Severe Acute Respiratory Infection Cases Research Articles

Genetic characterization of pediatric SARI-associated human adenoviruses in eight Chinese provinces during 2017-2021.

Human adenovirus (HAdV) is a significant viral pathogen causing severe acute respiratory infections (SARIs) in children. To improve the understanding of type distribution and viral genetic characterization of HAdV in severe cases, this study enrolled 3404 pediatric SARI cases from eight provinces of China spanning 2017-2021, resulting in the acquisition of 112 HAdV strains. HAdV-type identification, based on three target genes (penton base, hexon, and fiber), confirmed the diversity of HAdV types in SARI cases. Twelve types were identified, including species B (HAdV-3, 7, 55), species C (HAdV-1, 2, 6, 89, 108, P89H5F5, Px1/Ps3H1F1, Px1/Ps3H5F5), and E (HAdV-4). Among these, HAdV-3 exhibited the highest detection rate (44.6%), followed by HAdV-7 (19.6%), HAdV-1 (12.5%), and HAdV-108 (9.8%). All HAdV-3, 7, 55, 4 in this study belonged to dominant lineages circulating worldwide, and the sequences of the three genes demonstrated significant conservation and stability. Concerning HAdV-C, excluding the novel type Px1/Ps3H1F1 found in this study, the other seven types were detected both in China and abroad, with HAdV-1 and HAdV-108 considered the two main types of HAdV-C prevalent in China. Two recombinant strains, including P89H5F5 and Px1/Ps3H1F1, could cause SARI as a single pathogen, warranting close monitoring and investigation for potential public health implications. In conclusion, 5 years of SARI surveillance in China provided crucial insights into HAdV-associated respiratory infections among hospitalized pediatric patients.

Cross-sectional study of influenza trends and costs in Malaysia between 2016 and 2018.

While influenza circulates year-round in Malaysia, research data on its incidence is scarce. Yet, this information is vital to the improvement of public health through evidence-based policies. In this cross-sectional study, we aimed to determine the trends and financial costs of influenza. Data for the years 2016 through 2018 were gathered retrospectively from several sources. These were existing Ministry of Health (MOH) influenza sentinel sites data, two teaching hospitals, and two private medical institutions in the Klang Valley, Malaysia. Expert consensus determined the final estimates of burden for laboratory-confirmed influenza-like illness (ILI) and severe acute respiratory infection (SARI). Economic burden was estimated separately using secondary data supplemented by MOH casemix costing. Altogether, data for 11,652 cases of ILI and 5,764 cases of SARI were extracted. The influenza B subtype was found to be predominant in 2016, while influenza A was more prevalent in 2017 and 2018. The distribution timeline revealed that the highest frequency of cases occurred in March and April of all three years. The costs of influenza amounted to MYR 310.9 million over the full three-year period. The study provides valuable insights into the dynamic landscape of influenza in Malaysia. The findings reveal a consistent year-round presence of influenza with irregular seasonal peaks, including a notable influenza A epidemic in 2017 and consistent surges in influenza B incidence during March across three years. These findings underscore the significance of continuous monitoring influenza subtypes for informed healthcare strategies as well as advocate for the integration of influenza vaccination into Malaysia's national immunization program, enhancing overall pandemic preparedness.

Predictors of severity and prolonged hospital stay of viral acute respiratory infections (ARI) among children under five years in Burkina Faso, 2016–2019

BackgroundViruses are the leading etiology of acute respiratory infections (ARI) in children. However, there is limited knowledge on drivers of severe acute respiratory infection (SARI) cases involving viruses. We aimed to identify factors associated with severity and prolonged hospitalization of viral SARI among children < 5 years in Burkina Faso.MethodsData were collected from four SARI sentinel surveillance sites during October 2016 through April 2019. A SARI case was a child < 5 years with an acute respiratory infection with history of fever or measured fever ≥ 38 °C and cough with onset within the last ten days, requiring hospitalization. Very severe ARI cases required intensive care or had at least one danger sign. Oropharyngeal/nasopharyngeal specimens were collected and analyzed by multiplex real-time reverse-transcription polymerase chain reaction (rRT-PCR) using FTD-33 Kit. For this analysis, we included only SARI cases with rRT-PCR positive test results for at least one respiratory virus. We used simple and multilevel logistic regression models to assess factors associated with very severe viral ARI and viral SARI with prolonged hospitalization.ResultsOverall, 1159 viral SARI cases were included in the analysis after excluding exclusively bacterial SARI cases (n = 273)very severe viral ARI cases were common among children living in urban areas (AdjOR = 1.3; 95% CI: 1.1–1.6), those < 3 months old (AdjOR = 1.5; 95% CI: 1.1–2.3), and those coinfected with Klebsiella pneumoniae (AdjOR = 1.9; 95% CI: 1.2–2.2). Malnutrition (AdjOR = 2.2; 95% CI: 1.1–4.2), hospitalization during the rainy season (AdjOR = 1.71; 95% CI: 1.2–2.5), and infection with human CoronavirusOC43 (AdjOR = 3; 95% CI: 1.2-8) were significantly associated with prolonged length of hospital stay (> 7 days).ConclusionYounger age, malnutrition, codetection of Klebsiella pneumoniae, and illness during the rainy season were associated with very severe cases and prolonged hospitalization of SARI involving viruses in children under five years. These findings emphasize the need for preventive actions targeting these factors in young children.

Infective Versus Non-Infective Respiratory Illness Admissions: Comparative cost analysis in a tertiary hospital in Malaysia

Background: Severe Acute Respiratory Infection (SARI) that is mainly caused by the Influenza virus, poses a significant public health threat, demanding timely detection and preventive measures. This study assesses the financial implications of managing two distinct respiratory conditions: SARI and Acute Exacerbation of Bronchial Asthma (AEBA). Method: Data were collected for 100 patients, with 50 cases of SARI and 50 cases of AEBA, admitted to Hospital Canselor Tuanku Muhriz (HCTM) from July to December 2022. Cost analysis was conducted from a provider perspective, considering factors such as building, asset, emolument, overhead, utility, medication, consumables, and laboratory and imaging expenses. Results: The study revealed that the average total cost of treating SARI patients was RM 1,587.11 ($US334.80), significantly higher (30.7%) than AEBA patients at RM 1,214.41 ($US256.18).This was mainly due to the acute and severe nature of SARI, requiring more intensive medical interventions, potentially leading to complications and greater strain on healthcare resources. The study highlighted the economic challenges posed by SARI, provided valuable insights for resource allocation and public health planning. The study's limitations include retrospective data collection and potential underestimation of actual costs due to top-down costing methodology. Conclusion: SARI, especially in the elderly population, leads to substantial healthcare costs and economic impact. Effective preventive measures, such as vaccination, are crucial in reducing the burden of influenza-related illnesses. Health financing plays a vital role in addressing communicable diseases and ensuring the well-being of the population.

Patterns of Non-influenza Respiratory Viruses Among Severe Acute Respiratory Infection Cases in Burkina Faso: A Surveillance Study.

Although influenza viruses cause only one-fifth of severe acute respiratory infections (SARI) in Burkina Faso, the other viral causes of SARI remain poorly investigated to inform clinical and preventive decision making. Between 2016 and 2019, we prospectively enrolled inpatients meeting the World Health Organization (WHO) case definition of SARI in Burkina Faso. Results of viral etiologies among inpatients tested negative for influenza using the Fast Track Diagnostics Respiratory Kits (FTD-33) were reported. Of 1541 specimens tested, at least one respiratory virus was detected in 76.1% of the 1231 specimens negative for influenza virus. Human rhinoviruses (hRVs) were the most detected pathogens (476; 38.7%), followed by human adenoviruses (hAdV) (17.1%, 210/1231), human respiratory syncytial virus (hRSV) (15.4%, 189/1231), enterovirus (EnV) (11.2%, 138/1231), human bocavirus (hBoV) (7.9%, 97/1231), parainfluenza 3 (hPIV3) (6.1%, 75/1231), human metapneumovirus (hMPV) (6.0%,74/1321), parainfluenza 4 (hPIV4) (4.1%, 51/1231), human coronavirus OC43 (hCoV-OC43) (3.4%, 42/1231), human coronavirus HKU1(hCoV-HKU1) (2.7%, 33/1231), human coronavirus NL63 (hCoV-NL63) (2.5%, 31/1231), parainfluenza 1 (hPIV1) (2.0%, 25/1231), parainfluenza 2 (hPIV2) (1.8%, 22/1231), human parechovirus (PeV) (1.1%, 14/1231), and human coronavirus 229E (hCoV-229E) (0.9%, 11/1231). Among SARI cases, infants aged 1-4 years were mostly affected (50.7%; 622/1231), followed by those <1 year of age (35.7%; 438/1231). Most detected pathogens had year-long circulation patterns, with seasonal peaks mainly observed during the cold and dry seasons. Several non-influenza viruses are cause of SARI in Burkina Faso. The integration of the most common pathogens into the routine influenza surveillance system might be beneficial.

Spatiotemporal dynamics and epidemiological impact of SARS-CoV-2 XBB lineage dissemination in Brazil in 2023.

Brazil was one the most affected countries by the SARS-CoV-2 pandemic, with more than 700,000 deaths by mid-2023. This study reconstructs the dissemination of the virus in the country in the first half of 2023, a period characterized by the dissemination of descendants of XBB.1, a recombinant of Omicron BA.2 lineages evolved in late 2022. The analysis supports that XBB dissemination was marked by the continuous emergence of indigenous lineages bearing similar mutations in key sites of their Spike protein, a process followed by continuous increments in transmissibility, and without repercussions in the incidence of severe cases. Thus, the results suggest that the epidemiological impact of the spread of a SARS-CoV-2 variant is influenced by an intricate interplay of factors that extend beyond the virus's transmissibility alone. The study also underlines the need for SARS-CoV-2 genomic surveillance that allows the monitoring of its ever-shifting composition.

Respiratory Syncytial Virus-Associated Deaths among Children under Five before and during the COVID-19 Pandemic in Bangladesh.

Respiratory syncytial virus (RSV) is a leading cause of acute lower respiratory infections in young children worldwide. RSV-associated deaths in children are underreported in Bangladesh. We analyzed hospital-based surveillance data on severe acute respiratory infections (SARIs) in under-five children before (August 2009-February 2020) and during the COVID-19 pandemic (March 2020-March 2022). Using the World Health Organization definition, we identified SARI cases in 14 tertiary-level hospitals. Nasopharyngeal and oropharyngeal swabs were collected for real-time reverse-transcriptase-polymerase chain reaction (rRT-PCR) testing of six respiratory viruses, including RSV. SARI deaths during the pandemic (2.6%, 66) were higher than pre-pandemic (1.8%, 159; p < 0.001). Nearly half of pandemic deaths (47%) had underlying respiratory viruses, similar to the pre-pandemic rate (45%). RSV detection in deaths was consistent pre-pandemic (13%, 20/159) and during the pandemic (12%, 8/66). Children aged < 6 months constituted 57% (16) of RSV-related deaths. Evaluating interventions like maternal vaccination and infant monoclonal antibody prophylaxis is crucial to address RSV, a major contributor to under-five SARI deaths.

Respiratory syncytial virus among hospitalized patients of severe acute respiratory infection in Bhutan: Cross-sectional study.

Respiratory syncytial virus (RSV) is a leading cause of lower respiratory tract infections worldwide, particularly in young children. In Bhutan, respiratory disease continues to be among the top 10 diseases of morbidity for several years. This study aimed to estimate the prevalence of RSV among hospitalized patients with severe acute respiratory infection (SARI) in Bhutan. Respiratory specimens were collected from SARI patients of all ages in 2016 and 2018 following influenza surveillance guidelines. Specimens were tested for influenza and RSV, human metapneumovirus, adenovirus, and human parainfluenza virus types 1, 2, and 3 using real-time reverse-transcription polymerase chain reaction assay. Descriptive statistics were used to analyze the result in STATA 16.1. Of the 1339 SARI specimens tested, 34.8% were positive for at least one viral pathogen. RSV was detected in 18.5% of SARI cases, followed by influenza in 13.4% and other respiratory viruses in 3%. The median age of SARI cases was 3 (IQR: 0.8-21 years)years. RSV detection was higher among children aged 0-6 (Adj OR: 3.03; 95% CI: 1.7-5.39) and 7-23 months (Adj OR: 3.01; 95% CI: 1.77-5.12) compared with the children aged 5-15 years. RSV was also associated with breathing difficulty (Adj OR: 1.73; 95% CI: 1.17-2.56) and pre-existing lung disease, including asthma (Adj OR: 2.78; 95% CI: 0.99-7.8). Respiratory viruses were detected in a substantial proportion of SARI hospitalizations in Bhutan.

Impact of BioFire FilmArray Multiplex PCR in the Detection of Microbial Agents causing Severe Acute Respiratory Infection in the COVID-19 Era: A Cross-sectional Study from a Tertiary Care Hospital in Central India

Introduction: Many viral and bacterial respiratory tract infections can present with respiratory signs and progress to complicated pneumonia. In the recent Coronavirus Disease2019 (COVID-19) pandemic, it is crucial to test all Severe Acute Respiratory Infection (SARI) patients for other microbial infections in addition to COVID-19, enabling timely diagnosis and treatment to reduce morbidity and mortality. The automated system, BioFire FilmArray, utilises multiplex Polymerase Chain Reaction (PCR) to rapidly detect and identify multiple respiratory pathogens, including selected Antimicrobial Resistance (AMR) genes, within an hour. Aim: To detect bacterial and/or viral pathogens associated with hospitalised COVID-19-negative SARI patients using the BioFire FilmArray Pneumonia Panel (BFPP). Materials and Methods: This laboratory-based cross-sectional study was conducted at All India Institute of Medical Sciences (AIIMS), Nagpur, Maharashtra, India, from June 2020 to February 2021. Respiratory samples, such as sputum, tracheal aspirate, Endotracheal (ET) secretions, and Bronchoalveolar Lavage (BAL), were collected from COVID-19-negative hospitalised SARI cases. A total of 81 patients were included in the study. The samples were tested using the BFPP (multiplex PCR) system and processed using conventional culture techniques. Patient characteristics, clinical and laboratory investigation data, and findings of respiratory viral and bacterial agents, as well as antibiotic resistance genes detected by BioFire FilmArray, were recorded using paper case reports. The data were collected and analysed using Statistical Package for Social Sciences (SPSS) software. Results: Out of the 81 clinical samples processed, the BFPP detected 168 bacterial and 18 viral pathogens. Bacterial-viral codetection was observed in 13 (16%) samples. Atypical bacteria were detected in 3% of cases. Among the bacterial pathogens, the AMR gene for New Delhi Metallo-beta-lactamases (NDM) was detected in 42 (25.9%) cases, followed by CTX-M betalactamases, VIM, and the oxacillinase group of β-lactamases. Conclusion: The BFPP test is a valuable tool for the rapid detection of a wide range of pathogens, including associated AMR genes, with high sensitivity and specificity. This can greatly aid in treatment decisions.

Epidemiology and burden of Severe Acute Respiratory Infections (SARI) in the aftermath of COVID-19 pandemic: A prospective sentinel surveillance study in a Tunisian Medical ICU, 2022/2023.

Severe Acute Respiratory Infections (SARI) caused by influenza and other respiratory viruses pose significant global health challenges, and the COVID-19 pandemic has further strained healthcare systems. As the focus shifts from the pandemic to other respiratory infections, assessing the epidemiology and burden of SARI is crucial for healthcare planning and resource allocation. Aim: to understand the impact of the post-pandemic period on the epidemiology of SARI cases, clinical outcomes, and healthcare resource utilization in Tunisia. This is a prospective study conducted in a Tunisian MICU part of a national sentinel surveillance system, focusing on enhanced SARI surveillance. SARI cases from week 39/2022, 26 September to week 19/2023, 13 May were included, according to a standardized case definition. Samples were collected for virological RT-PCR testing, and an electronic system ensured standardized and accurate data collection. Descriptive statistics were performed to assess epidemiology, trends, and outcomes of SARI cases, and univariate/multivariate analyses to assess factors associated with mortality. Among 312 MICU patients, 164 SARI cases were identified during the study period. 64(39%) RT-PCR were returned positive for at least one pathogen, with influenza A and B strains accounting for 20.7% of cases at the early stages of the influenza season. The MICU experienced a significant peak in admissions during weeks 1-11/2023, leading to resource mobilization and the creation of a surge unit. SARI cases utilized 1664/3120 of the MICU-stay days and required 1157 mechanical ventilation days. The overall mortality rate among SARI cases was 22.6%. Age, non-COPD, and ARDS were identified as independent predictors of mortality. The present study identified a relatively high rate of SARI cases, with 39% positivity for at least one respiratory virus, with influenza A and B strains occurring predominantly during the early stages of the influenza season. The findings shed light on the considerable resource utilization and mortality associated with these infections, underscoring the urgency for proactive management and efficient resource allocation strategies.

2637. Activity of Respiratory Viruses in Georgia 2020-2022

Abstract Background The emergence of SARS-CoV-2 in early 2020 with subsequent implementation of public health and social measures influenced the epidemiology of respiratory viruses worldwide. This study describes circulation of respiratory viruses during two winter seasons and inter-seasonal periods in Georgia. Methods We aggregated data obtained from Influenza like illness (ILI) and Severe Acute Respiratory Infection (SARI) cases during 2020/21 and 2021/22 (weeks 40-20) and inter-seasonal (weeks 21-39) periods in Georgia. All specimens from patients were screened on 22 respiratory viruses by real time RT-PCR. Results During 2020/21 season 50% (868/1729) specimens tested positive on at least one virus. No influenza virus and few RSV detections were observed in Georgia. Mostly identified virus was Rhino (44.8%) circulating almost all season; followed by Coronavirus OC43 (23.7%), primarily seen in weeks 12-18 and SARS-Cov-2 (15%) with highest detection rates during weeks 48-52. In 2021 inter-season 54% (825/1513) of specimens were positive. A gradual increase in RSV detections was observed in summer. Most seen viruses were Rhino (30%), HMPV (22%) and Parainfluenza virus 3 (21%) circulating mainly in June and July. During 2021/22 season 44% (2012/4545) of specimens screened positive, out of which RSV (25.7%) with earlier circulation in weeks 40-2 and Rhino (25.7%) with most detections in the beginning and at the end of the season. Unusually influenza A/H3 (17%) peaked in late spring (weeks 12-18). SARS-Cov-2, Parainfluenza viruses 3 and 4, Adenoviruses, Human bocavirus, enteroviruses were actively co-circulating too. In 2022 inter-season 54% (1320/2456) of samples tested positive. Influenza A/H3 circulation continued until July. SARS-Cov-2 (27.7%), Rhino (22%), HMPV (14.5%), Parainfluenza virus 3 (12.7%), RSV (10.8%) were mostly seen viruses predominantly in June. Conclusion Wider range respiratory viruses with higher positivity rates were detected among ILI and SARI cases in 2021/22 season compared to 2020/21 presumably due to mitigation of public health and social measures. Low detection rates of SARS-CoV-2 at sentinel sites could be explained by referral of COVID-19 patients to dedicated clinics. RSV and Influenza circulations were unusual in summer months in Georgia. Disclosures All Authors: No reported disclosures

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.

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.

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.

Phylogenetic characteristics and recombination analysis of echovirus 5 associated with severe acute respiratory infection in China.

Echovirus 5 (E5) belongs to the enterovirus B (EV-B) species, which is one of the pathogens causing respiratory diseases. Only two whole genome sequences (WGSs) of E5 are available in GenBank, and few studies on E5 have been reported worldwide. In this study, human rhabdomyosarcoma (RD) cells were used to isolate E5 from respiratory samples associated with severe acute respiratory infection (SARI). The nucleotide sequence of the VP1 region and the WGSs of two E5 strains were sequenced using Sanger sequencing and high-throughput sequencing technology, respectively. Together with 31 E5 VP1 sequences and 2 WGSs downloaded from GenBank, a total of 33 complete VP1 sequences and 4 WGSs were used for genetic characterization and evolutionary analysis. Phylogenetic analysis revealed five genotypes (A-E) based on complete VP1 sequences. Evolutionary analysis showed that the time to the most recent common ancestor of E5 was approximately 1952 (95% highest posterior density [HPD] range, 1948-1953]), with a mean substitution rate of 7.74 × 10-3 subs/site/year (95% HPD range, 6.44-9.11 × 10-3). In addition, the WGS analyses showed that the nucleotide and amino acid similarities of the coding regions of the two strains obtained in this study with the prototype of the E5 strain Noyce were 80.2% and 97.2%, respectively. Recombination analysis showed that the two E5 strains may have intraspecific recombination with E6, EV-B85, and CVA9 serotypes in the nonstructural region. This study reports the isolation of E5 from SARI cases for the first time, and genetic characterization and evolutionary analysis provide valuable information on global E5 molecular epidemiology.IMPORTANCEThis study is the first report of echovirus 5 (E5) associated with severe acute respiratory infection and obtained the first E5 whole-genome sequence in China. Combined with the sequences available in the GenBank database, the first genotyping, phylogenetic characteristics, recombination, and genetic evolutionary analysis of E5 was performed in this study. Our findings providing valuable information on global E5 molecular epidemiology.

Lessons learned from identifying clusters of severe acute respiratory infections with influenza sentinel surveillance, Bangladesh, 2009-2020.

We explored whether hospital-based surveillance is useful in detecting severe acute respiratory infection (SARI) clusters and how often these events result in outbreak investigation and community mitigation. During May 2009-December 2020, physicians at 14 sentinel hospitals prospectively identified SARI clusters (i.e., ≥2 SARI cases who developed symptoms ≤10 days of each other and lived <30 min walk or <3 km from each other). Oropharyngeal and nasopharyngeal swabs were tested for influenza and other respiratory viruses by real-time reverse transcriptase-polymerase chain reaction (rRT-PCR). We describe the demographic of persons within clusters, laboratory results, and outbreak investigations. Field staff identified 464 clusters comprising 1427 SARI cases (range 0-13 clusters per month). Sixty percent of clusters had three, 23% had two, and 17% had ≥4 cases. Their median age was 2 years (inter-quartile range [IQR] 0.4-25) and 63% were male. Laboratory results were available for the 464 clusters with a median of 9 days (IQR = 6-13 days) after cluster identification. Less than one in five clusters had cases that tested positive for the same virus: respiratory syncytial virus (RSV) in 58 (13%), influenza viruses in 24 (5%), human metapneumovirus (HMPV) in five (1%), human parainfluenza virus (HPIV) in three (0.6%), adenovirus in two (0.4%). While 102/464 (22%) had poultry exposure, none tested positive for influenza A (H5N1) or A (H7N9). None of the 464 clusters led to field deployments for outbreak response. For 11 years, none of the hundreds of identified clusters led to an emergency response. The value of this event-based surveillance might be improved by seeking larger clusters, with stronger epidemiologic ties or decedents.

Protocol for establishing a model for integrated influenza surveillance in Tamil Nadu, India.

The potential for influenza viruses to cause public health emergencies is great. The World Health Organisation (WHO) in 2005 concluded that the world was unprepared to respond to an influenza pandemic. Available surveillance guidelines for pandemic influenza lack the specificity that would enable many countries to establish operational surveillance plans. A well-designed epidemiological and virological surveillance is required to strengthen a country's capacity for seasonal, novel, and pandemic influenza detection and prevention. Here, we describe the protocol to establish a novel mechanism for influenza and SARS-CoV-2 surveillance in the four identified districts of Tamil Nadu, India. This project will be carried out as an implementation research. Each district will identify one medical college and two primary health centres (PHCs) as sentinel sites for collecting severe acute respiratory infections (SARI) and influenza like illness (ILI) related information, respectively. For virological testing, 15 ILI and 10 SARI cases will be sampled and tested for influenza A, influenza B, and SARS-CoV-2 every week. Situation analysis using the WHO situation analysis tool will be done to identify the gaps and needs in the existing surveillance systems. Training for staff involved in disease surveillance will be given periodically. To enhance the reporting of ILI/SARI for sentinel surveillance, trained project staff will collect information from all ILI/SARI patients attending the sentinel sites using pre-tested tools. Using time, place, and person analysis, alerts for abnormal increases in cases will be generated and communicated to health authorities to initiate response activities. Advanced epidemiological analysis will be used to model influenza trends over time. Integrating virological and epidemiological surveillance data with advanced analysis and timely communication can enhance local preparedness for public health emergencies. Good quality surveillance data will facilitate an understanding outbreak severity and disease seasonality. Real-time data will help provide early warning signals for prevention and control of influenza and COVID-19 outbreaks. The implementation strategies found to be effective in this project can be scaled up to other parts of the country for replication and integration.

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.

Antibiotic use among SARI patients according to the AWaRe classification before and during the COVID-19 pandemic in Bangladesh

Background: Irrational antibiotic use among hospitalized patients can lead to antibiotic resistance. For rational use, the WHO introduced the Access, Watch, and Reserve (AWaRe) classification of antibiotics. We explored antibiotic use according to the AWaRe classification among patients hospitalized with severe acute respiratory infection (SARI) between the prepandemic and COVID-19 pandemic periods in Bangladesh. Methods: From June 2017 to November 2022, we analyzed SARI inpatient data from the hospital-based influenza surveillance platform at 9 tertiary-level hospitals in Bangladesh. We defined June 2017–February 2020 as the prepandemic period and March 2020–November 2022 as the pandemic period. Physicians identified inpatients meeting the WHO SARI case definition and recorded patient demographics, clinical characteristics, and antibiotics received during hospitalization. We used descriptive statistics to summarize the data. Results: We enrolled 20,640 SARI patients (median age, 20 years; IQR, 1.6–50; 63% male); and among them, 18,197 (88%) received antibiotics (26% of those received &gt;1 different course of antibiotics). Compared to the prepandemic period, the proportion of antibiotic use among SARI patients was higher during the pandemic: 93% (9,887 of 10,655) versus 83% (8,310 of 9,985) (P &lt; .001). According to AWaRe classification, Access, Watch, and Reserve groups accounted for 32% (n = 2,623), 86% (n = 7,158), and 0.05% (n = 4), respectively, before the pandemic and 32% (n = 3,194), 90% (n = 8,850), and 0.08% (n = 8), respectively, during the pandemic (Fig.). The most common antibiotic prescribed for children aged &lt;5 years during the prepandemic was ceftriaxone (n = 1,940, 74%), followed by amikacin (n = 325, 13%) and flucloxacillin (n = 300, 12%); similarly, during the pandemic, most common antibiotic prescribed was ceftriaxone (n = 3,097, 79%), followed by amikacin (n = 723, 18%) and flucloxacillin (n = 348, 9%). The most common antibiotic prescribed for patients aged ≥5 years during the prepandemic period was ceftriaxone (n = 3,174, 54%), followed by amoxicillin-clavulanic acid (n = 1,304, 22%) and azithromycin (n = 1,038, 18%). During the pandemic, the most common antibiotic prescribed for patients aged ≥5 years was ceftriaxone (n = 3,793, 64%), followed by amoxicillin-clavulanic acid (n = 1,327, 22%) and clarithromycin (n = 797, 13%). Among children aged &lt;5 years, use of the Watch group of antibiotics during the prepandemic and pandemic periods was similar: 94% (n = 3,688) versus 95% (n = 2,347) (P = .099). However, among patients aged ≥5 years, the use of Watch antibiotics was higher during the pandemic compared to the prepandemic period: 87% (n = 5,163) versus 82% (n = 4,811) (P &lt; .001). Conclusions: Use of antibiotics in the Watch group was predominant among SARI patients both before and during the COVID-19 pandemic, and it increased among SARI patients aged ≥5 years during the pandemic period in Bangladesh. Promoting antibiotic stewardship programs for physicians, including in-service training on antibiotic use, could reduce irrational antibiotic use, which might contribute to mitigating antibiotic resistance in the country.Financial support: This study was funded by the CDC.Disclosures: None

COVID-19 and Severe Acute Respiratory Infections: Monitoring Trends in 421 German Hospitals During the First Four Pandemic Waves.

Reliable surveillance systems to monitor trends of COVID-19 case numbers and the associated healthcare burden play a central role in efficient pandemic management. In Germany, the federal government agency Robert-Koch-Institute uses an ICD-code-based inpatient surveillance system, ICOSARI, to assess temporal trends of severe acute respiratory infection (SARI) and COVID-19 hospitalization numbers. In a similar approach, we present a large-scale analysis covering four pandemic waves derived from the Initiative of Quality Medicine (IQM), a German-wide network of acute care hospitals. Routine data from 421 hospitals for the years 2019-2021 with a "pre-pandemic" period (01-01-2019 to 03-03-2020) and a "pandemic" period (04-03-2020 to 31-12-2021) was analysed. SARI cases were defined by ICD-codes J09-J22 and COVID-19 by ICD-codes U07.1 and U07.2. The following outcomes were analysed: intensive care treatment, mechanical ventilation, in-hospital mortality. Over 1.1 million cases of SARI and COVID-19 were identified. Patients with COVID-19 and additional codes for SARI were at higher risk for adverse outcomes when compared to non-COVID SARI and COVID-19 without any coding for SARI. During the pandemic period, non-COVID SARI cases were associated with 28%, 23% and 27% higher odds for intensive care treatment, mechanical ventilation and in-hospital mortality, respectively, compared to pre-pandemic SARI. The nationwide IQM network could serve as an excellent data source to enhance COVID-19 and SARI surveillance in view of the ongoing pandemic. Future developments of COVID-19/SARI case numbers and associated outcomes should be closely monitored to identify specific trends, especially considering novel virus variants.