scholarly journals Utility and Challenges of a Multi-pathogen Diagnostic Platform for Characterizing Public Health Threats of Severe Acute Respiratory Infections in Six Countries

2017 ◽  
Vol 4 (suppl_1) ◽  
pp. S17-S18
Author(s):  
Jennifer Milucky ◽  
Keyword(s):  
Public Health ◽  
Influenza A ◽  
Age Distribution ◽  
Simultaneous Detection ◽  
Case Fatality ◽  
Influenza B ◽  
Upper Respiratory Tract ◽  
Severe Acute Respiratory Infection ◽  
Syncytial Virus ◽  
Multiple Pathogens

Abstract Background Pneumonia causes significant morbidity and mortality worldwide. Comprehensive etiology studies of pneumonia in adults are limited; however, new diagnostics enable simultaneous detection of multiple pathogens in respiratory specimens. Characterizing the public health threat of severe acute respiratory infection (SARI) may enhance global health security. We studied potential etiologies of SARI among adults in six countries over a 12-month period using multi-pathogen diagnostics. Methods We enrolled SARI cases (acute onset of fever and cough, requiring hospitalization, in an adult) from Global Disease Detection sites in Bangladesh, China, Egypt, Guatemala, Kenya, and Thailand and healthy frequency-matched controls (2 controls: 5 cases) by time (onset), age group (18–49, 50–64, 65+ years), and catchment area. Demographics, clinical data, and nasopharyngeal and oropharyngeal specimens were collected from cases and controls. Specimens were tested for 16 viruses and 14 bacteria using Taqman® Array Card, which uses real-time reverse transcriptase polymerase chain reaction. Results We enrolled 2,388 cases and 1,135 controls from Oct 2013 through Oct 2015. Age distribution (Figure) and seasonality varied by site: enrollment peaked in summer months in Bangladesh, Thailand, and China, and in winter months in Egypt, but was stable throughout the year in Guatemala and Kenya. Case fatality rate across all study locations was 2.3% (range 0–7.0%). One or more pathogens was detected in 76% of cases and in 67% of controls; ≥2 pathogens were detected in 42% of cases and 37% of controls. Pathogens more commonly detected among cases than controls included influenza A (OR 13.3, CI 7.0–25.2; 12.8% of cases vs. 1.1% of controls), influenza B (OR: 27.0, CI 8.6–84.8; 8.1% vs. 0.3%), and respiratory syncytial virus (RSV) (OR: 9.4, CI 3.4–25.8; 4.0% vs. 0.4%). Conclusion In this SARI study, frequent detection of multiple pathogens in the oro- and nasopharynx of both cases and controls made etiology attribution difficult. Influenza and RSV, however, were likely to be causes of SARI. Because upper respiratory tract specimens may not accurately reflect disease in the lung, better specimens are needed to determine pneumonia etiology, particularly for bacteria. Disclosures All authors: No reported disclosures.

scholarly journals Evaluation of the Xpert Xpress SARS-CoV-2/Flu/RSV assay for simultaneous detection of SARS-CoV-2, Influenza A/B and Respiratory Syncytial Viruses in nasopharyngeal specimens

2021 ◽  
Author(s):  
Eddie Chi-man Leung ◽  
Viola Chi-ying Chow ◽  
May Kin-ping Lee ◽  
Kevin Pui-san Tang ◽  
Daniel Kwok-cheung Li ◽  
...  
Keyword(s):  
Influenza A ◽  
Simultaneous Detection ◽  
Threshold Value ◽  
Influenza B ◽  
Upper Respiratory Tract ◽  
Prevention Measures ◽  
Kappa Value ◽  
High Concordance ◽  
Syncytial Virus ◽  
Value Association

Patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), influenza A (flu A), influenza B (flu B), and respiratory syncytial virus (RSV) have overlapping clinical presentations, but the approaches to treatment and management of infections caused by these viruses are different. Therefore, rapid diagnosis in conjunction with infection prevention measures is important to prevent transmission of the diseases. Recently, a new Xpert Xpress SARS-CoV-2/Flu/RSV (Xpert 4-in-1) assay enables the detection and differentiation of SARS-CoV-2, flu A, flu B, and RSV in upper respiratory tract specimens. In this study, we evaluated the performance of the Xpert 4-in-1 assay by comparing it with the Xpert Xpress SARS-CoV-2 and Xpert Xpress Flu/RSV assays for the detection of the four viruses in nasopharyngeal (NP) specimens. A total of 279 NP specimens, including 66, 56, 64 and 53 positive specimens for SARS-CoV-2, flu A, flu B and RSV respectively, were included. The Xpert 4-in-1 assay demonstrated high concordance with the comparator assays, with overall agreement for SARS-CoV-2, flu A, flu B, and RSV at 99.64%, 100%, 99.64%, and 100%, respectively, and a high kappa value ranging from 0.99 to 1.00, indicating an almost perfect correlation between assays. The cycle threshold value association between positive samples also showed a good correlation between assays. In conclusion, the overall performance of the Xpert 4-in-1 assay was highly comparable to that of the Xpert SARS-CoV-2 and Xpert Flu/RSV assays for the detection and differentiation of SARS CoV-2, flu A, flu B, and RSV in NP specimens.

scholarly journals Analytical performances of the AMPLIQUICK® Respiratory Triplex assay for simultaneous detection and differentiation of SARS-CoV-2, influenza A/B and respiratory syncytial viruses in respiratory specimens

PLoS ONE ◽  
2022 ◽  
Vol 17 (1) ◽  
pp. e0262258
Author(s):  
Ralph-Sydney Mboumba Bouassa ◽  
Serge Tonen-Wolyec ◽  
David Veyer ◽  
Hélène Péré ◽  
Laurent Bélec
Keyword(s):  
Influenza A ◽  
Viral Infections ◽  
Simultaneous Detection ◽  
Influenza B ◽  
The Novel ◽  
Perfect Agreement ◽  
Qualitative Detection ◽  
High Concordance ◽  
Syncytial Virus ◽  
Respiratory Specimens

Although patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), influenza A, influenza B and respiratory syncytial virus (RSV) show comparable or very similar manifestations, the therapeutic approaches of these respiratory viral infections are different, which requires an accurate diagnosis. Recently, the novel multiplex real-time reverse transcription-polymerase chain reaction assay AMPLIQUICK® Respiratory Triplex (BioSynex SA, Illkirch-Graffenstaden, France) allows simultaneous detection and differentiation of SARS-CoV-2, influenza A, influenza B, and RSV in respiratory tract samples. We herein evaluated the performance of the AMPLIQUICK® Respiratory Triplex for the detection of the four viruses in respiratory specimens, using Allplex™ Respiratory Panel 1 and 2019-nCoV assays (Seegene, Seoul, Korea) as reference comparator assays. A total of 359 archived predetermined respiratory samples, including 83, 145, 19 and 95 positive specimens for SARS-CoV-2, influenza A, influenza B and RSV respectively, were included. The AMPLIQUICK® Respiratory Triplex showed high concordance with the reference assays, with an overall agreement for SARS-CoV-2, influenza A, influenza B, and RSV at 97.6%, 98.8%, 98.3% and 100.0%, respectively, and high κ values ranging from 0.93 to 1.00, indicating an almost perfect agreement between assays. Furthermore, high correlations of cycle threshold (Ct) values were observed for positive samples of the four viruses between the AMPLIQUICK® Respiratory Triplex and comparator assays, with an overall high agreement between Ct values assessed by Bland-Altman analyses. In conclusion, these observations demonstrate that the multiplex AMPLIQUICK® Respiratory Triplex is a reliable assay for the qualitative detection and differentiation of SARS-CoV-2, influenza A, influenza B, and RSV in respiratory specimens, which may prove useful for streamlining diagnostics during the winter influenza-seasons.

scholarly journals Multi-center Evaluation of the Cepheid Xpert® Xpress SARS-CoV-2/Flu/RSV Test

2020 ◽  
Author(s):  
Heba H. Mostafa ◽  
Karen C. Carroll ◽  
Rachel Hicken ◽  
Gregory J. Berry ◽  
Ryhana Manji ◽  
...  
Keyword(s):  
Public Health ◽  
Los Angeles ◽  
Influenza A ◽  
Respiratory Virus ◽  
Medical Center ◽  
Standard Of Care ◽  
Nucleic Acid Amplification ◽  
Nasopharyngeal Swab ◽  
Influenza B ◽  
Syncytial Virus

With the approach of respiratory virus season in the Northern Hemisphere, clinical microbiology and public health laboratories will need rapid diagnostic assays to distinguish SARS-CoV-2 from influenza and respiratory syncytial virus (RSV) infections for diagnosis and surveillance. In this study, the clinical performance of the Xpert® Xpress SARS-CoV-2/Flu/RSV test (Cepheid, Sunnyvale, CA, USA) for nasopharyngeal swab specimens was evaluated in four centers: Johns Hopkins Medical Microbiology Laboratory, Northwell Health Laboratories, NYC Public Health Laboratory, and Los Angeles County/University of Southern California (LAC+USC) Medical Center. A total of 319 nasopharyngeal swab specimens, positive for SARS-CoV-2 (n = 75), influenza A (n = 65), influenza B (n = 50), RSV (n = 38), or negative (n = 91) by the standard of care nucleic acid amplification tests at each site were tested using the Cepheid panel test. The overall positive percent agreement for the SARS-CoV-2 target was 98.7% (n= 74/75) and the negative agreement was 100% (n= 91) with all other analytes showing 100% total agreement (n= 153). Standard of care tests to which the Cepheid panel was compared included the Cepheid Xpert Xpress SARS-CoV-2, Cepheid Xpert Xpress Flu/RSV, the GenMark ePlex respiratory panel, the BioFire Respiratory panels 2.1 and v1.7, the DiaSorin Simplexa COVID-19 Direct, and the Hologic Panther Fusion SARS-CoV-2 assays. The Xpert Xpress SARS-CoV-2/Flu/RSV test showed high sensitivity and accuracy for all analytes included in the test. This test will provide a valuable clinical diagnostic and public health solution for detecting and differentiating SARS-CoV-2, influenza A and B, and RSV infections during the current respiratory virus season.

Bacteria and Viral Profile of Severe Acute Respiratory Infections of Children Attending Yangon Children’s Hospital and Yankin Children’s Hospital

2019 ◽  
Vol 31 (1) ◽  
pp. 44-51
Keyword(s):  
Influenza A ◽  
Respiratory Infections ◽  
Antibiotic Sensitivity ◽  
Parainfluenza Virus ◽  
Sensitivity Testing ◽  
E Coli ◽  
Children's Hospital ◽  
Severe Acute Respiratory Infection ◽  
Children’S Hospital ◽  
Syncytial Virus

Objectives of study are (1) to reinforce the national capacity for diagnosis and antibiogram of some infectious diseases causing severe acute respiratory infection (SARI) and (2) to build a network between hospital and laboratory for the diagnosis and surveillance of SARI in Yangon. This study is a crosssectional hospital- and laboratory-based descriptive study. A total of 825 samples including respiratory samples and blood samples from 511 children attending Yangon Children’s Hospital and Yankin Children’s Hospital from December 2014 to April 2016 for treatment of SARI were included. Identification and antibiotic sensitivity testing were done using Vitek 2. Out of 129 gram-negative bacilli (GNB), K. pneumoniae 32%, P. aeruginosa 18%, A. baumannii 13%, E. coli 9% were mostly isolated. Among 35 gram-positive cocci (GPC), S. aureus 42% and S. pneumoniae 6% were mostly isolated. Multidrug resistance rates were E. coli 100%, K. pneumoniae 95%, A. baumanii 82% and P. aeruginosa 17%. Extended-spectrum beta-latamase (ESBL)-producing K. pneumoniae and E. coli was 6 out of 10 tested organisms. Carbarpenemase-producing GNB and methicillin-resistant Staphylococcus aureus (MRSA) were 21% and 33%, respectively. Virology section tested 529 samples of 490 patients using the FTD33 Multiplex PCR method which can detect 33 pathogens including 20 viruses, 12 bacteria and 1 fungus. Out of 490 patients, 374 were PCR positive. Different types of samples including nasopharyngeal, throat, endotracheal and laryngeal swab, tracheal secretion and bronchoalveolar lavage, were tested. Out of 566 viruses, respiratory syncytial virus (RSV) (19.3%), rhinovirus (17.0%), parechovirus (14.3%), bocavirus (11.1%), adenovirus (10.2%), metapneumo-virus A and B (10.2%), parainfluenza virus (5.7%), enterovirus (3.0%), influenza A virus (2.8%), coronavirus (4%), parainfluenza virus (0.9%) and influenza C virus (0.4%) were detected. This study highlighted the etiological agents of bacteria, viruses and drug-resistant bacterial pathogens in SARI.

Pneumocystis carinii Pneumonitis in Young Immunocompetent Infants

PEDIATRICS ◽  
1980 ◽  
Vol 66 (1) ◽  
pp. 56-62
Author(s):  
Sergio Stagno ◽  
Linda L. Pifer ◽  
Walter T. Hughes ◽  
Dana M. Brasfield ◽  
Ralph E. Tiller
Keyword(s):  
Influenza A ◽  
Pneumocystis Carinii ◽  
Open Lung Biopsy ◽  
Influenza B ◽  
Severe Respiratory Distress ◽  
Number Of Patients ◽  
Circulating Antigens ◽  
Cytomegalovirus Pneumonia ◽  
Syncytial Virus ◽  
A Prospective Study

Of 67 infants enrolled in a prospective study of infant pneumonia ten (14%) had evidence of Pneumocystis carinii infection. Diagnosis was achieved by demonstrating circulating P carinii antigens by counterimmunoelectrophoresis in all ten cases and by histopathology in the only infant who underwent an open lung biopsy. Antigenemia did not occur in 64 control infants (P = .003), nor in 57 patients of similar age who were hospitalized with pneumonitis due to Chlamydia trachomatis, respiratory syncytial virus, cytomegalovirus, adenovirus, and influenza A and influenza B viruses. None of the ten infants with P carinii pneumonitis had evidence of a primary immunodeficiency nor had any received immunosuppressive medication. These patients were hospitalized at a mean age of 6 weeks (range 2 to 12) and their illness was characterized by its afebrile course, presentation in crisis with severe respiratory distress, apnea, tachypnea, cough, increased IgM, and bilateral pulmonary infiltrates with hyperaeration. The clinical features of P carinii pneumonitis were indistinguishable from those of C trachomatis and cytomegalovirus pneumonia. Treatment with trimethoprim-sulfamethoxazole was associated with rapid disappearance of circulating antigens; however, the small number of patients studied did not permit an analysis of its clinical efficacy. These results indicate that P carinii singly or in combination with other infectious agents may be an important cause of pneumonitis in young, immunocompetent infants with no underlying illnesses.

scholarly journals Rapid disappearance of influenza following the implementation of COVID-19 mitigation measures in Hamilton, Ontario

2021 ◽  
Vol 47 (04) ◽  
pp. 202-208
Author(s):  
Kevin Zhang ◽  
Avika Misra ◽  
Patrick J Kim ◽  
Seyed M Moghadas ◽  
Joanne M Langley ◽  
...  
Keyword(s):  
Public Health ◽  
Influenza A ◽  
Respiratory Virus ◽  
Respiratory Viruses ◽  
Mitigation Measures ◽  
Nasopharyngeal Swab ◽  
Health Measures ◽  
Bayesian Linear Regression ◽  
Syncytial Virus ◽  
The Impact

Background: Public health measures, such as physical distancing and closure of schools and non-essential services, were rapidly implemented in Canada to interrupt the spread of the coronavirus disease 2019 (COVID-19). We sought to investigate the impact of mitigation measures during the spring wave of COVID-19 on the incidence of other laboratory-confirmed respiratory viruses in Hamilton, Ontario. Methods: All nasopharyngeal swab specimens (n=57,503) submitted for routine respiratory virus testing at a regional laboratory serving all acute-care hospitals in Hamilton between January 2010 and June 2020 were reviewed. Testing for influenza A and B, respiratory syncytial virus, human metapneumovirus, parainfluenza I–III, adenovirus, and rhinovirus/enterovirus was done routinely using a laboratory-developed polymerase chain reaction multiplex respiratory viral panel. A Bayesian linear regression model was used to determine the trend of positivity rates of all influenza samples for the first 26 weeks of each year from 2010 to 2019. The mean positivity rate of Bayesian inference was compared with the weekly reported positivity rate of influenza samples in 2020. Results: The positivity rate of influenza in 2020 diminished sharply following the population-wide implementation of COVID-19 interventions. Weeks 12–26 reported 0% positivity for influenza, with the exception of 0.1% reported in week 13. Conclusion: Public health measures implemented during the COVID-19 pandemic were associated with a reduced incidence of other respiratory viruses and should be considered to mitigate severe seasonal influenza and other respiratory virus pandemics.

scholarly journals No evidence of SARS-CoV-2 in hospitalized patients with severe acute respiratory syndrome in five Italian hospitals from 1st November 2019 to 29th February 2020

PLoS ONE ◽  
2021 ◽  
Vol 16 (12) ◽  
pp. e0260947
Author(s):  
Donatella Panatto ◽  
Andrea Orsi ◽  
Beatrice Marina Pennati ◽  
Piero Luigi Lai ◽  
Stefano Mosca ◽  
...  
Keyword(s):  
Phase I ◽  
Influenza A ◽  
Hospitalized Patients ◽  
Influenza Viruses ◽  
Influenza B ◽  
Molecular Testing ◽  
Rt Pcr ◽  
The Real ◽  
Severe Acute Respiratory Infection ◽  
Novel Coronavirus

Background On 9th January 2020, China CDC reported a novel coronavirus (later named SARS-CoV-2) as the causative agent of the coronavirus disease 2019 (COVID-19). Identifying the first appearance of virus is of epidemiological importance to tracking and mapping the spread of SARS-CoV-2 in a country. We therefore conducted a retrospective observational study to detect SARS-CoV-2 in oropharyngeal samples collected from hospitalized patients with a Severe Acute Respiratory Infection (SARI) enrolled in the DRIVE (Development of Robust and Innovative Vaccine Effectiveness) study in five Italian hospitals (CIRI-IT BIVE hospitals network) (1st November 2019 – 29th February 2020). Objectives To acquire new information on the real trend in SARS-CoV-2 infection during pandemic phase I and to determine the possible early appearance of the virus in Italy. Materials and methods Samples were tested for influenza [RT-PCR assay (A/H1N1, A/H3N2, B/Yam, B/Vic)] in accordance with the DRIVE study protocol. Subsequently, swabs underwent molecular testing for SARS-COV-2. [one-step real-time multiplex retro-transcription (RT) PCR]. Results In the 1683 samples collected, no evidence of SARS-CoV-2 was found. Moreover, 28.3% (477/1683) of swabs were positive for influenza viruses, the majority being type A (358 vs 119 type B). A/H3N2 was predominant among influenza A viruses (55%); among influenza B viruses, B/Victoria was prevalent. The highest influenza incidence rate was reported in patients aged 0–17 years (40.3%) followed by those aged 18–64 years (24.4%) and ≥65 years (14.8%). Conclusions In Italy, some studies have shown the early circulation of SARS-CoV-2 in northern regions, those most severely affected during phase I of the pandemic. In central and southern regions, by contrast no early circulation of the virus was registered. These results are in line with ours. These findings highlight the need to continue to carry out retrospective studies, in order to understand the epidemiology of the novel coronavirus, to better identify the clinical characteristics of COVID-19 in comparison with other acute respiratory illnesses (ARI), and to evaluate the real burden of COVID-19 on the healthcare system.

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

2021 ◽  
Author(s):  
Paul Stamm ◽  
Ingo Sagoschen ◽  
Kerstin Weise ◽  
Bodo Plachter ◽  
Thomas Münzel ◽  
...  
Keyword(s):  
Emergency Room ◽  
Influenza A ◽  
Point Of Care ◽  
Respiratory Viruses ◽  
Pediatric Emergency ◽  
Influenza B ◽  
Complete Suppression ◽  
Emergency Room Patients ◽  
Syncytial Virus ◽  
Point Of Care Tests

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.

scholarly journals Public health implications of influenza B outbreaks in closed settings in the United Kingdom in the 2007/08 influenza season

2008 ◽  
Vol 13 (38) ◽  
Author(s):  
P Mook ◽  
J Ellis ◽  
J M Watson ◽  
CI Thompson ◽  
M Zambon ◽  
...  
Keyword(s):  
Public Health ◽  
United Kingdom ◽  
Burden Of Disease ◽  
Influenza A ◽  
Health Management ◽  
Influenza Season ◽  
Influenza B ◽  
Influenza A Viruses ◽  
School Aged Children ◽  
The United Kingdom

Several influenza B outbreaks occurred in closed settings late in the 2007/08 influenza season (October to mid-May) in the United Kingdom (UK), with implications for public health management. Influenza B viruses usually circulate late in the season and cause a milder disease than influenza A viruses [1]. Epidemics of influenza B usually occur every two to three years with the burden of disease falling predominantly on school-aged children [2].

scholarly journals Human Metapneumovirus: Etiological Agent of Severe Acute Respiratory Infections in Hospitalized and Deceased Patients with a Negative Diagnosis of Influenza

Pathogens ◽  
2020 ◽  
Vol 9 (2) ◽  
pp. 85
Author(s):  
Gisela Barrera-Badillo ◽  
Beatriz Olivares-Flores ◽  
Adriana Ruiz-López ◽  
Miguel Ángel Fierro-Valdez ◽  
Rosaura Idania Gutiérrez-Vargas ◽  
...  
Keyword(s):  
Young Children ◽  
Age Groups ◽  
Simultaneous Detection ◽  
Respiratory Viruses ◽  
Human Metapneumovirus ◽  
Late Winter ◽  
Older Individuals ◽  
Severe Acute Respiratory Infection ◽  
Syncytial Virus ◽  
Tract Infections

Human metapneumovirus (HMPV) is one of the four major viral pathogens associated with acute respiratory tract infections (ARI) and creates a substantial burden of disease, particularly in young children (<5 years) and older individuals (≥65 years). The objective of this study was to determine the epidemiological behavior of HMPV in Mexico. This retrospective study was conducted over a nine-year period and used 7283 influenza-negative respiratory samples from hospitalized and deceased patients who presented Severe Acute Respiratory Infection (SARI). The samples were processed with the help of qualitative multiplex RT-PCR for simultaneous detection of 14 respiratory viruses (xTAG® RVP FAST v2). 40.8% of the samples were positive for respiratory viruses, mainly rhinovirus/enterovirus (47.6%), respiratory syncytial virus (15.9%), HMPV (11.1%) and parainfluenza virus (8.9%). Other respiratory viruses and co-infections accounted for 16.5%. HMPV infects all age groups, but the most affected group was infants between 29 days and 9 years of age (65.6%) and adults who are 40 years and older (25.7%). HMPV circulates every year from November to April, and the highest circulation was observed in late winter. The results of this study aim to raise awareness among clinicians about the high epidemiological impact of HMPV in young children and older individuals in order to reduce the economic burden in terms of health care costs.

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