RT-qPCR Test Research Articles

Side of chute does not affect the sensitivity of Tritrichomonas foetus sample collection in bulls when using dominant hand for collection

Tritrichomonas foetus, a sexually transmitted disease in cattle, continues to plague the cattle industry despite years of control programs. One reason for this continued prevalence through­out the U.S. and the world is that accurate diagnosis is compli­cated in the fact that retrieval of organisms for diagnosis and subsequent testing may be compromised by multiple factors in­cluding, but not limited to, how samples are collected. A commonly used sampling technique for diagnosing T. foetus in bulls is scraping of the preputial and penile mucosa with ei­ther an artificial insemination pipette or specially designed T. foetus testing device such as the Pizzle Stick Trich Testing De­vice (Lane Manufacturing Denver, CO). Parker et al. noted that right-hand dominant practitioners were more commonly suc­cessful in retrieving T. foetus in known positive bulls when col­lecting from the right side of the bull compared to the left; how­ever, the opposite was not investigated for left-hand dominant practitioners and only cultures were used to declare whether a sample was positive or not. The objective of this study was to determine if using current RT-qPCR testing if there is a differ­ence in rate of positive tests pending side of chute and use of dominant hand for testing.

Evaluation of combined disinfection methods of infectious myonecrosis virus (IMNV) in seawater using Pacific white shrimp (Penaeus vannamei)

The global spread of infectious myonecrosis virus (IMNV) poses a serious threat to the shrimp aquaculture industry and urgent actions are needed to control its transmission and prevalence. Aquaculture water serves as an important route of IMN transmission, and disinfection of aquaculture water is crucial to ensure the health and stable production of shrimp. In this study, we introduced the purified IMNV into seawater and then subjected the seawater to different disinfection treatments (PMS, PMS + PVP-I and ClO2 + PVP-I) before culturing shrimp. By performing RT-qPCR tests on both the seawater and Pacific white shrimp (Penaeus vannamei) samples, we evaluated the effectiveness of the different disinfection methods in eradicating IMNV from the seawater. The results showed that peroxymonosulfate (PMS) could effectively reduce the viral load of IMNV in seawater samples. The combined disinfection approach (10 ppm) of PMS disinfection (combined with povidone‑iodine) followed by a standing time of at least 2 days, or 10 ppm chlorine dioxide disinfection (combined with povidone‑iodine) followed by a standing time of at least 4 days, were found to be successful in the efficient disinfection of IMNV. This research provides a method to effectively remove IMNV from marine aquaculture water, thereby contributing to reducing the risk of IMN disease transmission and providing a sound basis for the sustainable and healthy development of the shrimp aquaculture industry.

Identification of unique electromagnetic signatures from GLRaV-3 infected grapevine leaves in different stages of virus development.

Grapevine leafroll associated virus 3 (GLRaV-3) is one of the most common viruses that adversely affect grape production quality around the world. Grapevine virus is usually detected by polymerase chain reaction (PCR) tests, but the main diagnostic challenges with the PCR are uneven distribution of symptoms, low virus titers in early stage, and the tests are time consuming and expensive. In the absence of effective control and treatment for grapevine virus, the recommendation is to remove infected vines before they become a source of transmission and a rapid and early detection method for viruses is urgently needed. This study investigated how GLRaV-3 infection affects spectral behavior of grapevine leaves and the use of remote sensing tools to identify changes caused by the biotic stress. A Real-Time RT-qPCR test was performed to select representative vines with healthy and GLRaV-3 infection, and changes in electromagnetic (EM) spectrum of leaves were observed with a portable hyperspectral spectrometer and a multispectral sensor on a remotely piloted aircraft system (RPAS). The results of this study suggest that foliar EM reflectance may differ depending on the presence or absence of visible symptoms of infected leaves and different stages of virus infection progress could be indicated by changes in the relative rate of reflectance around 700 nm. This research also confirmed that the development of a narrow-band hyperspectral index for the detection of grapevine virus is feasible, further research is recommended in a much more comprehensive investigation including a combination of hyperspectral sensor and chlorophyll fluorescence sensors, interpolation of suspect wavebands into ratios or indices, larger sample sizes and a more controlled study environment.

Viral SARS-CoV-2 Rebound Rates in Linked Commercial Pharmacy-Based Testing and Health Care Claims.

Viral SARS-CoV-2 rebound (viral RNA rebound) is challenging to characterize in large cohorts due to the logistics of collecting frequent and regular diagnostic test results. Pharmacy-based testing data provide an opportunity to study the phenomenon in a large population, also enabling subgroup analyses. The current real-world evidence approach complements approaches focused on smaller, prospective study designs. We linked real-time reverse transcription quantitative polymerase chain reaction test data from national pharmacy-based testing to health care claims data via tokenization to calculate the cumulative incidence of viral RNA rebound within 28 days following positive test results in nirmatrelvir/ritonavir (NMV-r)-treated and untreated individuals during the Omicron era (December 2021-November 2022) and prior to the Omicron era (October 2020-November 2021). Among 30 646 patients, the rate of viral RNA rebound was 3.5% (95% CI, 2.0%-5.7%) in NMV-r-treated infections as compared with 1.5% (95% CI, 1.3%-1.7%) in untreated infections during the Omicron era and 1.9% (95% CI, 1.7%-2.1%) prior to the Omicron era. Viral RNA rebound in patients who were vaccinated (n = 8151), high risk (n = 4411), or older (≥65 years, n = 4411) occurred at comparable rates to the overall cohort (range, 1.1%-4.8%). Viral rebounds to high RNA levels in NMV-r-treated infections occurred in 8% of viral rebounds as compared with 5% to 11% in untreated infections. Rates of hospitalization were comparable between patients with NMV-r-treated infections with viral RNA rebound (0%) and untreated patients with viral RNA rebound (0%-1.2%). Our findings suggest viral RNA rebound is rare (< 5%), with rates that were consistent with those from the EPIC-HR trial (Evaluation of Protease Inhibition for COVID-19 in High-Risk Patients). Most occurrences of viral RNA rebound were associated with low viral RNA levels, and viral RNA rebound progression to severe disease was not observed.

Elevated TRPV2 expression in the facial nerve of rats by cold stimulation: Implications for Bell's palsy

ObjectiveBell's palsy, also referred to as clinical manifestations of unilateral facial nerve palsy, encompasses downward angling of the corners of the mouth, the absence of forehead creases, and unilateral incomplete eyelid closure. The incidence of Bell's palsy has increased progressively in recent years, but the underlying mechanism of its occurrence remains unknown; therefore, it is essential to investigate both the cause and treatment of Bell's palsy. Member 2 of the Subfamily V Transient Receptor Potential Cation Channel is a mechanically and thermally sensitive ion channel that plays a crucial role in neural growth and development. Using a novel modeling technique, we endeavored to develop an animal model of Bell's palsy and determine whether TRPV2 expression is altered throughout the course of a facial nerve injury. Materials and methodsThe rats were categorized into 3 groups, and their facial nerve function was assessed using RT-qPCR, WB, and pathologic testing, respectively, after undergoing unilateral cold air stimulation for 1, 3, and 7 days. TRPV2 expression was identified using these techniques. ResultsIn response to cold stimulation, rats exhibited facial nerve paralysis symptoms, demyelinating lesions in the facial nerve, and increased TRPV2 expression. ConclusionsExtended cold stimulation of the facial nerve in rats may lead to an imbalance in facial nerve homeostasis and increased TRPV2 expression. These findings will contribute to the understanding of the potential mechanism by which cold stimulation affects the facial nerve. Moreover, this finding implies that TRPV2 could possibly function as an additional diagnostic marker or therapeutic target in the context of Bell's palsy.

Evaluating and optimizing Acid-pH and Direct Lysis RNA extraction for SARS-CoV-2 RNA detection in whole saliva

COVID-19 has been a global public health and economic challenge. Screening for the SARS-CoV-2 virus has been a key part of disease mitigation while the world continues to move forward, and lessons learned will benefit disease detection beyond COVID-19. Saliva specimen collection offers a less invasive, time- and cost-effective alternative to standard nasopharyngeal swabs. We optimized two different methods of saliva sample processing for RT-qPCR testing. Two methods were optimized to provide two cost-efficient ways to do testing for a minimum of four samples by pooling in a 2.0 mL tube and decrease the need for more highly trained personnel. Acid-pH-based RNA extraction method can be done without the need for expensive kits. Direct Lysis is a quick one-step reaction that can be applied quickly. Our optimized Acid-pH and Direct Lysis protocols are reliable and reproducible, detecting the beta-2 microglobulin (B2M) mRNA in saliva as an internal control from 97 to 96.7% of samples, respectively. The cycle threshold (Ct) values for B2M were significantly higher in the Direct Lysis protocol than in the Acid-pH protocol. The limit of detection for N1 gene was higher in Direct Lysis at ≤ 5 copies/μL than Acid-pH. Saliva samples collected over the course of several days from two COVID-positive individuals demonstrated Ct values for N1 that were consistently higher from Direct Lysis compared to Acid-pH. Collectively, this work supports that each of these techniques can be used to screen for SARS-CoV-2 in saliva for a cost-effective screening platform.

Effect of simultaneous and sequential use of TGF-β1 and TGF-β3 with FGF-2 on teno/ligamentogenic differentiation of periodontal ligament stem cells

ObjectiveThe periodontal ligament is a crucial part of the periodontium, and its regeneration is challenging. This study compares the effect of simultaneous and sequential use of FGF-2 and TGF-β1 with FGF-2 and TGF-β3 on the periodontal ligament stem cells (PDLSCs) teno/ligamentogenic differentiation. DesignThis study comprises ten different groups. A control group with only PDLSCs; FGF-2 group containing PDLSCs with a medium culture supplemented with FGF-2 (50 ng/mL). In other experimental groups, different concentrations (5 ng/mL or 10 ng/mL) of TGF-β1&-β3 simultaneously or sequentially were combined with FGF-2 on the cultured PDLSCs. TGF-β was added to the medium after day 3 in the sequential groups. Methyl Thiazolyl Tetrazolium (MTT) assay on days 3, 5, and 7 and Quantitative Real-time Polymerase Chain Reaction (RT-qPCR) analysis after day 7 were conducted to investigate PLAP1, SCX, and COL3A1, RUNX2 genes. All experiments were conducted in a triplicate. The One-way and Two-way ANOVA with Tukey post hoc were utilized to analyze the results of the MTT and RT-qPCR tests, respectively. A p-value less than 0.05 is considered significant. ResultsThe proliferation of cells on days 3, 5, and 7 was not significantly different among different experimental groups (P > 0.05). A higher expression of the PLAP1, SCX, and COL3A1 have been seen in groups with sequential use of growth factors; among these groups, the group using 5 ng/mL of TGF-β3 led other groups with the most amount of significant upregulation in PLAP1(17.69 ± 1.11 fold; P < 0.0001), SCX (5.71 ± 0.38 fold; P < 0.0001), and COL1A3 (6.35 ± 0.39 fold; P < 0.0001) expression, compared to the control group. The expression of the RUNX2 decreased in all groups compared to the control group; this reduction was more in groups with sequential use of growth factors. ConclusionThe sequential use of growth factors can be more effective than simultaneous use in teno/ligamentogenic differentiation of PDLSCs. Moreover, treatment with 5 ng/mL TGF-β3 after FGF-2 was more effective than TGF-β1.

Development and Optimization of a Multiplex Real-Time RT-PCR to Detect SARS-CoV-2 in Human Samples.

PCR and its variants (RT-PCR and qRT-PCR) are valuable and innovative molecular techniques for studying nucleic acids. qPCR has proven to be highly sensitive, efficient, and reproducible, generating reliable results that are easy to analyze. During the COVID-19 pandemic, qPCR became the gold standard technique for detecting the SARS-CoV-2 virus that allowed to confirm the infection event, and those asymptomatic ones, and thus save millions of lives. In-house multiplex qPCR tests were developed worldwide to detect different viral targets and ensure results, follow the infections, and favor the containment of a pandemic. Here, we present the detailed fundamentals of the qPCR technique based on fluorogenic probes and processes to develop and optimize a successful multiplex RT-qPCR test for detecting SARS-CoV-2 that could be used to diagnose COVID-19 accurately.

SARS-CoV-2 infection prevalence and associated factors among primary healthcare workers in France after the third COVID-19 wave

Data on the SARS-CoV-2 infection among primary health care workers (PHCWs) are scarce but essential to reflect on policy regarding prevention and control measures. We assessed the prevalence of PHCWs who have been infected by SARS-CoV-2 in comparison with modeling from the general population in metropolitan France, and associated factors. A cross-sectional study was conducted among general practitioners (GPs), pediatricians, dental and pharmacy workers in primary care between May and August 2021. Participants volunteered to provide a dried-blood spot for SARS-CoV-2 antibody assessment and completed a questionnaire. The primary outcome was defined as the detection of infection-induced antibodies (anti-nucleocapsid IgG, and for non-vaccinees: anti-Spike IgG and neutralizing antibodies) or previous self-reported infection (positive RT-qPCR or antigenic test, or positive ELISA test before vaccination). Estimates were adjusted using weights for representativeness and compared with prediction from the general population. Poisson regressions were used to quantify associated factors. The analysis included 1612 PHCWs. Weighted prevalences were: 31.7% (95% CI 27.5–36.0) for GPs, 28.7% (95% CI 24.4–33.0) for pediatricians, 25.2% (95% CI 20.6–31.0) for dentists, and 25.5% (95% CI 18.2–34.0) for pharmacists. Estimates were compatible with model predictions for the general population. PHCWs more likely to be infected were: GPs compared to pharmacist assistants (adjusted prevalence ratio [aPR] = 2.26; CI 95% 1.01–5.07), those living in Île-de-France (aPR = 1.53; CI 95% 1.14–2.05), South-East (aPR = 1.57; CI 95% 1.19–2.08), North-East (aPR = 1.81; CI 95% 1.38–2.37), and those having an unprotected contact with a COVID-19 case within the household (aPR = 1.48; CI 95% 1.22–1.80). Occupational factors were not associated with infection. In conclusion, the risk of SARS-CoV-2 exposure for PHCWs was more likely to have occurred in the community rather than at their workplace.

Quantitative detection of chikungunya, Zika, and dengue viruses by one-step real-time PCR in different cell substrates.

Chikungunya (CHIKV), Zika (ZIKV), and dengue viruses (DENV) are vector-borne pathogens that cause emerging and re-emerging epidemics throughout tropical and subtropical countries. The symptomatology is similar among these viruses and frequently co-circulates in the same areas, making the diagnosis arduous. Although there are different methods for detecting and quantifying pathogens, real-time reverse transcription-polymerase chain reaction (real-time RT-qPCR) has become a leading technique for detecting viruses. However, the currently developed assays frequently involve probes and high-cost reagents, limiting access in low-income countries. Therefore, this study aims to design and evaluate a quantitative one-step RT-qPCR assay to detect CHIKV, ZIKV, and DENV with high specificity, reproducibility, and low cost in multiple cell substrates. We established a DNA intercalating green dye-based RT-qPCR test that targets nsP1 of CHIKV, and NS5 gene of ZIKV, and DENV for the amplification reaction. The assay exhibited a high specificity confirmed by the melting curve analysis. No cross-reactivity was observed between the three viruses or unspecific amplification of host RNA. The sensitivity of the reaction was evaluated for each virus assay, getting a limit of detection of one RNA copy per virus. Standard curves were constructed, obtaining a reaction efficiency of ~ 100%, a correlation coefficient (R2) of ~ 0.97, and a slope of -3.3. The coefficient of variation (CV) ranged from 0.02 to 1.43. In addition, the method was optimized for viral quantification and tested in Vero, BHK-21, C6/36, LULO, and the Aedes cell lines. Thus, the DNA intercalating green dye-based RT-qPCR assay was a highly specific, sensitive, reproducible, and effective method for detecting and quantifying CHIKV, ZIKV, and DENV in different cell substrates that could also be applied in clinical samples.

The first confirmed cases of pigeon rotavirus A (RVA) infection in domestic pigeons (Columba livia) in Poland

Abstract Introduction Although the presence of rotaviruses in pigeon samples has been reported since the 1980s, its importance as an aetiological agent of the “classical” young pigeon disease (YPD) was not proven until 2020, when the Henle–Koch postulates were confirmed for pigeon-type rotavirus A (RVA) genotype G18P(17). Material and Methods From 2011 to 2020, archived liver samples from 117 pigeons submitted by 74 individual lofts were tested for the presence of pigeon-type RVA using a VP6-specific RT-qPCR test. For four positive racing pigeons, a more detailed necropsy and histopathological analysis was performed. Results Indicators of an acute RVA infection were found in 24 out of 117 (20.5%) samples tested, the earliest in 2014. Necropsies of the four selected RVA-positive pigeons showed changes mainly in the liver, spleen and kidneys similar to those described by other researchers. The histopathological examination revealed mainly hyperaemia and necrosis in the liver, as well as mononuclear cell infiltrates in these organs. Conclusion Pigeon-type RVA is also a cause of YPD in Poland and is a serious challenge for racing pigeon breeders and veterinarians, especially during the training and flights of young pigeons.

Occurrence and characteristics of elderly With Covid-19 in southern Brazil

This study aimed to describe the occurrence of COVID-19 in elderly patients treated at public health services in southern Brazil cities and their clinical and sociodemographic characteristics. This is a cross-sectional, observational, and retrospective study. From July 2020 to May 2021, medical records of elderly patients who underwent a test for COVID-19 at the molecular diagnostics laboratory of the University of Cruz Alta were selected. 310 elderly patients, with an average age of 60 to 99 years, were included in the study. Information was collected regarding the result of the RT-qPCR test, gender, symptoms, and comorbidities. We identified that 24.2% of the elderly evaluated in the study had a positive molecular diagnosis for COVID-19. The average age of the sample studied was 69 years (±8.89). Females had a higher proportion of positive cases (69.3%) compared to males (30.7%) (p=0.017). A higher proportion of individuals infected with SARS-Cov2 among those who reported cough, fever &gt;37°C and pre-existing cardiovascular diseases (p = 0.028; 0.015; 0.017 respectively) was also identified. Learning the clinical and sociodemographic profile of the elderly with COVID-19 can contribute to strategies for care and prevention of the disease in this group. The study findings indicate that greater attention should be given to the elderly with heart diseases and those who have fevers and coughs.

Endoplasmic reticulum stress-related features predict the prognosis of osteosarcoma and reveal STC2 as a novel risk indicator for disease progression.

Endoplasmic reticulum (ER) stress exerts significant effects on cell growth, proliferation, migration, invasion, chemoresistance, and angiogenesis in various cancers. However, the impact of ER stress on the outcomes of osteosarcoma patients remains unclear. In this study, we established an ER stress risk model based on The Cancer Genome Atlas (TARGET) osteosarcoma dataset to reflect immune features and predict the prognosis of osteosarcoma patients. Survival analysis revealed significant differences in overall survival among osteosarcoma patients with different ER stress-related risk scores. Furthermore, ER stress-related risk features were significantly associated with the clinical pathological characteristics of osteosarcoma patients and could serve as independent prognostic indicators. Functional enrichment analysis indicated associations of the risk model with cell chemotaxis, leukocyte migration, and regulation of leukocyte migration. Additionally, the ER stress-related risk model suggested the presence of an immunosuppressive microenvironment and immune checkpoint responses. We validated the significance of 7 ER stress-related genes obtained from LASSO regression analysis through RT-qPCR testing on osteosarcoma samples from a local hospital, and inferred the importance of STC2 based on the literature. Subsequently, IHC experiments using samples from 70 osteosarcoma cases and 21 adjacent tissue samples confirmed differential expression of STC2 between cancer and normal tissues, and explored the gene's expression in pan-cancer and its association with clinical pathological parameters of osteosarcoma. In conclusion, we have proposed an ER stress risk model as an independent prognostic factor and identified STC2 as a novel risk indicator for disease progression, providing a promising direction for further research and treatment of osteosarcoma.

Unlocking potential of oxytocin: improving intracranial lymphatic drainage for Alzheimer's disease treatment.

Background: The impediment to β-amyloid (Aβ) clearance caused by the invalid intracranial lymphatic drainage in Alzheimer's disease is pivotal to its pathogenesis, and finding reliable clinical available solutions to address this challenge remains elusive. Methods: The potential role and underlying mechanisms of intranasal oxytocin administration, an approved clinical intervention, in improving intracranial lymphatic drainage in middle-old-aged APP/PS1 mice were investigated by live mouse imaging, ASL/CEST-MRI scanning, in vivo two-photon imaging, immunofluorescence staining, ELISA, RT-qPCR, Western blotting, RNA-seq analysis, and cognitive behavioral tests. Results: Benefiting from multifaceted modulation of cerebral hemodynamics, aquaporin-4 polarization, meningeal lymphangiogenesis and transcriptional profiles, oxytocin administration normalized the structure and function of both the glymphatic and meningeal lymphatic systems severely impaired in middle-old-aged APP/PS1 mice. Consequently, this intervention facilitated the efficient drainage of Aβ from the brain parenchyma to the cerebrospinal fluid and then to the deep cervical lymph nodes for efficient clearance, as well as improvements in cognitive deficits. Conclusion: This work broadens the underlying neuroprotective mechanisms and clinical applications of oxytocin medication, showcasing its promising therapeutic prospects in central nervous system diseases with intracranial lymphatic dysfunction.

419. Viral SARS-CoV-2 rebound rates in linked commercial pharmacy-based SARS-CoV-2 RT-qPCR testing and healthcare claims

Abstract Background Viral SARS-CoV-2 RNA rebound has been described as a positive viral antigen or PCR test that follows a negative test. Although early descriptions of this phenomenon were linked to nirmatrelvir/ritonavir (NMV-r) treatment, subsequent studies have shown that viral rebound occurs both in untreated patients and patients treated with other antiviral therapies and is not associated with progression to severe disease. The rate of viral SARS-CoV-2 rebound has not been well characterized in large cohorts outside of clinical trials. Schematic representation of study population (Upper) High frequency testing and (Lower) High frequency testing with viral RNA rebound, along with relevant clinical information indicated by dashed lines. Each circle represents a SARS-CoV-2 RT-qPCR test with the darker shade indicating the minimum required tests to meet the definition and the lighter shade to reflect the possibility of &amp;gt;3 tests. The index date is the first positive test within 28-days. Methods In this large retrospective US-based cohort study, RT-qPCR SARS-CoV-2 test data were linked to healthcare claims to calculate the viral rebound rate in treated and untreated individuals, among subjects tested at least 3 times during a SARS-CoV-2 infection. This cohort of 30,646 unique patients includes SARS-CoV-2 vaccinated patients, patients infected during the Omicron era, and high risk patients (those with underlying medical conditions associated with a higher risk for severe SARS-CoV-2 infection). Results The observed rate of viral SARS-CoV-2 RNA rebound was approximately 3.5% in NMV-r treated infections compared to 1.5% in untreated infections during the Omicron era. Viral rebound in vaccinated, high-risk, or older patients occurred at comparable rates to the overall cohort. Viral rebounds to high RNA levels in NMV-r treated infections were rare (8% of viral rebounds) and comparable in frequency to those in untreated infections (11% of viral rebounds) during the Omicron era. Viral RNA rebound rates Viral RNA rebound rates and characteristics of the patient cohort, stratified by risk group, Omicron era, and NMV-r treatment. Untreated groups exclude patients who received NMV-r or a different SARS-CoV-2 treatment 28 days post-index date. Conclusion This study demonstrates that SARS-CoV-2 viral RNA rebound is rare and occurs in both treated and untreated SARS-CoV-2 infections, with rates comparable to those seen in the EPIC-HR clinical trial for NMV-r. Even when viral rebound occurs, only a small minority of cases rebound to a high viral RNA level and rarely result in progression to severe disease. Disclosures Shishi Luo, PhD, Helix: Employee Lisa M. McEwen, PhD, Helix: Employee Scott P. Kelly, PhD, Pfizer: Employee|Pfizer: Stocks/Bonds Magnus Isaksson, PhD, Helix: Employee Sarah Murphy, n/a, Helix: Former employee Simon White, n/a, Helix: Employee JT McCrone, PhD, Helix: Employment Geraint Levan, n/a, Helix: Employee Mary Lynn Baniecki, PhD, Pfizer Inc: Employee|Pfizer Inc: Stocks/Bonds Candace Bramson, MD, Pfizer Inc: Employee|Pfizer Inc: Stocks/Bonds Heather Rubino, PhD, MS, Pfizer: Stocks/Bonds Victoria Hendrick, BSc, Pfizer: Employee|Pfizer: Stocks/Bonds Holly Soares, PhD, Pfizer: Stocks/Bonds Jennifer Hammond, PhD, Pfizer: Employee|Pfizer: Stocks/Bonds

Clinical evaluation of a new COVID-19 antigen rapid test kit for detection of SARS-CoV-2

The antigen rapid diagnostic test (Ag-RDT) is an assay kit for detecting the SARS-COV-2 nucleocapsid proteins, based on the colloidal gold method.Accurate diagnosis has an important role in limiting the transmission of SARS-COV-2, and also helps patients to receive earlier treatment .The object of this study was to perform the clinical evaluation of a novel Ag-RDTs with samples collected from two different swabs.DEEPBLUE®COVID-19 antigen detection kit used for the examination of the subjects in the experiment.For antigen testing on samples collected with nasal swabs, sensitivity was 91.7 % (95 % CI 83.6-96.6 %) and specificity was 100 %(95 %CI 98.1-100 %).For nasopharyngeal swabs, the sensitivity was 96.8 % (95 % CI 93.6-98.7 %) and the specificity was 100 % (95 % CI 98.2-100 %).Fisher Precision test showed a significant correlation between nasopharyngeal swab Ag-RDTs and nasal swab Ag-RDTs and RT-qPCR test (p-value <0.001).The results showed that the patients use the kit for testing were comparable to the RT-qPCR.

Effectiveness of COVID-19 vaccines in Ecuador: A test-negative design

BackgroundThe COVID-19 pandemic poses a significant global health threat, characterized by high morbidity, severity, and the emergence of concerning variants. Latin America has been greatly affected, with high infection and mortality rates. Vaccination plays a crucial role in mitigating severe disease and controlling the pandemic. This study aims to assess the effectiveness of COVID-19 vaccines in preventing SARS-CoV-2 severe acute respiratory infections (SARI) in hospitalized vaccination target groups in Ecuador. MethodsThis is a test-negative design study. We used data reported through sentinel surveillance of SARI between May 2021 and March 2022 in Ecuador. Patients with case criteria of SARI and hospitalized for a minimum of 24 hours were included in the study. Cases were defined as patients with SARI with a positive RT-qPCR test for SARS-CoV-2 and controls were those with a negative result. Information on vaccination status was obtained from the national vaccination registry, a valid dose of vaccination was considered when it was administered at least 14 days prior to symptom onset. Vaccine effectiveness (VE) (1-OR/OR) was calculated using a logistic regression. ResultsA total of 1,277 patients were included in the analysis of VE. The adjusted vaccine effectiveness (aVE) in preventing hospitalization, adjusted for sex, age group, presence of one or more comorbidities, and period of the predominance of the omicron variant, was 44.5% for the partial primary schedule, 74.7% for the complete primary schedule, and 79.9% for the complete primary schedule plus booster doses. The aVE in avoiding ICU admissions was close to 80% with both the complete primary schedule and the booster doses, and in avoiding deaths, the aVE was 89% and 98%, respectively. ConclusionsIn Ecuador, COVID-19 vaccination prevents hospitalizations, ICU admissions, and deaths. The effectiveness of the vaccines improves with more doses, offering increased protection across all age groups.

SARS-CoV-2 testing in the Slovak Republic from March 2020 to September 2022 - summary of the pandemic trends.

The COVID-19 pandemic has been part of Slovakia since March 2020. Intensive laboratory testing ended in October 2022, when the number of tests dropped significantly, but the state of the pandemic continues to this day. For the management of COVID-19, it is important to find an indicator that can predict pandemic changes in the community. The average daily/weekly Ct value with a certain time delay can predict changes in the number of cases of SARS-CoV-2 infection, which can be a useful indicator for the healthcare system. The study analyzed the results of 1,420,572 RT-qPCR tests provided by one accredited laboratory during the ongoing pandemic in Slovakia from March 2020 to September 2022. The total positivity of the analyzed tests was 24.64%. The average Ct values found were the highest in the age group of 3-5 years, equal to the number 30.75; the lowest were in the age group >65 years, equal to the number 27. The average weekly Ct values ranged from 22.33 (pandemic wave week) to 30.12 (summer week). We have summarized the results of SARS-CoV-2 diagnostic testing in Slovakia with the scope defined by the rate and positivity of tests carried out at Medirex a.s. laboratories.

Supervised Machine Learning Methods for Seasonal Influenza Diagnosis.

Influenza has been a stationary disease in Mexico since 2009, and this causes a high cost for the national public health system, including its detection using RT-qPCR tests, treatments, and absenteeism in the workplace. Despite influenza's relevance, the main clinical features to detect the disease defined by international institutions like the World Health Organization (WHO) and the United States Centers for Disease Control and Prevention (CDC) do not follow the same pattern in all populations. The aim of this work is to find a machine learning method to facilitate decision making in the clinical differentiation between positive and negative influenza patients, based on their symptoms and demographic features. The research sample consisted of 15480 records, including clinical and demographic data of patients with a positive/negative RT-qPCR influenza tests, from 2010 to 2020 in the public healthcare institutions of Mexico City. The performance of the methods for classifying influenza cases were evaluated with indices like accuracy, specificity, sensitivity, precision, the f1-measure and the area under the curve (AUC). Results indicate that random forest and bagging classifiers were the best supervised methods; they showed promise in supporting clinical diagnosis, especially in places where performing molecular tests might be challenging or not feasible.

Evaluation of the analytical performance of the 15-minute point-of-care DASH™ SARS-CoV-2 RT-qPCR test

Accurate and timely diagnosis for COVID-19 diagnosis allows highly effective antiviral medications to be prescribed. The DASH™ Rapid PCR System is a sample-to-answer point-of-care platform combining state-of-the-art PCR kinetics with sequence specific hybridization. The platform's first assay, the DASH™ SARS-CoV-2/S test for anterior nares direct swab specimens, received FDA Emergency Use Authorization in March 2022 for point-of-care use. Here we report the analytical characteristics of the assay including limit of detection, dynamic range, and robustness of SARS-CoV-2 variant detection. The limit of detection was determined by testing swabs contrived with one hundred copies of wild type or Omicron BA.5 virus and detecting 20/20 and 19/20, respectively. The dynamic range was assessed with contrived swabs containing 102-106 copies; the log-linear relationship between Cq and copy input was plotted, and the qPCR efficiency calculated from the slope of the line was 101.4%. Detection of seven SARS-CoV-2 variants was demonstrated.