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1.
Hepatology ; 76(Supplement 1):S402, 2022.
Article in English | EMBASE | ID: covidwho-2157787

ABSTRACT

Background: Achievement of WHO goals for HCV elimination needs scaling up of diagnosis and treatment capacities in low-income and middle-income countries, where HCV is highly endemic. However, in these regions, access to HCV diagnostic tools is severely limited. The current diagnostic algorithm is based on using two steps;rapid diagnostic test (RDTs) and viral load confirmation. So there is a need for simple point of care (POC) test that can be done in the field. Recently, we developed a novel technology for extraction and enrichment of HCV antigen using temperature-sensitive Smart Polymer, which used previously For enabling affinity enrichment of current coronavirus (SARS-CoV- 2) to improve its diagnostic sensitivity Our aim is to design a novel method for extraction and enrichment of HCV antigen using temperature-responsive smart polymer 'NIPAAm-co- HIPAAm- co- SAKIPAAm' (Patent: 2019/2002) for enabling affinity enrichment of HCV antigen to be used as a part of POC test to improve the cascade of care Methods: We used temperature-responsive smart polymer 'NIPAAm-co- HIPAAm- co- SAKIPAAm' (Patent: 2019/2002) for extraction and enrichment HCV antigen for 15 positive HCV serum samples and 5 negative HCV serum samples confirmed by PCR technique. After extraction and enrichment of HCV antigen by temperature-responsive smart polymer 'NIPAAm-co- HIPAAm- co- SAKIPAAm' samples undergo amplification and detection by thermal cycler as amplification and detection of Rt-PCR technique (SLAN-96P Real-Time PCR System ). Result(s): . The time needed for extraction and enrichment of HCV Antigen using temperature-sensitive smart polymer (10mins) which is shorter than extraction time in RT-PCR ( One hour). The results showed that HCV antigen extracted and enriched by temperature-responsive smart polymer gave the same results with positive and negative HCV samples detected by PCR, Sensitivity 100%, Specificity 100% Conclusion(s): The novel temperature-responsive smart polymer 'NIPAAm-co- HIPAAm- co- SAKIPAAm' (Patent: 2019/2002) is able to extract and enrich HCV antigen in the same sensitivity and specificity like the current PCR. The time needed for this simple technique may make it be suitable to be a part of POC test for rapid, affordable, easy-to- use test in comparison to PCR technique which needs dedicated facilities and highly qualified personnel.

2.
Journal of Pharmaceutical Negative Results ; 13:733-740, 2022.
Article in English | EMBASE | ID: covidwho-2156348

ABSTRACT

Background: Severe Acute Respiratory Syndrome Coronavirus-type 2 (SARS-CoV-2) was identified as the RNA virus causing 'Coronavirus Disease 2019' (COVID -19). Diagnostic test of choice had varying degree of sensitivity, with serology test being of use in giving idea on the timing of the infection. This pandemic associated with delay in providing care to many surgical emergencies, with more complicated presentations found. Aim of study: To estimate the effect of current and previous COVID 19 infections on the diagnosis and rate of complications of acute appendicitis. Patients & methods: A prospective case control study was conducted at Al-Kindy teaching hospital department of general surgery over 18 months The studied sample were collected from all admitted patients suffering from signs of acute appendicitis and had positive serology test result for COVID 19. Other 100 cases of appendicitis without COVID 19 symptoms and negative serology and polymerase chain reaction considered control group. According to the serology results the case group further divided into previous infection and current infection. Result(s): Two hundred fifteen cases were included in our study 19.1% had current infection, 34.4% had previous infection, 46.5% the control group. Cases of COVID 19 had increased duration of symptoms before seeking medical care. This duration was single independent predictor of the development of perforated appendicitis. While readmission rate was higher in cases of COVID 19 and this related to the complications of appendicitis other than COVID 19 infection. COVID 19 infection was single independent predictor of increased hospital stay. Conclusion(s): COVID 19 infection per se not associated with increase in complication rate. It was associated with delayed in seeking medical care. Copyright © 2022 Wolters Kluwer Medknow Publications. All rights reserved.

3.
International Journal of Pharmaceutical Sciences and Research ; 13(12):5050-5056, 2022.
Article in English | EMBASE | ID: covidwho-2155832

ABSTRACT

Background: Severe Acute Respiratory Syndrome Corona Virus Disease 2019 (COVID-19) is responsible for the COVID-19 pandemic causing respiratory illness worldwide. Hence there is an urgent need for simple, rapid, and accurate tests for diagnosis. Performance characteristic of Rapid Antigen detection test for identifying sensitivity and specificity with gold standard Real-Time Polymerase Chain Reaction and correlate the significance of non-specific parameters like CRP(C- Reactive Protein), IL-6(Interleukin-6), Procalcitonin for diagnosis of COVID-19. Method(s): The Rapid Antigen Detection test was compared with Real-Time Polymerase Chain Reaction to detect SARS CoV-2 in respiratory specimens. 100 respiratory samples (mainly nasopharyngeal and throat swab) and for CRP, IL6, and Procalcitonin serum samples were obtained from COVID-19 suspected cases, mostly in-patients at Saveetha Medical College from April 2021- to September 2021. Result(s): Out of 100 samples, 67% were positive, 33% were negative for SARS-CoV2 RNA by RT-PCR assay. When compared with Rapid Antigen Test, the RT-PCR test showed 83.8% sensitivity and 59.3% specificity, while non-specific parameters correlation in diagnosis of COVID-19 showed CRP insignificant, IL-6 and Procalcitonin significant. Conclusion(s): RT-PCR is considered the standard gold method for diagnosing COVID-19. On comparing RT-PCR with other non-specific tests like CRP, Procalcitonin, IL-6 showed Procalcitonin and IL-6 can be considered non-specific tests for diagnosing COVID-19. Copyright © 2022 are reserved by International Journal of Pharmaceutical Sciences and Research. This Journal licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License.

4.
Medical Journal of Malaysia ; 77(Supplement 4):25, 2022.
Article in English | EMBASE | ID: covidwho-2147652

ABSTRACT

SARS-CoV-2, cause of the COVID-19 pandemic, is a RNA virus with genome size of 29.9 kbases. The importance of genome sequences of SARS-CoV-2 is clear in epidemiological surveillance, tracking of variants, development of therapies and diagnostics, pathogenesis studies, and others. This has driven global expansion of sequencing facilities and sharing of sequences, such that over 11.5 million sequences were available, as of June 2022. Our research laboratory started whole genome sequencing (WGS) of SARS-CoV-2 in April 2020, and have since completed and shared over 800 sequences using Illumina and Nanopore technologies. In this talk, I will share how we used the generated SARS-CoV-2 sequences in conjunction with a clinical diagnostic microbiology service in our associated teaching hospital: (1) to contribute to surveillance of SARS-CoV-2 linages both nationally and within our hospital;(2) to investigate clusters within our hospital, and how this impacted clinical protocols;(3) to determine suspected individual cases of reinfection or persistent infection;and (4) to evaluate reduced performance in a commercial diagnostic PCR assay, leading to modified primers and probes. WGS has become increasingly accessible and affordable, with numerous publicly available databases, protocols, training and bioinformatics tools, to help overcome technical and analytical challenges. Sequencing data has a variety of clinical and epidemiological uses.

5.
Rivista Italiana della Medicina di Laboratorio ; 18(2):102-107, 2022.
Article in Italian | EMBASE | ID: covidwho-2146107

ABSTRACT

Background: Detection and surveillance of SARS-CoV-2 is of eminent importance, particularly due to the rapid emergence of variants of concern (VOCs). Since September 2020, the TaqPath COVID-19 assay (Thermo Fisher Scientific, Waltham, MA, USA) has been used to identify viral strains of the new lineage B.1.1.7, since it previously failed to detect the S-gene 69/70 deletion. Rapid detection of these variants of concern can help to contain them and prevent widely spreading throughout the population. This study evaluated S-gene mutations screening with a commercially available qualitative real-time PCR (RT-PCR) assay to detect likely variant of SARS-CoV-2 by the S gene amplification curve non-sigmoidal fluorescence profile. Method(s): The viral RNA of the samples was extracted using the Seegene STARlet automated system combined with StarMag 96x4 Viral DNA/RNA 200C. All samples were subjected to Real Time RT-PCR with the AllplexTM SARS-CoV-2 Assay kit (Seegene Inc, Seul, South Korea) for the qualitative detection of four target genes: E, N, RdRp, and S genes. PCR has been performed by a CFX-96 real-time thermocycler (Bio-Rad Laboratories Inc, Hercules, CA, USA) and Ct values were acquired from the fluorescence channels by the fluorophores FAM (E gene), Quasar 670 (N gene), Cal Red 610 (RdRp and S genes), and HEX (internal control). Gene target amplification curve analysis was performed using Seegene Viewer ver 3.24 (Seegene). The samples tested positive for SARS-CoV-2 viral genome, which presented abnormalities in the fluorescence profile of the amplification curve of the RdRP/S genes, were further subjected to the amplification protocol by the GSD NovaTYpe SARS-CoV-2 amplification kit (Nova Tec Immunodiagnostica, Dietzenbach, Hessen, Germany), and to definitively confirm the presence of the English variant (lineage B.1.1.7), subsequently subjected to Next Generation Sequencing (NGS). Result(s): Thirty respiratory samples subjected to amplification using the AllplexTM SARS-CoV-2 Assay in early January 2021, showed a reduction in amplification efficiency on the fluorescence profile of RdRP/S genes with slope and inflection point variations. The profile of the SARS-CoV-2 English variant (lineage B.1.1.7) for the 30 samples, was performed first by qualitative test in RT-PCR, GSD Nova TYpe SARS-CoV-2, and subsequently confirmed by NGS technology (analysis performed in an external laboratory). Both analytical methodologies identified all 30 samples with the B.1.1.7. lineage of SARS-CoV-2. This last diagnostic proof pushed our working group to evaluate the presence and degree of spread of the English variant in the area of the Napoli 3 Sud ASL, testing the viral genome of 900 samples to RT-PCR using the Allplex TM SARS-Cov-2 kit, alterations in the fluorescence profile of the amplification curves related to the S gene were observed and confirmed using the GSD NovaTYpe SARS-CoV-2 kit. Conclusion(s): Since late 2020, several variants of SARS-CoV-2 have emerged around the world. The gold standard molecular method to detect a specific variant consists in the total or partial sequencing of the virus genome, but today the latter remains expensive and time-consuming, limiting its implementation in all diagnostic samples. PCR-based screening approaches are relatively cheaper, and results can be verified in a few hours. The indirect approach in RT-PCR, on SARS-Cov-2 diagnostic tests of positive samples, of the non-sigmoidal fluorescence profile of the S gene using AllplexTM SARS-CoV-2 PCR assay allows a quick and cheaper prediction of the lineage B.1.1.7. Therefore, using Allplex SARS-COV 2 can be used as an early and first-line screening, before eventually using the sequencing of the viral genome. Copyright © 2022 EDIZIONI MINERVA MEDICA.

6.
Open Access Macedonian Journal of Medical Sciences ; Part A. 10:1505-1511, 2022.
Article in English | EMBASE | ID: covidwho-2143915

ABSTRACT

BACKGROUND: Detection of positive 2019-nCoV nucleic acids by real-time reverse transcriptase-polymerase chain reaction (rRT-PCR)-based assays performed on the upper and lower respiratory samples remains the gold standard for the diagnosis of COVID-19. However, antigen-detecting rapid diagnostic tests can offer a faster (15-30 min) and less expensive way to diagnose active severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection than nucleic acid amplification tests. AIM: Hence, the present study aimed to compare and evaluate the results of different SARS-CoV-2 rapid point-of-care antigen tests with SARS-CoV-2 PCR as a reference method. METHOD(S): Sixty-five nasopharyngeal swab specimens were collected from attendees of the Reference Laboratory of Egyptian university hospitals. The samples were placed in viral transport medium for RNA extraction. The remaining part of the suspension was stored at -70degreeC until use for COVID-19 antigen testing. All samples were processed for the COVID-19 Ag rapid test and RT-PCR simultaneously. RESULT(S): RT-PCR assay revealed 46 (70.8%) positive samples and 19 (29.2%) negative samples for COVID-19. All eight rapid antigen assays indicated specificity and positive predictive value of 100% each. As for the other parameters, the sensitivity, negative predictive value (NPV), and accuracy ranged from 43.8 to 93.8, 33.3 to 90, and 60 to 96, respectively. Biozak exhibited the best performance with the highest sensitivities 91.3, 81.8, and 93.75, respectively, while Viro and Standard Q were the worst among the tested kits with sensitivity, NPV, and accuracy of 50, 33.3, and 60 each. Regarding the relationship between the viral load of COVID-19 detected by RT-PCR and the results of the eight rapid antigen tests (RAT), we deduced that the higher the viral load, the better the sensitivity observed. CONCLUSION(S): The RATs used, in our study, exhibited heterogeneous diagnostic performance, where some of them showed very promising results in comparison to the reference RT-PCR assay. Copyright © 2022 Ghada Ismail, Dalia H. Abdelhamid, Rania Abdel Halim, Marwa Salah Mostafa, Hossam Abdelghaffar, Noha Alaa Eldin Fahim, Ahmed Elshafei, Menna Asker, Nashwa Naguib Omar.

7.
Multiple Sclerosis Journal ; 28(3 Supplement):211-212, 2022.
Article in English | EMBASE | ID: covidwho-2138892

ABSTRACT

Introduction: The 'coronavirus disease of 2019' (COVID-19) is an acute infection caused by the novel 'severe acute respiratory syndrome coronavirus-2' which has evolved into an ongoing pandemic with more than six million case fatalities to date. Evidence from large-scale observational studies has consistently shown that simply having MS does not make affected subjects more susceptible to contract COVID-19 nor to become severely ill from the infection, as compared to the general population. Risk factors are similar in both settings and include older age, male gender, cardiovascular comorbidities, African- American ethnicity, progressive disease and B-cell depleting agents. However, the reverse relationship - i.e., the impact of COVID-19 on clinical disability related to MS - remains less well described. Objective(s): To explore whether COVID-19 is associated with accelerated disability worsening in patients with MS. Method(s): Since March 2020, demographics and COVID-19 severity (categorized as ambulatory, hospitalized, death) of patients with MS have been collected at the Belgian National MS Center in Melsbroek in case of COVID-19 diagnosis (i.e., positive polymerase chain reaction test). On February 28, 2022, this database was locked and consisted of 234 unique cases. Clinical disability measures - including Expanded Disability Status Scale (EDSS), Timed 25-Foot Walk Test, 9-Hole Peg Test and Symbol Digit Modalities Test scores - were available from a larger local database, obtained during routine medical follow-up. For each of these parameters, the first two assessments before COVID-19 diagnosis (labelled T0 and T1, respectively;T1 is the closest to COVID-19 diagnosis), and the first thereafter (labelled T2), were retrieved for every COVID-19 case. Result(s): Mortality and hospitalisation rate in this cohort was 5/234 (2.1%) and 37/234 (15.8%), respectively. Among the survivors with complete EDSS data (N = 139), mean annualized EDSS score changes between T1 and T2 (i.e., including the COVID-19 infection) were significantly increased, as compared with the respective changes between T0 and T1 (i.e., not including the COVID-19 infection) (0.09 versus 0.36, p = 0.008). Similar effects were not found for the other clinical outcome measures. Conclusion(s): COVID-19 infection is associated with global disability worsening in patients with MS. Our findings highlight the importance of preventive measures against COVID-19 spreading within this population.

8.
Research and Practice in Thrombosis and Haemostasis Conference ; 6(Supplement 1), 2022.
Article in English | EMBASE | ID: covidwho-2128236

ABSTRACT

Background: Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV- 2) is associated with a prothrombotic phenotype with an increased risk for thrombosis. Aim(s): To investigate whether COVID-19 is associated with changes in coagulation parameters upon presentation at the emergency department and whether these changes are associated with the development of thrombotic complications in patients with SARS-CoV- 2 infection. Method(s): A single centre, cross-sectional cohort study: The MArkers in COVID-19 And Relations to Outcomes in the Netherlands (MACARON) study was conducted. All patients suspected of SARS-CoV- 2 infection referred to the emergency department of the Meander Medical Center between March-May 2020 were included. 519 patients (26% PCR positive, median age 66 (range 19-97 years), 52.2% male) were included from whom an oro-and nasopharyngeal swab was obtained for detection of SARS-CoV- 2 by polymerase chain reaction (PCR). Blood samples for laboratory analysis were obtained from all patients. Thrombosis was defined as a clinical diagnosis of venous thromboembolism or atherothrombotic event based upon radiology and laboratory results. Result(s): SARS-CoV- 2 PCR positive patients had increased fibrinogen levels (5.41 g/L vs. 4.21 g/L, p < 0.001) and decreased levels of protein C (85.1% vs. 96.1%, p < 0.001) and alpha2-macroglobulin (4.41 muM vs. 5.11 muM, p < 0.001) compared to the PCR negative patients. In addition, we found more acquired activated protein C resistance in PCR positive patients. Furthermore, we found that elevated levels of factor VIII (208% vs. 162%, p = 0.028) and von Willebrand Factor (208% vs. 186%, p = 0.038) and decreased ADAMTS-13 levels (597 ng/ml vs. 691 ng/ml, p < 0.001) were associated with increased occurrence of thrombosis in PCR positive patients (thrombosis vs. non-thrombosis). Conclusion(s): We found that PCR positive patients had a more pronounced prothrombotic phenotype with endothelial activation upon hospital admission showing that coagulation tests may be considered useful to discriminate severe cases of COVID-19 at risk for thrombosis.

9.
Research and Practice in Thrombosis and Haemostasis Conference ; 6(Supplement 1), 2022.
Article in English | EMBASE | ID: covidwho-2128069

ABSTRACT

Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is associated with an increased risk of venous and arterial thrombosis but the underlying mechanism if still unclear. Aim(s): The study would identify a mechanism implicated in platelet activation and thrombus growth during SARS-CoV-2 infection. Method(s): We performed a cross-sectional analysis of platelet function in 30 SARS-CoV-2 and 20 healthy subjects (HS) by measuring Nox2-derived oxidative stress and thromboxane (Tx) B2 and investigated if administration of monoclonal antibodies against the Spike(S) protein of SARS-CoV-2 affects platelet activation. Furthermore, we investigated in vitro if the Spike(S) protein of SARS-CoV-2 or plasma from SARS-CoV-2 enhanced platelet activation. Result(s): Ex vivo studies showed enhanced platelet Nox2-derived oxidative stress and TxB2 biosynthesis and under laminar flow platelet-dependent thrombus growth in SARS-CoV-2 compared to controls;both effects were lowered by Nox2 and Toll-like receptor 4(TLR4) inhibitors. Two hours after administration of monoclonal antibodies a significant inhibition of platelet activation was observed in SARS-CoV-2 patients compared to untreated ones. In vitro study showed that S protein functionally interacts with platelet TLR4, and a docking simulation analysis suggested that TLR4 binds to S protein via three receptor-binding domains;furthermore, in platelets from SARS-CoV-2 S protein co-immunoprecipitated with TLR4. Plasma from SARS-CoV-2 patients incubated with normal platelets enhanced platelet activation and Nox2-related oxidative stress, an effect blunted by TNF-alpha inhibitor;this effect was recapitulated by an in vitro study documenting that TNF-alpha alone promoted platelet activation and amplified the platelet response to S protein via p47phox up-regulation. Conclusion(s): The study identifies two TLR4-dependent and independent pathways promoting platelet-dependent thrombus growth and suggests inhibition of TLR4 or p47phox as a tool to counteract thrombosis in SARS-CoV-2.

10.
United European Gastroenterology Journal ; 10(Supplement 8):206, 2022.
Article in English | EMBASE | ID: covidwho-2115145

ABSTRACT

Introduction: Gastrointestinal manifestations are common during coronavirus disease (COVID-19) infection. They can occur before respiratory symptoms, resulting in a diagnostic delay and an increased risk of disease transmission. Aims & Methods: The current study reports major gastrointestinal manifestations as initial symptoms of COVID-19. This prospective, descriptive, cross-sectional, and single-center study of 713 cases was conducted in a field hospital over a 5-week period from June 21 to July 25, 2020. Result(s): The average age of our patients was 31.95 years. Clinically, on admission, anorexia was the main symptom, present in 32.3% of patients. Gastrointestinal manifestations were present in 14.9% of patients, including watery diarrhea in 8.6% of cases, nausea and/or vomiting in 4.6% of cases, and abdominal pain in 1.6% of cases. Six hundred thirty-two patients were treated in accordance with one of the two therapeutic protocols recommended by the National Ministry of Health. The treatment-related effects that occurred in 61.4% of patients were primarily digestive in 55.3% of cases. In multivariate analysis, following adjustment of the studied parameters, only the presence of gastroin- testinal manifestations (odds ratio [OR]: 1.478 confidence interval [CI]: 1.286-1.698;p < 0.001) and treat- ment side effects (OR = 1.069, CI: 1.020-1.119, p = 0.005) altered the rate of negative polymerase chain reaction (PCR) tests on day 10. Conclusion(s): Gastrointestinal manifestations are common during COVID- 19 and seem to be linked to a longer duration of disease. SARS-CoV-2 (the causative virus of COVID-19) can persist in the digestive tract, with the possibility of fecal-oral transmission. Therefore, hygiene is extremely important, espe- cially handwashing and strict precautions when performing gastrointestinal endoscopy and handling stools from infected patients.

11.
Journal of the Pakistan Medical Association ; 72(11):2229-2232, 2022.
Article in English | EMBASE | ID: covidwho-2114060

ABSTRACT

Objective: To determine the symptoms and risk factors associated with gender-specific mortality among coronavirus disease-2019 patients. Method(s): The retrospective, descriptive, cross-sectional study was conducted at the coronavirus disease-2019 ward of the Jinnah Hospital, Lahore, Pakistan, and comprised record of confirmed cases of coronavirus disease-2019 diagnosed on the basis of characteristic clinical symptoms, radiological findings and polymerase chain reaction positivity from May 1 to August 31, 2020. Clinical symptoms, comorbidities and outcomes were extracted from the medical records. Data was analysed using SPSS 23. Result(s): Of 337 cases, 132(39.2%) died. Among the deceased, 84(64%) were males with median age 61.5 (interquartile range: 22) and 48(36%) were females with median age 54.5 (interquartile range: 25).There were more female non-survivors who suffered from kidney disease 10(66.7%) than male non-survivors 5(33.3%) (p<0.05). Ischaemic heart disease was more common among males than females (p=1.62). Conclusion(s): The mortality rate in males was higher compared to females. The symptoms and risk factors associated with mortality varied between the genders. Copyright © 2022 Pakistan Medical Association. All rights reserved.

12.
Eesti Arst ; 101(Supplement 4):43, 2022.
Article in English | EMBASE | ID: covidwho-2111974

ABSTRACT

Objectives. Due to the rapid spread of the SARS-CoV-2 Omicron variant (B. 1.1.529) in Latvia at the end of 2021 and the beginning of 2022, it has become essential to determine the rate of its epidemiological spread and the rate of its dominance over the SARS-CoV-2 Delta variant (B.1. 617.2). The aim of the study was to determine the rate of Omicron variant prevalence in Latvia and, at the same time, differentiate Omicron subtypes BA.1 (variant B.1.1.529.1) and BA.2 (variant B.1.1.529.2). METHODS. The presence of the SARS-CoV-2 virus in nasopharyngeal and oropharyngeal swab samples was determined by RNA extraction and reverse transcription polymerase chain reaction. Altogether 36,719 samples were tested for mutations E484A, N501Y and deletion 69/70del. The RNA was extracted by fully automated nucleic acid extraction device Seegene NIMBUS and using STARMag 96 X 4 Universal Cartridge Kit (Seegene Inc.) reagents. For the RT-PCR reaction, the NovaplexTM SARS-CoV-2 Variants VII Assay (Seegene Inc.) reagent kit was used. The RT-PCR test kit can determine SARS-CoV-2 Omicron variant specific mutations (E484A and N501Y) as well as deletion 69/70del, with which it is possible to determine the sample affiliation to the Omicron subtypes BA.1 (with the deletion) or BA.2 (without the deletion). RESULTS. SARS-CoV-2 Omicron variant (B.1.1.529) became a dominant SARS-CoV-2 virus variant within 10 weeks in the territory of Latvia. Its presence in the population in the 48th week of 2021 was determined as 2% and in the 5th week of 2022 hit the rate of 98%. The highest increase took place in the first and second week of 2022 with an overall increase rate of 17%. The change of SARS-CoV-2 Omicron (B.1.1.529) subvariant BA.1 to BA.2 was found to happen within 6 weeks. The spread of the BA.2 subtype in the population in the 52nd week of 2021 was at the rate of 12%, however, in the 5th week of 2022, it hit almost 100%. The BA.2 subtype became a dominant subvariant in the 2nd week of 2022. CONCLUSIONS. The SARS-CoV-2 Omicron variant (B.1.1.529) became a dominant variant of the virus in the population of Latvia at the end of 2021 and the beginning of 2022. The rapid spread of the Omicron variant can be associated with its high infectivity.

13.
Eesti Arst ; 101(Supplement 4):42, 2022.
Article in English | EMBASE | ID: covidwho-2111967

ABSTRACT

Objectives. The main goal of the study was to develop laboratory-developed tests (LDT) for monitoring SARS-CoV-2 variants of concern (VOC) currently present in Latvia. METHODS. We have studied the latest scientific articles to prognose specific mutations that could be indicators of VOC. Mutations responsible for immune escape were chosen as targets for our LDTs. Multiple TaqMan RT-PCR LDTs detecting alfa, beta, gamma, delta and omicron strains in nasopharyngeal swab and saliva samples were developed and validated in our laboratory. RESULTS. More than 15,000 SARS-CoV-2 positive samples were tested. In total, 10,874 different VOCs of SARS-CoV-2 were found by our LDTs. Beta, delta and omicron strains were first detected in Latvia by E. Gulbis Laboratory. Sanger sequencing methods for RT-PCR result confirmation were also developed. The first cases of VOCs detected by the RT-PCR method were also confirmed in our laboratory by Sanger sequencing. Our results were later confirmed by the National Reference Laboratory. CONCLUSIONS. Using our laboratory capacity and intellectual potential, we have developed skills for an urgent response to future VOCs of SARS-CoV-2 or other potentially harmful infectious diseases.

14.
Oto-Rhino-Laryngology Tokyo ; 64(3):145-149, 2021.
Article in Japanese | EMBASE | ID: covidwho-2067222

ABSTRACT

Reverse -transcription polymerase chain reaction (RT-PCR)testing is necessary for the definitive diagnosis of coronavirus disease 2019(COVID-19), and is most often performed on pharyngeal swabs. However, it has become clear that even if the RT-PCR is negative, COVID-19 cannot be ruled out altogether. We encountered a patient who developed COVID-19 after a tracheostomy. He developed fever and respiratory failure and was suspected as having developed COVID-19, but RT-PCR conducted on upper airway specimens was negative twice in succession;a third RT-PCR test conducted on a sputum specimen later confirmed a positive result for severe acute respiratory syndrome coronavirus 2(SARS-CoV-2). In cases with clinically suspected infection with SARS-CoV-2, RT-PCR should be repeated, and lower respiratory tract specimens should be used from the beginning if the infection occurs before or after tracheostomy. Copyright © 2021 Society of Oto-Rhino-Laryngology Tokyo. All rights reserved.

15.
Indian Journal of Critical Care Medicine ; 26(10):1091-1098, 2022.
Article in English | EMBASE | ID: covidwho-2066996

ABSTRACT

Background: It is known that coronavirus disease-2019 (COVID-19) pneumonia causes cytokine storm, and treatment modalities are being developed on inhibition of proinflammatory cytokines. We aimed to investigate the effects of anticytokine therapy on clinical improvement and the differences between anticytokine treatments. Method(s): A total of 90 patients with positive COVID-19 polymerase chain reaction (PCR) test were divided into three groups, group I (n = 30) was given anakinra, group II (n = 30) was given tocilizumab, and group III (n = 30) was given standard treatment. Group I was treated with anakinra for 10 days;tocilizumab, intravenously, was given in group II. Group III patients were selected from those who did not receive any anticytokine treatment other than the standard treatment. Laboratory values, Glasgow coma scale (GCS), and PaO2/FiO2 values were analyzed on days 1, 7, and 14. Result(s): The seventh-day mortality rates were 6.7% in group II, 23.3% in group I, and 16.7% in group III. In group II, the ferritin levels on the 7th and 14th days were significantly lower (p = 0.004), and the lymphocyte levels on the seventh day were significantly higher (p = 0.018). Examining the changes between the first intubation days, in the early period (seventh day), group I was found to be 21.7%, group II was 26.9%, and group III was 47.6%. Conclusion(s): We observed the positive effects of the use of tocilizumab on clinical improvement in the early period;mechanical ventilation requirement was delayed and at a lower rate. Anakinra treatment did not change mortality and PaO2/FiO2 rates. Mechanical ventilation requirements occurred earlier in the patients who were not receiving any anticytokine therapy. Studies with larger patient populations are needed to demonstrate the potential efficacy of anticytokine therapy. Copyright © The Author(s).

16.
Mediterranean Journal of Infection, Microbes and Antimicrobials ; 11(1) (no pagination), 2022.
Article in English | EMBASE | ID: covidwho-2066934

ABSTRACT

Introduction: Severe acute respiratory syndrome-Coronavirus-2 (SARS-CoV-2) antibodies are produced in persons who have been infected by the virus or have received the vaccine. Many features of these antibodies, including their dynamics and neutralization capacities, are still unclear. Understanding the immune response of the host is very important for the development of appropriate treatment methods, vaccines, and epidemiological control strategies. The present study aimed to monitor the change in antibody levels over time in individuals diagnosed with SARSCoV- 2 infections and to determine their neutralization capacity. Material(s) and Method(s): Anti-nucleocapsid and anti-spike antibody titers were measured using different kits on monthly obtained serum samples of patients of patients with SARS-CoV-2 infection. The neutralizing antibodies were evaluated using a microneutralization assay. Result(s): A total of 134 serum samples taken from 43 patients with a mild-moderate disease course were analyzed. Anti-spike antibody positivity was detected on day seven at the earliest and day 334 at the latest following a positive polymerase chain reaction (PCR) test. The mean antibody levels were observed to increase gradually to a peak after three months, and then started to decrease after month six. Anti-nucleocapsid IgM and IgG antibodies were detected alone or in combination. The highest neutralizing antibody titer was 1/80 in the first month, which was seen to drop below 1/10 after four months. Conclusion(s): The combined use of kits for the detection of antibodies against different antigens or testing total antibodies would result in a more accurate and earlier detection of the antibodies that start to emerge on the seventh day and decrease six months after SARS-CoV-2 PCR positivity. In addition, the dramatic decrease in neutralizing antibody titers after four months may be one of the causes of early reinfections. Copyright © 2022 by the Infectious Diseases and Clinical Microbiology Specialty Society of Turkey.

17.
American Journal of Transplantation ; 22(Supplement 3):1059, 2022.
Article in English | EMBASE | ID: covidwho-2063485

ABSTRACT

Purpose: The purpose of this study was to evaluate long term humoral and cellular immunity generated following SARS-CoV-2 infection in solid organ transplant recipients (SOTR). Method(s): Patients included had an active graft of an organ transplant as an adult, a positive polymerase chain reaction nasopharyngeal swab for SARS-CoV-2 after transplant, and had not received convalescent plasma, vaccination, or monoclonal antibody for SARS-CoV-2. Whole blood was obtained 6 months (+/- 1 month) after infection. Serology measured IgG and IgM titer to the SARS-CoV-2 spike protein receptor binding domain, reported as signal/ cut-off ratio (s/co). CD4+ and CD8+ T-cell reactivity was measured by Activation Induced Marker assays following stimulation of peripheral blood mononuclear cells with SARS-CoV-2 peptide pools encompassing the SARS-CoV-2 spike protein. Result(s): Of 25 subjects, 19 (76.0%) were hospitalized, 4 (16.0%) developed hypoxia, but none required mechanical ventilation. Biopsy-proven graft rejection occurred in 3 (12.0%), but none had graft loss. At 6 months, 8 (16%) had persistent symptoms and 2 (4.0%) were re-infected within one year. In the immunity study, 22 (88.0%) had reactive IgG testing and 11 (44.0%) had reactive IgM testing. Median IgG titer was 3.68 s/co (range 0.19-36.44) and IgM titer was 0.79 s/co (range 0.02-16.41). Virus-specific CD4+ T-cell reactivity was noted in 23 (92%), but only 10 (40.0%) had reactive CD8+ T-cell testing. Moderate correlation was observed between IgG and IgM titer (r=.51, p= 0.009) and between IgG titer and percent virus-specific CD4+ T-cells (r=.46, p=0.02). CD8+ T-cell reactivity was correlated with greater illness severity (p=0.043). Use of Tacrolimus, mycophenolate, or corticosteroids at time of infection was not associated with T-cell or antibody reactivity. Conclusion(s): In summary, this cohort of SOTR evaluated six months after noncritical COVID-19 illness demonstrated robust IgG and CD4+ T-cell responses, and CD8+ T-cell reactivity was correlated with higher disease severity.

18.
American Journal of Transplantation ; 22(Supplement 3):1066, 2022.
Article in English | EMBASE | ID: covidwho-2063484

ABSTRACT

Purpose: The purpose of this study was to study our cohort of adult solid organ transplant recipients who had been infected with SARS-CoV-2 to describe the incidence density of SARS-CoV-2 re-infection, as well as the clinical features and convalescent immunity profile. Method(s): Incidence density was calculated as the total cases of re-infection divided by total days after initial diagnosis with active graft. We included those with initial infection diagnosed by polymerase chain reaction before or after transplantation, and cycle threshold values were obtained when possible. Two recipients had immunity evaluated in the weeks prior to re-infection, by measuring IgG antibody titer to the SARS-CoV-2 receptor binding domain and virus-specific CD4+ and CD8+ T-cell reactivity following stimulation with SARS-CoV-2 peptide pools and using activation induced marker assays. Result(s): Out of 210 infected recipients, 5 (2.4%) developed re-infection, including two that had received full mRNA vaccination, but none developed hypoxia. The incidence density was 9.4 (95% confidence interval 3.9-22.6) cases/100,000 patient days. Two cases of re-infection had participated in our immunity study and had convalescent immunity data from a blood draw approximately six months after initial infection and prior to re-infection. Both mounted virus specific CD4 T cell responses prior to re-infection (1.19% and 0.28% of total CD4 T cells) and both had reactive IgG testing (1.30 and 4.99 signal/cut off ratio). Conclusion(s): This suggests that SOT recipients infected with SARS-CoV-2 remain at high risk for re-infection even after generating reactive cellular and humoral immune responses.

19.
American Journal of Transplantation ; 22(Supplement 3):645-646, 2022.
Article in English | EMBASE | ID: covidwho-2063439

ABSTRACT

Purpose: Kidney transplant recipients (KTRs) are at higher risk for severe COVID- 19 caused by the severe acute respiratory syndrome coronavirus-2 (SARS646 All Infections (Excluding Kidney & Viral Hepatitis) I CoV-2). Sotrovimab decreases the risk of disease progression in the general population, but efficacy and safety in KTRs is unknown. Herein, we describe our experience in treating COVID-19 infected KTRs with sotrovimab. Method(s): We performed a retrospective, single-center cohort study of KTRs diagnosed with COVID-19 by polymerase chain reaction from 07/15/21-11/30/21. KTRs with COVID-19 were admitted to the hospital to expedite evaluation and treatment. KTRs with COVID-19 were eligible for sotrovimab if they 1) were not requiring oxygen at admission, 2) were unvaccinated or if SARS-CoV-2 spike antibody (SAb) after vaccination was <100 U/mL, and 3) duration of symptoms/day of illness (DOI) was <=7 days. COVID-19 disease requiring oxygen therapy was treated with remdesevir + dexamethasone. Immunomodulator therapy (baricitinib or tocilizimab) was given for rapidly progressive disease requiring high-flow oxygen or ICU care. Baseline characteristics, treatments, and outcomes including oxygen supplementation, ICU admission, and mortality were manually ed and evaluated. Result(s): In all, 36 KTRs were diagnosed with COVID-19 - mean age 59 years, 72% male, 67% Chinese, 64% diabetic and 17% obese;72% were deceased donor and 28% were living donor KTRs presenting a mean 11 years from transplant. The majority (69%) were vaccinated with >=2 doses of mRNA-based SARS-CoV-2 vaccines, 22% received 3 doses, and 15% were unvaccinated. Among KTRs who received >=2 doses, SAb was reactive in 36% and >100 U/mL in 16%. In all, 14 (39%) required oxygen, 11 (31%) required ICU admission, 5 (14%) were mechanically ventilated, and 4 (11%) died (Table). Sotrovimab was given to 27 eligible KTRs at median DOI 2 (range 0-6). Of these, 8 (30%) required oxygen, 5 (19%) required ICU admission, 2 (7%) were mechanically ventilated, and 1 died (4%). KTRs receiving sotrovimab at DOI <=3 vs >3 were less likely to require oxygen (p=0.01) or ICU admission (p=0.02). Sotrovimab was well tolerated with one associated adverse event (self-limiting diarrhea). Conclusion(s): KTRs remain at high risk for severe COVID-19. Sotrovimab administered early in the disease course is associated with a lower rate of severe COVID-19. Outcomes of KTRs with COVID-19 overall and among those receiving sotrovimab by day of illness (Figure Presented).

20.
American Journal of Transplantation ; 22(Supplement 3):441, 2022.
Article in English | EMBASE | ID: covidwho-2063357

ABSTRACT

Purpose: Rapid evolution of the SARS-CoV-2 pandemic over the past 24 months has demanded agility in managing selection criteria for deceased organ donors, with the goal of saving every possible life while avoiding disease transmission to recipients. At 1 large organ procurement organization (OPO), the detection of any SARS-CoV-2 in a naso-pharyngeal (NP) specimen by polymerase chain reaction (PCR) was initially an absolute contraindication to organ donation. That approach gradually became more refined utilizing clinical evidence along with detection of low levels of viremia. Method(s): A retrospective analysis of all patients with authorization for organ donation after brain death or circulatory death from 3/16/2020 - 11/9/2021 was undertaken. Patients with any positive result for a COVID-19 test were identified. Donors with any positive result of an NP +/- broncho-alveolar fluid (BAL) PCR were selected for this analysis. Organ allocation was accompanied by the expectation of written confirmation that the recipient had provided informed consent for use of an organ from a SARS-CoV-2 donor. Result(s): A total of 18 deceased donors from whom 49 organs were transplanted, were identified. Multiple test results were often available for a single patient. Results were mixed in all 18 donors. At least one of the positive NP PCR test results included a cycle threshold in 16/18 patients and ranged from 31.4 to 42.5. In 2 donors a BAL PCR was also positive;1 heart was donated from one of these donors. With a follow-up of > 53 days for all transplants, no known transmission of SARS-CoV-2 to recipients or transplant teams has been reported. Conclusion(s): Available laboratory testing for SARS-CoV-2 and deepening understanding of COVID-19, increasing treatment options, and evolution of infection prevention practices have facilitated a growing confidence in safely transplanting non-lung organs from donors with a positive SARS-CoV-2 test. (Figure Presented).

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