BACKGROUND:Rapid Diagnostic Tests (RDTs) for SARS-CoV-2 have been pivotal for diagnostics, and shaping policies regarding self-isolation. In case of decreased sensitivity of RDTs to novel virus variants, viral spread can increase. In order to monitor for reduced sensitivity of RDTs we used a collection of SARS-CoV-2 positive samples from RDT negative patients. Infectieradar, a national participatory surveillance that registers respiratory symptoms and investigates the causative pathogen(s), is used here as a framework to study false-negative RDT results and possible relation of the emergence of new virus variants. METHODS:Participants reported weekly on RDT use and symptoms linked to Acute Respiratory Illness (ARI). Each week, all RDT-positive samples and a subset of 200 symptomatic, participants with RDT negative samples were invited to send in nose throat swabs (NTS). SARS-CoV-2 Ct-values were determined using RT-PCR on RDT-positive and RDT-negative NTS samples and compared using unpaired T-tests. Sequencing was performed on all eligible samples to compare the proportion of mutations in the N encoding gene and investigate the clustering patterns of genome sequences through analyses. NTS samples of participants with discordant RT-PCR and RDT results were also analyzed using RDTs by professionals in the laboratory. Between October 2022 and October 2023, our study had 16,893 participants and we collected 1,757 self-test-positive/NTS PCR-positive samples (RDT+/PCR+) and 359 self-test-negative/NTS PCR positive samples (RDT-/PCR+), which is 4.3% of RDT-negative samples. RESULTS:We observed overall higher Ct-values in the RDT-negative group, but saw no changes in viral loads throughout our sampling period. Few and relatively small differences in prevalence of amino acid substitutions were observed when we compared the RDT-negative group and to RDT-positive group. No specific clusters within the phylogenetic tree were observed from the RDT-negative sequences, which suggested there were no distinctive genetic properties of RDT-negative specimens. This was further confirmed by laboratory analyses. CONCLUSIONS:Evaluating RDT performance in the Dutch population and in-depth analysis of false-negative RDT specimens, led to no evidence for SARS-CoV-2 evolution affecting RDT sensitivity of the tests used. The participatory surveillance program Infectieradar is a powerful tool for our national surveillance of acute respiratory illnesses, as well as for research purposes. Since this framework offered both self-testing and the gold standard of PCR testing results.

Respiratory infections remain a major global health burden, causing substantial morbidity and mortality worldwide. The responsible viruses circulate concurrently, potentially affecting each other’s dynamics, yet the extent and direction of such interactions remain poorly understood. Characterising these cross-pathogen effects at the population level is essential for elucidating transmission dynamics and guiding mitigation strategies. Using incidence data from a participatory syndromic surveillance system with multiplex PCR (polymerase chain reaction) confirmation of specific pathogens, we applied complementary statistical approaches, including multivariate regression, endemic–epidemic, and distributed-lag models, to characterise immediate and delayed associations among seven major respiratory diseases. We show that these pathogens form a connected system of temporal associations in which some pairs, such as SARS-CoV-2 and human seasonal coronaviruses, exhibit positive associations in their temporal incidence patterns, primarily from SARS-CoV-2 to human seasonal coronaviruses, whereas others, such as influenza and rhinovirus or parainfluenza virus show negative associations in circulation dynamics. Associations were often directional rather than reciprocal: for instance, rhinovirus was negatively associated with subsequent human seasonal coronaviruses, whereas the reverse pattern was not observed, while positive bidirectional associations between human metapneumovirus and parainfluenza virus were observed in several models. Temporal association patterns were largely consistent across analytical frameworks, suggesting persistent co-circulation dynamics among the studied respiratory viruses. By integrating multiple analytic frameworks, our study provides a comprehensive, data-driven view of patterns of co-circulation and statistical association among respiratory viruses, offering crucial insights for improved epidemic forecasting and mitigation strategies.

BACKGROUND:With the introduction of metagenomics in clinical diagnostics unfolding and the expanding role of pathogen genomics in national surveillance, conditions are favourable for the further maturation of these approaches in public health surveillance. In this study, we aimed to pilot the use of probe-based metagenomics for nationwide sentinel surveillance through general practitioner (GP) networks and for the genomic characterisation of both anticipated and emerging respiratory viruses in primary care. METHODS:This prospective, pilot study included patients with acute respiratory illness attending GP practices participating in nationwide sentinel virological surveillance in the Netherlands, from Jan 10, 2025, to April 25, 2025. On predefined selection days, 90-100 combined nasopharyngeal and oropharyngeal swab specimens were analysed through parallel metagenomic testing using probes targeting 15 488 strains of human and animal viruses. Results were compared with a standard two-tiered surveillance strategy comprising PCR targeting 17 viruses, followed by amplicon-based nanopore whole-genome sequencing of influenza viruses, SARS-CoV-2, and respiratory syncytial virus (RSV). The primary outcome was detection and in-depth genomic characterisation of viruses within and beyond the scope of standard screening. Sensitivity, specificity, positive and negative predictive values, and genome coverage were analysed. FINDINGS:93 patients were included, with a median age of 51 years (IQR 33-67); 55 (59%) were women and 38 (41%) were men. Overall, 74 (80%) specimens tested positive through standard PCR-based screening. Metagenomic surveillance detected viruses in 88 (95%) specimens, including DNA viruses known to establish latent infections. For viruses targeted by routine PCR, metagenomics showed a pooled sensitivity of 93·8% (95% CI 88·1-98·7), specificity of 99·8% (95% CI 99·5-100·0), positive predictive value of 96·2% (95% CI 91·8-100·0), and negative predictive value of 99·7% (95% CI 91·8-100·0), with a median genome coverage of 99·4% (IQR 96·9-99·9%). Metagenomic data enabled simultaneous full genomic characterisation of circulating viruses targeted by current amplicon-based surveillance, including influenza viruses (success rate 30 [86%] of 35 detections) and RSV (six [86%] of seven), and of viruses that were post hoc characterised by whole-genome sequencing in response to epidemiological findings during the study period (human metapneumoviruses [hMPV], five [50·0%] of ten), and non-targeted viruses such as adenoviruses. The data facilitated characterisation of a reassortant A(H3N2) influenza virus, potential vaccine escape mutants, markers of susceptibility to influenza antiviral drugs and RSV monoclonal antibodies, and a human A(H1N2)v influenza virus infection. INTERPRETATION:The technically robust and comprehensive performance across heterogeneous circulating viruses shown here supports evaluation in larger prospective studies in high-prevalence settings, where implementation might be most cost-efficient. Further optimisation of probe-based enrichment strategies could reduce turnaround time and facilitate integration into routine public health surveillance. FUNDING:The Netherlands Organisation for Health Research and Development (ZonMw), and the Ministry of Health, Welfare and Sport (VWS).

Background:Seasonal human influenza viruses can escape from antibody-mediated neutralization when amino acid changes occur in the hemagglutinin protein. Routine surveillance identified circulation of an A(H3N2) virus variant in the Netherlands with amino acid substitutions at hemagglutinin positions 158 and 189. These amino acid positions were previously responsible for antigenic change of influenza A(H3N2) viruses and potentially lead to escape of this variant from vaccine-mediated immunity. Aim:To characterize the emergence and antigenic properties of N158K and K189R double substitution virus variants. Methods:We analyzed the geographical and temporal dynamics of the double-substitution variant using a phylogeographic approach and used hemagglutination inhibition assays and antigenic cartography methods to map its antigenic properties. Results:A(H3N2) viruses carrying K189R were first detected in Guatemala in June 2024, before subsequently gaining the N158K substitution, which was intially detected in Colombia in November 2024, followed by detection in the Netherlands in December 2024. However, detections within Europe remained almost entirely confined to the Netherlands. The proportion of viruses carrying the N158K and K189R substitutions increased to 16% - 24% per collection week of sequenced Dutch viruses during the peak of the epidemic of the 2024-2025 respiratory season. Antigenic characterization of viruses with N158K and K189R substitutions indicated that these are antigenically distinct from the A(H3N2) components of 2025-2026 Northern Hemisphere vaccines, showing 8-192-fold reduction in hemagglutination inhibition titers with antisera against the vaccine strain compared to antisera against the homologous virus. Conclusions:Influenza A(H3N2) viruses with N158K and K189R escaped recognition by antibodies raised against the 2024-2025 and 2025/2026 Northern Hemipshere vaccine strains in hemagglutination inhibition assays. These variants circulated widely in the Netherlands during the 2024-2025 influenza season, raising concerns about reduced vaccine-mediated protection if such variants would spread more broadly during 2025-2026 Northern Hemipshere season.

INTRODUCTION:We estimated vaccine effectiveness (VE) of JN.1 COVID-19 vaccination against SARS-CoV-2 infection by (sub)variant between 23 September 2024 and 23 February 2025. METHODS:JN.1 vaccine-eligible participants of an ongoing prospective cohort study (VAccine Study COvid-19; VASCO) were included: individuals aged ≥60 years, and individuals aged <60 years with a medical risk condition or who were healthcare workers. In VASCO, questionnaire and serology data are regularly collected and self-tests are provided. SARS-CoV-2 infection was based on reported positive self-tests and/or anti-nucleoprotein serology results. The variant of infection was determined by whole genome sequencing of viral genetic material in positive self-tests. VE against infection was estimated using Cox regression with JN.1-vaccination as time-varying exposure, and VE against JN.1 subvariants KP.3.1.1 and XEC using multinomial logistic regression with matching of infected and uninfected participants by calendar week. Models were adjusted for age group, sex, education level, medical risk condition and SARS-CoV-2 infection history. RESULTS:Of 4490 JN.1-vaccine eligible participants <60 years, 1283 (29%) were vaccinated. Of 19,349 participants ≥60 years, 14,400 (74%) were vaccinated. During follow-up 2142 infections occurred, of which the majority was self-reported (72%). VE was 16% (95%CI: -11-36) in participants <60 years and 13% (95%CI: 2-23) in participants ≥60 years. VE against KP.3.1.1 (n = 251;27%) did not differ significantly from the VE against XEC (n = 195;5%)(OR:1.3; 0.8-2.1). CONCLUSION:We found that, during a 5-month study period with low incidence, JN.1-vaccination provided limited added protection in preventing SARS-CoV-2 infection. The observed VE estimates indicate potentially lower protection against XEC than KP.3.1.1, but the power to detect such a difference was low.

OBJECTIVES:Here, we investigate symptoms linked to the new SARS-CoV-2 variant XFG using an evidence-based method to determine possible elevated levels of sore throat and severity as suggested by on-line news reports and social media. STUDY DESIGN:Participants (n = 39,937) in the participatory surveillance program, Infectieradar, weekly report respiratory symptoms and severity of disease. In addition, SARS-CoV-2 self-test results are reported and a representative subsample of all participants with symptoms sent a nose-throat swab for molecular diagnostic testing and sequencing. METHODS:We compared symptom prevalence, symptom burden and severity of disease in week 28 to week 40 in 2025, when SARS-CoV-2 strain XFG was dominant, with the same period in 2024, in which the KP.3 variant was most abundant. We compared these two periods through adjusted odds ratios and estimated marginal means to provide evidence for possibly altered symptomatology or disease severity. RESULTS:Sore throat was not significantly higher during the COVID-19 wave in 2025, compared to 2024, nor were any other symptoms. Additionally, the number of symptoms and severity of disease in the two periods is comparable. CONCLUSIONS:We conclude that sore throat is not indicative for the emerging XFG variant, nor that worse severity of disease is experienced during current COVID-19 cases in the general population.

BACKGROUND:Since 2022, highly pathogenic H5N1 influenza A virus clade 2.3.4.4b has caused global outbreaks among wild birds and poultry, with increasing mammalian and sporadic human infections. This elevates concerns about zoonotic transmission and pandemic risk, highlighting the need for accurate detection and identification of animal influenza A viruses by human clinical diagnostic laboratories (hCDL). METHODS:To evaluate routine diagnostic performance, an External Quality Assessment (EQA) panel containing inactivated influenza A viruses of avian (three subtype H5, one H7), swine (two H1, one H3), and human (one H1pdm09, one H3) origin was distributed to 50 hCDL in the Netherlands, Aruba, Bonaire, and Curaçao. Laboratories conducted their routine molecular influenza virus detection and, if available, subtyping workflows. RESULTS:A total of 118 detection workflows were reported. Of these, 109 (91 %) successfully detected influenza A virus in all positive specimens. At least one workflow in 49/50 (98 %) laboratories reliably detected all animal influenza viruses as type A influenza virus. Most false negatives occurred with swine H1N1v. Only 24 workflows from 20 laboratories attempted subtyping for one or multiple panel specimens (total 109 subtype-specific results reported): for human viruses, 37/39 results were correct; for avian viruses, 13/14 were correct (including 12/12 for H5); for swine viruses, only 2/56 were correct (both swine H3N2 using broad-reactive H3 assays). CONCLUSIONS:hCDL in the Netherlands demonstrate high performance for detecting animal influenza A viruses. However, subtyping capacity is limited, necessitating referral of specimens of suspected zoonotic influenza cases to the National Influenza Centre for further characterization.

Zoonotic influenza A viruses (zIAV) originating from avian and swine reservoirs present a serious concern for public health. Since the emergence of zIAV A(H5N1) in 1996, the virus has spread globally, impacting wild birds, poultry, wild and domestic mammals, including cattle and pigs, and sporadically infecting humans. Challenges persist in detecting and characterising zIAV, particularly at the human-animal interface. Recent external quality assessments conducted in the Netherlands and at European level have evaluated the capacity of human clinical diagnostic and national reference laboratories to detect, subtype and characterise potential zIAV. Based on these results, we reflect on the status and challenges of methods used for identifying cases of zIAV infection in Europe. While all laboratories are largely successful in generic detection of influenza A virus, subtyping is not widely used in clinical diagnostic laboratories. For national reference laboratories, subtyping specifically of swine-origin viruses remains challenging, often requiring sequencing for accurate identification. Although sequencing offers greater potential for characterising zIAV, training in the appropriate use of bioinformatics tools is needed. Raising awareness among healthcare professionals to document animal exposure in patient disease histories is also critical, as early suspicion of zoonotic infections is needed to direct laboratory testing, including subtyping.

This prospective study assessed the prevalence, type, and consequences of persistent symptoms following a nonhospitalized SARS-CoV-2 infection by comparing infected and noninfected children and adults of Dutch households. Two comparable prospective household studies were conducted during two pandemic phases. At baseline, all household members were tested for SARS-CoV-2 with 10 consecutive saliva samples during a 6-week period using RT-PCR. Questionnaires assessing persistent symptoms, health-related quality of life (HRQoL), anxiety, and depressive symptoms were collected at 6 and 12 months. Of the 297 included participants (median age 34 years, IQR 12-48), 201 (67.7%) tested positive for SARS-CoV-2. At 6 months, only one child reported persistent symptoms. SARS-CoV-2-infected adults (> 18 years) reported more pulmonary symptoms (15.2% vs. 3.4%, p = 0.023), and tended to report more fatigue (12.8% vs. 3.4%, p = 0.061) and exertion-related symptoms (8.8% vs. 1.7%, p = 0.107) compared to the negative adults. Adult participants with persistent symptoms reported decreased HRQoL and increased anxiety and depressive symptoms. This study found that SARS-CoV-2-positive adults tended to have higher prevalence of respiratory symptoms, fatigue, and exertion-related symptoms 6 months after SARS-CoV-2 infection, whereas children rarely reported persistent symptoms. Persistent symptoms were associated with a reduced HRQoL and increased anxiety and depression.

BACKGROUND:Knowledge of SARS-CoV-2 household transmission dynamics guides infection control and vaccination measures. This household cohort study prospectively assessed the impact of the Omicron BA.2 variant and immunity on household transmission using dense saliva sampling and sequence analysis. METHOD:Households consisting of a polymerase chain reaction-confirmed index and at least 2 household members were enrolled in March and April 2022 during the Omicron BA.2 wave in the Netherlands. SARS-CoV-2 polymerase chain reaction was performed on 10 consecutive saliva samples. Serum antibodies were measured at baseline and day 42. Household and per-person secondary attack rates (SARs) were calculated to measure transmission. Whole genome sequencing was performed for phylogenetic analysis, followed by sensitivity analysis, to correct for multiple household introductions and index definition. Results were compared with the identical, early-pandemic, preimmunization predecessor study. RESULTS:Sixty-seven households were included, consisting of 241 individuals (median age, 33.0 years; IQR, 12.0-46.0). Maximum household SAR was 59.7% and per-person SAR 41.5%. Pediatric index cases were more likely to transmit. Transmission was negatively affected by household members' immunity. Phylogenetic analysis showed multiple introductions in 4 households. Sensitivity analysis resulted in a minimal household SAR of 51.0% and per-person SAR of 28.5%. CONCLUSIONS:The Omicron BA.2 variant is highly transmissible within households. However, the transmission rate is lower when compared with previous studies with other SARS-CoV-2 variants, highlighting the effect of immunity. Regardless of immune status, children have a crucial role in Omicron household transmission. Intensive sampling and phylogenetic analysis are beneficial for correctly calculating transmission rates, especially during periods of minimal behavioral restrictions.

BACKGROUND:During the COVID-19 pandemic, the spread and diversity of SARS-CoV-2 was monitored non-invasively in more than 99% of Dutch households by a comprehensive wastewater-based epidemiology (WBE) programme which analysed viral RNA in wastewater samples taken at every household wastewater-treatment plant (WWTP) in the Netherlands. In this study, we analyse next-generation sequencing data generated from these wastewater samples for tracking SARS-CoV-2 lineages. We aimed to determine how well patterns of lineage abundances correspond to findings from individual surveillance, including community testing and testing at hospitals, and how WBE can be employed efficiently for future surveillance of SARS-CoV-2. METHODS:Whole-genome short-read sequencing was performed on 16,631 wastewater samples collected between Apr 9, 2021, and Dec 31, 2023, at 311 WWTPs. Observed lineages were grouped and week-aggregate estimates were compared to estimates from 138,374 individual surveillance sequences generated during the same period. Furthermore, we used resampling to examine the effect of sample size and catchment type on observed lineage dynamics. RESULTS:WBE enabled monitoring of SARS-CoV-2 lineages even during periods of reduced circulation in the Dutch population. Wastewater lineage proportions consistently mirrored those of individual surveillance. During periods of low turnover of dominant lineages, nationally representative lineage estimates can be obtained by sequencing only 24 samples per week, whereby population density or total population size of catchment areas would have a negligible effect on country-wide aggregate lineage estimates. CONCLUSIONS:WBE at household WWTPs is a valuable tool for SARS-CoV-2 surveillance, whereby comparatively little sequence data can be generated to identify lineage dynamics trends in large populations, and which can be scaled up and down in response to emerging lineages of concern. As such, it provides a useful complement to existing surveillance tools, to ensure optimal insight into pathogen diversity and spread.

Cas13 is activated by the hybridization of a CRISPR RNA to a complementary single-stranded RNA protospacer in a target RNA. While Cas13 is not activated by double-stranded RNA in vitro, it robustly targets RNA in cellular environments where RNAs are highly structured. The mechanism by which Cas13 targets structured RNAs remains unknown. Here, we systematically probe the effects of secondary structure on Cas13. We find that secondary structure in the protospacer and 3' to it inhibits Cas13 activity and quantitatively explains the former effect through a strand displacement framework. We then harness strand displacement to generate an 'occluded' Cas13, which enhances mismatch discrimination up to 50-fold and enables sequence-agnostic mutation identification at low (<1%) allele frequencies. Using occluded Cas13, we identify human-adaptive mutations in SARS-CoV-2 and human and avian influenza A viruses, as well as oncogenic mutations in KRAS. Our work leverages improved mechanistic understanding of Cas13 to expand the scope of RNA diagnostics and enable structure-informed Cas13 approaches.

This study compared the dynamics of SARS-CoV-2 viral shedding in saliva between wild-type virus-infected and Omicron-infected household cohorts. Preexisting immunity in participants likely shortens the viral RNA shedding duration and lowers viral load peaks. Frequent saliva sampling can be a convenient tool to study viral load dynamics.

During the winter 2023-2024, an upsurge of Mycoplasma pneumoniae (M.pneumoniae) was noted in the Netherlands. To investigate the distribution of M.pneumoniae sequence types from different patient populations and to explore genotypic macrolide resistance which is common in East Asia but not (yet) in Europe. M.pneumoniae positive throat/nasal samples from participatory respiratory surveillance, patients visiting general practitioners with an acute respiratory infection including community acquired pneumonia (CAP) and hospitalised patients with CAP were included, representing different disease severity. The M.pneumoniae were typed with multilocus sequence typing and the 23 S rRNA region was sequenced to determine macrolide resistance markers. In total, 153 M.pneumoniae were sequenced, six sequence types (STs) and only one bacterium with macrolide resistance marker were detected. No link between STs or bacterial load (PCR cycle threshold) and source population of M.pneumoniae was detected. In the Netherlands, the M.pneumoniae upsurge in 2023-2024 existed of multiple commonly found STs. No link between ST and severity of illness was detected. Macrolide resistance remained sporadic.

OBJECTIVES:To analyze changes over time in symptomatology and symptom burden of SARS-CoV-2 infected individuals. METHODS:Data from symptomatic individuals from Infectieradar, an online community-based, participatory surveillance platform in the Netherlands, were analyzed (November 2020-April 2025). Weekly questionnaires collected self-reported data on SARS-CoV-2 testing, health score (scale: 0-100), medication use, and healthcare visits. Longitudinal trends were evaluated using logistic regression models adjusted for age, sex, and comorbidities. RESULTS:During 4.5 years, 18,600 participants reported a positive SARS-CoV-2 test at least once. Upper respiratory symptoms became more prominent over time, and loss of smell and taste less. The self-reported health score and the proportion of symptomatic SARS-CoV-2-positive individuals with a high number of symptoms (more than 10 symptoms) remained relatively stable over time (October 2022-April 2025), with a health impact comparable to influenza virus infections (n = 768). CONCLUSION:The findings suggest that the clinical presentation of COVID-19 has evolved toward upper respiratory symptoms. Despite shifting symptoms, the impact on reported well-being in this population was remarkably stable, without a significantly lower endemic symptomatic burden. The health impact of COVID-19 is more comparable to influenza than to other common respiratory infections.

OBJECTIVES:Evaluation of the presence and effect of SARS-CoV-2 co-infections on disease severity. METHODS:We collected both symptom data and nose- and throat samples from symptomatic people during the 2022/2023 respiratory season in a large participatory surveillance study in the Netherlands, and tested these for 18 respiratory viruses, including SARS-CoV-2. We compared reported health status, symptoms and odds of having a single respiratory viral infection or co-infection with SARS-CoV-2 and another respiratory virus. RESULTS:In total, 4655 samples were included with 22% (n=1017) testing SARS-CoV-2 positive. Of these 11% (n=116) also tested positive for a second respiratory virus. The most frequently occurring co-infections in SARS-CoV-2 positive participants were with rhinovirus (59%; n=69), seasonal coronaviruses (15%; n=17), and adenovirus (7%; n=8). Participants with a co-infection with one of these three viruses did not report more severe disease compared to those with a SARS-CoV-2 mono-infection. The odds of experiencing SARS-CoV-2 co-infection with seasonal coronavirus or rhinovirus were lower compared to the odds of the respective non-SARS-CoV-2 mono-infection (OR: 0.16, CI 95%: 0.10 - 0.24; OR: 0.21 CI 95%: 0.17 - 0.26; respectively). CONCLUSIONS:SARS-CoV-2 co-infections with rhinovirus, seasonal coronavirus, and adenovirus are frequently observed in the general population, but are not associated with more severe disease compared to SARS-CoV-2 mono-infections. Furthermore, we found indications for inter-virus interaction with rhinovirus and seasonal coronavirus, possibly decreasing the risk of co-infection.

BackgroundSwine influenza has a considerable impact on pig populations and poses a pandemic threat to humans. However, little is known about the influenza A viruses circulating among pigs in the Netherlands.AimWe piloted a surveillance programme aimed at enabling swine influenza A virus (swIAV) surveillance in the Netherlands: investigated prevalence, genomic characteristics and recent evolution of circulating swIAV variants and compared them with relevant human and swine influenza viruses from the Netherlands and other European countries.MethodsWe collected and tested respiratory samples from pigs (2019-2023) for swIAV, characterised the viruses with molecular and virological methods and shared molecular data of swine and relevant human influenza A viruses in a national platform.ResultsWe detected swIAV throughout the year in 342 (42%) of 824 respiratory samples from 90 farms. Complete genome sequencing identified 73 H1N1, 51 H1N2 and one H3N2 viruses. Phylogenetic analyses identified viruses from each of the three H1 swine lineages (1A/B/C) and four subclades. Viruses from the 1A lineage clustered into three subgroups with distinct antigenic properties, which seemed descendent from separate introductions of human seasonal A(H1N1)pdm09 viruses. Phenotypically, no reduced susceptibility to existing antiviral drugs oseltamivir and zanamivir was found.ConclusionWe provided insights into swIAVs in pigs in the Netherlands, including antiviral susceptibility and antigenic differences. It highlighted occasional virus transmission between humans and pigs. Sharing swIAV data at a national level will be continued to reduce influenza burden in swine and support identification and characterisation of emerging swIAVs with zoonotic potential.

Non-human primates are important for preclinical vaccine evaluation. In depth characterization of the antibody response requires representative immunoglobulin (IG) germline gene databases for correct gene and allele assignments and assessment of affinity maturation of antigen-specific antibodies. Current IG-reference databases do not cover the genetic diversity observed in frequently used macaque species and it is unclear to what extent closely related animals express shared alleles at similar levels. Here, IG-germline alleles of sixteen cynomolgus macaques (CynoSet), some of which were related, were characterized and compared with previously described Mauritian and Indonesian origin cynomolgus macaque datasets. Although the CynoSet showed more overlap with the Mauritian origin dataset, compared to an Indonesian origin dataset, there were clear differences in allelic expression patterns, independent of family relationship. Calculation of somatic hypermutation levels in post-infection influenza hemagglutinin-specific B cells demonstrated the need for individualized IG-genotyping for accurate evaluation of the antigen-specific B cell response.

OBJECTIVE:This individual patient data meta-analysis investigates the impact of SARS-CoV-2 infection with or without other respiratory viruses on Acute Respiratory Illness (ARI) occurrence and severity. METHODS:We pooled individual participant data from 11 prospective COVID-19 community and healthcare cohorts (2020-2024). A subject's first respiratory sample was tested for SARS-CoV-2 and a panel of respiratory viruses. The association of SARS-CoV-2 single versus viral co-infection with ARI occurrence and severity was analyzed using mixed effects regression. The analysis was repeated for Human Rhinovirus (HRV). RESULTS:Of 1606 SARS-CoV-2 positive episodes (1597 subjects), 124 (7.7%) were co-infected with another respiratory virus, the majority with HRV (66.1%). SARS-CoV-2 Co-infection was associated with a lower odds of ARI than SARS-CoV-2 single infection in community cohorts (adjusted (a) OR: 0.39; 95%CI: 0.21-0.71). This association was not observed for ARI severity in healthcare cohorts (aOR: 1.76; 95%CI: 0.67-4.61). Co-infection versus single infection with HRV was associated with higher ARI occurrence and severity in both settings (community: aOR: 1.72 and healthcare: aOR: 6.04). CONCLUSION:In community settings, SARS-CoV-2 co-infection with another virus, particularly HRV, attenuates ARI compared to SARS-CoV-2 single infection. The low number of detected co-infections with other viruses, such as influenza or RSV, limits generalizability to other combinations of co-infecting viruses.

During the COVID-19 pandemic participatory digital surveillance of symptoms (syndromic surveillance) re-established itself as a worthy addition to the surveillance pyramid, as they are scalable, flexible and function independent from the health care system or health care seeking behaviour. A limitation of syndromic surveillance however is the inability of pathogen identification. We describe our experiences regarding integrating self-swabs with centralized testing into a participatory syndromic surveillance system in the Netherlands (Infectieradar). In the 2022/2023 winter season Infectieradar was extended to include nose- and throat swabs. Participants received test-kits including SARS-CoV-2 antigen tests for home use as well as nose- and throat swabs. All SARS-CoV-2 positive participants and a random sample of symptomatic SARS-CoV-2 self-test negative participants were asked to return a nose- and throat swab by regular post. Self-test negative swabs were tested by multiplex-PCR on 22 pathogens, including SARS-CoV-2. Self-test SARS-CoV-2 positive samples with a Ct-value < 30 were sequenced for variant analysis. Over 17,000 participants were included in the study, which involved relatively older persons and relatively more women compared to the general Dutch population. We collected 1,475 (median: 37 per week) swabs from participants with positive and 4,096 swabs (median: 136 per week) from participants with negative SARS-CoV-2 antigen self-tests (74% of those who requested to send in a swab). Of the swabs following a negative self-test, 47.7% tested positive in the multiplex-PCR, with rhinovirus/enterovirus being the most frequently detected pathogen (24.5%). Self-test SARS-CoV-2 positivity was laboratory-confirmed in 96.1% of swabs and showed parallel variant distributions as the national SARS-CoV-2 variant surveillance. This large-scale, centralized participatory surveillance system provides a comprehensive approach for performing syndromic and virological surveillance in the general population, including respiratory pathogen detection by self-test or multiplex-PCR. Despite the non-representative sample it was possible to monitor the variant distribution. Given the continuous collection of samples among those who don't seek care, the system provides valuable insights into circulating respiratory pathogens and is part of an answer on how to study the transmission, competition, virulence and evolution of circulating pathogens in interpandemic periods.