Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR

Enhanced testing can substantially improve defense against several types of respiratory virus pandemic

Mass testing to identify and isolate infected individuals is a promising approach for reducing harm from the next acute respiratory virus pandemic. It offers the prospect of averting hospitalizations and deaths whilst avoiding the need for indiscriminate social distancing measures. To understand scenarios where mass testing might or might not be a viable intervention, here we modeled how effectiveness depends both on characteristics of the pathogen (R0, time to peak viral load) and on the testing strategy (limit of detection, testing frequency, test turnaround time, adherence). We base time-dependent test sensitivity and time-dependent infectiousness on an underlying viral load trajectory model. We show that given moderately high public adherence, frequent testing can prevent as many transmissions as more costly interventions such as school or business closures. With very high adherence and fast, frequent, and sensitive testing, we show that most respiratory virus pandemics could be controlled with mass testing alone.

Intranasal recombinant protein subunit vaccine targeting TLR3 induces respiratory tract IgA and CD8 T cell responses and protects against respiratory virus infection

BACKGROUND

Intranasal vaccines against respiratory viruses are desired due to ease of administration and potential to protect against virus infection of the upper respiratory tract.

METHODS

We tested a cationic liposomal adjuvant delivering the TLR3 agonist Poly (I:C) (CAF®09b) for intranasal administration, by formulating this with SARS-CoV-2 spike trimeric protein and assessing airway mucosal immune responses in mice. The vaccine was further evaluated in SARS-CoV-2 virus challenge models, using mice expressing the human ACE2 receptor and Syrian hamsters.

FINDINGS

The intranasal vaccine elicited both serum neutralising antibody responses and IgA responses in the upper respiratory tract. Uniquely, it also elicited high-magnitude CD4 and CD8 T cell responses in the lung parenchyma and nasal-associated lymphoid tissue. In contrast, parenteral administration of the same vaccine, or the mRNA-1273 (Spikevax®) vaccine, led to systemic antibody responses and vaccine-induced CD4 T cells were mainly found in circulation. The intranasal vaccine protected against homologous SARS-CoV-2 (Wuhan-Hu-1) challenge in K18-hACE2 mice, preventing weight loss and virus infection in the upper and lower airways. In Syrian hamsters, the vaccine prevented weight loss and significantly reduced virus load after challenge with the homologous strain and Omicron BA.5.

INTERPRETATION

This study demonstrates that intranasal subunit vaccines containing TLR3-stimulating cationic liposomes effectively induce airway IgA and T cell responses, which could be utilised in future viral pandemics.

FUNDING

This work was primarily supported by the European Union Horizon 2020 research and innovation program under grant agreement no. 101003653.

A humanised ACE2, TMPRSS2, and FCGRT mouse model reveals the protective efficacy of anti-receptor binding domain antibodies elicited by SARS-CoV-2 hybrid immunity

BACKGROUND

Despite the importance of vaccination- and infection-elicited antibodies (Abs) to SARS-CoV-2 immunity, current mouse models do not fully capture the dynamics of Ab-mediated immunity in vivo, including potential contributions of the neonatal Fc receptor, encoded by FCGRT.

METHODS

We generated triple knock-in (TKI) mice expressing human ACE2, TMPRSS2, and FCGRT; and evaluated the protective efficacy of anti-SARS-CoV-2 monoclonal Abs (mAbs) and plasma from individuals with immunity elicited by vaccination alone plus SARS-CoV-2 infection-induced (hybrid) immunity.

FINDINGS

A human anti-SARS-CoV-2 mAb harbouring a half-life-extending mutation, but not the wild-type mAb, exhibited prolonged half-life in TKI mice and protected against lung infection with Omicron BA.2, validating the utility of these mice for evaluating therapeutic Abs. Pooled plasma from individuals with hybrid immunity to Delta, but not from vaccinated-only individuals, cleared infectious Delta from the lungs of TKI mice (P < 0.01), even though the two plasma pools had similar Delta-binding and -neutralising Ab titres in vitro. Similarly, plasma from individuals with hybrid Omicron BA.1/2 immunity, but not hybrid Delta immunity, decreased lung infection (P < 0.05) with BA.5 in TKI mice, despite the plasma pools having comparable BA.5-binding and -neutralising titres in vitro. Depletion of receptor-binding domain-targeting Abs from hybrid immune plasma abrogated their protection against infection.

INTERPRETATION

These results demonstrate the utility of TKI mice as a tool for the development of anti-SARS-CoV-2 mAb therapeutics, show that in vitro neutralisation assays do not accurately predict in vivo protection, and highlight the importance of hybrid immunity for eliciting protective anti-receptor-binding domain Abs.

FUNDING

This work was funded by grants from the e-Asia Joint Research Program (N10A650706 and N10A660577 to MLM, in collaboration with SS); the NIH (U19 AI142790-02S1 to EOS and SS and R44 AI157900 to KJ); the GHR Foundation (to SS and EOS); the Overton family (to SS and EOS); the Arvin Gottlieb Foundation (to SS and EOS), the Prebys Foundation (to SS); and the American Association of Immunologists Fellowship Program for Career Reentry (to FASB).

Transfusion safety concerns during the COVID-19 pandemic in Taiwan: Altered by evolving control strategies

BACKGROUND

In 2022, the SARS-CoV-2 Omicron surge affected 8.8 million people in Taiwan. This study delves into how the transition from containment to mitigation strategies in COVID-19 control has altered concerns regarding transfusion safety.

METHODS

Blood donations during 2020-2022 in Taiwan were included. Donation details and post-donation information (PDI) were retrieved to assess donation fluctuations and incidences of various PDI. The main effects of PDI reporting were assessed using chi-square test and logistic regression. Additionally, from April to August 2022, we collected disease information from COVID-19 donors, and tested their repository specimens for SARS-CoV-2 RNA and antibodies.

RESULTS

Before 2022, when containment measures were in place, only 8 blood donors with COVID-19 reported PDI. However, by mid-2021, there was a significant decrease in blood donations. In 2022, with mitigation strategies implemented, a total of 3483 donations reported COVID-19 PDI. The incidence of all cause PDI increased from 10.5 per 10,000 donations in 2020-2021 to 29.9 per 10,000 in 2022, with nearly 70% of PDI being related to COVID-19. Female donors reported more PDI events. Additionally, the incidence significantly decreased with age. A total of 1148 repository specimens from COVID-19 donor were tested, revealing no detection of SARS-CoV-2 RNA. The seroprevalence rates of anti-nucleocapsid(N) and anti-spike(S) antibodies were 0.61% and 98.4%, respectively.

CONCLUSION

Transfusion safety concerns in Taiwan progressed alongside the evolution of control strategies, with a one-year delay following the pandemic started. The absence of RNAemia among COVID-19 donors indicates that precautionary measures were commensurate with the risk.

Enhancing public health outcomes with AI-powered clinical surveillance: Precise detection of COVID-19 variants using qPCR and nanopore sequencing

BACKGROUND

We aimed to evaluate the efficacy of integrating the Varia5 multiplex assay (qPCR) and whole genome sequencing (WGS) for monitoring SARS-CoV-2, focusing on their overall performance in identifying various virus variants.

METHODS

This study included 140 naso-pharyngeal swab samples from individuals with suspected COVID-19. We utilized our self-developed Varia5 multiplex assay, which targets five viral genes linked to COVID-19 mutations, in conjunction with comprehensive genomic analysis performed through whole genome sequencing (WGS) using the Oxford Nanopore system. Machine learning was integrated to optimize the qPCR conditions and enhance the detection efficiency.

RESULTS

The Varia5 assay identified the prevalent BA.2.75 variant in 92 samples compared to that in 81 samples detected via WGS. The BA.5.2 variant, indicative of higher viral loads, was identified in 15 samples via Varia5 and in 14 samples via WGS.Furthermore, rare variants, such as BA.2.10, were identified. The mean Ct value was 18.36, with significant viral load differences noted between specific variants.

CONCLUSION

Our findings demonstrate that while WGS offers enhanced sensitivity and specificity for variant detection, qPCR remains crucial for large-scale testing because of its cost and time efficiency. The integrated approach, which combines both techniques, represents a more comprehensive monitoring algorithm that can improve public health strategies against pandemics such as COVID-19.

Cross-Species Surveillance of Respiratory Viruses in Domestic and Wild Mammals of an Urban Atlantic Forest from Brazil

Our aim was to investigate respiratory viruses circulating in animals from the urban Atlantic Forest, which is located in the most densely populated area near Rio de Janeiro in Brazil. This study focused on the detection of Influenza A viruses and diverse coronaviruses, including SARS-CoV-2, in domestic and wild animals, including bats, nonhuman primates, rodents, and marsupials. From August 2020 to September 2022, biological samples were collected from a total of 72 pets, 66 primates, 20 rodents, 36 marsupials, and 390 bats. Samples were tested using RT-PCR for Influenza A and coronaviruses, and positive samples were sequenced. When blood samples were available, they were tested for SARS-CoV-2 antibodies. All terrestrial animals were negative for evidence of infection with SARS-CoV-2 and Influenza A viruses. However, samples from 17 phyllostomid bats, including Great fruit-eating bat (Artibeus lituratus), Silky short-tailed bat (Carollia brevicauda), Seba's short-tailed bat (Carollia perspicillata), Common big-eared bat (Micronycteris microtis), Greater spear-nosed bat (Phyllostomus hastatus), White-lined broad-nosed bat (Platyrrhinus lineatus), Little yellow-shouldered bat (Sturnira lilium), Greater round-eared bat (Tonatia bidens), and Common vampire bat (Desmodus rotundus), were positive for bat coronaviruses classified as Alphacoronavirus. Our study adds new information on the occurrence of coronaviruses in bats and contributes to a long-term program of Influenza surveillance. Developing active surveillance for viruses in wildlife species, as implemented in this study, is crucial for understanding zoonotic risks and preventing future global pandemics.

Fluorogenic oligonucleotide cleavage probes with a branched linker improve RNA detection

Fluorescent probe-based quantitative polymerase chain reaction (qPCR) is essential for DNA/RNA quantification widely used in research and clinical diagnostics. The performance of fluorogenic probes depends heavily on their design, particularly the identities of the fluorophore and quencher moieties, and the linkers used to attach them to oligonucleotides. Here we report a highly modular, three-way branched glycerol 'X' linker in fluorogenic TaqMan® type oligonucleotide probes for multiplexed, reverse transcription qPCR (RT-qPCR). The flexible 'X' linker served as an internal attachment point for various quenchers (BHQ1, BHQ2) in probes containing a variable fluorophore at the 5' end (Flu, Hex, Cy5, Cy5.5). A four-color RT-qPCR 'tetraplex' assay was thereby developed for distinguishing between RNA genomes from SARS-CoV-2, influenza A, and influenza B viruses in a single reaction. The 'X' linker exhibited superior performance with single-molecule detection limits approaching four copies, compared to an internal arabinoside-based (ara) linker strategy, demonstrating the presence of competing processes during primer extension, one where Taq exonuclease activity cleaves the fluorogenic X probe leading to productive fluorescence, and the second where the ara probe is displaced from the PCR template without cleavage. Together these results demonstrate the importance of linker structure selection in oligonucleotides for developing highly effective fluorogenic probes for qPCR.

A hybrid inception-dilated-ResNet architecture for deep learning-based prediction of COVID-19 severity

Chest computed tomography (CT) scans are essential for accurately assessing the severity of the novel Coronavirus (COVID-19), facilitating appropriate therapeutic interventions and monitoring disease progression. However, determining COVID-19 severity requires a radiologist with significant expertise. This study introduces a pioneering utilization of deep learning (DL) for evaluate COVID-19 severity using lung CT images, presenting a novel and effective method for assessing the severity of pulmonary manifestations in COVID-19 patients. Inception-Residual networks (Inception-ResNet), advanced hybrid models known for their compactness and effectiveness, were used to extract relevant features from CT scans. Inception-ResNet incorporates the dilated mechanism into its ResNet component, enhancing its ability to accurately classify lung involvement stages. This study demonstrates that dilated residual networks (dResNet) outperform their non-dilated counterparts in image classification tasks, as their architectural designs allow the systems to acquire comprehensive global data by expanding their receptive fields. Our study utilized an initial dataset of 1548 human thoracic CT scans, meticulously annotated by two experienced specialists. Lung involvement was determined by calculating a percentage based on observations made at each scan. The hybrid methodology successfully distinguished the ten distinct severity levels associated with COVID-19, achieving a maximum accuracy of 96.40%. This system demonstrates its effectiveness as a diagnostic framework for assessing lung involvement in COVID-19-affected individuals, facilitating disease progression tracking.

COVID-19 extracellular vesicles display heterogeneity based on viral and host RNA expression: implications for host immune response

Viral RNA and miRNAs released by immune cells contribute to inflammation in COVID-19 patients. Here, we investigated the role of SARS-CoV2 RNA and host miRNAs carried within extracellular vesicles (EVs) in modulating inflammation. EVs were classified as positive or negative depending on their viral RNA cargo. To assess the function of viral RNA, EVs, and lipopolysaccharide (LPS) were used to stimulate whole blood samples from healthy subjects, and the secretion of 27 serum analytes was measured. EVs alone did not induce cytokines, chemokines, or growth factors. However, under LPS stimulation, (SARS-CoV2+) EVs increased IL-12 and decreased IL-13 secretion, while (SARS-CoV2-) EVs increased MIP-1α and IL-1β secretion. Host miR-19a-3p, -192-5p, -let-7c-5p, and -92b-3a were differentially expressed in association with viral RNA. EVs from COVID-19 patients exhibited differences in viral RNA and miRNA expression profiles that modulate LPS responses. This knowledge sheds light on the immunopathology of COVID-19.

4D-DIA Proteomics Uncovers New Insights into Host Salivary Response Following SARS-CoV-2 Omicron Infection

Since late 2021, Omicron variants have dominated the epidemiological scenario as the most successful severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sublineages, driving new and breakthrough infections globally over the past two years. In this study, we investigated for the first time the host salivary response of COVID-19 patients infected with Omicron variants (BA.1, BA.2, and BA.4/5) by using an untargeted four-dimensional data-independent acquisition (4D-DIA)-based proteomics approach. We identified 137 proteins whose abundance levels differed between the COVID-19 positive and negative groups. Salivary signatures were mainly enriched in ribosomal proteins, linked to mRNAviral translation, protein synthesis and processing, immune innate, and antiapoptotic signaling. The higher abundance of 14-3-3 proteins (YWHAG, YWHAQ, YWHAE, and SFN) in saliva, first reported here, may be associated with increased infectivity and improved viral replicative fitness. We also identified seven proteins (ACTN1, H2AC2, GSN, NDKA, CD109, GGH, and PCYOX) that yielded comprehension into Omicron infection and performed outstandingly in screening patients with COVID-19 in a hospital setting. This panel also presented an enhanced anti-COVID-19 and anti-inflammatory signature, providing insights into disease severity, supported by comparisons with other proteome data sets. The salivary signature provided valuable insights into the host's response to SARS-CoV-2 Omicron infection, shedding light on the pathophysiology of COVID-19, particularly in cases associated with mild disease. It also underscores the potential clinical applications of saliva for disease screening in hospital settings. Data are available via ProteomeXchange with the identifier PXD054133.

Phase-resolved Functional Lung (PREFUL) MRI May Reveal Distinct Pulmonary Perfusion Defects in Postacute COVID-19 Syndrome: Sex, Hospitalization, and Dyspnea Heterogeneity

BACKGROUND

Pulmonary perfusion defects have been observed in patients with coronavirus disease 2019 (COVID-19). Currently, there is a need for further data on non-contrast-enhanced MRI in COVID patients. The early identification of heterogeneity in pulmonary perfusion defects among COVID-19 patients is beneficial for their timely clinical intervention and management.

PURPOSE

To investigate the utility of phase-resolved functional lung (PREFUL) MRI in detecting pulmonary perfusion disturbances in individuals with postacute COVID-19 syndrome (PACS).

STUDY TYPE

Prospective.

SUBJECTS

Forty-four participants (19 females, mean age 64.1 years) with PACS and 44 healthy subjects (19 females, mean age 59.5 years). Moreover, among the 44 patients, there were 19 inpatients and 25 outpatients; 19 were female and 25 were male; 18 with non-dyspnea and 26 with dyspnea.

FIELD STRENGTH/SEQUENCE

3-T, two-dimensional (2D) spoiled gradient-echo sequence.

ASSESSMENT

Ventilation and perfusion-weighted maps were extracted from five coronal slices using PREFUL analysis. Subsequently, perfusion defect percentage (QDP), ventilation defect percentage (VDP), and ventilation-perfusion match healthy (VQM) were calculated based on segmented lung parenchyma ventilation and perfusion-weighted maps. Additionally, clinical features, including demographic data (such as sex and age) and serum biomarkers (such as D-dimer levels), were evaluated.

STATISTICAL TESTS

Spearman correlation coefficients to explore relationships between clinical features and QDP, VDP, and VQM. Propensity score matching analysis to reduce the confounding bias between patients with PACS and healthy controls. The Mann-Whitney U tests and Chi-squared tests to detect differences between groups. Multivariable linear regression analyses to identify factors related to QDP, VDP, and VQM. A P-value <0.05 was considered statistically significant.

RESULTS

QDP significantly exceeded that of healthy controls in individuals with PACS (39.8% ± 15.0% vs. 11.0% ± 4.9%) and was significantly higher in inpatients than in outpatients (46.8% ± 17.0% vs. 34.5% ± 10.8%). Moreover, males exhibited pulmonary perfusion defects significantly more frequently than females (43.9% ± 16.8% vs. 34.4% ± 10.2%), and dyspneic participants displayed significantly higher perfusion defects than non-dyspneic patients (44.8% ± 15.8% vs. 32.6% ± 10.3%). QDP showed a significant positive relationship with age (β = 0.50) and D-dimer level (β = 0.72).

DATA CONCLUSION

PREFUL MRI may show pulmonary perfusion defects in patients with PACS. Furthermore, perfusion impairments may be more pronounced in males, inpatients, and dyspneic patients.

EVIDENCE LEVEL

2 TECHNICAL EFFICACY: Stage 2.

Comparison of Airborne SARS-CoV-2 Omicron and Pre-Delta Variants Around Infected Patients

Transmissibility has increased during the evolution of SARS-CoV-2, possibly by improved airborne transmission. An increased transmission was noted also in many hospitals. We analyzed SARS-CoV-2 in room air of hospitalized Omicron infected patients and compared results with previous findings with pre-Delta variants to study if SARS-CoV-2 was more prevalent in patient rooms after the introduction of Omicron. Only 4 of 75 (5%) air samples, from 3 of 43 included patients, were positive during the early Omicron wave, compared to 14/120 (12%), from 10 of 60 included patients during the initial wave. No certain statistical difference between virus variants could be established, but the tendency was a lower occurrence at Omicron infected patients, also when adjusting for relevant confounders. These finding do not support the initial hypothesis that increased SARS-CoV-2 aerosol emission from diagnosed patients with Omicron could explain any increased risk of hospital transmission.

Effect of wearing N95 masks for 10 hours on ambulatory blood pressure in healthy adults

The impact of wearing a face mask for an extended duration is unknown. This study aimed to determine if wearing a face mask for 10 h impacts blood pressure (BP) and arterial stiffness. Subjects received an ambulatory blood pressure cuff and were asked to wear it for 10 h while readings were taken every 15 min. During the face mask trial, subjects wore an N95 mask for 10 h. During the control, subjects did not wear a mask. Subjects were randomized to start their trial. An accelerometer was given to ensure no physical activity differences. Linear mixed models were used to determine group differences, and McNemar test was used to assess frequency differences when determining BP load. Twelve college-aged (20.5 ± 1.5 years) male ( n  = 5) and female ( n  = 7) individuals with normal BP participated in this study. There were no differences in time spent in any physical activity domain (all P  > 0.05). There was no difference in brachial SBP ( P  = 0.688), brachial DBP ( P  = 0.063), central SBP ( P  = 0.875), central DBP ( P  = 0.246), heart rate ( P  = 0.125), and augmentation pressure ( P  = 0.158) between conditions. During mask condition, augmentation pressure was reduced by 5.2 ± 3.1% compared to control ( P  < 0.001). There were no frequency differences in the number of BP readings above 140 mmHg for SBP ( P  = 0.479) and >90 mmHg for DBP ( P  = 0.212). The current study found that wearing an N95 mask for 10 h did not affect brachial or central BP but significantly decreased augmentation pressure.

Creating respiratory pathogen-free environments in healthcare and nursing-care settings: a comprehensive review

Hospital- and nursing-care-acquired infections are a growing problem worldwide, especially during epidemics, posing a significant threat to older adults in geriatric settings. Intense research during the COVID-19 pandemic highlighted the prominent role of aerosol transmission of pathogens. Aerosol particles can easily adsorb different airborne pathogens, carrying them for a long time. Understanding the dynamics of airborne pathogen transmission is essential for controlling the spread of many well-known pathogens, like the influenza virus, and emerging ones like SARS-CoV-2. Particles smaller than 50 to 100 µm remain airborne and significantly contribute to pathogen transmission. This review explores the journey of pathogen-carrying particles from formation in the airways, through airborne travel, to deposition in the lungs. The physicochemical properties of emitted particles depend on health status and emission modes, such as breathing, speaking, singing, coughing, sneezing, playing wind instruments, and medical interventions. After emission, sedimentation and evaporation primarily determine particle fate. Lung deposition of inhaled aerosol particles can be studied through in vivo, in vitro, or in silico methods. We discuss several numerical lung models, such as the Human Respiratory Tract Model, the LUng Dose Evaluation Program software (LUDEP), the Stochastic Lung Model, and the Computational Fluid Dynamics (CFD) techniques, and real-time or post-evaluation methods for detecting and characterizing these particles. Various air purification methods, particularly filtration, are reviewed for their effectiveness in healthcare settings. In the discussion, we analyze how this knowledge can help create environments with reduced PM2.5 and pathogen levels, enhancing safety in healthcare and nursing-care settings. This is particularly crucial for protecting older adults, who are more vulnerable to infections due to weaker immune systems and the higher prevalence of chronic conditions. By implementing effective airborne pathogen control measures, we can significantly improve health outcomes in geriatric settings.

Making Accessible and Attractive Porosities in Block Copolymer Nanofibers for Highly Permeable and Durable Air Filtration

Submicron particulate matter (PM) can penetrate deeply into human tissue, posing a serious threat to human health. However, the electrostatic charge of commercial respirators is easily dissipated, making it difficult to maintain long-term filtration. Herein, a hierarchically porous filter based on nanofibers with accessible porosity and particulate-attractive surfaces, achieving significant filtration performance is developed through polarity-driven interactions. This is achieved by selective swelling of electrospun nanofibers of the block copolymer of polysulfone and poly(ethylene glycol) (PSF-b-PEG), in which the originally solid nanofibers are 3D perforated with the PEG chains lined along the pore walls. Thus-produces nanofiber filters exhibit a long-term continuous filtration with an efficiency of over 95% for PM0.3 and a low pressure drop of only 40 Pa. In particular, it maintains superior filtration performance even under high particle concentrations and high humidity conditions. Additionally, the filter exhibits high air permeability (10814 m3 m-2 h-1 kPa-1) and water vapor transmission rate (3707 g m-2 d-1). This work provides new strategies and understandings on the development of porous structures simultaneously exhibiting high gas permeability and efficient particulate rejection.

Subgenomic RNA Detection in SARS-CoV-2 Assessing Replication and Inactivation Through Serial Passages, RT-qPCR, and Electron Microscopy

Subgenomic RNAs (sgRNAs) are potential markers of active SARS-CoV-2 replication, serving as templates for the synthesis of structural and accessory proteins in infectious viral particles. This study aimed to use RT-qPCR to quantify sgRNA and negative RNA intermediates, assessing viral replication in virus samples inactivated by β-propiolactone (βPL). Inactivated viruses subjected to five blind serial passages (BSs) were amplified by RT-qPCR using primers to target the envelope (ENV) and nucleoproteins (N1 and N2) of genomic genes, subgenomic envelope RNA (sgENV), and intermediate envelope RNA (ENV-). All positive controls showed consistent viral titers across passages (10 log10 copies/mL in N1/N2 and 11 log10 copies/mL in ENV) during BSs. Inactivated viral samples for ENV and ENV- targets ranged from 11.34 log10 copies/mL in BS1 to 11.20 log10 copies/mL in BS5. The sgENV was no longer detected in the inactivated SARS-CoV-2 samples after the second passage, suggesting successful inactivation. Replication kinetics showed consistent profiles for N1/N2, ENV, and ENV- targets in the first three post-infection hours (pih) and maintained approximately 5 log10 copies/mL at 1 pih, 2 pih, and 3 pih. A sharp exponential increase in the viral titer was observed from 24 pih onwards, peaking at 11.64 log10 copies/mL at 48 pih. Transmission electron microscopy confirmed viral particles only in cells infected with active SARS-CoV-2. These results support the use of sgRNA as a reliable marker for SARS-CoV-2 replication, especially in distinguishing between active replication and non-viable particles and in the development of diagnostic and therapeutic strategies.

Leveraging deep transfer learning and explainable AI for accurate COVID-19 diagnosis: Insights from a multi-national chest CT scan study

The COVID-19 pandemic has emerged as a global health crisis, impacting millions worldwide. Although chest computed tomography (CT) scan images are pivotal in diagnosing COVID-19, their manual interpretation by radiologists is time-consuming and potentially subjective. Automated computer-aided diagnostic (CAD) frameworks offer efficient and objective solutions. However, machine or deep learning methods often face challenges in their reproducibility due to underlying biases and methodological flaws. To address these issues, we propose XCT-COVID, an explainable, transferable, and reproducible CAD framework based on deep transfer learning to predict COVID-19 infection from CT scan images accurately. This is the first study to develop three distinct models within a unified framework by leveraging a previously unexplored large dataset and two widely used smaller datasets. We employed five known convolutional neural network architectures, both with and without pretrained weights, on the larger dataset. We optimized hyperparameters through extensive grid search and 5-fold cross-validation (CV), significantly enhancing the model performance. Experimental results from the larger dataset showed that the VGG16 architecture (XCT-COVID-L) with pretrained weights consistently outperformed other architectures, achieving the best performance, on both 5-fold CV and independent test. When evaluated with the external datasets, XCT-COVID-L performed well with data with similar distributions, demonstrating its transferability. However, its performance significantly decreased on smaller datasets with lower-quality images. To address this, we developed other models, XCT-COVID-S1 and XCT-COVID-S2, specifically for the smaller datasets, outperforming existing methods. Moreover, eXplainable Artificial Intelligence (XAI) analyses were employed to interpret the models' functionalities. For prediction and reproducibility purposes, the implementation of XCT-COVID is publicly accessible at https://github.com/cbbl-skku-org/XCT-COVID/.

Predicting COVID-19 Patient Disposition Using the National Early Warning Score 2: A Retrospective Cohort Study

Objectives To evaluate the effectiveness of the National Early Warning Score 2 (NEWS2) in predicting the need for hospital admission and close monitoring of suspected patients with COVID-19 presenting to the Emergency Department (ED). This study aims to determine whether NEWS2 can aid in identifying high-risk patients with COVID-19 requiring urgent care and admission. Methodology Retrospective data from electronic health records of 300 patients with COVID-19 who presented to Mediclinic Parkview Hospital ED between January 1, 2021, and June 30, 2021, were analyzed. Collected variables included age, gender, body mass index (BMI), vital signs, and patient disposition. Statistical analysis was conducted to assess the ability of NEWS2 to predict COVID-19 patient disposition. Results A total of 300 patients were included, and their NEWS2 scores were analyzed to predict clinical deterioration. NEWS2, with a cutoff value of 2, predicted hospital admission with 86% sensitivity and 75% specificity. It achieved an average area under the curve (AUC) of 0.86 for predicting outcomes at 24 to 72 hours from the time of initial presentation to the ED. Conclusions NEWS2 demonstrates high sensitivity in predicting the disposition of patients with COVID-19. Our findings support the use of NEWS2 as a useful tool for the initial assessment of patients with COVID-19 presenting to the ED, assisting in identifying patients at risk of deterioration.

Molecular detection of coronavirus in camelids and bovines using real-time quantitative polymerase chain reaction in Wasit Province, Iraq

Background

Coronaviruses (CoVs) are a diverse group of RNA viruses that cause respiratory and gastrointestinal diseases in humans and animals. Over the past two decades, outbreaks of Middle East Respiratory Syndrome Coronavirus (MERS-CoV) and bovine coronavirus (BCoV) have affected animal populations, especially in regions with close animal-human interactions, such as the Arabian Peninsula and Iraq. Given the potential for zoonotic transmission, understanding the prevalence and spread of CoVs among livestock is essential for managing potential risks to animal and human health.

Aim

This study aimed to investigate the prevalence of MERS-CoV in camels and BCoV in bovines within the Wasit Governorate of Iraq to assess the infection rates and potential interspecies transmission risks.

Methods

One hundred and fifty nasal swab samples (75 from camels and 75 from bovines) were collected between November 2022 and April 2023. The samples were analyzed for the presence of MERS-CoV and BCoV using real- time quantitative reverse transcription PCR (qRT-PCR) targeting the nucleocapsid (N) gene for each virus. Standard procedures for RNA extraction were followed, and qRT-PCR assays were conducted using specific primers to ensure high sensitivity and specificity.

Results

MERS-CoV was present in (42%) of the camel samples, whereas BCoV was detected in (34%) of the bovine samples. Statistical analysis indicated a significant difference (p < 0.05) in infection rates between camels and bovines, with a higher prevalence observed in camels. The clinical signs observed in infected camels included fever, nasal discharge, and appetite loss, whereas infected bovines exhibited symptoms such as diarrhea and respiratory distress.

Conclusion

The high prevalence of MERS-CoV and BCoV in camels and bovines in the Wasit region indicates a substantial risk for the continued spread of these viruses within animal populations. These findings underscore the importance of surveillance and biosecurity measures to control the spread of coronavirus among livestock, potentially reducing zoonotic transmission risks. Further research is required to understand the transmission dynamics of CoVs in mixed livestock farming systems.

Respiratory Shedding of Infectious SARS-CoV-2 Omicron XBB.1.41.1 Lineage among Captive White-Tailed Deer, Texas, USA

White-tailed deer (Odocoileus virginianus) have high value for research, conservation, agriculture, and recreation and might be key SARS-CoV-2 reservoirs. In November 2023, we sampled 15 female deer in a captive facility in Texas, USA. All deer had neutralizing antibodies to SARS-CoV-2; respiratory swab samples from 11 deer were SARS-CoV-2-positive by quantitative reverse transcription PCR, and 1 deer also had a positive rectal swab sample. Six of the 11 respiratory swab samples yielded infectious virus; replication kinetics of most samples displayed lower growth 24-48 hours postinfection in vitro than Omicron lineages isolated from humans in Texas in the same period. Virus growth was similar between groups by 72 hours, suggesting no strong attenuation of deer-derived virus. All deer viruses clustered in XBB Omicron clade and demonstrated more mutations than expected compared with contemporaneous viruses in humans, suggesting that crossing the species barrier was accompanied by a high substitution rate.

Alpha and Betacoronavirus Detection in Neotropical Bats from Northeast Brazil Suggests Wide Geographical Distribution and Persistence in Natural Populations

The emergence of zoonotic viral diseases, notably exemplified by the recent coronavirus disease pandemic in 2019 (COVID-19), underscores the critical need to understand the dynamics of viruses circulating in wildlife populations. This study aimed to investigate the diversity of coronaviruses in bat populations from northeastern Brazil, particularly in the state of Ceará, where little research on bat pathogens has been conducted previously. Bat sampling was performed between March 2021 and March 2022 across three municipalities, resulting in the collection of oral and rectal swabs from 298 captured individuals. Molecular analyses revealed alphacoronaviruses in multiple bat species. Additionally, a novel Betacoronavirus was identified in Artibeus planirostris, which did not fall within an established subgenus. Phylogenetic placement of these new coronavirus sequences suggests that closely related coronavirus lineages can infect a wide range of bat species sampled in distantly related Brazilian states and biomes. No SARS-CoV-2 and influenza A viruses were found in the sampled bats. These findings expand our understanding of coronavirus diversity in Brazilian bats. The detection of coronaviruses in various bat species underscores the importance of bats as reservoirs for these viruses. The absence of SARS-CoV-2 in the sampled bats indicates a lack of spillback events from human or environmental sources. However, the potential for future transmission events underscores the importance of ongoing surveillance and transmission mitigation protocols in wildlife management practices.

Mixed lipopeptide-based mucosal vaccine candidate induces cross-variant immunity and protects against SARS-CoV-2 infection in hamsters

The global dissemination of SARS-CoV-2 led to a worldwide pandemic in March 2020. Even after the official downgrading of the COVID-19 pandemic, infection with SARS-CoV-2 variants continues. The rapid development and deployment of SARS-CoV-2 vaccines helped to mitigate the pandemic to a great extent. However, the current vaccines are suboptimal; they elicit incomplete and short-lived protection and are ineffective against evolving virus variants. Updating the spike antigen according to the prevailing variant and repeated boosters is not the long-term solution. We have designed a lipopeptide-based, mucosal, pan-coronavirus vaccine candidate, derived from highly conserved and/or functional regions of the SARS-CoV-2 spike, nucleocapsid, and membrane proteins. Our studies demonstrate that the designed lipopeptides (LPMix) induced both cellular and humoral (mucosal and systemic) immune responses upon intranasal immunization in mice. Furthermore, the antibodies bound to the wild-type and mutated S proteins of SARS-CoV-2 variants of concern, including Alpha, Beta, Delta and Omicron, and also led to efficient neutralization in a surrogate viral neutralization assay. Our sequence alignment and 3-dimensional molecular modeling studies demonstrated that spike-derived epitopes, P1 and P2, are sequentially and/or structurally conserved among the SARS-CoV-2 variants. The addition of a novel mucosal adjuvant, heat-killed Caulobacter crescentus, to the lipopeptide vaccine significantly bolstered mucosal antibody responses. Finally, the lipopeptide-based intranasal vaccine demonstrated significant improvement in lung pathologies in a hamster model of SARS-CoV-2 infection. These studies are fundamentally important and open new avenues in the investigation of an innovative, broadly protective intranasal vaccine platform for SARS-CoV-2 and its variants.

The immune landscape and viral shedding of Omicron SARS-CoV-2 variants implicate immune escape

Background

Three years into the SARS-CoV-2 pandemic, the virus continues to mutate despite widespread vaccination, posing ongoing challenges for epidemic prevention and control. The relationship between viral shedding and immune escape remains under investigation. This study aims to examine the association between viral shedding and immune escape in the BA.4/5 and BF.7 variants.

Method

We included 542 patients infected with the Omicron variant from Beijing Xiaotangshan shelter hospital. Based on the viral strain, patients were divided into BA.4/5 group and BF.7 group. Additionally, we categorized patients into rapid viral shedding and slow viral shedding groups according to their viral shedding rates. We explored the relationship between viral shedding and immune-related clinical indicators during this period.

Result

Of the 542 patients, 118 were infected with BA.4/5 variant, and 424 were infected with BF.7 variant. The viral shedding duration differed significantly between BA.4/5 and BF.7 groups (p < 0.0001). However, there was no statistically significant correlation between viral shedding duration and immune-related indicators, such as WBC, Hb, PLT, Neu, Lym, CRP, allergy, fever, and vaccination status (p > 0.05). Furthermore, viral shedding duration was not associated with vaccination status, intervals between vaccinations, or vaccine types (p > 0.05).

Conclusion

The duration of viral shedding in patients infected with Omicron variants BA.4/5 and BF.7 is not associated with WBC, Hb, Lym, CRP, fever, allergy, or vaccine-related indicators. This lack of association may be attributed to immune escape mechanisms.

Research Trends and Development Dynamics of qPCR-based Biomarkers: A Comprehensive Bibliometric Analysis

Quantitative polymerase chain reaction (qPCR) is a vital molecular technique for biomarker detection; however, its clinical application is impeded by the scarcity of robust biomarkers and the inherent limitations of the technology. This study conducted a bibliometric analysis of 4063 qPCR-based biomarker studies sourced from the Web of Science (WOS) database, employing VOSviewer and CiteSpace to generate multi-dimensional structural insights into this field. The results reveal a growing trend in research within this domain, with gene expression analysis playing a central role in the identification of potential biomarkers. Among these, cancer-related biomarkers are the most prominent, while research on biomarkers for other diseases remains limited. Liquid biopsy biomarkers, including microRNA (miRNA), circulating free DNA (cfDNA), and circulating tumor DNA (ctDNA), are increasingly being explored. The integration of bioinformatics, omics analysis, and high-throughput technologies with qPCR is accelerating biomarker discovery. Furthermore, large-scale parallel sequencing is emerging as a potential alternative to relative quantification and microarray techniques. Nevertheless, qPCR remains essential for validating specific biomarkers, and further standardization of its protocols is necessary to enhance reliability. This study provides a systematic analysis of qPCR-based biomarker research and underscores the need for future technological integration and standardization to facilitate broader clinical applications.

An integrated methodological framework for the validation and verification of clinical testing by qRT-PCR

This paper outlines a practical method for validating quantitative-qualitative techniques used to detect genetic material through qRT-PCR, specifically focusing on SARS-CoV-2 testing and adhering to ISO/IEC 17025:2018 accreditation standards. Despite the prevalence of quantitative-qualitative screening in genetic testing, comprehensive validation guidelines remain a notable gap in the field. Such guidelines could be applied to other molecular testing areas that rely on these techniques, particularly those involving sample handling, automated extraction, and amplification processes, which can significantly impact results. This work describes the statistical approaches behind qRT-PCR protocols, followed by a technical characterization profile of the validation process. Modifications to the gold standard method allowed us to establish a technical limit of detection (LOD) of 5,09 copies/reaction at a 95 % confidence interval.

Utility of Protein Markers in COVID-19 Patients

COVID-19 has been a challenge at the healthcare level not only in the early stages of the pandemic, but also in the subsequent appearance of long-term COVID-19. Several investigations have attempted to identify proteomic biomarkers in an attempt to improve clinical care, guide treatment and predict possible patient outcomes. Proteins such as C-reactive protein (CRP) or interleukin 6 (IL-6) are clear markers of severe disease, but many others have been proposed that could help in risk stratification and in the prediction of specific complications. This review aims to bring together the most relevant studies in this regard, providing information to identify the most notable biomarkers in relation to COVID-19 found to date.

Effectiveness and user experience of nose and throat swabbing techniques for SARS-CoV-2 detection: results from the UK COVID-19 National Testing Programme

BACKGROUND

The UK's National Health Service Test and Trace (NHSTT) program aimed to provide the most effective and accessible SARS-CoV-2 testing approach possible. Early user feedback indicated that there were accessibility issues associated with throat swabbing. We report the results of service evaluations performed by NHSTT to assess the effectiveness and user acceptance of swabbing approaches, as well as qualitative findings of user experiences from research reports, surveys, and incident reports. Our intent is to present and summarize our findings about the application of alternative swabbing approaches during the COVID-19 pandemic in the UK.

METHODS

From May 2020 to December 2021, NHSTT conducted a series of service evaluations assessing self-swabbing and assisted swabbing of the nose and throat, and nose only (anterior nares/mid-turbinate) using polymerase chain reaction (PCR) and lateral flow devices (LFDs), for diagnostic suitability within the COVID-19 National Testing Programme. Outcomes included observational user feedback on swabbing approaches and quantitative testing performance (concordance, sensitivity, and specificity). A post-hoc indirect comparison of swabbing approaches was also performed. Additionally, an analysis of existing cross-service research was conducted in April 2021 to determine user feedback regarding swabbing approaches.

RESULTS

Observational data from cross-service research indicated a user preference for nose swabbing over throat swabbing. Significantly more users reported that nose swabbing was easier to perform than throat swabbing (50% vs. 12%) and there were significantly fewer reported incidents. In the service evaluations, while there was reduced sensitivity for nose-only swabbing for PCR (88%) compared with nose and throat swabbing, similar sensitivities were observed for nose-only and nose and throat swabbing for LFDs. The sensitivity of nose-only swabbing for LFDs was higher for individuals with higher viral concentrations.

CONCLUSIONS

User experience analyses supported a preference for nose-only swabbing. Nose-only swabbing for LFDs provided sufficient diagnostic accuracy, supporting its use as a viable option in the COVID-19 National Testing Programme. Less invasive swabbing approaches are important to maximize testing accessibility and alongside other behavioral interventions, increase user uptake.

Evolution of Omicron lineage towards increased fitness in the upper respiratory tract in the absence of severe lung pathology

The emergence of the Omicron lineage represented a major genetic drift in SARS-CoV-2 evolution. This was associated with phenotypic changes including evasion of pre-existing immunity and decreased disease severity. Continuous evolution within the Omicron lineage raised concerns of potential increased transmissibility and/or disease severity. To address this, we evaluate the fitness and pathogenesis of contemporary Omicron variants XBB.1.5, XBB.1.16, EG.5.1, and JN.1 in the upper (URT) and lower respiratory tract (LRT). We compare in vivo infection in Syrian hamsters with infection in primary human nasal and lung epithelium cells and assess differences in transmissibility, antigenicity, and innate immune activation. Omicron variants replicate efficiently in the URT but display limited pathology in the lungs compared to previous variants and fail to replicate in human lung organoids. JN.1 is attenuated in both URT and LRT compared to other Omicron variants and fails to transmit in the male hamster model. Our data demonstrate that Omicron lineage evolution has favored increased fitness in the URT.

Laboratory readiness and genomic surveillance of Covid-19 in the capital of Brazil

This study aims to analyze the diagnostic readiness to Covid-19 and the genomic surveillance of SARS-CoV-2 in Brasília, the capital of Brazil. This is a retrospective, cross-sectional study, with data from: cases/deaths-Ministry of Health; RT-PCR analyses Brasília Central Public Health Laboratory (LACEN); genomics-Global Initiative on Sharing All Influenza Data (GISAID). It was found that in March 2021, with the Gamma variant was predominant, RT-PCR diagnostic tests administered by LACEN reached their peak, followed by a reduction, possibly due to the start of vaccination. New peaks were observed in September 2021 and January 2022. The average time for releasing RT-PCR results was reduced from eight days (July 2020), to around eight hours in 2023. The participation of private laboratories was evident in sequencing the SARS-CoV-2 variants of concern in Brasília (n = 1,897). LACEN sequenced 50% of the samples received (571). A decrease in the incidence of cases and deaths due to Covid-19 was noted in the years 2022 to 2023, following the national trend. LACEN maintained RT-PCR diagnostic tests administered satisfactorily throughout the period. Regarding the genomic surveillance of SARS-CoV-2, the vast majority of samples were sequenced by private laboratories when compared to the public laboratory.

A Truncated Multi-Thiol Aptamer-Based SARS-CoV-2 Electrochemical Biosensor: Towards Variant-Specific Point-of-Care Detection with Optimized Fabrication

With the goal of fast and accurate diagnosis of infectious diseases, this study presents a novel electrochemical biosensor that employs a refined aptamer (C9t) for the detection of spike (S) protein SARS-CoV-2 variants in a flexible multielectrode aptasensor array with PoC capabilities. Two aptamer modifications were employed: removing the primer binding sites and including two dithiol phosphoramidite anchor molecules. Thus, reducing fabrication time from 24 to 3 h and increasing the stability and sparseness for multi-thiol aptasensors compared to a standard aptasensor using single thiols, without a reduction in aptamer density. The biosensor fabrication, optimization, and detection were verified in detail by electrochemistry, QCM-D, SPR, and XPS. The analyte-receptor binding was further confirmed spectroscopically at the level of individual molecules by AFM-IR. The aptasensor possesses a low limit of detection (8.0 fg/mL), the highest sensitivity reported for S protein (209.5 signal per concentration decade), and a wide dynamic detection range (8.0 fg/mL-38 ng/mL) in nasopharyngeal samples, covering the clinically relevant range. Furthermore, the C9t aptasensor showed high selectivity for SARS-CoV-2 S proteins over biomarkers for MERS-CoV, RSV, and Influenza. Even more, it showed a three times higher sensitivity for the Omicron in comparison to the Wuhan strain (wild type), alpha, and beta variants of the SARS-CoV-2 virus. Those results demonstrate the creation of an affordable and variant-selective refined C9t aptasensor that outperformed current rapid diagnosis tests.

Investigating the Role of Gut Microbiota in Pediatric Patients with Severe COVID-19 or MIS-C

Severe COVID-19 and MIS-C are rare but serious outcomes associated with SARS-CoV-2 infection. The onset of MIS-C often involves the gastrointestinal system, suggesting a potential connection with gut microbiota. This study aims to compare the gut microbiota of children with severe COVID-19 and those with MIS-C using various biomolecular approaches. Gut microbiota composition and specific microbial modulations were analyzed using fecal samples collected at hospital admission. The study included hospitalized patients (mean age 6 ± 5 years) diagnosed with severe COVID-19 (37 patients) or MIS-C (37 patients). Microbial differences were assessed using both NGS and qRT-PCR methodologies. In 75% of cases, pharmacological treatments included antibiotics and corticosteroids, which influenced the microbiota composition. Early age was found to have the most significant impact on microbiota diversity. Significant differences in alpha and beta diversity were observed between COVID-19 and MIS-C patients, particularly concerning low-abundance species. Levels of Bacteroides spp., Bifidobacterium spp., and Akkermansia muciniphila were comparable between groups, while an increased activity of Bifidobacterium spp. was noted in children with positive fecal samples (p = 0.019). An in-depth evaluation of lesser-known gut species may be key to reducing the risk of severe outcomes and developing microbiota-based biomarkers for the early diagnosis of MIS-C.

Nasal Mucociliary Epithelial Cell Culture Models for Studying Viral Infections

Respiratory nasal or lung epithelial cells serve as a valuable in vitro model for studying respiratory viral infections due to their physiological relevance and ability to recapitulate key aspects of the nasal or lung mucosa. In this chapter, we discuss the use of primary nasal epithelial cell cultures in studying viral infections, including their advantages, production methods, quality control, and identifiable disadvantages. Different methods for quantifying infection are presented with a special emphasis on how to adapt automated imaging methods and image analysis tools to the pseudostratified nasal epithelial cell models where cells are grown at the air-liquid interphase.

Inhibitors of dihydroorotate dehydrogenase synergize with the broad antiviral activity of 4'-fluorouridine

RNA viruses present a constant threat to human health, often with limited options for vaccination or therapy. Notable examples include influenza viruses and coronaviruses, which have pandemic potential. Filo- and henipaviruses cause more limited outbreaks, but with high case fatality rates. All RNA viruses rely on the activity of a virus-encoded RNA-dependent RNA polymerase (RdRp). An antiviral nucleoside analogue, 4'-Fluorouridine (4'-FlU), targets RdRp and diminishes the replication of several RNA viruses, including influenza A virus and SARS-CoV-2, through incorporation into nascent viral RNA and delayed chain termination. However, the effective concentration of 4'-FlU varied among different viruses, raising the need to fortify its efficacy. Here we show that inhibitors of dihydroorotate dehydrogenase (DHODH), an enzyme essential for pyrimidine biosynthesis, can synergistically enhance the antiviral effect of 4'-FlU against influenza A viruses, SARS-CoV-2, henipaviruses, and Ebola virus. Even 4'-FlU-resistant mutant influenza A virus was re-sensitized towards 4'-FlU by DHODH inhibition. The addition of uridine rescued influenza A virus replication, strongly suggesting uridine depletion as a mechanism of this synergy. 4'-FlU was also highly effective against SARS-CoV-2 in a hamster model of COVID. We propose that the impairment of endogenous uridine synthesis by DHODH inhibition enhances the incorporation of 4'-FlU into viral RNAs. This strategy may be broadly applicable to enhance the efficacy of pyrimidine nucleoside analogues for antiviral therapy.

Safety, tolerability, and efficacy of intranasally-administered detoxified LTh(αK) in mild-to-moderate COVID-19 patients: A randomized, double-blinded, placebo-controlled phase 2 study

The objective of the study was to assess the safety, tolerability, and potential efficacy of intranasally administered AD17002, a detoxified form of Escherichia coli heat-labile enterotoxin, in treating individuals with mild-to-moderate coronavirus disease of 2019 (COVID-19). In this randomized, double-blinded, and placebo-controlled phase 2a study, a total of 30 adults aged 20-70 years with mild-to-moderate COVID-19 were recruited from three medical centers in Taiwan in 2022-2023. The trial comprised two cohorts, and participants were randomly assigned to receive intranasal administrations of either three doses of AD17002 immunomodulator or a placebo formulation buffer. Outcome analyses were conducted on the intention-to-treat set, and the safety set that included all randomized participants exposed to the AD17002. The proportion of cycle threshold (Ct) ≥30 and time to the recovery of key symptoms were assessed. An exploratory study was conducted to analyze the integrity of the viral genome after treatment. Administering 20 μg of AD17002 three times, either at 1-week or 1-day intervals, proved to be safe and well tolerated in subjects with mild-to-moderate COVID-19. AD17002 demonstrated a rapid and positive outcome in reducing the viral load in patients receiving the treatment. Impact of AD17002 treatment was further supported by the analysis of viral genome integrity following the treatment. The enhancement in clinical recovery by AD17002 within 5 days after symptom onset was observed but did not achieve statistical significance. According to the results, intranasal administration of AD17002 was safe, well-tolerated, and potentially effective for treating mild-to-moderate COVID-19.

Quality and resilience of clinical laboratories in Rwanda: a need for sustainable strategies

BACKGROUND

Quality healthcare is a global priority, reliant on robust health systems for evidence-based medicine. Clinical laboratories are the backbone of quality healthcare facilitating diagnostics, treatment, patient monitoring, and disease surveillance. Their effectiveness depends on sustainable delivery of accurate test results. Although the Strengthening Laboratory Management Towards Accreditation (SLMTA) programme has enhanced laboratory quality in low-income countries, the long-term sustainability of this improvement remains uncertain.

OBJECTIVE

To explore the sustainability of quality performance in clinical laboratories in Rwanda following the conclusion of SLMTA.

METHODS

A quasi-experimental design was adopted, involving 47 laboratories divided into three groups with distinct interventions. While one group received continuous mentorship and annual assessments (group two), interventions for the other groups (groups one and three) ceased following the conclusion of SLMTA. SLMTA experts collected data for 10 years through assessments using WHO's StepwiseLaboratory Quality Improvement Process Towards Accreditation (SLIPTA) checklist. Descriptive and t-test analyses were conducted for statistical evaluation.

RESULTS

Improvements in quality were noted between baseline and exit assessments across all laboratory groups (mean baseline: 35.3%, exit: 65.8%, p < 0.001). However, groups one and three experienced performance declines following SLMTA phase-out (mean group one: 64.6% in reference to 85.8%, p = 0.01; mean group three: 57.3% in reference to 64.7%, p < 0.001). In contrast, group two continued to enhance performance even years later (mean: 86.6%compared to 70.6%, p = 0.03).

CONCLUSION

A coordinated implementation of quality improvement plan that enables regular laboratory assessments to pinpoint and address the quality gaps is essential for sustaining quality services in clinical laboratories.

Whispering gallery mode optical resonators for biological and chemical detection: current practices, future perspectives, and challenges

Sensors are important for a wide variety of applications include medical diagnostics and environmental monitoring. Due to their long photon confinement times, whispering gallery mode (WGM) sensors are among the most sensitive sensors currently in existence. We briefly discuss what are WGM sensors, the principles of WGM sensing, and the history of the field, beginning with Mie theory. We discuss recent work in the field on using these WGM resonators as sensors, focusing particularly on biological and chemical sensing applications. We discuss how sensorgrams are acquired and fundamental measurement limits. In addition, we discuss how to interpret binding curves and extract physical parameters such as binding affinity constants. We discuss the controversy surrounding single-molecule detection and discuss hybrid WGM nanoparticle sensors. In addition, we place these sensors in context with others sensing technologies both labeled and label-free. Finally, we discuss what we believe are the most promising applications for these devices, outline remaining challenges, and provide an outlook for the future.

From Tradition to Innovation: Diverse Molecular Techniques in the Fight Against Infectious Diseases

Infectious diseases impose a significant burden on global health systems due to high morbidity and mortality rates. According to the World Health Organization, millions die from infectious diseases annually, often due to delays in accurate diagnosis. Traditional diagnostic methods in clinical microbiology, primarily culture-based techniques, are time-consuming and may fail with hard-to-culture pathogens. Molecular biology advancements, notably the polymerase chain reaction (PCR), have revolutionized infectious disease diagnostics by allowing rapid and sensitive detection of pathogens' genetic material. PCR has become the gold standard for many infections, particularly highlighted during the COVID-19 pandemic. Following PCR, next-generation sequencing (NGS) has emerged, enabling comprehensive genomic analysis of pathogens, thus facilitating the detection of new strains and antibiotic resistance tracking. Innovative approaches like CRISPR technology are also enhancing diagnostic precision by identifying specific DNA/RNA sequences. However, the implementation of these methods faces challenges, particularly in low- and middle-income countries due to infrastructural and financial constraints. This review will explore the role of molecular diagnostic methods in infectious disease diagnosis, comparing their advantages and limitations, with a focus on PCR and NGS technologies and their future potential.

Microbiota-related metabolites correlated with the severity of COVID-19 patients

BACKGROUND

Coronavirus disease 2019 (COVID-19) is a global pandemic with high mortality, and the treatment options for the severe patients remain limited. Previous studies reported the altered gut microbiota in severe COVID-19. But there are no comprehensive data on the role of microbial metabolites in COVID-19 patients.

METHODS

We identified 153 serum microbial metabolites and assessed the changes in 72 COVID-19 patients upon admission and one-month after their discharge, comparing these changes to those in 133 healthy control individuals from the outpatient department during the same period.

RESULTS

Our study revealed that microbial metabolites varied across different stages and severity of COVID-19 patients. These altered microbial metabolites included tryptophan, bile acids, fatty acids, amino acids, vitamins and those containing benzene. A total of 13 distinct microbial metabolites were identified in COVID-19 patients compared to healthy controls. Notably, correlations were found among these disrupted metabolites and organ injury and inflammatory responses related to COVID-19. Furthermore, these metabolites did not restore to the normal levels one month after discharge. Importantly, two microbial metabolites were the core microbial metabolites related to the severity of COVID-19 patients.

CONCLUSIONS

The microbial metabolites were altered in the acute and recovery stage, correlating with disease severity of COVID-19. These results indicated the important role of gut microbiota in the progression of COVID-19, and facilitated the potential therapeutic microbial target for severe COVID-19 patients.

"The COVID-19 pandemic in BRICS: Milestones, interventions, and molecular epidemiology"

Brazil, Russia, India, China, and South Africa (BRICS) are a group of developing countries with shared economic, healthcare, and scientific interests. These countries navigate multiple syndemics, and the COVID-19 pandemic placed severe strain on already burdened BRICS' healthcare systems, hampering effective pandemic interventions. Genomic surveillance and molecular epidemiology remain indispensable tools for facilitating informed pandemic intervention. To evaluate the combined manner in which the pandemic unfolded in BRICS countries, we reviewed the BRICS pandemic epidemiological and genomic milestones, which included the first reported cases and deaths, and pharmaceutical and non-pharmaceutical interventions implemented in these countries. To assess the development of genomic surveillance capacity and efficiency over the pandemic, we analyzed the turnaround time from sample collection to data availability and the technologies used for genomic analysis. This data provided information on the laboratory capacities that enable the detection of emerging SARS-CoV-2 variants and highlight their potential for monitoring other pathogens in ongoing public health efforts. Our analyses indicated that BRICS suffered >105.6M COVID-19 infections, resulting in >1.7M deaths. BRICS countries detected intricate genetic combinations of SARS-CoV-2 variants that fueled country-specific pandemic waves. BRICS' genomic surveillance programs enabled the identification and characterization of the majority of globally circulating Variants of Concern (VOCs) and their descending lineages. Pandemic intervention strategies first implemented by BRICS countries included non-pharmaceutical interventions during the onset of the pandemic, such as nationwide lockdowns, quarantine procedures, the establishment of fever clinics, and mask mandates- which were emulated internationally. Vaccination rollout strategies complemented this, some representing the first of their kind. Improvements in BRICS sequencing and data generation turnaround time facilitated quicker detection of circulating and emerging variants, supported by investments in sequencing and bioinformatic infrastructure. Intra-BRICS cooperation contributed to the ongoing intervention in COVID-19 and other pandemics, enhancing collective capabilities in addressing these health challenges. The data generated continues to inform BRICS-centric pandemic intervention strategies and influences global health matters. The increased laboratory and bioinformatic capacity post-COVID-19 will support the detection of emerging pathogens.

Co-immunization with spike and nucleocapsid based DNA vaccines for long-term protective immunity against SARS-CoV-2 Omicron

The continuing evolution of SARS-CoV-2 variants challenges the durability of existing spike (S)-based COVID-19 vaccines. We hypothesized that vaccines composed of both S and nucleocapsid (N) antigens would increase the durability of protection by strengthening and broadening cellular immunity compared with S-based vaccines. To test this, we examined the immunogenicity and efficacy of wild-type SARS-CoV-2 S- and N-based DNA vaccines administered individually or together to K18-hACE2 mice. S, N, and S + N vaccines all elicited polyfunctional CD4+ and CD8+ T cell responses and provided short-term cross-protection against Beta and Omicron BA.2 variants, but only co-immunization with S + N vaccines provided long-term protection against Omicron BA.2. Depletion of CD4+ and CD8+ T cells reduced the long-term efficacy, demonstrating a crucial role for T cells in the durability of protection. These findings underscore the potential to enhance long-lived protection against SARS-CoV-2 variants by combining S and N antigens in next-generation COVID-19 vaccines.

AI-empowered visualization of nucleic acid testing

AIMS

The visualization of nucleic acid testing (NAT) results plays a critical role in diagnosing and monitoring infectious and genetic diseases. The review aims to review the current status of AI-based NAT result visualization. It systematically introduces commonly used AI-based methods and techniques for NAT, emphasizing the importance of result visualization for accessible, clear, and rapid interpretation. This highlights the importance of developing a NAT visualization platform that is user-friendly and efficient, setting a clear direction for future advancements in making nucleic acid testing more accessible and effective for everyday applications.

METHOD

This review explores both the commonly used NAT methods and AI-based techniques for NAT result visualization. The focus then shifts to AI-based methodologies, such as color detection and result interpretation through AI algorithms. The article presents the advantages and disadvantages of these techniques, while also comparing the performance of various NAT platforms in different experimental contexts. Furthermore, it explores the role of AI in enhancing the accuracy, speed, and user accessibility of NAT results, highlighting visualization technologies adapted from other fields of experimentation.

SIGNIFICANCE

This review offers valuable insights for researchers and everyday users, aiming to develop effective visualization platforms for NAT, ultimately enhancing disease diagnosis and monitoring.

Comparison of a SARS-CoV-2 mRNA booster immunization containing additional antigens to a spike-based mRNA vaccine against Omicron BA.5 infection in hACE2 mice

The emergence of SARS-CoV-2 variants presents challenges to vaccine effectiveness, underlining the necessity for next-generation vaccines with multiple antigens beyond the spike protein. Here, we investigated a multiantigenic booster containing spike and a chimeric construct composed of nucleoprotein (N) and membrane (M) proteins, comparing its efficacy to a spike-only booster against Omicron BA.5 in K18-hACE2 mice. Initially, mice were primed and boosted with Beta (B.1.351) spike-only mRNA, showing strong spike-specific T cell responses and neutralizing antibodies, albeit with limited cross-neutralization to Omicron variants. Subsequently, a spike-NM multiantigenic vaccine was then examined as a second booster dose for protection in hACE2-transgenic mice. Mice receiving either homologous spike-only or heterologous spike-NM booster had nearly complete inhibition of infectious virus shedding in oral swabs and reduced viral burdens in both lung and nasal tissues following BA.5 challenge. Examination of lung pathology further revealed that both spike-only and spike-NM boosters provided comparable protection against inflammatory infiltrates and fibrosis. Moreover, the spike-NM booster demonstrated neutralization efficacy in a pseudovirus assay against Wuhan-Hu-1, Beta, and Omicron variants akin to the spike-only booster. These findings indicate that supplementing spike with additional SARS-CoV-2 targets in a booster immunization confers equivalent immunity and protection against Omicron BA.5. This work highlights a promising strategy for individuals previously vaccinated with spike-only vaccines, potentially offering enhanced protection against emerging coronaviruses.

SARS-CoV-2 seroprevalence and antibody trajectories after easing of COVID-19 restrictions: a longitudinal study in China

Background

We aimed to evaluate the seroprevalence of SARS-CoV-2 and investigate the trajectories of protective immunity and associated risk factors in eastern China between March and November 2023 after the easing of COVID-19 restrictions.

Materials and methods

We conducted repeated population-based seroepidemiologic studies using a multistage, population-stratified, cluster random sampling method. We measured neutralizing antibodies (nAbs) using a fluorescence immunoassay. We calculated both overall and stratified seroprevalence. The latent class growth mixed model (LCGMM) was used to analyze the dynamic trajectories of antibodies, and a multinomial logistic regression model was used to identify factors associated with different antibody trajectory patterns.

Results

A total of 6,147 participants were included at baseline, with a median age of 53.61 years. Both observed and adjusted seroprevalence remained high and stable throughout the study period. The LCGMM identified four distinct antibody trajectories: 75.22% of participants had a high and stable antibody trajectory, while nearly 8% of them exhibited an increase, decline, or low-stable antibody trajectory. Younger participants, women, those fully vaccinated, and individuals with a history of previous infection were more likely to have high and stable antibody trajectories.

Conclusion

The majority of the population maintained sustained protective immunity after the outbreak, following the easing of COVID-19 restrictions across the country.

An Outbreak of SARS-CoV-2 in Captive Armadillos Associated with Gamma Variant in Argentina

The current pandemic produced by SARS-CoV-2 and its variants represent an example of the one health concept in which humans and animals are components of the same epidemiologic chain. Animal reservoirs of these viruses are thus the focus of surveillance programs, to monitor their circulation and evolution in potentially new hosts and reservoirs. In this work, we report the detection of the SARS-CoV-2 Gamma variant infection in four specimens of Chaetophractus villosus (big hairy armadillo/armadillo peludo) in Argentina. In addition to the finding of a new wildlife species susceptible to SARS-CoV-2 infection, the identification of the Gamma variant three months after its last detection in humans in Argentina is a noteworthy result, which can be due to alternative non-exclusive scenarios, such as unidentified viral reservoirs, unrecognized circulation in humans or species-specific variation in incubation periods.

Wastewater-based epidemiology for COVID-19 surveillance and beyond: A survey

The pandemic of COVID-19 has imposed tremendous pressure on public health systems and social economic ecosystems over the past years. To alleviate its social impact, it is important to proactively track the prevalence of COVID-19 within communities. The traditional way to estimate the disease prevalence is to estimate from reported clinical test data or surveys. However, the coverage of clinical tests is often limited and the tests can be labor-intensive, requires reliable and timely results, and consistent diagnostic and reporting criteria. Recent studies revealed that patients who are diagnosed with COVID-19 often undergo fecal shedding of SARS-CoV-2 virus into wastewater, which makes wastewater-based epidemiology for COVID-19 surveillance a promising approach to complement traditional clinical testing. In this paper, we survey the existing literature regarding wastewater-based epidemiology for COVID-19 surveillance and summarize the current advances in the area. Specifically, we have covered the key aspects of wastewater sampling, sample testing, and presented a comprehensive and organized summary of wastewater data analytical methods. Finally, we provide the open challenges on current wastewater-based COVID-19 surveillance studies, aiming to encourage new ideas to advance the development of effective wastewater-based surveillance systems for general infectious diseases.

Profile of Cytokines and T Cell Subsets Transcription Factors in Cerebrospinal Fluid of Patients with Viral Encephalitis

This study investigates the demographic, clinical characteristics, virological profiles, and immunological responses of patients with viral encephalitis (VE) compared with a control group. The VE group displayed a wide range of neurological symptoms. Virological analysis revealed the predominance of Herpesviridae family viruses. Immune responses in cerebrospinal fluid (CSF) from patients with VE were examined, highlighting an immunological shift toward T helper 1 (Th1) cells dominance, altered T helper 17 cells/regulatory T cells (Th17/Tregs) balance, and high interleukin-6 expression. These findings provide insights into the complex immunological landscape of VE, highlighting the role of specific cytokines and T cell subsets in its pathogenesis and potentially guiding targeted therapeutic strategies.

Wild red foxes (Vulpes vulpes) do not participate in SARS-CoV-2 circulation in Poland

BACKGROUND

Biomonitoring is an essential activity for identifying possible vectors and reservoirs of pathogens and predicting potential outbreaks. Wild red foxes are present in both sylvatic and synanthropic environments, making them potential carriers of zoonotic pathogens. Experimental studies have shown that both coyotes and red foxes can transmit SARS-CoV-2. This study aimed to assess the prevalence and seroprevalence of SARS-CoV-2 in wild red foxes hunted in northern Poland.

METHODS

Oral swabs, blood clots or heat tissue samples were collected from 292 red foxes hunted in northern Poland. We used both molecular (RT-PCR) and serological (IFA) approaches to detect SARS-CoV-2 infections in the sampled animals.

RESULTS

We did not find any evidence of SARS-CoV-2 infection in the collected samples, using both molecular and serological methods.

CONCLUSIONS

Despite foxes having frequent contact with humans, human waste, and other animals, they do not appear to participate in the circulation of the SARS-CoV-2 virus in our geographical region. Nevertheless, we believe that continuous biomonitoring should be performed to assess the SARS-CoV-2 epidemiological situation in the wild.

Development of new RT-PCR assays for the specific detection of BA.2.86 SARS-CoV-2 and its descendent sublineages

The SARS-CoV-2 BA.2.86 variant, also known as Pirola, has acquired over 30 amino acid changes in the Spike protein, evolving into >150 sublineages within ten months of its emergence. Among these, the JN.1, has been rapidly increasing globally becoming the most prevalent variant. To facilitate the identification of BA.2.86 sublineages, we designed the PiroMet-1 and PiroMet-2 assays in silico and validated them using BA.2.86 viral RNA and clinical samples to ascertain analytical specificity and sensitivity. Both assays resulted very specific with limit of detection of about 1-2 RNA copies/μL. The assays were then applied in a digital RT-PCR format to wastewater samples, combined with the OmMet assay (which identifies Omicron sublineages except BA.2.86 and its descendants) and the JRC-UCE.2 assay (which can universally recognize all SARS-CoV-2 variants). When used together with the OmMet and JRC-CoV-UCE.2 assays, the PiroMet assays accurately quantified BA.2.86 sublineages in wastewater samples. Our findings support the integration of these assays into routine SARS-CoV-2 wastewater surveillance as a timely and cost-effective complement to sequencing for monitoring the prevalence and spread of BA.2.86 sublineages within communities.

Development of multiplex allele-specific RT-qPCR assays for differentiation of SARS-CoV-2 Omicron subvariants

Quick differentiation of current circulating variants and the emerging recombinant variants of SARS-CoV-2 is essential to monitor their transmissions. However, the widely applied gene sequencing method is time-consuming and costly especially when facing recombinant variants, because a large part or whole genome sequencing is required. Allele-specific reverse transcriptase real time RT-PCR (RT-qPCR) represents a quick and cost-effective method for SNP (single nucleotide polymorphism) genotyping and has been successfully applied for SARS-CoV-2 variant screening. In the present study, we developed a panel of 5 multiplex allele-specific RT-qPCR assays targeting 20 key mutations for quick differentiation of the Omicron subvariants (BA.1 to BA.5 and their descendants) and the recombinant variants (XBB.1 and XBB.1.5). Two parallel multiplex RT-qPCR reactions were designed to separately target the prototype allele and the mutated allele of each mutation in the allele-specific RT-qPCR assay. Optimal annealing temperatures, primer and probe dosage, and time for annealing/extension for each reaction were determined by multi-factor and multi-level orthogonal test. The variation of Cp (crossing point) values (ΔCp) between the two multiplex RT-qPCR reactions was applied to determine if a mutation occurs or not. SARS-CoV-2 subvariants and related recombinant variants were differentiated by their unique mutation patterns. The developed multiplex allele-specific RT-qPCR assays exhibited excellent analytical sensitivities (with limits of detection (LoDs) of 1.47-18.52 copies per reaction), wide linear detection ranges (109-100 copies per reaction), good amplification efficiencies (88.25 to 110.68%), excellent reproducibility (coefficient of variations (CVs) < 5% in both intra-assay and inter-assay tests), and good clinical performances (99.5-100% consistencies with Sanger sequencing). The developed multiplex allele-specific RT-qPCR assays in the present study provide an alternative tool for quick differentiation of the SARS-CoV-2 Omicron subvariants and their recombinant variants. KEY POINTS: • A panel of five multiplex allele-specific RT-qPCR assays for quick differentiation of 11 SARS-CoV-2 Omicron subvariants (BA.1, BA.2, BA.4, BA.5, and their descendants) and 2 recombinant variants (XBB.1 and XBB.1.5). • The developed assays exhibited good analytical sensitivities and reproducibility, wide linear detection ranges, and good clinical performances, providing an alternative tool for quick differentiation of the SARS-CoV-2 Omicron subvariants and their recombinant variants.

Impaired mucosal IgA response in patients with severe COVID-19

Several studies have investigated the antibody response to SARS-CoV-2, focusing particularly on the systemic humoral immune response and the production of immunoglobulin G (IgG) antibodies. IgA antibodies play a crucial role in protecting against respiratory viral infections but have also been associated with the pathophysiology of COVID-19. We performed a prospective study of 169 COVID-19 patients - 50 with critical/severe (ICU), 47 with moderate (Non-ICU), and 72 with asymptomatic COVID-19 - to explore the humoral immune response to SARS-CoV-2 infection. We found that the early systemic IgA response strongly induced in patients with severe disease did not block IgG neutralization functions and activated FcRs more effectively than IgG. However, even if SIgA levels were high, mucosal IgA antibodies could not control the infection effectively in patients with severe disease. Our findings highlight the complexity of the immune response to SARS-CoV-2 exhibiting high systemic levels of IgA with strong neutralizing capacity in severe cases, together with higher levels of IgA-FcR activation than in asymptomatic patients. They also suggest the need for further research to fully understand the role of IgA and its structural alterations in mucosal tissues in cases of severe disease and the impact of these antibodies on disease progression.