Respiratory Virus Surveillance Research Articles

Cohort profile: A population-based record linkage platform to address critical epidemiological evidence gaps in respiratory syncytial virus and other respiratory infections

IntroductionThe Western Australia (WA) Respiratory Infections Linked Data Platform is a population-based cohort established to investigate the epidemiology of RSV and other respiratory infections in children aged 0-10 years, incorporating microbiological testing patterns, hospital admissions, emergency department presentations, and socio-demographic data. MethodsThe cohort was formed through individual linkages between datasets from the WA Department of Health including the Birth and Death Registry, Midwives Notification System (MNS), Hospital Morbidity Data Collection, Emergency Department Data Collection, WA Notifiable Diseases Database, WA Register of Developmental Anomalies, WA Cerebral Palsy Register, WA Antenatal Vaccination Database, WA Family Connections, and PathWest Respiratory Virus Surveillance Data. Hospitalisations and emergency department presentations were temporally linked to routine respiratory viral surveillance data. ResultsThe cohort consists of 368,830 WA births between 1 January 2010 and 31 December 2020 with accompanying perinatal and demographic data, and with secondary care follow-up to 30 June 2022. Of these births, 24,660 (6.7%) identify as Aboriginal. A total of 4,077 (1.1%) children died from all causes during the study period (2010-2020), and 9.2% (33,818) of children were born preterm (<37 weeks). ConclusionThe Respiratory Infections Linked Data Platform enables epidemiological investigations, identifying virus-specific risk groups, risk factors, clinical presentation, viral testing patterns, long-term impacts and accurate measures of viral incidence rates in risk and population sub-groups This will not only aid in the calculation of cost-effectiveness estimates of interventions such as immunisations, but also provide guidance for design and implementation of such programs to priority groups. The Respiratory Infections Linked Data Platform will also enable evaluation of the direct and indirect effects of maternal and infant vaccines and new therapeutics. Analyses using this platform will also generate epidemiological data needed for other respiratory viruses on the vaccine pipeline such as parainfluenza virus and human metapneumovirus.

Rapid identification of SARS-CoV-2 variants using stable high-frequency mutation sites.

Respiratory infectious viruses, including SARS-CoV-2, undergo rapid genetic evolution, resulting in diverse subtypes with complex mutations. Detecting and differentiating these subtypes pose significant challenges in respiratory virus surveillance. To address these challenges, we integrated ARMS-PCR with molecular beacon probes, allowing selective amplification and discrimination of subtypes based on adjacent mutation sites. The method exhibited high specificity and sensitivity, detecting as low as 104 copies/mL via direct fluorescence analysis and ~106 copies/mL using real-time PCR. Our robust detection approach offers a reliable and efficient solution for monitoring evolving respiratory infections, aiding early diagnosis and control measures. Further research could extend its application to other respiratory viruses and optimize its implementation in clinical settings.

Burden of disease of respiratory syncytial virus in infants, young children and pregnant women and people.

Passive immunization products for infants and pregnant women and people have sparked interest in understanding Canada's respiratory syncytial virus (RSV) burden. This rapid review examines RSV burden of disease in infants, young children and pregnant women and people. Electronic databases were searched to identify studies and systematic reviews reporting data on outpatient visits, hospitalizations, intensive care unit admissions, deaths and preterm labour associated with RSV. We also contacted Canadian respiratory virus surveillance experts for additional data. Overall, 17 studies on infants and young children and 10 studies on pregnant women and people were included, in addition to primary surveillance data from one Canadian territory (Yukon). There were higher rates of medical utilization for infants than older children. Hospitalization rates were highest in infants under six months (more than 1% annually), with 5% needing intensive care unit admission, but mortality was low. Severe outcomes often occurred in healthy full-term infants and burden was higher than influenza. Respiratory syncytial virus attack rate was 10%-13% among pregnant women and people. Only one study found a higher hospitalization rate in pregnant women and people compared to non-pregnant women and people. Limited evidence was found on intensive care unit admission, death and preterm birth for pregnant women and people. While risk of severe outcomes is larger in high-risk infants and children, healthcare burden is greatest in healthy term infants. The RSV severity for pregnant women and people appears to be similar to that for non-pregnant women and people.

Key Challenges for Respiratory Virus Surveillance while Transitioning out of Acute Phase of COVID-19 Pandemic.

To support the ongoing management of viral respiratory diseases while transitioning out of the acute phase of the COVID-19 pandemic, many countries are moving toward an integrated model of surveillance for SARS-CoV-2, influenza virus, and other respiratory pathogens. Although many surveillance approaches catalyzed by the COVID-19 pandemic provide novel epidemiologic insight, continuing them as implemented during the pandemic is unlikely to be feasible for nonemergency surveillance, and many have already been scaled back. Furthermore, given anticipated cocirculation of SARS-CoV-2 and influenza virus, surveillance activities in place before the pandemic require review and adjustment to ensure their ongoing value for public health. In this report, we highlight key challenges for the development of integrated models of surveillance. We discuss the relative strengths and limitations of different surveillance practices and studies as well as their contribution to epidemiologic assessment, forecasting, and public health decision-making.

The role of human rhinovirus in COPD exacerbations in Abu Dhabi: molecular epidemiology and clinical significance

ABSTRACT This study aimed to describe the molecular epidemiology and seasonality of human rhinovirus (HRV) in chronic obstructive pulmonary disease (COPD) and its association with COPD exacerbations in Abu Dhabi, the United Arab Emirates (UAE). Sputum specimens were collected for analysis from all COPD patients who visited a medical center from November 2021 to October 2022. The real-time quantitative polymerase chain reaction (qPCR) test was used to detect HRV. Of the 78 COPD patients included in the study, 58 (74%) patients presented with one or more exacerbation episodes. The incidence of COPD exacerbation peaked over the winter and substantially decreased during the summer. HRV positivity in patients during exacerbation (E1) was 11/58 (19%) and 15/58 (26%) two weeks after the exacerbation episode (E2). There was no significant difference in the HRV load in these patients. No statistically significant difference was observed in the detection of HRV during exacerbation compared to patients with stable COPD. This is the first study to assess the association between HRV detection by qPCR and COPD exacerbations in the UAE. The high sensitivity of the detection technology helped collect reliable epidemiologic data. Few studies have provided similar Middle East data. This study’s pattern of COPD exacerbations and HRV detection parallels that of temperate countries. This information can help with future, more extensive surveillance of respiratory viruses in the UAE and the Middle East and their association with COPD exacerbations.

Syndromic surveillance performance in Canada throughout the COVID-19 pandemic, March 1, 2020 to March 4, 2023.

The coronavirus disease 2019 (COVID-19) pandemic has highlighted the need for robust surveillance of respiratory viruses. Syndromic surveillance continues to be an important surveillance component recommended by the World Health Organization (WHO). While FluWatchers, Canada's syndromic surveillance system, has been in place since 2015, the COVID-19 pandemic provided a valuable opportunity to expand the program's scope and underlying technology infrastructure. Following some structural changes to FluWatchers syndromic questionnaire, participants are now able to contribute valuable data to the non-specific surveillance of respiratory virus activity across Canada. This article examines the performance of FluWatchers' syndromic surveillance over the three years of the COVID-19 pandemic in Canada. More specifically, this article examines FluWatchers' performance with respect to the correlation between the FluWatchers influenza-like illness (ILI) and acute respiratory infection (ARI) indicators and total respiratory virus detections (RVDs) in Canada, including influenza, respiratory syncytial virus (RSV), severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and other respiratory viruses.

2652. Detection of respiratory viruses by air sampling and student and staff surveillance testing in two elementary schools

Abstract Background The COVID-19 pandemic highlighted the need for better data to understand how ventilation may impact respiratory virus transmission. We evaluated if there was an association between respiratory viruses detected in school room air samples and nasal swabs from students/ staff in the same room. Methods We performed air and respiratory sampling to detect respiratory viruses at 3 time points between Feb 27 - Mar 28, 2023 in 2 elementary schools. Three classrooms, a multipurpose room, and school nurse’s office in each school had 1 air sample/ room collected using Thermo Scientific AerosolSense™ sampler during 8 school hours. Concomitant respiratory viral testing, using self-collected nasal swabs, was performed in students/ staff enrolled in a respiratory virus surveillance school testing program. Air and respiratory specimens were tested for adenovirus (AdV); coronaviruses (CoV) 229E, HKU1, NL63, OC43; human metapneumovirus (hMPV), influenza A and B (Flu), parainfluenza virus 1-4 (PIV), respiratory syncytial virus (RSV), rhinovirus/ enterovirus (RV/EV), and SARS-CoV-2 using the Hologic® Panther Fusion® Respiratory Assay. Detected respiratory viruses in room air and respiratory samples were compared to determine likelihood of capturing current human respiratory viral infections in room air and additional viruses circulating from unsampled students/ staff in the same room. RV and AdV in human respiratory samples were typed by partial genomic sequencing to understand if viruses were similar. Results Ten rooms, including 6 classrooms with ≈25 people/ room, were sampled at 3 occasions. At least 1 respiratory virus was detected in 27/ 30 (90%) air samples. 59 samples were obtained from 20 students and 5 staff in these rooms; 24 (41%) were positive for ≥1 virus and 11/24 (46%) rooms with concomitant air and respiratory samples had the same viruses detected (Table). RV typing demonstrates that both participants from Room E, Round 1 and 2 had RV-B27. Both participants from Room F, Round 2 with single AdV infections had AdV B3.Table.Concomitant respiratory virus detection from student and staff nasal swabs and air samplers (N=student/staff tested per room) Conclusion Concomitant respiratory virus surveillance in air samples and students/ staff can be performed to better understand the role of ventilation and respiratory virus transmission. Additional studies, including sequencing data and symptom assessment, are needed. Disclosures Rangaraj Selvarangan, BVSc, PhD, D(ABMM), FIDSA, FAAM, Abbott: Honoraria|Altona Diagnostics: Grant/Research Support|Baebies Inc: Advisor/Consultant|BioMerieux: Advisor/Consultant|BioMerieux: Grant/Research Support|Bio-Rad: Grant/Research Support|Cepheid: Grant/Research Support|GSK: Advisor/Consultant|Hologic: Grant/Research Support|Lab Simply: Advisor/Consultant|Luminex: Grant/Research Support

2074. Longitudinal wastewater surveillance for endemic respiratory viruses and its correlation with clinically confirmed cases in Calgary, Canada

Abstract Background Wastewater (WW)-based surveillance of SARS-CoV-2 is an established tool for COVID-19 pandemic monitoring, providing a leading indicator to cases and hospitalizations. However, its potential for monitoring endemic respiratory viruses has not been elucidated. We assessed the occurrence of Influenza A (IAV), Influenza B (IBV), and Respiratory Syncytial Virus (RSV) RNA in WW treatment plants (WWTP) in Alberta's largest city and its correlation with clinical disease. Methods Twenty-four-hour composite WW samples were collected weekly from three WWTP in Calgary between Mar'22/Apr'23. WW was concentrated and RNA extracted using the 4S-Silica Column. Viral RNA was quantified using a commercial TaqMan assay (IAV, Assay ID Vi99990011 po, Applied Biosystems) and established RT-qPCR assays targeting: the hemagglutinin gene (IBV) and nucleocapsid gene (RSV). Flow rates at each WWTP were used to create a composite city-wide metric for each target. WW values were compared to clinical data reported by Alberta Health Services and reported as total cases and test positivity rates across the Calgary Zone (or entire Province if granular data was unavailable). Results IAV peaked in Calgary's WW between November-December 2022, IBV between February-April 2023 and RSV between November 2022-February 2023 (Figure 1,2,3). The composite-IAV signal positively correlated with weekly confirmed clinical cases within the Calgary Zone (Spearman's r= 0.83, p< 0.0001 for signals recorded the same week, and r= 0.85, p< 0.0001 for the prior week). The positive correlation existed regardless of influenza typed as H3N2, H1N1 or untyped. Furthermore, specimen test positivity rates across the entire province correlated with Calgary's WW measured IAV (Spearman's r= 0.88, p< 0.0001). The IBV WW signal correlated with clinical cases (Spearman's r= 0.63, p< 0.0001) and test positivity rates (Spearman's r= 0.74, p< 0.0001) across the entire province. Calgary's RSV WW correlated with clinical cases (Spearman's r= 0.56, p=0.001) and test positivity rates (Spearman's r= 0.50, p=0.007) across Alberta.Figure 1.Comparison of aggregate WW IAV in Calgary compared to locally confirmed clinical cases.Figure 2.Trend of aggregate WW IBV signal in Calgary compared to clinically confirmed cases.Figure 3.Trend of aggregate signal in Alberta for RSV compared to clinically confirmed cases over time measured. There is a peak in the RSV signal from November 2022 to February 2023, with a correlation to Alberta’s weekly confirmed clinical cases. Conclusion WW surveillance is an emerging technology enabling objective, unbiased and inclusive population-level monitoring of endemic respiratory viral infections. Disclosures All Authors: No reported disclosures

1745. Respiratory Syncytial Virus Surveillance of Child Care Attendees, Family Members, and Child Care Providers

Abstract Background Respiratory syncytial virus (RSV) is a leading cause of severe respiratory illness among young children. In the U.S., a third of these children attend child care centers (CCC), where RSV can spread rapidly and be transmitted to family members. The study objective was to determine the incidence of RSV in CCC attendees and their household contacts. Methods The prospective cohort enrolled students (< 6 years old), their household contacts and child care providers (CCP) at six CCC in Ann Arbor, MI from May 2021 to March 2022. Participants completed a symptom diary and weekly nasal swabs. RT-PCR was used to detect RSV. Incidence rates were calculated using Poisson regression. Results A total of 2,342 swabs were collected during 19,121 person-days from 32 students, 13 household child contacts (7 of whom were also students), 45 household adult contacts, and 10 CCP. The incidence rates per 10,000 person-days (95% CI) for total vs. asymptomatic cases were 10.2 (4.2, 24.5) vs. 2.0 (0.3, 14.5) for students, 8.4 (2.1, 33.7) vs. 4.2 (0.6, 30.0) for child contacts, and 5.4 (2.2, 12.9) vs. 1.1 (0.2, 7.6) for adult contacts, respectively. Twelve people tested positive for RSV: 5 (15.6%) were students, 2 (15.4%) were child contacts, 5 (11.1%) were adult contacts, and none were CCP. Semiquantitative cycle threshold was comparable between samples from asymptomatic and symptomatic cases. Three students, 1 child contact and 3 adult contacts had serial positive swabs for a single illness. Asymptomatic cases were detected in 1 (20%) student, 1 (20%) adult contact, and 1 (50%) child contact. Suspected transmission events were observed in 3/24 (12.5%) households with documented infection. All cases were detected between 9/6/21 and 1/17/22, coinciding with RSV circulation in Michigan during the study period. Conclusion This study demonstrates the continued presence of RSV in CCC, including during times of increased disease mitigation, and transmission between children and household contacts may have occurred. Asymptomatic infection was detected, albeit at lower rates than symptomatic infections. Given the incidence of RSV detected, our findings underscore the importance of implementing additional surveillance and infection prevention policies in CCC to mitigate the impact of RSV on vulnerable populations. Disclosures Khalil Chedid, MPH, MD, PHD, Merck: Grant/Research Support Timothy Shope, MD MPH, Merck: Grant/Research Support Andrew Hashikawa, MD, Merck: Grant/Research Support Anna Wang-Erickson, PhD, Merck: Grant/Research Support John V. Williams, MD, Merck: Grant/Research Support|Quidel: Board Member Emily T. Martin, PhD, MPH, Merck: Grant/Research Support

546. COVID-19 Monoclonal Antibody Use at a Stand Alone Children’s Hospital

Abstract Background Texas Children’s Hospital (TCH) implemented an outpatient clinic for eligible patients to receive infusions when COVID monoclonal antibodies (mAbs) were approved for use in non-hospitalized, high-risk patients with mild to moderate COVID-19. There are limited data evaluating the use of outpatient COVID mAbs in pediatric patients. We describe the clinical characteristics and outcomes of the patients treated with COVID mAbs at TCH. Methods Patients that were referred to receive COVID mAbs from 12/1/2020 to 5/5/2022 were included. Information collected included demographics, comorbidities, refusal reason, adverse events, emergency center (EC) visits or admission within 14 days after final dose, and EC visit or admission within 14 days of referral if patients did not receive COVID mAbs. Chi-square was used to determine differences between the groups. Results There were 262 patients referred during the study period. The median age of all referred patients was 15.8 years (IQR 14-17.4 years). Majority of referrals were for treatment of COVID-19 infection rather than post-exposure prophylaxis (92.8% vs 7.2%). Of the 262 referrals, 134 patients received COVID mAbs (51.2%) while 128 patients were not treated. Majority of the patients received casirivimab-imdevimab (73.9%). The comorbidities of all patients are shown in Figure 1. The most common reasons for patients to not receive COVID mAbs were no drug available or not listed, and the full list of reasons are listed in Figure 2. The median time from reported symptom onset to infusion was 4 days (IQR 2-6 days). Of the 134 infused patients, 8 patients (6%) visited the EC within 14 days from infusion, and 6 (4.5%) were admitted while 4 patients (3.1%) that did not receive an antibody visited the EC resulting in 3 admissions (2.3%) (EC visits p=0.27; admissions p=0.34). There were 11 patients (8.2%) that experienced adverse events from their infusion, which led to 5 of the 8 EC visits. Comorbidities were similar across the infused and non-infused groups (p=0.16). Number of high-risk conditions represented by all referred, high-risk patients Number of patients for each reason for not receiving a COVID-19 antibody infusion Conclusion COVID mAb treatments were well tolerated among pediatric patients. Majority of patients in both groups did not require EC visit or hospitalization. More data are needed to determine the clinical efficacy of mAbs patients. Disclosures Flor M. Munoz, MD, MSc, CDC respiratory virus surveillance: Grant/Research Support|Gilead: Grant/Research Support|Moderna, sanofi, aztra zeneca, Merck, GSK: Advisor/Consultant|NIH: DSMB|NIH COVID-19 vaccines in pregnancy: Grant/Research Support|Pfizer Pediatric COVID-19 vaccines: Grant/Research Support|Pfizer, Dynavax, Monderna, Meissa, NIH: DSMB Lisa Forbes Satter, MD, ADMA: Advisor/Consultant|CsL Behring: Advisor/Consultant|Grifols: Advisor/Consultant|incyte: Advisor/Consultant|Pharming: Advisor/Consultant|Takeda: Advisor/Consultant

Respiratory Viruses Causing Influenza Like Illness/Severe Acute Respiratory Infection During COVID-19 Pandemic

Background: Respiratory tract infections caused by viruses are among the most common diseases in humans worldwide. The diagnosis remains difficult as the symptoms overlap significantly with each other. Objectives: The objective of this study is to identify the respiratory viruses other than SARS-CoV- -2 causing Influenza-like illness (ILI) /severe acute respiratory infection (SARI) during COVID-19 pandemic Methods: A total of 100 samples, including COVID-19 positive (n=50) and negative (n=50), were included in the study. The detailed case record form was filled for each patient including relevant history. Nasopharyngeal and Oropharyngeal swabs were subjected to standardized RT-PCR for the detection of SARS-CoV-2 followed by Multiplex RT-PCR for other respiratory viruses. Results: Other respiratory viruses causing ILI/SARI symptoms similar to SARS-CoV2 during COVID-19 pandemic in non-COVID-19 patients aged more than 18 years were found to be Human metapneumovirus (2%), Human adenovirus (1%), Human parainfluenza virus-1 (1%). The result suggested that other respiratory viral infections are significantly higher among COVID-19 negative individuals presenting with respiratory illness as compared to COVID-19 positive individuals, possibly due to viral interference and competitive advantage of SARS-CoV-2 in modulating the host immune system. Conclusion: The other respiratory viruses in SARS-CoV-2 negative patients had mild to moderate ILI/SARI symptoms, which usually do not require hospitalization but need to be monitored, especially in high-risk patients. Human metapneumovirus, Adenovirus, Parainfluenza virus-1 most commonly occured in more than 60 years age group with comorbidity which can be useful in stratification for future surveillance of other respiratory viruses in health care settings.

Characteristics of respiratory viruses' circulation through a six-year period (2016-2022) in a pediatric population in Normandy, France, and the impact of COVID-19 pandemic.

The impact of COVID-19 on the circulation of respiratory viruses has highlighted the need for ongoing surveillance and preparedness for emerging infectious diseases. The aim of this study was to provide information on the dynamics of respiratory viruses in pediatric populations to inform public health policies and strategies for the prevention and control of respiratory infections. This study analyzed data on the detection of respiratory viruses in pediatric populations from 2016 to 2022. The weekly number of tests and positive results for respiratory viruses were collected and analyzed from the two major university hospitals, Caen and Rouen. Different assays, including multiplex panels and rapid detection kits, were used for testing. The study analyzed the epidemiological trends of respiratory viruses in a French region during the COVID-19 pandemic. The data set included 37,969 tests, with a significant increase in the number of tests in 2020-2021 and 2021-2022. The rate of positive tests fell below 50% in 2021-2022. Enteroviruses (EV)/rhinoviruses (RV) and respiratory syncytial viruses (RSV) were the most frequently identified viruses, except in 2021-2022, when Flu ranked second. The Flu epidemic appeared slightly earlier in 2021-2022 and lasted for 25 weeks, with a doubling time of 4.03. The RSV epidemic occurred earlier in 2021-2022 and had similar dynamics to pre-pandemic years. EV/RV continued to circulate throughout the lockdowns, while low numbers of other viruses were detected. Our results emphasize the importance of continuing active surveillance of respiratory virus circulation and the need for new recommendations for respiratory virus detection in pediatric patients.IMPORTANCEThe report highlights an epidemiological change in the circulation of respiratory viruses in pediatric populations due to strategies adopted against COVID-19 pandemic. COVID-19 has resulted in a significant increase in requests for multiplex respiratory research to identify the virus responsible for the symptoms. The diagnostic needs have increased, and the number of samples analyzed in 2021-2022 is equal to the samples analyzed over the four epidemic periods preceding the pandemic. The report suggests the importance of active surveillance of respiratory viruses' circulation and new recommendations for respiratory virus detection in pediatric patients.

Respiratory virus surveillance in hospitalized children less than two-years of age in Kenema, Sierra Leone during the COVID-19 pandemic (October 2020- October 2021).

Globally, viral pathogens are the leading cause of acute respiratory infection in children under-five years. We aim to describe the epidemiology of viral respiratory pathogens in hospitalized children under-two years of age in Eastern Province of Sierra Leone, during the second year of the SARS-CoV-2 pandemic. We conducted a prospective study of children hospitalized with respiratory symptoms between October 2020 and October 2021. We collected demographic and clinical characteristics and calculated each participant´s respiratory symptom severity. Nose and throat swabs were collected at enrollment. Total nucleic acid was purified and tested for multiple respiratory viruses. Statistical analysis was performed using R version 4.2.0 software. 502 children less than two-years of age were enrolled. 376 (74.9%) had at least one respiratory virus detected. The most common viruses isolated were HRV/EV (28.2%), RSV (19.5%) and PIV (13.1%). Influenza and SARS-CoV-2 were identified in only 9.2% and 3.9% of children, respectively. Viral co-detection was common. Human metapneumovirus and RSV had more than two-fold higher odds of requiring O2 therapy while hospitalized. Viral pathogen prevalence was high (74.9%) in our study population. Despite this, 100% of children received antibiotics, underscoring a need to expand laboratory diagnostic capacity and to revisit clinical guidelines implementation in these children. Continuous surveillance and serologic studies among more diverse age groups, with greater geographic breadth, are needed in Sierra Leone to better characterize the long-term impact of COVID-19 on respiratory virus prevalence and to better characterize the seasonality of respiratory viruses in Sierra Leone.

Respiratory virus infections in decedents in a large, urban medical examiner's office

ObjectiveMost respiratory virus surveillance relies on medically attended respiratory illness, but an understanding of the true patterns of infection independent of care-seeking behaviour would enhance clinical and public health responses to respiratory virus outbreaks. We evaluated the potential of decedent surveillance by estimating the burden of respiratory virus infection in decedents in a large, urban medical examiner's office. Study designObservational. MethodsIn 2020–2022, we tested nasopharyngeal swabs from 4121 decedents in Detroit, Michigan for 15 respiratory viruses, including SARS-CoV-2, respiratory syncytial virus, and influenza virus A and B. We analysed infection prevalence over time and by age, sex, race/ethnicity, and manner of death. ResultsOf 4113 valid tests, 30.2% were positive for at least one virus, and 6.1% were positive for multiple viruses. All viruses were detected except for influenza A/H1N1 and influenza B. The most prevalent viruses were SARS-CoV-2 (15.7%), rhinovirus (11.2%), and adenovirus (4.9%), which were detected in all months. Most viruses exhibited decreasing prevalence with age, higher prevalence among Black and Hispanic than among White decedents and lower prevalence among deaths from natural causes; SARS-CoV-2 was a notable exception to the patterns by age and manner of death, instead reflecting community trends in catchment counties. ConclusionsThere was high prevalence and diversity of respiratory viruses in decedents entering a large, urban medical examiner's office. Decedent surveillance could offer a clearer picture of the true underlying burden of infection, motivating public health priorities for intervention and vaccine development, and augmenting data for real-time response to respiratory virus outbreaks.

Surveillance of respiratory viruses at health facilities from across Kenya, 2014

Background: Acute respiratory illnesses (ARI) are a major cause of morbidity and mortality globally. With (re)emergence of novel viruses and increased access to childhood bacterial vaccines, viruses have assumed greater importance in the aetiology of ARI. There are now promising candidate vaccines against some of the most common endemic respiratory viruses. Optimal delivery strategies for these vaccines, and the need for interventions against other respiratory viruses, requires geographically diverse data capturing temporal variations in virus circulation. Methods: We leveraged three health facility-based respiratory illness surveillance platforms operating in 11 sites across Kenya. Nasopharyngeal (NP) and/or oropharyngeal (OP) specimens, patient demographic, and clinical characteristics were collected in 2014 from individuals of various ages presenting with respiratory symptoms at the surveillance facilities. Real time multiplex polymerase chain reaction was used to detect rhinoviruses, respiratory syncytial virus (RSV), influenza virus, human coronaviruses (hCoV), and adenoviruses. Results: From 11 sites, 5451 NP/OP specimens were collected and tested from patients. Of these, 40.2% were positive for at least one of the targeted respiratory viruses. The most frequently detected were rhinoviruses (17.0%) and RSV A/B (10.5%), followed by influenza A (6.2%), adenovirus (6.0%) and hCoV (4.2%). RSV was most prevalent among infants aged <12 months old (18.9%), adenovirus among children aged 12–23 months old (11.0%), influenza A among children aged 24–59 months (9.3%), and rhinovirus across all age groups (range, 12.7–19.0%). The overall percent virus positivity varied by surveillance site, health facility type and case definition used in surveillance. Conclusions: We identify rhinoviruses, RSV, and influenza A as the most prevalent respiratory viruses. Higher RSV positivity in inpatient settings compared to outpatient clinics strengthen the case for RSV vaccination. To inform the design and delivery of public health interventions, long-term surveillance is required to establish regional heterogeneities in respiratory virus circulation and seasonality.

Rapidly developed, optimized, and applied wastewater surveillance system for real-time monitoring of low-incidence, high-impact MPOX outbreak.

Recent MPOX viral resurgences have mobilized public health agencies around the world. Recognizing the significant risk of MPOX outbreaks, large-scale human testing, and immunization campaigns have been initiated by local, national, and global public health authorities. Recently, traditional clinical surveillance campaigns for MPOX have been complemented with wastewater surveillance (WWS), building on the effectiveness of existing wastewater programs that were built to monitor SARS-CoV-2 and recently expanded to include influenza and respiratory syncytial virus surveillance in wastewaters. In the present study, we demonstrate and further support the finding that MPOX viral fragments agglomerate in the wastewater solids fraction. Furthermore, this study demonstrates that the current, most commonly used MPOX assays are equally effective at detecting low titers of MPOX viral signal in wastewaters. Finally, MPOX WWS is shown to be more effective at passively tracking outbreaks and/or resurgences of the disease than clinical testing alone in smaller communities with low human clinical case counts of MPOX.

Seasonal respiratory virus trends in pediatric patients during the COVID-19 pandemic in Brazil.

Acute respiratory infections are a constant public health problem causing childhood morbidity and mortality worldwide. Reported cases of major respiratory infections decreased in 2020 after restrictive measures were adopted to contain the COVID-19 pandemic, but there is little data on the impact after these measures were relaxed in the subsequent years. This study conducted molecular analysis to identify rhinovirus, respiratory syncytial virus, influenza A virus, and adenovirus in SARS-CoV-2-negative samples taken from symptomatic pediatric patients during 2021 and 2022 to ascertain the impact of pandemic response measures within the broader epidemiological scenario. The positivity rates found were 28.3% and 50.8%, in 2021 and 2022, respectively, representing a significant increase (1.8 times) in the circulation of non-SARS-CoV-2 viruses after the reduction of non-pharmacological measures to contain the COVID-19 pandemic. Within the positive samples, rhinovirus and respiratory syncytial virus were most frequent (44.4 and 18% in 2021; 44.5 and 22.5% in 2022), whereas influenza A and adenovirus were found in lower frequency (12.5 and 5.5% in 2021; 13.4 and 4.9% in 2022, respectively). Because these different respiratory virus diseases produce similar symptoms, diagnosis based on clinical condition alone can be inaccurate, and more reliable testing is required to select the best therapeutic approach for each case. The loosening of restrictive measures to contain the COVID-19 pandemic led to higher numbers of other respiratory infections in pediatric patients. Ongoing surveillance and differential diagnosis of respiratory viruses are required to better understand their seasonal patterns after the COVID-19 pandemic to guide prevention and control strategies.

Influenza transmission during COVID-19 measures downscaling in Greece, August 2022: evidence for the need of continuous integrated surveillance of respiratory viruses.

After the near absence of influenza and other respiratory viruses during the first 2 years of the COVID-19 pandemic, an increased activity of mainly influenza A(H3N2) was detected at the beginning of August 2022 in Greece on three islands. Of 33 cases with respiratory symptoms testing negative for SARS-CoV-2 with rapid antigen tests, 24 were positive for influenza: 20 as A(H3N2) subtype and four as A(H1N1)pdm09 subtype. Phylogenetic analysis of selected samples from both subtypes was performed and they fell into clusters within subclades that included the 2022/23 vaccine strains. Our data suggest that influenza can be transmitted even in the presence of another highly infectious pathogen, such as SARS-CoV-2, with a similar transmission mode. We highlight the need for implementing changes in the current influenza surveillance and suggest a move from seasonal to continuous surveillance, especially in areas with a high number of tourists. Year-round surveillance would allow for a timelier start of vaccination campaigns and antiviral drugs procurement processes.

Burden of long COVID among adults experiencing sheltered homelessness: a longitudinal cohort study in King County, WA between September 2020—April 2022

BackgroundPeople experiencing homelessness (PEH) are at increased risk for acquiring SARS-CoV-2, but the burden of long COVID in this population is unknown.MethodsWe conducted a matched prospective cohort study to assess the prevalence, characteristics, and impact of long COVID among sheltered PEH in Seattle, WA between September 2020—April 2022. Adults ≥ 18 years, residing across nine homeless shelters with active respiratory virus surveillance, were eligible to complete in-person baseline surveys and interval follow-up phone surveys. We included a subset of 22 COVID-19-positive cases who tested positive or inconclusive for SARS-CoV-2 and 44 COVID-19-negative controls who tested negative for SARS-CoV-2, frequency matched on age and sex. Among controls, 22 were positive and 22 were negative for one of 27 other respiratory virus pathogens. To assess the impact of COVID-19 on the risk of symptom presence at follow-up (day 30–225 post-enrollment test), we performed log-linear regression with robust standard errors, adjusting for confounding by shelter site and demographic variables determined a priori.ResultsOf 53 eligible COVID-19 cases, 22 (42%) completed ≥ 1 follow-up survey. While five (23%) cases reported ≥ 1 symptom at baseline, this increased to 77% (10/13) between day 30–59 and 33% (4/12) day 90 + . The most commonly reported symptoms day 30 + were fatigue (27%) and rhinorrhea (27%), with 8 (36%) reporting symptoms that interfered with or prevented daily activities. Four (33%) symptomatic cases reported receiving medical care outside of a medical provider at an isolation facility. Of 44 controls, 12 (27%) reported any symptoms day 90 + . Risk of any symptoms at follow-up was 5.4 times higher among COVID-19 cases compared to controls (95% CI: 2.7–10.5).ConclusionsShelter residents reported a high prevalence of symptoms 30 + days after their SARS-CoV-2 detection, though few accessed medical care for persistent illness. The impact of COVID-19 extends beyond acute illness and may exacerbate existing challenges that marginalized populations face in maintaining their health and wellbeing.

Respiratory syncytial virus and other respiratory virus infections in residents of homeless shelters - King County, Washington, 2019-2021.

Respiratory syncytial virus (RSV) causes disproportionate morbidity and mortality in vulnerable populations. We tested residents of homeless shelters in Seattle, Washington for RSV in a repeated cross-sectional study as part of community surveillance for respiratory viruses. Of 15 364 specimens tested, 35 had RSV detected, compared to 77 with influenza. The most common symptoms for both RSV and influenza were cough and rhinorrhea. Many individuals with RSV (39%) and influenza (58%) reported that their illness significantly impacted their ability to perform their regular activities. RSV and influenza demonstrated similar clinical presentations and burden of illness in vulnerable populations living in congregate settings.