scholarly journals Diagnostic Performance of Automated SARS-CoV-2 Antigen Assay in Nasal Swab during COVID-19 Vaccination Campaign

Diagnostics ◽  
2021 ◽  
Vol 11 (11) ◽  
pp. 2110
Author(s):  
Haya Altawalah ◽  
Wadha Alfouzan ◽  
Talal Al-Fadalah ◽  
Sayeh Ezzikouri
Keyword(s):  
Viral Load ◽  
Diagnostic Performance ◽  
Vaccination Campaign ◽  
Real Life ◽  
High Viral Load ◽  
Laboratory Method ◽  
Life Study ◽  
Viral Loads ◽  
Antigen Assay ◽  
A Prospective Study

Background: To control the spread of the pandemic brought about by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, it is necessary to have an automated reliable diagnostic assay. To date, the RT-PCR (RT-qPCR) has been the recommended laboratory method to diagnose SARS-CoV-2 infection, but there is a need for more automated and reliable tests. The aim of this real-life study was to assess the diagnostic performance of DiaSorin’s LIAISON SARS-CoV-2 antigen (Ag) chemiluminescence immunoassay in detecting SARS-CoV-2 in vaccinated and unvaccinated individuals. Methods: A prospective study was performed on 300 nasopharyngeal swabs randomly collected from 31 May to 6 July 2021. Nasopharyngeal samples were assayed with DiaSorin’s LIAISON SARS-CoV-2 Ag and TaqPath™ COVID-19 multiplex RT-qPCR. Results: Of 300 participants, 150 had a RT-qPCR confirmed SARS-CoV-2 infection of whom 113 (75.33%) were also detected by the DiaSorin LIAISON SARS-CoV-2 Ag. Taking RT-qPCR as a reference, the sensitivity and specificity of the DiaSorin LIAISON SARS-CoV-2 Ag assay were evaluated as 75.33% (95% CI = 67.64–82) and 100% (95% CI = 97.57–100), respectively. When a viral load cut-off was applied for high viral load (median cycle threshold (Ct) < 18.57), the overall sensitivity was increased to 96.55% (95% CI = 88.09–99.58). Interestingly, median RT-qPCR Ct and SARS-CoV-2 Ag values were similar between fully vaccinated and unvaccinated subjects. Conclusions: Automated, quantitative LIAISON SARS-CoV-2 Ag assay shows good performance to identify SARS-CoV-2-infected individuals with moderate to high viral loads. LIAISON SARS-CoV-2 Ag testing could be used as frontline testing for COVID-19 diagnosis and be more suitable for large utilization.

scholarly journals Rapid diagnosis of SARS-CoV-2 pneumonia on lower respiratory tract specimens

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Vanessa De Pace ◽  
Patrizia Caligiuri ◽  
Valentina Ricucci ◽  
Nicola Nigro ◽  
Barbara Galano ◽  
...  
Keyword(s):  
Intensive Care ◽  
Viral Load ◽  
Lower Respiratory Tract ◽  
Diagnostic Performance ◽  
High Viral Load ◽  
Load Cycle ◽  
Rt Pcr ◽  
Cycle Threshold ◽  
Viral Loads ◽  
Rapid Pcr

Abstract Background The ongoing SARS-CoV-2 pandemic requires the availability of accurate and rapid diagnostic tests, especially in such clinical settings as emergency and intensive care units. The objective of this study was to evaluate the diagnostic performance of the Vivalytic SARS-CoV-2 rapid PCR kit in lower respiratory tract (LRT) specimens. Methods Consecutive LRT specimens (bronchoalveolar lavage and bronchoaspirates) were collected from Intensive Care Units of San Martino Hospital (Genoa, Italy) between November 2020 and January 2021. All samples underwent RT-PCR testing by means of the Allplex™ SARS-CoV-2 assay (Seegene Inc., South Korea). On the basis of RT-PCR results, specimens were categorized as negative, positive with high viral load [cycle threshold (Ct) ≤ 30] and positive with low viral load (Ct of 31–35). A 1:1:1 ratio was used to achieve a sample size of 75. All specimens were subsequently tested by means of the Vivalytic SARS-CoV-2 rapid PCR assay (Bosch Healthcare Solutions GmbH, Germany). The diagnostic performance of this assay was assessed against RT-PCR through the calculation of accuracy, Cohen’s κ, sensitivity, specificity and expected positive (PPV) and negative (NPV) predictive values. Results The overall diagnostic accuracy of the Vivalytic SARS-CoV-2 was 97.3% (95% CI: 90.9–99.3%), with an excellent Cohen’s κ of 0.94 (95% CI: 0.72–1). Sensitivity and specificity were 96% (95% CI: 86.5–98.9%) and 100% (95% CI: 86.7–100%), respectively. In samples with high viral loads, sensitivity was 100% (Table 1). The distributions of E gene Ct values were similar (Wilcoxon’s test: p = 0.070), with medians of 35 (IQR: 25–36) and 35 (IQR: 25–35) on Vivalytic and RT-PCR, respectively (Fig. 1). NPV and PPV was 92.6% and 100%, respectively.Table 1 Demographic characteristics and data sample type of the study cases (N = 75) Male, N (%) 56 (74.6%) Age (yr), Median (IQR) 65 (31–81) BAS, N (%) 43 (57.3%)  Negative 30.2%  Positive—High viral load [Ct ≤ 30] 27.9%  Positive—Low viral load [Ct 31–35] 41.9% BAL, N (%) 32 (42.7%)  Negative 37.5%  Positive—High viral load [Ct ≤ 30] 40.6%  Positive—Low viral load [Ct 31–35] 21.9% Data were expressed as proportions for categorical variables. Specimens were categorized into negative, positive with high viral load [cycle threshold (Ct) ≤ 30] and positive with low viral load (Ct of 31–35). BAS bronchoaspirates, BAL bronchoalveolar lavage, Ct cycle threshold Conclusions Vivalytic SARS-CoV-2 can be used effectively on LRT specimens following sample liquefaction. It is a feasible and highly accurate molecular procedure, especially in samples with high viral loads. This assay yields results in about 40 min, and may therefore accelerate clinical decision-making in urgent/emergency situations.

scholarly journals Performance of the Innova SARS-CoV-2 antigen rapid lateral flow test in the Liverpool asymptomatic testing pilot: population based cohort study

BMJ ◽  
2021 ◽  
pp. n1637 ◽  
Author(s):  
Marta García-Fiñana ◽  
David M Hughes ◽  
Christopher P Cheyne ◽  
Girvan Burnside ◽  
Mark Stockbridge ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Viral Load ◽  
Predictive Value ◽  
High Viral Load ◽  
Test Results ◽  
Chain Reaction ◽  
Viral Loads ◽  
Flow Test ◽  
Polymerase Chain ◽  
Lateral Flow Test

Abstract Objective To assess the performance of the SARS-CoV-2 antigen rapid lateral flow test (LFT) versus polymerase chain reaction testing in the asymptomatic general population attending testing centres. Design Observational cohort study. Setting Community LFT pilot at covid-19 testing sites in Liverpool, UK. Participants 5869 asymptomatic adults (≥18 years) voluntarily attending one of 48 testing sites during 6-29 November 2020. Interventions Participants were tested using both an Innova LFT and a quantitative reverse-transcriptase polymerase chain reaction (RT-qPCR) test based on supervised self-administered swabbing at testing sites. Main outcome measures Sensitivity, specificity, and predictive values of LFT compared with RT-qPCR in an epidemic steady state of covid-19 among adults with no classic symptoms of the disease. Results Of 5869 test results, 22 (0.4%) LFT results and 343 (5.8%) RT-qPCR results were void (that is, when the control line fails to appear within 30 minutes). Excluding the void results, the LFT versus RT-qPCR showed a sensitivity of 40.0% (95% confidence interval 28.5% to 52.4%; 28/70), specificity of 99.9% (99.8% to 99.99%; 5431/5434), positive predictive value of 90.3% (74.2% to 98.0%; 28/31), and negative predictive value of 99.2% (99.0% to 99.4%; 5431/5473). When the void samples were assumed to be negative, a sensitivity was observed for LFT of 37.8% (26.8% to 49.9%; 28/74), specificity of 99.6% (99.4% to 99.8%; 5431/5452), positive predictive value of 84.8% (68.1% to 94.9%; 28/33), and negative predictive value of 93.4% (92.7% to 94.0%; 5431/5814). The sensitivity in participants with an RT-qPCR cycle threshold (Ct) of <18.3 (approximate viral loads >10 6 RNA copies/mL) was 90.9% (58.7% to 99.8%; 10/11), a Ct of <24.4 (>10 4 RNA copies/mL) was 69.4% (51.9% to 83.7%; 25/36), and a Ct of >24.4 (<10 4 RNA copies/mL) was 9.7% (1.9% to 23.7%; 3/34). LFT is likely to detect at least three fifths and at most 998 in every 1000 people with a positive RT-qPCR test result with high viral load. Conclusions The Innova LFT can be useful for identifying infections among adults who report no symptoms of covid-19, particularly those with high viral load who are more likely to infect others. The number of asymptomatic adults with lower Ct (indicating higher viral load) missed by LFT, although small, should be considered when using single LFT in high consequence settings. Clear and accurate communication with the public about how to interpret test results is important, given the chance of missing some cases, even at high viral loads. Further research is needed to understand how infectiousness is reflected in the viral antigen shedding detected by LFT versus the viral loads approximated by RT-qPCR.

scholarly journals SARS-CoV-2 Persistence in Immunocompromised Children

2021 ◽  
Author(s):  
Susan Dolan ◽  
Jean Mulcahy Levy ◽  
Angla Moss ◽  
Kelly Pearce ◽  
Samuel Dominguez ◽  
...  
Keyword(s):  
Viral Load ◽  
Median Time ◽  
Immunosuppressive Treatment ◽  
Viral Persistence ◽  
High Viral Load ◽  
Viral Loads ◽  
Mild Disease ◽  
Kaplan Meier ◽  
Diagnostic Panel ◽  
Event Times

Introduction/Objectives: We evaluated the length of time immunocompromised children (ICC) remain positive for SARS-CoV-2, identified factors associated with viral persistence and determined cycle threshold (CT) values of children with viral persistence as a surrogate of viral load. Methods: We conducted a retrospective cohort study of ICC at a pediatric hospital from March 2020-2021. Immunocompromised status was defined as primary, secondary or acquired due to medical comorbidities/immunosuppressive treatment. The primary outcome was time to first-of-two consecutive negative SARS-CoV-2 Polymerase chain reaction (PCR) tests at least 24 hours apart. Testing of sequential clinical specimens from the same subject was conducted using the Centers for Disease Control (CDC) 2019-nCoV Real-Time RT-PCR Diagnostic Panel assay. Descriptive statistics, Kaplan-Meier curve median event times and log-rank-sum tests were used to compare outcomes between groups. Results: Ninety-one children met inclusion criteria. Median age was 15.5 years (IQR 8-18 yrs), 64% were male, 58% were white, and 43% were Hispanic/Latinx. Most (67%) were tested in outpatient settings and 58% were asymptomatic. The median time to two negative tests was 42 days (IQR 25.0,55.0), with no differences in median time by illness presentation or level of immunosuppression. Seven children had >1 sample available for repeat testing, and 5/7 (71%) children had initial CT values of <30, (moderate to high viral load); 4 children had CT values of <30 3-4 weeks later, suggesting persistent moderate to high viral loads. Conclusions: Most ICC with SARS-CoV-2 infection had mild disease, with prolonged viral persistence >6 weeks and moderate to high viral load.

scholarly journals Evaluation of saliva sampling procedures for SARS-CoV-2 diagnostics reveals differential sensitivity and association with viral load

2020 ◽  
Author(s):  
Pieter Mestdagh ◽  
Michel Gillard ◽  
Marc Arbyn ◽  
Jean-Paul Pirnay ◽  
Jeroen Poels ◽  
...  
Keyword(s):  
Viral Load ◽  
High Risk ◽  
Health Professionals ◽  
High Viral Load ◽  
Sampling Procedure ◽  
Differential Sensitivity ◽  
Collection Method ◽  
Viral Loads ◽  
Saliva Collection ◽  
Sampling Procedures

AbstractNasopharyngeal sampling has been the preferential collection method for SARS-CoV-2 diagnostics. Alternative sampling procedures that are less invasive and do not require a healthcare professional would be more preferable for patients and health professionals. Saliva collection has been proposed as such a possible alternative sampling procedure. We evaluated the sensitivity of SARS-CoV-2 testing on two different saliva collection devices (spitting versus swabbing) compared to nasopharyngeal swabs in over 2500 individuals that were either symptomatic or had high-risk contacts with infected individuals. We observed an overall poor sensitivity in saliva for SARS-CoV-2 detection (30.8% and 22.4% for spitting and swabbing, respectively). However, when focusing on individuals with medium to high viral load, sensitivity increased substantially (97.0% and 76.7% for spitting and swabbing, respectively), irrespective of symptomatic status. Our results suggest that saliva cannot readily replace nasopharyngeal sampling for SARS-CoV-2 diagnostics but may enable identification of cases with medium to high viral loads.

scholarly journals High Resolution Analysis of Respiratory Syncytial Virus Infection In Vivo

Viruses ◽  
2019 ◽  
Vol 11 (10) ◽  
pp. 926 ◽  
Author(s):  
Waleed Aljabr ◽  
Stuart Armstrong ◽  
Natasha Y. Rickett ◽  
Georgios Pollakis ◽  
Olivier Touzelet ◽  
...  
Keyword(s):  
Viral Load ◽  
Respiratory Syncytial Virus ◽  
The Elderly ◽  
High Viral Load ◽  
Label Free ◽  
Respiratory Problems ◽  
Viral Loads ◽  
High Resolution Analysis ◽  
Syncytial Virus

Human respiratory syncytial virus (HRSV) is a major cause of pediatric infection and also causes disease in the elderly and those with underlying respiratory problems. There is no vaccine for HRSV and anti-viral therapeutics are not broadly applicable. To investigate the effect of HRSV biology in children, nasopharyngeal aspirates were taken from children with different viral loads and a combined high throughput RNAseq and label free quantitative proteomics approach was used to characterize the nucleic acid and proteins in these samples. HRSV proteins were identified in the nasopharyngeal aspirates from infected children, and their abundance correlated with viral load (Ct value), confirming HRSV infection. Analysis of the HRSV genome indicated that the children were infected with sub-group A virus and that minor variants in nucleotide frequency occurred in discrete clusters along the HRSV genome, and within a patient clustered distinctly within the glycoprotein gene. Data from the samples were binned into four groups; no-HRSV infection (control), high viral load (Ct < 20), medium viral load (Ct = 20–25), and low viral load (Ct > 25). Cellular proteins associated with the anti-viral response (e.g., ISG15) were identified in the nasopharyngeal aspirates and their abundance was correlated with viral load. These combined approaches have not been used before to study HRSV biology in vivo and can be readily applied to the study the variation of virus host interactions.

scholarly journals Feasibility and Effectiveness Assessment of SARS-CoV-2 Antigenic Tests in Mass Screening of a Pediatric Population and Correlation with the Kinetics of Viral Loads

Viruses ◽  
2021 ◽  
Vol 13 (10) ◽  
pp. 2071
Author(s):  
Marcello Lanari ◽  
Giovanni Battista Biserni ◽  
Matteo Pavoni ◽  
Eva Caterina Borgatti ◽  
Marta Leone ◽  
...  
Keyword(s):  
Viral Load ◽  
Mass Screening ◽  
Point Of Care ◽  
Pediatric Population ◽  
Late Phase ◽  
High Viral Load ◽  
Pediatric Emergency ◽  
Nucleic Acid Amplification ◽  
Baseline Sensitivity ◽  
Viral Loads

The gold standard for diagnosis of SARS-CoV-2 infection has been nucleic acid amplification tests (NAAT). However, rapid antigen detection kits (Ag-RDTs), may offer advantages over NAAT in mass screening, generating results in minutes, both as laboratory-based test or point-of-care (POC) use for clinicians, at a lower cost. We assessed two different POC Ag-RDTs in mass screening versus NAAT for SARS-CoV-2 in a cohort of pediatric patients admitted to the Pediatric Emergency Unit of IRCCS—Polyclinic of Sant’Orsola, Bologna (from November 2020 to April 2021). All patients were screened with nasopharyngeal swabs for the detection of SARS-CoV-2-RNA and for antigen tests. Results were obtained from 1146 patients. The COVID-19 Ag FIA kit showed a baseline sensitivity of 53.8% (CI 35.4–71.4%), baseline specificity 99.7% (CI 98.4–100%) and overall accuracy of 80% (95% CI 0.68–0.91); the AFIAS COVID-19 Ag kit, baseline sensitivity of 86.4% (CI 75.0–93.9%), baseline specificity 98.3% (CI 97.1–99.1%) and overall accuracy of 95.3% (95% CI 0.92–0.99). In both tests, some samples showed very low viral load and negative Ag-RDT. This disagreement may reflect the positive inability of Ag-RDTs of detecting antigen in late phase of infection. Among all cases with positive molecular test and negative antigen test, none showed viral loads > 106 copies/mL. Finally, we found one false Ag-RDTs negative result (low cycle thresholds; 9 × 105 copies/mL). Our results suggest that both Ag-RDTs showed good performances in detection of high viral load samples, making it a feasible and effective tool for mass screening in actively infected children.

scholarly journals Viral loads of Delta-variant SARS-CoV2 breakthrough infections following vaccination and booster with the BNT162b2 vaccine

2021 ◽  
Author(s):  
Matan Levine-Tiefenbrun ◽  
Idan Yelin ◽  
Hillel Alapi ◽  
Rachel Katz ◽  
Esma Herzel ◽  
...  
Keyword(s):  
Viral Load ◽  
Real Life ◽  
Load Reduction ◽  
Protective Effects ◽  
Breakthrough Infection ◽  
Life Effectiveness ◽  
Post Vaccination ◽  
Viral Loads ◽  
Booster Vaccine ◽  
Viral Load Reduction

The BNT162b2 vaccine showed high real-life effectiveness both at preventing disease and in reducing viral loads of breakthrough infections, but coincidental with the rise of the Delta-variant SARS-CoV2, these protective effects have been decreasing, prompting a third, booster, vaccine inoculation. Here, analyzing viral loads of over 11,000 infections during the current wave in Israel, we find that even though this wave is dominated by the Delta-variant, breakthrough infections in recently vaccinated patients, still within 2 months post their second vaccine inoculation, do have lower viral loads compared to unvaccinated patients, with the extent of viral load reduction similar to pre-Delta breakthrough observations. Yet, this infectiousness protection starts diminishing for patients two months post vaccination and ultimately vanishes for patients 6 months or longer post vaccination. Encouragingly, we find that this diminishing vaccine effectiveness on breakthrough infection viral loads is restored following the booster vaccine. These results suggest that the vaccine is initially effective in reducing infectiousness of breakthrough infections even with the Delta variant, and that while this protectiveness effect declines with time it can be restored, at least temporarily, with a booster vaccine.

scholarly journals SARS-CoV-2 infectivity correlates with high viral loads and detection of viral antigen and is terminated by seroconversion

2021 ◽  
Author(s):  
Felix Buder ◽  
Markus Bauswein ◽  
Clara L Magnus ◽  
Franz Audebert ◽  
Henriette Lang ◽  
...  
Keyword(s):  
Viral Load ◽  
Symptom Onset ◽  
Viral Antigen ◽  
Virus Isolation ◽  
Point Of Care ◽  
High Viral Load ◽  
University Hospital ◽  
Public Health Perspective ◽  
Viral Loads ◽  
Restrictive Measures

Abstract Background From a public health perspective, effective containment strategies for SARS-CoV-2 should be balanced with individual liberties. Methods We collected 79 respiratory samples from 59 patients monitored in an outpatient center or in the intensive care unit of the University Hospital Regensburg. We analyzed viral load by quantitative real-time PCR, viral antigen by point-of-care assay, time since onset of symptoms and presence of SARS-CoV-2 IgG antibodies in the context of virus isolation from respiratory specimen. Results The odds ratio for virus isolation increased 1.9-fold for each log10 level of SARS-CoV-2 RNA and 7.4-fold with detection of viral antigen, while it decreased 6.3-fold beyond 10 days of symptoms and 20.0-fold with presence of SARS-CoV-2 antibodies. The latter was confirmed for B.1.1.7 strains. The positive predictive value for virus isolation was 60.0% for viral loads above 10 7 RNA copies/mL and 50.0% for the presence of viral antigen. Symptom onset before 10 days and seroconversion predicted lack of infectivity with 93.8% and 96.0%. Conclusions Our data support quarantining patients with high viral load and detection of viral antigen, and lifting restrictive measures with increasing time to symptom onset and seroconversion. Delay of antibody formation may prolong infectivity.

scholarly journals The Comparison of Honeybee Viral Loads for Six Honeybee Viruses (ABPV, BQCV, CBPV, DWV, LSV3 and SBV) in Healthy and Clinically Affected Honeybees with TaqMan Quantitative Real-Time RT-PCR Assays

Viruses ◽  
2021 ◽  
Vol 13 (7) ◽  
pp. 1340
Author(s):  
Laura Šimenc ◽  
Tanja Knific ◽  
Ivan Toplak
Keyword(s):  
Viral Load ◽  
Real Time ◽  
Viral Infections ◽  
Clinical Signs ◽  
High Viral Load ◽  
Deformed Wing Virus ◽  
Viral Loads ◽  
Additional Information ◽  
Queen Cell ◽  
Paralysis Virus

The viral loads of acute bee paralysis virus (ABPV), black queen cell virus (BQCV), chronic bee paralysis virus (CBPV), deformed wing virus (DWV), Lake Sinai virus 3 (LSV3), and sacbrood bee virus (SBV) were determined in samples with the use of quantitative TaqMan real-time reverse transcription and polymerase chain reaction (RT-qPCR). A total of 108 samples of healthy adult honeybees from four differently located apiaries and samples of honeybees showing different clinical signs of viral infections from 89 apiaries were collected throughout Slovenia. The aim of this study was to discover correlations between viral loads and clinical signs in adult honeybees and confirm previously set threshold viral load levels between healthy and clinically affected honeybees. Within this study, two new RT-qPCR assays for quantification of LSV3 and SBV were developed. Statistically significant differences in viral loads of positive samples were identified between healthy and clinically affected honeybees for ABPV, CBPV, DWV, and SBV, while for BQCV and LSV3, no statistical differences were observed between both groups. Despite high detected LSV3 prevalence and viral loads around 6.00 log10 viral copies/bee, this lineage probably has a limited impact on the health status of honeybee colonies. The determined viral loads between 3.94 log10 and 13.17 log10 in positive samples for six viruses, collected over 10 consecutive months, including winter, present additional information of high viral load variations in healthy honeybee colonies.

scholarly journals Ultrastructural analysis of nasopharyngeal epithelial cells from patients with SARS-CoV-2 infection

2021 ◽  
Author(s):  
Karina LA Saraiva ◽  
Luydson RS Vasconcelos ◽  
Matheus F Bezerra ◽  
Rodrigo ML Arcoverde ◽  
Sinval P Brandao-Filho ◽  
...  
Keyword(s):  
Viral Load ◽  
Primary Cilium ◽  
High Viral Load ◽  
Ultrastructural Changes ◽  
Multivesicular Bodies ◽  
Ciliated Cells ◽  
Squamous Cells ◽  
Viral Loads ◽  
Distinct Disease ◽  
Shed Light

The nasal epithelium is an initial site for SARS-CoV-2 infection, responsible for the ongoing COVID-19 pandemic. However, the pathogenicity and morphological impact of SARS-CoV-2 on the nasopharynx cells from symptomatic patients with different viral loads remain poorly understood. Here, we investigated the ultrastructure of nasal cells obtained from individuals at distinct disease days and with high and low SARS-CoV-2 loads. Squamous and ciliated cells were the main cells observed in SARS-CoV-2 negative samples. We identified virus-like particles (VLPs) and replication organelles (RO)-like structures in the squamous cells from high viral load samples after 3- and 4-days of symptoms. Ultrastructural changes were found in those cells, such as the loss of microvilli and primary cilium, the increase of multivesicular bodies and autophagosomes, and signs of cell death. No ciliated cells were found in those samples. Squamous cells from low viral load sample after 5 days of symptoms showed few microvilli and no primary cilium. VLPs and RO-like structures were found in the ciliated cells only. No ultrastructural alterations were seen in the cells from low viral load individuals after 10- and 14-days of symptoms. Our results shed light on the ultrastructural effects of SARS-CoV-2 infection on the human nasopharyngeal cells.

Sign in / Sign up

Export Citation Format

Share Document