathematical modeling enables the quantification of aspects of the intra-host immune response that are difficult to assess experimentally. In this narrative review, we highlight important mechanisms of IAV coinfection with bacterial and viral pathogens and survey mathematical models of coinfection and the insights gained from them. We discuss current challenges and limitations facing coinfection modeling, as well as current trends and future directions toward a complete understanding of coinfection using mathematical modeling and computer simulation.

Positive and negative viral associations in patients with acute respiratory tract infections in primary care: the ECOVIR study

Introduction

Acute respiratory infections (ARIs) are the most common viral infections encountered in primary care settings. The identification of causal viruses is still not available in routine practice. Although new strategies of prevention are being identified, knowledge of the relationships between respiratory viruses remains limited.

Materials and methods

ECOVIR was a multicentric prospective study in primary care, which took place during two pre-pandemic seasons (2018-2019 and 2019-2020). Patients presenting to their General practitioner (GP) with ARIs were included, without selecting for age or clinical conditions. Viruses were detected on nasal swab samples using a multiplex Polymerase Chain Reaction test focused on 17 viruses [Respiratory Syncytial Virus-A (RSV-A), RSV-B, Rhinovirus/Enterovirus (HRV), human Metapneumovirus (hMPV), Adenovirus (ADV), Coronaviruses (CoV) HKU1, NL63, 229E, OC43, Influenza virus (H1 and H3 subtypes), Influenza virus B, Para-Influenza viruses (PIVs) 1-4, and Bocavirus (BoV)].

Results

Among the 668 analyzed samples, 66% were positive for at least one virus, of which 7.9% were viral codetections. The viral detection was negatively associated with the age of patients. BoV, ADV, and HRV occurred more significantly in younger patients than the other viruses (p < 0.05). Codetections were significantly associated with RSV, HRV, BoV, hMPV, and ADV and not associated with influenza viruses, CoV, and PIVs. HRV and influenza viruses were negatively associated with all the viruses. Conversely, a positive association was found between ADV and BoV and between PIVs and BoV.

Conclusion

Our study provides additional information on the relationships between respiratory viruses, which remains limited in primary care.

Effect of cross-immunity in a two-strain cholera model with aquatic component

The bacteria Vibrio cholerae relies heavily upon an aquatic reservoir as a transmission route with two distinct serotypes observed in many recent outbreaks. In this paper, we extend previously studied ordinary differential equation epidemiological models to create a two-strain SIRP (susceptible-infectious-recovered-pathogen) system which incorporates both partial cross-immunity between disease strains and environmental pathogen transmission. Of particular interest are undamped anti-phase periodic solutions, as these display a type of coexistence where strains routinely switch dominance, and understanding what drives this switch can optimize the efficiency of the host population's control measures against the disease. We derive the basic reproduction number R0 and use stability analysis to examine the disease free and single-strain equilibria. We formulate a unique coexistence equilibrium and prove uniform persistence of both strains when R0>1. In addition, we simulate solutions to this system, along with seasonally forced versions of the model with and without host coinfection. Cross-immunity and transmission pathways influence damped or sustained oscillatory dynamics, where the presence of seasonality can modify, amplify or synchronize the period and phase of serotypes, driving epidemic waves. Cycling of serotypes over large time intervals, similar to observed data, is found for a range of cross-immunity levels, and the inclusion of coinfection in the model contributes to sustained anti-phase periodic solutions.

Gastrointestinal Infections Modulate the Risk for Insulin Autoantibodies as the First-Appearing Autoantibody in the TEDDY Study

OBJECTIVE

To investigate gastrointestinal infection episodes (GIEs) in relation to the appearance of islet autoantibodies in The Environmental Determinants of Diabetes in the Young (TEDDY) cohort.

RESEARCH DESIGN AND METHODS

GIEs on risk of autoantibodies against either insulin (IAA) or GAD (GADA) as the first-appearing autoantibody were assessed in a 10-year follow-up of 7,867 children. Stool virome was characterized in a nested case-control study.

RESULTS

GIE reports (odds ratio [OR] 2.17 [95% CI 1.39-3.39]) as well as Norwalk viruses found in stool (OR 5.69 [1.36-23.7]) at <1 year of age were associated with an increased IAA risk at 2-4 years of age. GIEs reported at age 1 to <2 years correlated with a lower risk of IAA up to 10 years of age (OR 0.48 [0.35-0.68]). GIE reports at any other age were associated with an increase in IAA risk (OR 2.04 for IAA when GIE was observed 12-23 months prior [1.41-2.96]). Impacts on GADA risk were limited to GIEs <6 months prior to autoantibody development in children <4 years of age (OR 2.16 [1.54-3.02]).

CONCLUSIONS

Bidirectional associations were observed. GIEs were associated with increased IAA risk when reported before 1 year of age or 12-23 months prior to IAA. Norwalk virus was identified as one possible candidate factor. GIEs reported during the 2nd year of life were associated with a decreased IAA risk.

Respiratory virus surveillance in hospitalized children less than two-years of age in Kenema, Sierra Leone during the COVID-19 pandemic (October 2020- October 2021)

Globally, viral pathogens are the leading cause of acute respiratory infection in children under-five years. We aim to describe the epidemiology of viral respiratory pathogens in hospitalized children under-two years of age in Eastern Province of Sierra Leone, during the second year of the SARS-CoV-2 pandemic. We conducted a prospective study of children hospitalized with respiratory symptoms between October 2020 and October 2021. We collected demographic and clinical characteristics and calculated each participant´s respiratory symptom severity. Nose and throat swabs were collected at enrollment. Total nucleic acid was purified and tested for multiple respiratory viruses. Statistical analysis was performed using R version 4.2.0 software. 502 children less than two-years of age were enrolled. 376 (74.9%) had at least one respiratory virus detected. The most common viruses isolated were HRV/EV (28.2%), RSV (19.5%) and PIV (13.1%). Influenza and SARS-CoV-2 were identified in only 9.2% and 3.9% of children, respectively. Viral co-detection was common. Human metapneumovirus and RSV had more than two-fold higher odds of requiring O2 therapy while hospitalized. Viral pathogen prevalence was high (74.9%) in our study population. Despite this, 100% of children received antibiotics, underscoring a need to expand laboratory diagnostic capacity and to revisit clinical guidelines implementation in these children. Continuous surveillance and serologic studies among more diverse age groups, with greater geographic breadth, are needed in Sierra Leone to better characterize the long-term impact of COVID-19 on respiratory virus prevalence and to better characterize the seasonality of respiratory viruses in Sierra Leone.

Shifting Patterns of Influenza Circulation during the COVID-19 Pandemic, Senegal

Historically low levels of seasonal influenza circulation were reported during the first years of the COVID-19 pandemic and were mainly attributed to implementation of nonpharmaceutical interventions. In tropical regions, influenza's seasonality differs largely, and data on this topic are scarce. We analyzed data from Senegal's sentinel syndromic surveillance network before and after the start of the COVID-19 pandemic to assess changes in influenza circulation. We found that influenza shows year-round circulation in Senegal and has 2 distinct epidemic peaks: during January-March and during the rainy season in August-October. During 2021-2022, the expected January-March influenza peak completely disappeared, corresponding to periods of active SARS-CoV-2 circulation. We noted an unexpected influenza epidemic peak during May-July 2022. The observed reciprocal circulation of SARS-CoV-2 and influenza suggests that factors such as viral interference might be at play and should be further investigated in tropical settings.

Statistical Analysis of Common Respiratory Viruses Reveals the Binary of Virus-Virus Interaction

Respiratory viruses may interfere with each other and affect the epidemic trend of the virus. However, the understanding of the interactions between respiratory viruses at the population level is still very limited. We here conducted a prospective laboratory-based etiological study by enrolling 14,426 patients suffered from acute respiratory infection (ARI) in Beijing, China during 2005 to 2015. All 18 respiratory viruses were simultaneously tested for each nasal and throat swabs collected from enrolled patients using molecular tests. The virus correlations were quantitatively evaluated, and the respiratory viruses could be divided into two panels according to the positive and negative correlations. One included influenza viruses (IFVs) A, B, and respiratory syncytial virus (RSV), while the other included human parainfluenza viruses (HPIVs) 1/3, 2/4, adenovirus (Adv), human metapneumovirus (hMPV), and enterovirus (including rhinovirus, named picoRNA), α and β human coronaviruses (HCoVs). The viruses were positive-correlated in each panel, while negative-correlated between panels. After adjusting the confounding factors by vector autoregressive model, positive interaction between IFV-A and RSV and negative interaction between IFV-A and picoRNA are still be observed. The asynchronous interference of IFV-A significantly delayed the peak of β human coronaviruses epidemic. The binary property of the respiratory virus interactions provides new insights into the viral epidemic dynamics in human population, facilitating the development of infectious disease control and prevention strategies. IMPORTANCE Systematic quantitative assessment of the interactions between different respiratory viruses is pivotal for the prevention of infectious diseases and the development of vaccine strategies. Our data showed stable interactions among respiratory viruses at human population level, which are season irrelevant. Respiratory viruses could be divided into two panels according to their positive and negative correlations. One included influenza virus and respiratory syncytial virus, while the other included other common respiratory viruses. It showed negative correlations between the two panels. The asynchronous interference between influenza virus and β human coronaviruses significantly delayed the peak of β human coronaviruses epidemic. The binary property of the viruses indicated transient immunity induced by one kind of virus would play role on subsequent infection, which provides important data for the development of epidemic surveillance strategies.

Influence of COVID-19 pandemic on the virus spectrum in children with respiratory infection in Xuzhou, China: a long-term active surveillance study from 2015 to 2021

BACKGROUND

To investigate the impact of the coronavirus disease 2019 (COVID-19) outbreak on the prevalence of respiratory viruses among pediatric patients with acute respiratory infections in Xuzhou from 2015-2021.

METHODS

Severe acute respiratory infection (SARI) cases in hospitalized children were collected from 2015-2021 in Xuzhou, China. Influenza virus(IFV), respiratory syncytial virus (RSV), human parainfluenza virus type 3(hPIV-3), human rhinovirus (hRV), human adenovirus(hAdV), human coronavirus(hCoV) were detected by real-time fluorescence polymerase chain reaction(RT-qPCR), and the results were statistically analyzed by SPSS 23.0 software.

RESULTS

A total of 1663 samples with SARI were collected from 2015-2021, with a male-to-female ratio of 1.67:1 and a total virus detection rate of 38.5% (641/1663). The total detection rate of respiratory viruses decreased from 46.2% (2015-2019) to 36% (2020-2021) under the control measures for COVID-19 (P < 0.01). The three viruses with the highest detection rates changed from hRV, RSV, and hPIV-3 to hRV, RSV, and hCoV. The epidemic trend of hPIV-3 and hAdV was upside down before and after control measures(P < 0.01); however, the epidemic trend of RV and RSV had not changed from 2015 to 2021(P > 0.05). After the control measures, the detection rate of hPIV-3 decreased in all age groups, and the detection rate of hCoV increased in all except the 1 ~ 3 years old group.

CONCLUSIONS

Implementing control measures for COVID-19 outbreak curbed the spread of respiratory viruses among children as a whole. However, the epidemic of RV and RSV was not affected by the COVID-19 control policy.

Severe Acute Respiratory Distress Syndrome Secondary to Concomitant Influenza A and Rhinovirus Infection Complicated by Methicillin-resistant Staphylococcus aureus Pneumonia in an Early Pregnancy Patient With Vaping-induced Lung Injury

Acute respiratory distress syndrome (ARDS) is a life-threatening lung injury characterized by rapid onset of widespread inflammation in the lungs. Multiple risk factors, including pneumonia, non-pulmonary sepsis, aspiration of gastric contents or inhalation injury, have been reported, to cause ARDS. We present a case of a healthy young woman in her first trimester with vaping-induced lung injury who presented with spontaneous pneumothorax and acute respiratory distress syndrome with concomitant influenza A and rhinovirus infection followed by methicillin-resistant Staphylococcus aureus pneumonia.

Contribution of the FilmArray BioFire® Technology in the Diagnosis of Viral Respiratory Infections during the COVID-19 Pandemic at Ibn Sina University Hospital Center in Rabat: Epidemiological Study about 503 Cases

Respiratory viruses are the most involved pathogens in acute respiratory infections. During the COVID-19 pandemic, new elements have been brought to this topic, especially at the diagnostic and therapeutic level. The objective of this work is to describe the epidemiology of respiratory viruses in patients admitted to the Ibn Sina University Hospital of Rabat during a period characterized by the emergence and spread of SARS-CoV-2. We conducted a retrospective study from January 1 to December 31. We included all patients treated for acute respiratory infection and for whom a multiplex respiratory panel PCR was requested. Virus detection was performed using a FilmArray RP 2.1 plus BioFire multiplex respiratory panel. The study population was relatively adults with a mean age of 39 years. The sex ratio M/F was 1.20. The survey revealed a high prevalence of 42.3% of patients hospitalized in the adult intensive care unit whose respiratory distress was the most common reason for hospitalization (58%). The positivity rate was 48.1%. This rate was higher in the pediatric population 83.13% compared to adults 29.7%. Monoinfection was found in 36.4% of cases, and codetection in 11.7% of cases. This survey revealed that a total of 322 viruses were detected, HRV being the most incriminated virus (48.7%), followed by RSV in 13.8% of patients. Considering the five most detected viruses in our study (HRV, RSV, PIV3, ADV, and hMPV), we found that the incidence was significantly higher in the pediatric population. SARS-CoV-2 was detected only in adult's population. In our study, we found that influenza A and B viruses, PIV2, MERS, and all bacteria were not detected by this kit during the study period. Regarding the seasonal distribution, RSV and hMPV showed a significantly high incidence during autumn and summer and SARS-CoV-2 and CoV OC43 showed a high peak during winter. In this study, we found a lack of detection of influenza virus and a shift in the usual winter peak of RSV to the summer, while the detection of ADV and HRV was less affected. This difference in detection could be due on the one hand to the difference in stability between enveloped and nonenveloped viruses and on the other hand to the escape of certain viruses to the different sanitary measures introduced after the declaration of the COVID-19 pandemic. These same measures were effective against enveloped viruses such as RSV and influenza viruses. The emergence of SARS-CoV-2 has modified the epidemiology of other respiratory viruses, either directly by viral interference or indirectly by the preventive measures taken.

2021/22 and 2022/23 Post-Pandemic Bronchiolitis Seasons in Two Major Italian Cities: A Prospective Study

Objectives: Bronchiolitis remains a major cause of morbidity and mortality in children under 24 months. During the first year of the pandemic, non-pharmacological interventions resulted in a significant reduction of bronchiolitis cases. Early in 2021, a rebound of bronchiolitis was reported with a description of out-of-season outbreaks. In this study, we prospectively evaluated the impact of bronchiolitis in two Italian University centers located in different geographical areas, aiming to compare two post-pandemic bronchiolitis seasons (2021/22 and 2022/23) in terms of severity, outcomes, microbiology and temporal distribution. Methods: This was a bicentric prospective observational cohort study. All consecutive children under 24 months of age assessed in the participating institutions during the specified seasons and receiving a clinical diagnosis of bronchiolitis were included. Results: A total of 900 patients were enrolled. Patients in the second season were globally younger and had comorbidities less often. Temporal distribution changed between the two seasons. Of the patients, 56% were tested for RSV; 60% of these was positive. Patients with RSV were globally younger (3.5 months vs. 4.9, p < 0.001), more often had a need for any kind of respiratory and fluid support and more often needed ward or PICU admission. At the end of the ED visit, 430 patients were discharged home, 372 (41.3%) were admitted to an inpatient ward and 46 (5.1%) to a pediatric intensive care unit. Conclusions: The 2022/23 post-COVID bronchiolitis was mostly similar to that of 2021/22, and was in line with pre-pandemic expectations.

How Interactions during Viral-Viral Coinfection Can Shape Infection Kinetics

Respiratory viral infections are a leading global cause of disease with multiple viruses detected in 20-30% of cases, and several viruses simultaneously circulating. Some infections with unique viral copathogens result in reduced pathogenicity, while other viral pairings can worsen disease. The mechanisms driving these dichotomous outcomes are likely variable and have only begun to be examined in the laboratory and clinic. To better understand viral-viral coinfections and predict potential mechanisms that result in distinct disease outcomes, we first systematically fit mathematical models to viral load data from ferrets infected with respiratory syncytial virus (RSV), followed by influenza A virus (IAV) after 3 days. The results suggest that IAV reduced the rate of RSV production, while RSV reduced the rate of IAV infected cell clearance. We then explored the realm of possible dynamics for scenarios that had not been examined experimentally, including a different infection order, coinfection timing, interaction mechanisms, and viral pairings. IAV coinfection with rhinovirus (RV) or SARS-CoV-2 (CoV2) was examined by using human viral load data from single infections together with murine weight-loss data from IAV-RV, RV-IAV, and IAV-CoV2 coinfections to guide the interpretation of the model results. Similar to the results with RSV-IAV coinfection, this analysis shows that the increased disease severity observed during murine IAV-RV or IAV-CoV2 coinfection was likely due to the slower clearance of IAV-infected cells by the other viruses. The improved outcome when IAV followed RV, on the other hand, could be replicated when the rate of RV infected cell clearance was reduced by IAV. Simulating viral-viral coinfections in this way provides new insights about how viral-viral interactions can regulate disease severity during coinfection and yields testable hypotheses ripe for experimental evaluation.

Prolonged Primary Rhinovirus Infection of Human Nasal Epithelial Cells Diminishes the Viral Load of Secondary Influenza H3N2 Infection via the Antiviral State Mediated by RIG-I and Interferon-Stimulated Genes

Our previous study revealed that prolonged human rhinovirus (HRV) infection rapidly induces antiviral interferons (IFNs) and chemokines during the acute stage of infection. It also showed that expression levels of RIG-I and interferon-stimulated genes (ISGs) were sustained in tandem with the persistent expression of HRV RNA and HRV proteins at the late stage of the 14-day infection period. Some studies have explored the protective effects of initial acute HRV infection on secondary influenza A virus (IAV) infection. However, the susceptibility of human nasal epithelial cells (hNECs) to re-infection by the same HRV serotype, and to secondary IAV infection following prolonged primary HRV infection, has not been studied in detail. Therefore, the aim of this study was to investigate the effects and underlying mechanisms of HRV persistence on the susceptibility of hNECs against HRV re-infection and secondary IAV infection. We analyzed the viral replication and innate immune responses of hNECs infected with the same HRV serotype A16 and IAV H3N2 at 14 days after initial HRV-A16 infection. Prolonged primary HRV infection significantly diminished the IAV load of secondary H3N2 infection, but not the HRV load of HRV-A16 re-infection. The reduced IAV load of secondary H3N2 infection may be explained by increased baseline expression levels of RIG-I and ISGs, specifically MX1 and IFITM1, which are induced by prolonged primary HRV infection. As is congruent with this finding, in those cells that received early and multi-dose pre-treatment with Rupintrivir (HRV 3C protease inhibitor) prior to secondary IAV infection, the reduction in IAV load was abolished compared to the group without pre-treatment with Rupintrivir. In conclusion, the antiviral state induced from prolonged primary HRV infection mediated by RIG-I and ISGs (including MX1 and IFITM1) can confer a protective innate immune defense mechanism against secondary influenza infection.

How Interactions During Viral-Viral Coinfection Can Shape Infection Kinetics

Respiratory virus infections are a leading cause of disease worldwide with multiple viruses detected in 20-30% of cases and several viruses simultaneously circulating. Some infections with viral copathogens have been shown to result in reduced pathogenicity while other virus pairings can worsen disease. The mechanisms driving these dichotomous outcomes are likely variable and have only begun to be examined in the laboratory and clinic. To better understand viral-viral coinfections and predict potential mechanisms that result in distinct disease outcomes, we first systematically fit mathematical models to viral load data from ferrets infected with respiratory syncytial virus (RSV) followed by influenza A virus (IAV) after 3 days. The results suggested that IAV reduced the rate of RSV production while RSV reduced the rate of IAV infected cell clearance. We then explored the realm of possible dynamics for scenarios not examined experimentally, including different infection order, coinfection timing, interaction mechanisms, and viral pairings. IAV coinfection with rhinovirus (RV) or SARS-CoV-2 (CoV2) was examined by using human viral load data from single infections together with murine weight loss data from IAV-RV, RV-IAV, and IAV-CoV2 coinfections to guide the interpretation of the model results. Similar to the results with RSV-IAV coinfection, this analysis showed that the increased disease severity observed during murine IAV-RV or IAV-CoV2 coinfection was likely due to slower clearance of IAV infected cells by the other viruses. On the contrary, the improved outcome when IAV followed RV could be replicated when the rate of RV infected cell clearance was reduced by IAV. Simulating viral-viral coinfections in this way provides new insights about how viral-viral interactions can regulate disease severity during coinfection and yields testable hypotheses ripe for experimental evaluation.

Circulation of respiratory viruses during the COVID-19 pandemic in The Gambia

Background: In many countries, non-pharmaceutical interventions to limit severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission resulted in significant reductions in other respiratory viruses. However, similar data from Africa are limited. We explored the extent to which viruses such as influenza and rhinovirus co-circulated with SARS-CoV-2 in The Gambia during the COVID-19 pandemic.  Methods: Between April 2020 and March 2022, respiratory viruses were detected using RT-PCR in nasopharyngeal swabs from 1397 participants with influenza-like illness. An assay to detect SARS-CoV-2 and a viral multiplex RT-PCR assay was used as previously described  to detect influenza A and B, respiratory syncytial virus (RSV) A and B, parainfluenza viruses 1-4, human metapneumovirus (HMPV), adenovirus, seasonal coronaviruses (229E, OC43, NL63) and human rhinovirus. Results: Overall virus positivity was 44.2%, with prevalence higher in children <5 years (80%) compared to children aged 5-17 years (53.1%), adults aged 18-50 (39.5%) and >50 years (39.9%), p<0.0001. After SARS-CoV-2 (18.3%), rhinoviruses (10.5%) and influenza viruses (5.5%) were the most prevalent. SARS-CoV-2 positivity was lower in children <5 (4.3%) and 5-17 years (12.7%) than in adults aged 18-50 (19.3%) and >50 years (24.3%), p<0.0001. In contrast, rhinoviruses were most prevalent in children <5 years (28.7%), followed by children aged 5-17 (15.8%), adults aged 18-50 (8.3%) and >50 years (6.3%), p<0.0001. Four SARS-CoV-2 waves occurred, with 36.1%-52.4% SARS-CoV-2 positivity during peak months. Influenza infections were observed in both 2020 and 2021 during the rainy season as expected (peak positivity 16.4%-23.5%). Peaks of rhinovirus were asynchronous to the months when SARS-CoV-2 and influenza peaked. Conclusion: Our data show that many respiratory viruses continued to circulate during the COVID-19 pandemic in The Gambia, including human rhinoviruses, despite the presence of NPIs during the early stages of the pandemic, and influenza peaks during expected months.

The effects of the COVID-19 pandemic on community respiratory virus activity

The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused substantial global morbidity and deaths, leading governments to turn to non-pharmaceutical interventions to slow down the spread of infection and lessen the burden on health care systems. These policies have evolved over the course of the COVID-19 pandemic, including after the availability of COVID-19 vaccines, with regional and country-level differences in their ongoing use. The COVID-19 pandemic has been associated with changes in respiratory virus infections worldwide, which have differed between virus types. Reductions in respiratory virus infections, including by influenza virus and respiratory syncytial virus, were most notable at the onset of the COVID-19 pandemic and continued in varying degrees through subsequent waves of SARS-CoV-2 infections. The decreases in community infection burden have resulted in reduced hospitalizations and deaths associated with non-SARS-CoV-2 respiratory infections. Respiratory virus evolution relies on the maintaining of a diverse genetic pool, but evidence of genetic bottlenecking brought on by case reduction during the COVID-19 pandemic has resulted in reduced genetic diversity of some respiratory viruses, including influenza virus. By describing the differences in these changes between viral species across different geographies over the course of the COVID-19 pandemic, we may better understand the complex factors involved in community co-circulation of respiratory viruses.

The bronchiolitis epidemic in 2021-2022 during the SARS-CoV-2 pandemic: experience of a third level centre in Northern Italy

BACKGROUND

The aim of this study is to compare the 2021-2022 bronchiolitis season to the four previous years (2017-2018, 2018-2019, 2019-2020, 2020-2021) to see if there was an anticipation of the peak, an overall increase of cases, and an increased need of intensive care.

METHODS

A retrospective single-centre study in the San Gerardo Hospital Fondazione MBBM, Monza, Italy was performed. Emergency Departments (ED) visits of patients aged < 18 years and ≤ 12 months were analyzed: the incidence of bronchiolitis on total assessments, the urgency level at triage and the hospitalization rate were compared. Data of children admitted to the Pediatric Department due to bronchiolitis were analyzed in terms of need of intensive care, respiratory support (type and duration), length of hospital stay, main etiological agent, patient characteristics.

RESULTS

During 2020-2021 (first pandemic period) an important reduction in the ED attendance for bronchiolitis was observed, while in 2021-2022 there was an increase in incidence of bronchiolitis (13% of visits in infants < 1 year) and in the rate of urgent accesses (p = 0.0002), but hospitalization rates did not differ compared to previous years. Furthermore, an anticipated peak in November 2021 was observed. In the 2021-2022 cohort of admitted children to the Pediatric Department, a statistically significative increased need of intensive care unit was detected (Odds Ratio 3.1, 95% CI 1.4-6.8 after adjustment for severity and clinical characteristics). Instead, respiratory support (type and duration) and length of hospital stay did not differ. RSV was the main etiological agent and RSV-bronchiolitis determined a more severe infection (type and duration of breathing support, intensive care need and length of hospital stay).

CONCLUSIONS

During Sars-CoV-2 lockdowns (2020-2021), there was a dramatic decrease of bronchiolitis and others respiratory infections. In the following season, 2021-2022, an overall increase of cases with an anticipated peak was observed and data analysis confirmed that patients in 2021-2022 required more intensive care than children in the four previous seasons.

Circulation of respiratory viruses during the COVID-19 pandemic in The Gambia

Background: In many countries, non-pharmaceutical interventions to limit severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission resulted in significant reductions in other respiratory viruses. However, similar data from Africa are limited. We explored the extent to which viruses such as influenza and rhinovirus co-circulated with SARS-CoV-2 in The Gambia during the COVID-19 pandemic.  Methods: Between April 2020 and March 2022, respiratory viruses were detected using RT-PCR in nasopharyngeal swabs from 1397 participants with influenza-like illness. An assay to detect SARS-CoV-2 and a viral multiplex RT-PCR assay was used as previously described  to detect influenza A and B, respiratory syncytial virus (RSV) A and B, parainfluenza viruses 1-4, human metapneumovirus (HMPV), adenovirus, seasonal coronaviruses (229E, OC43, NL63) and human rhinovirus. Results: Overall virus positivity was 44.2%, with prevalence higher in children <5 years (80%) compared to children aged 5-17 years (53.1%), adults aged 18-50 (39.5%) and >50 years (39.9%), p<0.0001. After SARS-CoV-2 (18.3%), rhinoviruses (10.5%) and influenza viruses (5.5%) were the most prevalent. SARS-CoV-2 positivity was lower in children <5 (4.3%) and 5-17 years (12.7%) than in adults aged 18-50 (19.3%) and >50 years (24.3%), p<0.0001. In contrast, rhinoviruses were most prevalent in children <5 years (28.7%), followed by children aged 5-17 (15.8%), adults aged 18-50 (8.3%) and >50 years (6.3%), p<0.0001. Four SARS-CoV-2 waves occurred, with 36.1%-52.4% SARS-CoV-2 positivity during peak months. Influenza infections were observed in both 2020 and 2021 during the rainy season as expected (peak positivity 16.4%-23.5%). Peaks of rhinovirus were asynchronous to the months when SARS-CoV-2 and influenza peaked. Conclusion: Our data show that many respiratory viruses continued to circulate during the COVID-19 pandemic in The Gambia, including human rhinoviruses, despite the presence of NPIs during the early stages of the pandemic, and influenza peaks during expected months.

Counterintuitive effect of antiviral therapy on influenza A-SARS-CoV-2 coinfection due to viral interference

The resurgence of influenza and continued circulation of SARS-CoV-2 raise the question of how these viruses interact in a co-exposed host. Here we studied virus-virus and host-virus interactions during influenza A virus (IAV) -SARS-CoV-2 coinfection using differentiated cultures of the human airway epithelium. Coexposure to IAV enhanced the tissue antiviral response during SARS-CoV-2 infection and suppressed SARS-CoV-2 replication. Oseltamivir, an antiviral targeting influenza, reduced IAV replication during coinfection but also reduced the antiviral response and paradoxically restored SARS-CoV-2 replication. These results highlight the importance of diagnosing coinfections and compel further study of how coinfections impact the outcome of antiviral therapy.

Influenza's Plummeting During the COVID-19 Pandemic: The Roles of Mask-Wearing, Mobility Change, and SARS-CoV-2 Interference

Seasonal influenza activity typically peaks in the winter months but plummeted globally during the current coronavirus disease 2019 (COVID-19) pandemic. Unraveling lessons from influenza's unprecedented low profile is critical in informing preparedness for incoming influenza seasons. Here, we explored a country-specific inference model to estimate the effects of mask-wearing, mobility changes (international and domestic), and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) interference in China, England, and the United States. We found that a one-week increase in mask-wearing intervention had a percent reduction of 11.3%-35.2% in influenza activity in these areas. The one-week mobility mitigation had smaller effects for the international (1.7%-6.5%) and the domestic community (1.6%-2.8%). In 2020-2021, the mask-wearing intervention alone could decline percent positivity by 13.3-19.8. The mobility change alone could reduce percent positivity by 5.2-14.0, of which 79.8%-98.2% were attributed to the deflected international travel. Only in 2019-2020, SARS-CoV-2 interference had statistically significant effects. There was a reduction in percent positivity of 7.6 (2.4-14.4) and 10.2 (7.2-13.6) in northern China and England, respectively. Our results have implications for understanding how influenza evolves under non-pharmaceutical interventions and other respiratory diseases and will inform health policy and the design of tailored public health measures.

Influenza's Plummeting During the COVID-19 Pandemic: The Roles of Mask-Wearing, Mobility Change, and SARS-CoV-2 Interference

Seasonal influenza activity typically peaks in the winter months but plummeted globally during the current coronavirus disease 2019 (COVID-19) pandemic. Unraveling lessons from influenza's unprecedented low profile is critical in informing preparedness for incoming influenza seasons. Here, we explored a country-specific inference model to estimate the effects of mask-wearing, mobility changes (international and domestic), and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) interference in China, England, and the United States. We found that a one-week increase in mask-wearing intervention had a percent reduction of 11.3%-35.2% in influenza activity in these areas. The one-week mobility mitigation had smaller effects for the international (1.7%-6.5%) and the domestic community (1.6%-2.8%). In 2020-2021, the mask-wearing intervention alone could decline percent positivity by 13.3-19.8. The mobility change alone could reduce percent positivity by 5.2-14.0, of which 79.8%-98.2% were attributed to the deflected international travel. Only in 2019-2020, SARS-CoV-2 interference had statistically significant effects. There was a reduction in percent positivity of 7.6 (2.4-14.4) and 10.2 (7.2-13.6) in northern China and England, respectively. Our results have implications for understanding how influenza evolves under non-pharmaceutical interventions and other respiratory diseases and will inform health policy and the design of tailored public health measures.

Adapting an integrated acute respiratory infections sentinel surveillance to the COVID-19 pandemic requirements, Egypt, 2020-2022

Objectives

In Egypt, an integrated surveillance for acute respiratory infections (ARIs) was established in 2016 to identify the causes of ARIs. The surveillance system includes 19 governmental hospitals. In response to the coronavirus disease 2019 (COVID-19) pandemic, the World Health Organisation (WHO) requested surveillance adaptation to address the emerging challenges. This study aims to describe the experience in Egypt of adapting ARI surveillance to the COVID-19 pandemic.

Methods

WHO case definitions were used to identify patients with ARIs. Nasopharyngeal/oropharyngeal swabs were collected for SARS-CoV-2 and influenza testing. Demographic and clinical information were obtained by interviewing patients at the hospitals. During the COVID-19 pandemic, the first two outpatients daily and every fifth admitted patient were enrolled in the study. To determine the status of ARIs in Egypt during the pandemic, patient demographic, clinical and laboratory data from 2020 to 2022 were obtained and descriptive analyses were performed.

Results

Overall, 18,160 patients were enrolled in the study, including 7923 (43.6%) seen at outpatient clinics and 10,237 (56.4%) inpatients. Of the study participants, 6453 (35.5%) tested positive for ARIs, including 5620 (87.1%) for SARS-CoV-2, 781 (12.1%) for influenza and 52 (0.8%) for SARS-CoV-2/influenza coinfection. SARS-CoV-2 was the cause for 95.3% of admitted patients and 65.4% of outpatients. Influenza subtypes included A/H3 (55.7%), Influenza-B (29.1%) and H1/pdm09 (14.2%). Compared with influenza, SARS-CoV-2 tended to infect the elderly, in warm weather and in urban governorates, and resulted in more hospitalisations, longer hospital stays and higher case fatalities (16.3% vs 6.6%, p < 0.001).

Conclusions

ARI surveillance in Egypt was successfully adapted to the COVID-19 pandemic and effectively described the clinical characteristics and severity of circulating viruses. Surveillance reported the re-emergence of influenza with a severe course and high fatality. Surveillance is essential for monitoring the activity of respiratory viruses with the aim of guiding clinical management, including preventative and control measures.

SARS-CoV-2 Related Viral Respiratory Co-Infections: A Narrative Review

Background

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is the new coronavirus originating from Wuhan, China, responsible for the illness known as coronavirus disease 2019 (COVID-19). Early experience and the recent literature have shown that co-infection of SARS-CoV-2 with another respiratory virus might occur. Similar symptoms of acute respiratory infections (ARIs) and COVID-19 represent a challenge for diagnostic and therapeutic efficacy and may modify COVID-19 outcomes.

Materials and Methods

We reviewed the literature on the epidemic pattern and major learning points on important aspects of SARS-CoV-2-related viral respiratory co-infections during the COVID-19 pandemic. Databases such as PubMed, Scopus, Science Direct, and Google Scholar were used to conduct a comprehensive search.

Results

The circulation of respiratory viruses changed as the COVID-19 epidemic continues. Phenomena like viral interference, resource competition, and differences in virus-host range might explain why simultaneous viral respiratory infections have seemed to vanish with the spread of SARS-CoV-2.

Conclusion

Key research to be conducted during this pandemic should include the simultaneous screening of other respiratory pathogens with many available commercial platforms for transmission containment and appropriate clinical management.