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      Performance Evaluation of TaqMan SARS-CoV-2, Flu A/B, RSV RT-PCR Multiplex Assay for the Detection of Respiratory Viruses

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          Abstract

          Purpose

          To detect and differentiate co-infection with influenza and respiratory syncytial virus during the COVID pandemic, a rapid method that can detect multiple pathogens in a single test is a significant diagnostic advance to analyze the outcomes and clinical implications of co-infection. Therefore, we validated and evaluated the performance characteristics of TaqMan SARS-CoV-2, Flu A/B, RSV RT-PCR multiplex assay for the detection of SARS-CoV-2, Flu A/B, and RSV using nasopharyngeal and saliva samples.

          Materials and Methods

          The method validation was performed by using culture fluids of Influenza A virus (H3N2) (A/Wisconsin/67/2005), Influenza B virus (B/Virginia/ATCC4/2009), RSV A2 cpts-248, SARS-CoV-2 (USA-WA1/2020) and quantitative RNA controls of Influenza A virus (H1N1) strain A/PR/8/34 (VR-95DQ), RSV A2 (VR-1540DQ) and SARS-CoV-2 (MN908947.3 Wuhan-Hu-1) from ATCC and Zeptometrix, NY, USA. A total of 110 nasopharyngeal specimens and 70 saliva samples were used for the SARS-CoV-2 detection, and a total of 70 nasopharyngeal specimens were used for Influenza and RSV detection. Total RNA was extracted from all the samples and multiplex PCR was performed using TaqMan SARS-CoV-2, Flu A/B, RSV RT-PCR multiplex assay. The assay was used for SARS-CoV-2 variant (B.1.1.7_601443, B.1.617.1_1662307, P.1_792683, B.1.351_678597, B.1.1.529/BA.1).

          Results

          Validation controls showed accurate and precise results. The correlation study found the accuracy of 96.38 to 100% (95% CI) in nasopharyngeal and 94.87 to 100% (95% CI) in saliva for SARS-CoV-2 and 91.1 to 100% (95% CI) for both Influenza A/B and RSV. The diagnostic efficiency of this assay was not affected by SARS-CoV-2 variant, including Omicron.

          Conclusion

          The TaqMan SARS-CoV-2, Flu A/B, RSV RT-PCR multiplex assay is a rapid method to detect and differentiate SAR-CoV-2, Flu A and B, and RSV in nasopharyngeal and saliva samples. It has a significant role in the diagnosis and management of respiratory illnesses and the clinical implications of co-infection.

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          Most cited references18

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          Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and coronavirus disease-2019 (COVID-19): The epidemic and the challenges

          Chih-Cheng Lai, Tzu-Ping Shih, Wen-Chien Ko … (2020)
          Highlights • Emergence of 2019 novel coronavirus (2019-nCoV) in China has caused a large global outbreak and major public health issue. • At 9 February 2020, data from the WHO has shown >37 000 confirmed cases in 28 countries (>99% of cases detected in China). • 2019-nCoV is spread by human-to-human transmission via droplets or direct contact. • Infection estimated to have an incubation period of 2–14 days and a basic reproduction number of 2.24–3.58. • Controlling infection to prevent spread of the 2019-nCoV is the primary intervention being used.
          Article 0 comments Cited 2410 times – based on 0 reviews     Review now
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            Mortality associated with influenza and respiratory syncytial virus in the United States.

            William W Thompson, David Shay (2003)
            Influenza and respiratory syncytial virus (RSV) cause substantial morbidity and mortality. Statistical methods used to estimate deaths in the United States attributable to influenza have not accounted for RSV circulation. To develop a statistical model using national mortality and viral surveillance data to estimate annual influenza- and RSV-associated deaths in the United States, by age group, virus, and influenza type and subtype. Age-specific Poisson regression models using national viral surveillance data for the 1976-1977 through 1998-1999 seasons were used to estimate influenza-associated deaths. Influenza- and RSV-associated deaths were simultaneously estimated for the 1990-1991 through 1998-1999 seasons. Attributable deaths for 3 categories: underlying pneumonia and influenza, underlying respiratory and circulatory, and all causes. Annual estimates of influenza-associated deaths increased significantly between the 1976-1977 and 1998-1999 seasons for all 3 death categories (P<.001 for each category). For the 1990-1991 through 1998-1999 seasons, the greatest mean numbers of deaths were associated with influenza A(H3N2) viruses, followed by RSV, influenza B, and influenza A(H1N1). Influenza viruses and RSV, respectively, were associated with annual means (SD) of 8097 (3084) and 2707 (196) underlying pneumonia and influenza deaths, 36 155 (11 055) and 11 321 (668) underlying respiratory and circulatory deaths, and 51 203 (15 081) and 17 358 (1086) all-cause deaths. For underlying respiratory and circulatory deaths, 90% of influenza- and 78% of RSV-associated deaths occurred among persons aged 65 years or older. Influenza was associated with more deaths than RSV in all age groups except for children younger than 1 year. On average, influenza was associated with 3 times as many deaths as RSV. Mortality associated with both influenza and RSV circulation disproportionately affects elderly persons. Influenza deaths have increased substantially in the last 2 decades, in part because of aging of the population, underscoring the need for better prevention measures, including more effective vaccines and vaccination programs for elderly persons.
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              Co-infection with respiratory pathogens among COVID-2019 cases

              Xiaojuan Zhu, Yiyue Ge, Tao Wu … (2020)
              Highlights • We describe the presence of 24 respiratory pathogens as co-infections in COVID-19 patients. • Most of these co-infections occurred 1–4 days after the onset of disease in COVID-19 patients. • The proportion of viral co-infections, fungal co-infections and bacterial-fungal co-infections were the highest in severe COVID-19 cases.
              Article 0 comments Cited 275 times – based on 0 reviews     Review now
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                Author and article information

                Journal
                Journal ID (nlm-ta): Infect Drug Resist
                Journal ID (iso-abbrev): Infect Drug Resist
                Journal ID (publisher-id): idr
                Title: Infection and Drug Resistance
                Publisher: Dove
                ISSN (Electronic): 1178-6973
                Publication date (Electronic): 12 September 2022
                Publication date Collection: 2022
                Volume: 15
                Pages: 5411-5423
                Affiliations
                [1 ]Patients Choice Laboratories , Indianapolis, IN, 46278, USA
                Author notes
                Correspondence: Safedin Beqaj, Patients Choice Laboratories , 7026 Corporate Dr, Indianapolis, IN, 46278, USA, Email sajo@pclabsindiana.com
                Author information
                http://orcid.org/0000-0001-6081-1305
                Article
                Publisher ID: 373748
                DOI: 10.2147/IDR.S373748
                PMC ID: 9480588
                PubMed ID: 36119638
                SO-VID: 116435dd-6366-4865-9bf0-2a8dd9275c9e
                Copyright © © 2022 Neopane et al.
                License:

                This work is published and licensed by Dove Medical Press Limited. The full terms of this license are available at https://www.dovepress.com/terms.php and incorporate the Creative Commons Attribution – Non Commercial (unported, v3.0) License ( http://creativecommons.org/licenses/by-nc/3.0/). By accessing the work you hereby accept the Terms. Non-commercial uses of the work are permitted without any further permission from Dove Medical Press Limited, provided the work is properly attributed. For permission for commercial use of this work, please see paragraphs 4.2 and 5 of our Terms ( https://www.dovepress.com/terms.php).

                History
                Date received : 11 May 2022
                Date accepted : 24 August 2022
                Page count
                Figures: 2, Tables: 8, References: 27, Pages: 13
                Categories
                Subject: Original Research

                ScienceOpen disciplines: Infectious disease & Microbiology
                Keywords: taqman,sars-cov-2,flu a/b,respiratory syncytial virus,rsv,multiplex
                Data availability:
                ScienceOpen disciplines: Infectious disease & Microbiology
                Keywords: taqman, sars-cov-2, flu a/b, respiratory syncytial virus, rsv, multiplex

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