Respiratory Virus Surveillance Research Articles

Characterization of neuraminidase inhibitor-resistant influenza virus isolates from immunocompromised patients in the Republic of Korea

BackgroundThe emergence of influenza viruses resistant to anti-influenza drugs is a threat to global public health. The Korea Centers for Disease Control and Prevention operates the Korea Influenza and Respiratory Viruses Surveillance System (KINRESS) to monitor epidemics of influenza and Severe Acute Respiratory Infection (SARI) to identify mutated influenza viruses affecting drug resistance, pathogenesis, and transmission.MethodsOropharyngeal swab samples were collected from KINRESS and SARI during the 2018–2019 season. The specimens confirmed influenza virus using real-time RT-PCR on inoculated MDCK cells. HA and NA sequences of the influenza viruses were analyzed for phylogeny and mutations. Neuraminidase inhibition and hemagglutination inhibition assays were utilized to characterize the isolates.ResultsTwo A(H1N1)pdm09 isolates harboring an H275Y substitution in the neuraminidase sequence were detected in patients with acute hematologic cancer. They had prolonged respiratory symptoms, with the virus present in the respiratory tract despite oseltamivir and peramivir treatment. Through the neuraminidase inhibition assay, both viruses were found to be resistant to oseltamivir and peramivir, but not to zanamivir. Although hemagglutinin and neuraminidase phylogenetic analyses suggested that the 2 A(H1N1)pdm09 isolates were not identical, their antigenicity was similar to that of the 2018–19 influenza vaccine virus.ConclusionsOur data indicate the utility of monitoring influenza-infected immunocompromised patients in general hospitals for the early detection of emerging neuraminidase inhibitor-resistant viruses and maintaining continuous laboratory surveillance of patients with influenza-like illness in sentinel clinics to monitor the spread of such new variants. Finally, characterization of the virus can inform the risk assessment for future epidemics and pandemics caused by drug-resistant influenza viruses.

Early trends for SARS-CoV-2 infection in central and north Texas and impact on other circulating respiratory viruses.

Rapid diagnosis and isolation are key to containing the quick spread of a pandemic agent like severe acute respiratory syndrome‐related coronavirus 2 (SARS‐CoV‐2), which has spread globally since its initial outbreak in Wuhan province in China. SARS‐CoV‐2 is novel and the effect on typically prevalent seasonal viruses is just becoming apparent. We present our initial data on the prevalence of respiratory viruses in the month of March 2020. This is a retrospective cohort study post launching of SARS‐CoV‐2 testing at Baylor Scott and White Hospital (BSWH), Temple, Texas. Testing for SARS‐CoV‐2 was performed by real‐time reverse transcription polymerase chain reaction assay and results were shared with State public health officials for immediate interventions. More than 3500 tests were performed during the first 2 weeks of testing for SARS‐CoV‐2 and identified 168 (4.7%) positive patients. Sixty‐two (3.2%) of the 1912 ambulatory patients and 106 (6.3%) of the 1659 emergency department/inpatients tested were positive. The highest rate of infection (6.9%) was seen in patients aged 25 to 34 years, while the lowest rate of infection was seen among patients aged <25 years old (2%). County‐specific patient demographic information was shared with respective public health departments for epidemiological interventions. Incidentally, this study showed that there was a significant decrease in the occurrence of seasonal respiratory virus infections, perhaps due to increased epidemiological awareness about SARS‐CoV‐2 among the general public, as well as the social distancing measures implemented in response to SARS‐CoV‐2. Data extracted for BSWH from the Centers for Disease Control and Prevention's National Respiratory and Enteric Virus Surveillance System site revealed that Influenza incidence was 8.7% in March 2020, compared with 25% in March 2019. This study was intended to provide an initial experience of dealing with a pandemic and the role of laboratories in crisis management. This study provided SARS‐CoV‐2 testing data from ambulatory and inpatient population. Epidemiological interventions depend on timely availability of accurate diagnostic tests and throughput capacity of such systems during large outbreaks like SARS‐CoV‐2.

Surveillance of respiratory viruses among children attending a primary school in rural coastal Kenya

Background: Respiratory viruses are primary agents of respiratory tract diseases. Knowledge on the types and frequency of respiratory viruses affecting school-children is important in determining the role of schools in transmission in the community and identifying targets for interventions. Methods: We conducted a one-year (term-time) surveillance of respiratory viruses in a rural primary school in Kilifi County, coastal Kenya between May 2017 and April 2018. A sample of 60 students with symptoms of ARI were targeted for nasopharyngeal swab (NPS) collection weekly. Swabs were screened for 15 respiratory virus targets using real time PCR diagnostics. Data from respiratory virus surveillance at the local primary healthcare facility was used for comparison. Results: Overall, 469 students aged 2-19 years were followed up for 220 days. A total of 1726 samples were collected from 325 symptomatic students; median age of 7 years (IQR 5-11). At least one virus target was detected in 384 (22%) of the samples with a frequency of 288 (16.7%) for rhinovirus, 47 (2.7%) parainfluenza virus, 35 (2.0%) coronavirus, 15 (0.9%) adenovirus, 11 (0.6%) respiratory syncytial virus (RSV) and 5 (0.3%) influenza virus. The proportion of virus positive samples was higher among lower grades compared to upper grades (25.9% vs 17.5% respectively; χ 2 = 17.2, P -value <0.001). Individual virus target frequencies did not differ by age, sex, grade, school term or class size. Rhinovirus was predominant in both the school and outpatient setting. Conclusion: Multiple respiratory viruses circulated in this rural school population. Rhinovirus was dominant in both the school and outpatient setting and RSV was of notably low frequency in the school. The role of school children in transmitting viruses to the household setting is still unclear and further studies linking molecular data to contact patterns between the school children and their households are required.

Interactive, semi-automatized and open source computational model applied to respiratory viruses surveillance

Acute respiratory infections (ARI) are an important cause of morbidity and mortality worldwide, affecting mainly children and the elderly. They are associated with a high economic burden, increased number of medical visits and hospitalizations. The surveillance of the circulation of respiratory viruses can reduce the health care associated costs, and to optimize the health response. A platform based on R and its package Shiny was designed, to create an interactive and friendly web interface for gathering, analysis and publication of the data. The data from the Chilean metropolitan respiratory viruses surveillance network, available since 2006, was uploaded into the platform. Using this platform, the researcher spends less than 1 minute to upload the data, and the analysis and publication is immediate, available to be seen by any user with a device connected to Internet, who can choose the variables to be displayed. With a very low cost, in a short time, and using the R programming language, it was possible to create a simple, and interactive platform, considerably decreasing the upload and analysis time, and increasing the impact and availability of this surveillance.

The clinical benefit of instituting a prospective clinical community-acquired respiratory virus surveillance program in allogeneic hematopoietic stem cell transplantation

BackgroundThere is a lack of studies comparing clinical outcomes among retrospective versus prospective cohorts of allogeneic stem cell transplant (allo-HCT) recipients with community acquired respiratory virus (CARV) infections. MethodsWe compare outcomes in two consecutive cohorts of allo-HCT recipients with CARV infections. The retrospective cohort included 63 allo-HCT recipients with 108 CARV infections from January 2013 to April 2016 who were screened and managed following standard clinical practice based on influenza and respiratory syncytial virus rapid antigen detection methods. The prospective cohort was comprised of 144 consecutive recipients with 297 CARV episodes included in a prospective interventional clinical surveillance program (ProClinCarvSur-P) based on syndromic multiplex PCR as first-line test from May 2016 to December 2018 at a single transplant center. ResultsCARV infections in the retrospective cohort showed more severe clinical features at the time of diagnosis compared to the prospective cohort (fever 83% vs. 57%, hospital admission 69% vs. 28% and lower respiratory tract 58% vs. 31%, respectively, p ≤ 0.002 for all comparisons). Antiviral therapy was more commonly prescribed in the prospective cohort (69 vs. 43 treated CARV episodes), particularly at the upper respiratory tract disease stage (34 vs. 12 treated CARV episodes). Three-month all-cause mortality was significantly higher in the retrospective cohort (n = 23, 37% vs. n = 10, 7%, p < 0.0001). Multivariate logistic regression analysis showed that recipients included in ProClinCarvSur-P had lower mortality rate [odds ratio 0.31, 95% confidence interval 0.12–0.7, p = 0.01]. ConclusionThis study report on outcome differences when reporting retrospective vs. prospective CARV infections after allo-HCT. Recipients included in a ProClinCarvSur-P had lower mortality.

Human parainfluenza virus circulation, United States, 2011–2019

BackgroundHuman parainfluenza viruses (HPIVs) cause upper and lower respiratory tract illnesses, most frequently among infants and young children, but also in the elderly. While seasonal patterns of HPIV types 1–3 have been described, less is known about national patterns of HPIV-4 circulation. ObjectivesTo describe patterns of HPIVs circulation in the United States (US). Study designWe used data from the National Respiratory and Enteric Virus Surveillance System (NREVSS), a voluntary passive laboratory-based surveillance system, to characterize the epidemiology and circulation patterns of HPIVs in the US during 2011–2019. We summarized the number of weekly aggregated HPIV detections nationally and by US census region, and used a subset of data submitted to NREVSS from public health laboratories and several clinical laboratories during 2015–2019 to analyze differences in patient demographics. ResultsDuring July 2011 - June 2019, 2,700,135 HPIV tests were reported; 122,852 (5 %) were positive for any HPIV including 22,446 for HPIV-1 (18 %), 17,474 for HPIV-2 (14 %), 67,649 for HPIV-3 (55 %), and 15,283 for HPIV-4 (13 %). HPIV testing increased substantially each year. The majority of detections occurred in children aged ≤ 2 years (36 %) with fluctuations in the distribution of age by type. ConclusionsHPIVs were detected year-round during 2011–2019, with type-specific year-to-year variations in circulation patterns. Among HPIV detections where age was known, the majority were aged ≤ 2 years. HPIV-4 exhibited an annual fall-winter seasonality, both nationally and regionally. Continued surveillance is needed to better understand national patterns of HPIV circulation.

A Mini-Review of Adverse Lung Transplant Outcomes Associated With Respiratory Viruses.

Due to their overall immunocompromised state, lung transplant recipients (LTRs) are at increased risk for the development of viral respiratory infections compared to the general population. Such respiratory infections often lead to poor transplant outcomes. We performed a systematic review of the last 30 years of medical literature to summarize the impact of specific respiratory viruses on LTRs. After screening 2,150 articles for potential inclusion, 39 manuscripts were chosen for final review. We found evidence for an association of respiratory viruses including respiratory syncytial virus (RSV), parainfluenza virus, and influenza viruses with increased morbidity following transplant. Through the literature search, we also documented associations of RSV and adenovirus infections with increased mortality among LTRs. We posit that the medical literature supports aggressive surveillance for respiratory viruses among this population.

Respiratory viruses in individuals with a high frequency of animal exposure in southern and highland Vietnam.

Active surveillance for zoonotic respiratory viruses is essential to inform the development of appropriate interventions and outbreak responses. Here we target individuals with a high frequency of animal exposure in Vietnam. Three‐year community‐based surveillance was conducted in Vietnam during 2013‐2016. We enrolled a total of 581 individuals (animal‐raising farmers, slaughterers, animal‐health workers, and rat traders), and utilized reverse transcription‐polymerase chain reaction to detect 15 common respiratory viruses in pooled nasal‐throat swabs collected at baseline or acute respiratory disease episodes. A respiratory virus was detected in 7.9% (58 of 732) of baseline samples, and 17.7% (136 of 770) of disease episode samples (P < .001), with enteroviruses (EVs), rhinoviruses and influenza A virus being the predominant viruses detected. There were temporal and spatial fluctuations in the frequencies of the detected viruses over the study period, for example, EVs and influenza A viruses were more often detected during rainy seasons. We reported the detection of common respiratory viruses in individuals with a high frequency of animal exposure in Vietnam, an emerging infectious disease hotspot. The results show the value of baseline/control sampling in delineating the causative relationships and have revealed important insights into the ecological aspects of EVs, rhinoviruses and influenza A and their contributions to the burden posed by respiratory infections in Vietnam.

Performance of surveillance case definitions for respiratory syncytial virus infections through the sentinel influenza surveillance system, Portugal, 2010 to 2018.

BackgroundWell-established influenza surveillance systems (ISS) can be used for respiratory syncytial virus (RSV) surveillance. In Portugal, RSV cases are detected through the ISS using the European Union (EU) influenza-like illness (ILI) case definition.AimTo investigate clinical predictors for RSV infection and how three case definitions (EU ILI, a modified EU acute respiratory infection, and one respiratory symptom) performed in detecting RSV infections in Portugal.MethodsThis observational retrospective study used epidemiological and laboratory surveillance data (October 2010–May 2018). Associations between clinical characteristics and RSV detection were analysed using logistic regression. Accuracy of case definitions was assessed through sensitivity, specificity, and area under the receiver operating characteristic curve (AUC). A 0.05 significance level was accepted.ResultsThe study involved 6,523 persons, including 190 (2.9%) RSV cases. Among 183 cases with age information, RSV infection was significantly more frequent among individuals < 5 years (n = 23; 12.6%) and ≥ 65 years (n = 45; 24.6%) compared with other age groups (p < 0.0001). Cough (odds ratio (OR): 2.4; 95% confidence interval (CI): 1.2–6.5) was the best RSV-infection predictor considering all age groups, while shortness of breath was particularly associated with RSV-positivity among ≤ 14 year olds (OR: 6.7; 95% CI: 2.6–17.4 for 0–4 year olds and OR: 6.7; 95% CI: 1.5–28.8 for 5–14 year olds). Systemic symptoms were significantly associated with RSV-negative and influenza-positive cases. None of the case definitions were suitable to detect RSV infections (AUC = 0.51).ConclusionTo avoid underestimating the RSV disease burden, RSV surveillance within the Portuguese sentinel ISS would require a more sensitive case definition than ILI and, even a different case definition according to age.

Clinical characteristics, predictors, and performance of case definition-Interim results from the WHO global respiratory syncytial virus surveillance pilot.

BackgroundThe lack of a uniform surveillance case definition poses a challenge to characterize the epidemiology, clinical features, and disease burden of the respiratory syncytial virus (RSV). Global standards for RSV surveillance will inform immunization policy when RSV vaccines become available.MethodsThe WHO RSV surveillance pilot leverages the capacities of the Global Influenza Surveillance and Response System (GISRS). Hospitalized and non‐hospitalized medically attended patients of any age were tested for RSV using standardized molecular diagnostics throughout the year in fourteen countries. An extended severe acute respiratory infection (extended SARI) or an acute respiratory infection (ARI) case definition was used that did not require fever as a criterion.ResultsAmongst 21 221 patients tested for RSV between January 2017 and September 2018, 15 428 (73%) were hospital admissions. Amongst hospitalized RSV‐positive patients, 50% were aged <6 months and 88% <2 years. The percentage of patients testing positive for RSV was 37% in children <6 months and 25% in those aged 6 months to 2 years. Patients with fever were less likely to be RSV positive compared to those without fever (OR 0.74; 95% CI: 0.63‐0.86). For infants <6 months, 29% of RSV ARI cases did not have fever.ConclusionRequiring fever in a case definition for RSV lowers the sensitivity to detect cases in young children. Countries should consider ways to leverage the GISRS platform to implement RSV surveillance with an augmented case definition amongst the young pediatric population.

93. Trends in the Laboratory Detection of Rotavirus Before and After Implementation of Routine Rotavirus Vaccination: the United States, 2000–2018

BackgroundBefore the introduction of rotavirus vaccine in the United States in 2006, rotavirus infection was the leading cause of severe gastroenteritis among US children.MethodsTo evaluate the long-term impact of rotavirus vaccination on disease burden in the United States, CDC analyzed national laboratory testing data for rotavirus from laboratories participating in CDC’s National Respiratory and Enteric Viruses Surveillance System (NREVSS) during the pre- (2000–2006) and post-vaccine (2007–2018) periods.ResultsNationally, the median annual percentage of positive rotavirus tests declined from 25.6% (range: 25.2–29.4%) in the pre-vaccine era to 6.1% (range: 2.6–11.1%) in the post-vaccine period. When comparing the pre- and post-vaccine era, the annual peak in rotavirus positivity declined from a median of 43.1% (range: 43.8–56.3%) to a median 14.0% (range: 4.8–27.3%) while the season duration was reduced from a median of 26 weeks (range: 23–27 weeks) to 9 weeks (range: 0–18 weeks). In the post-vaccine period, a biennial pattern emerged with alternating years of low and high rotavirus activity.ConclusionThe implementation of rotavirus vaccine has dramatically reduced the disease burden and altered seasonal patterns of rotavirus in the United States; these changes have been sustained over 11 post-vaccine introduction seasons.Disclosures All Authors: No reported Disclosures.

Approaches to use the WHO respiratory syncytial virus surveillance platform to estimate disease burden.

The World Health Organization (WHO) recently completed the first phase of a RSV surveillance pilot study in fourteen countries (two to three in each WHO region) building on the Global Influenza Surveillance and Response System (GISRS). This active surveillance strategy had several objectives including understanding RSV‐related health burden in a variety of settings. A range of approaches can be used to estimate disease burden; most approaches could not be applied by participating countries in the WHO surveillance pilot. This article provides the recommendations made by WHO for strengthening and expanding the scope of the RSV surveillance in the next phase to enable burden estimation.

Current practices for respiratory syncytial virus surveillance across the EU/EEA Member States, 2017.

BackgroundRespiratory syncytial virus (RSV) is a major contributor to lower respiratory tract infections worldwide and several vaccine candidates are currently in development. Following vaccine introduction, reliable RSV surveillance should enable monitoring of vaccination impact. Data on the RSV disease burden in the European Union and European Economic Area (EU/EEA) are sparse.AimThe aim of this study was to gather knowledge on current practices of national RSV surveillance in the EU/EEA.MethodsNational Coordinators and National Focal Points for Influenza (epidemiologists and virologists) from the EU/EEA countries (n = 31) were invited to participate in an online survey in August and September 2017. The questionnaire covered questions on epidemiological and laboratory aspects of RSV surveillance.ResultsAll EU/EEA countries except Liechtenstein replied to the survey. Eighteen countries reported to have a sentinel surveillance system, 26 countries a non-sentinel surveillance system and three countries to have neither. RSV data collection was mostly done within the context of influenza surveillance. A wide range of diagnostic and characterisation assays was used for the detection of RSV.DiscussionThe majority of EU/EEA countries have some surveillance for RSV in place. The prevailing integration of RSV surveillance into the existing influenza sentinel surveillance system may lead to under-reporting of RSV. The documented variations in existing RSV surveillance systems and their outputs indicate that there is scope for developing guidelines on establishing comparable methods and outcomes for RSV surveillance across the EU/EEA, to ensure the availability of a consistent evidence base for assessing future vaccination programmes.

Cold Weather Viruses.

1. Asif Noor, MD* 2. Theresa Fiorito, MD* 3. Leonard R. Krilov, MD*,† 1. *Department of Pediatrics, Children's Medical Center, NYU Winthrop Hospital, Mineola, NY 2. †Department of Pediatrics, State University of New York, Stony Brook School of Medicine, Stony Brook, NY * Abbreviations: AAP: : American Academy of Pediatrics Adv: : adenovirus CDC: : Centers for Disease Control and Prevention FDA: : Food and Drug Administration hMPV: : human metapneumovirus PCR: : polymerase chain reaction PIV: : parainfluenza virus RSV: : respiratory syncytial virus RV: : rhinovirus Clinicians must learn to identify viral infections in children during the winter months and must practice caution with the use of unnecessary medications in such cases. Recognition of the clinical pattern of viral infection (eg, bronchiolitis) in conjunction with judicious use of viral tests (either office-based immunoassays or newer molecular tests) may assist in epidemiological monitoring, cohorting patients in the hospital, withholding unnecessary therapies, and providing a definitive diagnosis. After completing this article, readers should be able to: 1. Review the epidemiological aspects and clinical signs and symptoms of common cold weather viruses. 2. Recognize situations in which viral testing is indicated. 3. Recognize situations in which treatment is indicated. In early November you are evaluating a 9-month-old boy born at 33 weeks of gestation. The infant presents with 2 days of fevers (101°F–102°F [38.3°C–38.8°C]), copious rhinorrhea, and 1 day of coughing with difficulty breathing. He is otherwise feeding well and has had adequate urination. His 4-year-older sister has an upper respiratory tract infection. On physical examination, the infant has a respiratory rate of 45 breaths/min without chest wall retractions. On auscultation there is good air entry with scattered rhonchi bilaterally. What is the most appropriate next step in management? 1. Obtain respiratory syncytial virus (RSV) and influenza antigen testing. 2. Obtain a chest radiograph to look for focal infiltrate. 3. Provide supportive care with nasal …

Has Rotavirus Vaccination Decreased the Prevalence of Biliary Atresia?

Biliary atresia (BA) is a rare neonatal liver disease that causes cholestasis and is the leading indication for pediatric liver transplantation. Although the exact etiology of BA remains unknown, evidence from murine models supports the role of rotavirus infection in the development of BA. In 2006, universal rotavirus vaccination was implemented in the United States. The goal of this study was to determine if the prevalence of BA correlated with the number of annual rotavirus infections. We utilized data from the 1997 to 2012 Kids' Inpatient Database and the 1988 to 2015 Organ Procurement and Transplantation Network to determine the annual number of infant discharges with a primary diagnosis of BA and the number of infants with BA who received a liver transplant, respectively. We obtained the number of annual rotavirus infections from the National Respiratory and Enteric Virus Surveillance System and examined whether trends existed between the data from these 3 sources over time. From 1997 to 2006, the number of positive rotavirus antigen tests remained steady, however a rapid decrease was observed from 2006 to 2012 (8774 to 1277), coinciding with the uptake of rotavirus immunizations nationwide. The number of BA discharges doubled from 1997 to 2003 and again increased from 2006 to 2012 (67 to 137 and 117 to 156), while the number of liver transplants for BA changed very little from 1997 to 2012. The recent implementation of rotavirus vaccination has not had any substantial influence on the prevalence of BA in the United States.

Leveraging the Global Influenza Surveillance and Response System for global respiratory syncytial virus surveillance-opportunities and challenges.

BackgroundRespiratory syncytial virus (RSV)‐associated acute lower respiratory infection is a common cause for hospitalization and hospital deaths in young children globally. There is urgent need to generate evidence to inform immunization policies when RSV vaccines become available. The WHO piloted a RSV surveillance strategy that leverages the existing capacities of the Global Influenza Surveillance and Response System (GISRS) to better understand RSV seasonality, high‐risk groups, validate case definitions, and develop laboratory and surveillance standards for RSV.MethodsThe RSV sentinel surveillance strategy was piloted in 14 countries. Patients across all age groups presenting to sentinel hospitals and clinics were screened all year‐round using extended severe acute respiratory infection (SARI) and acute respiratory infection (ARI) case definitions for hospital and primary care settings, respectively. Respiratory specimens were tested for RSV at the National Influenza Centre (NIC) using standardized molecular diagnostics that had been validated by an External Quality Assurance program. The WHO FluMart data platform was adapted to receive case‐based RSV data and visualize interactive visualization outputs.ResultsLaboratory standards for detecting RSV by RT‐PCR were developed. A review assessed the feasibility and the low incremental costs for RSV surveillance. Several challenges were addressed related to case definitions, sampling strategies, the need to focus surveillance on young children, and the data required for burden estimation.ConclusionsThere was no evidence of any significant adverse impact on the functioning of GISRS which is primarily intended for virologic and epidemiological surveillance of influenza.

Investigation of an outbreak of acute respiratory disease in an indigenous village in Brazil: Contribution of Influenza A(H1N1)pdm09 and human respiratory syncytial viruses.

Analyses of the 2009 H1N1 influenza pandemic and post-pandemic years showed high attack rates and severity among indigenous populations. This study presents the characteristics of the first documented influenza outbreak in indigenous peoples in Brazil, that occurred from 30th March to 14th April 2016 in a Guarani village in Southeast Region. Acute respiratory infections were prospectively investigated. The majority of the 73 cases were influenza-like illness (ILI) (63.0%) or severe acute respiratory infection (SARI) (20.5%). The ILI+SARI attack rate (35.9%) decreased with increasing age. There was a high influenza vaccination rate (86.3%), but no statistically significant difference in vaccination rates between severe and non-severe cases was seen (p = 0.334). Molecular analyses of 19.2% of the cases showed 100% positivity for influenza A(H1N1)pdm09 and/or hRSV. Influenza A(H1N1)pdm09 was included in the 6B.1 genetic group, a distinct cluster with 13 amino acid substitutions of A/California/07/2009-like. The hRSV were clustered in the BA-like genetic group. The early arrival of the influenza season overlapping usual hRSV season, the circulation of a drifted influenza virus not covered by vaccine and the high prevalence of risk factors for infection and severity in the village jointly can explain the high attack rate of ARI, even with a high rate of influenza vaccination. The results reinforce the importance of surveillance of respiratory viruses, timely vaccination and controlling risk factors for infection and severity of in the indigenous populations in order to preventing disease and related deaths, particularly in children.

Validation of the Seegene RV15 multiplex PCR for the detection of influenza A subtypes and influenza B lineages during national influenza surveillance in hospitalized adults.

Background The Serious Outcomes Surveillance Network of the Canadian Immunization Research Network (CIRN SOS) has been performing active influenza surveillance since 2009 (ClinicalTrials.gov identifier: NCT01517191). Influenza A and B viruses are identified and characterized using real-time reverse-transcriptase polymerase chain reaction (RT-PCR), and multiplex testing has been performed on a subset of patients to identify other respiratory virus aetiologies. Since both methods can identify influenza A and B, a direct comparison was performed.Methods Validated real-time RT-PCRs from the World Health Organization (WHO) to identify influenza A and B viruses, characterize influenza A viruses into the H1N1 or H3N2 subtypes and describe influenza B viruses belonging to the Yamagata or Victoria lineages. In a subset of patients, the Seeplex RV15 One-Step ACE Detection assay (RV15) kit was also used for the detection of other respiratory viruses.Results In total, 1111 nasopharyngeal swabs were tested by RV15 and real-time RT-PCRs for influenza A and B identification and characterization. For influenza A, RV15 showed 98.0 % sensitivity, 100 % specificity and 99.7 % accuracy. The performance characteristics of RV15 were similar for influenza A subtypes H1N1 and H3N2. For influenza B, RV15 had 99.2 % sensitivity, 100 % specificity and 99.8 % accuracy, with similar assay performance being shown for both the Yamagata and Victoria lineages.Conclusions Overall, the detection of circulating subtypes of influenza A and lineages of influenza B by RV15 was similar to detection by real-time RT-PCR. Multiplex testing with RV15 allows for a more comprehensive respiratory virus surveillance in hospitalized adults, without significantly compromising the reliability of influenza A or B virus detection.

Trends in the Laboratory Detection of Rotavirus Before and After Implementation of Routine Rotavirus Vaccination - United States, 2000-2018.

Before the introduction of rotavirus vaccine in the United States in 2006, rotavirus infection was the leading cause of severe gastroenteritis among U.S. children (1). To evaluate the long-term impact of rotavirus vaccination on disease prevalence and seasonality in the United States, CDC analyzed national laboratory testing data for rotavirus from laboratories participating in CDC's National Respiratory and Enteric Viruses Surveillance System (NREVSS) during the prevaccine (2000-2006) and postvaccine (2007-2018) periods. Nationally, the median annual percentage of tests positive for rotavirus declined from 25.6% (range=25.2-29.4) in the prevaccine period to 6.1% (range=2.6-11.1) in the postvaccine period. When compared with the prevaccine period, the postvaccine period saw declines in the annual peak in rotavirus positivity from a median of 43.1% (range=43.8-56.3) to a median of 14.0% (range=4.8-27.3) and in the season duration from a median of 26 weeks (range=23-27) to a median of 9 weeks (range=0-18). In the postvaccine period, a biennial pattern emerged, with alternating years of low and high rotavirus activity. Implementation of the rotavirus vaccination program has substantially reduced prevalence of the disease and altered seasonal patterns of rotavirus in the United States; these changes have been sustained over 11 seasons after vaccine introduction. Ongoing efforts to improve coverage and on-time vaccination (2) can help maximize the public health impact of rotavirus vaccination.

Surveillance of Respiratory Viruses in Long Term Care Facilities

ObjectiveTo assess the feasibility of conducting respiratory virus surveillance for residents of long term care facilities (LTCF) using simple nasal swab specimens and to describe the virology of acute respiratory infections (ARI) in LCTFs.IntroductionAlthough residents of LTCFs have high morbidity and mortality associated with ARIs, there is very limited information on the virology of ARI in LTCFs.[1,2] Moreover, most virological testing of LCTF residents is reactive and is triggered by a resident meeting selected surveillance criteria. We report on incidental findings from a prospective trial of introducing rapid influenza diagnostic testing (RIDT) in ten Wisconsin LTCFs over a two-year period with an approach of testing any resident with ARI.MethodsAny resident with new onset of respiratory symptoms consistent with ARI had a nasal swab specimen collected for RIDT by nursing staff. Following processing for RIDT (Quidel Sofia Influenza A+B FIA), the residual swab was placed into viral transport medium and forwarded to the Wisconsin State Laboratory of Hygiene and tested for influenza using RT-PCR (IVD CDC Human Influenza Virus Real-Time RT-PCR Diagnostic Panel), and for 17 viruses (Luminex NxTAG Respiratory Pathogen Panel [RPP]). The numbers of viruses in each of 7 categories [influenza A (FluA ), influenza B (FluB), coronaviruses (COR), human metapneumovirus (hMPV), parainfluenza (PARA), respiratory syncytial virus (RSV) and rhinovirus/enterovirus (R/E)], across the two years were compared using chi-square.ResultsTotals of 164 and 190 specimens were submitted during 2016-2017 and 2017-2018, respectively. RPP identified viruses in 56.2% of specimens, with no difference in capture rate between years (55.5% vs. 56.8%). Influenza A (21.5%), influenza B (16.5%), RSV (19.0%) and hMPV (16.5%) accounted for 73.5% of all detections, while coronaviruses (15.5%), rhino/enteroviruses (8.5%) and parainfluenza (2.5%) were less common. Specific distribution of viruses varied significantly across the two years (Table: X2=48.1, df=6; p&lt;0.001).ConclusionsSurveillance in LTCFs using nasal swabs collected for RIDT is highly feasible and yields virus identification rates similar to those obtained in clinical surveillance of ARI with collection of nasopharyngeal specimens by clinicians and those obtained in a school-based surveillance project of ARI with collection of combined nasal and oropharyngeal specimens collected by trained research assistants. Significant differences in virus composition occurred across the two study years. RSV varied little between years while hMPV demonstrated wide variation. Simple approaches to surveillance may provide a more comprehensive assessment of respiratory viruses in LTCF settings.References(1) Uršič T, Gorišek Miksić N, Lusa L, Strle F, Petrovec M. Viral respiratory infections in a nursing home: a six-month prospective study. BMC Infect Dis. 2016; 16: 637. Published online 2016 Nov 4. doi: 10.1186/s12879-016-1962-8(2) Masse S, Capai L, Falchi A. Epidemiology of Respiratory Pathogens among Elderly Nursing Home Residents with Acute Respiratory Infections in Corsica, France, 2013–2017. Biomed Res Int. 2017; 2017: 1423718. Published online 2017 Dec 17. doi: 10.1155/2017/1423718