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1.
Curr Osteoporos Rep ; 20(3): 186-193, 2022 06.
Article in English | MEDLINE | ID: covidwho-1820676

ABSTRACT

PURPOSE OF REVIEW: To review the mechanisms by which vitamin D and its metabolites regulate the immune system to facilitate the ability of the body to prevent and/or treat SARS-CoV2 and other respiratory infections and encourage further research into the role that vitamin D supplementation plays in preventing/treating such infections. RECENT FINDINGS: Vitamin D deficiency is associated with an increased risk of SARS-CoV2 and other respiratory infections. Clinical trials in general demonstrate that correction of vitamin D deficiency reduces the risk of hospitalization, ICU admission, and death from SARS-CoV2 infection. The airway epithelium and alveolar macrophages express the enzyme, CYP27B1, that produces the active metabolite of vitamin D, 1,25(OH)2D, and the vitamin D receptor, VDR. Vitamin D and its metabolites promote the innate immune response, which provides the first line of defense against viral and bacterial infections while restricting the adaptive immune response, which if unchecked promotes the inflammatory response leading to the acute respiratory distress syndrome and death. The rationale for treating vitamin D deficiency to reduce the risk of SARS-CoV2 infection and supplementing patients with vitamin D early in the course of SARS-CoV2 infection rests primarily on the ability of vitamin D metabolites to promote an effective immune response to the infection.


Subject(s)
COVID-19 , Vitamin D Deficiency , Humans , Immunity, Innate/physiology , RNA, Viral , SARS-CoV-2 , Vitamin D/metabolism , Vitamin D Deficiency/complications
2.
Jpn J Infect Dis ; 75(4): 411-414, 2022 Jul 22.
Article in English | MEDLINE | ID: covidwho-2100391

ABSTRACT

The World Health Organization designated Omicron (B.1.1.529 lineage) of SARS-CoV-2 as a new variant of concern on November 26, 2021. The risk to public health conferred by the Omicron variant is still not completely clear, although its numerous gene mutations have raised concerns regarding its potential for increased transmissibility and immune escape. In this study, we describe the development of two single-nucleotide polymorphism genotyping assays targeting the G339D or T547K mutations of the spike protein to screen for the Omicron variant. A specificity test revealed that the two assays successfully discriminated the Omicron variant from the Delta and Alpha variants, each with a single nucleotide mismatch. In addition, a sensitivity test showed that the G339D and T547K assays detected at least 2.60 and 3.36 RNA copies of the Omicron variant, respectively, and 1.59 RNA copies of the Delta variant. These results demonstrate that both assays could be useful for detecting and discriminating the Omicron variant from other strains. In addition, because of the rapid and unpredictable evolution of SARS-CoV-2, combining our assays with previously developed assays for detecting other mutations may lead to a more accurate diagnostic system.


Subject(s)
COVID-19 , Genotyping Techniques , Humans , COVID-19/diagnosis , COVID-19/virology , Genotype , RNA , RNA, Viral/genetics , Polymorphism, Single Nucleotide
3.
Trials ; 23(1): 218, 2022 Mar 18.
Article in English | MEDLINE | ID: covidwho-2098433

ABSTRACT

BACKGROUND: Non-invasive ventilation (NIV) is indicated to avoid orotracheal intubation (OTI) to reduce hospital stay and mortality. Patients infected by SARS-CoV2 can progress to respiratory failure (RF); however, in the initial phase, they can be submitted to oxygen therapy and NIV. Such resources can produce aerosol and can cause a high risk of contagion to health professionals. Safe NIV strategies are sought, and therefore, the authors adapted diving masks to be used as NIV masks (called an Owner mask). OBJECTIVE: To assess the Owner mask safety and effectiveness regarding conventional orofacial mask for patients in respiratory failure with and without confirmation or suspicion of COVID-19. METHODS: A Brazilian multicentric study to assess patients admitted to the intensive care unit regarding their clinical, sociodemographic and anthropometric data. The primary outcome will be the rate of tracheal intubation, and secondary outcomes will include in-hospital mortality, the difference in PaO2/FiO2 ratio and PaCO2 levels, time in the intensive care unit and hospitalization time, adverse effects, degree of comfort and level of satisfaction of the mask use, success rate of NIV (not progressing to OTI), and behavior of the ventilatory variables obtained in NIV with an Owner mask and with a conventional face mask. Patients with COVID-19 and clinical signs indicative of RF will be submitted to NIV with an Owner mask [NIV Owner COVID Group (n = 63)] or with a conventional orofacial mask [NIV orofacial COVID Group (n = 63)], and those patients in RF due to causes not related to COVID-19 will be allocated into the NIV Owner Non-COVID Group (n = 97) or to the NIV Orofacial Non-COVID Group (n = 97) in a randomized way, which will total 383 patients, admitting 20% for loss to follow-up. DISCUSSION: This is the first randomized and controlled trial during the COVID-19 pandemic about the safety and effectiveness of the Owner mask compared to the conventional orofacial mask. Experimental studies have shown that the Owner mask enables adequate sealing on the patient's face and the present study is relevant as it aims to minimize the aerosolization of the virus in the environment and improve the safety of health professionals. TRIAL REGISTRATION: Brazilian Registry of Clinical Trials (ReBEC): RBR - 7xmbgsz . Registered on 15 April 2021.


Subject(s)
COVID-19 , Diving , Noninvasive Ventilation , Humans , Noninvasive Ventilation/adverse effects , Noninvasive Ventilation/methods , Pandemics/prevention & control , RNA, Viral , Randomized Controlled Trials as Topic , SARS-CoV-2
4.
Am J Respir Crit Care Med ; 206(9): 1178-1179, 2022 Nov 01.
Article in English | MEDLINE | ID: covidwho-2098113
5.
J Clin Microbiol ; 60(11): e0105822, 2022 11 16.
Article in English | MEDLINE | ID: covidwho-2097912

ABSTRACT

Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has been the cause of human pandemic infection since late 2019. SARS-CoV-2 infection in animals has also been reported both naturally and experimentally, rendering awareness about a potential source of infection for one health concern. Here, we describe an epidemiological investigation of SARS-CoV-2 infection in 639 cats and 224 dogs throughout multiple waves of COVID-19 outbreaks in Thailand. To indicate the potential source of infection, we performed SARS-CoV-2 genomic sequencing of samples obtained from pets and contacted humans, combined with in-depth interviews to support the epidemiological investigation. In the tested animals, SARS-CoV-2 RNA was present in 23 cases (19 cats and 4 dogs). Whole-genome sequencing of selected samples showed various SARS-CoV-2 variants of concern, which included the original European lineage (B.1), Alpha (B.1.1.7), Delta (B.1.617), and Omicron (BA.2). Among SARS-CoV-2-positive pets, 34.78% had evidence of contact with infected humans. Together with genomic analysis and an overlapping timeline, we revealed evidence of viral transmission from infected humans as the primary source, which spread to household cats via an undefined mode of transmission and most likely circulated between cohoused cats and caretakers within the weeks before the investigation. The SARS-CoV-2 surface glycoprotein (spike gene) obtained from caretakers of individual cats contained sequence signatures found in the sequences of infected cats, indicating possible exposure to the virus excreted by cats. Although pet-to-human transmission of SARS-CoV-2 is considered relatively rare, our study provides suspected episodes of human infection from animals that were initially infected through contact with infected humans.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , Cats , Dogs , Animals , SARS-CoV-2/genetics , COVID-19/veterinary , RNA, Viral , Thailand/epidemiology
6.
Semin Neurol ; 42(4): 512-522, 2022 Aug.
Article in English | MEDLINE | ID: covidwho-2096904

ABSTRACT

Medication overuse headache (MOH), new daily persistent headache (NDPH), and persistent refractory headache attributed to severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) infection represent a significant burden in terms of disability and quality of life, and a challenge in terms of definition, pathophysiology, and treatment. Regarding MOH, prevention without withdrawal is not inferior to prevention with withdrawal. Preventive medications like topiramate, onabotulinumtoxinA, and calcitonin gene-related peptide (CGRP) monoclonal antibodies improve chronic migraine with MOH regardless of withdrawal. The differential diagnosis of NDPH is broad and should be carefully examined. There are no guidelines for the treatment of NDPH, but options include a short course of steroids, nerve blocks, topiramate, nortriptyline, gabapentin, CGRP monoclonal antibodies, and onabotulinumtoxinA. The persistence of headache 3 months after SARS-CoV2 infection is a predictor of poor prognosis.


Subject(s)
Botulinum Toxins, Type A , COVID-19 , Headache Disorders, Secondary , Headache Disorders , Humans , Calcitonin Gene-Related Peptide/therapeutic use , Botulinum Toxins, Type A/therapeutic use , Quality of Life , Topiramate/therapeutic use , RNA, Viral/therapeutic use , COVID-19/complications , COVID-19/drug therapy , SARS-CoV-2 , Headache Disorders, Secondary/diagnosis , Headache Disorders, Secondary/drug therapy , Headache/diagnosis , Headache/drug therapy , Antibodies, Monoclonal/therapeutic use
8.
Med (N Y) ; 3(9): 636-643.e4, 2022 09 09.
Article in English | MEDLINE | ID: covidwho-2095786

ABSTRACT

BACKGROUND: Throughout the SARS-CoV-2 pandemic, multiple waves of variants of concern have swept across populations, leading to a chain of new and yet more contagious variants dominating COVID-19 cases. Here, we tracked the remarkably rapid shift from Omicron BA.1 to BA.2 sublineage dominance in the Swedish population in early 2022 at a day-by-day basis. METHODS: Using a custom SARS-CoV-2 Omicron BA.1 lineage-typing RT-PCR assay, we analyzed 174,933 clinical upper airway samples collected during January to March 2022. FINDINGS: Our study demonstrates the feasibility and reliability of parallel lineage assignment of select variants at population scale, tracking the dominant sublineage transition from BA.1 to BA.2 at day-to-day resolution and uncovering nearly 2-fold higher levels of viral RNA in cases infected with Omicron BA.2 relative to BA.1. CONCLUSIONS: Our data provide unique insights into the Omicron BA.1 to BA.2 transition that occurred in Sweden during early 2022, and later, across the world. This may help to understand the increased transmissibility of the BA.2 variant.


Subject(s)
COVID-19 , RNA, Viral , COVID-19/epidemiology , Humans , RNA, Viral/genetics , Reproducibility of Results , SARS-CoV-2/genetics , Sweden/epidemiology
9.
Int J Mol Sci ; 23(21)2022 Oct 28.
Article in English | MEDLINE | ID: covidwho-2090209

ABSTRACT

Consistently emerging variants and the life-threatening consequences of SARS-CoV-2 have prompted worldwide concern about human health, necessitating rapid and accurate point-of-care diagnostics to limit the spread of COVID-19. Still, However, the availability of such diagnostics for COVID-19 remains a major rate-limiting factor in containing the outbreaks. Apart from the conventional reverse transcription polymerase chain reaction, loop-mediated isothermal amplification-based (LAMP) assays have emerged as rapid and efficient systems to detect COVID-19. The present study aims to develop RT-LAMP-based assay system for detecting multiple targets in N, ORF1ab, E, and S genes of the SARS-CoV-2 genome, where the end-products were quantified using spectrophotometry, paper-based lateral-flow devices, and electrochemical sensors. The spectrophotometric method shows a LOD of 10 agµL-1 for N, ORF1ab, E genes and 100 agµL-1 for S gene in SARS-CoV-2. The developed lateral-flow devices showed an LOD of 10 agµL-1 for all four gene targets in SARS-CoV-2. An electrochemical sensor developed for N-gene showed an LOD and E-strip sensitivity of log 1.79 ± 0.427 pgµL-1 and log 0.067 µA/pg µL-1/mm2, respectively. The developed assay systems were validated with the clinical samples from COVID-19 outbreaks in 2020 and 2021. This multigene target approach can effectively detect emerging COVID-19 variants using combination of various analytical techniques at testing facilities and in point-of-care settings.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , SARS-CoV-2/genetics , COVID-19/diagnosis , Sensitivity and Specificity , Nucleic Acid Amplification Techniques/methods , Molecular Diagnostic Techniques/methods , RNA, Viral/genetics
10.
Opt Express ; 30(22): 40277-40291, 2022 Oct 24.
Article in English | MEDLINE | ID: covidwho-2089309

ABSTRACT

We conceptualized and numerically investigated a photonic crystal fiber (PCF)-based surface plasmon resonance (SPR) sensor for rapid detection and quantification of novel coronavirus. The plasmonic gold-based optical sensor permits three different ways to quantify the virus concentrations inside patient's body based on different ligand-analyte conjugate pairs. This photonic biosensor demonstrates viable detections of SARS-CoV-2 spike receptor-binding-domain (RBD), mutated viral single-stranded ribonucleic acid (RNA) and human monoclonal antibody immunoglobulin G (IgG). A marquise-shaped core is introduced to facilitate efficient light-tailoring. Analytes are dissolved in sterile phosphate buffered saline (PBS) and surfaced on the plasmonic metal layer for realizing detection. The 1-pyrene butyric acid n-hydroxy-succinimide ester is numerically used to immobilize the analytes on the sensing interface. Using the finite element method (FEM), the proposed sensor is studied critically and optimized for the refractive index (RI) range from 1.3348-1.3576, since the target analytes RIs fluctuate within this range depending on the severity of the viral infection. The polarization-dependent sensor exhibits dominant sensing attributes for x-polarized mode, where it shows the average wavelength sensitivities of 2,009 nm/RIU, 2,745 nm/RIU and 1,984 nm/RIU for analytes: spike RBD, extracted coronavirus RNA and antibody IgG, respectively. The corresponding median amplitude sensitivities are 135 RIU-1, 196 RIU-1 and 140 RIU-1, respectively. The maximum sensor resolution and figure of merit are found 2.53 × 10-5 RIU and 101 RIU-1, respectively for viral RNA detection. Also, a significant limit of detection (LOD) of 6.42 × 10-9 RIU2/nm is obtained. Considering modern bioassays, the proposed compact photonic sensor will be well-suited for rapid point-of-care COVID testing.


Subject(s)
Biosensing Techniques , COVID-19 , Humans , SARS-CoV-2 , Ligands , Butyric Acid , COVID-19 Testing , RNA, Viral , COVID-19/diagnosis , Gold/chemistry , Immunoglobulin G , Succinimides , Pyrenes , Antibodies, Monoclonal , Esters , Phosphates
11.
BMC Immunol ; 23(1): 51, 2022 10 26.
Article in English | MEDLINE | ID: covidwho-2089161

ABSTRACT

BACKGROUND: Plasmacytoid and myeloid dendritic cells play a vital role in the protection against viral infections. In COVID-19, there is an impairment of dendritic cell (DC) function and interferon secretion which has been correlated with disease severity. RESULTS: In this study, we described the frequency of DC subsets and the plasma levels of Type I (IFNα, IFNß) and Type III Interferons (IFNλ1), IFNλ2) and IFNλ3) in seven groups of COVID-19 individuals, classified based on days since RT-PCR confirmation of SARS-CoV2 infection. Our data shows that the frequencies of pDC and mDC increase from Days 15-30 to Days 61-90 and plateau thereafter. Similarly, the levels of IFNα, IFNß, IFNλ1, IFNλ2 and IFNλ3 increase from Days 15-30 to Days 61-90 and plateau thereafter. COVID-19 patients with severe disease exhibit diminished frequencies of pDC and mDC and decreased levels of IFNα, IFNß, IFNλ1, IFNλ2 and IFNλ3. Finally, the percentages of DC subsets positively correlated with the levels of Type I and Type III IFNs. CONCLUSION: Thus, our study provides evidence of restoration of homeostatic levels in DC subset frequencies and circulating levels of Type I and Type III IFNs in convalescent COVID-19 individuals.


Subject(s)
COVID-19 , Interferon Type I , Humans , Interferon Type I/metabolism , RNA, Viral/metabolism , SARS-CoV-2 , Dendritic Cells/metabolism , Homeostasis
12.
Indoor Air ; 32(10): e13118, 2022 Oct.
Article in English | MEDLINE | ID: covidwho-2088231

ABSTRACT

SARS-CoV-2 has been detected both in air and on surfaces, but questions remain about the patient-specific and environmental factors affecting virus transmission. Additionally, more detailed information on viral sampling of the air is needed. This prospective cohort study (N = 56) presents results from 258 air and 252 surface samples from the surroundings of 23 hospitalized and eight home-treated COVID-19 index patients between July 2020 and March 2021 and compares the results between the measured environments and patient factors. Additionally, epidemiological and experimental investigations were performed. The proportions of qRT-PCR-positive air (10.7% hospital/17.6% homes) and surface samples (8.8%/12.9%) showed statistical similarity in hospital and homes. Significant SARS-CoV-2 air contamination was observed in a large (655.25 m3 ) mechanically ventilated (1.67 air changes per hour, 32.4-421 L/s/patient) patient hall even with only two patients present. All positive air samples were obtained in the absence of aerosol-generating procedures. In four cases, positive environmental samples were detected after the patients had developed a neutralizing IgG response. SARS-CoV-2 RNA was detected in the following particle sizes: 0.65-4.7 µm, 7.0-12.0 µm, >10 µm, and <100 µm. Appropriate infection control against airborne and surface transmission routes is needed in both environments, even after antibody production has begun.


Subject(s)
Air Pollution, Indoor , COVID-19 , Humans , SARS-CoV-2 , COVID-19/epidemiology , RNA, Viral , Prospective Studies , Respiratory Aerosols and Droplets
13.
Commun Biol ; 5(1): 1140, 2022 Oct 27.
Article in English | MEDLINE | ID: covidwho-2087322

ABSTRACT

Defective interfering (DI) particles arise during virus propagation, are conditional on parental virus for replication and packaging, and interfere with viral expansion. There is much interest in developing DIs as anti-viral agents. Here we characterize DI particles that arose following serial passaging of SARS-CoV-2 at high multiplicity of infection. The prominent DIs identified have lost ~84% of the SARS-CoV-2 genome and are capable of attenuating parental viral titers. Synthetic variants of the DI genomes also interfere with infection and can be used as conditional, gene delivery vehicles. In addition, the DI genomes encode an Nsp1-10 fusion protein capable of attenuating viral replication. These results identify naturally selected defective viral genomes that emerged and stably propagated in the presence of parental virus.


Subject(s)
COVID-19 , Defective Viruses , Humans , Defective Viruses/genetics , SARS-CoV-2/genetics , Defective Interfering Viruses , RNA, Viral/genetics
14.
Anal Biochem ; 659: 114960, 2022 Dec 15.
Article in English | MEDLINE | ID: covidwho-2085839

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.


Subject(s)
COVID-19 , RNA, Viral , Humans , Clinical Laboratory Techniques/methods , COVID-19 Testing , Nucleic Acid Amplification Techniques/methods , Pandemics , Reproducibility of Results , Reverse Transcriptase Polymerase Chain Reaction , RNA, Viral/genetics , RNA, Viral/analysis , RNA-Directed DNA Polymerase/genetics , SARS-CoV-2/genetics , Sensitivity and Specificity , Taq Polymerase/metabolism
15.
Vaccine ; 40(48): 6900-6907, 2022 Nov 15.
Article in English | MEDLINE | ID: covidwho-2083107

ABSTRACT

BACKGROUND: The associations of doses of vaccine received with symptomatic infection with SARS-CoV-2 and negative conversion rate of viral RNA by BMI, diabetes, and age are unclear. METHODS: Included were adult cases of SARS-CoV-2 infection hospitalized at a makeshift hospital in Shanghai (N = 38,592). Each case received a real-time reverse transcriptase-polymerase chain reaction (RT-PCR) test every day until discharge. Symptomatic cases had ≥1 pre-specified symptoms. Negative conversion time (NCT) was the duration between the specimen collection date associated with the first positive RT-PCR test and the first test date of the two consecutive negative tests at least 24 h apart. BMI-, diabetes- and age-stratified multivariable logistic and Poisson regressions were applied. FINDINGS: Coexistence of overweight/obesity and diabetes was associated with a higher risk of symptomatic infection and a longer NCT compared with coexistence of normal weight and without diabetes, but this association was primarily attributed to underlying comorbidities. Compared with absence of vaccination, booster vaccination, but not full vaccination, was consistently associated with a 42 %-56 % lower odds of symptomatic infection and ∼1.6-1.8 days of shorter NCT across different strata separately for weight and diabetes. Age-stratified analyses found that the effectiveness of booster vaccination did not attenuate with age, except for preventing symptomatic infection among adults with diabetes. INTERPRETATION: BMI and diabetes co-determined their associations with symptomatic infection and NCT. Booster vaccination but not full vaccination was associated a lower risk of symptomatic infection, a shorter NCT or both regardless of BMI, diabetes status and age.


Subject(s)
COVID-19 , Diabetes Mellitus , Adult , Humans , SARS-CoV-2 , RNA, Viral/genetics , Body Mass Index , China , Diabetes Mellitus/epidemiology , Vaccination
16.
J Mol Diagn ; 24(9): 963-976, 2022 Sep.
Article in English | MEDLINE | ID: covidwho-2083089

ABSTRACT

Amplicon-based sequencing methods are central in characterizing the diversity, transmission, and evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), but need to be rigorously assessed for clinical utility. Herein, we validated the Swift Biosciences' SARS-CoV-2 Swift Normalase Amplicon Panels using remnant clinical specimens. High-quality genomes meeting our established library and sequence quality criteria were recovered from positive specimens, with 95% limit of detection of 40.08 SARS-CoV-2 copies/PCR. Breadth of genome recovery was evaluated across a range of CT values (11.3 to 36.7; median, 21.6). Of 428 positive samples, 413 (96.5%) generated genomes with <10% unknown bases, with a mean genome coverage of 13,545× ± SD 8382×. No genomes were recovered from PCR-negative specimens (n = 30) or from specimens positive for non-SARS-CoV-2 respiratory viruses (n = 20). Compared with whole-genome shotgun metagenomic sequencing (n = 14) or Sanger sequencing for the spike gene (n = 11), pairwise identity between consensus sequences was 100% in all cases, with highly concordant allele frequencies (R2 = 0.99) between Swift and shotgun libraries. When samples from different clades were mixed at varying ratios, expected variants were detected even in 1:99 mixtures. When deployed as a clinical test, 268 tests were performed in the first 23 weeks, with a median turnaround time of 11 days, ordered primarily for outbreak investigations and infection control.


Subject(s)
COVID-19 , SARS-CoV-2 , COVID-19/genetics , Genome, Viral , Humans , RNA, Viral/genetics , SARS-CoV-2/genetics , Whole Genome Sequencing/methods
17.
Int J Mol Sci ; 23(21)2022 Oct 25.
Article in English | MEDLINE | ID: covidwho-2081940

ABSTRACT

In order to assess SARS-CoV-2 real time quantitative polymerase chain reaction (RT-qPCR) results in a real-life setting, three independent laboratories in Graz (Austria) set up a continuous cross comparison schedule. The following test systems were used: The QIAGEN NeuMoDx SARS-CoV-2 Assay, the Allplex™ 2019-nCoV Assay (Seegene) on a MicroLab Nimbus (Hamilton) platform combined with RealStar SARS-CoV-2 RT-PCR Assay (Altona Diagnostics GmbH), and the cobas SARS-CoV-2 test on a fully automated cobas 6800 system (Roche). A total of 200 samples were analysed, 184 (92%) were found to be concordant with all testing platforms, 14 (7%) discordant. Two (1%) samples tested invalid on a single platform and were excluded from further analysis. Discordant results were distributed randomly across the assays. The Ct values from all assays correlated closely with each other. All discordant samples showed Ct values ≥ 26. SARS-CoV-2 RT-qPCR assays may show considerable variability, especially in samples with low viral RNA concentrations. Decision makers should thus balance the advantages and disadvantages of RT-qPCR for mass screening and adopt suitable strategies that ensure a rational management of positive samples with high Ct values.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , SARS-CoV-2/genetics , RNA, Viral/genetics , COVID-19 Testing , COVID-19/diagnosis , Real-Time Polymerase Chain Reaction/methods , Sensitivity and Specificity
18.
Clin Lab ; 68(10)2022 Oct 01.
Article in English | MEDLINE | ID: covidwho-2080871

ABSTRACT

BACKGROUND: Diagnosis with reverse transcriptase polymerase chain reaction (RT-PCR) test is a very important step for the control of the COVID-19 pandemic. The aim of this study is to compare the RT-PCR results of the samples taken directly from the viral transport medium (VTM) without extraction with the RT-PCR results of two different extraction methods, one automated and the other manual, in the diagnosis of COVID-19. METHODS: Among the respiratory tract samples sent to Sakarya Training and Research Hospital Microbiology Laboratory for COVID-PCR study, 20 negative and 43 positive samples with different cycle threshold (CT) values were included in the study. Both manual nucleic acid isolation with the vNAT isolation kit (Bioeksen, Turkey) and automatic nucleic acid isolation with the EZ1 Virus Mini Kit v2.0 in the isolation device were performed simulta-neously from the patient samples included in the study and the results were compared. RESULTS: The mean Ct values of the samples were found to be 21.58 using manual vNAT as the extraction method, 17.63 using the automated magnetic bead method, and 21.45 in PCR from direct VTM without extraction. When the automatic magnetic beads extraction method was taken as the reference method, the sensitivity of direct PCR was 97.3%, the specificity was 95%, the positive predictive value was 97.3%, and the negative predictive value was 95%. Phi coefficients were found to be 0.927 between vNAT and direct PCR, 1 between vNAT and EZ1, and 0.922 between direct PCR and EZ1. CONCLUSIONS: Direct PCR has advantages such as eliminating RNA extraction and purification steps, providing a shorter detection time, and using less labor and less consumables without reducing the diagnostic accuracy. It is thought that this method can help as a useful process management for the control of the epidemic in countries with limited resources.


Subject(s)
COVID-19 , Nucleic Acids , COVID-19/diagnosis , COVID-19 Testing , Humans , Pandemics , RNA , RNA, Viral/analysis , Reverse Transcriptase Polymerase Chain Reaction , SARS-CoV-2/genetics , Sensitivity and Specificity
19.
Transpl Int ; 35: 10677, 2022.
Article in English | MEDLINE | ID: covidwho-2080318

ABSTRACT

Protection of adult kidney transplant recipients against SARS-CoV2 was shown to be strongly impaired owing to low reactogenicity of available vaccines. So far, data on vaccination outcomes in adolescents are scarce due to later vaccination approval for this age group. We therefore comprehensively analyzed vaccination-specific humoral-, T- and B-cell responses in kidney transplanted adolescents aged 12-18 years in comparison to healthy controls 6 weeks after standard two-dose BNT162b2 ("Comirnaty"; Pfizer/BioNTech) vaccination. Importantly, 90% (18/20) of transplanted adolescents showed IgG seroconversion with 75% (15/20) developing neutralizing titers. Still, both features were significantly diminished in magnitude compared to controls. Correspondingly, spike-specific B cells were quantitatively reduced and enriched for non-isotype-class-switched IgD+27+ memory cells in patients. Whereas spike specific CD4+ T cell frequencies were similar in both groups, cytokine production and memory differentiation were significantly impaired in transplant recipients. Although our data identify limitations in all arms of vaccine-specific immunity, the majority of our adolescent patients showed robust humoral responses despite antimetabolite-based treatment being associated with poor vaccination outcomes in adults.


Subject(s)
COVID-19 , Kidney Transplantation , Adolescent , Adult , Antibodies, Viral , BNT162 Vaccine/administration & dosage , BNT162 Vaccine/adverse effects , COVID-19/prevention & control , Humans , Immunity, Humoral , Kidney Transplantation/adverse effects , RNA, Viral , SARS-CoV-2 , Vaccination , Vaccines, Synthetic , mRNA Vaccines
20.
Front Public Health ; 10: 871010, 2022.
Article in English | MEDLINE | ID: covidwho-2080280

ABSTRACT

Background: Studies began investigating occupational exposures as a source of contamination to SARS-CoV-2, yet few considered the variation in SARS-Cov2 pandemic activity for these exposures. Several indicators were built to assess SARS-Cov2 activity though they usually serve a specific purpose and have limitations. The aim was to compare qualitatively different estimators of the SARS-CoV-2 pandemic activity and to create an estimator of pandemic activity level based on daily hospital admissions for job-exposure matrices (JEM) usage. Methods: From publicly available French databases, we retrieved all data from March 19, 2020 (first day available) to March 25, 2021 (day of data collection) on four different estimators: percentage of intensive care bed occupied, reproductive number, tests' positive rate and number positive tests. An indicator based on new daily hospital admissions was created for a COVID JEM. Due to the heterogeneity of the estimators, a qualitative comparison was carried out. Results: During the study period, three major outbreaks took place. Though the number of positive tests was the first indicator to worsen during the 2nd outbreak, it failed to identify variation during the outbreak. Though each indicators behaved differently during the study period, the indicator based on new daily hospital admissions and the positive rate seemed to be the closest to one another. Conclusion: This study highlights the heterogeneity of the indicators used during the first and second SARS-Cov2 outbreaks in France. An indicator based on new daily hospital admissions seems to be a good candidate for estimating SARS-CoV-2 epidemic activity for COVID JEMs and is easily available in countries where usual indicators are not commonly accessible.


Subject(s)
COVID-19 , Pandemics , Humans , SARS-CoV-2 , RNA, Viral , COVID-19/epidemiology , Disease Outbreaks
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