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

SARS-CoV-2 BA.2.86 enters lung cells and evades neutralizing antibodies with high efficiency

BA.2.86, a recently identified descendant of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron BA.2 sublineage, contains ∼35 mutations in the spike (S) protein and spreads in multiple countries. Here, we investigated whether the virus exhibits altered biological traits, focusing on S protein-driven viral entry. Employing pseudotyped particles, we show that BA.2.86, unlike other Omicron sublineages, enters Calu-3 lung cells with high efficiency and in a serine- but not cysteine-protease-dependent manner. Robust lung cell infection was confirmed with authentic BA.2.86, but the virus exhibited low specific infectivity. Further, BA.2.86 was highly resistant against all therapeutic antibodies tested, efficiently evading neutralization by antibodies induced by non-adapted vaccines. In contrast, BA.2.86 and the currently circulating EG.5.1 sublineage were appreciably neutralized by antibodies induced by the XBB.1.5-adapted vaccine. Collectively, BA.2.86 has regained a trait characteristic of early SARS-CoV-2 lineages, robust lung cell entry, and evades neutralizing antibodies. However, BA.2.86 exhibits low specific infectivity, which might limit transmissibility.

Molecular Investigation of SARS-CoV-2 Circulating in Iranian Bats Using Real-Time RT-PCR for Detection of Envelop (E) Gene of the Virus

Background

The COVID-19 was first reported in 2019 to cause pneumonia in people of Wuhan, Hubei province, China, is now associated with high mortality worldwide. Phylogenetic analysis revealed that SARS-CoV-2 (2019-nCoV) is closely (88%-89% similarity) related to the coronavirus circulating in Rhinolophus (horseshoe bats). More than 50 bat species belonging to eight families have been reported from Iran of which five species belong to the Rhinolophidae family. So far, no study has been done on COVID-19 infection in Iranian bats.

Aim

The current study was performed, for the first time, to investigate the infection of Iranian bats with SARS-CoV-2.

Methods

This cross-sectional study was conducted in 2021 using 183 bat samples collected from three caves in the south (Fars province) and two caves in the northwest (Kermanshah and Kurdistan provinces) of Iran. Bats' digestive and respiratory system samples were collected from each bat of different species. The samples were evaluated by real-time PCR and by targeting a 221 bp fragment of the envelop (E) genes of SARS-CoV-2.

Results

COVID-19 was detected in alimentary specimens of two of the Mediterranean horseshoe (Rhinolophus Euryale) bats.

Conclusion

Although, based on the findings of the molecular evaluation, the infection of bats with COVID-19 was determined in this study, further studies are needed on a larger number of bats, particularly horseshoe bats, to confirm the potential infection of Iranian bats with COVID-19.

Highly efficient and sensitive membrane-based concentration process allows quantification, surveillance, and sequencing of viruses in large volumes of wastewater

Wastewater-based epidemiology is experiencing exponential development. Despite undeniable advantages compared to patient-centered approaches (cost, anonymity, survey of large populations without bias, detection of asymptomatic infected peoples…), major technical limitations persist. Among them is the low sensitivity of the current methods used for quantifying and sequencing viral genomes from wastewater. In situations of low viral circulation, during initial stages of viral emergences, or in areas experiencing heavy rains, the extremely low concentrations of viruses in wastewater may fall below the limit of detection of the current methods. The availability during crisis and the cost of the commercial kits, as well as the requirement of expensive materials such as high-speed centrifuge, can also present major blocks to the development of wastewater-based epidemiological survey, specifically in low-income countries. Thereby, highly sensitive, low cost and standardized methods are still needed, to increase the predictability of the viral emergences, to survey low-circulating viruses and to make the results from different labs comparable. Here, we outline and characterize new protocols for concentrating and quantifying SARS-CoV-2 from large volumes (500 mL-1 L) of untreated wastewater. In addition, we report that the methods are applicable for monitoring and sequencing. Our nucleic acid extraction technique (the routine C: 5 mL method) does not require sophisticated equipment such as automatons and is not reliant on commercial kits, making it readily available to a broader range of laboratories for routine epidemiological survey. Furthermore, we demonstrate the efficiency, the repeatability, and the high sensitivity of a new membrane-based concentration method (MBC: 500 mL method) for enveloped (SARS-CoV-2) and non-enveloped (F-specific RNA phages of genogroup II / FRNAPH GGII) viruses. We show that the MBC method allows the quantification and the monitoring of viruses in wastewater with a significantly improved sensitivity compared to the routine C method. In contexts of low viral circulation, we report quantifications of SARS-CoV-2 in wastewater at concentrations as low as 40 genome copies per liter. In highly diluted samples collected in wastewater treatment plants of French Guiana, we confirmed the accuracy of the MBC method compared to the estimations done with the routine C method. Finally, we demonstrate that both the routine C method processing 5 mL and the MBC method processing 500 mL of untreated wastewater are both compatible with SARS-CoV-2 sequencing. We show that the quality of the sequence is correlated with the concentration of the extracted viral genome. Of note, the quality of the sequences obtained with some MBC processed wastewater was improved by dilutions or enzyme substitutions suggesting the presence of specific enzyme inhibitors in some wastewater. To the best of our knowledge, our MBC method is one of the first efficient, sensitive, and repeatable method characterized for SARS-CoV-2 quantification and sequencing from large volumes of wastewater.

An Insight into the Present Pandemic Scenario (COVID-19) with Respect to Maxfac Speciality

The December 2019 pandemic killed about 2 million people and impacted countless more. SARS-CoV-2 causes COVID-19. The sickness causes dyspnea, high temperature, dry cough, loss of taste smell, etc., Due to the disease's fast spread, oral and maxillofacial surgical practices must be reconsidered. The World Health Organization, Association of Oral and Maxillofacial Surgeons of India, and other reputable bodies have released guidelines for safe and efficient COVID-19 therapy. This poll seeks surgeons' awareness of these worldwide and national bodies' guidance. A social media poll generated 173 replies, which were analyzed and interpreted. Many surgeons were aware of the recommendations and safety precautions, but others were unaware of the modifications in oral and maxillofacial surgery practice procedures.

Impact of the COVID-19 related border restrictions on influenza and other common respiratory viral infections in New Zealand

BACKGROUND

New Zealand's (NZ) complete absence of community transmission of influenza and respiratory syncytial virus (RSV) after May 2020, likely due to COVID-19 elimination measures, provided a rare opportunity to assess the impact of border restrictions on common respiratory viral infections over the ensuing 2 years.

METHODS

We collected the data from multiple surveillance systems, including hospital-based severe acute respiratory infection surveillance, SHIVERS-II, -III and -IV community cohorts for acute respiratory infection (ARI) surveillance, HealthStat sentinel general practice (GP) based influenza-like illness surveillance and SHIVERS-V sentinel GP-based ARI surveillance, SHIVERS-V traveller ARI surveillance and laboratory-based surveillance. We described the data on influenza, RSV and other respiratory viral infections in NZ before, during and after various stages of the COVID related border restrictions.

RESULTS

We observed that border closure to most people, and mandatory government-managed isolation and quarantine on arrival for those allowed to enter, appeared to be effective in keeping influenza and RSV infections out of the NZ community. Border restrictions did not affect community transmission of other respiratory viruses such as rhinovirus and parainfluenza virus type-1. Partial border relaxations through quarantine-free travel with Australia and other countries were quickly followed by importation of RSV in 2021 and influenza in 2022.

CONCLUSION

Our findings inform future pandemic preparedness and strategies to model and manage the impact of influenza and other respiratory viral threats.

Human conjunctiva organoids to study ocular surface homeostasis and disease

The conjunctival epithelium covering the eye contains two main cell types: mucus-producing goblet cells and water-secreting keratinocytes, which present mucins on their apical surface. Here, we describe long-term expanding organoids and air-liquid interface representing mouse and human conjunctiva. A single-cell RNA expression atlas of primary and cultured human conjunctiva reveals that keratinocytes express multiple antimicrobial peptides and identifies conjunctival tuft cells. IL-4/-13 exposure increases goblet and tuft cell differentiation and drastically modifies the conjunctiva secretome. Human NGFR+ basal cells are identified as bipotent conjunctiva stem cells. Conjunctival cultures can be infected by herpes simplex virus 1 (HSV1), human adenovirus 8 (hAdV8), and SARS-CoV-2. HSV1 infection was reversed by acyclovir addition, whereas hAdV8 infection, which lacks an approved drug therapy, was inhibited by cidofovir. We document transcriptional programs induced by HSV1 and hAdV8. Finally, conjunctival organoids can be transplanted. Together, human conjunctiva organoid cultures enable the study of conjunctival (patho)-physiology.

Pipette-free field-deployable molecular diagnostic kit for bimodal visual detection of infectious RNA viruses

Here, we developed a field-deployable molecular diagnostic kit for the detection of RNA viruses that operates in a pipette-free manner. The kit is composed of acrylic sticks, PCR tubes, and palm-sized three-dimensional(3D)-printed heaters operated by batteries. The kit performs RNA extraction, reverse transcriptase loop-mediated isothermal amplification (RT-LAMP), and visual detection in one kit. An acrylic stick was engraved with one shallow and one deep cylindrical chamber at each end for the insertion of an FTA card and ethidium homodimer-1 (EthD-1), respectively, to perform RNA extraction/purification and bimodal visual detection of the target amplicons. First, an intercalation of EthD-1 into the target DNA initially produces fluorescence upon UV illumination. Next, the addition of a strong oxidant, in this case sodium (meta) periodate (NaIO4 ), produces intense aggregates in the presence of EthD-1-intercalated DNA, realized by electrostatic interaction. In the absence of the target amplicon, no fluorescence or aggregates are observed. Using this kit, two major infectious viruses-severe fever with thrombocytopenia syndrome virus (SFTSV) and severe acute respiratory syndrome coronavirus (SARS-CoV-2)-were successfully detected in 1 h, and the limits of detection (LOD) were approximately 1 virus μL-1 for SFTSV and 103 copies μL-1 for SARS-CoV-2 RNA. The introduced kit is portable, end-user-friendly, and can be operated in a pipette-free manner, paving the way for simple and convenient virus detection in resource-limited settings.

Clinical decision support systems (CDSS) in assistance to COVID-19 diagnosis: A scoping review on types and evaluation methods

Background and Aims

Due to the COVID-19 pandemic, a precise and reliable diagnosis of this disease is critical. The use of clinical decision support systems (CDSS) can help facilitate the diagnosis of COVID-19. This scoping review aimed to investigate the role of CDSS in diagnosing COVID-19.

Methods

We searched four databases (Web of Science, PubMed, Scopus, and Embase) using three groups of keywords related to CDSS, COVID-19, and diagnosis. To collect data from studies, we utilized a data extraction form that consisted of eight fields. Three researchers selected relevant articles and extracted data using a data collection form. To resolve any disagreements, we consulted with a fourth researcher.

Results

A search of the databases retrieved 2199 articles, of which 68 were included in this review after removing duplicates and irrelevant articles. The studies used nonknowledge-based CDSS (n = 52) and knowledge-based CDSS (n = 16). Convolutional Neural Networks (CNN) (n = 33) and Support Vector Machine (SVM) (n = 8) were employed to design the CDSS in most of the studies. Accuracy (n = 43) and sensitivity (n = 35) were the most common metrics for evaluating CDSS.

Conclusion

CDSS for COVID-19 diagnosis have been developed mainly through machine learning (ML) methods. The greater use of these techniques can be due to their availability of public data sets about chest imaging. Although these studies indicate high accuracy for CDSS based on ML, their novelty and data set biases raise questions about replacing these systems as clinician assistants in decision-making. Further studies are needed to improve and compare the robustness and reliability of nonknowledge-based and knowledge-based CDSS in COVID-19 diagnosis.

Stacked deep learning approach for efficient SARS-CoV-2 detection in blood samples

Identifying COVID-19 through blood sample analysis is crucial in managing the disease and improving patient outcomes. Despite its advantages, the current test demands certified laboratories, expensive equipment, trained personnel, and 3-4 h for results, with a notable false-negative rate of 15%-20%. This study proposes a stacked deep-learning approach for detecting COVID-19 in blood samples to distinguish uninfected individuals from those infected with the virus. Three stacked deep learning architectures, namely the StackMean, StackMax, and StackRF algorithms, are introduced to improve the detection quality of single deep learning models. To counter the class imbalance phenomenon in the training data, the Synthetic Minority Oversampling Technique (SMOTE) algorithm is also implemented, resulting in increased specificity and sensitivity. The efficacy of the methods is assessed by utilizing blood samples obtained from hospitals in Brazil and Italy. Results revealed that the StackMax method greatly boosted the deep learning and traditional machine learning methods' capability to distinguish COVID-19-positive cases from normal cases, while SMOTE increased the specificity and sensitivity of the stacked models. Hypothesis testing is performed to determine if there is a significant statistical difference in the performance between the compared detection methods. Additionally, the significance of blood sample features in identifying COVID-19 is analyzed using the XGBoost (eXtreme Gradient Boosting) technique for feature importance identification. Overall, this methodology could potentially enhance the timely and precise identification of COVID-19 in blood samples.

TXM peptides inhibit SARS-CoV-2 infection, syncytia formation, and lower inflammatory consequences

After three years of the SARS-CoV-2 pandemic, the search and availability of relatively low-cost benchtop therapeutics for people not at high risk for a severe disease are still ongoing. Although vaccines and new SARS-CoV-2 variants reduce the death toll, the long COVID-19 along with neurologic symptoms can develop and persist even after a mild initial infection. Reinfections, which further increase the risk of sequelae in multiple organ systems as well as the risk of death, continue to require caution. The spike protein of SARS-CoV-2 is an important target for both vaccines and therapeutics. The presence of disulfide bonds in the receptor binding domain (RBD) of the spike protein is essential for its binding to the human ACE2 receptor and cell entry. Here, we demonstrate that thiol-reducing peptides based on the active site of oxidoreductase thioredoxin 1, called thioredoxin mimetic (TXM) peptides, can prevent syncytia formation, SARS-CoV-2 entry into cells, and infection in a mouse model. We also show that TXM peptides inhibit the redox-sensitive HIV pseudotyped viral cell entry. These results support disulfide targeting as a common therapeutic strategy for treating infections caused by viruses using redox-sensitive fusion. Furthermore, TXM peptides exert anti-inflammatory properties by lowering the activation of NF-κB and IRF signaling pathways, mitogen-activated protein kinases (MAPKs) and lipopolysaccharide (LPS)-induced cytokines in mice. The antioxidant and anti-inflammatory effects of the TXM peptides, which also cross the blood-brain barrier, in combination with prevention of viral infections, may provide a beneficial clinical strategy to lower viral infections and mitigate severe consequences of COVID-19.

Clinical Performance of the Reverse Transcription-Loop-Mediated Isothermal Amplification Assay for the Diagnosis of COVID-19 in a Thai Community Hospital at the Thailand-Myanmar Border

INTRODUCTION

Coronavirus disease 2019 (COVID-19) continues to be a global health threat and is a public health issue in Thailand and other countries. The extensive cross-border between Thailand and Myanmar is considered to be at a potentially high risk for COVID-19 distribution in this region. In this instance, simple and cost-effective tests for rapid and early detection of COVID-19 would be useful for effective patient management and control of the disease.

METHODS

This study was conducted at Mae Sot Hospital on the border of Thailand-Myanmar to evaluate the diagnostic performance of a simple colorimetric reverse transcription-loop-mediated isothermal amplification (RT-LAMP) assay developed recently for the rapid detection of SARS-CoV-2. Nasopharyngeal specimens were routinely collected and processed through automated nucleic acid extraction followed by real-time reverse transcription-polymerase chain reaction (rRT-PCR) using the Molaccu® COVID-19 Detection Kit. The RT-LAMP assay was further performed on remnant RNA samples, and the visual results were compared to those of rRT-PCR as a reference.

RESULTS

Of the 727 samples tested, the RT-LAMP assay could detect 322 out of 374 samples positive for SARS-CoV-2 by rRT-PCR with 100% (n = 353/353) negative agreement. The comparative analysis demonstrated the overall accuracy, sensitivity, specificity, positive predictive value, and negative predictive value of the RT-LAMP at 92.85% (n = 675/727, 95% CI: 90.73-94.61), 86.10% (n = 322/374, 95% CI: 82.17-89.44), 100% (n = 353/353, 95% CI: 98.96-100), 100% (n = 322/322, 95% CI: 98.86-100), and 87.16% (n = 353/405, 95% CI: 84.06-89.73), respectively.

CONCLUSION

This RT-LAMP assay showed good diagnostic performance in the hospital setting. It can increase laboratory capacity for rapid SARS-CoV-2 testing and has the potential for use as an alternative or a backup assay at the point of need, especially where alternatives are unavailable for any reason, such as a decline in COVID-19 cases.

SARS-CoV and SARS-CoV-2 display limited neuronal infection and lack the ability to transmit within synaptically connected axons in stem cell-derived human neurons

Sarbecoviruses such as SARS and SARS-CoV-2 have been responsible for two major outbreaks in humans, the latter resulting in a global pandemic. While sarbecoviruses primarily cause an acute respiratory infection, they have been shown to infect the nervous system. However, mechanisms of sarbecovirus neuroinvasion and neuropathogenesis remain unclear. In this study, we examined the infectivity and trans-synaptic transmission potential of the sarbecoviruses SARS and SARS-CoV-2 in human stem cell-derived neural model systems. We demonstrated limited ability of sarbecoviruses to infect and replicate in human stem cell-derived neurons. Furthermore, we demonstrated an inability of sarbecoviruses to transmit between synaptically connected human stem cell-derived neurons. Finally, we determined an absence of SARS-CoV-2 infection in olfactory neurons in experimentally infected ferrets. Collectively, this study indicates that sarbecoviruses exhibit low potential to infect human stem cell-derived neurons, lack an ability to infect ferret olfactory neurons, and lack an inbuilt molecular mechanism to utilise retrograde axonal trafficking and trans-synaptic transmission to spread within the human nervous system.

Human coronavirus OC43-elicited CD4+ T cells protect against SARS-CoV-2 in HLA transgenic mice

SARS-CoV-2-reactive T cells are detected in some healthy unexposed individuals. Human studies indicate these T cells could be elicited by the common cold coronavirus OC43. To directly test this assumption and define the role of OC43-elicited T cells that are cross-reactive with SARS-CoV-2, we develop a model of sequential infections with OC43 followed by SARS-CoV-2 in HLA-B*0702 and HLA-DRB1*0101 Ifnar1-/- transgenic mice. We find that OC43 infection can elicit polyfunctional CD8+ and CD4+ effector T cells that cross-react with SARS-CoV-2 peptides. Furthermore, pre-exposure to OC43 reduces subsequent SARS-CoV-2 infection and disease in the lung for a short-term in HLA-DRB1*0101 Ifnar1-/- transgenic mice, and a longer-term in HLA-B*0702 Ifnar1-/- transgenic mice. Depletion of CD4+ T cells in HLA-DRB1*0101 Ifnar1-/- transgenic mice with prior OC43 exposure results in increased viral burden in the lung but no change in virus-induced lung damage following infection with SARS-CoV-2 (versus CD4+ T cell-sufficient mice), demonstrating that the OC43-elicited SARS-CoV-2 cross-reactive T cell-mediated cross-protection against SARS-CoV-2 is partially dependent on CD4+ T cells. These findings contribute to our understanding of the origin of pre-existing SARS-CoV-2-reactive T cells and their effects on SARS-CoV-2 clinical outcomes, and also carry implications for development of broadly protective betacoronavirus vaccines.

Development and validation of cost-effective SYBR Green-based RT-qPCR and its evaluation in a sample pooling strategy for detecting SARS-CoV-2 infection in the Indonesian setting

A low-cost SYBR Green-based RT-qPCR method to detect SARS-CoV-2 were developed and validated. Primers targeting a conserved and vital region of the N genes of SARS-CoV-2 were designed. In-silico study was performed to analyse the compatibility of the selected primer pair with Indonesian SARS-CoV-2 genome sequences available from the GISAID database. We determined the linearity of our new assay using serial dilution of SARS-CoV-2 RNA from clinical samples with known virus concentration. The assay was then evaluated using clinically relevant samples in comparison to a commercial TaqMan-based test kit. Finally, we applied the assay in sample pooling strategies for SARS-CoV-2 detection. The SYBR Green-based RT-qPCR method was successfully developed with sufficient sensitivity. There is a very low prevalence of genome variation in the selected N primer binding regions, indicating their high conservation. The validation of the assay using clinical samples demonstrated similar performance to the TaqMan method suggesting the SYBR methods is reliable. The pooling strategy by combining 5 RNA samples for SARS-CoV-2 detection using the SYBR RT-qPCR methods is feasible and provides a high diagnostic yield. However, when dealing with samples having a very low viral load, it may increase the risk of missing positive cases.

SARS-CoV-2 produces a microRNA CoV2-miR-O8 in patients with COVID-19 infection

Many viruses produce microRNAs (miRNAs), termed viral miRNAs (v-miRNAs), with the capacity to target host gene expression. Bioinformatic and cell culture studies suggest that SARS-CoV-2 can also generate v-miRNAs. This patient-based study defines the SARS-CoV-2 encoded small RNAs present in nasopharyngeal swabs of patients with COVID-19 infection using small RNA-seq. A specific conserved sequence (CoV2-miR-O8) is defined that is not expressed in other coronaviruses but is preserved in all SARS-CoV-2 variants. CoV2-miR-O8 is highly represented in nasopharyngeal samples from patients with COVID-19 infection, is detected by RT-PCR assays in patients, has features consistent with Dicer and Drosha generation as well as interaction with Argonaute and targets specific human microRNAs.

"KAIZEN" method realizing implementation of deep-learning models for COVID-19 CT diagnosis in real world hospitals

Numerous COVID-19 diagnostic imaging Artificial Intelligence (AI) studies exist. However, none of their models were of potential clinical use, primarily owing to methodological defects and the lack of implementation considerations for inference. In this study, all development processes of the deep-learning models are performed based on strict criteria of the "KAIZEN checklist", which is proposed based on previous AI development guidelines to overcome the deficiencies mentioned above. We develop and evaluate two binary-classification deep-learning models to triage COVID-19: a slice model examining a Computed Tomography (CT) slice to find COVID-19 lesions; a series model examining a series of CT images to find an infected patient. We collected 2,400,200 CT slices from twelve emergency centers in Japan. Area Under Curve (AUC) and accuracy were calculated for classification performance. The inference time of the system that includes these two models were measured. For validation data, the slice and series models recognized COVID-19 with AUCs and accuracies of 0.989 and 0.982, 95.9% and 93.0% respectively. For test data, the models' AUCs and accuracies were 0.958 and 0.953, 90.0% and 91.4% respectively. The average inference time per case was 2.83 s. Our deep-learning system realizes accuracy and inference speed high enough for practical use. The systems have already been implemented in four hospitals and eight are under progression. We released an application software and implementation code for free in a highly usable state to allow its use in Japan and globally.

Parental Willingness and Factors Influencing COVID-19 Vaccination for Children in Saudi Arabia

Purpose

The study aimed to examine the parents' willingness and its association with demographic factors, attitudes, and practices to vaccinate their child against COVID-19.

Patients and Methods

The study involved 2500 participants from various regions of Saudi Arabia and was conducted between July 1, 2021, and August 31, 2021. Information was gathered via an online questionnaire comprising 26 questions, distributed across social media platforms. Informed consent was obtained from all participants before the commencement of the study. A chi-square test was applied to analyze the association among variables, utilizing a subset of 2127 participants based on study inclusion criteria. A chi-square test was applied to observe the association.

Results

The willingness of parents to vaccinae their children against COVID-19 was found 61%. The main reason for taking was "Protect the child" by 1094 (51.4%%) and the main reason for refusing was "Side effects/safety concerns" by 477 (22.4%). 1846 (86.8%) participants, received the COVID-19 vaccine or were planning to receive it.

Conclusion

Our study concluded that parent's willingness to vaccinate their children against COVID-19 was relatively high in our sample as about two-thirds of them accept the vaccine for their child once it is available. The use of the health belief model demonstrated the urgent requirement for awareness and education campaigns in the private and public sectors to increase awareness of parents not only related to COVID-19 but also to cater to any unexpected or suspected pandemic of infectious disease in the future full capacity.

Augmentation of Omicron BA.1 pathogenicity in hamsters using intratracheal inoculation

The Omicron BA.1 variant of SARS-CoV-2 displays an attenuated phenotype in the Syrian hamster after intranasal inoculation. This is characterized by reduced viral replication and lung pathology in the lower respiratory tract. Here, we report that intratracheal inoculation with Omicron BA.1 recovers the lower respiratory tract replication and pathogenicity as observed with other lineages.

High quality of SARS-CoV-2 molecular diagnostics in a diverse laboratory landscape through supported benchmark testing and External Quality Assessment

A two-step strategy combining assisted benchmark testing (entry controls) and External Quality Assessments (EQAs) with blinded simulated clinical specimens to enhance and maintain the quality of nucleic acid amplification testing was developed. This strategy was successfully applied to 71 diagnostic laboratories in The Netherlands when upscaling the national diagnostic capacity during the SARS-CoV-2 pandemic. The availability of benchmark testing in combination with advice for improvement substantially enhanced the quality of the laboratory testing procedures for SARS-CoV-2 detection. The three subsequent EQA rounds demonstrated high quality testing with regard to specificity (99.6% correctly identified) and sensitivity (93.3% correctly identified). Even with the implementation of novel assays, changing workflows using diverse equipment and a high degree of assay heterogeneity, the overall high quality was maintained using this two-step strategy. We show that in contrast to the limited value of Cq value for absolute proxies of viral load, these Cq values can, in combination with metadata on strategies and techniques, provide valuable information for laboratories to improve their procedures. In conclusion, our two-step strategy (preparation phase followed by a series of EQAs) is a rapid and flexible system capable of scaling, improving, and maintaining high quality diagnostics even in a rapidly evolving (e.g. pandemic) situation.

Rapid classification of SARS-CoV-2 variant strains using machine learning-based label-free SERS strategy

The spread of COVID-19 over the past three years is largely due to the continuous mutation of the virus, which has significantly impeded global efforts to prevent and control this epidemic. Specifically, mutations in the amino acid sequence of the surface spike (S) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have directly impacted its biological functions, leading to enhanced transmission and triggering an immune escape effect. Therefore, prompt identification of these mutations is crucial for formulating targeted treatment plans and implementing precise prevention and control measures. In this study, the label-free surface-enhanced Raman scattering (SERS) technology combined with machine learning (ML) algorithms provide a potential solution for accurate identification of SARS-CoV-2 variants. We establish a SERS spectral database of SARS-CoV-2 variants and demonstrate that a diagnostic classifier using a logistic regression (LR) algorithm can provide accurate results within 10 min. Our classifier achieves 100% accuracy for Beta (B.1.351/501Y.V2), Delta (B.1.617), Wuhan (COVID-19) and Omicron (BA.1) variants. In addition, our method achieves 100% accuracy in blind tests of positive and negative human nasal swabs based on the LR model. This method enables detection and classification of variants in complex biological samples. Therefore, ML-based SERS technology is expected to accurately discriminate various SARS-CoV-2 variants and may be used for rapid diagnosis and therapeutic decision-making.

Proteolytic cleavage and inactivation of the TRMT1 tRNA modification enzyme by SARS-CoV-2 main protease

Nonstructural protein 5 (Nsp5) is the main protease of SARS-CoV-2 that cleaves viral polyproteins into individual polypeptides necessary for viral replication. Here, we show that Nsp5 binds and cleaves human tRNA methyltransferase 1 (TRMT1), a host enzyme required for a prevalent post-transcriptional modification in tRNAs. Human cells infected with SARS-CoV-2 exhibit a decrease in TRMT1 protein levels and TRMT1-catalyzed tRNA modifications, consistent with TRMT1 cleavage and inactivation by Nsp5. Nsp5 cleaves TRMT1 at a specific position that matches the consensus sequence of SARS-CoV-2 polyprotein cleavage sites, and a single mutation within the sequence inhibits Nsp5-dependent proteolysis of TRMT1. The TRMT1 cleavage fragments exhibit altered RNA binding activity and are unable to rescue tRNA modification in TRMT1-deficient human cells. Compared to wildtype human cells, TRMT1-deficient human cells infected with SARS-CoV-2 exhibit reduced levels of intracellular viral RNA. These findings provide evidence that Nsp5-dependent cleavage of TRMT1 and perturbation of tRNA modification patterns contribute to the cellular pathogenesis of SARS-CoV-2 infection.

A high-performance polymer composite column for coronavirus nucleic acid purification

Here, we report the development of a novel polymer composite (PC) purification column and kit. The performance of the PC columns was compared to conventional silica gel (SG) columns for the purification of nucleic acids from coronaviruses, including SARS-CoV-2, in 82 clinical samples. The results shows that PC-based purification outperforms silica gel (SG)-based purification by enabling a higher sensitivity (94%), accuracy (97%), and by eliminating false positives (100% specificity). The high specificity is critical for efficient patient triage and resource management during pandemics. Furthermore, PC-based purification exhibits three times higher analytical precision than a commonly used SG-based nucleic acid purification thereby enabling a more accurate quantification of viral loads and higher reproducibility.

Evidence of the simultaneous replications of active viruses in specimens positive for multiple respiratory viruses

IMPORTANCE

Since the pandemic of coronavirus diseases 2019, the use of real-time PCR assay has become widespread among people who were not familiar with it in virus detection. As a result, whether a high real-time PCR value in one time test indicates virus transmissibly became a complicated social problem, regardless of the difference in assays and/or amplification conditions, the time and number of diagnostic test during the time course of infection. In addition, the multiple positives in the test of respiratory viruses further add to the confusion in the interpretation of the infection. To address this issue, we performed virus isolation using pediatric SARI (severe acute respiratory infections) specimens on air-liquid interface culture of human bronchial/tracheal epithelial cell culture. The result of this study can be a strong evidence that the specimens showing positivity for multiple agents in real-time PCR tests possibly contain infectious viruses.

Halogenated Rocaglate Derivatives: Pan-antiviral Agents against Hepatitis E Virus and Emerging Viruses

The synthesis of a library of halogenated rocaglate derivatives belonging to the flavagline class of natural products, of which silvestrol is the most prominent example, is reported. Their antiviral activity and cytotoxicity profile against a wide range of pathogenic viruses, including hepatitis E, Chikungunya, Rift Valley Fever virus and SARS-CoV-2, were determined. The incorporation of halogen substituents at positions 4', 6 and 8 was shown to have a significant effect on the antiviral activity of rocaglates, some of which even showed enhanced activity compared to CR-31-B and silvestrol.

Spatiotemporal analysis of SARS-CoV-2 infection reveals an expansive wave of monocyte-derived macrophages associated with vascular damage and virus clearance in hamster lungs

IMPORTANCE

We present the first study of the 3D kinetics of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and the early host response in a large lung volume using a combination of tissue imaging and transcriptomics. This approach allowed us to make a number of important findings: Spatially restricted antiviral response is shown, including the formation of monocytic macrophage clusters and upregulation of the major histocompatibility complex II in infected epithelial cells. The monocyte-derived macrophages are linked to SARS-CoV-2 clearance, and the appearance of these cells is associated with post-infection endothelial damage; thus, we shed light on the role of these cells in infected tissue. An early onset of tissue repair occurring simultaneously with inflammatory and necrotizing processes provides the basis for longer-term alterations in the lungs.

Evaluation of colorimetric RT-LAMP for screening of SARS-CoV-2 in untreated wastewater

This study compared reverse transcription-loop-mediated isothermal amplification (RT-LAMP) and three reverse transcription-quantitative polymerase chain reaction (RT-qPCR) assays targeting the N and E genes of the SARS-CoV-2 genome for detecting RNA in untreated wastewater samples. RT-qPCR assays exhibited consistent amplification down to 2 × 102 GC/reaction, with greater analytical sensitivity at 2 × 101 GC/reaction by US CDC N1 and US CDC N2 assays. In contrast, RT-LAMP exhibited lower sensitivity, detecting SARS-CoV-2 only at or above 2 × 103 GC/reaction. For SARS-CoV-2 seeded wastewater samples, the US CDC N1 assay exhibited greater analytical sensitivity than the US CDC N2, E_Sarbeco, and RT-LAMP assays. Out of 30 wastewater samples, RT-qPCR detected endogenous SARS-CoV-2 RNA in 29 samples, while RT-LAMP identified 27 positive samples, with 20 displaying consistent amplifications in all three RT-LAMP technical replicates. Agreement analysis revealed a strong concordance between RT-LAMP and the US CDC N1 and E_Sarbeco RT-qPCR assays (κ = 0.474) but lower agreement with the US CDC N2 RT-qPCR assay (κ = 0.359). Quantification of SARS-CoV-2 RNA in positive samples revealed a strong correlation between the US CDC N1 and E_Sarbeco assays, while the US CDC N1 and US CDC N2 assays exhibited weak correlation. Logistic regression analysis indicated that RT-LAMP results correlated with RNA quantified by the US CDC N1 and E_Sarbeco assays, with 95 % limits of detection of 3.99 and 3.47 log10 GC/15 mL, respectively. In conclusion, despite lower sensitivity compared to RT-qPCR assays, RT-LAMP may offer advantages for wastewater surveillance, such as rapid results (estimated as twice as fast), and simplicity, making it a valuable tool in the shifting landscape of COVID-19 wastewater surveillance. Furthermore, LAMP positive wastewater samples might be prioritized for SARS-CoV-2 sequencing due to reduced analytical sensitivity. These findings support the use of RT-LAMP as a specific and efficient method for screening wastewater samples for SARS-CoV-2, particularly in resource-limited settings.

Estimates of early outbreak-specific SARS-CoV-2 epidemiological parameters from genomic data

We estimate the basic reproductive number and case counts for 15 distinct Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreaks, distributed across 11 populations (10 countries and one cruise ship), based solely on phylodynamic analyses of genomic data. Our results indicate that, prior to significant public health interventions, the reproductive numbers for 10 (out of 15) of these outbreaks are similar, with median posterior estimates ranging between 1.4 and 2.8. These estimates provide a view which is complementary to that provided by those based on traditional line listing data. The genomic-based view is arguably less susceptible to biases resulting from differences in testing protocols, testing intensity, and import of cases into the community of interest. In the analyses reported here, the genomic data primarily provide information regarding which samples belong to a particular outbreak. We observe that once these outbreaks are identified, the sampling dates carry the majority of the information regarding the reproductive number. Finally, we provide genome-based estimates of the cumulative number of infections for each outbreak. For 7 out of 11 of the populations studied, the number of confirmed cases is much bigger than the cumulative number of infections estimated from the sequence data, a possible explanation being the presence of unsequenced outbreaks in these populations.

Airborne transmission efficiency of SARS-CoV-2 in Syrian hamsters is not influenced by environmental conditions

Several human respiratory viruses display a clear seasonal pattern with a higher incidence in the winter season in temperate regions. We previously determined that SARS-CoV-2 is more stable at low-temperature and low-humidity conditions compared to warmer temperature and higher-humidity. To determine if this translates into differential airborne transmission rates in vivo, we performed airborne transmission experiments in the Syrian hamster model under three different environmental conditions (10 °C, 45% relative humidity (RH), 22 °C, 45% RH, and 27 °C, 65% RH). We compared the ancestral SARS-CoV-2 Lineage A with the more transmissible Delta Variant of Concern (VOC). Airborne transmission was evaluated using SARS-CoV-2 infected donor animals at 24 h post inoculation. Sentinels were placed at a 90 cm distance in a transmission set-up and exposed for 1-h to infected donor animals. While environmental conditions moderately impacted lung RNA titers, the shedding kinetics of the donors were not affected by the environmental conditions and did not differ significantly between variants on day 1. Overall, the highest transmission efficiency was observed at 22 °C, 40%RH for Delta (62.5%, based on seroconversion), and ranged between 37.5 and 50% for all other conditions. However, these differences were not significant. To elucidate this further, we performed aerosol stability comparisons and found that infectious virus remained stable during a 1-h time window across all conditions. Our data suggest that even when environmental conditions affect the stability of SARS-CoV-2, this may not directly be translatable to measurable impacts on transmission in an experimental setting when exposure time is restricted.

Multiple redox switches of the SARS-CoV-2 main protease in vitro provide opportunities for drug design

Besides vaccines, the development of antiviral drugs targeting SARS-CoV-2 is critical for preventing future COVID outbreaks. The SARS-CoV-2 main protease (Mpro), a cysteine protease with essential functions in viral replication, has been validated as an effective drug target. Here, we show that Mpro is subject to redox regulation in vitro and reversibly switches between the enzymatically active dimer and the functionally dormant monomer through redox modifications of cysteine residues. These include a disulfide-dithiol switch between the catalytic cysteine C145 and cysteine C117, and generation of an allosteric cysteine-lysine-cysteine SONOS bridge that is required for structural stability under oxidative stress conditions, such as those exerted by the innate immune system. We identify homo- and heterobifunctional reagents that mimic the redox switching and inhibit Mpro activity. The discovered redox switches are conserved in main proteases from other coronaviruses, e.g. MERS-CoV and SARS-CoV, indicating their potential as common druggable sites.

Validation of Diagnostic Accuracy and Disease Severity Correlation of Chest Computed Tomography Severity Scores in Patients with COVID-19 Pneumonia

The aim of our study was to establish and compare the diagnostic accuracy and clinical applicability of published chest CT severity scoring systems used for COVID-19 pneumonia assessment and to propose the most efficient CT scoring system with the highest diagnostic performance and the most accurate prediction of disease severity. This retrospective study included 218 patients with PCR-confirmed SARS-CoV-2 infection and chest CT. Two radiologists blindly evaluated CT scans and calculated nine different CT severity scores (CT SSs). The diagnostic validity of CT SSs was tested by ROC analysis. Interobserver agreement was excellent (intraclass correlation coefficient: 0.982-0.995). The predominance of either consolidations or a combination of consolidations and ground-glass opacities (GGOs) was a predictor of more severe disease (both p < 0.005), while GGO prevalence alone was not. Correlation between all CT SSs was high, ranging from 0.848 to 0.971. CT SS 30 had the highest diagnostic accuracy (AUC = 0.805) in discriminating mild from severe COVID-19 disease compared to all the other proposed scoring systems (AUC range 0.755-0.788). In conclusion, CT SS 30 achieved the highest diagnostic accuracy in predicting the severity of COVID-19 disease while maintaining simplicity, reproducibility, and applicability in complex clinical settings.

Performance Analysis of Serodiagnostic Tests to Characterize the Incline and Decline of the Individual Humoral Immune Response in COVID-19 Patients: Impact on Diagnostic Management

Serodiagnostic tests for antibody detection to estimate the immunoprotective status regarding SARS-CoV-2 support diagnostic management. This study aimed to investigate the performance of serological assays for COVID-19 and elaborate on test-specific characteristics. Sequential samples (n = 636) of four panels (acute COVID-19, convalescent COVID-19 (partly vaccinated post-infection), pre-pandemic, and cross-reactive) were tested for IgG by indirect immunofluorescence test (IIFT) and EUROIMMUN EUROLINE Anti-SARS-CoV-2 Profile (IgG). Neutralizing antibodies were determined by a virus neutralization test (VNT) and two surrogate neutralization tests (sVNT, GenScript cPass, and EUROIMMUN SARS-CoV-2 NeutraLISA). Analysis of the acute and convalescent panels revealed high positive (78.3% and 91.6%) and negative (91.6%) agreement between IIFT and Profile IgG. The sVNTs revealed differences in their positive (cPass: 89.4% and 97.0%, NeutraLISA: 71.5% and 72.1%) and negative agreement with VNT (cPass: 92.3% and 50.0%, NeutraLISA: 95.1% and 92.5%) at a diagnostic specificity of 100% for all tests. The cPass showed higher inhibition rates than NeutraLISA at VNT titers below 1:640. Cross-reactivities were only found by cPass (57.1%). Serodiagnostic tests, which showed substantial agreement and fast runtime, could provide alternatives for cell-based assays. The findings of this study suggest that careful interpretation of serodiagnostic results obtained at different times after SARS-CoV-2 antigen exposure is crucial to support decision-making in diagnostic management.

COVID-19 pneumonia assessed at a private hospital, a field hospital, and a public-referral hospital: population analysis, chest computed tomography findings, and outcomes

Objective

To compare a private quaternary referral hospital, a public tertiary hospital, and a field hospital dedicated to patients with COVID-19, regarding patients' characteristics, clinical parameters, laboratory, imaging findings, and outcomes of patients with confirmed diagnosis of COVID-19.

Methods

Retrospective multicenter observational study that assessed the association of clinical, laboratory and CT data of 453 patients with COVID-19, and also their outcomes (hospital discharge or admission, intensive care unit admission, need for mechanical ventilation, and mortality caused by COVID-19).

Results

The mean age of patients was 55 years (±16 years), 58.1% of them were male, and 41.9% were female. Considering stratification by the hospital of care, significant differences were observed in the dyspnea, fever, cough, hypertension, diabetes mellitus parameters, and CT score (p < 0.05). Significant differences were observed in ward admission rates, with a lower rate in the private hospital (40.0%), followed by the public hospital (74.1%), and a higher rate in the field hospital (89.4%). Regarding intensive care unit admission, there was a higher rate in the public hospital (25.2%), followed by the private hospital (15.5%), and a lower rate in the field hospital (9.9%). In the analysis of the discharge and death outcomes, it was found that there was a higher number of patients discharged from the private hospital (94.2%), compared to the field hospital (90.1%) and public hospital (82.3%) and a higher number of deaths in the public hospital (17.7%) compared to the private hospital and field hospital (5.8 and 0% respectively).

Conclusion

The analysis of the data regarding the population treated with COVID-19 during the first wave in different levels of care in the public and private health systems in the city of São Paulo revealed statistically significant differences between the populations, reflecting distinct outcomes.

Exploring the relationship of cognitive function with and without COVID-19 recovered schizophrenic patients

Background

The Coronavirus disease 2019 (COVID-19) is linked to the deterioration of cognitive function among individuals suffering from schizophrenia. The purpose of this study was to compare the cognitive performance of schizophrenic patients before and after COVID-19.

Methods

A longitudinal cohort study involving a sample of 219 individuals diagnosed with schizophrenia was enrolled between June 2022 and May 2023. The participants were split into two groups infected with COVID-19 (n = 165) and not infected with COVID-19 (n = 54). The data were gathered via a questionnaire on demographic characteristics, the Brief Assessment of Cognition in Schizophrenia (BACS), the Positive and Negative Syndrome Scale (PANSS), the Calgary Depression Scale for Schizophrenia (CDSS), the Activities of Daily Living (ADL) scale, and the Insomnia Severity Index (ISI).

Results

The repeated-measures ANOVA showed that Among patients diagnosed with COVID-19, there was a deterioration in global cognitive function (before COVID-19 = -2.45 vs. after COVID-19 = -3.02, p = 0.007), working memory (before COVID-19 = -2.76 vs. after COVID-19 = -3.34, p < 0.00 1), motor speed (before COVID-19 = -1.64 vs. after COVID-19 = -2.12, p < 0.001), attention and speed of information processing (before COVID-19 = -1.93 vs. after COVID-19 = -1.16, p = 0.008). multi-variable analysis showed that several factors as having a secondary grade of education (β = 0.434), experiencing insomnia (β = 0.411)and the interaction between COVID-19 diagnosis and cognition at baseline (β = 0.796) were significantly associated with cognitive deficits. At the same time, no significant associations were found between global cognition and clinical symptoms, autonomy, or depression (p > 0.05).

Conclusion

The COVID-19 pandemic has significantly impacted various cognitive functions, such as verbal memory, working memory, and global cognition. Insomnia has been identified as the predominant determinant of cognitive impairment, alongside the confirmation of a COVID-19 diagnosis. Additional research is imperative to elucidate the diversification of cognitive functionality observed in individuals diagnosed with schizophrenia who have acquired COVID-19.

Distinct phenotype of SARS-CoV-2 Omicron BA.1 in human primary cells but no increased host range in cell lines of putative mammalian reservoir species

SARS-CoV-2's genetic plasticity has led to several variants of concern (VOCs). Here we studied replicative capacity for seven SARS-CoV-2 isolates (B.1, Alpha, Beta, Gamma, Delta, Zeta, and Omicron BA.1) in primary reconstituted airway epithelia (HAE) and lung-derived cell lines. Furthermore, to investigate the host range of Delta and Omicron compared to ancestral SARS-CoV-2, we assessed replication in 17 cell lines from 11 non-primate mammalian species, including bats, rodents, insectivores and carnivores. Only Omicron's phenotype differed in vitro, with rapid but short replication and efficient production of infectious virus in nasal HAEs, in contrast to other VOCs, but not in lung cell lines. No increased infection efficiency for other species was observed, but Delta and Omicron infection efficiency was increased in A549 cells. Notably replication in A549 and Calu3 cells was lower than in nasal HAE. Our results suggest better adaptation of VOCs towards humans, without an extended host range, and may be relevant to the search for the putative intermediate host and reservoirs prior to the pandemic.

Epidemiology and clinical features of respiratory syncytial virus (RSV) infection in hospitalized children during the COVID-19 pandemic in Gorgan, Iran

Background and Aims

Respiratory syncytial virus (RSV) is a leading cause of acute respiratory infection in infants and young children. Given the altered circulation patterns of respiratory viruses during the coronavirus disease pandemic-2019 (COVID-19), the study aimed to evaluate epidemiology and clinical features of RSV infections in hospitalized children during the COVID-19 pandemic in Gorgan, northeastern Iran. Molecular epidemiology studies on respiratory viral infections are necessary to monitor circulating viruses, disease severity, and clinical symptoms, in addition to early warning of new outbreaks.

Methods

Overall, 411 respiratory swab samples from hospitalized children from October 2021 to March 2022 were collected at Taleghani Children's Hospital, Gorgan, Iran. The incidence of RSV, as well as the circulating subgroups and genotypes, were investigated and confirmed using PCR methods. Additionally, all samples tested for severe acute respiratory syndrome-associated coronavirus 2 (SARS-CoV-2) and influenza, and demographic and clinical data were analyzed using SPSS software.

Results

The share of RSV, SARS-CoV-2, and influenza among hospitalized children with acute lower respiratory infections (ALRI) were 27%, 16.5%, and 4.1%, respectively. The RSV subgroup A (genotype ON1) was dominant over subgroup B (genotype BA9), with more severe clinical symptoms. Compared with the prepandemic era there were high numbers of hospitalized SARS-CoV-2 positive children and low numbers of other respiratory viruses. Despite this, the prevalence of ALRI-related RSV-disease among hospitalized children in our specialized pediatric center was higher than COVID-19 disease in the same cohort.

Conclusions

Studying the epidemiology of respiratory viruses and determining the circulating strains can contribute to effective infection control and treatment strategies.

One-step and Rapid Identification of SARS-CoV-2 using Real-Time Reverse Transcription Loop-Mediated Isothermal Amplification (RT-LAMP)

Background

SARS-CoV-2 as the cause of novel coronavirus disease (COVID-19) is a member of the family Coronaviridea that has generated an emerging global health concern. Controlling and preventing the spread of the disease requires a simple, portable, and rapid diagnostic method. Today, a standard method for detecting SARS-CoV-2 is quantitative real-time reverse transcription PCR, which is time-consuming and needs an advanced device. The aim of this study was to evaluate a faster and more cost-effective field-based testing method at the point of risk. We utilized a one-step RT-LAMP assay and developed, for the first time, a simple and rapid screening detection assay targeting the Envelope (E) gene, using specific primers.

Methods

For this, the total RNA was extracted from respiratory samples of COVID-19 infected patients and applied to one-step a RT-LAMP reaction. The LAMP products were visualized using green fluorescence (SYBR Green I). Sensitivity testing was conducted using different concentrations of the designed recombinant plasmid (TA-E) as positive control constructs. Additionally, selectivity testing was performed using the influenza H1N1 genome. Finally, the results were compared using with conventional real time RT-PCR.

Results

It was shown that the RT-LAMP assay has a sensitivity of approximately 15 ng for the E gene of SARS-CoV-2 when using extracted total RNA. Additionally, a sensitivity of 112 pg was achieved when using an artificially prepared TA-E plasmid. Accordingly, for the detection of SARS-CoV-2 infection, the RT-LAMP had high sensitivity and specificity and also could be an alternative method for real-time RT-PCR.

Conclusion

Overall, this method can be used as a portable, rapid, and easy method for detecting SARS-CoV-2 in the field and clinical laboratories.

Proteomics-based mass spectrometry profiling of SARS-CoV-2 infection from human nasopharyngeal samples

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of the on-going global pandemic of coronavirus disease 2019 (COVID-19) that continues to pose a significant threat to public health worldwide. SARS-CoV-2 encodes four structural proteins namely membrane, nucleocapsid, spike, and envelope proteins that play essential roles in viral entry, fusion, and attachment to the host cell. Extensively glycosylated spike protein efficiently binds to the host angiotensin-converting enzyme 2 initiating viral entry and pathogenesis. Reverse transcriptase polymerase chain reaction on nasopharyngeal swab is the preferred method of sample collection and viral detection because it is a rapid, specific, and high-throughput technique. Alternate strategies such as proteomics and glycoproteomics-based mass spectrometry enable a more detailed and holistic view of the viral proteins and host-pathogen interactions and help in detection of potential disease markers. In this review, we highlight the use of mass spectrometry methods to profile the SARS-CoV-2 proteome from clinical nasopharyngeal swab samples. We also highlight the necessity for a comprehensive glycoproteomics mapping of SARS-CoV-2 from biological complex matrices to identify potential COVID-19 markers.

AttentionCovidNet: Efficient ECG-based diagnosis of COVID-19

The novel coronavirus caused a worldwide pandemic. Rapid detection of COVID-19 can help reduce the spread of the novel coronavirus as well as the burden on healthcare systems worldwide. The current method of detecting COVID-19 suffers from low sensitivity, with estimates of 50%-70% in clinical settings. Therefore, in this study, we propose AttentionCovidNet, an efficient model for the detection of COVID-19 based on a channel attention convolutional neural network for electrocardiograms. The electrocardiogram is a non-invasive test, and so can be more easily obtained from a patient. We show that the proposed model achieves state-of-the-art results compared to recent models in the field, achieving metrics of 0.993, 0.997, 0.993, and 0.995 for accuracy, precision, recall, and F1 score, respectively. These results indicate both the promise of the proposed model as an alternative test for COVID-19, as well as the potential of ECG data as a diagnostic tool for COVID-19.

Innovation and Patenting Activities During COVID-19 and Advancement of Biochemical and Molecular Diagnosis in the Post- COVID-19 Era

The COVID-19 pandemic is to escalate globally and acquire new mutations quickly, so accurate diagnostic technologies play a vital role in controlling and understanding the epidemiology of the disease. A plethora of technologies acquires diagnosis of individuals and informs clinical management of COVID. Some important biochemical parameters for COVID diagnosis are the elevation of liver enzymes, creatinine, and nonspecific inflammatory markers such as C-reactive protein (CRP) and Interleukin 6 (IL-6). The main progression predictors are lymphopenia, elevated D-dimer, and hyperferritinemia, although it is also necessary to consider LDH, CPK, and troponin in the marker panel of diagnosis. Owing to the greater sensitivity and accuracy, molecular technologies such as conventional polymerase chain reaction (PCR), reverse transcription (RT)-PCR, nested PCR, loop-mediated isothermal amplification (LAMP), and xMAP technology have been extensively used for COVID diagnosis for some time now. To make so many diagnostics accessible to general people, many techniques may be exploited, including point of care (POC), also called bedside testing, which is developing as a portable promising tool in pathogen identification. Some other lateral flow assay (LFA)-centered techniques like SHERLOCK, CRISPR-Cas12a (AIOD-CRISPR), and FNCAS9 editor limited uniform detection assay (FELUDA), etc. have shown auspicious results in the rapid detection of pathogens. More recently, low-cost sequencing and advancements in big data management have resulted in a slow but steady rise of next-generation sequencing (NGS)-based approaches for diagnosis that have potential relevance for clinical purposes and may pave the way toward a better future. Due to the COVID-19 pandemic, various institutions provided free, specialized websites and tools to promote research and access to critically needed advanced solutions by alleviating research and analysis of data within a substantial body of scientific and patent literature regarding biochemical and molecular diagnosis published since January 2020. This circumstance is unquestionably unique and difficult for anyone using patent information to find pertinent disclosures at a specific date in a trustworthy manner.

Evaluation of the fully automated, sample-to-result Seegene STARlet-AIOS platform for detection of SARS-CoV-2, influenza virus A, influenza virus B, and RSV

Early, accurate, and bulk detection of respiratory pathogens is essential for patient management and infection control. STARlet-All-in-One System (AIOS) (Seegene) is a new, fully automated, sample-to-result, molecular diagnostic platform. This study describes the first evaluation of STARlet-AIOS, by testing the Allplex™ SARS-CoV-2 (AS) and Allplex™ SARS-CoV-2/FluA/FluB/RSV combination (AC) assays in comparison to the SARS-CoV-2 assays used at our institute. Over a 3-week period, all naso-/oropharyngeal specimens tested for SARS-CoV-2 using either GeneXpert, Panther, or in-house developed test (LDT) were tested on the AIOS using the AS or AC assays. In addition, retrospective cohorts of specimens containing SARS-CoV-2, influenza virus A, influenza virus B, and RSV were tested. Discrepant results were re-tested with another assay used in this study. Hands-on time (HOT) and turn-around time (TAT) of the different systems were monitored and compared. A total of 738 specimens were tested on the AIOS using the AS assay. In addition, 210 specimens were tested using the AC assay. Overall agreement for SARS-CoV-2 detection was established as 98.5% and 95.2% for the AS and AC assay, respectively. Retrospective testing revealed high agreements for all targets, except for influenza virus A (agreement of 87.5%). HOT of the system was comparable to the HOT of GeneXpert and Panther and TAT comparable to Panther and LDT. The AIOS proved to be a robust sample-to-result system with low HOT and moderate TAT. This study showed reliable detection of SARS-CoV-2, influenza virus B, and RSV, whereas detection of influenza virus A using the AC assay appeared to be suboptimal.

Comparison of gene targets and sampling regimes for SARS-CoV-2 quantification for wastewater epidemiology in UK prisons

Prisons are high-risk settings for infectious disease transmission, due to their enclosed and semi-enclosed environments. The proximity between prisoners and staff, and the diversity of prisons reduces the effectiveness of non-pharmaceutical interventions, such as social distancing. Therefore, alternative health monitoring methods, such as wastewater-based epidemiology (WBE), are needed to track pathogens, including SARS-CoV-2. This pilot study assessed WBE to quantify SARS-CoV-2 prevalence in prison wastewater to determine its utility within a health protection system for residents. The study analysed 266 samples from six prisons in England over a 12-week period for nucleoprotein 1 (N1 gene) and envelope protein (E gene) using quantitative reverse transcriptase-polymerase chain reaction. Both gene assays successfully detected SARS-CoV-2 fragments in wastewater samples, with both genes significantly correlating with COVID-19 case numbers across the prisons (p < 0.01). However, in 25% of the SARS-positive samples, only one gene target was detected, suggesting that both genes be used to reduce false-negative results. No significant differences were observed between 14- and 2-h composite samples, although 2-h samples showed greater signal variance. Population normalisation did not improve correlations between the N1 and E genes and COVID-19 case data. Overall, WBE shows considerable promise for health protection in prison settings.

Environmental monitoring of SARS-CoV-2 in the metropolitan area of Porto Alegre, Rio Grande do Sul (RS), Brazil

Since starts the coronavirus disease 2019 (COVID-19) pandemic identified the presence of genomic fragments of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in various environmental matrices: domestic sewage, surface waters, and contaminated freshwater. Environmental monitoring of SARS-CoV-2 is a tool for evaluating trend curves over the months, compared to several clinical cases of the disease. The objective of this study was to monitor the SARS-CoV-2 in environmental samples collected in different sites in a metropolitan area of Porto Alegre, Southern Brazil. During 10 months from 2020 to 2021, 300 samples were collected weekly and biweekly from nine points located in 3 cities: one point from a wastewater treatment plant (WWTP) in São Leopoldo (fortnightly collection), two points in Dilúvio Stream in Porto Alegre (fortnightly collection), two points in Pampa and Luiz Rau Streams (weekly collection), and two points in public fountains (fortnightly collection) in Novo Hamburgo. After collection, samples were concentrated by ultracentrifugation, and viral nucleic acids were extracted using MagMax® Core Nucleic Acid Purifications kits and submitted to RT-qPCR, using E, N1, and N2 gene targets of SARS-CoV-2. Only 7% (3/41) samples from public fountains were positive, with a mean viral load (VL) of SARS-CoV-2 RNA of 5.02 × 101 gc/l (2.41~8.59 × 101 gc/l), while the streams had average VL of 7.43 × 105 gc/l (Pampa), 7.06 × 105 gc/l (Luiz Rau), 2.01 × 105 gc/l (Dilúvio), and 4.46 × 105 cg/l (WWTP). The results showed varying levels of viral presence in different sample types, with a demonstrated correlation between environmental viral load and clinical COVID-19 cases. These findings contribute to understanding virus persistence and transmission pathways in the environment. Continuous monitoring, especially in less developed regions, is crucial for early detection of vaccine resistance, new variants, and potential COVID-19 resurgence.

Predictors of Functional Impairment in Severe COVID-19 Patients Two Months After Discharge

Background

The Post-COVID-19 Functional Status (PCFS) scale is a validated tool used to measure the functional status of patients discharged from the hospital.

Objectives

To describe the functional limitations of hospitalized COVID-19 patients at the time of discharge and two months afterward, and to identify risk factors associated with functional impairment.

Design

Retrospective study.

Methods

A total of 540 patients were included in this monocentric study. The functional status assessment using the PCFS scale and ventilatory needs were recorded at discharge and two months later. Univariate and multivariate analyses were performed in order to identify the risk factors of a high PCFS score.

Results

Two months after discharge, the PCFS grade was 0 in 60,6% of the survivors, 1 in 24.5%, 2 in 6.9%, 3 in 2.8%, and 4 in 5.3%. The identified risk factors of a high PCFS scale were: age, arterial hypertension, diabetes mellitus, immunosuppression, cardiovascular disease, high need for oxygen and high News2 score at admission, a high percentage of ground glass at chest CT scan performed at admission or during follow-up, elevated leukocytes, neutrophils, LDH, D-dimers, procalcitonin, and serum creatinine levels. During the hospital stay, treatment with steroids, tocilizumab, longer duration of hospitalization, ICU admission and prolonged stay, and the occurrence of thromboembolic or hemorrhagic events were also significantly associated with a higher PCFS. Multivariate analysis identified that only age and a high News2 score at admission were independent risk factors of a low PCFS score.

Conclusion

Multiple risk factors for a higher PCFS score were identified, but only age and a high News2 score at admission were found to be independent risk factors.

Seroprevalence of Anti-SARS-CoV-2 Remained Extremely Low in Taiwan Until the Vaccination Program Was Implemented

Background

The Taiwanese government made a concerted effort to contain a coronavirus disease 2019 (COVID-19) nosocomial outbreak of variant B.1.429, shortly before universal vaccination program implementation. This study aimed to investigate seroprevalence in the highest-risk regions.

Methods

Between January and February 2021, we retrieved 10 000 repository serum samples from blood donors to examine for antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleocapsid (N) and spike (S) antigens. A positive result was confirmed if anti-N and anti-S antibodies were positive. Overall, 2000 donors residing in the highest-risk district and donating blood in January 2021 were further examined for SARS-CoV-2 RNA. We estimated seroprevalence and compared the epidemic curve between confirmed COVID-19 cases and blood donors with positive antibodies or viral RNA.

Results

Twenty-one cases with COVID-19 were confirmed in the nosocomial cluster, with an incidence of 1.27/100 000 in the COVID-affected districts. Among 4888 close contacts of the nosocomial cases, 20 (0.4%) became confirmed cases during isolation. Anti-SARS-CoV-2 was detected in 2 of the 10000 blood donors, showing a seroprevalence of 2/10000 (95% CI, 0.55-7.29). None of the 2000 donors who underwent tests for SARS-CoV-2 RNA were positive. The SARS-CoV-2 infection epidemic curve was observed sporadically in blood donors compared with the nosocomial cluster.

Conclusions

In early 2021, an extremely low anti-SARS-CoV-2 seroprevalence among blood donors was observed. Epidemic control measures through precise close contact tracing, testing, and isolation effectively contained SARS-CoV-2 transmission before universal vaccination program implementation.

Manually pressurized droplet digital PCR chip for rapid SARS-CoV-2 diagnostics

Droplet digital PCR (ddPCR) is a technique in which PCR reaction is divided into thousands of nanoliter-sized droplets and has proven to be a great tool in virus diagnostics. Compared to the gold standard system quantitative real-time PCR (RT-qPCR), ddPCR functions particularly well when dealing with samples with low template counts, such as viral concentration. This feature makes the technique suitable for early detection of the virus. In this study, a novel portable PDMS ddPCR chip is introduced. The chip functions without external pumps using manual pressurization with a multichannel pipet. The created droplets are monodispersed and form a monolayer on the chip's collection chamber, from where they can be effortlessly imaged. Droplets were analyzed and counted using artificial intelligence. The use of the manually pressurized chip was demonstrated for a SARS-CoV-2 assay, which takes advantage of isothermal strand invasion-based amplification (SIBA) technology, allowing quick and accurate, even point-of-care analysis of the sample. The results demonstrate that SIBA assays can be divided into nanoliter-sized droplets and used as quantitative assays, giving an approximation of the samples' viral count.

Management of neonates with maternal prenatal coronavirus infection and influencing factors

The coronavirus disease 2019 (COVID-19) in pregnancy causes adverse outcomes for both the mother and the fetus. Neonates are at risk of vertical transmission and in-utero infection. Additionally, intensive care unit (ICU) admission and impairment in the organ systems of the mother are associated with neonatal outcomes, including impaired intrauterine growth, prematurity, and neonatal ICU admission. The management of neonates born from infected mothers has changed over the progress of the pandemic. At the beginning of the pandemic, cesarean section, immediate separation of mother-infant dyads, isolation of neonates, and avoiding of skin-to-skin contact, breast milk, and breastfeeding were the main practices to reduce vertical and horizontal transmission risk in the era of insufficient knowledge. The effects of antenatal steroids and delayed cord clamping on COVID-19 were also not known. As the pandemic progressed, data showed that prenatal, delivery room, and postnatal care of neonates can be performed as pre-pandemic practices. Variants and vaccines that affect clinical course and outcomes have emerged during the pandemic. The severity of the disease and the timing of infection in pregnancy also influence maternal and neonatal outcomes. The knowledge and lessons from COVID-19 will be helpful for the next pandemic if it happens. IMPACT: Prenatal infection with COVID-19 is associated with adverse maternal and neonatal outcomes. Our review includes the management of neonates with prenatal COVID-19 infection exposure, maternal-fetal, delivery room, and postnatal care of neonates, clinical features, treatment of neonates, and influencing factors such as variants, vaccination, severity of maternal disease, and timing of infection during pregnancy. There is a growing body of data and evidence about the COVID-19 pandemic. The knowledge and lessons from the pandemic will be helpful for the next pandemic if it happens.

Nanobodies to multiple spike variants and inhalation of nanobody-containing aerosols neutralize SARS-CoV-2 in cell culture and hamsters

The ongoing threat of COVID-19 has highlighted the need for effective prophylaxis and convenient therapies, especially for outpatient settings. We have previously developed highly potent single-domain (VHH) antibodies, also known as nanobodies, that target the Receptor Binding Domain (RBD) of the SARS-CoV-2 Spike protein and neutralize the Wuhan strain of the virus. In this study, we present a new generation of anti-RBD nanobodies with superior properties. The primary representative of this group, Re32D03, neutralizes Alpha to Delta as well as Omicron BA.2.75; other members neutralize, in addition, Omicron BA.1, BA.2, BA.4/5, and XBB.1. Crystal structures of RBD-nanobody complexes reveal how ACE2-binding is blocked and also explain the nanobodies' tolerance to immune escape mutations. Through the cryo-EM structure of the Ma16B06-BA.1 Spike complex, we demonstrated how a single nanobody molecule can neutralize a trimeric spike. We also describe a method for large-scale production of these nanobodies in Pichia pastoris, and for formulating them into aerosols. Exposing hamsters to these aerosols, before or even 24 h after infection with SARS-CoV-2, significantly reduced virus load, weight loss and pathogenicity. These results show the potential of aerosolized nanobodies for prophylaxis and therapy of coronavirus infections.

Natural SARS-CoV-2 infection in dogs: Determination of viral loads, distributions, localizations, and pathology

Instances of reverse zoonosis involving severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been documented in both controlled experiments and spontaneous cases. Although dogs are susceptible to infection, clinical significance is limited to mild or asymptomatic. Here, we investigate the fatal cases of natural SARS-CoV-2 infection in dogs in Thailand. Pathological findings of SARS-CoV-2-infected dogs reveal severe diffuse alveolar damage, pulmonary hyalinization and fibrosis, and syncytial formation, together with minor lesions in brain and kidney. Employing reverse transcription-digital PCR, substantial viral loads of SARS-CoV-2 were detected in lung, kidney, brain, trachea, tonsil, tracheobronchial lymph node, liver, and intestine, respectively. Localization of SARS-CoV-2 within various tissues was examined through immunohistochemistry (IHC), where the co-localization of the viral spike protein and the angiotensin-converting enzyme 2 (ACE2) receptor was illustrated using double IHC. SARS-CoV-2 localization was markedly identified in the epithelial cells of the lung, trachea, intestine and kidneys, and moderately presented in the salivary gland and gall bladder, where the co-localization with the ACE2 was also evident. Neurons in the brainstem where exhibited lymphocytic perivascular cuffing were also found to be positive for SARS-CoV-2 in IHC testing, despite lacking ACE2 receptor expression. In addition, SARS-CoV-2 replication within the lungs of infected dogs was confirmed by transmission electron microscopy, visualizing free viral particles within the cytosol or the endoplasmic reticulum of syncytial cells within the lung. This study considerably expanded on the knowledge of the pathology associated with natural SARS-CoV-2 infection in dogs, a scenario that is relatively infrequent but occasionally leads to fatal outcome. Furthermore, these findings suggest the potential utility of dogs as a model for studying SARS-CoV-2 infection in humans, warranting further investigation.

Long COVID: Molecular Mechanisms and Detection Techniques

Long COVID, also known as post-acute sequelae of SARS-CoV-2 infection (PASC), has emerged as a significant health concern following the COVID-19 pandemic. Molecular mechanisms underlying the occurrence and progression of long COVID include viral persistence, immune dysregulation, endothelial dysfunction, and neurological involvement, and highlight the need for further research to develop targeted therapies for this condition. While a clearer picture of the clinical symptomatology is shaping, many molecular mechanisms are yet to be unraveled, given their complexity and high level of interaction with other metabolic pathways. This review summarizes some of the most important symptoms and associated molecular mechanisms that occur in long COVID, as well as the most relevant molecular techniques that can be used in understanding the viral pathogen, its affinity towards the host, and the possible outcomes of host-pathogen interaction.

Evaluating the sensitivity of droplet digital PCR for the quantification of SARS-CoV-2 in wastewater

Wastewater surveillance for SARS-CoV-2 has been demonstrated to be a valuable tool in monitoring community-level virus circulation and assessing new outbreaks. It may become a useful tool in the early detection and response to future pandemics, enabling public health authorities to implement timely interventions and mitigate the spread of infectious diseases with the fecal excretion of their agents. It also offers a chance for cost-effective surveillance. Reverse transcription-quantitative polymerase chain reaction (RTqPCR) is the most commonly used method for viral RNA detection in wastewater due to its sensitivity, reliability, and widespread availability. However, recent studies have indicated that reverse transcription droplet digital PCR (RTddPCR) has the potential to offer improved sensitivity and accuracy for quantifying SARS-CoV-2 RNA in wastewater samples. In this study, we compared the performance of RTqPCR and RTddPCR approaches for SARS-CoV-2 detection and quantification on wastewater samples collected during the third epidemic wave in Saxony, Germany, characterized by low-incidence infection periods. The determined limits of detection (LOD) and quantification (LOQ) were within the same order of magnitude, and no significant differences were observed between the PCR approaches with respect to the number of positive or quantifiable samples. Our results indicate that both RTqPCR and RTddPCR are highly sensitive methods for detecting SARS-CoV-2. Consequently, the actual gain in sensitivity associated with ddPCR lags behind theoretical expectations. Hence, the choice between the two PCR methods in further environmental surveillance programs is rather a matter of available resources and throughput requirements.