Influenza and Other Respiratory Viruses最新文献

Background

Nonpharmaceutical interventions, implemented during the COVID-19 pandemic, affected the transmission of other respiratory pathogens.

Methods

Systematically collected respiratory illness surveillance data and consistent case definitions were used to describe changes in influenza and respiratory syncytial virus (RSV)–associated outpatient visits and hospitalisations in South Africa during the first 3 years of the COVID-19 pandemic relative to a pre-COVID-19 pandemic period (2017–2019).

Results

In 2020, influenza circulation almost ceased. In 2021 an out-of-season circulation was observed with a return to prepandemic timing, albeit with a higher peak in 2022. During the pandemic period, influenza-associated influenza-like illness (ILI) was more common in those aged ≥ 5 years compared to < 6 months. Patients with influenza-associated severe respiratory illness (SRI) were less likely to be ≥ 45 years versus < 6 months and less likely to be admitted to ICU (aOR 0.2, 95% CI 0.04–0.8).

RSV circulation declined at the start of the pandemic, with an out-of-season spring resurgence in 2020 followed by a return to prepandemic timing in 2021 and a higher peak in 2022. During the pandemic, compared to the prepandemic period, patients with RSV-associated SRI were more likely to be aged 1–4 years (aOR 1.5, 95% CI 1.2–1.8) versus < 6 months and less likely to be admitted to ICU (aOR 0.5, 95% CI 0.3–0.8).

Conclusion

We report low levels of influenza circulation and out-of-season RSV circulation in 2020 with changes in the age distribution of cases and risk of ICU admission. Return to prepandemic timing was earlier for RSV, with higher seasonal peaks for influenza-associated ILI and RSV-associated SRI in 2022.

Background

Surveillance of influenza infections and virus characterisation are essential to guide prevention strategies. In the Central African Republic (CAR), data on influenza viruses are patchy and poorly documented.

Objective

To study the clinical, seasonal, genetic and phenotypic characteristics of influenza viruses circulating in the CAR population.

Materials and Methods

From January 2015 to December 2018, the presence of influenza A and B viruses in patients presenting with influenza-like illness (ILI) symptoms or severe acute respiratory infections (SARI) was investigated by RT-qPCR. Influenza genetic diversity was evaluated by phylogenetic analyses, and antigenic properties were investigated by haemagglutination inhibition assays, whereas reduced susceptibility to neuraminidase inhibitors was assessed through the presence of known genetic markers and neuraminidase assay. The relationship between patients' clinical characteristics and infection status was investigated using statistical analyses.

Results

Over the surveillance period influenza viruses were detected in 9.7% of samples (n = 6134), with the highest intensity of circulation occurring in 2016 (15.8%), attributed mainly to A(H3N2). Periods of increased influenza transmission (June to October) generally coincided with rainy seasons; however, variations in terms of monthly distribution of cases between years were evident. Hospitalisation rates (SARI) were most frequent in infants (0–11 months, 37.9%) and young children (1–4 years, 24.8%), whereas influenza prevalences were highest in the 15–49 (12.0%) and ≥ 50 (15.2%) years old categories. A new A(H1N1)pdm09 6B.1 hemagglutinin subgroup characterised by amino acid substitutions S84N, S162N and I216T was detected in 2015, with associated antigenic drift, and subsequently, two of these viruses showed highly reduced inhibition by oseltamivir.

Conclusion

This study showcases the value of local influenza sentinel networks to specifically inform vaccination strategies and highlights the need for improved strain characterisation in tropical regions.

Background and Objectives

Different COVID-19 vaccine platforms elicit variable immune responses, influenced by prior infection and booster vaccination. We aimed to compare the humoral immune responses elicited by mRNA and adenoviral vector (Ad-vector) COVID-19 vaccines in hospital employees and to assess the possible impact of prior SARS-CoV-2 infection on these responses.

Methods

We performed a prospective observational cohort study by recruiting employees of the Universitair Ziekenhuis Brussel who were vaccinated with an mRNA or Ad-vector vaccine. We assessed anti-spike (S) IgG and neutralising capacity at 1, 6 and 12 months (post-mRNA booster). Anti-S and anti-NCP IgG were measured by chemiluminescent microparticle immunoassay, and neutralising capacity was assessed using Genscript's cPASS. Non-parametric group comparisons used the Mann–Whitney U test, complemented by multiple linear regression.

Results

Following RVR, mRNA-vaccinated individuals (n = 380) exhibited higher anti-S IgG titres and neutralising capacity compared to those who received Ad-vector vaccines (n = 200). After the booster, anti-spike IgG remained higher in mRNA-vaccinated individuals than in Ad-vector recipients (q < 0.001); Ad-vector vaccinated individuals showed superior neutralising capacity. Natural SARS-CoV-2 infection prior to vaccination had varying impact on anti-S IgG and neutralising capacity, depending on vaccination type and time points.

Conclusion

Our findings underscore that both vaccine platforms and prior infections shape the magnitude and quality of the humoral immune response, highlighting the importance of considering priming strategy, booster design and hybrid immunity when optimising COVID-19 vaccination schedules for durable protection.

Background

Respiratory Syncytial Virus (RSV) causes significant respiratory infections, particularly in young children and elderly adults. Genetic variations in the fusion (F) protein can reduce the efficacy of vaccination and monoclonal antibody treatments, emphasizing the need for genomic surveillance of this virus.

Motivation

Current pipelines for RSV genome assembly focus on sequence reconstruction but often lack features for detecting genotypes, clinically relevant mutations, or presenting results in formats that are suitable for clinical researchers.

Results

We introduce RSVrecon, an advanced bioinformatics pipeline for comprehensive RSV genome assembly and phylogenetic analysis. RSVrecon processes raw FASTQ files into annotated variant reports and delivers results in multiple formats (CSV, PDF, and HTML) tailored to diverse end users. A key innovation of RSVrecon is not only its integrated detection of clinically critical features—including genotype classification and F protein mutation calling, capabilities absent in most analytical pipelines—but also its presentation of these results to clinicians via an integrated, graphical, and user-friendly interface. Its modular design, powered by Nextflow's modern framework, ensures a scalable and robust workflow, while user-friendly reports enable seamless translation of genomic data into actionable clinical insights. Benchmarking against existing pipelines using clinical datasets revealed that RSVrecon achieves comparable genomic assembly accuracy while excelling in three key dimensions: (1) expanded functional capabilities, (2) intuitive biological interpretation of the results, and (3) superior user experience and accessibility. By seamlessly translating RSV genomic data into clinically meaningful information, RSVrecon empowers research breakthroughs, guides clinical care decisions, and strengthens surveillance systems. With these features, RSVrecon offers an enhanced approach to RSV surveillance and research. The tool is freely available at https://github.com/stjudecab/rsvrecon with a Python implementation at https://github.com/stjudecab/RSVreconPy.

Background

Rapid and accurate detection and identification of viral pathogens have an impact on physician decision-making for patients with acute respiratory illness (ARI). We aimed to evaluate the Xpert Xpress Flu/RSV test for the management of antibiotic prescribing in pediatric outpatients with ARI.

Methods

We performed a prospective, quasi-randomized, controlled study in Beijing Children's Hospital between December 1, 2021 and April 28, 2022. Outpatients with ARI aged 28 days to 18 years were enrolled and randomly assigned to the Xpert Xpress Flu/RSV test (Xpert) group or the influenza (Flu) antigen test (control) group. Both tests were performed on site.

Results

A total of 771 patients were enrolled and assigned randomly to the Xpert (n = 398) and the control (n = 373) groups. There was no statistically significant difference in antibiotic prescriptions between the two groups, whereas a significant difference was observed for the prescriptions of oseltamivir (p < 0.001). In Flu B-positive patients, a statistically significant decrease in antibiotic use and increase in antiviral use were observed in both Xpert and control groups. Cephalosporin use was significantly decreased in respiratory syncytial virus (RSV)-positive patients in the Xpert group before (n = 8, 17.4%) and after (n = 1, 2.2%)visit (p = 0.035). Among clinical and laboratory parameters, shorter fever length (OR = 0.366) and positive Flu B or RSV (OR = 3.99) were two independent factors for antibiotic withdrawal by logistic regression analysis. There was no significant difference in duration of fever, clinical outcomes, and expenditure between the two groups at the 7-day and 30-day follow-up.

Conclusions

Use of Xpert Xpress Flu/RSV at point-of-care in pediatric outpatients with ARI reduced antibiotic prescription, which has the potential to improve antibiotic stewardship.

Background

Human metapneumovirus (hMPV) circulates globally, yet its seasonal dynamics remain incompletely defined. Here, we describe the global timing, amplitude and duration of hMPV outbreaks, comparing the pre- versus post-COVID-19 periods.

Methods

Surveillance data for hMPV were retrieved from WHO FluNet from Week 1/2016 until Week 26/2025. We examined the epidemic peak timing, amplitude and duration across seasons and latitudes and compared patterns in 2016–2019 with those in 2021–2025.

Results

Over the study period, approximately 145,000 hMPV detections were reported to the WHO FluNet database from a total of 54 countries worldwide. Among the 15 countries with sufficient data to analyse seasonality, the epidemic timing aligned with geographic latitude, with the peak occurring in June–September in the Southern Hemisphere, February–April in the Northern Hemisphere, while the timing was variable across the intertropical belt. The amplitude of the peak varied across countries, with some countries characterized by single, well-defined peaks and others with more widespread epidemics throughout the season. The median epidemic duration was 19.5 weeks (range 15–36). After the appearance of SARS-CoV-2, marked shifts in timing and amplitude were observed, with delays or dislocations in several countries compared with pre-pandemic seasons.

Conclusions

In this analysis of global surveillance data for hMPV (extended until June 2025), we highlighted latitudinal gradients in hMPV circulation, with disruptions associated with COVID-19. Our findings emphasize the importance of sustained, type-specific global surveillance to inform public health strategies and to characterize the post-COVID-19 global seasonality patterns of hMPV.