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Chang CK, Chen CS, Jian MJ, Chung HY, Chang FY, Lin JC, Hsieh SS, Tang SH, Perng CL, Chen CW, Chiu CH, Shang HS. Monitoring coronavirus disease progression and clinical impact through quantitative viral load testing. Clin Chim Acta 2024; 560:119731. [PMID: 38754576 DOI: 10.1016/j.cca.2024.119731] [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: 10/25/2023] [Revised: 04/13/2024] [Accepted: 05/13/2024] [Indexed: 05/18/2024]
Abstract
BACKGROUND The viral load (VL) in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-infected individuals is critical for improving clinical treatment strategies, care, and decisions. Several studies have reported that the initial SARS-CoV-2 VL is associated with disease severity and mortality. Cycle threshold (Ct) values and/or copies/mL are often used to quantify VL. However, a multitude of platforms, primer/probe sets of different SARS-CoV-2 target genes, and reference material manufacturers may cause inconsistent interlaboratory interpretations. The first International Standard for SARS-CoV-2 RNA quantitative assays has allowed diagnostic laboratories to transition SARS-CoV-2 VL results into international units per milliliter (IU/mL). The Cobas SARS-CoV-2 Duo quantitative assay provides VL results expressed in IU/mL. MATERIALS AND METHODS We enrolled 145 and 50 SARS-CoV-2-positive, hospitalized and 50-negative individuals at the Tri-Service General Hospital, Taiwan from January to May 2022. Each participant's electronic medical record was reviewed to determine asymptomatic, mild, moderate, and severe cases. Nasopharyngeal swabs were collected using universal transport medium. We investigated the association of SARS-CoV-2 VL with disease severity using the Cobas SARS-CoV-2 Duo quantitative assay and its functionality in clinical assessment and decision making to further improve clinical treatment strategies. Limit of detection (LOD) was assessed. RESULTS All 50 SARS-CoV-2-negative samples confirmed negative for SARS-CoV-2, demonstrating 100 % specificity of the Cobas SARS-CoV-2 Duo assay. Patients with severe symptoms had longer hospital stays, and the length of hospital stay (30.56 days on average) positively correlated with the VL (8.22 ± 1.21 log10 IU/mL). Asymptomatic patients had the lowest VL (5.54 ± 2.06 log10 IU/mL) at admission and the shortest hospital stay (14.1 days on average). CONCLUSIONS VL is associated with disease severity and duration of hospitalization; therefore, its quantification should be considered when making clinical care decisions and treatment strategies. The Cobas SARS-CoV-2 Duo assay provides a commutable unitage IU/mL for interlaboratory interpretations.
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Affiliation(s)
- Chih-Kai Chang
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, Republic of China
| | - Chi-Sheng Chen
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, Republic of China
| | - Ming-Jr Jian
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, Republic of China
| | - Hsing-Yi Chung
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, Republic of China
| | - Feng-Yee Chang
- Division of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, Republic of China
| | - Jung-Chung Lin
- Division of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, Republic of China
| | - Shan-Shan Hsieh
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, Republic of China
| | - Sheng-Hui Tang
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, Republic of China
| | - Cherng-Lih Perng
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, Republic of China
| | - Chien-Wen Chen
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, Republic of China
| | - Chun-Hsiang Chiu
- Division of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, Republic of China
| | - Hung-Sheng Shang
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, Republic of China.
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2
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Fisher LH, Kee JJ, Liu A, Espinosa CM, Randhawa AK, Ludwig J, Magaret CA, Robinson ST, Gilbert PB, Hyrien O, Kublin JG, Rouphael N, Falsey AR, Sobieszczyk ME, El Sahly HM, Grinsztejn B, Gray GE, Kotloff KL, Gay CL, Leav B, Hirsch I, Struyf F, Dunkle LM, Neuzil KM, Corey L, Huang Y, Goepfert PA, Walsh SR, Baden LR, Janes H. SARS-CoV-2 Viral Load in the Nasopharynx at Time of First Infection Among Unvaccinated Individuals: A Secondary Cross-Protocol Analysis of 4 Randomized Trials. JAMA Netw Open 2024; 7:e2412835. [PMID: 38780941 PMCID: PMC11117088 DOI: 10.1001/jamanetworkopen.2024.12835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 03/20/2024] [Indexed: 05/25/2024] Open
Abstract
Importance SARS-CoV-2 viral load (VL) in the nasopharynx is difficult to quantify and standardize across settings, but it may inform transmission potential and disease severity. Objective To characterize VL at COVID-19 diagnosis among previously uninfected and unvaccinated individuals by evaluating the association of demographic and clinical characteristics, viral variant, and trial with VL, as well as the ability of VL to predict severe disease. Design, Setting, and Participants This secondary cross-protocol analysis used individual-level data from placebo recipients from 4 harmonized, phase 3 COVID-19 vaccine efficacy trials sponsored by Moderna, AstraZeneca, Janssen, and Novavax. Participants were SARS-CoV-2 negative at baseline and acquired COVID-19 during the blinded phase of the trials. The setting included the US, Brazil, South Africa, Colombia, Argentina, Peru, Chile, and Mexico; start dates were July 27, 2020, to December 27, 2020; data cutoff dates were March 26, 2021, to July 30, 2021. Statistical analysis was performed from November 2022 to June 2023. Main Outcomes and Measures Linear regression was used to assess the association of demographic and clinical characteristics, viral variant, and trial with polymerase chain reaction-measured log10 VL in nasal and/or nasopharyngeal swabs taken at the time of COVID-19 diagnosis. Results Among 1667 participants studied (886 [53.1%] male; 995 [59.7%] enrolled in the US; mean [SD] age, 46.7 [14.7] years; 204 [12.2%] aged 65 years or older; 196 [11.8%] American Indian or Alaska Native, 150 [9%] Black or African American, 1112 [66.7%] White; 762 [45.7%] Hispanic or Latino), median (IQR) log10 VL at diagnosis was 6.18 (4.66-7.12) log10 copies/mL. Participant characteristics and viral variant explained only 5.9% of the variability in VL. The independent factor with the highest observed differences was trial: Janssen participants had 0.54 log10 copies/mL lower mean VL vs Moderna participants (95% CI, 0.20 to 0.87 log10 copies/mL lower). In the Janssen study, which captured the largest number of COVID-19 events and variants and used the most intensive post-COVID surveillance, neither VL at diagnosis nor averaged over days 1 to 28 post diagnosis was associated with COVID-19 severity. Conclusions and Relevance In this study of placebo recipients from 4 randomized phase 3 trials, high variability was observed in SARS-CoV-2 VL at the time of COVID-19 diagnosis, and only a fraction was explained by individual participant characteristics or viral variant. These results suggest challenges for future studies of interventions seeking to influence VL and elevates the importance of standardized methods for specimen collection and viral load quantitation.
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Affiliation(s)
- Leigh H. Fisher
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Jia Jin Kee
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Albert Liu
- Bridge HIV, San Francisco Department of Public Health, San Francisco, California
| | | | - April K. Randhawa
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington
| | - James Ludwig
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Craig A. Magaret
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Samuel T. Robinson
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Peter B. Gilbert
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Ollivier Hyrien
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington
| | - James G. Kublin
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington
| | | | - Ann R. Falsey
- Infectious Disease Division, University of Rochester, Rochester, New York
| | | | - Hana M. El Sahly
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas
| | - Beatriz Grinsztejn
- Evandro Chagas National Institute of Infectious Diseases-Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Glenda E. Gray
- South African Medical Research Council, Cape Town, South Africa
| | - Karen L. Kotloff
- Center for Vaccine Development and Global Health, Department of Pediatrics, University of Maryland School of Medicine, Baltimore
| | - Cynthia L. Gay
- University of North Carolina School of Medicine, Chapel Hill
| | | | - Ian Hirsch
- Vaccines & Immune Therapies, BioPharmaceuticals R&D, AstraZeneca, Cambridge, United Kingdom
| | - Frank Struyf
- Janssen Research and Development, Beerse, Belgium
| | | | - Kathleen M. Neuzil
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland
| | - Lawrence Corey
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Yunda Huang
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Paul A. Goepfert
- University of Alabama at Birmingham Heersink School of Medicine, Birmingham
| | | | | | - Holly Janes
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington
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Ibrahim F, Natasha A, Yasmon A, Rizal CT, Fithriyah, Karuniawati A, Saharman YR, Sudarmono P. Evaluation of SARS-CoV-2 quantification from oropharyngeal swabs, nasopharyngeal swabs, and naso-oropharyngeal swabs: A cross-sectional study. Heliyon 2024; 10:e28647. [PMID: 38586376 PMCID: PMC10998208 DOI: 10.1016/j.heliyon.2024.e28647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 03/17/2024] [Accepted: 03/21/2024] [Indexed: 04/09/2024] Open
Abstract
The current naso-oropharyngeal swab for SARS-CoV-2 detection faces several problems, such as waste issues and its use for quantitative studies. This study aimed to evaluate the total RNA and viral loads from different upper respiratory tract swabs types and whether SARS-CoV-2 quantification can use the current internal control for normalization. This cross-sectional study collected positive specimens with single oropharyngeal or nasopharyngeal swabs and naso-oropharyngeal swabs. The samples were extracted, tested with qualitative RT‒PCR, and then tested with quantitative RT‒PCR. The RNA eluate was measured for the total RNA concentration. The total RNA concentration, viral load, and RNaseP Ct values were collected and analysed statistically. The positive results came from 41 oropharyngeal swabs, 34 nasopharyngeal swabs, and 36 naso-oropharyngeal swabs. The total RNA increased significantly from oropharyngeal swabs to nasopharyngeal swabs to naso-oropharyngeal swabs. Significant differences in RNaseP Ct values between groups and their correlations with total RNA were found. In addition, the increase in the total RNA and the RNaseP Ct values were unrelated to the viral load. The physical features in the naso-oropharyngeal area and the swabbing procedures could affect the total RNA but not the viral load. However, since the virus particles could present inside and outside human cells, the increase in collected human cells may not always be followed by the viral load increase. Normalization using the RNaseP Ct value became unnecessary due to the factors mentioned above. Therefore, a careful approach is needed in viral load studies of swab specimens.
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Affiliation(s)
- Fera Ibrahim
- Department of Microbiology Faculty of Medicine Universitas Indonesia / Dr. Cipto Mangunkusumo Hospital, Pegangsaan Timur 16 Street, East Jakarta, 10430, Indonesia
| | - Augustine Natasha
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon 24252, Republic of Korea
| | - Andi Yasmon
- Department of Microbiology Faculty of Medicine Universitas Indonesia / Dr. Cipto Mangunkusumo Hospital, Pegangsaan Timur 16 Street, East Jakarta, 10430, Indonesia
| | - Chairunnisa Tawadhu Rizal
- Jakarta Health Laboratory Center, Ministry of Health, Percetakan Negara No.23B street, Central Jakarta, Indonesia
| | - Fithriyah
- Department of Microbiology Faculty of Medicine Universitas Indonesia / Dr. Cipto Mangunkusumo Hospital, Pegangsaan Timur 16 Street, East Jakarta, 10430, Indonesia
| | - Anis Karuniawati
- Department of Microbiology Faculty of Medicine Universitas Indonesia / Dr. Cipto Mangunkusumo Hospital, Pegangsaan Timur 16 Street, East Jakarta, 10430, Indonesia
| | - Yulia Rosa Saharman
- Department of Microbiology Faculty of Medicine Universitas Indonesia / Dr. Cipto Mangunkusumo Hospital, Pegangsaan Timur 16 Street, East Jakarta, 10430, Indonesia
| | - Pratiwi Sudarmono
- Department of Microbiology Faculty of Medicine Universitas Indonesia / Dr. Cipto Mangunkusumo Hospital, Pegangsaan Timur 16 Street, East Jakarta, 10430, Indonesia
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4
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Tao L, Chan A, Maris A, Schmitz JE. Internationally standardized respiratory viral load testing with limited resources: A derivative-of-care calibration strategy for SARS-CoV-2. Influenza Other Respir Viruses 2024; 18:e13207. [PMID: 38268611 PMCID: PMC10805620 DOI: 10.1111/irv.13207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 09/16/2023] [Accepted: 09/20/2023] [Indexed: 01/26/2024] Open
Abstract
Introduction SARS-CoV-2 has demonstrated that, in targeted circumstances, viral quantification within respiratory specimens can valuably inform patient management, as well as research. Nevertheless, the pandemic has illustrated concomitant challenges for obtaining high-quality (and broadly comparable) respiratory viral loads. This includes a critical need for standardization and calibration, even though the necessary resources may not always be available for emergent pathogens and non-bloodstream specimens. Methods To these ends, we describe a novel strategy for implementing quantitative SARS-CoV-2 testing with International Unit-based calibration. Earlier in the course of the pandemic-when analytic resources were far more limited-select residual SARS-CoV-2 positive specimens from routine care in our diagnostic laboratory were pooled to formulate a clinically realistic secondary standard of high volume and analyte concentration, which was cross-calibrated to the primary SARS-CoV-2 standard of the World Health Organization. Results The resultant calibrators were integrated into the original CDC RT-qPCR assay for SARS-CoV-2, whose (now broadened) performance characteristics were defined to generate a test appropriate for both clinical and research use. This test allowed for the quantification of virus in respiratory specimens down to a validated lower limit of quantification of 103.4 IU/ml. Conclusions By self-formulating calibrators from this derivative-of-care secondary standard, we successfully validated respiratory viral loads without the commercial availability (at that time) of quantitative assays or calibrators. As the SARS-CoV-2 pandemic continues to decline-and even beyond this pathogen-this strategy may be applicable for laboratories seeking to implement viral load testing for nontraditional specimen types despite limited resources.
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Affiliation(s)
- Lili Tao
- Department of Pathology, Microbiology, and ImmunologyVanderbilt University Medical CenterNashvilleTennesseeUSA
| | - Allison Chan
- Department of Pathology, Microbiology, and ImmunologyVanderbilt University Medical CenterNashvilleTennesseeUSA
| | - Alex Maris
- Department of Pathology, Microbiology, and ImmunologyVanderbilt University Medical CenterNashvilleTennesseeUSA
| | - Jonathan E. Schmitz
- Department of Pathology, Microbiology, and ImmunologyVanderbilt University Medical CenterNashvilleTennesseeUSA
- Department of UrologyVanderbilt University Medical CenterNashvilleTennesseeUSA
- Vanderbilt Institute for Infection, Immunology, and InflammationVanderbilt University Medical CenterNashvilleTennesseeUSA
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5
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Su YD, Lai CC, Lin TH, Chen WC, Hsueh PR. Performance evaluation of the cobas SARS-CoV-2 Duo, a novel qualitative and quantitative assay, for the detection of SARS-CoV-2 RNA. Microbiol Spectr 2023; 11:e0136923. [PMID: 37909752 PMCID: PMC10715196 DOI: 10.1128/spectrum.01369-23] [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: 04/03/2023] [Accepted: 09/27/2023] [Indexed: 11/03/2023] Open
Abstract
IMPORTANCE Quantitative SARS-CoV-2 tests for viral load are necessary to guide patient treatment, as well as to determine infection control measures and policies. Although the real-time RT-PCR assays can report the Ct value to estimate the viral load, there are several serious concerns regarding the use of Ct values. Importantly, Ct values can vary significantly among between- and within-run methods. The diagnostic performance of the cobas SARS-CoV-2 Duo is appropriate. It is a precise, accurate, and sensitive method for the detection of SARS-CoV-2 RNA and is comparable to two qualitative assays (the cobas SARS-CoV-2 and the Liat cobas SARS-CoV-2 and Inf A/B). In contrast, using the Ct value to estimate viral load is not reliable, and utilization of a quantitative detection test, such as the cobas SARS-CoV-2 Duo, to accurately measure the viral load is needed.
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Affiliation(s)
- Yang-Di Su
- Department of Laboratory Medicine, China Medical University Hospital, School of Medicine, China Medical University, Taichung, Taiwan
| | - Chih-Cheng Lai
- Department of Internal Medicine, Division of Hospital Medicine, Chi Mei Medical Center, Tainan, Taiwan
| | - Tsai-Hsiu Lin
- Department of Laboratory Medicine, China Medical University Hospital, School of Medicine, China Medical University, Taichung, Taiwan
| | - Wei-Cheng Chen
- Department of Internal Medicine, Division of Pulmonary and Critical Care Medicine,China Medical University Hospital, Taichung, Taiwan
- Graduate Institute of Biomedical Sciences and School of Medicine, College of Medicine, China Medical University, Taichung, Taiwan
| | - Po-Ren Hsueh
- Department of Laboratory Medicine, China Medical University Hospital, School of Medicine, China Medical University, Taichung, Taiwan
- Department of Internal Medicine, Division of Infectious Diseases, China Medical University Hospital, School of Medicine, China Medical University, Taichung, Taiwan
- PhD Program for Aging, School of Medicine, China Medical University, Taichung, Taiwan
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Riegler AN, Benson P, Long K, Leal SM. Differential activation of programmed cell death in patients with severe SARS-CoV-2 infection. Cell Death Discov 2023; 9:420. [PMID: 37985756 PMCID: PMC10662024 DOI: 10.1038/s41420-023-01715-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/26/2023] [Accepted: 11/07/2023] [Indexed: 11/22/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes severe lower airway disease and death in a subset of patients. Knowledge on the relative contribution of programmed cell death (PCD) to lung pathology is limited to few human autopsy studies with small sample size/scope, in vitro cell culture, and experimental model systems. In this study, we sought to identify, localize, and quantify activation of apoptosis, ferroptosis, pyroptosis, and necroptosis in FFPE lung tissues from patients that died from severe SARS-CoV-2 infection (n = 28) relative to uninfected controls (n = 13). Immunofluorescence (IF) staining, whole-slide imaging, and Image J software was used to localize and quantify expression of SARS-CoV-2 nucleoprotein and the following PCD protein markers: cleaved Caspase-3, pMLKL, cleaved Gasdermin D, and CD71, respectively. IF showed differential activation of each PCD pathway in infected lungs and dichotomous staining for SARS-CoV-2 nucleoprotein enabling distinction between high (n = 9) vs low viral burden (n = 19). No differences were observed in apoptosis and ferroptosis in SARS-CoV-2 infected lungs relative to uninfected controls. However, both pyroptosis and necroptosis were significantly increased in SARS-CoV-2-infected lungs. Increased pyroptosis was observed in SARS-CoV-2 infected lungs, irrespective of viral burden, suggesting an inflammation-driven mechanism. In contrast, necroptosis exhibited a very strong positive correlation with viral burden (R2 = 0.9925), suggesting a direct SARS-CoV-2 mediated effect. These data indicate a possible novel mechanism for viral-mediated necroptosis and a potential role for both lytic programmed cell death pathways, necroptosis and pyroptosis, in mediating infection outcome.
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Affiliation(s)
- Ashleigh N Riegler
- Division of Laboratory Medicine, Department of Pathology, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Paul Benson
- Division of Anatomic Pathology, Department of Pathology, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Kenneth Long
- Division of Infectious Diseases, Department of Medicine, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Sixto M Leal
- Division of Laboratory Medicine, Department of Pathology, The University of Alabama at Birmingham, Birmingham, AL, USA.
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Riegler A, Benson P, Long K, Leal S. Differential Activation of Programmed Cell Death in Patients with Severe SARS-CoV-2 Infection. RESEARCH SQUARE 2023:rs.3.rs-3059466. [PMID: 37461686 PMCID: PMC10350212 DOI: 10.21203/rs.3.rs-3059466/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/24/2023]
Abstract
SARS-CoV-2 (SARS-2) causes severe lower airway disease and death in a subset of patients. Knowledge on the relative contribution of programmed cell death (PCD) to lung pathology is limited to few human autopsy studies with small sample size/scope, in vitro cell culture, and experimental model systems. In this study, we sought to identify, localize, and quantify activation of apoptosis, ferroptosis, pyroptosis, and necroptosis in FFPE lung tissues from patients that died from severe SARS-2 infection (n=28) relative to uninfected controls (n=13). Immunofluorescence (IF) staining, whole-slide imaging, and Image J software was used to localize and quantify expression of SARS-2 nucleoprotein and the following PCD protein markers: cleaved Caspase-3, pMLKL, cleaved Gasdermin D, and CD71, respectively. IF showed differential activation of each PCD pathway in SARS-2 infected lungs and dichotomous staining for SARS-2 nucleoprotein enabling distinction between high (n=9) vs low viral burden (n= 19). No differences were observed in apoptosis and ferroptosis in SARS-2 infected lungs relative to uninfected controls. However, both pyroptosis and necroptosis were significantly increased in SARS-2 infected lungs. Increased pyroptosis was observed in SARS-2 infected lungs, irrespective of viral burden, suggesting an inflammation-driven mechanism. In contrast, necroptosis exhibited a very strong positive correlation with viral burden (R2=0.9925), suggesting a direct SARS-2 mediated effect. These data indicate a possible novel mechanism for viral-mediated necroptosis and a potential role for both lytic programmed cell death pathways, necroptosis and pyroptosis, in mediating infection outcome.
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8
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Bannick MS, Gao F, Brown ER, Janes HE. Retrospective, Observational Studies for Estimating Vaccine Effects on the Secondary Attack Rate of SARS-CoV-2. Am J Epidemiol 2023; 192:1016-1028. [PMID: 36883907 PMCID: PMC10505422 DOI: 10.1093/aje/kwad046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 11/21/2022] [Accepted: 02/23/2023] [Indexed: 03/09/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) vaccines are highly efficacious at preventing symptomatic infection, severe disease, and death. Most of the evidence that COVID-19 vaccines also reduce transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is based on retrospective, observational studies. Specifically, an increasing number of studies are evaluating vaccine effectiveness against the secondary attack rate of SARS-CoV-2 using data available in existing health-care databases or contact-tracing databases. Since these types of databases were designed for clinical diagnosis or management of COVID-19, they are limited in their ability to provide accurate information on infection, infection timing, and transmission events. We highlight challenges with using existing databases to identify transmission units and confirm potential SARS-CoV-2 transmission events. We discuss the impact of common diagnostic testing strategies, including event-prompted and infrequent testing, and illustrate their potential biases in estimating vaccine effectiveness against the secondary attack rate of SARS-CoV-2. We articulate the need for prospective observational studies of vaccine effectiveness against the SARS-CoV-2 secondary attack rate, and we provide design and reporting considerations for studies using retrospective databases.
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Affiliation(s)
- Marlena S Bannick
- Correspondence to Marlena Bannick, Department of Biostatistics, Hans Rosling Center for Population Health, Box 357232, University of Washington, Seattle, WA 98195 (e-mail: )
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9
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Gavina K, Franco LC, Robinson CM, Hymas W, Lei GS, Sinclair W, Hall T, Carlquist J, Lavik JP, Emery CL, Heaton PR, Hillyard D, Lopransi BK, Relich RF. Standardization of SARS-CoV-2 Cycle Threshold Values: Multisite Investigation Evaluating Viral Quantitation across Multiple Commercial COVID-19 Detection Platforms. Microbiol Spectr 2023; 11:e0447022. [PMID: 36651781 PMCID: PMC9927101 DOI: 10.1128/spectrum.04470-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 12/08/2022] [Indexed: 01/19/2023] Open
Abstract
The demand for testing during the coronavirus disease 2019 (COVID-19) pandemic has resulted in the production of several different commercial platforms and laboratory-developed assays for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This has created several challenges, including, but not limited to, the standardization of diagnostic testing, utilization of cycle threshold (CT) values for quantitation and clinical interpretation, and data harmonization. Using reference standards consisting of a linear range of SARS-CoV-2 concentrations quantitated by viral culture-based methods and droplet digital PCR, we investigated the commutability and standardization of SARS-CoV-2 quantitation across different laboratories in the United States. We assessed SARS-CoV-2 CT values generated on multiple reverse transcription-PCR (RT-PCR) platforms and analyzed PCR efficiencies, linearity, gene targets, and CT value agreement. Our results demonstrate the inappropriateness of using SARS-CoV-2 CT values without established standards for viral quantitation. Further, we emphasize the importance of using reference standards and controls validated to independent assays, to compare results across different testing platforms and move toward better harmonization of COVID-19 quantitative test results. IMPORTANCE From the onset of the COVID-19 pandemic, the demand for SARS-CoV-2 testing has resulted in an explosion of analytical tests with very different approaches and designs. The variability in testing modalities, compounded by the lack of available commercial reference materials for standardization early in the pandemic, has led to several challenges regarding data harmonization for viral quantitation. In this study, we assessed multiple commercially available RT-PCR platforms across different laboratories within the United States using standardized reference materials characterized by viral culture methods and droplet digital PCR. We observed variability in the results generated by different instruments and laboratories, further emphasizing the importance of utilizing validated reference standards for quantitation, to better harmonize SARS-CoV-2 test results.
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Affiliation(s)
- Kenneth Gavina
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Division of Clinical Microbiology, Indiana University Health, Indianapolis, Indiana, USA
| | - Lauren C. Franco
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Christopher M. Robinson
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Weston Hymas
- ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, Utah, USA
| | - Guang-Sheng Lei
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Will Sinclair
- Intermountain Laboratory Services, Department of Pathology, Intermountain Healthcare, Salt Lake City, Utah, USA
| | - Tara Hall
- Intermountain Laboratory Services, Department of Pathology, Intermountain Healthcare, Salt Lake City, Utah, USA
| | - John Carlquist
- Intermountain Laboratory Services, Department of Pathology, Intermountain Healthcare, Salt Lake City, Utah, USA
| | - John-Paul Lavik
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Division of Clinical Microbiology, Indiana University Health, Indianapolis, Indiana, USA
| | - Christopher L. Emery
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Division of Clinical Microbiology, Indiana University Health, Indianapolis, Indiana, USA
| | - Phillip R. Heaton
- Department of Pathology and Laboratory Medicine, Health Partners, Bloomington, Minnesota, USA
| | - David Hillyard
- ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, Utah, USA
| | - Bert K. Lopransi
- Intermountain Laboratory Services, Department of Pathology, Intermountain Healthcare, Salt Lake City, Utah, USA
| | - Ryan F. Relich
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Division of Clinical Microbiology, Indiana University Health, Indianapolis, Indiana, USA
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10
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Buchta C, Kollros D, Jovanovic J, Huf W, Delatour V, Puchhammer-Stöckl E, Mayerhofer M, Müller MM, Shenoy S, Griesmacher A, Aberle SW, Görzer I, Camp JV. Converting to an international unit system improves harmonization of results for SARS-CoV-2 quantification: Results from multiple external quality assessments. J Clin Virol 2023; 158:105352. [PMID: 36525853 PMCID: PMC9733965 DOI: 10.1016/j.jcv.2022.105352] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/30/2022] [Accepted: 12/07/2022] [Indexed: 12/13/2022]
Abstract
BACKGROUND The detection of SARS-CoV-2 vRNA in clinical samples has relied almost exclusively on RT-qPCR as the gold standard test. Published results from various external quality assessments ("ring trials") worldwide have shown that there is still a large variability in results reported for the same samples. As reference standards of SARS-CoV-2 RNA are available, we tested whether using standard curves to convert Ct values into copies/mL (cp/mL) improved harmonization. METHODS Nine laboratories using 23 test systems (15 of which were unique) prepared standard dilution curves to convert Ct values of 13 SARS-CoV-2 positive samples to cp/mL (hereafter IU/mL). The samples were provided in three rounds of a virus genome detection external quality assessment (EQA) scheme. We tested the precision and accuracy of results reported in IU/mL, and attempted to identify the sources of variability. RESULTS Reporting results as IU/mL improved the precision of the estimated concentrations of all samples compared to reporting Ct values, although some inaccuracy remained. Variance analysis showed that nearly all variability in data was explained by individual test systems within individual laboratories. When controlling for this effect, there was no significant difference between all other factors tested (test systems, EQA rounds, sample material). CONCLUSIONS Converting results to copies/mL improved precision across laboratory test systems. However, it seems the results are still very specific to test systems within laboratories. Further efforts could be made to improve accuracy and achieve full harmonization across diagnostic laboratories.
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Affiliation(s)
- Christoph Buchta
- Austrian Association for Quality Assurance and Standardization of Medical and Diagnostic Tests (ÖQUASTA), Vienna, Austria
| | - Dominik Kollros
- Austrian Association for Quality Assurance and Standardization of Medical and Diagnostic Tests (ÖQUASTA), Vienna, Austria
| | - Jovana Jovanovic
- Austrian Association for Quality Assurance and Standardization of Medical and Diagnostic Tests (ÖQUASTA), Vienna, Austria
| | - Wolfgang Huf
- Karl Landsteiner Institute for Clinical Risk Management, Vienna, Austria
| | - Vincent Delatour
- Laboratoire National de Métrologie et d'Essais (LNE), Paris, France
| | | | - Maximilian Mayerhofer
- Armament and Defence Technology Agency, NBC & Environmental Protection Technology Division, Vienna, Austria
| | - Mathias M. Müller
- Austrian Association for Quality Assurance and Standardization of Medical and Diagnostic Tests (ÖQUASTA), Vienna, Austria
| | - Santosh Shenoy
- Department of Surgery, Kansas City Veterans Medical Center, University of Missouri at Kansas City, Kansas City, MO, USA
| | - Andrea Griesmacher
- Austrian Association for Quality Assurance and Standardization of Medical and Diagnostic Tests (ÖQUASTA), Vienna, Austria
| | | | - Irene Görzer
- Center for Virology, Medical University of Vienna, Vienna, Austria
| | - Jeremy V. Camp
- Center for Virology, Medical University of Vienna, Vienna, Austria,Corresponding author at: Center for Virology, Medizinische Universitat Wien, Kinderspitalgasse 15, 1095 Vienna, Austria
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11
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Sakhabutdinova AR, Gazizov RR, Chemeris AV, Garafutdinov RR. Reverse transcriptase-free detection of viral RNA using Hemo Klentaq DNA polymerase. Anal Biochem 2022; 659:114960. [PMID: 36306819 PMCID: PMC9597527 DOI: 10.1016/j.ab.2022.114960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 10/07/2022] [Accepted: 10/17/2022] [Indexed: 12/14/2022]
Abstract
COVID-19 pandemic highlighted the demand for the fast and reliable detection of viral RNA. Although various methods for RNA amplification and detection have been proposed, some limitations, including those caused by reverse transcription (RT), need to be overcome. Here, we report on the direct detection of specific RNA by conventional polymerase chain reaction (PCR) requiring no prior RT step. It was found that Hemo KlenTaq (HKTaq), which is posed as DNA-dependent DNA polymerase, possesses reverse transcriptase activity and provides reproducible amplification of RNA targets with an efficiency comparable to common RT-PCR. Using nasopharyngeal swab extracts from COVID-19-positive patients, the high reliability of SARS-CoV-2 detection based on HKTaq was demonstrated. The most accurate detection of specific targets are provided by nearby primers, which allow to determine RNA in solutions affected to multiple freeze-thaw cycles. HKTaq can be used for elaboration of simplified amplification techniques intended for the analysis of any specific RNA and requiring only one DNA polymerase.
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12
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Braz BA, Hospinal-Santiani M, Martins G, Pinto CS, Zarbin AJG, Beirão BCB, Thomaz-Soccol V, Bergamini MF, Marcolino-Junior LH, Soccol CR. Graphene-Binding Peptide in Fusion with SARS-CoV-2 Antigen for Electrochemical Immunosensor Construction. BIOSENSORS 2022; 12:bios12100885. [PMID: 36291021 PMCID: PMC9599560 DOI: 10.3390/bios12100885] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/05/2022] [Accepted: 10/12/2022] [Indexed: 06/02/2023]
Abstract
The development of immunosensors to detect antibodies or antigens has stood out in the face of traditional methods for diagnosing emerging diseases such as the one caused by the SARS-CoV-2 virus. The present study reports the construction of a simplified electrochemical immunosensor using a graphene-binding peptide applied as a recognition site to detect SARS-CoV-2 antibodies. A screen-printed electrode was used for sensor preparation by adding a solution of peptide and reduced graphene oxide (rGO). The peptide-rGO suspension was characterized by scanning electron microscopy (SEM), Raman spectroscopy, and Fourier transform infrared spectroscopy (FT-IR). The electrochemical characterization (electrochemical impedance spectroscopy-EIS, cyclic voltammetry-CV and differential pulse voltammetry-DPV) was performed on the modified electrode. The immunosensor response is based on the decrease in the faradaic signal of an electrochemical probe resulting from immunocomplex formation. Using the best set of experimental conditions, the analytic curve obtained showed a good linear regression (r2 = 0.913) and a limit of detection (LOD) of 0.77 μg mL-1 for antibody detection. The CV and EIS results proved the efficiency of device assembly. The high selectivity of the platform, which can be attributed to the peptide, was demonstrated by the decrease in the current percentage for samples with antibody against the SARS-CoV-2 S protein and the increase in the other antibodies tested. Additionally, the DPV measurements showed a clearly distinguishable response in assays against human serum samples, with sera with a response above 95% being considered negative, whereas responses below this value were considered positive. The diagnostic platform developed with specific peptides is promising and has the potential for application in the diagnosis of other infections that lead to high antibody titers.
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Affiliation(s)
- Beatriz A. Braz
- Molecular Biology Laboratory, Graduate Program in Bioprocess Engineering and Biotechnology, Federal University of Paraná (UFPR), Curitiba 81531-980, PR, Brazil
- Laboratory of Electrochemical Sensors (LabSensE), Department of Chemistry, Federal University of Paraná (UFPR), Curitiba 81531-980, PR, Brazil
| | - Manuel Hospinal-Santiani
- Molecular Biology Laboratory, Graduate Program in Bioprocess Engineering and Biotechnology, Federal University of Paraná (UFPR), Curitiba 81531-980, PR, Brazil
| | - Gustavo Martins
- Laboratory of Electrochemical Sensors (LabSensE), Department of Chemistry, Federal University of Paraná (UFPR), Curitiba 81531-980, PR, Brazil
| | - Cristian S. Pinto
- Materials Chemistry Group (GQM), Department of Chemistry, Federal University of Paraná (UFPR), Curitiba 81531-980, PR, Brazil
| | - Aldo J. G. Zarbin
- Materials Chemistry Group (GQM), Department of Chemistry, Federal University of Paraná (UFPR), Curitiba 81531-980, PR, Brazil
| | - Breno C. B. Beirão
- Graduate Program in Microbiology, Parasitology, and Pathology, Federal University of Paraná (UFPR), Curitiba 81531-980, PR, Brazil
| | - Vanete Thomaz-Soccol
- Molecular Biology Laboratory, Graduate Program in Bioprocess Engineering and Biotechnology, Federal University of Paraná (UFPR), Curitiba 81531-980, PR, Brazil
| | - Márcio F. Bergamini
- Laboratory of Electrochemical Sensors (LabSensE), Department of Chemistry, Federal University of Paraná (UFPR), Curitiba 81531-980, PR, Brazil
| | - Luiz H. Marcolino-Junior
- Laboratory of Electrochemical Sensors (LabSensE), Department of Chemistry, Federal University of Paraná (UFPR), Curitiba 81531-980, PR, Brazil
| | - Carlos R. Soccol
- Molecular Biology Laboratory, Graduate Program in Bioprocess Engineering and Biotechnology, Federal University of Paraná (UFPR), Curitiba 81531-980, PR, Brazil
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