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Kanta P, Ghosh A, Goyal K, Kaur R, Baluni M, Sircar S, Kumar V, Kumar K, Vijay N, Singh MP. Effect of storage temperatures simulating transport conditions of nasopharyngeal swabs on the results of a chemiluminescence immunoassay (CLIA) to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antigen. Indian J Med Microbiol 2023; 44:100379. [PMID: 37356827 PMCID: PMC10163922 DOI: 10.1016/j.ijmmb.2023.100379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 02/24/2023] [Accepted: 04/20/2023] [Indexed: 06/27/2023]
Abstract
PURPOSE Chemiluminescence Immunoassay (CLIA) is high throughput, rapid diagnostic test which has recently come up for the detection of SARS-CoV-2 antigen. The present study evaluated performance of CLIA antigen test in nasopharyngeal swab samples stored at different temperatures for 7 days to simulate the transport conditions and transit time across the country from remote peripheral laboratories to central facilities. MATERIALS AND METHODS Limit of detection (LOD), sensitivity and specificity of VITROS® SARS-CoV-2 antigen assay was determined using Real-time reverse transcriptase PCR (rRT-PCR) confirmed SARS-CoV-2 positive and negative samples. To detect the effect of storage temperatures on VITROS ®SARS-CoV-2 antigen results, samples were stored at 4 °C, 25 °C & 37 °C for 7 days followed by detection of SARS-CoV-2 nucleocapsid antigen and compared with N-gene rRT-PCR. RESULTS The VITROS® SARS-CoV-2 antigen test was found to have a sensitivity and specificity of 78.9% and 100% respectively with high sensitivity of 88.1% for samples with Ct < 30. The LOD of VITROS assay was equivalent to 3800 copies of RNA per reactions as compared to 72 copies per reaction for rRT-PCR. We observed that more than 80% of samples with <30 Ct values could be detected by VITROS SARS-CoV-2 antigen assay at day 7 even when stored at 37 °C. For samples with Ct values between 26 and 30, on day 7 the positivity rate of N-antigen at 4 °C was 90.9% and 37 °C was 63.6%. CONCLUSIONS CLIA testing can be carried out for the detection of SARS-CoV-2 N-protein in NP-swab samples transported in cold chain even with 7 days transit time, particularly for Ct < 30 samples which represents cases with higher transmissibility. As drop in positivity for VITROS assay was lower as compared to rRT-PCR on day 7 in cold chain-maintained samples, the assay can be useful to screen samples received from remote peripheral areas before performing rRT-PCR.
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Affiliation(s)
- Poonam Kanta
- Department of Virology, PGIMER, Chandigarh, India
| | - Arnab Ghosh
- Department of Virology, PGIMER, Chandigarh, India
| | - Kapil Goyal
- Department of Virology, PGIMER, Chandigarh, India
| | | | | | | | - Vikas Kumar
- Department of Virology, PGIMER, Chandigarh, India
| | | | - Neetu Vijay
- Indian Council of Medical Research (ICMR), Department of Health Research, New Delhi, India
| | - Mini P Singh
- Department of Virology, PGIMER, Chandigarh, India.
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Van Poelvoorde LAE, Delcourt T, Vuylsteke M, De Keersmaecker SCJ, Thomas I, Van Gucht S, Saelens X, Roosens N, Vanneste K. A general approach to identify low-frequency variants within influenza samples collected during routine surveillance. Microb Genom 2022; 8. [PMID: 36169645 DOI: 10.1099/mgen.0.000867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Influenza viruses exhibit considerable diversity between hosts. Additionally, different quasispecies can be found within the same host. High-throughput sequencing technologies can be used to sequence a patient-derived virus population at sufficient depths to identify low-frequency variants (LFV) present in a quasispecies, but many challenges remain for reliable LFV detection because of experimental errors introduced during sample preparation and sequencing. High genomic copy numbers and extensive sequencing depths are required to differentiate false positive from real LFV, especially at low allelic frequencies (AFs). This study proposes a general approach for identifying LFV in patient-derived samples obtained during routine surveillance. Firstly, validated thresholds were determined for LFV detection, whilst balancing both the cost and feasibility of reliable LFV detection in clinical samples. Using a genetically well-defined population of influenza A viruses, thresholds of at least 104 genomes per microlitre and AF of ≥5 % were established as detection limits. Secondly, a subset of 59 retained influenza A (H3N2) samples from the 2016-2017 Belgian influenza season was composed. Thirdly, as a proof of concept for the added value of LFV for routine influenza monitoring, potential associations between patient data and whole genome sequencing data were investigated. A significant association was found between a high prevalence of LFV and disease severity. This study provides a general methodology for influenza LFV detection, which can also be adopted by other national influenza reference centres and for other viruses such as SARS-CoV-2. Additionally, this study suggests that the current relevance of LFV for routine influenza surveillance programmes might be undervalued.
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Affiliation(s)
- Laura A E Van Poelvoorde
- Transversal activities in Applied Genomics, Sciensano, Juliette Wytsmanstraat 14, Brussels, Belgium.,National Influenza Centre, Sciensano, Juliette Wytsmanstraat 14, Brussels, Belgium.,Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium.,VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
| | - Thomas Delcourt
- Transversal activities in Applied Genomics, Sciensano, Juliette Wytsmanstraat 14, Brussels, Belgium
| | | | | | - Isabelle Thomas
- National Influenza Centre, Sciensano, Juliette Wytsmanstraat 14, Brussels, Belgium
| | - Steven Van Gucht
- National Influenza Centre, Sciensano, Juliette Wytsmanstraat 14, Brussels, Belgium
| | - Xavier Saelens
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium.,VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
| | - Nancy Roosens
- Transversal activities in Applied Genomics, Sciensano, Juliette Wytsmanstraat 14, Brussels, Belgium
| | - Kevin Vanneste
- Transversal activities in Applied Genomics, Sciensano, Juliette Wytsmanstraat 14, Brussels, Belgium
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Bouzid D, Visseaux B, Perozziello A, Lescure X, Duval X, Casalino E, Lucet JC. Factors associated with single-room assignment among patients admitted through the emergency department during influenza epidemics. PLoS One 2020; 15:e0237214. [PMID: 32764788 PMCID: PMC7413401 DOI: 10.1371/journal.pone.0237214] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 07/22/2020] [Indexed: 11/18/2022] Open
Abstract
INTRODUCTION Every winter, emergency departments (EDs) face overcrowding with patients presenting influenza-like symptoms, and organisational issues such as single room assignment and droplet precautions to avoid hospital-acquired influenza. Our main objective was to assess the impact of PCR results and patient's severity on single room assignment. METHODS All patients admitted to Bichat-Claude Bernard Hospital through the ED and tested for influenza by PCR (GenXpert, Cepheid) or (FilmArray, BioMérieux) on a nasopharyngeal swab were retrospectively included during three influenza seasons (2015-2018. RESULTS Of 1,330 included patients, 278 (20.9%) had a positive PCR for influenza. The median time to obtain a PCR result was 19 hours, and 238 (18.3%) patients were assigned a single room. Among patients with positive and negative influenza PCR, 22.3% and 16.7% were assigned a single room (p = 0.03). The multivariable analysis was performed on the two first epidemic periods, excluding the third epidemic because of the concomitant use of influenza immune-chromatic test. Only level 1 of the Emergency severity index (ESI) (aOR, 1.9; 95% CI, 1.3-2.8; p < 0.01) was associated with single-room assignment. PCR result was not statistically associated with the decision of single room assignment (aOR, 1.4; 95%CI, 1.0-1.4; p = 0.07). CONCLUSION A PCR positive for influenza was not significantly associated with single-room assignment. Less than one quarter of influenza patients were adequately assigned a single room, likely due to the long turnaround time of PCR result and other conflicting indications for single room-assignment. Accelerating biological diagnosis could improve single-room assignment.
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Affiliation(s)
- Donia Bouzid
- IAME, INSERM, Université de Paris, Paris, France
- Emergency Department, AP-HP, University Hospital Bichat-Claude Bernard, Paris, France
| | - Benoit Visseaux
- IAME, INSERM, Université de Paris, Paris, France
- AP-HP, University Hospital Bichat-Claude Bernard, Virology, Paris, France
| | | | - Xavier Lescure
- IAME, INSERM, Université de Paris, Paris, France
- Infectious Disease Department, AP-HP, University Hospital Bichat-Claude Bernard, Paris, France
- Clinical Investigation Center, AP-HP, University Hospital Bichat-Claude Bernard, Paris, France
| | - Xavier Duval
- IAME, INSERM, Université de Paris, Paris, France
- Infection Control Unit, AP-HP, University Hospital Bichat-Claude, Paris, France
| | - Enrique Casalino
- IAME, INSERM, Université de Paris, Paris, France
- Emergency Department, AP-HP, University Hospital Bichat-Claude Bernard, Paris, France
| | - Jean Christophe Lucet
- IAME, INSERM, Université de Paris, Paris, France
- Infection Control Unit, AP-HP, University Hospital Bichat-Claude, Paris, France
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Simusika P, Tempia S, Chentulo E, Polansky L, Mazaba ML, Ndumba I, Mbewe QK, Monze M. An evaluation of the Zambia influenza sentinel surveillance system, 2011-2017. BMC Health Serv Res 2020; 20:35. [PMID: 31931793 PMCID: PMC6958603 DOI: 10.1186/s12913-019-4884-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 12/30/2019] [Indexed: 08/21/2023] Open
Abstract
Background Over the past decade, influenza surveillance has been established in several African countries including Zambia. However, information on the on data quality and reliability of established influenza surveillance systems in Africa are limited. Such information would enable countries to assess the performance of their surveillance systems, identify shortfalls for improvement and provide evidence of data reliability for policy making and public health interventions. Methods We used the Centers for Disease Control and Prevention guidelines to evaluate the performance of the influenza surveillance system (ISS) in Zambia during 2011–2017 using 9 attributes: (i) data quality and completeness, (ii) timeliness, (iii) representativeness, (iv) flexibility, (v) simplicity, (vi) acceptability, (vii) stability, (viii) utility, and (ix) sustainability. Each attribute was evaluated using pre-defined indicators. For each indicator we obtained the proportion (expressed as percentage) of the outcome of interest over the total. A scale from 1 to 3 was used to provide a score for each attribute as follows: < 60% (as obtained in the calculation above) scored 1 (weak performance); 60–79% scored 2 (moderate performance); ≥80% scored 3 (good performance). An overall score for each attribute and the ISS was obtained by averaging the scores of all evaluated attributes. Results The overall mean score for the ISS in Zambia was 2.6. Key strengths of the system were the quality of data generated (score: 2.9), its flexibility (score: 3.0) especially to monitor viral pathogens other than influenza viruses, its simplicity (score: 2.8), acceptability (score: 3.0) and stability (score: 2.6) over the review period and its relatively low cost ($310,000 per annum). Identified weaknesses related mainly to geographic representativeness (score: 2.0), timeliness (score: 2.5), especially in shipment of samples from remote sites, and sustainability (score: 1.0) in the absence of external funds. Conclusions The system performed moderately well in our evaluation. Key improvements would include improvements in the timeliness of samples shipments and geographical coverage. However, these improvements would result in increased cost and logistical complexity. The ISSS in Zambia is largely reliant on external funds and the acceptability of maintaining the surveillance system through national funds would require evaluation.
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Affiliation(s)
- Paul Simusika
- National Influenza Center, Virology Laboratory, University Teaching Hospital, Lusaka, Zambia.
| | - Stefano Tempia
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA, USA.,Influenza Program, Centers for Disease Control and Prevention, Pretoria, South Africa.,MassGenics, Duluth, GA, USA
| | - Edward Chentulo
- National Influenza Center, Virology Laboratory, University Teaching Hospital, Lusaka, Zambia
| | - Lauren Polansky
- Influenza Program, Centers for Disease Control and Prevention, Pretoria, South Africa
| | - Mazyanga Lucy Mazaba
- National Influenza Center, Virology Laboratory, University Teaching Hospital, Lusaka, Zambia
| | - Idah Ndumba
- National Influenza Center, Virology Laboratory, University Teaching Hospital, Lusaka, Zambia
| | - Quinn K Mbewe
- National Influenza Center, Virology Laboratory, University Teaching Hospital, Lusaka, Zambia
| | - Mwaka Monze
- National Influenza Center, Virology Laboratory, University Teaching Hospital, Lusaka, Zambia.
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Comparison of Respiratory Specimen Collection Methods for Detection of Influenza Virus Infection by Reverse Transcription-PCR: a Literature Review. J Clin Microbiol 2019; 57:JCM.00027-19. [PMID: 31217267 DOI: 10.1128/jcm.00027-19] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The detection of influenza virus in respiratory specimens from ill individuals is the most commonly used method to identify influenza virus infection. A number of respiratory specimen types may be used, including swabs, brush, aspirate, and wash, and specimens may be collected from numerous sites, including the anterior and posterior nasopharynx, oropharynx, and nares. Traditionally, respiratory specimens from the nasopharynx have been considered to have the highest sensitivity for viral detection. However, as molecular assays such as reverse transcription-PCR (RT-PCR) have increased the sensitivity of viral detection from respiratory specimens, the use of less-invasive and easier-to-obtain specimens has increased for the detection of influenza virus. This review presents and evaluates the sensitivities of respiratory specimen methods used in epidemiologic studies that used RT-PCR to detect influenza virus in respiratory specimens from ill patients. This literature review suggested that a combination of two less-invasive swabbing methods, such as nasal and oropharyngeal swabs, had about the same sensitivity as did nasopharyngeal specimens for influenza virus detection by RT-PCR. By combining two less-invasive collection methods, it may be possible to reduce barriers to enrollment without compromising influenza virus detection sensitivity.
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Ndegwa LK, Emukule G, Uyeki TM, Mailu E, Chaves SS, Widdowson MA, Lewa BV, Muiruri FK, Omoth P, Fields B, Mott JA. Evaluation of the point-of-care Becton Dickinson Veritor™ Rapid influenza diagnostic test in Kenya, 2013-2014. BMC Infect Dis 2017; 17:60. [PMID: 28077093 PMCID: PMC5225564 DOI: 10.1186/s12879-016-2131-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 12/15/2016] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND We evaluated the performance of the Becton Dickinson Veritor™ System Flu A + B rapid influenza diagnostic test (RIDT) to detect influenza viruses in respiratory specimens from patients enrolled at five surveillance sites in Kenya, a tropical country where influenza seasonality is variable. METHODS Nasal swab (NS) and nasopharyngeal (NP)/oropharyngeal (OP) swabs were collected from patients with influenza like illness and/or severe acute respiratory infection. The sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of the RIDT using NS specimens were evaluated against nasal swabs tested by real time reverse transcription polymerase chain reaction (rRT-PCR). The performance parameter results were expressed as 95% confidence intervals (CI) calculated using binomial exact methods, with P < 0.05 considered significant. Two-sample Z tests were used to test for differences in sample proportions. Analysis was performed using SAS software version 9.3. RESULTS From July 2013 to July 2014, 3,569 patients were recruited, of which 78.7% were aged <5 years. Overall, 14.4% of NS specimens were influenza-positive by RIDT. RIDT overall sensitivity was 77.1% (95% CI 72.8-81.0%) and specificity was 94.9% (95% CI 94.0-95.7%) compared to rRT-PCR using NS specimens. RIDT sensitivity for influenza A virus compared to rRT-PCR using NS specimens was 71.8% (95% CI 66.7-76.4%) and was significantly higher than for influenza B which was 43.8% (95% CI 33.8-54.2%). PPV ranged from 30%-80% depending on background prevalence of influenza. CONCLUSION Although the variable seasonality of influenza in tropical Africa presents unique challenges, RIDTs may have a role in making influenza surveillance sustainable in more remote areas of Africa, where laboratory capacity is limited.
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Affiliation(s)
- Linus K. Ndegwa
- DGHP, Centers for Disease Control and Prevention, Nairobi, Kenya
- Infection Control African Network (ICAN), Infection prevention network-Kenya (IPNET-K), Mbagathi Road off Mbagathi way, Village Market, PO Box 606, 00621 Nairobi, Kenya
| | - Gideon Emukule
- DGHP, Centers for Disease Control and Prevention, Nairobi, Kenya
| | - Timothy M. Uyeki
- Influenza Division, Centers for Disease Control and Prevention-Atlanta, Georgia, USA
| | - Eunice Mailu
- Kenya Medical Research Institute/Centers for Disease Control and Prevention-Kenya, Nairobi, Kenya
| | - Sandra S. Chaves
- DGHP, Centers for Disease Control and Prevention, Nairobi, Kenya
| | | | | | | | | | - Barry Fields
- DGHP, Centers for Disease Control and Prevention, Nairobi, Kenya
| | - Joshua A. Mott
- Influenza Division, Centers for Disease Control and Prevention-Atlanta, Georgia, USA
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Dare R, Zhu Y, Williams JV, Griffin M, Talbot HK. Detection of influenza by real time RT-PCR is not affected by delays in respiratory specimen processing. J Med Virol 2016; 88:1891-5. [PMID: 27089468 DOI: 10.1002/jmv.24549] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/07/2016] [Indexed: 11/06/2022]
Abstract
Sample processing for real-time reverse transcriptase polymerase chain reaction (rRT-PCR) based diagnostic assays requires stabilizing sample ribonucleic acid (RNA) in lysis buffer prior to testing. The stability of viral RNA prior to processing is difficult to assure. It is unknown whether clinical sample integrity is compromised by delays in processing, as may occur due to weekends and holidays. We sought to examine the integrity of respiratory specimens with variable processing times. Upper respiratory specimens were collected during three influenza seasons 2009-2012 and tested for influenza virus and internal control human RNase P (RNP) RNA by rRT-PCR. Time to processing was measured in hours from specimen collection to placement in lysis buffer. Six hundred thirty-five (11.4%) of 5,583 samples were influenza positive. Mean and median times to processing were 11.5 hr and 6.0 hr, respectively (min 0.1 hr, max 105.2 hr). There were no significant associations between time to processing and presence of RNP (OR = 1.0, P = 0.740), or detection of influenza (OR = 1.0, P = 0.060). Longer duration of illness was associated with a lower likelihood of influenza detection (OR = 0.92, P < 0.001) and with increased influenza A cycle threshold (Ct) values (P < 0.001), while older age was associated with increased influenza B Ct values (P = 0.001), indicating the presence of less amplifiable RNA. Delays in time to processing of upper respiratory specimens up to 105 hr were not associated with decreased detection of amplifiable RNA, suggesting specimen integrity is not compromised by such delays. J. Med. Virol. 88:1891-1895, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Ryan Dare
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Yuwei Zhu
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - John V Williams
- Department of Pediatrics, Children's Hospital of Pittsburgh of University of Pittsburgh Medical Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Marie Griffin
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee.,Department of Health Policy, Vanderbilt University Medical Center, Nashville, Tennessee.,Veterans Affairs Tennessee Valley Health Care System, Nashville, Tennessee
| | - H Keipp Talbot
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
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