Estimate false-negative RT-PCR rates for SARS-CoV-2. A systematic review and meta-analysis

A novel method for detecting SARS-CoV-2 IgM and IgG based on the gold immune chromatography assay

A novel method was proposed based on gold immune chromatography assay (GICA) including the detection of antibodies targeting different severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) epitopes to improve the SARS-CoV-2 IgM and IgG detection performance. Sera from 282 confirmed Coronavirus Disease 2019 (COVID-19) patients were obtained at different times as the SARS-CoV-2 IgM or IgG experimental group. Sera from 148 uninfected and unvaccinated individuals were used as the control. The serum single-epitope IgM and IgG antibodies against SARS-CoV-2 were detected via GICA; the two epitope antibodies with high detection performance were used to construct a novel method, and then compared with the chemiluminescence immunoassay (CLIA). The diagnostic specificity and screening sensitivity of S2-IgM and N-IgM combined detection of serum SARS-CoV-2 IgM antibodies based on GICA were 99.32% and 98.81%, respectively, which were higher than those of the CLIA test (83.78% and 82.14%; P < 0.001). The diagnostic specificity of RBD-IgG and N-IgG combined detection in the serum was 100.00%, the same as that of CLIA. The novel method showed excellent screening sensitivity and diagnostic specificity for serum SARS-CoV-2 IgM and IgG, effectively avoiding omissions and misdiagnoses in the early clinical stages of screening and diagnosing COVID-19.

The external validity of machine learning-based prediction scores from hematological parameters of COVID-19: A study using hospital records from Brazil, Italy, and Western Europe

The unprecedented worldwide pandemic caused by COVID-19 has motivated several research groups to develop machine-learning based approaches that aim to automate the diagnosis or screening of COVID-19, in large-scale. The gold standard for COVID-19 detection, quantitative-Real-Time-Polymerase-Chain-Reaction (qRT-PCR), is expensive and time-consuming. Alternatively, haematology-based detections were fast and near-accurate, although those were less explored. The external-validity of the haematology-based COVID-19-predictions on diverse populations are yet to be fully investigated. Here we report external-validity of machine learning-based prediction scores from haematological parameters recorded in different hospitals of Brazil, Italy, and Western Europe (raw sample size, 195554). The XGBoost classifier performed consistently better (out of seven ML classifiers) on all the datasets. The working models include a set of either four or fourteen haematological parameters. The internal performances of the XGBoost models (AUC scores range from 84% to 97%) were superior to ML models reported in the literature for some of these datasets (AUC scores range from 84% to 87%). The meta-validation on the external performances revealed the reliability of the performance (AUC score 86%) along with good accuracy of the probabilistic prediction (Brier score 14%), particularly when the model was trained and tested on fourteen haematological parameters from the same country (Brazil). The external performance was reduced when the model was trained on datasets from Italy and tested on Brazil (AUC score 69%) and Western Europe (AUC score 65%); presumably affected by factors, like, ethnicity, phenotype, immunity, reference ranges, across the populations. The state-of-the-art in the present study is the development of a COVID-19 prediction tool that is reliable and parsimonious, using a fewer number of hematological features, in comparison to the earlier study with meta-validation, based on sufficient sample size (n = 195554). Thus, current models can be applied at other demographic locations, preferably, with prior training of the model on the same population. Availability: https://covipred.bits-hyderabad.ac.in/home; https://github.com/debashreebanerjee/CoviPred.

The Histopathologic Features of Early COVID Pneumonia in a Pediatric Patient: New Insight into the Role of Macrophages

A life-threatening complication of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection is acute respiratory distress syndrome. Our understanding of the pathologic changes in coronavirus disease 2019 (COVID-19) is based almost exclusively on post-mortem analyses of adults. These studies established several hallmarks of SARS-CoV-2 lung infection, including diffuse alveolar damage, microvascular thrombi, and acute bronchopneumonia. We describe a fatal example of COVID pneumonia in a 9-year-old girl who presented with fever 10 months following the diagnosis of ALK-positive anaplastic large cell lymphoma (ALCL). A chest computed tomography scan revealed left upper lobe lung consolidation and nodular airspace disease, and an initial SARS-CoV-2 nasopharyngeal swab (RT-PCR) was negative. A subsequent lung biopsy performed due to concern for relapsed ALCL demonstrated sheets of intra-alveolar and interstitial macrophages, and macrophage-rich fibrinous exudates. Immunohistochemical and in-situ hybridization stains confirmed these macrophages as the predominant SARS-CoV-2-infected cell type. Subsequent RT-PCR testing of upper and lower respiratory tract samples was positive for SARS-CoV-2 infection. Whole genome sequencing confirmed the presence of the B.1.617.2 (Delta) variant. This biopsy illustrates the histopathologic features of early COVID pneumonia in antemortem lung tissue from a pediatric patient, and establishes macrophages as a potential source of SARS-CoV-2 amplification.

Exploring the causes of variability in quality of oropharyngeal swab sampling for SARS-CoV-2 nucleic acid testing and proposed improvement measures: a multicenter, double-blind study

Although coronavirus disease 2019 (COVID-19) has not been considered a public health emergency of international concern since last year, intermittent regional impacts still persist, and accurate testing remains crucial. Ribonuclease P protein subunit P30 (RPP30) RNA, known for its broad and stable expression in tissue cells, was used to evaluate samples from 10 hospitals with over 3,000 negative nucleic acid tests. The results revealed that the overall pass rate for the collected samples was consistently low and exhibited significant heterogeneity. After reassessing the evaluative effectiveness of RPP30 RNA Ct values from the samples of 132 positive individuals under quarantine observation, it was used to identify factors affecting sampling quality. These factors included different stages ranging from sample collection to PCR processing, various characteristics of both samplers and individuals being sampled, as well as sampling season and location. The results indicated that post-sampling handling had minimal impact, winter and fever clinic samples showed higher quality, whereas children's samples had lower quality. The key finding was that the characteristics of samplers were closely related to sampling quality, emphasizing the role of subjectivity. Quality control warnings led to substantial improvements, confirming this finding. Consequently, although there are various factors during the testing process, the most critical aspect is to improve, supervise, and maintain standardized practices among sampling staff.IMPORTANCEThis study further confirmed the reliability of internal references (IRs) in assessing sample quality, and utilized a large sample IR data to comprehensively and multidimensionally identify significant interference factors in nucleic acid test results. By further reminding and intervening in the subjective practices of specimen collectors, good results could be achieved.

ViralPrimer: a web server to monitor viral nucleic acid amplification tests' primer efficiency during pandemics, with emphasis on SARS-CoV-2 and Mpox

SUMMARY

Accurate pathogen identification is crucial during outbreaks, especially with the emergence of new variants requiring frequent primer updates. However, resources for maintaining up-to-date verification of primer sequences are often limited, which poses challenges for reliable diagnosis and hinders potential monitoring efforts based on genome sequencing. To address this, we introduce ViralPrimer, a web server facilitating primer design, SARS-CoV-2 and Mpox variant monitoring, and adaptation to future threats. ViralPrimer aims to enhance diagnostic accuracy with its comprehensive primer database, mutation analysis assistance, and user primer upload feature. Its adaptable design allows monitoring of other rapidly mutating pathogens, contributing to broader public health protection efforts.

AVAILABILITY AND IMPLEMENTATION

ViralPrimer is freely accessible and open to all users with no login requirement at https://viralprimer.elte.hu/. The application is hosted on a DJANGO v3.2.13 web server, with a PostgreSQL database, and the frontend was implemented using jQuery v3.6.0, vanilla JavaScript vES6, and Bootstrap v5.1.

Strategies to Overcome Erroneous Outcomes in Reverse Transcription-Polymerase Chain Reaction (RT-PCR) Testing: Insights From the COVID-19 Pandemic

The reverse transcription-polymerase chain reaction (RT-PCR) test to detect SARS-CoV-2, the virus causing COVID-19, has been regarded as the diagnostic gold standard. However, the excessive sensitivity of RT-PCR may cause false-positive outcomes from contamination. Again, its technical complexity increases the chances of false-negatives due to pre-analytical and analytical errors. This narrative review explores the elements contributing to inaccurate results during the COVID-19 pandemic and offers strategies to minimize these errors. False-positive results may occur due to specimen contamination, non-specific primer binding, residual viral RNA, and false-negatives, which may arise from improper sampling, timing, labeling, storage, low viral loads, mutations, and faulty test kits. Proposed mitigation strategies to enhance the accuracy of RT-PCR testing include comprehensive staff training in specimen collection, optimizing the timing of tests, analyzing multiple gene targets, incorporating clinical findings, workflow automation, and implementing stringent contamination control measures. Identifying and rectifying sources of error in RT-PCR diagnosis through quality control and standardized protocols is imperative for ensuring quality patient care and effective epidemic control.

COVID 19: Prevention and treatment through the Indian perspective

The most destructive period the world has experienced seems to be behind us. Not a single nation was spared by this disease, and many continue to struggle today. Even after recovering from COVID, patient may continue to experience some post-COVID effects, such as heart irregularities or a decline in lung vitality. In the past three years (2019-2022), the world has witnessed the power of a small entity, a single peculiar virus. Science initially appeared to be helpless in this regard, but due to the emergence of disease, pharmaceutics (the development of anti-covid drugs), immunology (the rapid antigen test), microbiology (the isolation of viruses from infected people), biotechnology (the development of recombinant vaccines), biochemistry (the blood profile, the D-dimer test), and biochemistry (blood profile, D-dimer test), biophysics (PCR, RT-PCR, CT Scan, MRI) had worked together to fight the disease. The results of these efforts are the development of new diagnostic techniques, possible treatment and finally the availability of vaccines against COVID-19. However, it is not proven that the treatment through the traditional medical system is directly active on SARS-CoV-2 but is instead indirectly acting on SARS-CoV-2 effects by improving symptoms derived from the viral disease. In India, the traditional system of medicine and tradition knowledge together worked in the pandemic and proved effective strategies in prevention and treatment of SARS-CoV-2. The use of effective masks, PPE kits, plasma therapy, yoga, lockdowns and social seclusion, use of modern antiviral drugs, monoclonal antibodies, herbal remedies, homoeopathy, hygienic practice, as well as the willpower of people, are all contributing to the fight against COVID. Which methods or practices will be effective against COVID nobody is aware since medical professionals who wear PPE kits do not live longer, and some people in India who remained unprotected and roamed freely were not susceptible to infection. The focus of this review is on the mode of transmission, diagnosis, preventive measures, vaccines currently under development, modern medicine developed against SARS-CoV-2, ayurvedic medicine used during pandemic, homoeopathic medicine used during pandemic, and specific yoga poses that can be used to lessen COVID-related symptoms.

Designing and optimizing clinical trials for long COVID

Long COVID is a debilitating, multisystemic illness following a SARS-CoV-2 infection whose duration may be indefinite. Over four years into the pandemic, little knowledge has been generated from clinical trials. We analyzed the information available on ClinicalTrials.gov, and found that the rigor and focus of trials vary widely, and that the majority test non-pharmacological interventions with insufficient evidence. We highlight promising trials underway, and encourage the proliferation of clinical trials for treating Long COVID and other infection-associated chronic conditions and illnesses (IACCIs). We recommend several guidelines for Long COVID trials: First, pharmaceutical trials with potentially curative, primary interventions should be prioritized, and both drug repurposing and new drug development should be pursued. Second, study designs should be both rigorous and accessible, e.g., triple-blinded randomized trials that can be conducted remotely, without participants needing to leave their homes. Third, studies should have multiple illness comparator cohorts for IACCIs such as myalgic encephalomyelitis (ME/CFS) and dysautonomia, and screen for the full spectrum of symptomatology and pathologies of these illnesses. Fourth, studies should consider inclusion/exclusion criteria with an eye towards equity and breadth of representation, including participants of all races, ethnicities, and genders most impacted by COVID-19, and including all levels of illness severity. Fifth, involving patient-researchers in all aspects of studies brings immensely valuable perspectives that will increase the impact of trials. We also encourage the development of efficient clinical trial designs including methods to study several therapies in parallel.

Comparison of clinical, laboratory and radiological characteristics between COVID-19 and Chlamydia psittaci pneumonia: a multicenter retrospective study

Chlamydia psittaci pneumonia (CPP) exhibits similar characteristics as of COVID-19 with respect to clustering outbreaks and onset symptoms. This study is aimed at exploring the different clinical manifestations of both pneumonias to establish a simple nomogram to distinguish them. This multicenter, retrospective, case-control study compared two independent cohorts of patients with CPP or COVID-19. The risk factors of CPP were analyzed using multivariate logistic regression, which was used to establish the nomogram. Both patients with CPP and COVID-19 exhibited similar clinical symptoms. As compared to patients with COVID-19, a higher proportion of patients with CPP had nervous system symptoms. Patients with CPP had higher inflammatory indicators, creatine kinase, and lower lymphocyte and albumin. They also had lower proportions of ground-glass opacity and bilateral lung involvement than COVID-19 patients. Furthermore, patients with CPP had higher 30 day mortality as well as higher rates of severe pneumonia, septic shock, and ICU admission. Multivariate logistic regression showed that nervous system symptoms, lymphocytes, creatine kinase, bilateral lung lesions, and ground-glass opacity were risk factors for CPP. Incorporating these five factors, the nomogram achieved good concordance index of 0.989 in differentiating CPP from COVID-19, and had well-fitted calibration curves. Despite similar clinical characteristics, nervous system symptoms, lymphocyte, creatine kinase, lesions in bilateral lungs, and ground-glass opacity may help in differentiating the pneumonias. These were combined into a clinically useful nomogram for rapid and early identification of CPP to avoid misdiagnosis and help in the decision-making process.

Sample-to-answer centrifugal microfluidic droplet PCR platform for quantitation of viral load

Droplet digital polymerase chain reaction (ddPCR) stands out as a highly sensitive diagnostic technique that is gaining traction in infectious disease diagnostics due to its ability to quantitate very low numbers of viral gene copies. By partitioning the sample into thousands of droplets, ddPCR enables precise and absolute quantification without relying on a standard curve. However, current ddPCR systems often exhibit relatively low levels of integration, and the analytical process remains dependent on elaborate workflows for up-front sample preparation. Here, we introduce a fully-integrated system seamlessly combining viral lysis, RNA extraction, emulsification, reverse transcription (RT) ddPCR, and fluorescence readout in a sample-to-answer format. The system comprises a disposable microfluidic cartridge housing buffers and reagents required for the assay, and a centrifugal platform that allows for pneumatic actuation of liquids during rotation, enabling automation of the workflow. Highly monodisperse droplets (∼50 μm in diameter) are produced using centrifugal step emulsification and automatically transferred to an integrated heating module for target amplification. The platform is equipped with a miniature fluorescence imaging system enabling on-chip read-out of droplets after RT-ddPCR. We demonstrate sample-to-answer detection of SARS-CoV-2 N and E genes, along with RNase P endogenous reference, using hydrolysis probes and multiplexed amplification within single droplets for concentrations as low as 0.1 copy per μL. We also tested 14 nasopharyngeal swab specimens from patients and were able to distinguish positive and negative SARS-CoV-2 samples with 100% accuracy, surpassing results obtained by conventional real-time amplification.

A droplet digital PCR method for the detection of scale drop disease virus in yellowfin seabream (Acanthopagrus latus)

In this study, a ddPCR method for the detection of scale drop disease virus (SDDV) in yellowfin seabream (Acanthopagrus latus) was established based on Real-time fluorescence quantitative PCR detection methods and principles. The reaction conditions were optimized, and the sensitivity, specificity, accuracy, and reproducibility were assessed. The results showed that threshold line position was determined to be 1900 by the ddPCR method; the optimum annealing temperature for SDDV detection by the ddPCR method was 60°C; the limit of detection was 1.4-1.7 copies/μL; the results of specific detection of other common viruses, except for SDDV specific amplification, were all negative; and the relative standard deviation (RSD) for the reproducibility validation was 0.77%. The samples of yellowfin seabream (Acanthopagrus latus) liver, spleen, kidney, heart, intestine, brain, blood, muscle, skin and ascites with three replicates, respectively, were tested using the ddPCR method, and the results were consistent with clinical findings. The ddPCR method established in this study has the advantages of high sensitivity, high specificity, good reproducibility and simple steps for the quantitative detection of SDDV, which could be used for the nucleic acid detection of clinical SDDV samples, and provided a new quantitative method for the diagnosis of yellowfin seabream SDDV in the early stage of pathogenesis.

Effects of post-acute COVID-19 syndrome on cerebral white matter and emotional health among non-hospitalized individuals

Introduction

Post-acute COVID syndrome (PACS) is a growing concern, given its impact on mental health and quality of life. However, its effects on cerebral white matter remain poorly understood, particularly in non-hospitalized cohorts. The goals of this cross-sectional, observational study were to examine (1) whether PACS was associated with distinct alterations in white matter microstructure, compared to symptom-matched non-COVID viral infection; and (2) whether microstructural alterations correlated with indices of post-COVID emotional health.

Methods

Data were collected for 54 symptomatic individuals who tested positive for COVID-19 (mean age 41 ± 12 yrs., 36 female) and 14 controls who tested negative for COVID-19 (mean age 41 ± 14 yrs., 8 female), with both groups assessed an average of 4-5 months after COVID testing. Diffusion magnetic resonance imaging data were collected, and emotional health was assessed via the NIH emotion toolbox, with summary scores indexing social satisfaction, well-being and negative affect.

Results

Despite similar symptoms, the COVID-19 group had reduced mean and axial diffusivity, along with increased mean kurtosis and neurite dispersion, in deep white matter. After adjusting for social satisfaction, higher levels of negative affect in the COVID-19 group were also correlated with increased mean kurtosis and reduced free water in white matter.

Discussion

These results provide preliminary evidence that indices of white matter microstructure distinguish PACS from symptomatic non-COVID infection. Moreover, white matter effects seen in PACS correlate with the severity of emotional sequelae, providing novel insights into this highly prevalent disorder.

Optical detection of infectious SARS-CoV-2 virions by counting spikes

Existing methods for the mass detection of viruses are limited to the registration of small amounts of a viral genome or specific protein markers. In spite of high sensitivity, the applied methods cannot distinguish between virulent viral particles and non-infectious viral particle debris. We report an approach to solve this long-standing challenge using the SARS-CoV-2 virus as an example. We show that wide-field optical microscopy with the state-of-the-art mesoscopic fluorescent labels, formed by a core-shell plasmonic nanoparticle with fluorescent dye molecules in the core-shell that are strongly coupled to the plasmonic nanoparticle, not only rapidly, i.e. in less than 20 minutes after sampling, detects SARS-CoV-2 virions directly in a patient sample without a pre-concentration step, but can also distinguish between infectious and non-infectious virus strains by counting the spikes on the lipid envelope of individual viral particles.

Does coronavirus disease 2019 affect peripheral and central auditory systems? Matched group cross-sectional study and six-month follow up

OBJECTIVE

This study aimed to compare the peripheral-to-central auditory systems of people with coronavirus disease 2019 to a well-matched control group and examine the long-term effects of coronavirus disease 2019 on the auditory system.

METHOD

Participants who were outpatients of coronavirus disease 2019 (n = 30) were compared with a well-matched control group (n = 30). Behavioural and electrophysiological tests were performed, and tests were repeated at six months in the coronavirus disease 2019 group.

RESULTS

Statistically significant differences were observed in the right ear at 10 kHz (p = 0.007) and 12.5 kHz (p = 0.028), and in the left ear at 10 kHz (p = 0.040) and 12.5 kHz (p = 0.040) between groups. The groups had no difference regarding the other audiological test results (p > 0.05).

CONCLUSION

Extended high-frequency thresholds were affected in the coronavirus disease 2019 patients. No other findings indicated that the peripheral-to-central auditory system was affected. The effect on extended high-frequency thresholds appeared permanent, but no clinically significant new, late-onset auditory system effects were observed.

Quality assurance of SARS-CoV-2 testing laboratories during the pandemic period in India - An experience from a designated provider laboratory

PURPOSE

Indian Council of Medical Research (ICMR) initiated an Inter-Laboratory Quality Control testing (ILQC) program for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) testing. Under this program, SARS-CoV-2 testing laboratories across the country submit specimens to the assigned State Quality Control (SQCs) laboratories for ILQC testing. This study aimed to investigate the performance of public and private SARS-CoV-2 testing laboratories in Delhi and highlights the country's effort in ramping up testing facility with close monitoring of the quality of Covid-19 testing results.

METHODS

In the present study, two-years of SARS-CoV-2 testing data is included. During July 2020 through February 2022, a total of 1791 anonymised specimens were received from 56 public and private laboratories. These specimens were processed by reverse transcriptase - polymerase chain reaction (RT-PCR) tests as per National Institute of Virology (NIV) protocol and the results were uploaded on the ICMR quality control/quality assurance (QC/QA) portal without directly conveying the results to respective participating laboratories. This portal generated a final report stating concordance and intimate results to individual laboratories.

RESULTS

Among the 1791 specimens, 25 were rejected and the remaining 1766 were tested. Among these specimens 1691 (95.75%) revealed concordance, and 75 (4.24%) were discordant. A total of 29 laboratories had 100% concordance, 21 laboratories had over 90% concordance and six laboratories had over 80% concordance.

CONCLUSIONS

The study demonstrates that the establishment of an inter-laboratory comparison program for SARS-CoV-2 testing helped in monitoring quality of SARS-CoV-2 testing in the country.

Global COVID-19 Pandemic Outcomes: A Cross-Country Comparison Study of Policy Strategies

This paper explores global COVID-19 treatment and containment strategies in 108 countries worldwide, specifically the correlation between COVID-19 deaths and the countries' vaccination rates. Comparison of data across states, provinces, territories, and countries relied upon a common method to evaluate data regarding the impact of COVID-19 policies in the last three years. Data from nine different databases were analyzed to determine if there were correlations between the percentage of countrywide COVID-19 deaths/population and countries' percent vaccinated. Secondary outcome measures include the effect of other variables on COVID-19 death rates per country population, including health expenditures and annual income per capita, COVID-19 tests per 1000 people, stringency index (a measure of each country's containment strategies), hydroxychloroquine/ivermectin scores (measure country use), hypertension, obesity, diabetes, and geographic locations. COVID-19 vaccination rates ranged from 0-99% in 108 countries. Bivariate analysis demonstrates the following independent variables to correlate with COVID-19 deaths/population (Spearman correlation coefficient, p value): countrywide COVID-19 vaccination rates (moderate relationship, r=0.39, P < .001); healthcare expenditures per capita per annum (US dollars) (moderate relationship, r=0.46, P < .001), net annual income per capita (moderate relationship, r=0.50, P < .001), COVID-19 tests per 1000 country population (moderate relationship, r=0.36, P < .003); stringency index per country (moderate relationship, r=0.28, P < .003); hydroxychloroquine index (negative relationship, r= 0.15, P = .125); and ivermectin index (negative relationship, r=0.23 P = .018). The authors found that the higher the percentage of a country's vaccination rate, stringent containment strategies, mass testing, etc., moderately correlated with higher COVID-19 death rates/population. Future studies are required to explore the findings of this study fully.

Using SCENTinel® to predict SARS-CoV-2 infection: insights from a community sample during dominance of Delta and Omicron variants

Introduction

Based on a large body of previous research suggesting that smell loss was a predictor of COVID-19, we investigated the ability of SCENTinel®, a newly validated rapid olfactory test that assesses odor detection, intensity, and identification, to predict SARS-CoV-2 infection in a community sample.

Methods

Between April 5, 2021, and July 5, 2022, 1,979 individuals took one SCENTinel® test, completed at least one physician-ordered SARS-CoV-2 PCR test, and endorsed a list of self-reported symptoms.

Results

Among the of SCENTinel® subtests, the self-rated odor intensity score, especially when dichotomized using a previously established threshold, was the strongest predictor of SARS-CoV-2 infection. SCENTinel® had high specificity and negative predictive value, indicating that those who passed SCENTinel® likely did not have a SARS-CoV-2 infection. Predictability of the SCENTinel® performance was stronger when the SARS-CoV-2 Delta variant was dominant rather than when the SARS-CoV-2 Omicron variant was dominant. Additionally, SCENTinel® predicted SARS-CoV-2 positivity better than using a self-reported symptom checklist alone.

Discussion

These results indicate that SCENTinel® is a rapid assessment tool that can be used for population-level screening to monitor abrupt changes in olfactory function, and to evaluate spread of viral infections like SARS-CoV-2 that often have smell loss as a symptom.

SARS-CoV-2 infection increases long-term multiple sclerosis disease activity and all-cause mortality in an underserved inner-city population

BACKGROUND

Although certain subsets patients with multiple sclerosis (MS), an immune-mediated disorder, are at higher risk of worse acute COVID-19 outcomes compared to the general population, it is not clear whether SARS-CoV-2 infection impacts long-term outcomes compared with MS patients without COVID-19 infection.

OBJECTIVES

This study investigated MS disease activity and mortality 3.5 years post SARS-CoV-2 infection and compared with MS patients without COVID-19.

METHODS

This retrospective study evaluated 1,633 patients with MS in the Montefiore Health System in the Bronx from January 2016 to July 2023. This health system serves a large minority population and was an epicenter for the early pandemic and subsequent surges of infection. Positive SARS-CoV-2 infection was determined by a positive polymerase-chain-reaction test. Primary outcomes were all-cause mortality, and optic neuritis post SARS-CoV-2 infection. Secondary outcomes included change in disease-modifying therapy (DMT), treatment with high-dose methylprednisolone, cerebellar deficits, relapse, and all-cause hospitalization post-infection.

RESULTS

MS patients with COVID-19 had similar demographics but higher prevalence of pre-existing major comorbidities (hypertension, type-2 diabetes, chronic obstructive pulmonary disease, congestive heart failure, chronic kidney disease, and coronary artery disease), optic neuritis, and history of high dose steroid treatment for relapses compared to MS patients without COVID-19. MS patients with COVID-19 had greater risk of mortality (adjusted HR=4.34[1.67, 11.30], p < 0.005), greater risk of post infection optic neuritis (adjusted HR=2.97[1.58, 5.58], p < 0.005), higher incidence of methylprednisolone treatment for post infection acute relapse (12.65% vs. 2.54 %, p < 0.001), and more hospitalization (78.92% vs. 66.81 %, p < 0.01), compared to MS patients without COVID-19.

CONCLUSIONS

MS patients who survived COVID-19 infection experienced worse long-term outcomes, as measured by treatment for relapse, hospitalization and mortality. Identifying risk factors for worse long-term outcomes may draw clinical attention to the need for careful follow-up of at-risk individuals post-SARS-CoV-2 infection.

Comparison of the Discrimination Performance of AI Scoring and the Brixia Score in Predicting COVID-19 Severity on Chest X-Ray Imaging: Diagnostic Accuracy Study

BACKGROUND

The artificial intelligence (AI) analysis of chest x-rays can increase the precision of binary COVID-19 diagnosis. However, it is unknown if AI-based chest x-rays can predict who will develop severe COVID-19, especially in low- and middle-income countries.

OBJECTIVE

The study aims to compare the performance of human radiologist Brixia scores versus 2 AI scoring systems in predicting the severity of COVID-19 pneumonia.

METHODS

We performed a cross-sectional study of 300 patients suspected with and with confirmed COVID-19 infection in Jakarta, Indonesia. A total of 2 AI scores were generated using CAD4COVID x-ray software.

RESULTS

The AI probability score had slightly lower discrimination (area under the curve [AUC] 0.787, 95% CI 0.722-0.852). The AI score for the affected lung area (AUC 0.857, 95% CI 0.809-0.905) was almost as good as the human Brixia score (AUC 0.863, 95% CI 0.818-0.908).

CONCLUSIONS

The AI score for the affected lung area and the human radiologist Brixia score had similar and good discrimination performance in predicting COVID-19 severity. Our study demonstrated that using AI-based diagnostic tools is possible, even in low-resource settings. However, before it is widely adopted in daily practice, more studies with a larger scale and that are prospective in nature are needed to confirm our findings.

Optimization of Screening Strategies for COVID-19: Scoping Review

BACKGROUND

COVID-19 screening is an effective nonpharmaceutical intervention for identifying infected individuals and interrupting viral transmission. However, questions have been raised regarding its effectiveness in controlling the spread of novel variants and its high socioeconomic costs. Therefore, the optimization of COVID-19 screening strategies has attracted great attention.

OBJECTIVE

This review aims to summarize the evidence and provide a reference basis for the optimization of screening strategies for the prevention and control of COVID-19.

METHODS

We applied a methodological framework for scoping reviews and the PRISMA-ScR (Preferred Reporting Items for Systematic Reviews and Meta-Analyses Extension for Scoping Reviews) checklist. We conducted a scoping review of the present publications on the optimization of COVID-19 screening strategies. We searched the PubMed, Web of Science, and Elsevier ScienceDirect databases for publications up to December 31, 2022. English publications related to screening and testing strategies for COVID-19 were included. A data-charting form, jointly developed by 2 reviewers, was used for data extraction according to the optimization directions of the screening strategies.

RESULTS

A total of 2770 unique publications were retrieved from the database search, and 95 abstracts were retained for full-text review. There were 62 studies included in the final review. We summarized the results in 4 major aspects: the screening population (people at various risk conditions such as different regions and occupations; 12/62, 19%), the timing of screening (when the target population is tested before travel or during an outbreak; 12/62, 19%), the frequency of screening (appropriate frequencies for outbreak prevention, outbreak response, or community transmission control; 6/62, 10%), and the screening and detection procedure (the choice of individual or pooled detection and optimization of the pooling approach; 35/62, 56%).

CONCLUSIONS

This review reveals gaps in the optimization of COVID-19 screening strategies and suggests that a number of factors such as prevalence, screening accuracy, effective allocation of resources, and feasibility of strategies should be carefully considered in the development of future screening strategies.

The evaluation of a rapid microfluidic immunofluorescence antigen test in detecting the infectiousness of COVID-19 patients

BACKGROUND

A test-based strategy against coronavirus disease 2019 (COVID-19) is one of the measures to assess the need for isolation and prevention of infection. However, testing with high sensitivity methods, such as quantitative RT-PCR, leads to unnecessary isolation, whereas the lateral flow antigen test shows low sensitivity and false negative results. The purpose of this study was to evaluate the performance of the LumiraDx SARS-CoV-2 Ag test (Lumira Ag), a rapid microfluidic immunofluorescence method, in assessing infectivity.

METHODS

This study was performed from March 2022 to July 2022. A pair of nasopharyngeal swab samples were obtained from each patient with mild COVID-19. One swab was used for Lumira Ag testing, and the other for quantitative RT-PCR testing and virus culture.

RESULTS

A total of 84 patients were included in the study. Among them, PCR, Lumira Ag test, and virus culture indicated positivity for 82, 66, and 24 patients, respectively. When comparing the Lumira Ag test to virus culture, its sensitivity was 100.0% (24/24), specificity, 30.0% (18/60); positive predictive value, 36.3% (24/66); and negative predictive value (NPV), 100.0% (18/18). The positive sample for virus culture was observed until the ninth day from the onset of symptoms, while the Lumira Ag test was observed until day 11.

CONCLUSIONS

The Lumira Ag test showed high sensitivity and NPV (100% each) compared to virus culture. A test-based strategy using the Lumira Ag test can effectively exclude COVID-19 infectiousness.

Universal Screening for SARS-CoV-2 in Obstetric Care: Clinical Characteristics and Maternofetal Outcomes in a Latin American High-Complexity Unit

The asymptomatic population's role in COVID-19 transmission poses challenges for control efforts. Pregnant women are susceptible to severe manifestations, increasing maternal and perinatal morbidity and mortality. This study describes the clinical characteristics, maternal and fetal outcomes, and our experience in universal severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) screening of pregnant women admitted to a high-complexity obstetric unit in Latin America. Of 568 pregnant women tested for SARS-CoV-2, 23 obtained a positive result. Among these patients, 17% had symptoms at admission, and 0.2% reported an epidemiological link. Pregnant women with positive were associated with an increased risk of eclampsia (16.7% vs 4.9%, P = .014) and acute respiratory distress (16.7% vs 4.9%, P = .014). In this group, 4 patients developed maternal near misses, and no maternal deaths were noted. Two early perinatal deaths occurred in the positive SARS-CoV-2 test group (2, 9.5% vs 17, 4.1%, P = .235). The high prevalence of asymptomatic pregnant women with SARS-CoV-2 and the adverse outcomes for those infected during pregnancy highlights the importance of universal screening upon hospital admission. This approach streamlines risk management, and enhances service structure, resource allocation, care pathways, patient management, follow-up, and overall outcomes.

The joint determination of morbidity and vaccination in the spatiotemporal epidemiology of COVID-19

This paper examines the mutual dependence between COVID-19 morbidity and vaccination rollout. A theory of endogenous immunization is proposed in which the decision to become vaccinated varies directly with the risks of contagion, and the public self-selects into self-protection. Hence, COVID-19 morbidity varies inversely with vaccination rollout, and vaccination rollout varies directly with COVID-19 morbidity. The paper leverages the natural sequencing between morbidity and immunization to identify the causal order in the dynamics of this relationship. A modified SIR model is estimated using spatial econometric methods for weekly panel data for Israel at a high level of spatial granularity. Connectivity between spatial units is measured using physical proximity and a unique mobility-based measure. Spatiotemporal models for morbidity and vaccination rollout show that not only does morbidity vary inversely with vaccination rollout, vaccination rollout varies directly with morbidity. The utility of the model for public health policy targeting, is highlighted.

Performance of Reverse Transcription Loop-Mediated Isothermal Amplification (RT-LAMP) Targeting the RNA Polymerase Gene for the Direct Detection of SARS-CoV2 in Nasopharyngeal Swabs

In 2020, a global pandemic caused by SARS-CoV-2 was declared. Different institutes proposed diagnostic molecular methods to detect the virus in clinical samples. This study aims to validate and standardize the use of a loop-mediated isothermal amplification (LAMP)-based methodology targeting the viral RP gene, as a faster and low-cost diagnostic method for SARS-CoV-2 infections. The results obtained with RT-LAMP (Reverse Transcriptase) were compared to the results of real-time polymerase chain reaction (RT-PCR) to assess its sensitivity and specificity. In total, 115 samples (nasopharyngeal samples) were used for detecting SARS-CoV-2 by RT-LAMP, with 43 positives and 72 negatives. The study showed a positive predictive value (PPV) of 90.7% and a negative predictive value (VPN) of 100%. The LAMP assay also demonstrated a high sensitivity of 90.7% and a specificity of 100% (confidence interval 77.9-97.4%) when using the lower detection limit of 40 copies/µL. The RT-LAMP described here has the potential to detect even the new variants of SARS-CoV-2, suggesting that it may not be significantly affected by gene mutations. The RT-LAMP targeting the RP viral region is faster and less expensive than other molecular approaches, making it an alternative for developing countries.

A systematic review of the barcoding strategy that contributes to COVID-19 diagnostics at a population level

The outbreak of SARS-CoV-2 has made us more alert to the importance of viral diagnostics at a population level to rapidly control the spread of the disease. The critical question would be how to scale up testing capacity and perform a diagnostic test in a high-throughput manner with robust results and affordable costs. Here, the latest 26 articles using barcoding technology for COVID-19 diagnostics and biologically-relevant studies are reviewed. Barcodes are molecular tags, that allow proceeding an array of samples at once. To date, barcoding technology followed by high-throughput sequencing has been made for molecular diagnostics for SARS-CoV-2 infections because it can synchronously analyze up to tens of thousands of clinical samples within a short diagnostic time. Essentially, this technology can also be used together with different biotechnologies, allowing for investigation with resolution of single molecules. In this Mini-Review, I first explain the general principle of the barcoding strategy and then put forward recent studies using this technology to accomplish COVID-19 diagnostics and basic research. In the meantime, I provide the viewpoint to improve the current COVID-19 diagnostic strategy with potential solutions. Finally, and importantly, two practical ideas about how barcodes can be further applied in studying SARS-CoV-2 to accelerate our understanding of this virus are proposed.

TRACE-Omicron: Policy Counterfactuals to Inform Mitigation of COVID-19 Spread in the United States

The Omicron wave was the largest wave of COVID-19 pandemic to date, more than doubling any other in terms of cases and hospitalizations in the United States. In this paper, we present a large-scale agent-based model of policy interventions that could have been implemented to mitigate the Omicron wave. Our model takes into account the behaviors of individuals and their interactions with one another within a nationally representative population, as well as the efficacy of various interventions such as social distancing, mask wearing, testing, tracing, and vaccination. We use the model to simulate the impact of different policy scenarios and evaluate their potential effectiveness in controlling the spread of the virus. Our results suggest the Omicron wave could have been substantially curtailed via a combination of interventions comparable in effectiveness to extreme and unpopular singular measures such as widespread closure of schools and workplaces, and highlight the importance of early and decisive action.

Evaluation of children and adults with post-COVID-19 persistent smell, taste and trigeminal chemosensory disorders: A hospital based study

BACKGROUND

Smell disorders are the most frequent persistent coronavirus disease 2019 (COVID-19) complications.

AIM

To describe the patterns and characteristics of persistent smell and taste disorders in Egyptian patients.

METHODS

Assessment was done to 185 patients (adults = 150, age: 31.41 ± 8.63 years; children = 35; age: 15.66 ± 1.63 years). Otolaryngology and neuropsychiatric evaluations were done. Measurements included: A clinical questionnaire (for smell and taste); sniffin' odor, taste and flavor identification tests and the Questionnaire of Olfactory Disorders-Negative Statements (sQOD-NS).

RESULTS

Duration of disorders was 11.53 ± 3.97 ms (6-24 ms). Parosmia (n = 119; 64.32%) was developed months after anosmia (3.05 ± 1.87 ms). Objective testing showed anosmia in all, ageusia and flavor loss in 20% (n = 37) and loss of nasal and oral trigeminal sensations in 18% (n = 33) and 20% (n = 37), respectively. Patients had low scoring of sQOD-NS (11.41 ± 3.66). There were no specific differences in other demographics and clinical variables which could distinguish post-COVID-19 smell and taste disorders in children from adults.

CONCLUSION

The course of small and taste disorders are supportive of the nasal and oral neuronal compromises. Post-COVID-19 taste and trigeminal disorders were less frequent compared to smell disorders. Post-COVID-19 flavor disorders were solely dependent on taste and not smell disorders. There were no demographics, clinical variables at onset or specific profile of these disorders in children compared to adults.

Rapid detection of intact SARS-CoV-2 using designer DNA Nets and a pocket-size smartphone-linked fluorimeter

Rapid, sensitive, and inexpensive point-of-care diagnosis is vital to controlling highly infectious diseases, including COVID-19. Here, we report the design and characterization of a compact fluorimeter called a "Virus Pod" (V-Pod) that enables sensitive self-testing of SARS-CoV-2 viral load in saliva. The rechargeable battery-operated device reads the fluorescence generated by Designer DNA Nanostructures (DDN) when they specifically interact with intact SARS-CoV-2 virions. DDNs are net-shaped self-assembling nucleic acid constructs that provide an array of highly specific aptamer-fluorescent quencher duplexes located at precise positions that match the pattern of spike proteins. The room-temperature assay is performed by mixing the test sample with DNA Net sensor in a conventional PCR tube and placing the tube into the V-Pod. Fluorescent signals are generated when multivalent aptamer-spike binding releases fluorescent quenchers, resulting in rapid (5-min) generation of dose-dependent output. The V-Pod instrument performs laser excitation, fluorescence intensity quantitation, and secure transmission of data to an App via Bluetooth™. We show that the V-Pod and DNA Net assay achieves clinically relevant detection limits of 3.92 × 103 viral-genome-copies/mL for pseudo-typed wild-type SARS-CoV-2 and 1.84 × 104, 9.69 × 104, 6.99 × 104 viral-genome-copies/mL for pathogenic Delta, Omicron, and D614G variants, representing sensitivity similar to laboratory-based PCR. The pocket-sized instrument (∼$294), inexpensive reagent-cost/test ($1.26), single-step, rapid sample-to-answer, and quantitative output represent a capability that is compatible with the needs of frequent self-testing in a consumer-friendly format that can link with medical service systems such as healthcare providers, contact tracing, and infectious disease reporting.

Comparison of the conventional tube and erythrocyte-magnetized technology in titration of red blood cell alloantibodies

BACKGROUND

Erythrocyte alloantibodies are mainly produced after immune stimulation, such as blood transfusion, pregnancy, and transplantation, and are the leading causes of severe hemolytic transfusion reactions and difficulty in blood grouping and matching. Therefore, antibody screening is critical to prevent and improve red cell alloantibodies. Routine tube assay is the primary detection method of antibody screening. Recently, erythrocyte-magnetized technology (EMT) has been increasingly used in clinical practice. This study intends to probe the application and efficacy of the conventional tube and EMT in red blood cell alloantibody titration to provide a reference for clinical blood transfusion.

AIM

To investigate the application value of conventional tube and EMT in red blood cell alloantibody titration and enhance the safety of blood transfusion practice.

METHODS

A total of 1298 blood samples were harvested from blood donors at the Department of Blood Transfusion of our hospital from March 2021 to December 2022. A 5 mL blood sample was collected in tubing, which was then cut, and the whole blood was put into a test tube for centrifugation to separate the serum. Different red blood cell blood group antibody titers were simultaneously detected using the tube polybrene test, tube antiglobulin test (AGT), and EMT screening irregular antibody methods to determine the best test method.

RESULTS

Simultaneous detection was performed through the tube polybrene test, tube AGT and EMT screening irregular antibodies. It was discovered that the EMT screening irregular antibody method could detect all immunoglobulin G (IgG) and immunoglobulin M (IgM) irregular antibodies, and the results of manual tube AGT were satisfactory, but the operation time was lengthy, and the equipment had a large footprint. The EMT screening irregular antibody assay was also conducted to determine its activity against type O Rh (D) red blood cells, and the outcomes were satisfactory. Furthermore, compared to the conventional tube method, the EMT screening irregular antibody method was more cost-effective and had significantly higher detection efficiency.

CONCLUSION

With a higher detection rate, the EMT screening irregular antibody method can detect both IgG and IgM irregular antibodies faster and more effectively than the conventional tube method.

MICaFVi: A Novel Magnetic Immuno-Capture Flow Virometry Nano-Based Diagnostic Tool for Detection of Coronaviruses

COVID-19 has resulted in a pandemic that aggravated the world's healthcare systems, economies, and education, and caused millions of global deaths. Until now, there has been no specific, reliable, and effective treatment to combat the virus and its variants. The current standard tedious PCR-based tests have limitations in terms of sensitivity, specificity, turnaround time, and false negative results. Thus, an alternative, rapid, accurate, and sensitive diagnostic tool that can detect viral particles, without the need for amplification or viral replication, is central to infectious disease surveillance. Here, we report MICaFVi (Magnetic Immuno-Capture Flow Virometry), a novel precise nano-biosensor diagnostic assay for coronavirus detection which combines the MNP-based immuno-capture of viruses for enrichment followed by flow-virometry analysis, enabling the sensitive detection of viral particles and pseudoviruses. As proof of concept, virus-mimicking spike-protein-coated silica particles (VM-SPs) were captured using anti-spike-antibody-conjugated MNPs (AS-MNPs) followed by detection using flow cytometry. Our results showed that MICaFVi can successfully detect viral MERS-CoV/SARS-CoV-2-mimicking particles as well as MERS-CoV pseudoviral particles (MERSpp) with high specificity and sensitivity, where a limit of detection (LOD) of 3.9 µg/mL (20 pmol/mL) was achieved. The proposed method has great potential for designing practical, specific, and point-of-care testing for rapid and sensitive diagnoses of coronavirus and other infectious diseases.

A comprehensive overview on the transmission, pathogenesis, diagnosis, treatment, and prevention of SARS-CoV-2

Severe acute respiratory syndrome coronavirus (SARS-CoV) is a single positive-strand RNA virus that is responsible for the current pandemic that the world has been facing since 2019. The primary route of transmission of SARS-CoV-2 is through respiratory tract transmission. However, other transmission routes such as fecal-oral, vertical transmission, and aerosol-eye also exist. In addition, it has been found that the pathogenesis of this virus involves the binding of the virus's S protein to its host cell surface receptor angiotensin-converting enzyme 2, which results in the subsequent membrane fusion that is required for SARS-CoV-2 to replicate and complete its entire life. The clinical symptoms of patients infected with SARS-CoV-2 can range from asymptomatic to severe. The most common symptoms seen include fever, dry cough, and fatigue. Once these symptoms are observed, a nucleic acid test is done using reverse transcription-polymerase chain reaction. This currently serves as the main confirmatory tool for COVID-19. Despite the fact that no cure has been found for SARS-CoV-2, prevention methods such as vaccines, specific facial mask, and social distancing have proven to be quite effective. It is imperative to have a complete understanding of the transmission and pathogenesis of this virus. To effectively develop new drugs as well as diagnostic tools, more knowledge about this virus would be needed.

SARS-CoV-2 Testing Strategies in the Diagnosis and Management of COVID-19 Patients in Low-Income Countries: A Scoping Review

The accuracy of diagnostic laboratory tests for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can impact downstream clinical procedures in managing and controlling the outbreak of coronavirus disease 2019 (COVID-19). To assess the effectiveness of laboratory tools for managing COVID-19 patients in low-income countries (LICs), we systematically searched the PubMed, Embase, Scopus and CINHAL databases for reports published between January 2020 and June 2022. We found that 22 of 1303 articles reported the performance of various SARS-CoV-2 detection tools across 10 LICs. These tools were (1) real-time reverse transcriptase polymerase chain reaction (RT-PCR); (2) reverse transcription loop-mediated isothermal amplification (RT-LAMP); (3) rapid diagnostic tests (RDTs); (4) enzyme-linked immunosorbent assay (ELISA); and (5) dot-blot immunoassay. The detection of COVID-19 is largely divided into two main streams-direct virus (antigen) detection and serology (immunoglobulin)-based detection. Point-of-care testing using antigen-based RDTs is preferred in LICs because of cost effectiveness and simplicity in the test procedures. The nucleic acid amplification technology (RT-PCR and RT-LAMP) has the highest diagnostic performance among the available tests, but it is not broadly used in this context due to costs and shortage of facilities/trained staff. The serology-based test method is affected by antibody interferences and varying amounts of SARS-CoV-2 immunoglobulins expressed at different stages of disease onset. We further discuss the effectiveness and shortcomings of each of these tools in the diagnosis and management of COVID-19. Using the LICs as the study model, our findings highlight ways to improve the quality and turnaround time of COVID-19 testing in resource-constrained settings, notably through local/international collaborative efforts to refine the molecular-based or immunoassay-based testing technologies.

What to Do if the qPCR Test for SARS-CoV-2 or Other Pathogen Lacks Endogenous Internal Control? A Simple Test on Housekeeping Genes

Some of the products for the molecular diagnosis of infections do not have an endogenous internal control, and this is necessary to ensure that the result is not a false negative. The aim of the project was to design a simple low-cost RT-qPCR test that can confirm the expression of basic metabolism proteins, thus confirming the quality of genetic material for molecular diagnostic tests. Two successful equivalent qPCR assays for the detection of the GADPH and ACTB genes were obtained. The course of standard curves is logarithmic, with a very high correlation coefficient R2 within the range of 0.9955-0.9956. The reaction yield was between 85.5 and 109.7%, and the detection limit (LOD) with 95% positive probability was estimated at 0.0057 ng/µL for GAPDH and 0.0036 ng/µL for ACTB. These tests are universal because they function on various types of samples (swabs, cytology, etc.) and can complement the diagnosis of SARS-CoV-2 and other pathogens, as well as potentially oncological diagnostics.

An update on lateral flow immunoassay for the rapid detection of SARS-CoV-2 antibodies

Over the last three years, after the outbreak of the COVID-19 pandemic, an unprecedented number of novel diagnostic tests have been developed. Assays to evaluate the immune response to SARS-CoV-2 have been widely considered as part of the control strategy. The lateral flow immunoassay (LFIA), to detect both IgM and IgG against SARS-CoV-2, has been widely studied as a point-of-care (POC) test. Compared to laboratory tests, LFIAs are faster, cheaper and user-friendly, thus available also in areas with low economic resources. Soon after the onset of the pandemic, numerous kits for rapid antibody detection were put on the market with an emergency use authorization. However, since then, scientists have tried to better define the accuracy of these tests and their usefulness in different contexts. In fact, while during the first phase of the pandemic LFIAs for antibody detection were auxiliary to molecular tests for the diagnosis of COVID-19, successively these tests became a tool of seroprevalence surveillance to address infection control policies. When in 2021 a massive vaccination campaign was implemented worldwide, the interest in LFIA reemerged due to the need to establish the extent and the longevity of immunization in the vaccinated population and to establish priorities to guide health policies in low-income countries with limited access to vaccines. Here, we summarize the accuracy, the advantages and limits of LFIAs as POC tests for antibody detection, highlighting the efforts that have been made to improve this technology over the last few years.

COVID-19 chest X-ray image classification in the presence of noisy labels

The Corona Virus Disease 2019 (COVID-19) has been declared a worldwide pandemic, and a key method for diagnosing COVID-19 is chest X-ray imaging. The application of convolutional neural network with medical imaging helps to diagnose the disease accurately, where the label quality plays an important role in the classification problem of COVID-19 chest X-rays. However, most of the existing classification methods ignore the problem that the labels are hardly completely true and effective, and noisy labels lead to a significant degradation in the performance of image classification frameworks. In addition, due to the wide distribution of lesions and the large number of local features of COVID-19 chest X-ray images, existing label recovery algorithms have to face the bottleneck problem of the difficult reuse of noisy samples. Therefore, this paper introduces a general classification framework for COVID-19 chest X-ray images with noisy labels and proposes a noisy label recovery algorithm based on subset label iterative propagation and replacement (SLIPR). Specifically, the proposed algorithm first obtains random subsets of the samples multiple times. Then, it integrates several techniques such as principal component analysis, low-rank representation, neighborhood graph regularization, and k-nearest neighbor for feature extraction and image classification. Finally, multi-level weight distribution and replacement are performed on the labels to cleanse the noise. In addition, for the label-recovered dataset, high confidence samples are further selected as the training set to improve the stability and accuracy of the classification framework without affecting its inherent performance. In this paper, three typical datasets are chosen to conduct extensive experiments and comparisons of existing algorithms under different metrics. Experimental results on three publicly available COVID-19 chest X-ray image datasets show that the proposed algorithm can effectively recover noisy labels and improve the accuracy of the image classification framework by 18.9% on the Tawsifur dataset, 19.92% on the Skytells dataset, and 16.72% on the CXRs dataset. Compared to the state-of-the-art algorithms, the gain of classification accuracy of SLIPR on the three datasets can reach 8.67%-19.38%, and the proposed algorithm also has certain scalability while ensuring data integrity.

COVID-associated acute limb ischemia during the Delta surge and the effect of vaccines

OBJECTIVE

Hypercoagulability is common in severe acute respiratory syndrome coronavirus 2 and has been associated with arterial thrombosis leading to acute limb ischemia (ALI). Our objective was to determine the outcomes of concurrent coronavirus disease 2019 (COVID-19) infection and ALI, particularly during the Delta variant surge and the impact of vaccination status.

METHODS

A retrospective review was performed of patients treated at a single health care system between March 2020 and December 2021 for ALI and recent (<14 days) COVID-19 infection or who developed ALI during hospitalization for the same disease. Patients were grouped by year as well as by pre and post Delta variant emergence in 2021 based on the World Health Organization timeline (January to May vs June to December). Baseline demographics, imaging, interventions, and outcomes were evaluated. A control cohort of all patients with ALI requiring surgical intervention for a 2-year period prior to the pandemic was used for comparison. Primary outcomes were in-hospital mortality and amputation-free survival. Kaplan-Meier survival and Cox proportional hazards analysis were performed.

RESULTS

Forty acutely ischemic limbs were identified in 36 patients with COVID-19, the majority during the Delta surge (52.8%) and after the wide availability of vaccines. The rate of COVID-19-associated ALI, although low overall, nearly doubled during the Delta surge (0.37% vs 0.20%; P = .09). Intervention (open or endovascular revascularization vs primary amputation) was performed on 31 limbs in 28 individuals, with the remaining eight treated with systemic anti-coagulation. Postoperative mortality was 48%, and overall mortality was 50%. Major amputation following revascularization was significantly higher with COVID-19 ALI (25% vs 3%; P = .006) compared with the pre-pandemic group. Thirty-day amputation-free survival was significantly lower (log-rank P < .001). COVID-19 infection (adjusted hazard ratio, 6.2; P < .001) and age (hazard ratio, 1.1; P = .006) were associated with 30-day amputation in multivariate analysis. Severity of COVID-19 infection, defined as vasopressor usage, was not associated with post-revascularization amputation. There was a higher incidence of re-thrombosis in the latter half of 2021 with the Delta surge, as reintervention for recurrent ischemia of the same limb was more common than our previous experience (21% vs 0%; P = .55). COVID-19-associated limb ischemia occurred almost exclusively in non-vaccinated patients (92%).

CONCLUSIONS

ALI observed with Delta appears more resistant to standard therapy. Unvaccinated status correlated highly with ALI occurrence in the setting of COVID-19 infection. Information of limb loss as a COVID-19 complication among non-vaccinated patients may help to increase compliance.

Performance Evaluation of a BZ COVID-19 NALF Assay for Rapid Diagnosis of SARS-CoV-2

Coronavirus disease (COVID-19) caused by SARS-CoV-2 infection has been a global pandemic for more than two years, and it is important to quickly and accurately diagnose and isolate patients with SARS-CoV-2 infection. The BZ COVID-19 NALF Assay could sensitively detect SARS-CoV-2 from a nasopharyngeal swab because it adopts both a loop-mediated isothermal amplification and lateral flow immunochromatography technology. In this study, a total of 389 nasopharyngeal swab samples, of which 182 were SARS-CoV-2 PCR positive and 207 were negative samples, were recruited. Compared to the Allplex™ SARS-CoV-2 Assay, the BZ COVID-19 NALF Assay showed 95.05% sensitivity and 99.03% specificity for detecting SARS-CoV-2. The concordance rate between the BZ COVID-19 NALF Assay and Allplex™ SARS-CoV-2 Assay was 97.69%. The turnaround time of the BZ COVID-19 NALF Assay is only about 40~55 min. The BZ COVID-19 NALF Assay is an accurate, easy, and quick molecular diagnostic test compared to the conventional PCR test for detection of SARS-CoV-2. In addition, the BZ COVID-19 NALF Assay is thought to be very useful in small size medical facilities or developing countries where it is difficult to operate a clinical laboratory.

A Multiplex Method for Detection of SARS-CoV-2 Variants Based on MALDI-TOF Mass Spectrometry

The recent outbreak of the coronavirus disease 2019 (COVID-19) pandemic and the continuous evolution of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have highlighted the significance of new detection methods for global monitoring and prevention. Although quantitative reverse transcription PCR (RT-qPCR), the current gold standard for diagnosis, performs excellently in genetic testing, its multiplexing capability is limited because of the signal crosstalk of various fluorophores. Herein, we present a highly efficient platform which combines 17-plex assays with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), enabling the targeting of 14 different mutation sites of the spike gene. Diagnosis using a set of 324 nasopharyngeal swab or sputum clinical samples with SARS-CoV-2 MS method was identical to that with the RT-qPCR. The detection consistency of mutation sites was 97.9% (47/48) compared to Sanger sequencing without cross-reaction with other respiratory-related pathogens. Therefore, the MS method is highly potent to track and assess SARS-CoV-2 changes in a timely manner, thereby aiding continuous response to viral variation and prevention of further transmission.

Unilateral Pleural Effusion after Third Dose of BNT162b2 mRNA Vaccination: Case Report

Vaccination remains the best strategy against coronavirus disease 2019 (COVID-19) in terms of prevention. The efficacy and safety of COVID-19 vaccines is supported by well-designed clinical trials that recruited many participants. It is well-known that vaccination is associated with local side effects related to the injection site, and mild, systemic side effects. However, there has been an increase in the occurrence of what is known as infrequent adverse effects in the population of vaccinated individuals in real life. We present the case of a 46-year-old woman with no past medical history, who presented with a sharp chest pain with deep inspiration, a few days after receiving the third dose of the Pfizer-BioNTech COVID-19 mRNA vaccine (BNT162b2). There is an association between the BNT16b2 vaccination and myocarditis, pericarditis, and even bilateral pleural effusions. To the best of our knowledge, this is the first report featuring a unilateral pleural effusion in a patient with no known past medical history, who did not develop cardiac involvement nor have any viral infection. The aim of our report is to inform health professionals of the possibility of encountering this rare adverse event in their daily practice, as the population of individuals who are receiving additional vaccine doses is increasing steadily.

SARS-CoV-2 Prevalence on and Incidence after Arrival in Travelers on Direct Flights from Cape Town, South Africa to Munich, Germany Shortly after Occurrence of the Omicron Variant in November/December 2021: Results from the OMTRAIR Study

The highly transmissible SARS-CoV-2-variant B.1.1.529 (Omicron) first appeared in South Africa in November 2021. In order to study Omicron entry to Germany, its occurrence related to incoming airline travel, symptomatology and compliance with entry regulations and recommendations, we conducted a cross-sectional study, followed by a retrospective cohort study among passengers and crew on 19 direct flights from Cape Town, South Africa, to Munich, Germany, between 26 November and 23 December 2021. Travelers were mandatorily PCR-tested on arrival and invited to complete an online questionnaire. SARS-CoV-2-prevalence on arrival was 3.3% (n = 90/2728), and 93% were Omicron. Of the passengers, 528 (19%) completed the questionnaire. Among participants who tested negative on arrival, self-reported SARS-CoV-2-incidence was 4.3% within 14 days, of whom 74% reported a negative PCR-test ≤ 48 h before boarding, 77% were fully vaccinated, and 90% reported wearing an FFP2/medical mask during flight. We found multiple associations between risk factors and infection on and after arrival, among which having a positive-tested travel partner was the most noteworthy. In conclusion, PCR testing before departure was insufficient to control the introduction of the Omicron variant. Additional measures (e.g., frequent testing, quarantine after arrival or travel ban) should be considered to delay virus introduction in such settings.

Comparison of risk factors for SARS-CoV-2 infection among healthcare workers during Omicron and Delta dominance periods in Japan

BACKGROUND

The risk factors for coronavirus disease (COVID-19) among healthcare workers (HCWs) might have changed since the emergence of the highly immune evasive Omicron variant.

AIM

To compare the risk factors for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection among HCWs during the Delta- and Omicron-predominant periods.

METHODS

Using data from repeated serosurveys among the staff of a medical research centre in Tokyo, two cohorts were established: Delta period cohort (N = 858) and Omicron period cohort (N = 652). The potential risk factors were assessed using a questionnaire. Acute/current or past SARS-CoV-2 infection was identified by polymerase chain reaction or anti-nucleocapsid antibody tests, respectively. Poisson regression was used to calculate the risk ratio (RR) of infection risk.

FINDINGS

The risk of SARS-CoV-2 infection during the early Omicron-predominant period was 3.4-fold higher than during the Delta-predominant period. Neither working in a COVID-19-related department nor having a higher degree of occupational exposure to SARS-CoV-2 was associated with an increased infection risk during both periods. During the Omicron-predominant period, infection risk was higher among those who spent ≥30 min in closed spaces, crowded spaces, and close-contact settings without wearing mask (≥3 times versus never: RR: 6.62; 95% confidence interval: 3.01-14.58), whereas no such association was found during the Delta period.

CONCLUSION

Occupational exposure to COVID-19-related work was not associated with the risk of SARS-CoV-2 infection in the Delta or Omicron period, whereas high-risk behaviours were associated with an increased infection risk during the Omicron period.

Accurate Detection of SARS-CoV-2 by Next-Generation Sequencing in Low Viral Load Specimens

As new SARS-CoV-2 variants emerge, there is an urgent need to increase the efficiency and availability of viral genome sequencing, notably to detect the lineage in samples with a low viral load. SARS-CoV-2 genome next-generation sequencing (NGS) was performed retrospectively in a single center on 175 positive samples from individuals. An automated workflow used the Ion AmpliSeq SARS-CoV-2 Insight Research Assay on the Genexus Sequencer. All samples were collected in the metropolitan area of the city of Nice (France) over a period of 32 weeks (from 19 July 2021 to 11 February 2022). In total, 76% of cases were identified with a low viral load (Ct ≥ 32, and ≤200 copies/µL). The NGS analysis was successful in 91% of cases, among which 57% of cases harbored the Delta variant, and 34% the Omicron BA.1.1 variant. Only 9% of cases had unreadable sequences. There was no significant difference in the viral load in patients infected with the Omicron variant compared to the Delta variant (Ct values, p = 0.0507; copy number, p = 0.252). We show that the NGS analysis of the SARS-CoV-2 genome provides reliable detection of the Delta and Omicron SARS-CoV-2 variants in low viral load samples.

Whole-genome sequencing of SARS-CoV-2 isolates from symptomatic and asymptomatic individuals in Tanzania

Background

Coronavirus Disease-2019 (COVID-19), caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) accounts for considerable morbidity and mortality globally. Paucity of SARS-CoV-2 genetic data from Tanzania challenges in-country tracking of the pandemic. We sequenced SARS-CoV-2 isolated in the country to determine circulating strains, mutations and phylogenies and finally enrich international genetic databases especially with sequences from Africa.

Methods

This cross-sectional study utilized nasopharyngeal swabs of symptomatic and asymptomatic adults with positive polymerase chain reaction tests for COVID-19 from January to May 2021. Viral genomic libraries were prepared using ARTIC nCoV-2019 sequencing protocol version three. Whole-genome sequencing (WGS) was performed using Oxford Nanopore Technologies MinION device. In silico genomic data analysis was done on ARTIC pipeline version 1.2.1 using ARTIC nCoV-2019 bioinformatics protocol version 1.1.0.

Results

Twenty-nine (42%) out of 69 samples qualified for sequencing based on gel electrophoretic band intensity of multiplex PCR amplicons. Out of 29 isolates, 26 were variants of concern [Beta (n = 22); and Delta (n = 4)]. Other variants included Eta (n = 2) and B.1.530 (n = 1). We found combination of mutations (S: D80A, S: D215G, S: K417N, ORF3a: Q57H, E: P71L) in all Beta variants and absent in other lineages. The B.1.530 lineage carried mutations with very low cumulative global prevalence, these were nsp13:M233I, nsp14:S434G, ORF3a:A99S, S: T22I and S: N164H. The B.1.530 lineage clustered phylogenetically with isolates first reported in south-east Kenya, suggesting regional evolution of SARS-CoV-2.

Conclusion

We provide evidence of existence of Beta, Delta, Eta variants and a locally evolving lineage (B.1.530) from samples collected in early 2021 in Tanzania. This work provides a model for ongoing WGS surveillance that will be required to inform on emerging and circulating SARS-CoV-2 diversity in Tanzania and East Africa.

Immune checkpoint inhibitor-related pneumonitis and COVID-19: a case-matched comparison of CT findings

OBJECTIVES

To compare the radiological findings of immune checkpoint inhibitor-related pneumonitis (IRP) and COVID-19 pneumonia, evaluating the potential of the CO-RADS score to differentiate between them.

METHODS

Two readers blindly reviewed chest CTs from age- and sex-matched groups of 33 patients with IRP and 33 patients with COVID-19 pneumonia. Each examiner evaluated the presence of 13 CT features, semiquantitatively scored lung involvement, and assigned a CO-RADS score. Inter-reader reliability in the assessment of CT features and CO-RADS categories was evaluated with Cohen's κ. Distribution differences between groups were evaluated with the χ², Fisher's, and Mann-Whitney U tests.

RESULTS

Substantial or higher inter-reader reliability was found in CO-RADS assignments (κ = 0.664) and in the evaluation of CT features (κ ≥ 0.638), among which the sole feature found to significantly differentiate IRP from COVID-19 pneumonia was unilateral presentation (p < 0.001). Lung involvement semiquantitative scores and CO-RADS scores were significantly higher (p < 0.001) in COVID patients (median involvement score 4, IQR 4-6; median CO-RADS score 5, IQR 4-5) than in IRP patients (median involvement score 2.5, IQR 2-4; median CO-RADS score 3, IQR 3-4) but exploratory analysis of CO-RADS specificity revealed comparatively low values, ranging between 51.5% (Reader 1) and 54.6% (Reader 2).

CONCLUSIONS

CT features of IRP and COVID-19 pneumonia frequently overlap, save for the extent of lung involvement and bilaterality. In the current SARS-CoV-2 pandemic, the low specificity of the CO-RADS score for the differential diagnosis of COVID-19 pneumonia and IRP may prompt to reconsider the role of imaging in IRP work-up.

Monthly transthoracic echocardiography in young adults for 6 months following SARS-CoV-2 infection

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can elicit acute and long-term effects on the myocardium among survivors, yet effects among otherwise healthy young adults remains unclear. Young adults with mild symptoms of SARS-CoV-2 (8M/8F, age: 21 ± 1 years, BMI: 23.5 ± 3.1 kg·m-2 ) underwent monthly transthoracic echocardiography (TTE) and testing of circulating cardiac troponin-I for months 1-6 (M1-M6) following a positive polymerase chain reaction test to better understand the acute effects and post-acute sequelae of SARS-CoV-2 on cardiac structure and function. Left heart structure and ejection fraction were unaltered from M1-M6 (p > 0.05). While most parameters of septal and lateral wall velocities, mitral and tricuspid valve, and pulmonary vein (PV) were unaltered from M1-M6 (p > 0.05), lateral wall s' wave velocity increased (M1: 0.113 ± 0.019 m·s-1 , M6: 0.135 ± 0.022 m·s-1 , p = 0.013); PV S wave velocity increased (M1: 0.596 ± 0.099 m·s-1 , M6: 0.824 ± 0.118 m·s-1 , p < 0.001); the difference between PV A wave and mitral valve (MV) A wave durations decreased (M1: 39.139 ± 43.715 ms, M6: 18.037 ± 7.227 ms, p = 0.002); the ratio of PV A duration to MV A duration increased (M1: 0.844 ± 0.205, M6: 1.013 ± 0.132, p = 0.013); and cardiac troponin-I levels decreased (M1: 0.38 ± 0.20 ng·ml-1 , M3: 0.28 ± 0.34 ng·ml-1 , M6: 0.29 ± 0.16 ng·ml-1 ; p = 0.002) over time. While young adults with mild symptoms of SARS-CoV-2 lacked changes to cardiac structure, the subclinical improvements to cardiac function and reduced inflammatory marker of cardiac troponin-I over 6 months following SARS-CoV-2 infection provide physiologic guidance to post-acute sequelae and recovery from SARS-CoV-2 and its variants using conventional TTE.

Habitat Imaging Biomarkers for Diagnosis and Prognosis in Cancer Patients Infected with COVID-19

OBJECTIVES

Cancer patients have worse outcomes from the COVID-19 infection and greater need for ventilator support and elevated mortality rates than the general population. However, previous artificial intelligence (AI) studies focused on patients without cancer to develop diagnosis and severity prediction models. Little is known about how the AI models perform in cancer patients. In this study, we aim to develop a computational framework for COVID-19 diagnosis and severity prediction particularly in a cancer population and further compare it head-to-head to a general population.

METHODS

We have enrolled multi-center international cohorts with 531 CT scans from 502 general patients and 420 CT scans from 414 cancer patients. In particular, the habitat imaging pipeline was developed to quantify the complex infection patterns by partitioning the whole lung regions into phenotypically different subregions. Subsequently, various machine learning models nested with feature selection were built for COVID-19 detection and severity prediction.

RESULTS

These models showed almost perfect performance in COVID-19 infection diagnosis and predicting its severity during cross validation. Our analysis revealed that models built separately on the cancer population performed significantly better than those built on the general population and locked to test on the cancer population. This may be because of the significant difference among the habitat features across the two different cohorts.

CONCLUSIONS

Taken together, our habitat imaging analysis as a proof-of-concept study has highlighted the unique radiologic features of cancer patients and demonstrated effectiveness of CT-based machine learning model in informing COVID-19 management in the cancer population.

Using a 29-mRNA Host Response Classifier To Detect Bacterial Coinfections and Predict Outcomes in COVID-19 Patients Presenting to the Emergency Department

Clinicians in the emergency department (ED) face challenges in concurrently assessing patients with suspected COVID-19 infection, detecting bacterial coinfection, and determining illness severity since current practices require separate workflows. Here, we explore the accuracy of the IMX-BVN-3/IMX-SEV-3 29 mRNA host response classifiers in simultaneously detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and bacterial coinfections and predicting clinical severity of COVID-19. A total of 161 patients with PCR-confirmed COVID-19 (52.2% female; median age, 50.0 years; 51% hospitalized; 5.6% deaths) were enrolled at the Stanford Hospital ED. RNA was extracted (2.5 mL whole blood in PAXgene blood RNA), and 29 host mRNAs in response to the infection were quantified using Nanostring nCounter. The IMX-BVN-3 classifier identified SARS-CoV-2 infection in 151 patients with a sensitivity of 93.8%. Six of 10 patients undetected by the classifier had positive COVID tests more than 9 days prior to enrollment, and the remaining patients oscillated between positive and negative results in subsequent tests. The classifier also predicted that 6 (3.7%) patients had a bacterial coinfection. Clinical adjudication confirmed that 5/6 (83.3%) of the patients had bacterial infections, i.e., Clostridioides difficile colitis (n = 1), urinary tract infection (n = 1), and clinically diagnosed bacterial infections (n = 3), for a specificity of 99.4%. Two of 101 (2.8%) patients in the IMX-SEV-3 "Low" severity classification and 7/60 (11.7%) in the "Moderate" severity classification died within 30 days of enrollment. IMX-BVN-3/IMX-SEV-3 classifiers accurately identified patients with COVID-19 and bacterial coinfections and predicted patients' risk of death. A point-of-care version of these classifiers, under development, could improve ED patient management, including more accurate treatment decisions and optimized resource utilization. IMPORTANCE We assay the utility of the single-test IMX-BVN-3/IMX-SEV-3 classifiers that require just 2.5 mL of patient blood in concurrently detecting viral and bacterial infections as well as predicting the severity and 30-day outcome from the infection. A point-of-care device, in development, will circumvent the need for blood culturing and drastically reduce the time needed to detect an infection. This will negate the need for empirical use of broad-spectrum antibiotics and allow for antibiotic use stewardship. Additionally, accurate classification of the severity of infection and the prediction of 30-day severe outcomes will allow for appropriate allocation of hospital resources.

Reverse transcriptase-free detection of viral RNA using Hemo Klentaq DNA polymerase

COVID-19 pandemic highlighted the demand for the fast and reliable detection of viral RNA. Although various methods for RNA amplification and detection have been proposed, some limitations, including those caused by reverse transcription (RT), need to be overcome. Here, we report on the direct detection of specific RNA by conventional polymerase chain reaction (PCR) requiring no prior RT step. It was found that Hemo KlenTaq (HKTaq), which is posed as DNA-dependent DNA polymerase, possesses reverse transcriptase activity and provides reproducible amplification of RNA targets with an efficiency comparable to common RT-PCR. Using nasopharyngeal swab extracts from COVID-19-positive patients, the high reliability of SARS-CoV-2 detection based on HKTaq was demonstrated. The most accurate detection of specific targets are provided by nearby primers, which allow to determine RNA in solutions affected to multiple freeze-thaw cycles. HKTaq can be used for elaboration of simplified amplification techniques intended for the analysis of any specific RNA and requiring only one DNA polymerase.

Clinical and Epidemiological Presentation of COVID-19 among Children in Conflict Setting

Background: This study aims to describe the observable symptoms of children with COVID-19 infection and analyze access to real-time polymerase chain reaction (RT-PCR) testing among children seeking care in Yemen. Method: In the period of March 2020−February 2022, data were obtained from 495 children suspected to have been infected with COVID-19 (from a larger register of 5634 patients) from the Diseases Surveillance and Infection Control Department at the Ministry of Public Health and Population in Aden, Yemen. Results: Overall, 21.4% of the children with confirmed COVID-19 infection were asymptomatic. Fever (71.4%) and cough (67.1%) were the most frequently reported symptoms among children, and children were less likely to have fever (p < 0.001), sore throat (p < 0.001) and cough (p < 0.001) compared to adults. A lower frequency of COVID-19-associated symptoms was reported among children with positive RT-PCR tests compared to children with negative tests. A lower rate of testing was conducted among children (25%) compared to adults (61%). Fewer tests were carried out among children <5 years (11%) compared to other age groups (p < 0.001), for children from other nationalities (4%) compared to Yemeni children (p < 0.001) and for girls (21%) compared to boys (30%) (p < 0.031). Conclusion: Understanding and addressing the cause of these disparities and improving guidelines for COVID-19 screening among children will improve access to care and control of the COVID-19 pandemic.