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

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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Multicenter Evaluation of the QIAstat-Dx Respiratory Panel for Detection of Viruses and Bacteria in Nasopharyngeal Swab Specimens

Journal of Clinical Microbiology ◽

10.1128/jcm.00155-20 ◽

2020 ◽

Vol 58 (5) ◽

Cited By ~ 5

Author(s):

Amy L. Leber ◽

Jan Gorm Lisby ◽

Glen Hansen ◽

Ryan F. Relich ◽

Uffe Vest Schneider ◽

...

Keyword(s):

Influenza A ◽

Parainfluenza Virus ◽

Nasopharyngeal Swab ◽

Influenza B ◽

Respiratory Pathogens ◽

Content Type ◽

Percent Agreement ◽

Influenza A H1n1 ◽

Syncytial Virus

ABSTRACT The QIAstat-Dx Respiratory Panel (QIAstat-Dx RP) is a multiplex in vitro diagnostic test for the qualitative detection of 20 pathogens directly from nasopharyngeal swab (NPS) specimens. The assay is performed using a simple sample-to-answer platform with results available in approximately 69 min. The pathogens identified are adenovirus, coronavirus 229E, coronavirus HKU1, coronavirus NL63, coronavirus OC43, human metapneumovirus A and B, influenza A, influenza A H1, influenza A H3, influenza A H1N1/2009, influenza B, parainfluenza virus 1, parainfluenza virus 2, parainfluenza virus 3, parainfluenza virus 4, rhinovirus/enterovirus, respiratory syncytial virus A and B, Bordetella pertussis, Chlamydophila pneumoniae, and Mycoplasma pneumoniae. This multicenter evaluation provides data obtained from 1,994 prospectively collected and 310 retrospectively collected (archived) NPS specimens with performance compared to that of the BioFire FilmArray Respiratory Panel, version 1.7. The overall percent agreement between QIAstat-Dx RP and the comparator testing was 99.5%. In the prospective cohort, the QIAstat-Dx RP demonstrated a positive percent agreement of 94.0% or greater for the detection of all but four analytes: coronaviruses 229E, NL63, and OC43 and rhinovirus/enterovirus. The test also demonstrated a negative percent agreement of ≥97.9% for all analytes. The QIAstat-Dx RP is a robust and accurate assay for rapid, comprehensive testing for respiratory pathogens.

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The viral aetiology of influenza-like illnesses in Kampala and Entebbe, Uganda, 2008

African Journal of Laboratory Medicine ◽

10.4102/ajlm.v2i1.65 ◽

2013 ◽

Vol 2 (1) ◽

Cited By ~ 2

Author(s):

Stephen Balinandi ◽

Barnabas Bakamutumaho ◽

John T. Kayiwa ◽

Juliette Ongus ◽

Joseph Oundo ◽

...

Keyword(s):

Influenza A ◽

Management Strategies ◽

Respiratory Viruses ◽

Cross Sectional Study ◽

Parainfluenza Virus ◽

Influenza B Virus ◽

Nasopharyngeal Swab ◽

Influenza B ◽

Cross Sectional ◽

Syncytial Virus

Background: As the threat of zoonoses and the emergence of pandemic-prone respiratory viruses increases, there is a need to establish baseline information on the incidence of endemic pathogens in countries worldwide.Objectives: To investigate the presence of viruses associated with influenza-like illnesses (ILI) in Uganda.Methods: A cross-sectional study was conducted in which nasopharyngeal swab specimens were collected from patients diagnosed with ILI in Kampala and Entebbe between 14 August2008 – 15 December 2008. A multiplex polymerase chain reaction assay for detecting 12 respiratory viruses was used.Results: A total of 369 patients (52.3% females) was enrolled; the median age was 6 years (range1–70). One or more respiratory viruses were detected in 172 (46.6%) cases and their prevalence were influenza A virus (19.2%), adenovirus (8.7%), human rhinovirus A (7.9%), coronavirusOC43 (4.3%), parainfluenza virus 1 (2.7%), parainfluenza virus 3 (2.7%), influenza B virus (2.2%),respiratory syncytial virus B (2.2%), human metapneumovirus (1.4%), respiratory syncytialvirus A (1.1%), parainfluenza virus 2 (0.5%) and coronavirus 229E (0.5%). There were 24 (14.0%) mixed infections.Conclusions: This study identified some of the respiratory viruses associated with ILI in Uganda.The circulation of some of the viruses was previously unknown in the study population. These results are useful in order to guide future surveillance and case management strategies involving respiratory illnesses in Uganda.

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

Canada Communicable Disease Report ◽

10.14745/ccdr.v47i04a04 ◽

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.

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

Medical Microbiology and Immunology ◽

10.1007/s00430-021-00720-7 ◽

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.

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Comparison of detection rate of 16 sampling methods for respiratory viruses: a Bayesian network meta-analysis of clinical data and systematic review

BMJ Global Health ◽

10.1136/bmjgh-2020-003053 ◽

2020 ◽

Vol 5 (11) ◽

pp. e003053

Author(s):

Nianzong Hou ◽

Kai Wang ◽

Haiyang Zhang ◽

Mingjian Bai ◽

Hao Chen ◽

...

Keyword(s):

Influenza A ◽

Detection Rate ◽

Sampling Methods ◽

Meta Analysis ◽

Random Effect ◽

Splitting Method ◽

Respiratory Viruses ◽

Nasopharyngeal Swab ◽

Specific Virus ◽

Syncytial Virus

BackgroundRespiratory viruses (RVs) is a common cause of illness in people of all ages, at present, different types of sampling methods are available for respiratory viral diagnosis. However, the diversity of available sampling methods and the limited direct comparisons in randomised controlled trials (RCTs) make decision-making difficult. We did a network meta-analysis, which accounted for both direct and indirect comparisons, to determine the detection rate of different sampling methods for RVs.MethodsRelevant articles were retrieved comprehensively by searching the online databases of PubMed, Embase and Cochrane published before 25 March 2020. With the help of R V.3.6.3 software and ‘GeMTC V.0.8.2’ package, network meta-analysis was performed within a Bayesian framework. Node-splitting method and I2 test combined leverage graphs and Gelman-Rubin-Brooks plots were conducted to evaluate the model’s accuracy. The rank probabilities in direct and cumulative rank plots were also incorporated to rank the corresponding sampling methods for overall and specific virus.Results16 sampling methods with 54 438 samples from 57 literatures were ultimately involved in this study. The model indicated good consistency and convergence but high heterogeneity, hence, random-effect analysis was applied. The top three sampling methods for RVs were nasopharyngeal wash (NPW), mid-turbinate swab (MTS) and nasopharyngeal swab (NPS). Despite certain differences, the results of virus-specific subanalysis were basically consistent with RVs: MTS, NPW and NPS for influenza; MTS, NPS and NPW for influenza-a and b; saliva, NPW and NPS for rhinovirus and parainfluenza; NPW, MTS and nasopharyngeal aspirate for respiratory syncytial virus; saliva, NPW and MTS for adenovirus and sputum; MTS and NPS for coronavirus.ConclusionThis network meta-analysis provides supporting evidences that NPW, MTS and NPS have higher diagnostic value regarding RVs infection, moreover, particular preferred methods should be considered in terms of specific virus pandemic. Of course, subsequent RCTs with larger samples are required to validate our findings.

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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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Prevalence and Genetic Characteristics of Human Bocaviruses Detected in Patients with Acute Respiratory Infections in Bulgaria

International Journal of Microbiology ◽

10.1155/2021/7035081 ◽

2021 ◽

Vol 2021 ◽

pp. 1-10

Author(s):

Neli Korsun ◽

Svetla Angelova ◽

Ivelina Trifonova ◽

Silvia Voleva ◽

Iliana Grigorova ◽

...

Keyword(s):

Amino Acid ◽

Influenza A ◽

Respiratory Infections ◽

Single Agent ◽

Respiratory Viruses ◽

Acute Respiratory Infections ◽

Vp2 Gene ◽

Genetic Characteristics ◽

Influenza A H1n1 ◽

Syncytial Virus

Нuman bocaviruses (hBoVs) are often associated with acute respiratory infections (ARIs). Information on the distribution and molecular epidemiology of hBoVs in Bulgaria is currently limited. The objectives of this study were to investigate the prevalence and genetic characteristics of hBoVs detected in patients with ARIs in Bulgaria. From October 2016 to September 2019, nasopharyngeal/oropharyngeal swabs were prospectively collected from 1842 patients of all ages and tested for 12 common respiratory viruses using a real-time RT-PCR. Phylogenetic and amino acid analyses of the hBoV VP1/VP2 gene/protein were performed. HBoV was identified in 98 (5.3%) patients and was the 6th most prevalent virus after respiratory-syncytial virus (20.4%), influenza A(H1N1)pdm09 (11.1%), A(H3N2) (10.5%), rhinoviruses (9.9%), and adenoviruses (6.8%). Coinfections with other respiratory viruses were detected in 51% of the hBoV-positive patients. Significant differences in the prevalence of hBoVs were found during the different study periods and in patients of different age groups. The detection rate of hBoV was the highest in patients aged 0–4 years (6.9%). In this age group, hBoV was the only identified virus in 9.7%, 5.8%, and 1.1% of the children diagnosed with laryngotracheitis, bronchiolitis, and pneumonia, respectively. Among patients aged ≥5 years, hBoV was detected as a single agent in 2.2% of cases of pneumonia. Phylogenetic analysis showed that all Bulgarian hBoV strains belonged to the hBoV1 genotype. A few amino acid substitutions were identified compared to the St1 prototype strain. This first study amongst an all-age population in Bulgaria showed a significant rate of hBoV detection in some serious respiratory illnesses in early childhood, year-to-year changes in the hBoV prevalence, and low genetic variability in the circulating strains.

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Incidence of medically attended acute respiratory illnesses due to respiratory viruses across the life course during the 2018/19 influenza season

Clinical Infectious Diseases ◽

10.1093/cid/ciab131 ◽

2021 ◽

Author(s):

Michael L Jackson ◽

Lea Starita ◽

Erika Kiniry ◽

C Hallie Phillips ◽

Stacie Wellwood ◽

...

Keyword(s):

Life Course ◽

Influenza A ◽

Influenza Season ◽

Respiratory Illness ◽

Respiratory Viruses ◽

Acute Respiratory Illness ◽

Common Cause ◽

Influenza A H1n1 ◽

Syncytial Virus ◽

The Life Course

Abstract Background While multiple respiratory viruses circulate in humans, few studies have compared the incidence of different viruses across the life course. We estimated the incidence of outpatient illness due to 12 different viruses during November 2018 through April 2019 in a fully enumerated population. Methods We conducted active surveillance for ambulatory care visits for acute respiratory illness (ARI) among members of Kaiser Permanente Washington (KPWA). Enrolled patients provided respiratory swab specimens which were tested for 12 respiratory viruses using RT-PCR. We estimated the cumulative incidence of infection due to each virus overall and by age group. Results The KPWA population under surveillance included 202,562 individuals, of whom 2,767 (1.4%) were enrolled in the study. Influenza A(H3N2) was the most commonly detected virus, with an overall incidence 21 medically attended illnesses per 1,000 population; the next most common viruses were influenza A(H1N1) (18 per 1,000), coronaviruses (13 per 1,000), respiratory syncytial virus (RSV, 13 per 1,000), and rhinovirus (9 per 1,000). RSV was the most common cause of medically attended ARI among children aged 1-4 years; coronaviruses were the most common among adults aged ≥65 years. Conclusions Consistent with other studies focused on single viruses, we found that influenza and RSV were major causes of acute respiratory illness in persons of all ages. In comparison, coronaviruses and rhinovirus were also important pathogens. Prior to the emergence of SARS-CoV-2, coronaviruses were the second-most common cause of medically attended ARI during the 2018/19 influenza season.

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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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Magnetofluidic platform for rapid multiplexed screening of SARS-CoV-2 variants and respiratory pathogens

10.1101/2021.05.10.21256995 ◽

2021 ◽

Author(s):

Alexander Y Trick ◽

Fan-En Chen ◽

Liben Chen ◽

Pei-Wei Lee ◽

Alexander C Hasnain ◽

...

Keyword(s):

Influenza A ◽

Respiratory Symptoms ◽

Limit Of Detection ◽

Respiratory Viruses ◽

Nasopharyngeal Swab ◽

Influenza B ◽

Respiratory Pathogens ◽

Multiplexed Detection ◽

New Challenges ◽

Sensitivity Specificity

The rise of highly transmissible SARS-CoV-2 variants brings new challenges and concerns with vaccine efficacy, diagnostic sensitivity, and public health responses in the fight to end the pandemic. Widespread detection of variant strains will be critical to inform policy decisions to mitigate further spread, and post-pandemic multiplexed screening of respiratory viruses will be necessary to properly manage patients presenting with similar respiratory symptoms. In this work, we have developed a portable, magnetofluidic cartridge platform for automated PCR testing in <30 min. Cartridges were designed for multiplexed detection of SARS-CoV-2 with either distinctive variant mutations or with Influenza A and B. The platform demonstrated a limit of detection down to 2 copies/μL SARS-CoV-2 RNA with successful identification of B.1.1.7 and B.1.351 variants. The multiplexed SARS-CoV-2/Flu assay was validated using archived clinical nasopharyngeal swab eluates (n = 116) with an overall sensitivity/specificity of 98.1%/95.2%, 85.7%/100%, 100%/98.2%, respectively, for SARS-CoV-2, Influenza A, and Influenza B. Further testing with saliva (n = 14) demonstrated successful detection of all SARS-CoV-2 positive samples with no false-positives.

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