MONITORING OF RESPIRATORY VIRUS COINFECTION IN SOUTHERN BRAZIL DURING COVID-19 PANDEMIC (preprint)

Since December 2019, the COVID-19 pandemic caused by SARS-CoV-2 has reached approximately 769 million people, leading to more than 7 million deaths worldwide. Faced with the possible presence of other respiratory pathogens that could co-infect and modify the clinical response of patients detected for SARS-CoV-2, some researchers have explored this line of investigation. The relationship between these co-infections remains unclear, leading to a need to deepen our knowledge about interactions among pathogens, and between pathogens and the host. Thus, the present study employed RT-qPCR to assess the presence of Human Adenovirus (HAdV), Influenza A (Flu A), Influenza B (Flu B), Human Metapneumovirus (HMPV), Respiratory Syncytial Virus (RSV), Human Rhinovirus (HRV), and Parainfluenza Virus (PIV). A total of 187 nasopharyngeal samples from adult patients exhibiting respiratory symptoms were collected between February 2021 and November 2022 at the University Hospital Polydoro Ernani de Sao Thiago in Florianopolis, SC, Brazil. Our findings revealed that 25.16% of samples tested positive for non-SARS-CoV-2 respiratory viruses (29.8% - HRV, 5.3% - PIV, 4.3%-RSV, and 1.1% - HMPV). From the 74.84% of SARS-CoV-2 positive patients, the presence of co-infection was observed in 9,7% of patients, with 7.5% being HRV, 1.1% HAdV and 1.1% Flu A. Since co-infections can potentially alter patient prognoses and impact local epidemiological dynamics, this study highlights the significance of ongoing monitoring and epidemiological assessment through genomic surveillance of other clinically relevant respiratory pathogens.

Validation of an unbiased metagenomic detection assay for RNA viruses in viral transport media and plasma (preprint)

Unbiased long read sequencing holds enormous potential for the detection of pathogen sequences in clinical samples. However, the untargeted nature of these methods precludes conventional PCR approaches, and the metagenomic content of each sample increases the challenge of bioinformatic analysis. Here, we evaluate a previously described novel workflow for unbiased RNA virus sequence identification in a series of contrived and real-world samples. The novel multiplex library preparation workflow was developed for the Oxford Nanopore Technologies (ONT) MinION sequencer using reverse transcription, whole genome amplification, and ONT's Ligation Sequencing Kit with Native Barcode Expansion. The workflow includes spiked MS2 Phage as an internal positive control and generates an 8-plex library with 6 samples, a negative control and a gfp transcript positive control. Targeted and untargeted data analysis was performed using the EPI2ME Labs framework and open access tools that are readily accessible to most clinical laboratories. Contrived samples composed of common respiratory pathogens (Influenza A, Respiratory Syncytial Virus and Human Coronavirus 229E) in viral transport media (VTM) and bloodborne pathogens (Zika Virus, Hepatitis A Virus, Yellow Fever Virus and Chikungunya Virus) in human plasma were used to establish the limits of detection for this assay. We also evaluated the diagnostic accuracy of the assay using remnant clinical samples and found that it showed 100% specificity and 62.9% clinical sensitivity. More studies are needed to further evaluate pathogen detection and better position thresholds for detection and non-detection in various clinical sample metagenomic mixtures.

Systematic computer-aided disulfide design as a general strategy to stabilize prefusion class I fusion proteins (preprint)

Numerous enveloped viruses, such as coronaviruses, influenza, and respiratory syncytial virus (RSV), utilize class I fusion proteins for cell entry. During this process, the proteins transition from a prefusion to a postfusion state, undergoing substantial and irreversible conformational changes. The prefusion conformation has repeatedly shown significant potential in vaccine development. However, the instability of this state poses challenges for its practical application in vaccines. While non-native disulfides have been effective in maintaining the prefusion structure, identifying stabilizing disulfide bonds remains an intricated task. Here, we present a general computational approach to systematically identify prefusion-stabilizing disulfides. Our method assesses the geometric constraints of disulfide bonds and introduces a ranking system to estimate their potential in stabilizing the prefusion conformation. We found, for the RSV F protein, that disulfides restricting the initial stages of the conformational switch can offer higher stability to the prefusion state than those preventing unfolding at a later stage. The implementation of our algorithm on the RSV F protein led to the discovery of prefusion-stabilizing disulfides, providing evidence that supports our hypothesis. Furthermore, the evaluation of our top design as a vaccine candidate in a cotton rat model demonstrated robust protection against RSV infection, highlighting the potential of our approach for vaccine development.

The unified proposal for classification of human respiratory syncytial virus below the subgroup level (preprint)

A globally implemented unified classification for human respiratory syncytial virus (HRSV) below the subgroup level remains elusive. Here, we formulate the global consensus of HRSV classification based on the challenges and limitations of our previous proposals and the future of genomic surveillance. From a high-quality dataset of 1,480 HRSV-A and 1,385 HRSV-B genomes submitted to NCBI and GISAID up to March 2023, we categorized HRSV-A/B sequences into lineages based on phylogenetic clades and amino acid markers. We defined 24 lineages within HRSV-A and 16 within HRSV-B, providing guidelines for prospective lineages definition. Our classification demonstrated robustness in its applicability to both complete and partial genomes. In addition, it allowed the observation of notable lineage replacements and the identification of lineages exclusively detected since the COVID-19 pandemic. We envision that this unified HRSV classification proposal will strengthen and facilitate HRSV molecular epidemiology on a global scale.

Increased pediatric RSV case counts following the emergence of SARS-CoV-2 are attributable to increased testing (preprint)

Background: The incidence of respiratory syncytial virus (RSV) dropped markedly early in the COVID-19 pandemic, followed by a resurgence with heightened case counts. The immunity debt hypothesis proposes that the RSV-naive pediatric population increased during the period of low transmission, resulting in a subsequent increased risk of infection. However, the evidence supporting this hypothesis is limited, and no studies have comprehensively evaluated the role of changing respiratory viral testing practices in the perceived surge. Methods: We conducted a multicenter, retrospective analysis of 342,530 RSV encounters and 980,546 RSV diagnostic tests occurring at 32 United States pediatric hospitals between 2013 and 2023. We used interrupted time series analysis to estimate pandemic-associated changes in RSV patient and testing volume, and to quantify changes in the proportions of patients admitted from the emergency department (ED), admitted to the intensive care unit (ICU), and receiving mechanical ventilation. We quantified the fraction of the observed shifts in case counts and in the age of diagnosed patients attributable to changes in RSV testing practices. Finally, we analyzed 524,404 influenza virus encounters and 1,768,526 influenza diagnostic tests to address the specificity of the findings to RSV. Findings: RSV patient volume increased 2.4-fold (95% CI: 1.7, 3.5) in 2021-2023 relative to the pre-pandemic phase, and was accompanied by an 18.9-fold increase (95% CI: 15.0, 23.9) in RSV test volume. Over two-thirds of the apparent shifts in patient volume and in patient age were attributable to increased testing, which was concentrated among older pediatric patients. The proportions of patients with RSV requiring hospitalization, intensive care, or mechanical ventilation declined significantly across all patient age groups. These declines were not observed for patients with influenza virus. Interpretation: A surge in RSV testing, rather than in viral circulation, likely underlies the increased case counts observed in 2021-2023. We identify expected consequences of increased testing, including the diagnosis of less severe cases and a shift in the patient age distribution. These findings warrant a critical assessment of the immunity debt hypothesis, while highlighting the importance of considering the testing denominator when surveillance strategies are dynamic.

Causal relationship between COVID-19 and the risk of asthma: A Mendelian Randomisation study (preprint)

Background Existing research has focused on new-onset asthma and viral infections, particularly respiratory syncytial virus (RSV). However, studies on whether COVID-19 can induce asthma are limited.Methods We performed bidirectional two-sample Mendelian Randomization (MR) to assess the potential causal relationship between COVID-19 and asthma using genome-wide association study (GWAS) summary data obtained from the COVID-19 Host Genetic Initiative GWAS Meta-analysis Round 5 (release date: 18 January 2021). Several methods (random-effects inverse variance weighted, weighted median, MR-Egger regression, and MR-PRESSO) were used to ensure the robustness of the causal effects. Heterogeneity was measured using Cochran's Q value. Horizontal pleiotropy was evaluated using MR-Egger regression and leave-one-out analyses.Results We observed a significant causal association between COVID-19 hospitalisation and asthma (odds ratio (OR) = 1.042, 95% Confidence Interval (CI) = 1.004–1.081, p = 0.031), indicating a significantly increased risk of COVID-19 hospitalisation associated with asthma. However, no statistically significant causal relationships were observed for COVID-19 susceptibility (OR = 1.023, 95% CI = 0.931–1.124, p = 0.637), COVID-19 severity (OR = 1.006, 95% CI = 0.978–1.035, p = 0.669), and asthma.Conclusions COVID-19 can trigger the onset of asthma. Individuals experiencing prolonged coughing, chest tightness, or difficulty in breathing long after recovery from COVID-19 should remain vigilant about the possibility of developing asthma.

Respiratory illness virus infections with special emphasis on Covid-19 (preprint)

Viruses that emerge pose challenges for treatment options as their uniqueness would not know completely. In spite of large diversity, viruses share common characteristics for infection. There are at least 12 different respiratory borne viruses that belong to different virus taxonomic families. Many of these viruses multiply and cause damage to the upper and lower respiratory tracts. The description about these viruses in comparison to each other with reference to their epidemiology, molecular characteristics, disease manifestations, diagnosis and treatment is lacking. Such information helps to diagnose, differentiate and for formulating the control measures at faster pace. The leading cause of acute illness worldwide are the acute respiratory infections (ARIs) and are being responsible for nearly 4 million deaths every year which are mostly in young children and infants. Among the above ARIs, influenza, respiratory syncytial virus (RSV), parainfluenza virus type 3 (PIV-3), Streptococcus pneumoniae, Haemophilus influenzae and corona viruses are the main infectious agents. WHO recognized respiratory syncytial virus, parainfluenza viruses, coronavirus, rhinovirus, and human metapneumovirus [non-influenza RNA respiratory viruses (NIRVs)], as considerable global health burden. Lower respiratory tract infections are the fourth most common cause of death globally, after the non-infectious chronic conditions. This review aimed at presenting the characteristics of different viruses causing the respiratory infections highlighting the uniqueness of Covid-19. We expect that this review would help in understanding the similarities and differences among the closely related viruses causing respiratory infections and hence to formulate the specific preventive or control measures.

Epidemiological characteristics of eleven common respiratory viral infections in children (preprint)

Background Lower respiratory tract infections (LRTIs) are one of the leading causes of hospital admissions among children. In this study, we aimed to describe the epidemiological characteristics of viral pathogens associated with LRTIs in hospitalized children in Yan'an; this has yet to be reported in the literature and may guide public health interventions and resource allocation in this region. Methods Between June 2021 and May 2023, we conducted a retrospective analysis of the results of viral detection using oral pharyngeal swabs from 4565 children with LRTIs in the Inpatient Department of Yan'an University Affiliated Hospital. Eleven respiratory viruses, including influenza A virus (Flu A), influenza A H1N1 virus (H1N1), seasonal influenza A H3N2 virus (H3N2), influenza B virus (Flu B), parainfluenza virus (HPIV), adenovirus (HADV), bocavirus (HBoV), rhinovirus (HRV), metapneumovirus (HNPV), coronavirus (HCoV), and respiratory syncytial virus (HRSV), were confirmed by applying a multiplex real-time polymerase chain reaction (PCR) kit for respiratory viruses. We evaluated the epidemiological features of infections caused by respiratory pathogens, including aging and the seasonal variations of different pathogens, and explored the high-risk factors associated with virus-caused pneumonia. Results At least one virus was detected in all 4565 cases; the positivity rate was 27.95%. We also detected a total of 1,276 cases with mixed infections (with two or more viruses). Of the positive cases, 59.3% were male and 40.7% were female (x2 = 0.41, P = 0.68). The highest positivity rates for respiratory pathogens were observed for HRSV, HRV, and HADV, at 5.98%, 5.67%, and 4.38%, respectively. We also observed variations in the number and positivity rates of respiratory pathogen infections by season and age. HPIV (x2 = 12.05，P < 0.05) and HADV (x2 = 11.73，P < 0.05) were more common in children under 3 years-of-age. Conclusions In conclusion, our analysis revealed that respiratory pathogen infections varied by gender, season, and age in the enrolled population of children.

Single Infection and Dual Co-infection With Respiratory Viruses Affect Cytokine and Chemokine Expression in Acute Respiratory Illness Negative for SARS-CoV-2 (preprint)

During the COVID-19 pandemic, the circulation of non–SARS-CoV-2 respiratory viruses changed throughout the world. This study aimed to analyze the effect of respiratory syncytial virus (RSV), metapneumovirus (MPV), rhinovirus (RV), and parainfluenza (PIV)-3 single infection, dual co-infection, and viral load on cytokine and chemokine expression in 300 Mexican patients with ARIs negative for SARS-CoV-2. Molecular detection and viral load were performed by RT-qPCR. Cytokine and chemokine expression was determined in samples positive for single RSV, MPV, RV, or PIV-3 infection, and in the most frequent dual co-infections, by a cytokine panel using a magnetic-bead-based multiplex immunoassay. Of the patients positive for viral infection, 91.7% had a single infection and 8.3% had dual co-infections. In this study, RSV was the respiratory virus with the highest prevalence, and the most common dual co-infection was RV+RSV. On the other hand, RV infections had the highest viral loads compared to the other viruses detected. FGF basic, MIP-1α IL-8, IP-10, MCP-1, IFN-γ, and RANTES showed differential expression between single infections and dual co-infections compared to healthy patients. We report, for the first time, the circulation of non-SARS-CoV-2 viruses in the south of Mexico and the cytokine and chemokine profiles associated with these viruses.

Altered RSV Epidemiology and Genetic Diversity Following the COVID-19 Pandemic (preprint)

Respiratory Syncytial Virus (RSV) is a leading cause of acute respiratory tract infection, with greatest impact on infants, immunocompromised individuals, and older adults. RSV prevalence decreased substantially following the implementation of non-pharmaceutical interventions to mitigate the COVID-19 pandemic but later rebounded with initially abnormal seasonality. The biological and epidemiological factors underlying this altered behavior remain poorly defined. In this retrospective cohort study, we examined RSV epidemiology, clinical severity, and genetic diversity in the years surrounding the COVID-19 pandemic. We found that changes in RSV diagnostic platforms drove increased detections in outpatient settings after 2020 and that hospitalized adults with RSV-A were at higher risk of needing intensive care than those with RSV-B. While the population structure of RSV-A remained unchanged, the population structure of RSV-B shifted in geographically distinct clusters. Mutations in the antigenic regions of the fusion protein suggest convergent evolution with potential implications for vaccine and therapeutic development.

RSV-bacterial co-infection is associated with increased illness severity in hospitalized children - Results from a prospective sentinel surveillance study (preprint)

Purpose: During the autumn/winter respiratory syncytial virus (RSV) epidemics, bacterial co-infection is common and affects the severity of the disease. We aimed to understand the relationship between RSV-bacterial co-infections and clinical severity since the change of RSV seasonality after the COVID-19 pandemic. Methods: We conducted a prospective, sentinel surveillance study at 20 sites in Portugal in children under two years old hospitalized with RSV, between April 2021 and January 2023. The effect of co-infection with potentially pathogenic bacteria (PPB) on the length of hospitalization and disease severity (defined by the need for ventilation or admission to an intensive care unit-ICU) was investigated using multivariate linear and log-binomial regression models. Age group (<6 months/≥6 months) and prematurity (yes/no) were included in models as potential confounders. Results: We report two RSV off-season epidemics: June 2021-February 2022 and May-October 2022. Among 678 RSV hospitalizations, 67.4 % occurred in children under 6 months old and 15.3 % in pre-term; 20.4 % tested positive for PPB; median length of hospitalization was five days (IQR: 3-7days); 5.8 % had at least one underlying condition. The most common bacteria were Haemophilus influenzae and Streptococcus pneumoniae. Children co-infected with PPB had a higher rate of ICU admission (29.7 % versus 3.5 %, p<0.001), resulting in more prolonged hospitalizations (median of 7 days versus 5 days, p<0.001) and a 13-fold risk of having severe disease (RR: 13.2, 95 CI: 7.3-23.9). Conclusion: RSV-bacterial co-infection was associated with increased length of hospitalization and severe illness during off-season epidemics. This risk is probably overestimated, as laboratory testing for bacterial infections is usually higher in severely ill-appearing children. Measures to prevent outgrowth of pathogenic bacteria within the respiratory tract should be discussed.

Adapting COVID-19 research infrastructure to capture Influenza and Respiratory Syncytial Virus alongside SARS-CoV-2 in UK healthcare workers Winter 2022/23 and beyond: protocol for a pragmatic sub-study (preprint)

IntroductionDuring the COVID-19 pandemic, extensive research was conducted on SARS-CoV-2, however important questions about other respiratory pathogens remain unanswered. A severe influenza season in 2022-2023 with simultaneous circulation of SARS-CoV2 and Respiratory Syncytial Virus (RSV) is anticipated. This sub-study aims to determine the incidence and impact of these respiratory viruses on healthcare workers (HCW), the symptoms they experienced, the effectiveness of both COVID-19 and influenza vaccination and the burden of these infections on the National Health Service (NHS) workforce. Methods and analysisThis is a longitudinal prospective cohort sub-study, utilising the population and infrastructure of SIREN, which focuses on hospital staff in the UK. Participants undergo fortnightly Nucleic Acid Amplification Testing (NAAT) on a multiplex assay including SARS-CoV-2, Influenza A&B and RSV, regardless of symptoms. Questionnaires are completed every two weeks, capturing symptoms, sick days, exposures, and vaccination records. Serum samples are collected monthly or quarterly from participants associated with a SIREN site. This sub-study commenced on 28/11/22 to align with the predicted influenza season and participants influenza vaccine status. The SIREN Participant Involvement Panel (PIP) shaped the aims and methods for the study, highlighting its acceptability. UK Devolved Administrations were supported to develop local protocols. Analysis plans include incidence of asymptomatic and symptomatic infection, comparisons of vaccination coverage; assessment of sick day burden, and effectiveness of seasonal influenza against infection and time off work. Data are also integrated into UKHSA nosocomial modelling. Ethics and disseminationThe protocol was approved by the Berkshire Research Ethics Committee (IRAS ID 284460, REC Reference 20SC0230) on 14/11/2022. Participants were informed in advance. As the frequency and method of sampling remained the same, implied consent processes were approved by the committee. Participants returning to the study give informed consent. Regular reports to advisory groups and peer-reviewed publications are planned to disseminate findings and inform decision making. Trial registration number: ISRCTN11041050. Strengths and limitations of this study- The positioning of this sub-study, led by public health agencies in collaboration with a network of NHS sites, facilitates horizon scanning enabling rapid adaptation of the study protocol and deployment to conduct relevant scientific research in a cohort of healthcare workers - To achieve target recruitment, deployment of a new postal pathway is underway, allowing for more direct communication between the central research team and participants - The multi-disciplinary partnerships including a network of academic centres established and embedded by SIREN can now be leveraged and extended to explore Flu and RSV - Decentralised study delivery, with testing at a network of NHS sites has both strengths and limitations. This includes enabling more in-depth relationships and communications between participants and their local research teams, however, introduce additional communication, governance, and data sharing requirements. - Some demographics are over-represented such as female staff, nurses and doctors, and some are under-represented such as staff from ethnic minorities, porters and estates. This is partly the consequence of a rapid recruitment drive at the beginning of the COVID-19 pandemic.

Loss of severe respiratory syncytial virus infection-associated antibody function during the peak of the COVID-19 pandemic mitigation measures (preprint)

Studies have linked reduced respiratory syncytial virus-specific Fc-mediated phagocytic function and complement deposition to more severe infection. This study shows a loss of these functions during the first year of COVID-19 pandemic. These findings corroborate other data supporting a general waning of RSV antibody functions in absence of viral circulation.

Evaluation of Incidence of Respiratory Syncytial Virus, SARS-CoV-2, Influenza A/B, and Adenovirus Cases via Rapid Tests in Community during the Winter 2023 Season. A Cross Sectional Study (preprint)

Respiratory infections constitute a major reason for infants and children seeking medical advice and visiting health facilities, thus remaining a significant public threat with high morbidity and mortality. The predominant viruses causing viral respiratory infections are influenza A and B viruses (Flu-A, Flu-B), Respiratory Syncytial Virus (RSV), Adenovirus and Coronaviruses. We aimed to record the incidence of RSV, SARS-CoV-2, Influenza A/B and Adenovirus cases with rapid antigen tests and validate the results with RT-PCR assay of upper respiratory specimens with a wide range of viral loads and (co)-infection patterns in children. Clinical samples were collected from early symptomatic children (presenting with fever and/or cough and/or headache within 5–7 days). The surveillance program was conducted in five private pediatrician dispensaries and one Pediatric care unit, from 10 January 2023 to 30 March 2023 in central Greece. The total sample of specimens collected was 784 young children and infants, of which 383 (48.8%) ware female and 401 were male (51.2%). The mean age of participants was 7.3 + 5.5 years. The sensitivity of FLU A & B test was 91.15% (95% CI: 84.33% -95.67%), and the specificity was 98.96% (95% CI: 97.86% - 99.58%). The sensitivity and specificity of the adenovirus and RSV test was {92.45% (95% CI: 81.79% - 97.91%), 99.32% (95% CI: 98.41% -99.78%)} and {92.59% (95% CI: 75.71% -99.09%), 99.47% (95% CI: 98.65% - 99.86%)} respectively. Lastly, the sensitivity of the SARS-CoV-2 test was 100.00% (95% CI: 79.41%-100.00%) and the specificity was 99.74% (95% CI: 99.06% - 99.97%). We recorded proportion of incidence for the Influenza-A and B, (14.3%), - (3.44%) correspondingly, followed by the adenovirus with a proportion (6.9%) and the RSV with (3.7%) incidence proportion and finally, the SARS-CoV-2 (2.3%). The combination of a new multiple rapid test with multiple antigens, will be probably a useful tool with financial impact for health systems targeting the early detection and right treatment of respiratory infections in the emergency departments in primary health care facilities.

Genomic and Immunological Characterisation Shows Increased Respiratory Syncytial Virus Cases Not Due to Waning Antibody Mediated Immunity (preprint)

Background: Seasonal epidemics of respiratory syncytial virus (RSV) in the Southern Hemisphere typically occur in late autumn and winter. However, implementation of public health measures for the Coronavirus Disease (COVID-19) pandemic resulted in an almost complete absence of RSV detections during the 2020 season. This was followed by unusual summer outbreaks worldwide throughout 2021, and in 2022 the seasonal RSV epidemic in Sydney (Australia) saw an unprecedented number of RSV detections.Methods: Whole genome sequences of RSV were generated from 264 RSV-infected infants and linked to case-matched clinical data from the 2022 Southern Hemisphere RSV season. We then performed immunological analysis of baseline RSV-specific humoral immunity in women of childbearing age before and throughout the COVID-19 pandemic.Findings: Clinical analysis found a high burden of disease across patients of all health backgrounds. Over half of RSV-related healthcare visits by infants resulted in hospitalization, and one quarter required high-flow respiratory support or a higher level of care. Viral phylogenetic analyses found that 2022 Sydney RSV sequences were closely related to viruses that were circulating globally since 2017, including those detected in recent USA outbreaks. Non-synonymous mutations within the palivizumab and nirsevimab binding sites were detected at low frequencies. There was no difference in baseline RSV-neutralizing antibody titres between 2020 and 2022.Interpretation: Collectively, these findings suggest an interplay of factors unrelated to changes in local host immunity to RSV contributed to the surge of RSV cases and hospitalisations in 2022. That is, we did not demonstrate the emergence of a novel RSV genotype or hypothesized immune debt associated with the increase in cases. Continued genomic and immunological surveillance is required to further understand factors driving outbreaks of RSV globally, and to inform guidelines for the rollout and ongoing use of recently developed immunotherapeutics and vaccines.Funding: Laboratory consumable costs were supported by the Thrasher Research Fund (Early Career Award, GW). This study was partly supported by MRFF (#2023323, PW, AB) and NHMRC (#2006755, AK, WR) grants.Declaration of Interest: The authors have no conflicts of interest to declare.Ethical Approval: This study was approved by the Sydney Children’s Hospitals Network Human Research Ethics Committee (2020/ETH00718).

Changes in Spectrum of Respiratory Pathogen Infections and Disease Severity Among Children in Hohhot: Impact of COVID-19 Prevention Measures (preprint)

Background Acute respiratory infections (ARIs) are caused by various pathogens, and the outbreak of the novel coronavirus has led to changes in the patterns of respiratory pathogen infections. Through long-term study of respiratory tract infection data in children from Hohhot, significant differences in the spectrum of respiratory pathogen infections, disease severity, and seasonal patterns have been discovered between 2022 and 2023.Methods Throat swabs were collected from 605 children with ARIs at the First Hospital of Hohhot, and pathogen detection was performed using microarray technology. Blood biomarkers, symptoms, and clinical diagnoses were evaluated.Results The study found that 56.03% of the patients were male, with an average age of 3.45 years. Pathogen dynamics revealed that SARS-CoV-2 was the most prevalent infection, accounting for 262 cases. It persisted from October 2022 to January 2023 and then disappeared. Influenza A virus (IAV) cases peaked in March 2023. Respiratory syncytial virus (RSV), Influenza B virus (IBV), Parainfluenza virus (PIV), Mycoplasma pneumoniae (M. pneumoniae), Escherichia coli (E. coli), Staphylococcus aureus (S. aureus), and Group A streptococcus (GAS) were not detected after December 2022. The proportion of mixed infections was 41.94% among SARS-CoV-2 patients, while other pathogens had mixed infection rates exceeding 57.14%. Before December 2022, the mean value of white blood cell (WBC) count for Streptococcus pneumoniae (S. pneumoniae), Haemophilus influenzae (H. influenzae), Epstein-Barr virus (EBV), and Cytomegalovirus (CMV) was 8.83*10^9/L, C-reactive protein (CRP) was 18.36 mg/L, and procalcitonin (PCT) was 1.11 ng /ml. After December 2022, these values decreased to 5.5*10^9/L, 6.33 mg/L, and 0.24 ng /ml, respectively. Similarly, the proportion of patients with cough, difficulty breathing, and running nose, as well as the diagnosis of lower respiratory tract infections, decreased in December 2022. However, the situation was different for SARS-CoV-2 infections.Conclusions Strict SARS-CoV-2 policies reduced the infection risk for S. pneumoniae, H. influenzae, EBV, and other pathogens before November 2022. However, patient symptoms worsened compared to after November 2022, possibly due to an excessive focus on SARS-CoV-2, neglecting other diseases, and reduced population immunity to respiratory infections.

Immunization technologies: Time to consider new preventative solutions for respiratory syncytial virus infections.

New technologies for the prevention of infectious diseases are emerging to address unmet medical needs, in particular, the use of long-acting monoclonal antibodies (mAb) to prevent Respiratory Syncytial Virus (RSV) lower respiratory tract disease in infants during their first RSV season. The lack of precedent for mAbs for broad population protection creates challenges in the assessment of upcoming prophylactic long-acting mAbs for RSV, with associated consequences in legislative and registration categorization, as well as in recommendation, funding, and implementation pathways. We suggest that the legislative and regulatory categorization of preventative solutions should be decided by the effect of the product in terms of its impact on the population and health-care systems rather than by the technology used or its mechanism of action. Immunization can be passive and active, both having the same objective of prevention of infectious diseases. Long-acting prophylactic mAbs work as passive immunization, as such, their recommendations for use should fall under the remit of National Immunization Technical Advisory Groups or other relevant recommending bodies for inclusion into National Immunization Programs. Current regulations, policy, and legislative frameworks need to evolve to embrace such innovative preventative technologies and acknowledge them as one of key immunization and public health tools.

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

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

Surveillance towards preventing paediatric incidence of respiratory syncytial virus attributable respiratory tract infection in primary and secondary/tertiary healthcare settings in Merseyside, Cheshire and Bristol, UK.

INTRODUCTION: Respiratory syncytial virus (RSV) is a common respiratory virus, particularly affecting children, and can cause respiratory infections such as croup and bronchiolitis. The latter is a leading cause of paediatric hospitalisation within the UK. Children <3 years of age and/or with underlying health conditions are more vulnerable to severe RSV infection.There are currently limited data on the incidence of laboratory-confirmed RSV, particularly within primary care settings and outside the typical 'RSV season', which in the Northern hemisphere tends to coincide with winter months. There is also a lack of data on the health economic impact of RSV infection on families and healthcare systems.This observational surveillance study aims to collect data on the incidence of laboratory-confirmed RSV-attributable respiratory tract infection (RTI) in children aged <3 years presenting to primary, secondary or tertiary care; it also aims to estimate the health economic and quality of life impact of RSV-attributable infection in this cohort. Such data will contribute to informing public health strategies to prevent RSV-associated infection, including use of preventative medications. METHODS AND ANALYSIS: Parents/carers of children <3 years of age with RTI symptoms will consent for a respiratory sample (nasal swab) to be taken. Laboratory PCR testing will assess for the presence of RSV and/or other pathogens. Data will be obtained from medical records on demographics, comorbidities, severity of infection and hospitalisation outcomes. Parents will complete questionnaires on the impact of ongoing infection symptoms at day 14 and 28 following enrolment. The primary outcome is incidence of laboratory-confirmed RSV in children <3 years presenting to primary, secondary or tertiary care with RTI symptoms leading to health-seeking behaviours. Recruitment will be carried out from December 2021 to March 2023, encompassing two UK winter seasons and intervening months. ETHICS AND DISSEMINATION: Ethical approval has been granted (21/WS/0142), and study findings will be published as per International Committee of Medical Journal Editors' guidelines.