Surveillance Of Acute Respiratory Infections Research Articles

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 > 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

Establishing severe acute respiratory infection (SARI) surveillance in a sentinel hospital, Ireland, 2021 to 2022.

BackgroundIn 2020, due to the COVID-19 pandemic, the European Centre for Disease Prevention and Control (ECDC) accelerated development of European-level severe acute respiratory infection (SARI) surveillance.AimWe aimed to establish SARI surveillance in one Irish hospital as part of a European network E-SARI-NET.MethodsWe used routine emergency department records to identify cases in one adult acute hospital. The SARI case definition was adapted from the ECDC clinical criteria for a possible COVID-19 case. Clinical data were collected using an online questionnaire. Cases were tested for SARS-CoV-2, influenza and respiratory syncytial virus (RSV), including whole genome sequencing (WGS) on SARS-CoV-2 RNA-positive samples and viral characterisation/sequencing on influenza RNA-positive samples. Descriptive analysis was conducted for SARI cases hospitalised between July 2021 and April 2022.ResultsOverall, we identified 437 SARI cases, the incidence ranged from two to 28 cases per week (0.7-9.2/100,000 hospital catchment population). Of 431 cases tested for SARS-CoV-2 RNA, 226 (52%) were positive. Of 349 (80%) cases tested for influenza and RSV RNA, 15 (4.3%) were positive for influenza and eight (2.3%) for RSV. Using WGS, we identified Delta- and Omicron-dominant periods. The resource-intensive nature of manual clinical data collection, specimen management and laboratory supply shortages for influenza and RSV testing were challenging.ConclusionWe successfully established SARI surveillance as part of E-SARI-NET. Expansion to additional sentinel sites is planned following formal evaluation of the existing system. SARI surveillance requires multidisciplinary collaboration, automated data collection where possible, and dedicated personnel resources, including for specimen management.

Resurgence of influenza and respiratory syncytial virus in Egypt following two years of decline during the COVID-19 pandemic: outpatient clinic survey of infants and children, October 2022

IntroductionTwo years after unprecedented low rates of circulation of most common respiratory viruses (SARS-CoV-2), the Egyptian ARI surveillance system detected an increase in acute respiratory infections (ARIs) with a reduced circulation of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), especially among school children. A national survey was conducted to estimate the burden and identify the viral causes of ARIs among children < 16 years of age.MethodsA one-day survey was carried out in 98 governmental outpatient clinics distributed all over Egypt 26 governorates. The four largest referral hospitals in each governorate where most influenza-like illness (ILI) patients seek care were selected. Using the WHO case definition, the first five patients < 16 years of age with ILI symptoms visiting the selected outpatient clinics on the survey day were enrolled. Basic demographic and clinical data of patients were collected using a linelist. Patients were swabbed and tested for SARS-CoV-2, influenza, and Respiratory Syncytial virus (RSV) by RT-PCR at the Central Laboratory in Cairo.ResultsOverall, 530 patients enrolled, their mean age was 5.8 ± 4.2, 57.1% were males, and 70.2% reside in rural or semi-rural areas. Of all patients, 134 (25.3%) had influenza, 111 (20.9%) RSV, and 14 (2.8%) coinfections. Influenza-positive children were older compared to RSV, (7.2 ± 4.1, 4.3 ± 4.1, p < 0.001), with more than half of them (53.0%) being school students. Dyspnea was reported in RSV more than in influenza (62.2% vs. 49.3%, p < 0.05). Among RSV patients, children < 2 years had a higher rate of dyspnea than others (86.7% vs. 53.1%, < 0.001).ConclusionsA resurgence of influenza and RSV was detected in Egypt in the 2022–2023 winter season. Influenza caused a higher rate of infection than RSV, while RSV caused more severe symptoms than influenza. Monitoring a broader range of respiratory pathogens is recommended to estimate the ARI burden and risky groups for severe disease in Egypt.

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.

Integrated environmental and clinical surveillance of viral acute respiratory infections in close communities: opportunities and challenges

Integrated environmental and clinical surveillance of viral acute respiratory infections in close communities: opportunities and challenges

An assessment of the current epidemiological and laboratory capacities for influenza-like illnesses and severe acute respiratory infection surveillance, Yemen 2022.

We aim to re-activate influenza sentinel surveillance system in Yemen after disruption related to repurposing for COVID-19 pandemic. WHO Country Office (CO) in collaboration with Yemen's Ministry of Public Health and Population (MOPH&P) jointly conducted an assessment mission to assess the current situation of the influenza sentinel surveillance system and assess its capacity to detect influenza epidemics and monitor trends in circulating influenza and other respiratory viruses of epidemic and pandemic potential. This study presents the results of the assessment for three sentinel sites located in Aden, Taiz, and Hadramout/Mukalla. A mixed methods approach was used to guide the assessment process and to help achieve the objectives. Data were collected as follows: desk review of the sentinel sites records and data; interviews with stakeholders, including key informants and partners; and direct observation through field visits to the sentinel sites, MOPH&P and the Central Public Health Laboratory (CPHL). Two assessment checklists were used: assessment of sentinel sites for SARI surveillance, and checklist for assessment of availability of SARI sentinel surveillance. COVID-19 has affected health systems and services, and this was demonstrated in this assessment. The influenza sentinel surveillance system in Yemen is not effectively functional; however, there is plenty of room for improvement if investment in the system's restructuring, training, building technical and laboratory capacities, and conducting continuous and regular supervision visits.

Immediate and long-term changes in the epidemiology, infection spectrum, and clinical characteristics of viral and bacterial respiratory infections in Western China after the COVID-19 outbreak: a modeling study.

The impact of COVID-19 on the epidemiology, clinical characteristics, and infection spectrum of viral and bacterial respiratory infections in Western China is unknown. We conducted an interrupted time series analysis based on surveillance of acute respiratory infections (ARI) in Western China to supplement the available data. The positive rates of influenza virus, Streptococcus pneumoniae, and viral and bacterial coinfections decreased, but parainfluenza virus, respiratory syncytial virus, human adenovirus, human rhinovirus, human bocavirus, non-typeable Haemophilus influenzae, Mycoplasma pneumoniae, and Chlamydia pneumoniae infections increased after the onset of the COVID-19 epidemic. The positive rate for viral infection in outpatients and children aged <5 years increased, but the positive rates of bacterial infection and viral and bacterial coinfections decreased, and the proportion patients with clinical symptoms of ARI decreased after the onset of the COVID-19 epidemic. Non-pharmacological interventions reduced the positive rates of viral and bacterial infections in the short term but did not have a long-term limiting effect. Moreover, the proportion of ARI patients with severe clinical symptoms (dyspnea and pleural effusion) increased in the short term after COVID-19, but in the long-term, it decreased. The epidemiology, clinical characteristics, and infection spectrum of viral and bacterial infections in Western China have changed, and children will be a high-risk group for ARI after the COVID-19 epidemic. In addition, the reluctance of ARI patients with mild clinical symptoms to seek medical care after COVID-19 should be considered. In the post-COVID-19 era, we need to strengthen the surveillance of respiratory pathogens.

Identification of Surveillance Procedures for Diseases and Deaths Potentially Caused by Air Pollution and Possible Solutions as a Proposal for a Binational Surveillance System: A Case Study of Mexicali B.C., México-Imperial Valley, United States

In this paper, an integrative analysis is conducted for both sides of the border of Mexicali B.C. and Imperial Valley, regarding the official procedures and ways in which the collection, organization and disposal of data is carried out for the following: pollutant molecules such as PM2.5, PM10, CO, and O3; meteorological data such as temperature and relative humidity; data produced by epidemiological surveillance of acute respiratory infections; and deaths from all causes minus external ones. Some points around the binational surveillance system, raised in a technical report, are collected, giving continuity to the previous work carried out on this matter. Challenges are identified, recommendations are made, and possible solutions are offered to achieve a binational, unified and integrative system that centralizes meteorological, clinical, and pollution data, and that guarantees the quality and expeditious availability of the data concerning of the effects of air pollution on respiratory diseases and/or natural deaths of the local population. According to our results, air monitoring in Mexicali, clinical data on acute respiratory infections, morbidity, and mortality records must be improved, as well as the cooperation and coordination with the institutions of Imperial Valley. Finally, we show that despite the deficiencies and limitations found in the data generated in the locality, especially data on pollution and clinical data, it is possible, with great effort, to build models that measure and explain the effects of air pollution on health. Examples include the relative risk of death from exposure to PM2.5, PM10, CO, and O3; particulate matter air pollution effects on activation of pulmonary tuberculosis; the association between personal PM10 exposure and pulmonary function; and the estimation of costs and public health benefits by PM10 mitigation, among others.

Clinical features and severe outcome predictors of COVID-19 vaccine breakthrough infection among hospitalized patients: results from Egypt severe acute respiratory infections sentinel surveillance, 2021–2022

BackgroundCOVID-19 vaccines are effective against infections and outcomes; however, breakthrough infections (VBT) are increasingly reported, possibly due to waning of vaccine-induced immunity or emerging variants. Most studies have focused on determining VBT rate based on antibody levels. This study aims at describing clinical features, risks, time trends, and outcomes of COVID-19 VBT among hospitalized patients in Egypt.MethodsData of SARS-CoV-2 confirmed patients hospitalized in 16 hospitals was obtained from the severe acute respiratory infections surveillance database, September 2021-April 2022. Data includes patients’ demographics, clinical picture, and outcomes. Descriptive analysis was performed and patients with VBT were compared to not fully vaccinated (UPV). Bivariate and multivariate analyses were performed using Epi Info7 with a significance level < 0.05 to identify VBT risk factors.ResultsOverall, 1,297 patients enrolled, their mean age 56.7 ± 17.0 years, 41.5% were males, 64.7% received inactivated, 25.% viral vector, and 7.7% mRNA vaccine. VBT was identified in 156(12.0%) patients with an increasing trend over time. VBT significantly was higher in (16–35 years) age, males, in those who received inactivated vaccine compared to corresponding groups of UPV (14.1 vs. 9.0%, p < 0.05 and 57.1 vs. 39.4%, p < 0.001 and 64.7 vs. 45.1, p < 0.01 respectively). Whereas receiving mRNA vaccine was significantly protective against VBT (7.7 vs. 21.6%, p < 001). VBT patients tend to have shorter hospital stays and lower case fatality (mean hospital days = 6.6 ± 5.5 vs. 7.9 ± 5.9, p < 0.01 and CFR = 28.2 vs. 33.1, p < 0.01 respectively). MVA identified younger ages, male gender, and inactivated vaccines as risks for VBT.ConclusionThe study indicated that COVID-19 vaccines significantly reduce hospital days and fatality. VBT trend is on the rise and males, young ages, and inactivated vaccine receivers are at higher risk. Caution regarding relaxation of personal preventive measures in areas with higher or increasing incidences of COVID-19, particularly for the at-risk group even if they are vaccinated. The vaccination strategy should be revised to reduce VBT rate and increase vaccine effectiveness.

Результаты эпидемиологического надзора за COVID-19 среди обучающихся и профессорско-преподавательского состава университета

Organization of training in the context of COVID-19 pandemic demanded the development and implementation of active epidemiological surveillance for acute respiratory infections in students and teaching staff of the Medical University. The study was aimed to identify the features of the COVID-19 epidemic process among students and teaching staff in 2020–2022. The analysis of COVID-19 incidence among students and teaching staff in the academic years 2020–2021 and 2021–2022 was carried out. The study was conducted on 6293 students enrolled in the academic year 2020–2021, 6148 students enrolled in the academic year 2021–2022, and 772 teaching staff members. In the academic year 2020–2021, COVID-19 was detected in 681 students, among whom the cumulative incidence (CI) was 10.83 (95% CI: 10.08-11.61) per 100 students, and 79 teaching staff members, among whom the CI was 10.23 (95% CI: 8.09–12.37); in the academic year 2021–2022 infection was detected in 690 students, the CI was 11.44 (95% CI: 10.64–12.24) per 100 students, and 75 teaching staff members, the CI was 9.71 (95% CI: 7.62%–11.80%). In 26.3% affected individuals, COVID-19 was detected when contacting the University outpatient clinic. The incidence among students living in the dormitories did not exceed that among students living in private apartments (p = 0.36), and no outbreaks were reported. There was a strong positive correlation between the incidence among residents of St. Petersburg and the incidence among students (r = 0.77). Over the entire period, probable setting of transmission was determined in 39.9% of infected individuals, contact most often (15.2%) occurred when working in the health care facilities. The incidence of novel coronavirus infection (COVID-19) among students and teaching staff members in the academic years 2020–2021 and 2021–2022 is directly related to their involvement in the COVID-19 epidemic process in St. Petersburg.

Monitoring COVID-19 and Influenza: The Added Value of a Severe Acute Respiratory Infection Surveillance System in Portugal.

Severe acute respiratory infections (SARI) surveillance is recommended to assess the severity of respiratory infections disease. In 2021, the National Institute of Health Doutor Ricardo Jorge, in collaboration with two general hospitals, implemented a SARI sentinel surveillance system based on electronic health registries. We describe its application in the 2021/2022 season and compare the evolution of SARI cases with the COVID-19 and influenza activity in two regions of Portugal. The main outcome of interest was the weekly incidence of patients hospitalized due to SARI, reported within the surveillance system. SARI cases were defined as patients containing ICD-10 codes for influenza-like illness, cardiovascular diagnosis, respiratory diagnosis, and respiratory infection in their primary admission diagnosis. Independent variables included weekly COVID-19 and influenza incidence in the North and Lisbon and Tagus Valley regions. Pearson and cross-correlations between SARI cases, COVID-19 incidence and influenza incidence were estimated. A high correlation between SARI cases or hospitalizations due to respiratory infection and COVID-19 incidence was obtained (ρ = 0.78 and ρ = 0.82, respectively). SARI cases detected the COVID-19 epidemic peak a week earlier. A weak correlation was observed between SARI and influenza cases (ρ = -0.20). However, if restricted to hospitalizations due to cardiovascular diagnosis, a moderate correlation was observed (ρ = 0.37). Moreover, hospitalizations due to cardiovascular diagnosis detected the increase of influenza epidemic activity a week earlier. In the 2021/2022 season, the Portuguese SARI sentinel surveillance system pilot was able to early detect the COVID-19 epidemic peak and the increase of influenza activity. Although cardiovascular manifestations associated with influenza infection are known, more seasons of surveillance are needed, to confirm the potential use of cardiovascular hospitalizations as an indicator of influenza activity.

Etiologies of influenza-like illness and severe acute respiratory infections in Tanzania, 2017-2019.

In 2016, Tanzania expanded sentinel surveillance for influenza-like illness (ILI) and severe acute respiratory infection (SARI) to include testing for non-influenza respiratory viruses (NIRVs) and additional respiratory pathogens at 9 sentinel sites. During 2017-2019, respiratory specimens from 2730 cases underwent expanded testing: 2475 specimens (90.7%) were tested using a U.S. Centers for Disease Control and Prevention (CDC)-developed assay covering 7 NIRVs (respiratory syncytial virus [RSV], rhinovirus, adenovirus, human metapneumovirus, parainfluenza virus 1, 2, and 3) and influenza A and B viruses. Additionally, 255 specimens (9.3%) were tested using the Fast-Track Diagnostics Respiratory Pathogens 33 (FTD-33) kit which covered the mentioned viruses and additional viral, bacterial, and fungal pathogens. Influenza viruses were identified in 7.5% of all specimens; however, use of the CDC assay and FTD-33 kit increased the number of specimens with a pathogen identified to 61.8% and 91.5%, respectively. Among the 9 common viruses between the CDC assay and FTD-33 kit, the most identified pathogens were RSV (22.9%), rhinovirus (21.8%), and adenovirus (14.0%); multi-pathogen co-detections were common. Odds of hospitalization (SARI vs. ILI) varied by sex, age, geographic zone, year of diagnosis, and pathogen identified; hospitalized illnesses were most common among children under the age of 5 years. The greatest number of specimens were submitted for testing during December-April, coinciding with rainy seasons in Tanzania, and several viral pathogens demonstrated seasonal variation (RSV, human metapneumovirus, influenza A and B, and parainfluenza viruses). This study demonstrates that expanding an existing influenza platform to include additional respiratory pathogens can provide valuable insight into the etiology, incidence, severity, and geographic/temporal patterns of respiratory illness. Continued respiratory surveillance in Tanzania, and globally, can provide valuable data, particularly in the context of emerging respiratory pathogens such as SARS-CoV-2, and guide public health interventions to reduce the burden of respiratory illnesses.

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

ObjectivesIn Egypt, an integrated surveillance for acute respiratory infections (ARIs) was established in 2016 to identify the causes of ARIs. The surveillance system includes 19 governmental hospitals. In response to the coronavirus disease 2019 (COVID-19) pandemic, the World Health Organisation (WHO) requested surveillance adaptation to address the emerging challenges. This study aims to describe the experience in Egypt of adapting ARI surveillance to the COVID-19 pandemic. MethodsWHO case definitions were used to identify patients with ARIs. Nasopharyngeal/oropharyngeal swabs were collected for SARS-CoV-2 and influenza testing. Demographic and clinical information were obtained by interviewing patients at the hospitals. During the COVID-19 pandemic, the first two outpatients daily and every fifth admitted patient were enrolled in the study. To determine the status of ARIs in Egypt during the pandemic, patient demographic, clinical and laboratory data from 2020 to 2022 were obtained and descriptive analyses were performed. ResultsOverall, 18,160 patients were enrolled in the study, including 7923 (43.6%) seen at outpatient clinics and 10,237 (56.4%) inpatients. Of the study participants, 6453 (35.5%) tested positive for ARIs, including 5620 (87.1%) for SARS-CoV-2, 781 (12.1%) for influenza and 52 (0.8%) for SARS-CoV-2/influenza coinfection. SARS-CoV-2 was the cause for 95.3% of admitted patients and 65.4% of outpatients. Influenza subtypes included A/H3 (55.7%), Influenza-B (29.1%) and H1/pdm09 (14.2%). Compared with influenza, SARS-CoV-2 tended to infect the elderly, in warm weather and in urban governorates, and resulted in more hospitalisations, longer hospital stays and higher case fatalities (16.3% vs 6.6%, p < 0.001). ConclusionsARI surveillance in Egypt was successfully adapted to the COVID-19 pandemic and effectively described the clinical characteristics and severity of circulating viruses. Surveillance reported the re-emergence of influenza with a severe course and high fatality. Surveillance is essential for monitoring the activity of respiratory viruses with the aim of guiding clinical management, including preventative and control measures.

Effectiveness of Oral Fluid in Pathogenic Surveillance of Acute Respiratory Infection

Objective: Oral fluid (OF) is a new safe, non-invasive, convenient, and efficient biological sample that can be used for virus nucleic acid and antibody detection. Because few studies have performed surveillance of multiple respiratory pathogens, this study sought to explore the application value of OF in this field. Methods: OF and throat swabs were collected from December 2020 to December 2021 in patients with acute respiratory tract infections in Beijing. Multiplex real-time PCR was performed, and the detection performance of two samples was compared. Results: A total of 769 OF and throat swab samples were collected. The detection rates of respiratory pathogens in throat swabs and OF were 29.26% (225/769) and 20.81% (160/769), respectively. The sensitivity and specificity of the OF assay, compared with the throat swab assay, were 71.11% (160/225) and 100% (544/544), respectively. The two assays had excellent agreement (kappa = 0.78). The detection consistency varied among pathogens. For OF samples, the most common pathogen was the influenza B virus, and the highest detection rate was in the ≤5-year-old group. The highest positivity rate was observed in December 2021. Conclusion: OF samples have excellent potential for the epidemiological surveillance of respiratory pathogens, and may have application prospects in preventing and controlling infectious diseases.

Impact of Nonpharmacological Interventions on Severe Acute Respiratory Infections in Children: From the National Surveillance Database.

Nonpharmacological interventions (NPIs) reduce the incidence of respiratory infections. After NPIs imposed during the coronavirus disease 2019 pandemic ceased, respiratory infections gradually increased worldwide. However, few studies have been conducted on severe respiratory infections requiring hospitalization in pediatric patients. This study compares epidemiological changes in severe respiratory infections during pre-NPI, NPI, and post-NPI periods in order to evaluate the effect of that NPI on severe respiratory infections in children. We retrospectively studied data collected at 13 Korean sentinel sites from January 2018 to October 2022 that were lodged in the national Severe Acute Respiratory Infections (SARIs) surveillance database. A total of 9,631 pediatric patients were admitted with SARIs during the pre-NPI period, 579 during the NPI period, and 1,580 during the post-NPI period. During the NPI period, the number of pediatric patients hospitalized with severe respiratory infections decreased dramatically, thus from 72.1 per 1,000 to 6.6 per 1,000. However, after NPIs ceased, the number increased to 22.8 per 1,000. During the post-NPI period, the positive test rate increased to the level noted before the pandemic. Strict NPIs including school and daycare center closures effectively reduced severe respiratory infections requiring hospitalization of children. However, childcare was severely compromised. To prepare for future respiratory infections, there is a need to develop a social consensus on NPIs that are appropriate for children.