Real-time Polymerase Chain Reaction Test Research Articles

Investigation of human anthrax outbreak in Koraput district of Odisha, India

BackgroundAnthrax is a zoonotic infection resulting from the bacteria Bacillus anthracis. Humans contract cutaneous anthrax by coming into contact, and gastrointestinal (GI) anthrax by consumption of infected animals or animal products. An outbreak investigation was conducted to confirm the occurrence of the anthrax outbreak, comprehend its extent, understand the epidemiological characteristics, identify the outbreak's cause, and propose control measures. MethodsA descriptive epidemiology was carried out for this outbreak investigation. We defined a suspected human cutaneous anthrax case as appearance of skin lesions and symptoms (itching/redness/swelling) and a suspected case of GI anthrax as appearance of diarrhoea/abdominal pain/vomiting in a resident of Koraput district after being associated with slaughtering and/or consumption of carcass during 5th April to 15th May 2023. The etiological hypothesis was formulated using descriptive epidemiological methods. Laboratory confirmation was performed by real-time polymerase chain reaction (RT-PCR). Statistical analyses were conducted using SPSS 25. ResultsA total of 47 clinically suspected anthrax cases were identified during the outbreak in five villages of Koraput district in Odisha. The epidemic curve indicated multiple point-source exposures starting from 13th April 2023. About 10 cases were identified by RT-PCR testing as confirmed cases of anthrax. No death was recorded in this outbreak investigation. ConclusionsBased on a thorough examination of epidemiological survey results and laboratory findings, we conclude that the outbreak was of human cutaneous and GI anthrax. Exposures from handling dead animals were associated with cutaneous anthrax, whereas eating uncooked meat of dead sheep was associated with gastrointestinal anthrax.

Setting up a specialized maternity unit in a tertiary hospital: An oasis for pregnant women with COVID-19 during the pandemic

ObjectiveThe COVID-19 pandemic has had an enormous impact on society and the medical environment in Taiwan in 2022. As pregnant women with COVID-19 are at higher risk for multiple complications, Taiwan needs a COVID-19 specialized maternity unit to improve the quality of maternal and neonatal care. Materials and methodsWe share our experience with specialized maternity unit for pregnant women with COVID-19 at the National Cheng Kung University Hospital, where we can have careful evaluation, safe birth, and comprehensive postpartum care. ResultsOur COVID-19 specialized maternity unit enrolled 253 pregnant women with COVID-19, 90 (35.6%) pregnant women were admitted to the specialized maternity unit, and 71 (28.1%) pregnant women gave birth during hospitalization in two months. All pregnant women recovery well and real-time polymerase chain reaction tests on all infants were negative for COVID-19. ConclusionA specialized maternity unit can provide pregnant women with a safe birth environment, immediate maternity care, and high medical quality. It can also help health workers in non-specialized maternity units deal with COVID-19-related psychological stress. Therefore, setting up one specialized maternity unit in the city during the pandemic should be guardedly considered.

Retrospective analysis of respiratory virus infections in adults with hematologic malignancies.

The study aimed to evaluate respiratory virus infections in adult patients with hematological malignancies (HM). The medical records of patients who were followed up by the hematology clinic at Başakşehir Çam and Sakura City Hospital between March 2021 and March 2023 with a diagnosis of HM and who underwent real-time polymerase chain reaction (RT-PCR) testing for nasopharyngeal/oropharyngeal specimens taken with suspected respiratory tract infection constituted the study data. Infections were symptomatic in 64.56% of patients, and the most common symptoms were fever (48.10%) and cough (18.99%). The mortality rate was 25.32% over a two-year period. When the samples were examined, positive test frequency was 43.04%, and the three most common pathogens were Influenza A (10.13%), SARS-CoV-2 (8.86%), and rhinovirus/enterovirus (7.59%). The frequency of positive tests from HMs was highest in patients with AML (p=0.042). Respiratory PCR kit positivity was higher in patients who had any symptoms (p=0.002) and cough (p=0.003). Test positivity was higher in patients with any pathological radiological finding (p=0.039) and ground glass appearance (p=0.010). The risk of death was found to be 5.848 times higher in patients with dyspnea compared to those without (OR: 5.848, 95% CI: 1.143-29.915, p=0.034). Respiratory tract virus panel PCR test positivity is more common in patients with HM presenting with respiratory tract infection symptoms in the presence of AML diagnosis, symptomatic infection, cough, radiological findings, and ground glass appearance. Mortality risk is high in HM patients with respiratory tract virus infection who have shortness of breath.

IL-6 serum level, ARDS, and AKI as risk factors for the COVID-19 infection's mortality in children.

Dysregulated immune responses are developed in Coronavirus disease-2019 (COVID-19) and Interleukin-6 (IL-6) levels are reflecting the severity of the clinical presentation. This study aimed to analyze IL-6 serum level, Acute Respiratory Distress Syndrome (ARDS), and Acute Kidney Injury (AKI) as risk factors for mortality in children with COVID-19. This prospective cohort study was conducted on children with COVID-19 infection confirmed by Real Time Polymerase Chain Reaction (RT-PCR) who were admitted to infection center at Dr. Wahidin Sudirohusodo Hospital from September 2021 to September 2022. Subjects were selected using the consecutive sampling method. A total of 2,060 COVID-19 RT-PCR tests were performed, and 1,065 children were confirmed positive. There were 291 cases that met the inclusion criteria, with 28.52 percent non-survives and 71.48% survives. The risk factors for mortality were IL-6, ARDS, AKI, Prothrombin Time / Activated Partial Thromboplastin Time (PT/aPTT), oxygen saturation, Absolut lymphocyte count (ALC), leukocytes, Length of Stay (LOS), and nutritional status (p<0.05). IL-6 levels increased in all patients (23.48-252.58 pq/ml). COVID-19 patients with AKI, ARDS, low oxygen saturation and thrombocytopenia had the highest levels of IL-6 (p 0.05). The IL-6 cut-off point was >80.97 pg/ml with 93% sensitivity and 90% specificity. Area Under Curve was 0.981 (95% CI), 0.960-1.000). A multivariate analysis showed IL-6 levels with OR 18.570 (95% CI 5.320-64.803), ARDS with Odds Ratio (OR) 10.177, (95% Confidence Interval (CI) 1.310-9.040), and AKI with OR 3.220 (95% CI 1.070-10.362). A combination of increased IL-6, ARDS, and AKI can predict a mortality probability as high as 98.3%. IL-6, ARDS, and AKI are risk factors for mortality in children with COVID-19. IL-6 level was the highest mortality risk factor.

A Population-Based Test-Negative Matched Case-Control Analysis of SARS-CoV-2 Vaccine Effectiveness Among Pregnant People in Ontario, Canada

ObjectivePregnancy is a risk factor for severe SARS-CoV-2 infection, which can result in adverse pregnancy outcomes, thus making understanding vaccine effectiveness (VE) in this population important. This study aimed to assess the VE of mRNA COVID-19 vaccines against symptomatic SARS-CoV-2 infection and COVID-19-related hospitalization in pregnant people. MethodsPopulation-based matched test-negative case-control study of pregnant people aged 18–49 years, of 12 or more weeks gestation in Ontario, Canada, symptomatic with possible SARS-CoV-2 infection, and having at least 1 positive (n = 1842) or negative (n = 8524) real-time polymerase chain reaction (RT-PCR) SARS-CoV-2 test between December 14, 2020, and December 31, 2021. The exposure was receipt of ≥1 dose of mRNA COVID-19 vaccine versus no vaccination. Exposure was further stratified by number and recency of doses. The primary outcome was a positive SARS-CoV-2 RT-PCR test. As a secondary outcome, VE for COVID-19-related hospitalization was assessed. ResultsIn the primary outcome analysis, there were 1821 positive cases, matched to 1821 negative controls. The mean (SD) maternal age was 31 (5) years. When compared to those unvaccinated, receipt of ≥1 dose was associated with an estimated VE of 39% (95% CI 29%–48%) for symptomatic infection, and 85% (95% CI 72%–92%) for COVID-19 hospitalization. VE estimates demonstrated waning with increased time since last vaccination. ConclusionsmRNA COVID-19 vaccines provide protection against symptomatic COVID-19 illness and are highly effective at preventing severe illness in pregnant people. The observed effect of vaccine waning highlights the importance of booster doses to provide optimal protection for pregnant people.

Bacterial Co-Infection in Patients with Coronavirus: A Rapid Review to Support COVID-19 Antimicrobial Prescription

The goal of this study was to determine the most common microorganisms present in COVID-19 patients with co-infections at the General Hospital of Mexicali. Bacterial co-infections have been reported in two previous global pandemics caused by viruses. In a retrospective observational study, we obtained information from 1979 patients. All had symptoms of respiratory disease, and we performed real-time Polymerase Chain Reaction tests on nasopharyngeal swab samples. Of the 1979 patients, 316 were negative; so, they were excluded. One thousand and sixty-three patients had positive results for COVID-19; one hundred and seventy-two (10.34%) had respiratory co-infections. These data were corroborated by positive growth results in culture media and identified using the MALDI-TOF MS System. Vitek 2® Compact, an automated identification system, determined the antimicrobial susceptibility testing results. We analyzed and determined the microorganisms in co-infected patients. Different microorganisms were found, including bacteria and fungi. The most prevalent of all the organisms was Acinetobacter baumannii, which was present in 64 patients (37.2%). We recommend improving the diagnostic and surveillance protocols for possible cases of co-infections in patients with COVID-19. Unlike co-infections in pandemic influenza, the spectrum of microorganisms that cause COVID-19 is too broad and varied to recommend empiric antibiotic therapy.

Investigation of Variants In SARS-CoV-2 Infections after Three Doses of COVID-19 Vaccine

Abstract&#x0D; Objective: Our study focused on retrospectively assessing variant of concern, specified by the World Health Organization (WHO), with one-step reverse transcription and real-time polymerase chain reaction (RT-PCR) test in SARS-CoV-2 positive patients after three doses of attenuated COVID-19 vaccine.&#x0D; Methods: 8.520 samples transported with viral nucleic acid buffer (vNAT) tubes between June 2021 and January 31, 2022, were tested and included in the study. All the patients whose samples were included in our research had 3 doses of CoronaVac (Sinovac Life Science Co, Ltd, Beijing, China). Gender distribution was 4686 (55%) female and 3834 ( 45%) males. Variant specific genome regions only found in B.1.351, P.1 and B.1.1.7 as well as ORF1ab and N gene regions are investigated by the Bio-Speedy® Emerging Plus kit (Bioeksen AR-GE Technologies, Turkey) used to identify the variants in the study.&#x0D; Results: All 8.520 samples were SARS-CoV-2 RT-PCR positive. Our study detected alpha and delta variants in 1460 (17.14%) and 3570 (41.9%) patients respectively. 2570 (30.16%) patients did not have any variants according to test results. It was observed that the spread of beta, gamma and other suspicious variants remained at relatively low rates.&#x0D; Conclusion: The delta variant became dominant from July until to the end of the year. Declining delta variant rates and increasing cases of suspected variants towards the beginning of December 2021 suggest the omicron variant. Therefore, molecular surveillance studies that are planned to take epidemiological data into consideration and to examine the prevalence and gene-based analysis of local and worldwide variants are required.

Molecular epidemiological analyses of Clostridioides difficile isolates in a university hospital in Japan

BackgroundWe performed molecular epidemiological analyses of Clostridioides difficile isolates in a university hospital in Japan to reveal the risk of C. difficile infection. MethodsCultured isolates from 919 stool samples from 869 patients obtained from July 2015 to August 2016 were subjected to toxin gene detection, ribotyping, multilocus sequence typing, antimicrobial susceptibility testing, and quantitative real-time polymerase chain reaction testing for C. difficile toxin gene expression. ResultsOf the 919 stool samples from 869 patients, C. difficile was isolated from 153 samples (16.6%), of which 49 (32%) and 104 (68%) were from patients with and without C. difficile infection, respectively. Analyses showed genetic diversity, with ST8 and ST17 strains of healthcare-associated infections, some of which caused C. difficile infections. There was no significant difference in the transcription levels of C. difficile toxin genes between isolates from patients with and without C. difficile infection. ConclusionsMajor Japanese clonal strains, ST8 and ST17, have been in the hospital environment for a long time and cause healthcare-associated C. difficile infections. The C. difficile toxin genes were transcribed in the isolates from both patients with and without C. difficile infection but were no significant relationship with the development of C. difficile infection.

Comparisons of parametric and non-parametric methods for analyzing RT-PCR experiment data

The real-time reverse-transcript polymerase chain reaction (RT-PCR) test is a widely used laboratory technique that is highly sensitive and reliable for measuring the quantification of gene expression levels and diagnosing various of diseases, including COVID-19. The RT-PCR experiments often have correlated technical replicates of a small number of samples. However, current statistical analysis of RT-PCR assumes a large sample size and does not account for correlated structure across the replicates. In this paper, we review popular statistical methods for analyzing RT-PCR data and propose a permutation method that accounts for the small sample size and the correlated structure of RT-PCR data. Our proposed method provides a more accurate and efficient analysis of RT-PCR data. We provide an R program to implement our method for practitioners.

Graphene Field Effect Biosensor for Concurrent and Specific Detection of SARS-CoV-2 and Influenza.

The SARS-CoV-2 pandemic has highlighted the need for devices capable of carrying out rapid differential detection of viruses that may manifest similar physiological symptoms yet demand tailored treatment plans. Seasonal influenza may be exacerbated by COVID-19 infections, increasing the burden on healthcare systems. In this work, we demonstrate a technology based on liquid-gated graphene field-effect transistors (GFETs), for rapid and ultraprecise sensing and differentiation of influenza and SARS-CoV-2 surface protein. Most distinctively, the device consists of 4 onboard GFETs arranged in a quadruple architecture, where each quarter is functionalized individually (with either antibodies or chemically passivated control) but measured jointly. The sensor platform was tested against a range of concentrations of viral surface proteins from both viruses with the lowest tested and detected concentration at ∼50 ag/mL, or 88 zM for COVID-19 and 227 zM for Flu, which is 5-fold lower than the values reported previously on a similar platform. Unlike the classic real-time polymerase chain reaction test, which has a turnaround time of a few hours, the graphene technology presents an ultrafast response time of ∼10 s even in complex and clinically relevant media such as saliva. Thus, we have developed a multianalyte, highly sensitive, and fault-tolerant technology for rapid diagnostic of contemporary, emerging, and future pandemics.

The usefulness of the modified deep convolutional neural network model in improving the detection of COVID-19 on chest X-ray images

Background: The COVID-19 pandemic has rapidly spread worldwide, leading to a global health crisis. Although the real-time polymerase chain reaction (RT-PCR) test is highly specific and sensitive in detecting COVID-19, chest X-rays have emerged as an optional diagnostic tool for COVID-19-induced lung lesions. Artificial intelligence (AI), particularly deep learning, is a rapidly evolving field with significant potential in medical image analysis, including the quick detection of COVID-19 to improve accuracy. Objectives: This study aims to enhance the accuracy of COVID-19 image detection on chest X-ray images by modifying the deep convolutional neural network. Materials and methods: We conducted lung segmentation and COVID-19 image classification experiments using a dataset of chest X-rays. The U-net algorithm was utilized for lung segmentation of COVID-19 and non-COVID-19 images. We developed a Modified Deep Convolutional Neural Network (MD-CNN) to classify the two image classes. The MD-CNN model was compared with two other models, ResNet and AlexNet, and evaluated for accuracy, sensitivity (recall), specificity, positive predictive value (precision), F1-score, and area under the curve (AUC). Results: Our experimental results demonstrate that the MD-CNN model achieved an accuracy of 97.95%, outperforming ResNet and AlexNet, which achieved 90.25% and 78.95%, respectively. The MD-CNN model also exhibited better sensitivity, F1-score, and AUC than the other models, while its specificity and precision were comparable to those of the ResNet model. Conclusion: The proposed MD-CNN model demonstrates significant potential for high accuracy in COVID-19 image detection compared to ResNet and AlexNet. It can serve as a useful tool for radiologists in the COVID-19 screening process, potentially reducing the workload, and improving the efficiency of COVID-19 diagnosis.

Anemia and COVID-19

Objectives: Coronavirus disease-19 (COVID-19) is an infective-inflammatory disease that mainly affects the lungs. Hematological symptoms such as thrombocytopenia, decreased eosinophil and lymphocyte counts are quite common and are of prognostic importance. Although it is known that the presence of anemia generally increases the severity of respiratory diseases, there is little data on the prevalence and importance of anemia in COVID-19. In this study, our aim is to evaluate the clinical features of patients with anemia in COVID-19 infection and to investigate the relationship between the presence of anemia and the prognosis of the disease. Methods: This retrospective, observational study included 353 patients who presented to our pandemic reference hospital between 15.04.2020 and 15.05.2020 and were diagnosed with SARS-CoV-2 infection confirmed by real-time reverse transcription polymerase chain reaction (PCR) test and typical clinical symptoms. Results: Our study included 167 female and 186 male patients. The mean age was 54.54 ± 18.28 years (range 19-99). One hundred forty-eight (41.93%) patients had anemia. In patients with anemia, age was higher than others (p &amp;lt; 0.001). The percentage of women was significantly higher in the anemia group (p &amp;lt; 0.001). Comorbidities were observed more in the anemia group. The percentages of intensive care stay (p = 0.003) and mortality (p = 0.001) were significantly higher in the anemia group compared to the group without anemia. Logistic regression analysis was performed to determine the important risk factors of death. We found patients with high age (p = 0.001), high red cell distribution width-coefficient of variation (RDW-CV) levels (p = 0.009), high D-dimer levels (p = 0.012) and high ferritin levels (p &amp;lt; 0.001) have higher risk of death. Anemia was found to be non-significant. Conclusions: Anemia is frequently observed in patients with severe COVID-19 disease and low hemoglobin values at presentation are thought to be associated with a worse prognosis. Being more sensitive to the hemoglobin levels of COVID-19 patients is important for early recognition of the high-risk patient group and for successful patient management. However, in our study, the presence of anemia was found to be effective in mortality in univariate analysis, but not in multivariate analysis. According to the multivariate analysis of this study, advanced age, high D-dimer, high ferritin and RDW-CV determine death.

Rapid Antigen Tests for COVID-19: Are Their Specificity, Sensivity and Accuracy Sufficient?

Objective: The aim of our study was to determine the sensitivity and specificity of rapid antigen and Real-Time Reverse Transcription Polymerase Chain Reaction (RT-PCR) tests which are widely used today in patients presenting with Covid-19 complaints and to evaluate these tests’ routine usability. Methods: Two samples were taken from oropharyngeal and nasopharyngeal from 100 patients (50 women, 50 men) who applied to the Covid-19 outpatient clinic of our hospital between April and May 2022. The patients attended to the study were volunteers between the ages of 18-90. One of the samples was studied with the BNG SARS-CoV-2 Antigen Rapid Test (Saliva) and evaluated with the naked eye after 15 minutes according to the company's recommendations. The other sample was studied with RT-PCR on BIO-RAD CFX Real Time System with DSCoronex Covid-19 QPCR Test Kit. The epidemiological data and clinical conditions of the patients were determined by questionnaires. The age, gender, symptoms (fever, cough, headache, diarrhea, sore throat, shortness of breath, loss of taste and smell, myalgia) of the patient and the day of the symptoms were noted down. Results: It is known that technically rapid antigen tests generally have lower sensitivity and higher specificity than RT-PCR. In our study, the sensitivity was 71% and the specificity was 100%. The Accuracy (Diagnostic Value) rate of the rapid antigen test was determined as 90%. Our results suggest that rapid antigen tests are inexpensive and practical tests to reduce transmission, especially in epidemics however they should be selected carefully by the health care authorities. Conclusion: The prevalence of self-reported FA based on web-based survey in Eastern Black Sea residents is relatively high and specific to the region.

General Hospitalization and Intensive Care Unit-Related Factors of COVID-19 Patients in Northeastern Colombia: Baseline Characteristics of a Cohort Study.

Objective This study aims to describe demographic and clinical characteristics and the factors associated with the risk of COVID-19 general hospitalization and intensive care unit (ICU) care of patients who consulted in a third-level hospital in Santander, Colombia. Methods We used baseline data from an ambidirectional cohort study. We included all patients with positive real-time polymerase chain reaction (PCR) tests for COVID-19 who came to the emergency room (ER) for respiratory symptoms related to COVID-19. Information regarding patients' baseline characteristics and symptoms was collected through telephone interviews and review of medical records. Vital signs were extracted from medical records as well. Results We enrolled 3,030 patients, predominantly men, with a median age of 60(interquartile range (IQR): 44-73). Symptoms of the acute phase varied between men and women. Men presented with more respiratory symptoms, and women had general symptoms. Hypertension, obesity, and diabetes were common risk factors for hospital admission. Antibiotic consumption may also play a role in hospital admission. Conclusions Male sex, older age,hypertension, obesity, prior thrombotic events, and self-medicated antibiotics were associated with general hospitalization. Hypertension, obesity, diabetes, and cancer were associated with ICU admission. The Charlson comorbidity index (CCI) is a powerful tool for evaluate the impact of pre-existing health conditions on COVID-19 hospital admission. We highlight the importance of these findings as possible predictors in our region.

Patients' characteristics and 30-day mortality for those undergoing elective surgeries during the COVID-19 pandemic in Bangladesh.

The COVID-19 pandemic has significantly impacted the surgical practice throughout the world, including elective surgical care. This study investigated the characteristics of patients undergoing elective surgery, the prevalence of COVID-19 infection, the surgical procedures performed, and 30-day mortality in general and pediatric surgical settings in selected tertiary-level hospitals in Bangladesh from November 2020 to August 2021. This serial cross-sectional study included 264 patients scheduled for elective surgeries during the study period. All patients underwent COVID-19 real-time polymerase chain reaction (RT-PCR) testing within 24 hours before surgery. Data on age, sex, common comorbidities, surgical procedures, and 30-day mortality were collected and analyzed. Furthermore, comparisons were made between COVID-19 positive and negative patients. The prevalence of COVID-19 infection among patients was 10.6%. Older age, a history of major surgery within the last three months, hypertension, and diabetes mellitus were significantly associated with COVID-19 infection. All COVID-19-negative patients underwent surgery, while only 46.4% of COVID-19-positive patients underwent surgery. The most common surgical procedures were related to the digestive system, breast, and urinary system. Only one patient (0.4%) died within 30 days after surgery among the COVID-19-negative patients, whereas two patients (7.1%) died among the COVID-19-positive patients: one before surgery and one after surgery. This study provides valuable insights into the characteristics, burden of COVID-19 infection, and 30-day mortality of patients undergoing elective surgery in tertiary care centers in Bangladesh during the pandemic.

Evaluation of Viral Respiratory Pathogens Among Patients Initially Tested Negative for SARS-CoV-2

Background: A number of ribonucleic acid (RNA) and deoxyribonucleic acid (DNA) viruses commonly circulating among vertebrates, such as influenza H1N1, respiratory syncytial virus (RSV), adenoviruses, and human coronavirus (HCoV)-229E, cause symptoms similar to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). These viruses are important causes of cold, pneumonia, and shortness of breath in humans, which have been overlooked during the coronavirus disease 2019 (COVID-19) pandemic. Furthermore, the diagnosis of infection with these viruses mostly relies on physical examination and clinical history, despite the fact that accurate molecular diagnosis is available. Objectives: This study aimed to evaluate the presence of respiratory viruses in patients who were suspected to be infected with COVID-19 yet initially tested negative for SARS-CoV-2, as it could be beneficial in developing effective control measures and more reliable testing and surveillance of such viruses. Methods: In this study, laboratory samples of 123 patients referred to Ghaem Hospital of Mashhad, Iran, were evaluated that tested negative for SARS-CoV-2 in the initial assessment while showing the clinical symptoms of COVID-19. Initial testing for SARS-CoV-2 was carried out by the TaqMan real-time polymerase chain reaction (PCR) method using a kit approved by the Ministry of Health (Pishtaz Teb, Iran). Further analysis for the presence of 17 respiratory viruses was carried out using Genova kits based on the virus genome conserved sequences of influenza H1N1, influenza B, influenza A, SARS-CoV-2, HCoV-HKU1, HCoV-OC43, HCoV-NL63, HCoV-229E, metapneumovirus, RSV, human bocavirus 1, 2, 3, parainfluenza 1, 2, 3, and adenovirus. Results: According to the results of the present evaluations, out of 123 samples that were acquired using nasal and throat swabs and that initially tested negative for SARS-CoV-2, 8 cases of influenza A (47.1%), 1 case of parainfluenza (5.9%), 1 case of HKU1/OC-43 (5.9%), 4 cases of RSV (23.5%), 1 case of HCoV-NL63/HCoV-229-E (5.9%), and 2 cases of SARS-CoV-2 (11.8%) were detected. Conclusions: Based on the results of real-time PCR tests obtained from patients who had clinical symptoms of SARS-CoV-2 infections, it can be mentioned that due to the similar symptoms of patients with respiratory viral infections, individuals with respiratory symptoms could be examined for other viral infections in addition to SARS-CoV-2 infection, and a suitable basis for their prevalence in the community could be provided.

Prevalence of asymptomatic strongyloidiasis co-infection in COVID-19 patients residing in endemic areas

BackgroundFatal forms of strongyloidiasis, hyperinfection syndrome (HS) and disseminated strongyloidiasis (DS), are caused by exaggerated autoinfection of the intestinal nematode, Strongyloides stercoralis (S. stercoralis). Corticosteroids, frequently administered to patients with severe COVID-19, can transform chronic asymptomatic strongyloidiasis into the above-mentioned fatal diseases. This study aimed to investigate the prevalence of strongyloidiasis in COVID-19 patients receiving corticosteroids in a hypoendemic region.MethodsThe present cross-sectional study enrolled 308 COVID-19 patients admitted to two hospitals in Ahvaz and Abadan in the southwest of Iran between 2020 and 2022. A real-time reverse transcription polymerase chain reaction (RT-PCR) test and chest computed tomography (CT) scan were employed to detect and monitor the disease’s severity in the patients, respectively. All patients were evaluated for IgG/IgM against S. stercoralis using Enzyme-linked immunosorbent assay (ELISA) test. Subsequently, individuals with a positive ELISA test were confirmed using parasitological methods, including direct smear and agar plate culture (APC).ResultsThe patients were between 15 and 94 years old, with a mean age of 57.99 ± 17.4 years. Of the 308 patients, 12 (3.9%) had a positive ELISA test, while 296 (96.1%) had negative results. Three of the 12 patients with a positive ELISA result died, and three failed to provide a stool sample. To this end, only six cases were examined parasitologically, in which S. stercoralis larvae were observed in five patients. Significant differences were found between S. stercoralis infection with sex (p = 0.037) and age (p = 0.027). Binary regression analysis revealed that strongyloidiasis was positively associated with sex (odds ratio [OR]: 5.137; 95% confidence interval [CI]: 1.107–23.847), age (OR: 5.647; 95% CI 1.216–26.218), and location (OR: 3.254; 95% CI: 0.864–12.257).ConclusionsOur findings suggest that screening for latent strongyloidiasis in COVID-19 patients in endemic areas using high-sensitivity diagnostic methods, particularly ELISA, before receiving suppressive drugs should be given more consideration.

Clinical application of a real-time polymerase chain reaction test for CYP2C19 genotyping based on genotype distribution in a healthy Korean population.

With the recent reports of additional alleles of the CYP2C19 gene with decreased or no function, the clinical utility of real-time polymerase chain reaction (PCR)-based testing that detects only a small number of variant targets needs to be evaluated. We retrospectively reviewed 7-year data for real-time PCR test records from a single hospital and analyzed CYP2C19 genotypes from publicly available whole-genome or whole-exome data from a healthy Korean population. Of the 2327 test results in this hospital, the *1 allele was most common (60.5%), followed by *2 (28.0%), *3 (10.1%), and *17 (1.4%). Among 5305 healthy Korean individuals, the frequencies of the *2, *3, and *17 alleles were 28.6%, 9.9%, and 1.0%, respectively, which were not statistically different from those of the hospital data (P = .4439, P = .6025, and P = .1142, respectively). Interestingly, the total frequency of additional nonfunctional alleles (*4, *6, *22, and *24) that could not be detected using real-time PCR was only 0.1%, with a total allele count of 8. Our study shows that the clinical utility of real-time PCR for CYP2C19 genotyping remains satisfactory. However, caution should be exercised because the test can miss patients with decreased CYP2C19 function.

An Integrated Microfluidic Biosensing System Based on a Versatile Valve and Recombinase Polymerase Amplification for Rapid and Sensitive Detection of Salmonella typhimurium.

Detecting foodborne pathogens on-site is crucial for ensuring food safety, necessitating the development of rapid, cost-effective, highly sensitive, and portable devices. This paper presents an integrated microfluidic biosensing system designed for the rapid and sensitive detection of Salmonella typhimurium (S. typhimurium). The biosensing system comprises a microfluidic chip with a versatile valve, a recombinase polymerase amplification (RPA) for nucleic acid detection, and a customized real-time fluorescence detection system. The versatile valve combines the functions of an active valve and a magnetic actuation mixer, enabling on-demand mixing and controlling fluid flow. Quantitative fluorescence is processed and detected through a custom-built smartphone application. The proposed integrated microfluidic biosensing system could detect Salmonella at concentrations as low as 1.0 × 102 copies/µL within 30 min, which was consistent with the results obtained from the real-time quantitative polymerase chain reaction (qPCR) tests. With its versatile valve, this integrated microfluidic biosensing system holds significant potential for on-site detection of foodborne pathogens.

Direct comparison of clinical diagnostic sensitivity of saliva from buccal swabs versus combined oro-/nasopharyngeal swabs in the detection of SARS-CoV-2 B.1.1.529 Omicron

While current guidelines recommend the use of respiratory tract specimens for the direct detection of SARS-CoV-2 infection, saliva has recently been suggested as preferred sample type for the sensitive detection of SARS-CoV-2 B.1.1.529 (Omicron). By comparing saliva collected using buccal swabs and oro-/nasopharyngeal swabs from patients hospitalized due to COVID-19, we aimed at identifying potential differences in virus detection sensitivity between these sample types. We compare the clinical diagnostic sensitivity of paired buccal swabs and combined oro-/nasopharyngeal swabs from hospitalized, symptomatic COVID-19 patients collected at median six days after symptom onset by real-time polymerase chain reaction (PCR) and antigen test. Of the tested SARS-CoV-2 positive sample pairs, 55.8% were identified as SARS-CoV-2 Omicron BA.1 and 44.2% as Omicron BA.2. Real-time PCR from buccal swabs generated significantly higher quantification cycle (Cq) values compared to those from matched combined oro-/nasopharyngeal swabs and resulted in an increased number of false-negative PCR results. Reduced diagnostic sensitivity of buccal swabs by real-time PCR was observed already at day one after symptom onset. Similarly, antigen test detection rates were reduced in buccal swabs compared to combined oro-/nasopharyngeal swabs. Our results suggest reduced clinical diagnostic sensitivity of saliva collected using buccal swabs when compared to combined oro-/nasopharyngeal swabs in the detection of SARS-CoV-2 Omicron in symptomatic individuals.