Influenza and RSV incidence during COVID-19 pandemic—an observational study from in-hospital point-of-care testing

AbstractThe severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has forced the implementation of unprecedented public health measures strategies which might also have a significant impact on the spreading of other viral pathogens such as influenza and Respiratory Syncytial Virus (RSV) . The present study compares the incidences of the most relevant respiratory viruses before and during the SARS-CoV-2 pandemic in emergency room patients. We analyzed the results of in total 14,946 polymerase chain reaction point-of-care tests (POCT-PCR) for Influenza A, Influenza B, RSV and SARS-CoV-2 in an adult and a pediatric emergency room between December 1, 2018 and March 31, 2021. Despite a fivefold increase in the number of tests performed, the positivity rate for Influenza A dropped from 19.32% (165 positives of 854 tests in 2018/19), 14.57% (149 positives of 1023 in 2019–20) to 0% (0 positives of 4915 tests) in 2020/21. In analogy, the positivity rate for Influenza B and RSV dropped from 0.35 to 1.47%, respectively, 10.65–21.08% to 0% for both in 2020/21. The positivity rate for SARS-CoV2 reached 9.74% (110 of 1129 tests performed) during the so-called second wave in December 2020. Compared to the two previous years, seasonal influenza and RSV incidence was eliminated during the COVID-19 pandemic. Corona-related measures and human behavior patterns could lead to a significant decline or even complete suppression of other respiratory viruses such as influenza and RSV.

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Performance of a Novel Point-of-Care Molecular Assay for Detection of Influenza A and B Viruses and Respiratory Syncytial Virus (Enigma MiniLab) in Children with Acute Respiratory Infection

Journal of Clinical Microbiology ◽

10.1128/jcm.02887-15 ◽

2015 ◽

Vol 54 (1) ◽

pp. 212-215 ◽

Cited By ~ 11

Author(s):

Sam T. Douthwaite ◽

Charlotte Walker ◽

Elisabeth J. Adams ◽

Catherine Mak ◽

Andres Vecino Ortiz ◽

...

Keyword(s):

Respiratory Syncytial Virus ◽

Influenza A ◽

Respiratory Virus ◽

Point Of Care ◽

Influenza B Virus ◽

Influenza B ◽

Molecular Assay ◽

B Virus ◽

Syncytial Virus ◽

Virus Influenza

The performance of the Enigma MiniLab assay for influenza A and B viruses and respiratory syncytial virus (RSV) was compared to a centralized laboratory respiratory virus panel. The positive and negative percent agreement for influenza A virus, influenza B virus, and RSV were 79.2% (95% confidence interval [95% CI], 57.8 to 92.9%) and 99.4% (95% CI, 98.4 to 99.9), 100% (95% CI, 47.8 to 100%) and 100% (95% CI, 99.3 to 100%), 98.5% (95% CI, 94.6 to 99.8%) and 94.5% (95% CI, 91.9 to 96.4%), respectively.

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Epidemiological and virological characteristics of respiratory tract infections in children during COVID-19 outbreak

BMC Pediatrics ◽

10.1186/s12887-021-02654-8 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Yueling Zhu ◽

Wei Li ◽

Binbin Yang ◽

Ruiying Qian ◽

Fang Wu ◽

...

Keyword(s):

Respiratory Tract ◽

Influenza A ◽

Respiratory Tract Infections ◽

Respiratory Viruses ◽

Influenza B ◽

Protective Measures ◽

Outpatient Visits ◽

Syncytial Virus ◽

Tract Infections ◽

The Impact

Abstract Background To investigate the impact of protective measures and isolation on respiratory tract infections in children during the COVID-19 outbreak. Methods We extracted data on outpatient visits and respiratory infection visits, and tests of respiratory viruses (adenovirus (ADV), influenza A (FluA), influenza B (FluB) and respiratory syncytial virus (RSV)) from electronic healthcare records in Children’s Hospital, Zhejiang University School of Medicine during the COVID-19 outbreak (January–April, 2020), compared with those in 2018 and 2019 during the same periods. Results We found that outpatient visits in January, 2020 was comparable with those in 2018 and 2019, but decreased by 59.9% (288,003 vs. 717,983) and 57.4% (288,003 vs. 676,704), respectively during the period of February-April, 2020, as compared with the same periods in 2018 and 2019. The total number of respiratory tract infections from January to April 2020 decreased by 65.7% (119,532 vs.348,762) and 59.0% (119,532 vs.291,557), respectively compared with the same periods in 2018 and 2019. The proportion of respiratory tract infections during the outbreak also dropped compared with the same periods in 2018 and 2019 (P<0.001). We also found significantly decreased number of completed tests for respiratory viruses and positive cases of ADV, FluA, FluB, and RSV during February-April, 2020. Conclusions In this study, we found that outpatient visits and respiratory tract infections in children significantly decreased during COVID-19 outbreak. Adequate protective measures and isolation in children may help to prevent respiratory virus infections in children.

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1791. Novel Metabolomics Approach for the Diagnosis of Respiratory Viruses Directly from Nasopharyngeal Specimens

Open Forum Infectious Diseases ◽

10.1093/ofid/ofz360.1654 ◽

2019 ◽

Vol 6 (Supplement_2) ◽

pp. S660-S660

Author(s):

Catherine Hogan ◽

Anthony T Le ◽

Justin Mak ◽

Malaya Kumar. Sahoo ◽

Tina Cowan ◽

...

Keyword(s):

Host Cell ◽

Influenza A ◽

Component Analysis ◽

Respiratory Viruses ◽

Primary Component ◽

Nasopharyngeal Swab ◽

Influenza B ◽

Compound Identification ◽

Influenza A H1n1 ◽

Syncytial Virus

Abstract Background Respiratory virus infections are important causes of morbidity and mortality among pediatric and adult patients. These viruses infect respiratory epithelial cells, where they may induce specific metabolite alterations. As a proof-of-concept, we investigate the novel use of liquid chromatography (LC) combined with quadrupole time-of-flight mass spectrometry (Q-TOF) for the study of host cell metabolite alterations to diagnose and differentiate respiratory viruses. Methods We studied nasopharyngeal swab samples positive for respiratory viruses by the eSensor Respiratory Viral Panel (GenMark Diagnostics, Carlsbad, CA). Banked, frozen samples (−80°C) stored in viral transport media were retrieved and thawed. Aliquots of 100 μL were centrifuged at 13.3 × g for 15 minutes, and the filtrate was analyzed by Agilent 6545 Quadrupole LC/Q-TOF (Agilent Technologies, Santa Clara, CA). Compounds were separated using a novel column arrangement based on hydrophobicity and charge using a quaternary solvent manager, followed by accurate mass analysis by LC/Q-TOF. Agilent Mass Profiler 3D principal component analysis was performed, and compound identification was completed using the METLIN metabolite database. Results A total of 235 specimens were tested by LC/Q-TOF, including 195 positive specimens [including adenovirus, coronavirus, influenza A H1N1 and H3N2, influenza B, human metapneumovirus, parainfluenza viruses 1, 2, 3, and 4, respiratory syncytial virus (RSV), and rhinovirus] as well as 40 negative clinical specimens. LC/Q-TOF primary component analysis (PCA) allowed preliminary identification of key metabolites that distinguished all virus-positive specimens compared with the negative group, and differentiated respiratory viruses from one another including between influenza A 2009 H1N1 and H3N2 subtypes (Figure 1). Conclusion Preliminary data from our LC/Q-TOF analysis show that respiratory viruses exhibit different host cell metabolomic profiles that allow viral differentiation to the species level, and for influenza A virus, the subtype level. This metabolomic approach has substantial potential for diagnostic applications in infectious diseases directly from patient samples, and may be eventually adapted for point-of-care testing. Disclosures All authors: No reported disclosures.

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Mortality Following Isolation of Various Respiratory Viruses in Nursing Home Residents

Infection Control and Hospital Epidemiology ◽

10.1086/501589 ◽

1999 ◽

Vol 20 (12) ◽

pp. 812-815 ◽

Cited By ~ 33

Author(s):

Paul J. Drinka ◽

Stefan Gravenstein ◽

Elizabeth Langer ◽

Peggy Krause ◽

Peter Shult

Keyword(s):

Nursing Home ◽

Influenza A ◽

Skilled Nursing Facility ◽

Nursing Home Residents ◽

Respiratory Illness ◽

Respiratory Viruses ◽

Influenza B ◽

Respiratory Pathogens ◽

Syncytial Virus ◽

Viral Respiratory

AbstractObjective:To compare mortality following isolation of influenza A to mortality following isolation of other respiratory viruses in a nursing home.Setting:The Wisconsin Veterans Home, a 688-bed skilled nursing facility for veterans and their spouses.Participants:All residents with respiratory viral isolates obtained between 1988 and 1999.Design:Thirty-day mortality was determined following each culture-proven illness.Results:Thirty-day mortality following isolation of viral respiratory pathogens was 4.7% (15/322) for influenza A 5.4% (7/129) for influenza B; 6.1% (3/49) for parainfluenza type 1; 0% (0/26) for parainfluenza types 2,3, and 4; 0% (0/26) for respiratory syncytial virus (RSV); and 1.6% (1/61) for rhinovirus.Conclusions:Mortality following isolation of certain other respiratory viruses may be comparable to that following influenza A (although influenza A mortality might be higher without vaccination and antiviral agents). The use of uniform secretion precautions for all viral respiratory illness deserves consideration in nursing homes.

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Epidemic characteristics of respiratory viruses in hospitals in a Chinese city during the SARS-CoV-2 epidemic

10.1101/2020.10.06.20207589 ◽

2020 ◽

Author(s):

Weihua Yang ◽

Jian Chen ◽

Mingjie Xu ◽

Jun Wang ◽

Huanjie Li ◽

...

Keyword(s):

Respiratory Syncytial Virus ◽

Nucleic Acid ◽

Influenza A ◽

Respiratory Viruses ◽

Influenza B ◽

Test Results ◽

Before And After ◽

Positive Rate ◽

Syncytial Virus ◽

Acid Test

AbstractThe SARS-CoV-2 virus first broke out in China in early 2020. The early symptoms of COVID-19 are similar to those of influenza. Therefore, during the epidemic, patients with similar symptoms will be tested for multiple pathogens at the same time. In order to control the spread of SARS-CoV-2, China has taken many measures. Under this special situation, have the types and epidemic characteristics of respiratory viruses changed? The nucleic acid test results of influenza A virus, influenza B virus and respiratory syncytial virus, as well as the antibody test results of 8 common respiratory viruses of Jinan Central Hospital were collected before and after the occurrence of SARS-CoV-2, and age distribution and time distribution characteristics were statisticed. Furthermore the epidemiological characteristics of this new virus before and after the SARS-CoV-2 epidemic was compared. In the early stage of the SARS-CoV-2 epidemic, influenza A, influenza B and respiratory syncytial virus nucleic acid test samples were large, and the positive rate of the three viruses was high. After that, the sample size and positive rate decreased significantly. No co-infection of SARS-CoV-2 and other viruses was found in our hospital. The sample size before the SARS-CoV-2 outbreak was larger than that after the outbreak, but the positive rate of the outbreak was lower than that after the outbreak. And the infection rate of children decreased in the middle and late stages of the epidemic. This is because since January 23, in order to prevent the spread of the new crown epidemic, my country has adopted measures such as wearing masks, not gathering together, and quarantining at home. This not only prevents the spread of the new crown virus, but also prevents the common respiratory tract. The spread of the virus has reduced the incidence of residents.

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Clinical and Financial Benefits of Rapid Detection of Respiratory Viruses: an Outcomes Study

Journal of Clinical Microbiology ◽

10.1128/jcm.38.8.2824-2828.2000 ◽

2000 ◽

Vol 38 (8) ◽

pp. 2824-2828 ◽

Cited By ~ 180

Author(s):

Joan Barenfanger ◽

Cheryl Drake ◽

Nidia Leon ◽

Tina Mueller ◽

Tammy Troutt

Keyword(s):

Length Of Stay ◽

Influenza A ◽

Respiratory Viruses ◽

Turnaround Time ◽

Influenza B Virus ◽

Influenza B ◽

Shell Vial ◽

The Mean ◽

Syncytial Virus ◽

Standard Techniques

To assess the expected benefits of rapid reporting of respiratory viruses, we compared patients whose samples were processed using standard techniques such as enzyme immunoassays, shell vial assays, and culture tube assays (year 1) to patients whose samples were processed with the same standard techniques in addition to immunofluorescent testing (FA) directly on cytocentrifuged samples (year 2). The cytospin FA screened for influenza A and B viruses, respiratory syncytial virus (RSV), parainfluenza viruses 1 to 3, and adenovirus (DAKO Diagnostics Ltd.). The specificity of the cytospin FA for all viruses was 100%. The sensitivities for influenza A virus and RSV were 90 and 98%, respectively, but the sensitivities for influenza B virus and adenovirus were unacceptable (14.3 and 0%, respectively). However, since the former viruses account for >85% of our isolates from clinical specimens, the cytospin FA is an excellent screening test since the positive result was available within hours. The mean turnaround time for all positive viruses was 4.5 days in year 1 and 0.9 day in year 2 (P = 0.001). This rapid reporting resulted in physicians having access to information sooner, enabling more appropriate treatment. The mean length of stay in the hospital for inpatients with respiratory viral isolates was 10.6 days for year 1 versus 5.3 days for year 2. Mean variable costs for these patients was $7,893 in year 1 and $2,177 in year 2. After subtracting reagent costs and technological time, the savings in variable costs was $144,332/year. Summarizing, the cytospin FA markedly decreased turnaround time and was associated with decreased mortality, length of stay, and costs and with better antibiotic stewardship.

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2220. Comparative Incidence and Burden of Respiratory Viruses Associated with Hospitalization in Adults

Open Forum Infectious Diseases ◽

10.1093/ofid/ofz360.1898 ◽

2019 ◽

Vol 6 (Supplement_2) ◽

pp. S757-S758

Author(s):

William Sieling ◽

Matthew Oberhardt ◽

Philip Zachariah ◽

Celibell Vargas ◽

Angela Barrett ◽

...

Keyword(s):

New York ◽

Market Share ◽

Influenza A ◽

Census Data ◽

Respiratory Viruses ◽

Population Based ◽

Influenza Viruses ◽

University Teaching ◽

Influenza B ◽

Syncytial Virus

Abstract Background The population-based incidence and burden of community-onset non-influenza respiratory viruses associated with hospitalization in adults has not been systematically assessed. Methods On admission, patients with respiratory symptoms are tested for respiratory viruses by multiplex polymerase chain reaction (BioFire FilmArray Respiratory Panel) as per standard of care at our university teaching hospital (1160 beds). A retrospective study was performed to identify adults who had influenza, parainfluenza virus (PIV), respiratory syncytial virus (RSV), human metapneumovirus (hMPV), or adenovirus (AV) detected within 3 days of admission from October 2017 to October 2018. To calculate population-based incidence per 100,000 persons (using 2010 US Census data), the number of cases was adjusted by the hospital’s percent market share for zip codes as determined by New York State’s all payer data reporting system. To improve the incidence estimate’s reliability, only cases living in zip codes for which the hospital had ≥ 60% market share were included. We compared median length of stay (LOS), ICU admission, and in-hospital mortality associated with each virus. Results Influenza A (H3) had the highest overall incidence followed by Influenza B and RSV. For each virus, the highest incidence was observed in adults ≥ 65 years old (figure). Overall, 12.9% of cases were hospitalized in the ICU and 4.7% died during hospitalization (table). AV, hMPV, and RSV were associated with the longest LOS. AV, PIV, and RSV were associated with the largest proportion of ICU admissions and deaths. Conclusion While Influenza A (H3) and Influenza B were associated with the highest population-based incidence, non-influenza respiratory viruses caused substantial morbidity in older adults. Compared with influenza viruses, AV, PIV, and RSV were associated with greater severity determined by ICU admissions and death. Disclosures All authors: No reported disclosures.

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Post-pandemic influenza A/H1N1pdm09 is associated with more severe outcomes than A/H3N2 and other respiratory viruses in adult hospitalisations

Epidemiology and Infection ◽

10.1017/s095026881900195x ◽

2019 ◽

Vol 147 ◽

Cited By ~ 5

Author(s):

C. A. Minney-Smith ◽

L. A. Selvey ◽

A. Levy ◽

D. W. Smith

Keyword(s):

Clinical Outcomes ◽

Influenza A ◽

Respiratory Virus ◽

Respiratory Illness ◽

Respiratory Viruses ◽

Influenza B ◽

Virus Infections ◽

Icu Admission ◽

Hospitalised Patients ◽

Syncytial Virus

Abstract This study compares the frequency and severity of influenza A/H1N1pdm09 (A/H1), influenza A/H3N2 (A/H3) and other respiratory virus infections in hospitalised patients. Data from 17 332 adult hospitalised patients admitted to Sir Charles Gairdner Hospital, Perth, Western Australia, with a respiratory illness between 2012 and 2015 were linked with data containing reverse transcription polymerase chain reaction results for respiratory viruses including A/H1, A/H3, influenza B, human metapneumovirus, respiratory syncytial virus and parainfluenza. Of these, 1753 (10.1%) had test results. Multivariable regression analyses were conducted to compare the viruses for clinical outcomes including ICU admission, ventilation, pneumonia, length of stay and death. Patients with A/H1 were more likely to experience severe outcomes such as ICU admission (OR 2.5, 95% CI 1.2–5.5, P = 0.016), pneumonia (OR 3.0, 95% CI 1.6–5.7, P < 0.001) and lower risk of discharge from hospital (indicating longer lengths of hospitalisation; HR 0.64 95% CI 0.47–0.88, P = 0.005), than patients with A/H3. Patients with a non-influenza respiratory virus were less likely to experience severe clinical outcomes than patients with A/H1, however, had similar likelihood when compared to patients with A/H3. Patients hospitalised with A/H1 had higher odds of severe outcomes than patients with A/H3 or other respiratory viruses. Knowledge of circulating influenza strains is important for healthcare preparedness.

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Using routine testing data to understand circulation patterns of influenza A, respiratory syncytial virus and other respiratory viruses in Victoria, Australia

Epidemiology and Infection ◽

10.1017/s0950268819001055 ◽

2019 ◽

Vol 147 ◽

Cited By ~ 6

Author(s):

O. H. Price ◽

S. G. Sullivan ◽

C. Sutterby ◽

J. Druce ◽

K. S. Carville

Keyword(s):

Respiratory Syncytial Virus ◽

Influenza A ◽

Respiratory Virus ◽

Respiratory Viruses ◽

Influenza B ◽

Routine Testing ◽

Circulation Patterns ◽

Cross Correlations ◽

Time Series Analyses ◽

Syncytial Virus

Abstract Several studies have reported evidence of interference between respiratory viruses: respiratory viruses rarely reach their epidemic peak concurrently and there appears to be a negative association between infection with one respiratory virus and co-infection with another. We used results spanning 16 years (2002–2017) of a routine diagnostic multiplex panel that tests for nine respiratory viruses to further investigate these interactions in Victoria, Australia. Time series analyses were used to plot the proportion positive for each virus. The seasonality of all viruses included was compared with respiratory syncytial virus (RSV) and influenza A virus using cross-correlations. Logistic regression was used to explore the likelihood of co-infection with one virus given infection with another. Seasonal peaks were observed each year for influenza A and RSV and less frequently for influenza B, coronavirus and parainfluenza virus. RSV circulated an average of 6 weeks before influenza A. Co-infection with another respiratory virus was less common with picornavirus, RSV or influenza A infection. Our findings provide further evidence of a temporal relationship in the circulation of respiratory viruses. A greater understanding of the interaction between respiratory viruses may enable better prediction of the timing and magnitude of respiratory virus epidemics.

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Virome of New York Presbyterian Hospital pediatric emergency

10.1101/2020.03.18.20038166 ◽

2020 ◽

Author(s):

Minhaz Ud-Dean ◽

Ioan Filip ◽

Marta Galanti ◽

Ruthie Birger ◽

Devon Comito ◽

...

Keyword(s):

New York ◽

Respiratory Syncytial Virus ◽

Respiratory Tract ◽

Emergency Room ◽

Influenza A ◽

Pediatric Emergency ◽

Human Rhinovirus ◽

Presbyterian Hospital ◽

Corona Virus ◽

Syncytial Virus

AbstractBackgroundViral infection of the respiratory tract is one of the major causes of hospital visits for young children. In this study, we report the occurrence and co-occurrence of different virus types and subtypes among the patients arriving at the pediatric emergency room of New York Presbyterian Hospital, a major urban hospital.MethodsWe collected nasal swabs from the patients and their accompanying persons. We also recorded the levels (None, Mild, High, and Severe) of their symptoms (Fever, Chill, Muscle Pain, Watery Eye, Runny Nose, Sneezing, Sore throat and Cough). The collected swabs were tested for the presence of common viruses infecting the respiratory tract.ResultsHuman Rhinovirus was the most common virus among the patients, followed Influenza and Respiratory Syncytial Virus. Human Rhinovirus was most common in summer, autumn and spring. In contrast, influenza was more common in winter. Further, Influenza A virus was more likely to co-occur with Corona Virus 229E. In comparison, Influenza was less likely to co-occur with Human Rhinovirus. Moreover, Influenza, Parainfluenza and Corona virus were associated with more severe symptoms, while Human Rhinovirus was associated with less severe symptoms. In addition, we observed that Influenza and Respiratory Syncytial Virus were more likely to infect a patient when these viruses also infected the accompanying person. We also found that it was difficult to distinguish among viruses based on the symptoms. The inability to distinguish among different virus types and subtypes is explained by the fact that multiple viruses lead to similar symptoms.ConclusionsThe findings of this study provide a better understanding of respiratory viral infections in small children presenting at a pediatric emergency room in New York.

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