Point-of-care testing for COVID-19: a simple two-step molecular diagnostic development and validation during the SARS-CoV-2 pandemic.

BACKGROUND: During the coronavirus disease 19 (COVID-19) pandemic, diagnostic testing of the general population proved challenging due to limitations of the gold-standard diagnostic procedure using reverse transcription real-time polymerase chain reaction (RT-qPCR) for large-scale testing on the centralised model, especially in low-resource areas. OBJECTIVES: To address this, a point-of-care (PoC) diagnostic protocol for COVID-19 was developed, providing fast, reliable, and affordable testing, particularly for low-mid develop areas. METHODS: The PoC diagnostic process combines a simple paper-based RNA extraction method housed within a 3D-printed plastic device with a colorimetric reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay. Nasopharyngeal/oropharyngeal swabs (NOS) and saliva samples were tested between 2020 and 2021, with the assistance of Santa Catarina's State Health Secretary, Brazil. FINDINGS: The developed diagnostic protocol showed a limit of detection of 9,900 copies and an overall diagnostic specificity of 98% for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from 1,348 clinical analysed samples. The diagnostic sensitivity was 95% for NOS samples, 85% for early morning saliva, and 69% for indiscriminate saliva. MAIN CONCLUSIONS: In conclusion, the developed device successfully extracted SARS-CoV-2 viral RNA from swabs and saliva clinical samples. When combined with colorimetric RT-LAMP, it provides results within 45 min using minimal resources, thus delivering a diagnostic kit protocol that is applicable in large-scale sampling.

Incremental Value of Radiomics Features of Epicardial Adipose Tissue for Detecting the Severity of COVID-19 Infection.

INTRODUCTION: Epicardial adipose tissue (EAT) is known for its pro-inflammatory properties and association with Coronavirus Disease 2019 (COVID-19) severity. However, existing detection methods for COVID-19 severity assessment often lack consideration of organs and tissues other than the lungs, which limits the accuracy and reliability of these predictive models. MATERIAL AND METHODS: The retrospective study included data from 515 COVID-19 patients (Cohort 1, n=415; Cohort 2, n=100) from two centers (Shanghai Public Health Center and Brazil Niteroi Hospital) between January 2020 and July 2020. Firstly, a three-stage EAT segmentation method was proposed by combining object detection and segmentation networks. Lung and EAT radiomics features were then extracted, and feature selection was performed. Finally, a hybrid model, based on seven machine learning models, was built for detecting COVID-19 severity. The hybrid model's performance and uncertainty were evaluated in both internal and external validation cohorts. RESULTS: For EAT extraction, the Dice similarity coefficients (DSC) of the two centers were 0.972 (±0.011) and 0.968 (±0.005), respectively. For severity detection, the area under the receiver operating characteristic curve (AUC), net reclassification improvement (NRI), and integrated discrimination improvement (IDI) of the hybrid model increased by 0.09 (p<0.001), 19.3 % (p<0.05), and 18.0 % (p<0.05) in the internal validation cohort, and by 0.06 (p<0.001), 18.0 % (p<0.05) and 18.0 % (p<0.05) in the external validation cohort, respectively. Uncertainty and radiomics features analysis confirmed the interpretability of increased certainty in case prediction after inclusion of EAT features. CONCLUSION: This study proposed a novel three-stage EAT extraction method. We demonstrated that adding EAT radiomics features to a COVID-19 severity detection model results in increased accuracy and reduced uncertainty. The value of these features was also confirmed through feature importance ranking and visualization.

Cost-effectiveness of SARS-CoV-2 self-testing at routine gatherings to minimize community-level infections in lower-middle income countries: A mathematical modeling study.

Places of worship serve as a venue for both mass and routine gathering around the world, and therefore are associated with risk of large-scale SARS-CoV-2 transmission. However, such routine gatherings also offer an opportunity to distribute self-tests to members of the community to potentially help mitigate transmission and reduce broader community spread of SARS-CoV-2. Over the past four years, self-testing strategies have been an impactful tool for countries' response to the COVID-19 pandemic, especially early on to mitigate the spread when vaccination and treatment options were limited. We used an agent-based mathematical model to estimate the impact of various strategies of symptomatic and asymptomatic self-testing for a fixed percentage of weekly routine gatherings at places of worship on community transmission of SARS-CoV-2 in Brazil, Georgia, and Zambia. Testing strategies assessed included weekly and bi-weekly self-testing across varying levels of vaccine effectiveness, vaccine coverage, and reproductive numbers to simulate developing stages of the COVID-19 pandemic. Self-testing symptomatic people attending routine gatherings can cost-effectively reduce the spread of SARS-CoV-2 within places of worship and the community, resulting in incremental cost-effectiveness ratios of $69-$303 USD. This trend is especially true in contexts where population level attendance at such gatherings is high, demonstrating that a distribution approach is more impactful when a greater proportion of the population is reached. Asymptomatic self-testing of attendees at 100% of places of worship in a country results in the greatest percent of infections averted and is consistently cost-effective but remains costly. Budgetary needs for asymptomatic testing are expensive and likely unaffordable for lower-middle income countries (520-1550x greater than that of symptomatic testing alone), promoting that strategies to strengthen symptomatic testing should remain a higher priority.

Detection of Neutralizing Antibodies in Serum Samples Using a SARS-CoV-2 Pseudotyped Virus Assay.

Conventional live virus research on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causal agent of coronavirus disease-19 (COVID-19), requires Biosafety Level 3 (BSL-3) facilities. SARS-CoV-2 pseudotyped viruses have emerged as valuable tools in virology, mimicking the entry process of the SARS-CoV-2 virus into human cells by expressing its spike glycoprotein in a surrogate system using recombinant plasmids. One significant application of this tool is in functional assays for the evaluation of neutralizing antibodies. Pseudotyped viruses have the advantage of being competent for only a single cycle of infection, providing better safety and versatility and allowing them to be studied in BSL-2 laboratories. Here, we describe three protocols for the detection of SARS-CoV-2 neutralizing antibodies through a pseudotyped virus assay. First, SARS-CoV-2 S pseudotyped viruses (PV SARS-CoV-2 S) are produced using a Moloney murine leukemia virus (MuLV) three-plasmid system. The plasmids are designed to express the GagPol packing proteins, enhanced green fluorescent protein (eGFP) as a readout system, and the SARS-CoV-2 S protein modified to remove the endoplasmic reticulum retention domain and to improve infection. Next, the internalization of PV SARS-CoV-2 S protein in human embryonic kidney 293T (HEK-293T) cells overexpressing angiotensin-converting enzyme 2 (HEK-293T-ACE2) is confirmed by fluorescence microscopy and quantified using flow cytometry. Finally, PV SARS-CoV-2 S is used to screen neutralizing antibodies in serum samples from convalescent COVID-19 patients; it can also be used for studying the cell entry mechanisms of different SARS-CoV-2 variants, evaluating antiviral agents, and designing vaccines. © 2024 Wiley Periodicals LLC. Basic Protocol 1: Generation of PV SARS-CoV-2 S pseudotyped virus Basic Protocol 2: Assay of PV SARS-CoV-2 S internalization in target cells. Basic Protocol 3: Detection of neutralizing antibodies in serum samples.

A novel viral RNA detection method based on the combined use of trans-acting ribozymes and HCR-FRET analyses.

The diagnoses of retroviruses are essential for controlling the rapid spread of pandemics. However, the real-time Reverse Transcriptase quantitative Polymerase Chain Reaction (RT-qPCR), which has been the gold standard for identifying viruses such as SARS-CoV-2 in the early stages of infection, is associated with high costs and logistical challenges. To innovate in viral RNA detection a novel molecular approach for detecting SARS-CoV-2 viral RNA, as a proof of concept, was developed. This method combines specific viral gene analysis, trans-acting ribozymes, and Fluorescence Resonance Energy Transfer (FRET)-based hybridization of fluorescent DNA hairpins. In this molecular mechanism, SARS-CoV-2 RNA is specifically recognized and cleaved by ribozymes, releasing an initiator fragment that triggers a hybridization chain reaction (HCR) with DNA hairpins containing fluorophores, leading to a FRET process. A consensus SARS-CoV-2 RNA target sequence was identified, and specific ribozymes were designed and transcribed in vitro to cleave the viral RNA into fragments. DNA hairpins labeled with Cy3/Cy5 fluorophores were then designed and synthesized for HCR-FRET assays targeting the RNA fragment sequences resulting from ribozyme cleavage. The results demonstrated that two of the three designed ribozymes effectively cleaved the target RNA within 10 minutes. Additionally, DNA hairpins labeled with Cy3/Cy5 pairs efficiently detected target RNA specifically and triggered detectable HCR-FRET reactions. This method is versatile and can be adapted for use with other viruses. Furthermore, the design and construction of a DIY photo-fluorometer prototype enabled us to explore the development of a simple and cost-effective point-of-care detection method based on digital image analysis.

Overcoming Limited Access to Virus Infection Rapid Testing: Development of a Lateral Flow Test for SARS-CoV-2 with Locally Available Resources.

The COVID-19 pandemic highlighted testing inequities in developing countries. Lack of lateral flow test (LFT) manufacturing capacity was a major COVID-19 response bottleneck in low- and middle-income regions. Here we report the development of an open-access LFT for SARS-CoV-2 detection comparable to commercial tests that requires only locally available supplies. The main critical resource is a locally developed horse polyclonal antibody (pAb) whose sensitivity and selectivity are greatly enhanced by affinity purification. We demonstrate that these Abs can perform similarly to commercial monoclonal antibodies (mAbs), as well as mAbs and other pAbs developed against the same antigen. We report a workflow for test optimization using nasopharyngeal swabs collected for RT-qPCR, spiked with the inactivated virus to determine analytical performance characteristics as the limit of detection, among others. Our final prototype showed a performance similar to available tests (sensitivity of 83.3% compared to RT-qPCR, and 90.9% compared to commercial antigen tests). Finally, we discuss the possibility and the challenges of utilizing affinity-purified pAbs as an alternative for the local development of antigen tests in an outbreak context and as a tool to address inequalities in access to rapid tests.

Pentraxin-3 (PTX-3) as a potential biomarker for predicting death in hospitalized patients with COVID-19.

BACKGROUND: Pentraxin 3 (PTX3) is an acute-phase protein that belongs to the pentraxin family, which plays an important role in the body's defense against pathogens. PTX3 levels have been associated with inflammatory processes, and it is a possible biomarker for the diagnosis and prognosis of different infectious diseases, including COVID-19. The objective of this study was to analyze the potential of PTX3 as a plasma biomarker for predicting death in patients hospitalized with COVID-19. METHODS: The study included a total of 312 patients with COVID-19, admitted from July 2020 to August 2021 to hospital ward and intensive care unit beds at two hospitals in the Northeast Region of Brazil. PTX3 was measured using ELISA in samples collected within 24 h after hospital admission. Maximally selected rank statistics were used to determine the PTX3 cutoff point that best distinguished patients who died from those who survived. A receiver operating characteristic (ROC) curve was used to determine the performance of the biomarker. Survival analysis was performed using a Kaplan-Meier curve, and a Cox regression model was used to determine predictors associated with death. RESULTS: Of the 312 patients included in the study, 233 recovered and 79 died. Patients who died had higher PTX3 levels at the time of admission, when compared to those who recovered (median: 52.84 versus 10.79 ng/mL; p < 0.001). PTX3 showed area under the ROC (AUC) = 0.834, higher than other markers used in clinical practice, such as C-reactive protein (AUC = 0.72) and D-dimer (AUC = 0.77). Furthermore, according to the Kaplan-Meier survival curve, patients with PTX3 concentrations above the cutoff point (27.3 ng/mL) had a lower survival rate (p = 0.014). In multivariate Cox regression, PTX3 > 27.3 ng/mL was an important predictor of death, regardless of other confounding factors (hazard ratio = 1.79; p = 0.027). CONCLUSION: PTX3 can be considered as a potential biomarker for predicting death in patients hospitalized with COVID-19.

Clinical characteristics and severity markers in hospitalized COVID-19 patients from western Mexico: a comparative analysis of Delta and Omicron variants.

Introduction: COVID-19 is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a virus notable for its rapid mutation rate, which has led to the emergence of various variants such as Delta and Omicron, each with potentially different levels of transmissibility and virulence. Therefore, this study aims to compare clinical charactheristics and markers associated with the severity of COVID-19 in hospitalized patients from western Mexico who were infected with the Delta and Omicron variants of SARS-CoV-2. Methods: This cross-sectional study involved 66 patients hospitalized for COVID-19, diagnosed by RT-qPCR. SARS-CoV-2 variants were identified through whole genome sequencing using the COVIDseq platform from Illumina. Upon admission, patients underwent a clinical history assessment, blood gas analysis, and blood biometry. Additionally, several tests and markers were measured, including the percentage of neutralizing antibodies, erythrocyte sedimentation rate (ESR), interleukin-6 (IL-6), tumor necrosis factor-alpha (TNFα), D-dimer, lactate dehydrogenase (LDH), C-reactive protein (CRP), and ferritin. Results and discussion: Patients hospitalized with the Omicron were found to be older, compared to those infected with the Delta (64 vs. 54 years, p = 0.006). Additionally, a higher proportion of male patients were observed in the Omicron compared to the Delta (p = 0.029). Both Omicron and Delta variants were associated with lymphopenia, although the lymphocyte count was lower in Omicron (0.9 vs. 0.56 10x3/L; p = 0.007). The COVID-GRAM scale indicated a high risk for severe disease in both groups, but the score was higher in Omicron compared to Delta (157 vs. 128 points; p = 0.0004). Patients infected with Omicron exhibited a lower percentage of neutralizing antibodies than those with Delta (35.99 vs. 81%; p < 0.05), regardless of their vaccination status. Among the markers assessed, globular ESR was found to be lower in Omicron compared to Delta (30.5 vs. 41.5 mm/h; p = 0.001), while ferritin levels were higher in patients infected with the Omicron (1,359 vs. 960.6 µg/L; p = 0.007). In patients with severe COVID-19, markers such as lymphopenia, neutralizing antibody levels, ferritin, and COVID-GRAM scores are elevated in the Omicron variant, while only the leukocyte count and ESR for the Delta variant.

Sleep disorder syndromes of post-acute sequelae of SARS-CoV-2 (PASC) / Long Covid.

INTRODUCTION: COVID-19 infection has resulted in a high prevalence of a post-infectious syndrome, known as post-acute sequelae of SARS-CoV-2 (PASC) or "Long COVID". PASC is a heterogeneous disease with a high prevalence of sleep disturbances, varying from an insomnia disorder to excessive daytime sleepiness. METHODS: Patients seen in the Covid Survivorship Program at the Beth Israel Deaconess Medical Center Boston, USA, were screened for sleep disorders as part of a comprehensive multi-system evaluation. Those who screened positive were referred for a comprehensive sleep evaluation in a dedicated COVID-19-Sleep clinic, followed by diagnostic sleep testing and treatment. This report summarizes patients who completed an American Academy of Sleep Medicine (AASM) accredited facility-based diagnostic evaluation. International Classification of Sleep Disorders 3rd Edition-Revised criteria were met for all diagnoses. RESULTS: In 42 patients with PASC, five categories of sleep disorder syndromes were observed following a sleep clinic evaluation, including obstructive sleep apnea, chronic insomnia disorder, primary hypersomnia, REM behavior disorder (RBD), and new onset circadian phase delay. Seven patients met criteria for idiopathic hypersomnia, and two had narcolepsy type 2. RBD patients were infected in three different waves; circadian disturbance patients were all infected in the winter wave of 2020/21, and the primary hypersomnolence group occurred during all waves, predominantly the initial wave of 2020. A peculiar form of insomnia was a persistent loss of sleep regularity. CONCLUSIONS: Specific sleep symptoms/syndromes are reported in this select group of patients with PASC/Long Covid. As new onset sleep complaints are prevalent in PASC, we recommend a complete clinical and investigative sleep evaluation for persistent severe sleep symptoms following COVID-19 infection.

A spatially resolved single-cell lung atlas integrated with clinical and blood signatures distinguishes COVID-19 disease trajectories.

COVID-19 is characterized by a broad range of symptoms and disease trajectories. Understanding the correlation between clinical biomarkers and lung pathology during acute COVID-19 is necessary to understand its diverse pathogenesis and inform more effective treatments. Here, we present an integrated analysis of longitudinal clinical parameters, peripheral blood markers, and lung pathology in 142 Brazilian patients hospitalized with COVID-19. We identified core clinical and peripheral blood signatures differentiating disease progression between patients who recovered from severe disease compared with those who succumbed to the disease. Signatures were heterogeneous among fatal cases yet clustered into two patient groups: "early death" (<15 days until death) and "late death" (>15 days). Progression to early death was characterized systemically and in lung histopathological samples by rapid endothelial and myeloid activation and the presence of thrombi associated with SARS-CoV-2+ macrophages. In contrast, progression to late death was associated with fibrosis, apoptosis, and SARS-CoV-2+ epithelial cells in postmortem lung tissue. In late death cases, cytotoxicity, interferon, and T helper 17 (TH17) signatures were only detectable in the peripheral blood after 2 weeks of hospitalization. Progression to recovery was associated with higher lymphocyte counts, TH2 responses, and anti-inflammatory-mediated responses. By integrating antemortem longitudinal blood signatures and spatial single-cell lung signatures from postmortem lung samples, we defined clinical parameters that could be used to help predict COVID-19 outcomes.

Questionnaire and polysomnographic evaluation of obstructive sleep apnea in a cohort of post-COVID-19 patients.

To evaluate the efficiency of 5 screening questionnaires for obstructive sleep apnea (OSA), OSA frequency, and the association between OSA and COVID-19 severity in recent COVID-19 cases, and to compare the use of the oxygen desaturation index (ODI) as an alternative measure for the respiratory disturbance index (RDI). This open cohort study recruited patients with recent COVID-19 (within 30-180 days) diagnosed using reverse transcription polymerase chain reaction. Participants were screened for OSA using the following 5 sleep disorder questionnaires prior to undergoing type I polysomnography: the Sleep Apnea Clinical Score (SACS), Epworth Sleepiness Scale (ESS), STOP-Bang score, No-Apnea score, and Berlin questionnaire. Polysomnography revealed that 77.5% of the participants had OSA and that these patients exhibited higher COVID-19-related hospitalization (58%) than those exhibited by non-apneic patients. The Kappa coefficient showed reasonable agreement between RDI > 5/h and No-Apnea score, RDI > 15/h and Berlin questionnaire score, and Epworth Sleepiness Scale and STOP-Bang score, but only moderate agreement between RDI > 15/h and No-Apnea score. An OSA-positive No-Apnea score increased the specificity of the SACS to 100% when RDI > 5/h. The intraclass correlation coefficient showed 95.2% agreement between RDI > 5/h and ODI > 10/h. The sequential application of the No-Apnea score and SACS was the most efficient screening method for OSA, which had a moderately high incidence among the post-COVID-19 group. We demonstrated an association between OSA and COVID-19 related hospitalization and that ODI could be a simple method with good performance for diagnosing OSA in this population.

Systematic review on molecular detection of congenital and neonatal infections caused by TORCH and SARS-CoV-2 in newborns' cerebrospinal fluid.

OBJECTIVE: To verify the use and identify advantages of molecular methods for congenital infections diagnosis in cerebrospinal fluid of neonates. DATA SOURCE: The review was registered in the International Prospective Register of Systematic Reviews (PROSPERO), under CRD42021274210. The literature search was performed in databases: PubMed, Virtual Health Library/ Latin American and Caribbean Center on Health Sciences Information (VHL/BIREME), Scopus, Web of Science, Excerpta Medica database (EMBASE), Cochrane, ProQuest, and EBSCOhost. The search was carried out from August to October 2021 and updated in December 2022, respecting the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. The selection sequence was: 1) Duplicate title removal; 2) Examination of titles and abstracts; 3) Full-text retrieval of potentially relevant reports; and 4) Evaluation of the full text according to eligibility criteria by two independent authors. Inclusion criteria considered randomized and non-randomized control trials, longitudinal, cross-sectional, and peer-reviewed studies in humans, published in English, Spanish, Italian, and Portuguese, with newborns up to 28 days old who had congenital neuroinfections by toxoplasmosis, rubella, cytomegalovirus, herpes simplex (TORCH), and others such as Treponema pallidum, Zika, parvovirus B-19, varicella zoster, Epstein-Barr, and SARS-CoV2, diagnosed by polymerase chain reaction (PCR). Two evaluators extracted the following information: author, year of publication, nationality, subjects, study type, methods, results, and conclusion. DATA SYNTHESIS: The most studied pathogen was herpes simplex. Several articles reported only nonspecific initial symptoms, motivating the collection of cerebrospinal fluid and performing PCR for etiological investigation. CONCLUSIONS: Molecular methods are effective to detect pathogen genomes in cerebrospinal fluid, which can impact clinical evolution and neurological prognosis.

Performance of the IMMY® sona Aspergillus lateral flow assay for the detection of galactomannan in tracheal aspirate samples from Brazilian patients with COVID-19-associated pulmonary aspergillosis: Cross-sectional and systematic review of literature.

During the COVID-19 pandemic, many patients in intensive care units (ICUs) were affected by invasive fungal infections, including aspergillosis, contributing to a high mortality rate. Diagnosing proven COVID-19-associated pulmonary aspergillosis (CAPA) requires clinical and radiological evaluations, along with laboratory testing of bronchoalveolar lavage samples or lung biopsies. However, these procedures and equipment are often inaccessible in developing countries or regions with limited resources, including Brazil. Consequently, alternative diagnostic methods, such as measuring Aspergillus galactomannan (GM) in tracheal aspirate (TA), have been explored for CAPA diagnosis. Nonetheless, research on the efficacy of TA-based diagnostic tests is limited. This study aimed to assess the performance of the IMMY® Sona Aspergillus lateral flow assay (LFA) for GM detection in TA samples from 60 ICU patients with suspected CAPA at two tertiary hospitals in Campo Grande, Brazil. The ELISA method (Platelia Aspergillus AG, Bio-Rad®) was used to detect Aspergillus GM in TA samples, serving as the microbiological criterion and reference test. Fifteen patients (12.4%) were identified as having possible CAPA. The overall accuracy of LFA was 94%, and the tests demonstrated an agreement of 93.1% (Cohen's kappa of 0.83). Based on our findings, the LFA for Aspergillus GM detection in TA samples exhibited excellent performance, proving to be a valuable diagnostic tool for potential CAPA. In a systematic review, two studies were included, and the meta-analysis revealed pooled estimates provided a sensitivity of 86% (95% CI, 80%-91%) and specificity of 93% (95% CI, 86%-97%). The diagnostic odds ratio (DOR) for identification of Aspergillus using LFA was 103.38 (95% CI, 38.03-281.03). Despite its lower sensitivity compared to our study, the LFA appears to be a promising diagnostic option for CAPA, particularly in suspected cases that have not received antifungal therapy. This enables timely antifungal treatment and could reduce mortality rates in regions where bronchoscopy is unavailable or limited.

Challenges in the Diagnosis of SARS-CoV-2 Infection in the Nervous System.

Neurological involvement has been widely reported in SARS-CoV-2 infection. However, viral identification in the cerebrospinal fluid (CSF) is rarely found. The aim of this study is to evaluate the accuracy of virological and immunological biomarkers in CSF for the diagnosis of neuroCOVID-19. We analyzed 69 CSF samples from patients with neurological manifestations: 14 with suspected/confirmed COVID-19, with 5 additional serial CSF samples (group A), and as a control, 50 non-COVID-19 cases (group B-26 with other neuroinflammatory diseases; group C-24 with non-inflammatory diseases). Real-time reverse-transcription polymerase chain reaction (real-time RT-PCR) was used to determine SARS-CoV-2, and specific IgG, IgM, neopterin, and protein 10 induced by gamma interferon (CXCL-10) were evaluated in the CSF samples. No samples were amplified for SARS-CoV-2 by real-time RT-PCR. The sensitivity levels of anti-SARS-CoV-2 IgG and IgM were 50% and 14.28%, respectively, with 100% specificity for both tests. CXCL-10 showed high sensitivity (95.83%) and specificity (95.83%) for detection of neuroinflammation. Serial CSF analysis showed an association between the neuroinflammatory biomarkers and outcome (death and hospital discharge) in two cases (meningoencephalitis and rhombencephalitis). The detection of SARS-CoV-2 RNA and specific immunoglobulins in the CSF can be used for neuroCOVID-19 confirmation. Additionally, CXCL-10 in the CSF may contribute to the diagnosis and monitoring of neuroCOVID-19.

Discrimination between Covid-19 positive and negative blood serum based on excitation-emission matrix fluorescence spectroscopy and chemometrics.

The outbreak of the disease caused by the SARS-CoV-2 virus (Covid-19) has resulted in a global health emergency that has caused millions of deaths in recent years. The control of the pandemic was significantly impacted by the availability of inputs and qualified labor to correctly diagnose the population. The challenges faced by numerous countries in conducting this extensive diagnosis, utilizing methods such as RT-PCR, emphasize the necessity for alternative testing strategies that are less reliant on expensive raw materials and can be implemented on a larger scale. This paper proposes a methodology for classifying blood serum samples as either positive or negative for Covid-19 infection using excitation-emission matrix (EEM) fluorescence spectroscopy associated with multivariate analysis. The proposed methodology uses EEM spectra of samples diagnosed by the reference method (RT-PCR) to train and validate classification models. Two approaches were tested: the first using PARAFAC and the second by unfolding the excitation-emission matrices. The DD-SIMCA model performed best in the PARAFAC approach, with an error rate of 0.05, sensitivity of 0.98 and specificity of 0.96. The PLS-DA and PCA-DA models in the second approach effectively distinguished between classes. The PCA-DA model performed the best with an error rate of 0.06 and sensitivity and specificity of 0.94. Fluorescence spectroscopy was found to be effective in analyzing serum samples and obtaining discrimination models to determine if a patient is infected with SARS-CoV-2. The findings are encouraging and could aid in the development of an inexpensive and reliable auxiliary diagnostic method.

Notable correlation between serum epidermal growth factor values and inflammatory status in patients with COVID-19.

INTRODUCTION: Despite its crucial role in Epidermal Growth Factor Receptor (EGFR) activation, and the resulting impact on the health-disease process, epidermal growth factor (EGF) is an underexplored molecule in relation to how its serum concentrations relate to other analytes and clinical variables in pathological contexts. OBJECTIVE: To clarify the possible correlation between EGF and clinical and analytical variables in the context of COVID-19. METHODS: Cross-sectional observational and analytical study, in patients with virological and clinical diagnosis of COVID-19, selected by simple random sampling, admitted between August and September 2021. UMELISA-EGF commercial kits were used. RESULTS: Differences in overall EGF values were observed between groups (566.04 vs. 910.53 pg/ml, p = .0430). In COVID-19 patients, no notable correlations were observed for neutrophil, platelet, triglyceride or liver enzyme values (p > .05). Significant correlations were observed with the neutrophil-lymphocyte indicator (r = 0.4711, p = .0128) as well as with the platelet-lymphocyte index (r = 0.4553, p = .0155). Statistical results of multivariate regression analysis suggest NLR (ß = .2232, p = .0353) and PLR (ß = .2117, p = .0411) are predictors of inflammation in patients with COVID-19. CONCLUSIONS: Serum EGF concentrations in COVID-19 correlate positively with prognostic inflammatory markers of severity and could presumably act as an independent risk factor for the development of inflammation in response to new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).

An end-point multiplex RT-PCR for SARS-CoV-2, Influenza A and B detection, including simultaneous RNAse P amplification: a timely tool for more accessible differential diagnosis.

The multiplex molecular diagnostic assays described for severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2), influenza A (IAV) and B (IBV) viruses have been mainly based on real-time reaction, which limits their access to many laboratories or diagnostic institutions. To contribute to available strategies and expand access to differential diagnosis, we describe an end-point multiplex RT-PCR targeting SARS-CoV-2, IAV and IBV with simultaneous endogenous control amplification. Initially, we looked for well-established primers sets for SARS-CoV-2, IAV, IBV and RNAse P whose amplicons could be distinguished on agarose gel. The multiplex assay was then standardized by optimizing the reaction mix and cycle conditions. The limit of detection (LoD) was determined using titrated viruses (for SARS-CoV-2 and IAV) and by dilution from a pool of IBV-positive samples. The diagnostic performance of the multiplex was evaluated by testing samples with different RNAse P and viral loads, previously identified as positive or negative for the target viruses. The amplicons of IAV (146 bp), SARS-CoV-2 (113 bp), IBV (103 bp) and RNAse P (65 bp) were adequately distinguished in our multiplex. The LoD for SARS-CoV-2, IAV and IBV was 0.02 TCID50/ml, 0.07 TCID50/ml and 10-3 from a pool of positive samples, respectively. All samples positive for SARS-CoV-2 (n=70, Ct 17.2-36.9), IAV (n=53, Ct 14-34.9) and IBV (n=12, Ct 23.9-31.9) remained positive in our multiplex assay. RNAse P from negative samples (n=40, Ct 25.2-30.2) was also amplified in the multiplex. Overall, our assay is a timely and alternative tool for detecting SARS-CoV-2 and influenza viruses in laboratories with limited access to supplies/equipment.

Identification of distinct phenotypes and improving prognosis using metabolic biomarkers in COVID-19 patients.

OBJECTIVE: To investigate the relationship between the levels of adipokines and other endocrine biomarkers and patient outcomes in hospitalized patients with COVID-19. METHODS: In a prospective study that included 213 subjects with COVID-19 admitted to the intensive care unit, we measured the levels of cortisol, C-peptide, glucagon-like peptide-1, insulin, peptide YY, ghrelin, leptin, and resistin.; their contributions to patient clustering, disease severity, and predicting in-hospital mortality were analyzed. RESULTS: Cortisol, resistin, leptin, insulin, and ghrelin levels significantly differed between severity groups, as defined by the World Health Organization severity scale. Additionally, lower ghrelin and higher cortisol levels were associated with mortality. Adding biomarkers to the clinical predictors of mortality significantly improved accuracy in determining prognosis. Phenotyping of subjects based on plasma biomarker levels yielded two different phenotypes that were associated with disease severity, but not mortality. CONCLUSION: As a single biomarker, only cortisol was independently associated with mortality; however, metabolic biomarkers could improve mortality prediction when added to clinical parameters. Metabolic biomarker phenotypes were differentially distributed according to COVID-19 severity but were not associated with mortality.

SARS-CoV-2 infection during pregnancy: clinical characteristics and vertical transmission in a referral hospital in Peru. / Infección por SARS-CoV-2 en el embarazo: características clínicas y trasmisión vertical en un hospital de referencia de Perú.

Motivation for the study. There is a gap in knowledge about vertical transmission of SARS- CoV-2 and its implications for maternal and neonatal health, despite evidence of multisystem involvement in pregnant women with COVID-19. Main findings. The study results suggest low incidence of vertical transmission during pregnancy, with only one PCR-positive case in the placenta and one asymptomatic neonate. Implications. Our results can inform strategies for prevention and management of COVID-19 in pregnant women, as well as guide the development of health policies aimed at protecting maternal and neonatal health during the pandemic. The aim of this study was to analyze the vertical transmission of SARS-CoV-2 in pregnant women with COVID-19 in the Gynecology and Obstetrics Department of the Edgardo Rebagliati Martins National Hospital (HNERM). Twelve pregnant women who met the inclusion criteria were included. Real-time PCR (RT-PCR) tests for SARS-CoV-2 were performed when each woman was admitted to the hospital, placenta samples were collected for pathological evaluation as well. The results showed that vertical transmission of the virus was rare, with an overall low positivity rate in newborns. Although the study has limitations, such as the small number of cases and the lack of electron microscope analysis, it is the first attempt to evaluate vertical transmission in Peru. It is concluded that more research is needed to better understand the relationship between COVID-19 infection and complications during pregnancy.

Se realizó un estudio en el departamento de Ginecología y Obstetricia del Hospital Nacional Edgardo Rebagliati Martins (HNERM) con el objetivo analizar la transmisión vertical del SARS-CoV-2 en mujeres embarazadas con COVID-19. Se incluyeron 12 gestantes que cumplían con los criterios de inclusión. Se realizaron pruebas diagnósticas de PCR en tiempo real (RT-PCR) para SARS-CoV-2 durante la admisión de cada gestante y se recolectaron muestras de placenta para su evaluación anatomopatológica. Los resultados mostraron que la transmisión vertical del virus fue poco común, con una tasa general de positividad baja en los recién nacidos. Aunque el estudio presenta limitaciones, como el número reducido de casos y la falta de análisis con microscopio electrónico, constituye el primer intento en Perú de evaluar la transmisión vertical. Se concluye que se necesita más investigación para comprender mejor la relación entre la infección por la COVID-19 y las complicaciones durante el embarazo. Motivación para realizar el estudio. A pesar de la evidencia de una afectación multisistémica en mujeres embarazadas con la COVID-19, existe un vacío de conocimiento sobre la transmisión vertical del virus y sus implicancias en la salud materna y neonatal. Principales hallazgos. Los resultados del estudio sugieren una baja incidencia de transmisión vertical durante el embarazo, con solo un caso positivo de PCR en la placenta y un neonato asintomático. Implicancias. Este resultado pueden informar las estrategias de prevención y manejo de la COVID-19 en mujeres embarazadas, así como guiar el desarrollo de políticas sanitarias dirigidas a proteger la salud materna y neonatal durante la pandemia.