scholarly journals Saliva swabs are the preferred sample for Omicron detection

2021 ◽  
Author(s):  
Gert Johannes Kruger Marais ◽  
Nei-yuan Hsiao ◽  
Arash Iranzadeh ◽  
Deelan Doolabh ◽  
Annabel Enoch ◽  
...  
Keyword(s):  
Disease Transmission ◽  
Ex Vivo ◽  
Diagnostic Testing ◽  
Standard Of Care ◽  
Relative Performance ◽  
Spike Protein ◽  
Tissue Tropism ◽  
Rt Pcr ◽  
Percent Agreement

The Omicron variant is characterised by more than 50 distinct mutations, the majority of which are located in the spike protein. The implications of these mutations for disease transmission, tissue tropism and diagnostic testing are still to be determined. We evaluated the relative performance of saliva and mid-turbinate swabs as RT-PCR samples for the Delta and Omicron variants. The positive percent agreement (PPA) of saliva swabs and mid-turbinate swabs to a composite standard was 71% (95% CI: 53-84%) and 100% (95% CI: 89-100%), respectively, for the Delta variant. However, for the Omicron variant saliva and mid-turbinate swabs had a 100% (95% CI: 90-100%) and 86% (95% CI: 71-94%) PPA, respectively. This finding supports ex-vivo data of altered tissue tropism from other labs for the Omicron variant. Reassessment of the diagnostic testing standard-of-care may be required as the Omicron variant becomes the dominant variant worldwide.

scholarly journals The Wild West of Emergency Use Authorizations for SARS-CoV-2 Testing: What Could Be the True Sensitivity?

2020 ◽  
Vol 154 (Supplement_1) ◽  
pp. S142-S143
Author(s):  
S Dalal ◽  
S Patel ◽  
J M Petersen ◽  
D Jhala
Keyword(s):  
Medical Center ◽  
Initial Result ◽  
Reference Laboratory ◽  
Test Results ◽  
Rt Pcr ◽  
Repeat Testing ◽  
Parallel Testing ◽  
Percent Agreement ◽  
Instructions For Use ◽  
Multiple Reference

Abstract Introduction/Objective SARS-CoV-2 is a pandemic that has required mobilization to meet urgent needs. In this mobilization, emergency use authorizations (EUA) have been issued by the FDA to expedite the deployment of these tests. This has led to a situation whereby sensitivity has not been rigorously studied for any of the assays with EUAs. Estimates can be extrapolated from the limited samples documented by the company in their instructions for use (IFU). Although the nationwide shortage of testing reagents prevent parallel testing of multiple platforms on all specimens, observations of repeat specimens at the Veteran Affairs Medical Center (VAMC) provides the first study in the literature of more complete data for SARS-CoV-2 nucleic acid (RT-PCR) assay on sensitivity on the Abbott (Abbott Park Ill) and Cepheid (Sunnyvale CA) assays. Methods A retrospective search was performed for all test results for SARS-CoV-2 by RT-PCR from 3/1/2020 to 4/14/2020 at Corporal Michael J. Crescenz Medical Center, in order to evaluate the sensitivity on Abbott m2000 and Cepheid platforms. Results across multiple reference laboratories and in-house testing platforms were collated in a table with all patients clinically requiring repeat testing recorded. Results 114/863 patients had repeat testing. The tests were performed initially by outside reference laboratories (25 patients), on the Abbott m2000 (63 patients), and Cepheid Infinity (26 patients). 15/114 (13%) had discordant results on repeat testing. This included 1 test initially done by a reference laboratory. 8 days after the initial result from the reference lab, a positive for the same patient was identified on the Abbott platform. 11 initial Abbott results were discordant on further repeat testing on two platforms - Abbott (6 patients) and Cepheid (5 patients) 1-6 days later. In addition, 3 initial Cepheid were discordant on further repeat testing by the same Cepheid platform (1-16 days later). Conclusion While the instructions for use for both platforms suggest 100% sensitivity and specificity (due to the 100% positive and negative percent agreement in limited specimens), the true sensitivity is less than 100%, particularly early in the course of the infection. In our study, the positive percent agreement (surrogate for sensitivity) was 83% for initial Abbott tests, 88% for initial Cepheid tests, and 95% by Reference laboratory platform.

scholarly journals Phenotypical and Functional Characteristics of Human Regulatory T Cells during Ex Vivo Maturation from CD4+ T Lymphocytes

2021 ◽  
Vol 11 (13) ◽  
pp. 5776
Author(s):  
Varvara G. Blinova ◽  
Natalia S. Novachly ◽  
Sofya N. Gippius ◽  
Abdullah Hilal ◽  
Yulia A. Gladilina ◽  
...  
Keyword(s):  
T Cells ◽  
Regulatory T Cells ◽  
Ex Vivo ◽  
Pcr Analysis ◽  
Mrna Levels ◽  
Rt Pcr ◽  
Inflammatory Reactions ◽  
Effector Cells ◽  
Cycle Regulation ◽  
Further Development

Regulatory T cells (Tregs) participate in the negative regulation of inflammatory reactions by suppressing effector cells. In a number of autoimmune disorders, the suppressive function and/or the number of Tregs is compromised. The lack of active functioning Tregs can be restored with adoptive transfer of expanded ex vivo autologous Tregs. In our study, we traced the differentiation and maturation of Tregs CD4+CD25+FoxP3+CD127low over 7 days of cultivation from initial CD4+ T cells under ex vivo conditions. The resulting ex vivo expanded cell population (eTregs) demonstrated the immune profile of Tregs with an increased capacity to suppress the proliferation of target effector cells. The expression of the FoxP3 gene was upregulated within the time of expansion and was associated with gradual demethylation in the promotor region of the T cell-specific demethylation region. Real-time RT-PCR analysis revealed changes in the expression profile of genes involved in cell cycle regulation. In addition to FOXP3, the cells displayed elevated mRNA levels of Ikaros zinc finger transcription factors and the main telomerase catalytic subunit hTERT. Alternative splicing of FoxP3, hTERT and IKZF family members was demonstrated to be involved in eTreg maturation. Our data indicate that expanded ex vivo eTregs develop a Treg-specific phenotype and functional suppressive activity. We suggest that eTregs are not just expanded but transformed cells with enhanced capacities of immune suppression. Our findings may influence further development of cell immunosuppressive therapy based on regulatory T cells.

scholarly journals Chemical, Mechanical, and Heat Cleaning to Decontaminate Hospital Drains Harboring Carbapenemase-Producing Enterobacteriales

2020 ◽  
Vol 41 (S1) ◽  
pp. s466-s467
Author(s):  
Alainna Juliette Jamal ◽  
Rajni Pantelidis ◽  
Rachael Sawicki ◽  
Angel Li ◽  
Wayne Chiu ◽  
...  
Keyword(s):  
Primary Outcome ◽  
Controlled Trial ◽  
Intervention Group ◽  
Group Versus ◽  
Brain Heart Infusion ◽  
Standard Of Care ◽  
Rt Pcr ◽  
Comparator Group ◽  
Carbapenemase Gene ◽  
Cleaning Intervention

Background: Carbapenemase-producing Enterobacteriales (CPE) outbreaks have been linked to contaminated wastewater drainage systems in hospitals. The optimal strategy for CPE decontamination of drains is unknown. In this randomized controlled trial, we aimed to determine whether combining chemical, mechanical, and heat cleaning was superior to routine cleaning for drain decontamination. Methods: We enrolled CPE-contaminated hospital drains at 2 geographic locations. Eligible drains were those initially found to be culture positive in a 2017 study and that remained positive (by RT-PCR) when retested twice in August 2018. Drains were stratified by type (sink versus shower) and randomized with a 1:1 allocation ratio (as per computer-generated randomization) to standard-of-care cleaning (comparator) or combined chemical, mechanical, and heat cleaning (intervention) on day 0. Drain tail pieces were swabbed on days 0 (before administration of the intervention), 1, 2, 3, 7, and 14, and at months 1, 2, 3, 4, 5, and 6. Swabs were placed into brain heart infusion with 10% Dey-Engley neutralizing broth and incubated overnight. Direct RT-PCR was performed to detect KPC, VIM, NDM, OXA-48–like, IMP, GES, and SME genes. The primary outcome was drain decontamination, defined as no detectable carbapenemase gene in the drain from day 1 to 7 (inclusive). Results: Overall, 33 CPE-contaminated drains were enrolled (7 sink and 26 shower); 17 and 16 drains were randomized to the intervention and comparator, respectively. Moreover, 12 (36%) drains met the primary outcome of decontamination, 18 (55%) remained contaminated, and 3 (9%) could not be assessed. Among drains that could be assessed, 11 of 15 (74%) in the intervention group met the primary outcome of decontamination compared to 1 of 15 (7%) in the comparator group (P = .0005). Of the 11 drains in the intervention group that were decontaminated, the carbapenemase gene present at enrollment was subsequently detected in 10 (91%): 1 (10%) at day 14, 3 (30%) at month 1, 4 (40%) at month 3, 1 (10%) at month 4, and 1 (10%) at month 6. The median time to a swab yielding CPE was 1 day in the comparator group versus 14 days in the intervention group (Fig. 1). Overall, 24 drains (73%) had a carbapenemase gene (that was not detectable at enrollment) appear in the follow-up. Of patients identified as CPE colonized or infected during this study, none occupied rooms with these drains. Conclusions: Chemical, mechanical, and heat cleaning were superior to standard cleaning for CPE decontamination of hospital drains at 7 days, but these trends were not sustained. Such cleaning may be useful if applied repeatedly.Funding: NoneDisclosures: Allison McGeer reports funds to her institution for studies for which she is the principal investigator from Pfizer and Merck as well as consulting fees from Sanofi-Pasteur, Sunovion, GSK, Pfizer, and Cidara.

scholarly journals Evaluation of SARS-CoV-2 antigen-based rapid diagnostic kits in Pakistan: formulation of COVID-19 national testing strategy

2021 ◽  
Vol 18 (1) ◽  
Author(s):  
Umar Saeed ◽  
Sara Rizwan Uppal ◽  
Zahra Zahid Piracha ◽  
Azhar Rasheed ◽  
Zubair Aftab ◽  
...  
Keyword(s):  
Gold Standard ◽  
Injection Drug Users ◽  
Drug Users ◽  
Diagnostic Testing ◽  
False Negative ◽  
Cross Sectional Study ◽  
Nasopharyngeal Swab ◽  
Rt Pcr ◽  
Cross Sectional ◽  
Negative Results

AbstractRapid diagnosis of SARS-CoV-2 during pandemic enables timely treatment and prevention of COVID-19. Evaluating the accuracy and reliability of rapid diagnostic testing kits is crucial for surveillance and diagnosis of SARS-CoV-2 infections in general population, injection drug users, multi-transfused populations, healthcare workers, prisoners, barbers and other high risk populations. The aim of this study was to evaluate performance and effectiveness of nasopharyngeal swab (NSP) and saliva based rapid antigen detection testing kits in comparison with USFDA approved triple target gold standard real-time polymerase chain reaction. A cross-sectional study was conducted on 33,000 COVID-19 suspected patients. From RT-PCR positive patients, nasopharyngeal swab (NSP) and saliva samples were obtained for evaluation of rapid COVID-19 testing kits (RDT). 100/33,000 (0.3%) of specimens were RT-PCR positive for SARS-CoV-2. Among RT-PCR positive, 62% were males, 34% were females, and 4% were children. The NSP-RDT (Lepu Medical China) analysis revealed 53% reactivity among males, 58% reactivity among females, and 25% reactivity among children. However saliva based RDT (Lepu Medical China) analysis showed 21% reactivity among males and 23% among females, and no reactivity in children. False negative results were significantly more pronounced in saliva based RDT as compared to NSP-RDT. The sensitivity of these NSP-RDT and saliva based RDT were 52% and 21% respectively. The RDTs evaluated in this study showed limited sensitivities in comparison to gold standard RT-PCR, indicating that there is a dire need in Pakistan for development of suitable testing to improve accurate COVID-19 diagnosis in line with national demands.

scholarly journals 528. Coronavirus Disease 2019 in Children Cared for at Texas Children’s Hospital: Implications of Repeat Testing on Infection Control Strategies

2020 ◽  
Vol 7 (Supplement_1) ◽  
pp. S331-S332
Author(s):  
Catherine Foster ◽  
Lucila Marquez ◽  
Tjin Koy ◽  
Ila Singh ◽  
Judith Campbell
Keyword(s):  
Infection Control ◽  
Median Time ◽  
Disease Transmission ◽  
Retrospective Chart Review ◽  
Source Control ◽  
Hospitalized Children ◽  
Rt Pcr ◽  
Repeat Testing ◽  
Children's Hospital ◽  
Children’S Hospital

Abstract Background Accurate diagnosis of coronavirus disease 2019 (COVID-19) is key for source control and interrupting disease transmission. To better understand the length of viral shedding in children and potential infection control implications, we describe 51 children with COVID-19 who underwent repeat testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) at Texas Children’s Hospital (TCH). Methods We performed a retrospective chart review of all pediatric patients (< 21 years of age) with ≥ 2 nasopharyngeal specimens tested for SARS-CoV-2 by reverse transcription-polymerase chain reaction (rt-PCR) and at least one positive result between 3/13/2020 and 6/7/2020 through the TCH Molecular Microbiology Laboratory. Results Fifty-one patients met inclusion criteria. The median age was 8.6 years (0.02–19.2 years). Sixteen (31%) children were hospitalized. Fourteen (27%) patients underwent testing for surveillance purposes (including 3 admitted patients). Two SARS-CoV-2 tests were performed in 25 (49%) children; while 12 (24%) children had 3 tests, 4 (8%) children had 4 tests, and 10 (20%) children had ≥ 5 tests (including 1 patient with underlying malignancy who had 9 SARS-CoV-2 PCRs performed). SARS-CoV-2 testing timeline for 9 hospitalized children is shown (Fig 1). The median time between collection of tests 1 and 2 was 14 days (n=51, range 1, 53 days). For children with conversion (first detected to first not-detected sample), the median time was 15 days (n=31, range 1, 45 days). For patients with consecutive positive SARS-CoV-2 PCRs, the median time of positivity was 10 days (n=19, range 2, 31). One patient with malignancy had 5 tests over 6 weeks in the outpatient setting and each time alternated between detected and not-detected. Following diagnosis with COVID-19, one patient with sickle cell disease likely had re-infection and had a positive test after having 2 consecutive negative tests; his last SARS-CoV-2 rt-PCR was positive 68 days after initial positive. Fig 1. Timing of Repeat SARS-CoV-2 PCRs in Select Hospitalized Children with COVID-19 Conclusion We observed variation in the duration of SARS-CoV-2 rt-PCR positivity in children with COVID-19. For children with COVID-19, a single negative molecular assay for SARS-CoV-2 may not be predictive of sustained negativity. Disclosures All Authors: No reported disclosures

scholarly journals SARS-CoV-2 full length spike protein for COVID-19 vaccine development and diagnostic testing

2021 ◽  
Vol 147 (2) ◽  
pp. AB152
Author(s):  
Crystal Richardson ◽  
Mayuresh Abhyankar ◽  
Jillian Bracaglia ◽  
Sayeh Agah ◽  
Zachary Schuhmacher ◽  
...  
Keyword(s):  
Vaccine Development ◽  
Diagnostic Testing ◽  
Full Length ◽  
Spike Protein

scholarly journals Automated Western immunoblotting detection of anti-SARS-CoV-2 serum antibodies

2021 ◽  
Author(s):  
Sophie Edouard ◽  
Rita Jaafar ◽  
Nicolas Orain ◽  
Philippe Parola ◽  
Philippe Colson ◽  
...  
Keyword(s):  
Negative Control ◽  
Cross Reactivity ◽  
Spike Protein ◽  
Rt Pcr ◽  
Substantial Agreement ◽  
Western Immunoblotting ◽  
Elisa Kit ◽  
Line Test ◽  
Serologic Assay ◽  
Control Samples

AbstractELISA and chemiluminescence serological assays for COVID-19 are currently incorporating only one or two SARS-CoV-2 antigens. We developed an automated Western immunoblotting as a complementary serologic assay for COVID-19. The JessTM Simple Western system, an automated capillary-based assay, was used, incorporating an inactivated SARS-CoV-2 lineage 20a strain as the source of antigen, and total immunoglobulins (IgG, IgM, IgA) detection. In total, 602 sera were tested including 223 from RT-PCR-confirmed COVID-19 patients, 76 from patients diagnosed with seasonal HCoVs and 303 from coronavirus-negative control sera. We also compared this assay with the EUROIMMUN® SARS-CoV-2 IgG ELISA kit. Among 223 sera obtained from RT-PCR-confirmed COVID-19 patients, 180/223 (81%) exhibited reactivity against the nucleocapsid and 70/223 (31%) against the spike protein. Nucleocapsid reactivity was further detected in 9/76 (14%) samples collected from patients diagnosed with seasonal HCoVs and in 15/303 (5%) coronavirus-negative control samples. In the subset of sera collected more than 2 weeks after the onset of symptoms, the sensitivity was 94% and the specificity 93%, the latter value probably reflecting cross-reactivity of SARS-CoV-2 with other coronaviruses. The automated Western immunoblotting presented a substantial agreement (90%) with the compared ELISA (Cohen’s Kappa=0.64). Automated Western immunoblotting may be used as a second line test to monitor exposure of people to HCoVs including SARS-CoV-2.

scholarly journals Utility of forensic detection of rabies virus in decomposed exhumed dog carcasses

2015 ◽  
Vol 86 (1) ◽  
Author(s):  
Wanda Markotter ◽  
Jessica Coertse ◽  
Kevin Le Roux ◽  
Joey Peens ◽  
Jacqueline Weyer ◽  
...  
Keyword(s):  
Rabies Virus ◽  
Gold Standard ◽  
Diagnostic Method ◽  
Diagnostic Testing ◽  
Domestic Dogs ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Brain Material ◽  
Polymerase Chain ◽  
Genomic Material

This report describes four suspected rabies cases in domestic dogs that were involved inhuman exposures. In all these cases, the animals were buried for substantial times beforerabies testing was performed. Animal rabies is endemic in South Africa and domestic dogsare the main vector for transmission to humans. Diagnosis of rabies in humans is complicated,and diagnosis in the animal vector can provide circumstantial evidence to support clinicaldiagnosis of rabies in humans. The gold standard diagnostic method, fluorescent antibodytest (FAT), only delivers reliable results when performed on fresh brain material and thereforedecomposed samples are rarely submitted for diagnostic testing. Severely decomposed brainmaterial was tested for the presence of rabies virus genomic material using a quantitativereal-time reverse transcription polymerase chain reaction (q-real-time RT-PCR) assaywhen conventional molecular methods were unsuccessful. This may be a useful tool in theinvestigation of cases where the opportunity to sample the suspected animals post mortem wasforfeited and which would not be possible with conventional testing methodologies becauseof the decomposition of the material.

Cross-contamination in molecular laboratories: A challenge to COVID-19 testing in Bangladesh

2021 ◽  
Vol 2 (5) ◽  
Author(s):  
Mohammad Jahidur Rahman Khan ◽  
◽  
Selim Reza ◽  
Farzana Mim ◽  
Md Abdullah Rumman ◽  
...  
Keyword(s):  
Public Health ◽  
Large Scale ◽  
Diagnostic Testing ◽  
Diagnostic Errors ◽  
Laboratory Diagnosis ◽  
Cross Contamination ◽  
Rt Pcr ◽  
Public Health Response ◽  
Surveillance Programs ◽  
The Government

Rapid and accurate laboratory diagnosis of SARS-CoV-2 infection is crucial for the management of COVID-19 patients and control of the spread of the virus. At the start of the COVID-19 pandemic, Bangladesh had only one government molecular laboratory where real-time RT-PCR will be performed to diagnose SARS-CoV-2 infection. With the increasing number of suspected cases requiring confirmation diagnostic testing, there was a requirement to quickly expand capacity for large-scale testing. The government of Bangladesh established over 100 molecular laboratories within one year to test COVID-19. To fulfil the requirement for expanded testing, the government was compelled to recruit laboratory employees with inadequate experience, technical knowledge, and skills in molecular assays, particularly in processing specimens, interpreting results, recognizing errors, and troubleshooting. As a result, the risk of diagnostic errors, such as cross-contamination, is increased, as is that the risk of false-positive results, which might risk the patient’s health and undermine the efficacy of public health policies, public health response, surveillance programs, and restrictive measures aimed toward containing the outbreak. This review article aims to explain different sources of crosscontamination in the COVID-19 RT-PCR laboratories and the way to forestall them in efficient and practical ways.

scholarly journals Untargeted saliva metabolomics reveals COVID-19 severity: Saliva Metabolomics for SARS-COV-2 Prognosis

2021 ◽  
Author(s):  
Melanie Bailey ◽  
Matt P Spick ◽  
Katie Longman ◽  
Cecile Frampas ◽  
Holly M Lewis ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Liquid Chromatography ◽  
Diagnostic Testing ◽  
Hospital Setting ◽  
Clinical Severity ◽  
Liquid Chromatography Mass Spectrometry ◽  
Percent Agreement ◽  
Chromatography Mass Spectrometry ◽  
Hospitalised Patients ◽  
Global Health Issue

ABSTRACT Background The COVID-19 pandemic is likely to represent an ongoing global health issue given the potential for vaccine escape and the low likelihood of eliminating all reservoirs of the disease. Whilst diagnostic testing has progressed at pace, there is an unmet clinical need to develop tests that are prognostic, to triage the high volumes of patients arriving in hospital settings. Recent research has shown that serum metabolomics has potential for prognosis of disease progression. 1 In a hospital setting, collection of saliva samples is more convenient for both staff and patients, and therefore offers an alternative sampling matrix to serum. We demonstrate here for the first time that saliva metabolomics can reveal COVID-19 severity. Methods 88 saliva samples were collected from hospitalised patients with clinical suspicion of COVID-19, alongside clinical metadata. COVID-19 diagnosis was confirmed using RT-PCR testing. COVID severity was classified using clinical descriptors first proposed by SR Knight et al. Metabolites were extracted from saliva samples and analysed using liquid chromatography mass spectrometry. Results In this work, positive percent agreement of 1.00 between a PLS-DA metabolomics model and the clinical diagnosis of COVID severity was achieved. The negative percent agreement with the clinical severity diagnosis was also 1.00, for overall percent agreement of 1.00. Conclusions This research demonstrates that liquid chromatography-mass spectrometry can identify salivary biomarkers capable of separating high severity COVID-19 patients from low severity COVID-19 patients in a small cohort study.

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