Surveillance Of Acute Respiratory Infections Research Articles

Real-Time Enterovirus D68 Outbreak Detection through Hospital Surveillance of Severe Acute Respiratory Infection, Senegal, 2023.

In December 2023, we observed through hospital-based surveillance a severe outbreak of enterovirus D68 infection in pediatric inpatients in Dakar, Senegal. Molecular characterization revealed that subclade B3, the dominant lineage in outbreaks worldwide, was responsible for the outbreak. Enhanced surveillance in inpatient settings, including among patients with neurologic illnesses, is needed.

Use of proxy indicators for automated surveillance of severe acute respiratory infection, the Netherlands, 2017 to 2023: a proof-of-concept study.

BackgroundEffective pandemic preparedness requires robust severe acute respiratory infection (SARI) surveillance. However, identifying SARI patients based on symptoms is time-consuming. Using the number of reverse transcription (RT)-PCR tests or contact and droplet precaution labels as a proxy for SARI could accurately reflect the epidemiology of patients presenting with SARI.AimWe aimed to compare the number of RT-PCR tests, contact and droplet precaution labels and SARI-related International Classification of Disease (ICD)-10 codes and evaluate their use as surveillance indicators.MethodsPatients from all age groups hospitalised at Leiden University Medical Center between 1 January 2017 up to and including 30 April 2023 were eligible for inclusion. We used a clinical data collection tool to extract data from electronic medical records. For each surveillance indicator, we plotted the absolute count for each week, the incidence proportion per week and the correlation between the three surveillance indicators.ResultsWe included 117,404 hospital admissions. The three surveillance indicators generally followed a similar pattern before and during the COVID-19 pandemic. The correlation was highest between contact and droplet precaution labels and ICD-10 diagnostic codes (Pearson correlation coefficient: 0.84). There was a strong increase in the number of RT-PCR tests after the start of the COVID-19 pandemic.DiscussionAll three surveillance indicators have advantages and disadvantages. ICD-10 diagnostic codes are suitable but are subject to reporting delays. Contact and droplet precaution labels are a feasible option for automated SARI surveillance, since these reflect trends in SARI incidence and may be available real-time.

Descriptive Epidemiology of Pathogens Associated with Acute Respiratory Infection in a Community-Based Study of K-12 School Children (2015-2023).

School-based outbreaks often precede increased incidence of acute respiratory infections in the greater community. We conducted acute respiratory infection surveillance among children to elucidate commonly detected pathogens in school settings and their unique characteristics and epidemiological patterns. The ORegon CHild Absenteeism due to Respiratory Disease Study (ORCHARDS) is a longitudinal, laboratory-supported, school-based, acute respiratory illness (ARI) surveillance study designed to evaluate the utility of cause-specific student absenteeism monitoring for early detection of increased activity of influenza and other respiratory viruses in schools from kindergarten through 12th grade. Eligible participants with ARIs provided demographic, epidemiologic, and symptom data, along with a nasal swab or oropharyngeal specimen. Multipathogen testing using reverse-transcription polymerase chain reaction (RT-PCR) was performed on all specimens for 18 respiratory viruses and 2 atypical bacterial pathogens (Chlamydia pneumoniae and Mycoplasma pneumoniae). Between 5 January 2015 and 9 June 2023, 3498 children participated. Pathogens were detected in 2455 of 3498 (70%) specimens. Rhinovirus/enteroviruses (36%) and influenza viruses A/B (35%) were most commonly identified in positive specimens. Rhinovirus/enteroviruses and parainfluenza viruses occurred early in the academic year, followed by seasonal coronaviruses, RSV, influenza viruses A/B, and human metapneumovirus. Since its emergence in 2020, SARS-CoV-2 was detected year-round and had a higher median age than the other pathogens. A better understanding of the etiologies, presentations, and patterns of pediatric acute respiratory infections can help inform medical and public health system responses.

Properties of influenza viruses that caused epidemic increases in morbidity in Russia and countries of the world during 2022–2023. The effectiveness of vaccine prophylaxis

The purpose of this work was to determine the characteristics of the circulation of various viral respiratory pathogens during the epidemic season 2022–2023 against the background of the ongoing evolutionary variability of SARS-CoV-2.
 Materials and methods. The article uses methods used in «traditional» and «hospital» epidemiological surveillance of acute respiratory viral infections.
 Results and discussion. The period from October 2022 to September 2023 was characterized by early and high activity of influenza A(H1N1)pdm09 virus, which was replaced by influenza B virus. The antigenic and genetic properties of strains were closely related to influenza vaccines viruses recommended by WHO experts for the current season. The effectiveness of influenza vaccines was confirmed (75.0%). All of the studied influenza A(H1N1)pdm09, A(H3N2) and B epidemic strais retained sensitivity to drugs with antineuraminidase activity. The structure and share of other ARVI pathogens have changed somewhat compared to the previous season: There was a tendency to increase the activity of HAdV and HMPV; almost equivalent activity of HRsV, HRV, HCoV and HBoV; and a decrease in HPIV activity. At the same time, the frequency of other ARVI pathogens did not reach the indicators of the pre-pandemic COVID-19 period. The rationale for updating the composition of influenza vaccines for the countries of the Northern Hemisphere in the 2023–2024 season is given.

Seasonality and Genotype Diversity of Human Rhinoviruses during an Eight-Year Period in Slovenia.

Due to the high socioeconomic burden of rhinoviruses, the development of prevention and treatment strategies is of high importance. Understanding the epidemiological and clinical features of rhinoviruses is essential in order to address these issues. Our study aimed to define the seasonality and molecular epidemiology of rhinoviruses in Slovenia. Over a period of eight years, a total of 20,425 patients from sentinel primary healthcare settings and sentinel hospitals were examined for a panel of respiratory viruses in the national programme for the surveillance of influenza-like illnesses and acute respiratory infections. The patients were from all age groups and had respiratory infections of various severity. Infection with a rhinovirus was confirmed using an RT-rPCR in 1834 patients, and 1480 rhinoviruses were genotyped. The molecular analysis was linked to demographical and meteorological data. We confirmed the year-round circulation of rhinoviruses with clear seasonal cycles, resulting in two seasonal waves with peaks in spring and autumn. High levels of genotype variability and co-circulation were confirmed between and within seasons and were analysed in terms of patient age, the patient source reflecting disease severity, and meteorological factors. Our study provides missing scientific information on the genotype diversity of rhinoviruses in Slovenia. As most previous investigations focused on exclusive segments of the population, such as children or hospitalised patients, and for shorter study periods, our study, with its design, size and length, contributes complementary aspects and new evidence-based knowledge to the regional and global understanding of rhinovirus seasonality and molecular epidemiology.

Impact of the COVID-19 related border restrictions on influenza and other common respiratory viral infections in New Zealand.

New Zealand's (NZ) complete absence of community transmission of influenza and respiratory syncytial virus (RSV) after May 2020, likely due to COVID-19 elimination measures, provided a rare opportunity to assess the impact of border restrictions on common respiratory viral infections over the ensuing 2 years. We collected the data from multiple surveillance systems, including hospital-based severe acute respiratory infection surveillance, SHIVERS-II, -III and -IV community cohorts for acute respiratory infection (ARI) surveillance, HealthStat sentinel general practice (GP) based influenza-like illness surveillance and SHIVERS-V sentinel GP-based ARI surveillance, SHIVERS-V traveller ARI surveillance and laboratory-based surveillance. We described the data on influenza, RSV and other respiratory viral infections in NZ before, during and after various stages of the COVID related border restrictions. We observed that border closure to most people, and mandatory government-managed isolation and quarantine on arrival for those allowed to enter, appeared to be effective in keeping influenza and RSV infections out of the NZ community. Border restrictions did not affect community transmission of other respiratory viruses such as rhinovirus and parainfluenza virus type-1. Partial border relaxations through quarantine-free travel with Australia and other countries were quickly followed by importation of RSV in 2021 and influenza in 2022. Our findings inform future pandemic preparedness and strategies to model and manage the impact of influenza and other respiratory viral threats.

Principal Component Patterns of Pediatric Respiratory Viral Testing Across Health Care Settings.

Factors prompting clinicians to request viral testing in children are unclear. We assessed patterns prompting clinicians to perform viral testing in children discharged from an emergency department (ED) or hospitalized with an acute respiratory infection (ARI). Using active ARI surveillance data collected from November 2017 through February 2020, children aged between 30 days and 17 years with fever or respiratory symptoms who had a research respiratory specimen tested were included. Children's presentation patterns from their initial evaluation at each health care setting were analyzed using principal components (PCs) analysis. PC-specific models using logistic regression with robust sandwich estimators were used to estimate odds ratios (ORs) and 95% confidence intervals (CIs) between PCs and provider-ordered viral testing. PCs were assigned respiratory virus/viruses names a priori based on the patterns represented. In total, 4107 children were enrolled and tested, with 2616 (64%) discharged from the ED and 1491 (36%) hospitalized. In the ED, children with a coviral presentation pattern had a 1.44-fold (95% CI, 1.24-1.68) increased odds of receiving a provider-ordered viral test than children showing clinical symptoms less representative of coviral-like infection. Whereas children in the ED and hospitalized with rhinovirus-like symptoms had 71% (OR, 0.29; 95% CI, 0.24-0.34) and 39% (OR, 0.61; 95% CI, 0.49-0.76) decreased odds, respectively, of receiving a provider-ordered viral test during their medical encounter. Viral tests are frequently ordered by clinicians, but presentation patterns vary by setting and influence the initiation of testing. Additional assessments of factors affecting provider decisions to use viral testing in pediatric ARI management are needed to maximize patient benefits of testing.

Comparative Analysis of Clinical Outcomes Using Propensity Score Matching: Coronavirus Disease 2019 vs. Seasonal Influenza in Korea.

The advent of the omicron variant and the formulation of diverse therapeutic strategies marked a new epoch in the realm of coronavirus disease 2019 (COVID-19). Studies have compared the clinical outcomes between COVID-19 and seasonal influenza, but such studies were conducted during the early stages of the pandemic when effective treatment strategies had not yet been developed, which limits the generalizability of the findings. Therefore, an updated evaluation of the comparative analysis of clinical outcomes between COVID-19 and seasonal influenza is requisite. This study used data from the severe acute respiratory infection surveillance system of South Korea. We extracted data for influenza patients who were infected between 2018 and 2019 and COVID-19 patients who were infected in 2021 (pre-omicron period) and 2022 (omicron period). Comparisons of outcomes were conducted among the pre-omicron, omicron, and influenza cohorts utilizing propensity score matching. The adjusted covariates in the propensity score matching included age, sex, smoking, and comorbidities. The study incorporated 1,227 patients in the pre-omicron cohort, 1,948 patients in the omicron cohort, and 920 patients in the influenza cohort. Following propensity score matching, 491 patients were included in each respective group. Clinical presentations exhibited similarities between the pre-omicron and omicron cohorts; however, COVID-19 patients demonstrated a higher prevalence of dyspnea and pulmonary infiltrates compared to their influenza counterparts. Both COVID-19 groups exhibited higher in-hospital mortality and longer hospital length of stay than the influenza group. The omicron group showed no significant improvement in clinical outcomes compared to the pre-omicron group. The omicron group did not demonstrate better clinical outcomes than the pre-omicron group, and exhibited significant disease severity compared to the influenza group. Considering the likely persistence of COVID-19 infections, it is imperative to sustain comprehensive studies and ongoing policy support for the virus to enhance the prognosis for individuals affected by COVID-19.

Provider-ordered viral testing and antibiotic administration practices among children with acute respiratory infections across healthcare settings in Nashville, Tennessee.

Evaluate the association between provider-ordered viral testing and antibiotic treatment practices among children discharged from an ED or hospitalized with an acute respiratory infection (ARI). Active, prospective ARI surveillance study from November 2017 to February 2020. Pediatric hospital and emergency department in Nashville, Tennessee. Children 30 days to 17 years old seeking medical care for fever and/or respiratory symptoms. Antibiotics prescribed during the child's ED visit or administered during hospitalization were categorized into (1) None administered; (2) Narrow-spectrum; and (3) Broad-spectrum. Setting-specific models were built using unconditional polytomous logistic regression with robust sandwich estimators to estimate the adjusted odds ratios and 95% confidence intervals between provider-ordered viral testing (ie, tested versus not tested) and viral test result (ie, positive test versus not tested and negative test versus not tested) and three-level antibiotic administration. 4,107 children were enrolled and tested, of which 2,616 (64%) were seen in the ED and 1,491 (36%) were hospitalized. In the ED, children who received a provider-ordered viral test had 25% decreased odds (aOR: 0.75; 95% CI: 0.54, 0.98) of receiving a narrow-spectrum antibiotic during their visit than those without testing. In the inpatient setting, children with a negative provider-ordered viral test had 57% increased odds (aOR: 1.57; 95% CI: 1.01, 2.44) of being administered a broad-spectrum antibiotic compared to children without testing. In our study, the impact of provider-ordered viral testing on antibiotic practices differed by setting. Additional studies evaluating the influence of viral testing on antibiotic stewardship and antibiotic prescribing practices are needed.

Surveillance of Acute Respiratory Infections in children and adolescents in a Pediatric Service

Introducción: Las infecciones agudas de vías respiratorias inferiores, de etiología viral, constituyen la principal causa de hospitalización y mortalidad infantil. El objetivo del presente estudio es conocer la frecuencia de las infecciones respiratorias agudas grave (IRAG) y los virus prevalentes en pacientes ≤15 años. Materiales y Métodos: Estudio observacional, descriptivo, producto de la vigilancia de IRAG, periodo enero/2019-mayo/2023. Se incluyeron todos los pacientes ≤15 años hospitalizados con diagnóstico de IRAG. Se analizaron datos demográficos, características clínicas y evolutivas. Resultados: Fueron hospitalizados 256 pacientes ≤15 años con diagnóstico de IRAG, 54,3%(139/256) de sexo masculino. El 69,1% correspondían a <2años, 15,6% de 2 a 4 años y 15,2% de 5 a 19 años. El 17,5% presentaban factores de riesgo. El 3,5% (9/256) tenía vacuna anti-influenza. El mayor número de casos se objetivó en 2019. En 2020 y 2021 se registró el menor número de casos, relacionado a la política de encierro durante la pandemia de COVID-19. El virus prevalente fue el Virus Sincitial Respiratorio (VSR). En el 2019, el VSR fue el virus más frecuente (p<0.0001.RR=1,56.IC95%= 1,18 - 2,06); el SARS - CoV2 fue el más frecuente en 2020. Según grupo etario el VSR fue más frecuente en <2 años (p<0.0001.RR=1,70.IC95%=1,18-2,06) y el SARS - CoV2 en los ≥2 años (p<0.0001.RR=2,50.IC95%=2,53-3,53). El VSR no fue asociado a factores de riesgo. El 39,4%(101/256) requirió ingreso a la UCIP, situación más frecuente en pacientes con factores de riesgo (21,7%vs14,8%,NS). El ingreso a UCI fue más frecuente en los <2 años (44,1% vs 29,1%;p<0,02.RR=1,51.IC95%=1,03-2,22). No hubo diferencias significativas del requerimiento de UCI y los virus aislados. La letalidad fue del 7,8%(20/256), más frecuente en el sexo femenino (p<0.02.RR=0,36.IC95%=0,1-0,9), no asociado a la edad ni etiología. Conclusion: La IRAG por VSR constituye una causa importante de hospitalización en <2 años, más frecuente en el sexo masculino. El ingreso a UCIP fue más frecuente en los <2años. La letalidad fue más frecuente en el sexo femenino.

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

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

Tracking severe acute respiratory syndrome coronavirus 2 transmission and co-infection with other acute respiratory pathogens using a sentinel surveillance system in Rift Valley, Kenya.

The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been the most significant public health challenge in over a century. SARS-CoV-2 has infected over 765 million people worldwide, resulting in over 6.9 million deaths. This study aimed to detect community transmission of SARS-CoV-2 and monitor the co-circulation of SARS-CoV-2 with other acute respiratory pathogens in Rift Valley, Kenya. We conducted a cross-sectional active sentinel surveillance for the SARS-CoV-2 virus among patients with acute respiratory infections at four sites in Rift Valley from January 2022 to December 2022. One thousand two hundred seventy-one patients aged between 3 years and 98 years presenting with influenza-like illness (ILI) were recruited into the study. Nasopharyngeal swab specimens from all study participants were screened using a reverse transcription-quantitative polymerase chain reaction (RT-qPCR) for SARS-CoV-2, influenza A, influenza B and respiratory syncytial virus (RSV). The samples that tested positive for influenza A (n = 73) and RSV (n = 12) were subtyped, while SARS-CoV-2 (n = 177) positive samples were further screened for 12 viral and seven bacterial respiratory pathogens. We had a prevalence of 13.9% for SARS-CoV-2, 5.7% for influenza A, 2% for influenza B and 1% for RSV. Influenza A-H1pdm09 and RSV B were the most dominant circulating subtypes of influenza A and RSV, respectively. The most common co-infecting pathogens were Streptococcus pneumoniae (n = 29) and Haemophilus influenzae (n = 19), accounting for 16.4% and 10.7% of all the SARS-CoV-2 positive samples. Augmenting syndromic testing in acute respiratory infections (ARIs) surveillance is crucial to inform evidence-based clinical and public health interventions.

Seasonal and inter-seasonal RSV activity in the European Region during the COVID-19 pandemic from autumn 2020 to summer 2022.

The emergence of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in early 2020 and subsequent implementation of public health and social measures (PHSM) disrupted the epidemiology of respiratory viruses. This work describes the epidemiology of respiratory syncytial virus (RSV) observed during two winter seasons (weeks 40-20) and inter-seasonal periods (weeks 21-39) during the pandemic between October 2020 and September 2022. Using data submitted to The European Surveillance System (TESSy) by countries or territories in the World Health Organization (WHO) European Region between weeks 40/2020 and 39/2022, we aggregated country-specific weekly RSV counts of sentinel, non-sentinel and Severe Acute Respiratory Infection (SARI) surveillance specimens and calculated percentage positivity. Results for both 2020/21 and 2021/22 seasons and inter-seasons were compared with pre-pandemic 2016/17 to 2019/20 seasons and inter-seasons. Although more specimens were tested than in pre-COVID-19 pandemic seasons, very few RSV detections were reported during the 2020/21 season in all surveillance systems. During the 2021 inter-season, a gradual increase in detections was observed in all systems. In 2021/22, all systems saw early peaks of RSV infection, and during the 2022 inter-seasonal period, patterns of detections were closer to those seen before the COVID-19 pandemic. RSV surveillance continued throughout the COVID-19 pandemic, with an initial reduction in transmission, followed by very high and out-of-season RSV circulation (summer 2021) and then an early start of the 2021/22 season. As of the 2022/23 season, RSV circulation had not yet normalised.

Sentinel Surveillance of Severe Acute Respiratory Infections in Serbia in 2022-2023 Season

Abstract Introduction Sentinel surveillance of severe acute respiratory infections (SARI) was implemented in Serbia in November 2009. Nine sentinel hospitals in 3 cities participated in the integrated SARI surveillance system. Four of them are children's hospitals. The aim of this study is to provide a review of integrated sentinel surveillance of SARI in Serbia in 2022-2023 influenza season, from October 2022 to April 2023. Methods Integrated Sentinel Surveillance of SARI has been done in accordance with professional guidance for epidemiological surveillance of influenza. Both epidemiological and virological data were collected on a weekly basis. All specimens were tested for influenza, SARS-CoV-2 and Respiratory syncytial virus (RSV). Intensive care units (ICUs), pediatric and respiratory disease wards were all represented. For laboratory confirmation, Real time polymerase chain reaction (RT-PCR) was used. Results Start of influenza season was registered in week 44/2022. A total of 3027 SARI cases were reported with 100% recorded age. Of these, 14% were 0-4 years old, 9% were 5-14, 7% were 15-29, 38% were 30-64 and 32% were ≥65. Among these cases, 607(20%) respiratory specimens were collected during the surveillance period. The number of positive samples for influenza was 208(34%), for SARS-CoV-2 was 37(6%) and for RSV 12(2%). The highest proportion of laboratory-confirmed influenza cases was 58% in week 51/2022. then, above 50% in week 7/2023 and 8/2023. All three influenza viruses were confirmed: A(H1)pdm09, A(H3) and type B. B viruses predominated, accounting for 38% of all sentinel SARI detections. There no were death associated to influenza, SARS-CoV-2 and RSV. Conclusions Integration epidemiological with laboratory surveillance as well as integrated sentinel SARI surveillance for influenza, SARS -CoV-2 and RSV highlights the importance of maintaining and improving national influenza surveillance capacity especially in the frame of International Health Regulations. Key messages • Quality, representativeness and sustainability are the guiding principles for integrated, SARS-CoV-2, RSV and influenza sentinel SARI surveillance. • The threat of influenza remains, and it is essential for countries to be vigilant for the emergence of non seasonal influenza viruses of pandemic potential and prepare for the next influenza season.

An evaluation of the severe acute respiratory infection (SARI) surveillance system in Ireland

Abstract Background Expansion of the current single hospital site Severe Acute Respiratory Infection (SARI) surveillance programme in Ireland, to create a sentinel network, will commence in 2023. This evaluation aimed to assess the performance of key surveillance system attributes to improve and guide expansion. Methods A mixed quantitative and qualitative evaluation was conducted from September 2021 to November 2022. SARI surveillance data were analysed to assess completeness, timeliness and positive predictive value (PPV). An online stakeholder questionnaire, semi-structured focus group discussions and key informant interviews evaluated usefulness, simplicity, flexibility and acceptability. Qualitative data were analysed using thematic analysis. Results Among SARI cases (n = 747), completeness of key variables including age, sex and outcome was 100%. Symptom data were completed in &amp;gt; 90%, COVID-19 vaccination status was completed in 89% and completeness of ethnicity data was 0.6%. Median times from hospitalisation to data entry commencement and completion were one day (IQR 1-3) and 48 days (IQR 21-81) respectively. Time to receipt of whole genome sequencing (WGS) results was 40 days (IQR 30-61). PPV was 95% (95% CI 93%-97%). The questionnaire response rate was 21% (75/362) and 96% (72/75) agreed that SARI surveillance is important. Key themes identified in the qualitative study (n = 11) were the complexity and importance of SARI surveillance. Suggested areas for improvement included process automation and additional designated resources to improve timeliness, flexibility and acceptability; particularly during epidemic or pandemic surge periods. Conclusions The SARI surveillance system reports high-quality data. Timeliness of WGS data and recording of vaccination status and equity stratifiers e.g., ethnicity should be improved. Priorities for expansion should be automation and adequate resource allocation to enable reliable SARI surveillance at all times. Key messages • The SARI surveillance system is a resource intensive, complex system that is an important component of national surveillance in Ireland and reports high-quality and timely surveillance data. • The priorities for expansion are process automation where possible and ensuring adequate resources, specifically skilled staff. These evaluation findings should inform SARI expansion in Ireland.

The Irish National SARS-CoV-2 Whole Genome Sequencing Surveillance Programme

Abstract Issue In response to the COVID-19 pandemic in Ireland, a national SARS-CoV-2 Whole Genome Sequencing (WGS) Surveillance Programme was set up in 2021 to track the molecular epidemiology of SARS-CoV-2 in Ireland to inform and enhance the urgent public health response to the COVID-19 pandemic. Description The Programme is a ‘hub and spoke’ model, led by the Health Protection Surveillance Centre with the National Virus Reference Laboratory (hub) and seven acute hospital laboratories (spokes), representing Ireland's six Regional Health Areas and Children's Health Ireland Hospitals. The two streams within the Programme's surveillance strategy are: 1. National surveillance of SARS-CoV-2 variants, including samples from GP sentinel sites and severe acute respiratory infection (SARI) surveillance, vaccine effectiveness studies, hospital in-patient, intensive care cases and deaths. 2. Targeted surveillance of risk groups e.g. outbreak cases, cases with unusual epidemiological/clinical characteristics. Results As of 30/03/2023, 103,258 COVID-19 cases (6% all notified cases in Ireland) have been sequenced since week 51, 2020. Data produced contribute to: public health policy in Ireland; local/national clinical and public health action; tracking variants nationally and variant shifts over time; the global community through reporting of WGS data to ECDC, WHO and global repository (GISAID). Lessons The hub and spoke model is an efficient and sustainable design for a laboratory public health programme. It is scalable, allowing addition of new spokes where needed. It ensures regional equity and builds capacity both nationally and regionally, increasing resilience and expertise throughout the country. Key messages • WGS will be key component of future epidemic/pandemic preparedness. • Programme successfully implements sustainable nationwide WGS surveillance and will expand to include other pathogens.

Pan-India influenza-like illness (ILI) and Severe acute respiratory infection (SARI) surveillance: epidemiological, clinical and genomic analysis.

Over time, COVID-19 testing has significantly declined across the world. However, it is critical to monitor the virus through surveillance. In late 2020, WHO released interim guidance advising the use of the existing Global Influenza Surveillance and Response System (GISRS) for the integrated surveillance of influenza and SARS-CoV-2. In July 2021, we initiated a pan-India integrated surveillance for influenza and SARS-CoV-2 through the geographically representative network of Virus Research and Diagnostic Laboratories (VRDLs) across 26 hospital and laboratory sites and 70 community sites. A total of 34,260 cases of influenza-like illness (ILI) and Severe acute respiratory infection (SARI) were enrolled from 4 July 2021 to 31 October 2022. Influenza A(H3) and B/Victoria dominated during 2021 monsoon season while A(H1N1)pdm09 dominated during 2022 monsoon season. The SARS-CoV-2 "variants of concern" (VoC) Delta and Omicron predominated in 2021 and 2022, respectively. Increased proportion of SARI was seen in extremes of age: 90% cases in < 1 year; 68% in 1 to 5 years and 61% in ≥ 8 years age group. Approximately 40.7% of enrolled cases only partially fulfilled WHO ILI and SARI case definitions. Influenza- and SARS-CoV-2-infected comorbid patients had higher risks of hospitalization, ICU admission, and oxygen requirement. The results depicted the varying strains and transmission dynamics of influenza and SARS-CoV-2 viruses over time, thus emphasizing the need to continue and expand surveillance across countries for improved decision making. The study also describes important information related to clinical outcomes of ILI and SARI patients and highlights the need to review existing WHO ILI and SARI case definitions.

Database derived from an electronic medical record-based surveillance network of US emergency department patients with acute respiratory illness

BackgroundFor surveillance of episodic illness, the emergency department (ED) represents one of the largest interfaces for generalizable data about segments of the US public experiencing a need for unscheduled care. This protocol manuscript describes the development and operation of a national network linking symptom, clinical, laboratory and disposition data that provides a public database dedicated to the surveillance of acute respiratory infections (ARIs) in EDs.MethodsThe Respiratory Virus Laboratory Emergency Department Network Surveillance (RESP-LENS) network includes 26 academic investigators, from 24 sites, with 91 hospitals, and the Centers for Disease Control and Prevention (CDC) to survey viral infections. All data originate from electronic medical records (EMRs) accessed by structured query language (SQL) coding. Each Tuesday, data are imported into the standard data form for ARI visits that occurred the prior week (termed the index file); outcomes at 30 days and ED volume are also recorded. Up to 325 data fields can be populated for each case. Data are transferred from sites into an encrypted Google Cloud Platform, then programmatically checked for compliance, parsed, and aggregated into a central database housed on a second cloud platform prior to transfer to CDC.ResultsAs of August, 2023, the network has reported data on over 870,000 ARI cases selected from approximately 5.2 million ED encounters. Post-contracting challenges to network execution have included local shifts in testing policies and platforms, delays in ICD-10 coding to detect ARI cases, and site-level personnel turnover. The network is addressing these challenges and is poised to begin streaming weekly data for dissemination.ConclusionsThe RESP-LENS network provides a weekly updated database that is a public health resource to survey the epidemiology, viral causes, and outcomes of ED patients with acute respiratory infections.

A decade of human metapneumovirus in hospitalized children with acute respiratory infection: molecular epidemiology in central Vietnam, 2007–2017

Human metapneumovirus (hMPV) can cause severe acute respiratory infection (ARI). We aimed to clarify the clinical and molecular epidemiological features of hMPV. We conducted an ARI surveillance targeting hospitalized children aged 1 month to 14 years in Nha Trang, Vietnam. Nasopharyngeal swabs were tested for respiratory viruses with PCR. We described the clinical characteristics of hMPV patients in comparison with those with respiratory syncytial virus (RSV) and those with neither RSV nor hMPV, and among different hMPV genotypes. Among 8822 patients, 278 (3.2%) were hMPV positive, with a median age of 21.0 months (interquartile range: 12.7–32.5). Among single virus-positive patients, hMPV cases were older than patients with RSV (p < 0.001) and without RSV (p = 0.003). The proportions of clinical pneumonia and wheezing in hMPV patients resembled those in RSV patients but were higher than in non-RSV non-hMPV patients. Seventy percent (n = 195) were genotyped (A2b: n = 40, 20.5%; A2c: n = 99, 50.8%; B1: n = 37, 19%; and B2: n = 19, 9.7%). The wheezing frequency was higher in A2b patients (76.7%) than in those with other genotypes (p = 0.033). In conclusion, we found a moderate variation in clinical features among hMPV patients with various genotypes. No seasonality was observed, and the multiple genotype co-circulation was evident.

Alarming case of avian influenza A (H5) in humans: call for urgent action in Ecuador

Alarming case of avian influenza A (H5) in humans: call for urgent action in Ecuador