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

The potential application of digital PCR in detecting different SARS-CoV-2 viral loads

Rapid, effective, and accurate detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is crucial. It is essential to control the spread of the virus and ensure accurate treatment for the disease. In the study, a total of 170 clinical specimens from 164 patients were collected and analyzed through digital PCR (dPCR) and real time quantitative reverse transcription PCR (RT-qPCR). The results showed an 86.41 % agreement between dPCR and RT-qPCR, with differences primarily noted in suspected cases. RT-qPCR exhibited a sensitivity of 84.78 %, specificity of 95.83 %, and accuracy of 86.42 %, which were comparatively lower than the 100 % accuracy of dPCR. Subsequently, we explored the potential correlation between these two methodologies based on Ct value groups. A strong negative correlation was observed between RT-qPCR and dPCR techniques in the Ct value group between 25 and 35, while the correlation was weakest in the Ct > 35 group. Moreover, the concordance rate for detecting the ORF1 (142/162) gene by RT-qPCR was lower compared to that of the N gene (149/162). Additionally, nucleic acid concentrations for ORF1 gene detection were lower than those for N gene detection in dPCR. In conclusion, this study shows that dPCR provides more reliable detection than RT-qPCR, especially for samples with low viral loads. Furthermore, dPCR effectively tracked changes in viral load during hospitalization, facilitating the diagnosis and treatment of COVID-19.

The frequency of SARS-CoV-2 in stool: A prospective study of healthy preschool children in Sweden

The study investigated the frequency of SARS-CoV-2 among healthy preschool children in two Swedish municipalities, a country where preschools remained uniquely opened throughout the pandemic. Stool samples were obtained from diapers collected at preschools in November-December 2021 and analyzed for SARS-CoV-2 using real-time reverse transcriptase polymerase chain reaction. Additionally, laboratory data concerning COVID-19 in the two regions were reviewed. Sixty-seven percent of invited preschools participated, providing 350 stool samples (Uppsala n=231, Gävle n=119). The children had a median age of 24 months (range 12-72). SARS-CoV-2 was not detected in any stool sample during the study period, which coincided with the initial omicron wave. The first pediatric omicron case appeared nearly two weeks after the first adult case. These findings suggest preschool children did not constitute a silent source nor played a major role in the transmission of SARS-CoV-2 during the first phases of the largest wave of COVID-19, so far.

FlexPCR: A streamlined multiplexed digital mRNA quantification platform with universal primers and limited fluorescence channels

Accurate quantification of multiple messenger RNA (mRNA) targets is essential for biomedical research and disease diagnosis. Current PCR-based methods for mRNA analysis are limited by the number of fluorescent labels and the complexities associated with multiple target-specific primers, leading to amplification bias and limited multiplexing capability. Here, we introduce Fluorescence-coding extension PCR (FlexPCR), a novel digital PCR-based assay that overcomes these limitations by employing a universal primer and probe strategy in conjugation with oligo extension. This method generates unique fluorescence-coded PCR templates for each mRNA target, enabling multiplexed detection using minimal fluorescence channels. FlexPCR simplifies assay design, reduces non-specific amplification, and enhances quantification accuracy. We demonstrate the efficacy by quantifying seven immune response mRNAs using only two fluorescence colors in various human total RNA samples. The results correlate strongly with gold-standard single-plex RT-qPCR, validating the accuracy of our method. FlexPCR offers a streamlined and scalable approach for multiplexed mRNA quantification with broad applications in gene expression analysis and molecular diagnostics.

Research on the histopathology of Larimichthys crocea affected by white gill disease and analysis of its bacterial and viral community characteristics

White gill disease (WGD) is one of the major diseases affecting Larimichthys crocea, although its etiology remains unclear. To investigate the causes of WGD, this study selected WGD-affected Larimichthys crocea (WG) and healthy Larimichthys crocea (NH) from multiple aquaculture regions for pathological analysis and analysis of bacterial and viral community characteristics. The results indicated severe tissue damage and significant inflammatory responses, as evidenced by clinical manifestations and electron microscopy. Two bacterial species, Photobacterium damselae and Vibrio campbellii, were isolated from all lesion tissues. Additionally, 16S full-length sequencing results showed that Photobacterium damselae and Vibrio campbellii dominated in the tissues of Larimichthys crocea, with a combined relative abundance of approximately 90 %. There were no significant differences in α-diversity and β-diversity between the NH group and WG group from the three aquaculture regions, and no significant biomarkers were identified. The diversity of DNA and RNA viruses did not show significant differences between the NH and WG groups, although both types of viruses exhibited notable synergistic and antagonistic relationships. Analyses from 16S full-length sequencing, metagenomics, and metatranscriptomics revealed that the related functional genes were primarily enriched in various metabolic pathways, including glycine biosynthesis, membrane transport, and energy metabolism. The metatranscriptomic analysis indicated that the expression levels of genes related to antibiotic resistance, biosynthesis, transport, and degradation processes were significantly downregulated in the WG group. Finally, through PCR, qPCR, and metagenomic sequencing, we were unable to detect iridovirus in Larimichthys crocea, further suggesting that the causes of WGD may differ across aquaculture regions compared to previous reports. This study indicates that the etiology of WGD may involve complex ecological and metabolic mechanisms, rather than being merely the result of a single pathogen infection. This research provides a comprehensive analysis of the microbial communities in WGD-affected Larimichthys crocea from multiple aquaculture regions for the first time, providing a theoretical basis for further elucidating the causes of WGD and developing preventive measures.

Advances in SERS detection method combined with microfluidic technology for bio-analytical applications

With the advancement of research on life systems and disease mechanisms, the precision of analysis tends to be at a single molecule or single gene level. The surface-enhanced Raman scattering (SERS) method is highly anticipated because of its sensitive detection ability down to a single molecule level. The SERS-based microfluidic platforms retain both advantages of SERS and microfluidics, working in a complementary way. The combination of microfluidics and SERS can provide rapid, non-destructive, high-sensitive, and high-throughput analysis for biological samples, which is of great significance to developing potential biomedical applications, thus occupying an outstanding position among the current research hot topics. This review briefly summarized the recent developments and applications of SERS-based microfluidic platforms in biological analysis. This paper first introduced the SERS-based microfluidic platforms and gave a classification of this method including continuous flow-based method, microarrays-based method, droplet-based method, lateral flow assay (LFA)-based method, and digital-based method. In particular, the bioanalytical applications of SERS-based microfluidic platforms in recent years, including biomolecule detection, cell analysis, and disease diagnosis, have been reviewed. It illustrated that SERS-based microfluidic platforms have great potential in bioanalysis.

Co-infection dynamics of SARS-CoV-2 and respiratory viruses in the 2022/2023 respiratory season in the Netherlands

OBJECTIVES

Evaluation of the presence and effect of SARS-CoV-2 co-infections on disease severity.

METHODS

We collected both symptom data and nose- and throat samples from symptomatic people during the 2022/2023 respiratory season in a large participatory surveillance study in the Netherlands, and tested these for 18 respiratory viruses, including SARS-CoV-2. We compared reported health status, symptoms and odds of having a single respiratory viral infection or co-infection with SARS-CoV-2 and another respiratory virus.

RESULTS

In total, 4655 samples were included with 22% (n=1017) testing SARS-CoV-2 positive. Of these 11% (n=116) also tested positive for a second respiratory virus. The most frequently occurring co-infections in SARS-CoV-2 positive participants were with rhinovirus (59%; n=69), seasonal coronaviruses (15%; n=17), and adenovirus (7%; n=8). Participants with a co-infection with one of these three viruses did not report more severe disease compared to those with a SARS-CoV-2 mono-infection. The odds of experiencing SARS-CoV-2 co-infection with seasonal coronavirus or rhinovirus were lower compared to the odds of the respective non-SARS-CoV-2 mono-infection (OR: 0.16, CI 95%: 0.10 - 0.24; OR: 0.21 CI 95%: 0.17 - 0.26; respectively).

CONCLUSIONS

SARS-CoV-2 co-infections with rhinovirus, seasonal coronavirus, and adenovirus are frequently observed in the general population, but are not associated with more severe disease compared to SARS-CoV-2 mono-infections. Furthermore, we found indications for inter-virus interaction with rhinovirus and seasonal coronavirus, possibly decreasing the risk of co-infection.

The pathogenic burden potential of airborne particles in emanating from the respiratory area of COVID-19 patients (a case study)

The pathogenic potential of airborne particles carrying the SARS-CoV-2 viral genome was examined by considering the size distribution of airborne particles at given distances from the respiratory zone of an infected patient after coughing or sneezing with a focus on time, temperature, and relative humidity. The results show an association between the size distribution of airborne particles, particularly PM1 and PM2.5, and the presence of viral genome in different stations affected by the distance from the respiratory zone and the passage of time. The correlation with time was strong with all the dependent factors except PM1. Also, the effect of time intervals on the median concentration of airborne PM in the range of PM7 and PM10 was significant. Accordingly, in the first 20 min after coughing, the COVID-19 patient was more likely to be exposed to PM-carrying RNA genomes of SARS-CoV-2. The other finding was that the two distances of 0.25 m to the patient's left of the respiratory zone and 1.0 m above the breathing zone showed positive results for the presence of SARS-CoV-2 in all studied time intervals. The patterns of results suggested that there was a high potential for distribution of the virus in an infected patient based on position and airflow and that the severity of infection and viral load may influence the presence of viral load in droplets when coughing. Based on the results, one can conclude that ventilation plays a key role in mitigating the risk of airborne virus transmission in indoor environments, and it has been shown that reductions in particulate concentrations occur when portable air purifiers are placed near the breathing zone. The use of personal protective equipment for the patient and healthcare personnel to minimize the distribution of virus particles in the air is recommended.

Strengthening diagnostic services in Latin America requires regional leadership, sustainable funding, and enhanced data sharing

Diagnostic services played a key role in government responses to the COVID-19 pandemic. In our work to support diagnostics in over 20 countries of the Global South, with a focus on Latin America, we observed common problems in resource-limited settings. We identify common constraints of (i) affordability of reagents, (ii) access to reagents, (iii) poor infrastructure, and (iv) limited human resources. Enhancing diagnostic services in resource-limited settings cannot be sustained only by international cooperation and philanthropic missions. Success depends on domestic leadership and regional cooperation of which the existent influenza or dengue networks in Latin America are prime examples. A Latin American Center for Disease Control and Prevention (CDC), as proposed by some, can only be successful if reliable funding and a clear mandate are secured. A stronger inclusion of diagnostic tool development and data sharing will be imperative for dealing with emerging pathogens.

COVID-19 activity screening by a smart-data-driven multi-band voice analysis

COVID-19 is a disease caused by the new coronavirus SARS-COV-2 which can lead to severe respiratory infections. Since its first detection it caused more than six million worldwide deaths. COVID-19 diagnosis non-invasive and low-cost methods with faster and accurate results are still needed for a fast disease control. In this research, 3 different signal analyses have been applied (per broadband, per sub-bands and per broadband & sub-bands) to Cough, Breathing & Speech signals of Coswara dataset to extract non-linear patterns (Energy, Entropies, Correlation Dimension, Detrended Fluctuation Analysis, Lyapunov Exponent & Fractal Dimensions) for feeding a XGBoost classifier to discriminate COVID-19 activity on its different stages. Classification accuracies ranged between 83.33% and 98.46% have been achieved, surpassing the state-of-art methods in some comparisons. It should be empathized the 98.46% of accuracy reached on pair Healthy Controls vs all COVID-19 stages. The results shows that the method may be adequate for COVID-19 diagnosis screening assistance.

Room temperature storage and shipping of encapsulated synthetic RNAs as quality control materials for SARS-CoV-2 molecular diagnostic assays

The Coronavirus pandemic unveiled the unprecedented need for diagnostic tests to rapidly detect the presence of pathogens in the population. Real-time RT-PCR and other nucleic acid amplification techniques are accurate and sensitive molecular techniques that necessitate quality control strategies and stable quality control materials. To meet this need, Twist Bioscience has developed and released synthetic RNA controls. However, RNA is an inherently unstable molecule needing cold storage, costly shipping, and resource-intensive logistics. Imagene provides a solution to this problem by encapsulating dehydrated RNA inside metallic capsules filled with anhydrous argon, allowing room temperature and eco-friendly storage and shipping. This technology initially developed for DNA storage has been successfully applied to RNA and other biospecimen and extensively validated through real time and accelerated aging. Here, RNA controls produced by Twist Bioscience were encapsulated in RNAshells and distributed to several laboratories that used them for COVID-19 detection tests by amplification. One RT-LAMP procedure, four different RT-PCR devices and 6 different PCR kits were used. The amplification targets were genes E, N; RdRp, Sarbeco-E and Orf1a/b. RNA retrieval was satisfactory, and the detection was reproducible. RNA stability was checked by real-time (3 years at room temperature) and accelerated aging (16h at 90 °C, corresponding to approximately 10 years of storage at 25 °C, according to our previously published Arrhenius study for encapsulated RNA). The results were not significantly different from those for unaged capsules. This room temperature RNA stability allows the preparation and distribution of large strategic batches which can be stored for more than 10 years a long time and used for standardization processes between detection sites. Moreover, this provides the advantage of single-use and field usability across varying temperatures. Consequently, this type of encapsulated synthetic RNA, processed at room temperature, can be used as internal quality control materials for the SARS-Cov-2 virus as well as for detection of other RNA viruses.

Validation of new equipment for SARS-CoV-2 diagnosis in Ecuador: Detection of the virus and antibodies generated by disease and vaccines with one POC device

The COVID-19 pandemic underscored the critical need to enhance screening capabilities and streamline diagnosis. Point-of-care (POC) tests offer a promising solution by decentralizing testing. We aimed to validate the PLUM device (LSK Technologies Inc.), a portable optical reader, to detect SARS-CoV-2 RNA using direct RT-LAMP targeting the ORF1a and E1 genes and patient antibodies by ELISA. The direct RT-LAMP assays employ nasopharyngeal swabs and bypass RNA extraction protocols through a brief chemical and physical lysis step. Test sensitivity and specificity were assessed against gold-standard detection methods in laboratory and field conditions. For samples with Ct values below 25, direct RT-LAMP showed 83% sensitivity and 90% specificity under laboratory conditions and 91% sensitivity and 92% specificity under field conditions. The nucleocapsid antigen antibody assay had 99% positive percent agreement (PPA) and 97% negative percent agreement (NPA), outperforming spike-RBD antigen (98% PPA, 92% NPA) and seroprevalence (98% PPA, 88% NPA) under laboratory conditions. Under field conditions, similar results were found for antibody detection for the nucleocapsid antigen (93% PPA; 100% NPA), spike-RBD (100% PPA; 94% NPA), and seroprevalence (90% PPA; 94% NPA). This study validated the PLUM device as a dual POC tool for direct RT-LAMP-based SARS-CoV-2 and ELISA-based COVID-19 antibody detection.

Shortened SARS-CoV-2 Viral RNA Shedding in Saliva During Early Omicron Compared to Wild-Type Pandemic Phase

This study compared the dynamics of SARS-CoV-2 viral shedding in saliva between wild-type virus-infected and Omicron-infected household cohorts. Preexisting immunity in participants likely shortens the viral RNA shedding duration and lowers viral load peaks. Frequent saliva sampling can be a convenient tool to study viral load dynamics.

Study of coronavirus diversity in wildlife in Northern Cambodia suggests continuous circulation of SARS-CoV-2-related viruses in bats

Since SARS-CoV-2's emergence, studies in Southeast Asia, including Cambodia, have identified related coronaviruses (CoVs) in rhinolophid bats. This pilot study investigates the prevalence and diversity of CoVs in wildlife from two Cambodian provinces known for wildlife trade and environmental changes, factors favoring zoonotic spillover risk. Samples were collected from 2020 to 2022 using active (capture and swabbing of bats and rodents) and non-invasive (collection of feces from bat caves and wildlife habitats) methods. RNA was screened for CoVs using conventional pan-CoVs and real-time Sarbecovirus-specific PCR systems. Positive samples were sequenced and phylogenetic analysis was performed on the partial RdRp gene. A total of 2608 samples were collected: 867 rectal swabs from bats, 159 from rodents, 41 from other wild animals, and 1541 fecal samples. The overall prevalence of CoVs was 2.0%, with a 3.3% positive rate in bats, 2.5% in rodents, and no CoVs detected in other wildlife species. Alpha-CoVs were exclusive to bats, while Beta-CoVs were found in both bats and rodents. Seven SARS-CoV-2-related viruses were identified in Rhinolophus shameli bats sampled in August 2020, March 2021, and December 2021. Our results highlight diverse CoVs in Cambodian bats and rodents and emphasize bats as significant reservoirs. They also suggest continuous circulation of bat SARS-CoV-2-related viruses may occur in a region where ecological and human factors could favor virus emergence. Continuous surveillance and integrated approaches are crucial to managing and mitigating emerging zoonotic diseases.

Emergence of influenza A(H1N1)pdm09 6B.1A.5a.2a and 6B.1A.5a.2a.1 subclades leading to subtyping failure in a commercial molecular assay

BACKGROUND

During the 2023-2024 and early 2024-2025 influenza seasons, several influenza A-positive specimens in our laboratory failed subtyping for H1, H1pdm09, and H3 using the Allplex Respiratory Panel 1 (Allplex RP1) (Seegene Inc.). This study aimed to identify the cause of these subtyping failures.

MATERIALS AND METHODS

Between August 2023 and December 2024, 23 nasopharyngeal specimens tested positive for influenza A but were unsubtypeable for H1, H1pdm09, and H3. Confirmatory testing by the manufacturer included target-specific PCR for the M and HA genes, followed by sequencing to determine subclades.

RESULTS

Among the 23 unsubtypeable specimens, 22 yielded PCR products for sequencing. Of these, 21 belonged to subclade 6B.1A.5a.2a.1 and one to 6B.1A.5a.2a. Sequence analysis revealed mismatches in the H1pdm09 primer/probe-binding regions of Allplex RP1, explaining the subtyping failures. Despite testing negative for H1pdm09 in Allplex RP1, sequencing confirmed their classification as H1N1pdm09 subclades with HA gene mutations.

CONCLUSIONS

Subclades 6B.1A.5a.2a.1 and 6B.1A.5a.2a harbour mutations that contributed to subtyping failures in some specimens tested with a commercial assay. While unsubtypeable influenza A results often raise concerns about emerging strains, sequencing confirmed that all unsubtypeable specimens tested with Allplex RP1 belonged to H1N1pdm09 within recognised subclades. Thus, such subtyping failures in this assay do not necessarily indicate a novel or zoonotic virus, though genomic surveillance remains essential.

External quality assessment of molecular detection and variant typing of SARS-CoV-2 in European expert laboratories in 2023

The COVID-19 pandemic highlighted the importance of laboratory preparedness. Regular monitoring of diagnostic tools via external quality assessments (EQAs) is key to maintaining robust public health response service. We hereby conducted a third SARS-CoV-2 EQA assessing the diagnostic capabilities of European expert public health laboratories. A 10 samples panel containing Alpha (used in previous EQA), BA.4, BA.5, and BQ.1.18 variants along with human seasonal coronaviruses and negative controls was produced and validated. Participants were invited by the European Centre for Disease Prevention and Control (ECDC) and asked to submit results and assay details via electronic forms. Thirty-eight laboratories from 31 European countries participated. Most (n = 32, 84%) identified all panel samples correctly and used in-house (11, 29%), commercial assays (22, 58%), or both (5, 13%). Compared to previous EQAs, correct detection of the SARS-CoV-2 samples in the panels increased: 8 (12%) in 2020, 45 (75%) in 2021, and 34 (90%) laboratories in 2023, respectively. The number of participants decreased to an average of one laboratory per country (range 1-3) compared to two (1-7) laboratories in both previous EQAs. The usage of commercial assays gradually increased in contrast to the usage of in-house or both approaches. The capacity for SARS-CoV-2 molecular diagnostics has markedly improved in Europe as evidenced by three consecutive EQAs carried out by expert public health laboratories. Routine monitoring of diagnostic and surveillance assays via EQAs remains key to maintaining rapid public health laboratory response systems.IMPORTANCEExternal quality assessments (EQAs) are crucial to ensure the reliability and consistency of diagnostic laboratories. They provide an objective framework for evaluating the performance of testing systems, enabling laboratories to identify weaknesses and implement improvements promptly. In the context of SARS-CoV-2, EQAs have become even more critical due to the high demand for accurate molecular diagnostics and the emergence of new variants. Accurate detection and typing of variants are especially essential for monitoring viral evolution. EQAs help standardize methodologies, ensuring that results across laboratories remain comparable and trustworthy. Moreover, they play a pivotal role in minimizing errors such as false positives or negatives. In this rapidly evolving landscape, regular EQAs are indispensable for maintaining high-quality standards in molecular diagnostics and variant surveillance. We demonstrate here that regular EQAs improve the molecular detection of SARS-CoV-2 in European laboratories.

Neuroinvasive and neurovirulent potential of SARS-CoV-2 in the acute and post-acute phase of intranasally inoculated ferrets

Severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) can cause systemic disease, including neurological complications, even after mild respiratory disease. Previous studies have shown that SARS-CoV-2 infection can induce neurovirulence through microglial activation in the brains of patients and experimentally inoculated animals, which are models representative for moderate to severe respiratory disease. Here, we aimed to investigate the neuroinvasive and neurovirulent potential of SARS-CoV-2 in intranasally inoculated ferrets, a model for subclinical to mild respiratory disease. The presence of viral RNA, histological lesions, virus-infected cells, and the number and surface area of microglia and astrocytes were investigated. Viral RNA was detected in various respiratory tissue samples by qPCR at 7 days post inoculation (dpi). Virus antigen was detected in the nasal turbinates of ferrets sacrificed at 7 dpi and was associated with inflammation. Viral RNA was detected in the brains of ferrets sacrificed 7 dpi, but in situ hybridization nor immunohistochemistry did confirm evidence for viral RNA or antigen in the brain. Histopathological analysis of the brains showed no evidence for an influx of inflammatory cells. Despite this, we observed an increased number of Alzheimer type II astrocytes in the hindbrains of SARS-CoV-2 inoculated ferrets. Additionally, we detected increased microglial activation in the olfactory bulb and hippocampus, and a decrease in the astrocytic activation status in the white matter and hippocampus of SARS-CoV-2 inoculated ferrets. In conclusion, although SARS-CoV-2 has limited neuroinvasive potential in this model for subclinical to mild respiratory disease, there is evidence for neurovirulent potential. This study highlights the value of this ferret model to study the neuropathogenecity of SARS-CoV-2 and reveals that a mild SARS-CoV-2 infection can affect both microglia and astrocytes in different parts of the brain.

Emergence, persistence, and positive selection of yellow fever virus in Colombia

Yellow fever virus (YFV) is an arbovirus that causes acute febrile illness (AFI), in tropical areas of South America and Africa. Through a 2020-2023 AFI study in Leticia, Colombia, leveraging metagenomic next-generation sequencing (mNGS), we identified and isolated YFV (LET1450). Phylogenetic analysis showed this strain belongs to South American genotype II (SamII), linked to Peruvian and Bolivian sequences emerging around 1989. Phylodynamic analysis indicates these strains, with a unique genetic makeup, could have reduced vaccine susceptibility, and due to positive Darwinian selection have an enhanced adaptive capacity. Antigenic analysis identified additional immune-evasive traits and this strain's potential for wider Latin American spread. Phylogeographic reconstruction demonstrated the persistence of YFV in Colombia is not due to repeated external introductions, but results from continuous, cryptic internal circulation. This study highlights the crucial role of mNGS in monitoring emerging strains and underscores the need for genomic surveillance of YFV and other arboviral infections.

Antiviral effect of Bromelain combined with acetylcysteine against SARS-CoV-2 Omicron variant

The recent pandemic represented one of the biggest challenges of modern civilization. SARS-CoV-2 remains an imminent public health threat and currently, there is no effective and greatly affordable treatment for severe COVID-19. Although standard management with dexamethasone, and physical management including physiotherapy, prone positioning and mechanical ventilation are used, severe disease patients may still succumb to infection. In this regard, BromAc® is a combination therapy of a refined protein derived from Bromelain and acetylcysteine, that shows significant mucolytic and anti-inflammatory properties. In the present study, we performed in vitro, and ex vivo analyses to assess the effect of BromAc® in inhibiting Omicron variant of SARS-CoV-2 at different levels. Here, we provide evidence of the in vitro virucidal activity of BromAc® in Vero-ACE2/TMPRSS2 cell line infected with the Omicron variant. BromAc® can also abrogate SARS-CoV-2 RNA genomic copies in tracheal aspirate (TA) samples from critically ill COVID-19 patients after long term exposure. These results were confirmed by lower spike expression observed in EpCAM+PanCKneg epithelial cells from tracheal aspirate samples after BromAc® treatment. Furthermore, atomized BromAc® promoted cleavage of the S1 Spike subunit in TA samples, demonstrating the mechanism of the antiviral activity displayed by BromAc® in human samples. These results bring novel evidence of antiviral activity in cell lines in vitro as well as in tracheal aspirate samples from critically ill COVID-19 patients, which support its potential use as an adjunct to COVID-19 management in future waves of Omicron subvariants.

Intranasal parainfluenza virus-vectored vaccine expressing SARS-CoV-2 spike protein of Delta or Omicron B.1.1.529 induces mucosal and systemic immunity and protects hamsters against homologous and heterologous challenge

The continuous emergence of new SARS-CoV-2 variants requires that COVID vaccines be updated to match circulating strains. We generated B/HPIV3-vectored vaccines expressing 6P-stabilized S protein of the ancestral, B.1.617.2/Delta, or B.1.1.529/Omicron variants as pediatric vaccines for intranasal immunization against HPIV3 and SARS-CoV-2 and characterized these in hamsters. Following intranasal immunization, these B/HPIV3 vectors replicated in the upper and lower respiratory tract and induced mucosal and serum anti-S IgA and IgG. B/HPIV3 expressing ancestral or B.1.617.2/Delta-derived S-6P induced serum antibodies that effectively neutralized SARS-CoV-2 of the ancestral and B.1.617.2/Delta lineages, while the cross-neutralizing potency of B.1.1.529/Omicron S-induced antibodies was lower. Despite the lower cross-neutralizing titers induced by B/HPIV3 expressing S-6P from B.1.1.529/Omicron, a single intranasal dose of all three versions of B/HPIV3 vectors was protective against matched or heterologous WA1/2020, B.1.617.2/Delta or BA.1 (B.1.1.529.1)/Omicron challenge; hamsters were protected from challenge virus replication in the lungs, while low levels of challenge virus were detectable in the upper respiratory tract of a small number of animals. Immunization also protected against lung inflammatory response after challenge, with mild inflammatory cytokine induction associated with the slightly lower level of cross-protection of WA1/2020 and B.1.617.2/Delta variants against the BA.1/Omicron variant. Serum antibodies elicited by all vaccine candidates were broadly reactive against 20 antigenic variants, but the antigenic breadth of antibodies elicited by B/HPIV3-expressed S-6P from the ancestral or B.1.617.2/Delta variant exceeded that of the S-6P B.1.1.529/Omicron expressing vector. These results will guide development of intranasal B/HPIV3 vectors with S antigens matching circulating SARS-CoV-2 variants.

Persistence and decay of neutralizing antibody responses elicited by SARS-CoV-2 infection and hybrid immunity in a Canadian cohort

A major challenge with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), has been assessing the intensity, dynamics, and determinants of the antibody responses after infection and/or vaccination. Therefore, we aimed to characterize the longitudinal dynamics of the antibody responses among naturally infected individuals and individuals who achieved hybrid immunity in a large Canadian cohort. We demonstrate that anti-Spike IgGs and neutralizing antibody dynamics vary greatly among individuals with COVID-19, in peak antibody levels, rate of waning, and longevity of the antibody response. Additionally, we found an association between robust antibody responses and individuals with severe COVID-19 clinical symptoms during the first-month post-symptom onset. For individuals who achieved hybrid immunity, a robust increase in anti-S1 IgGs and neutralizing antibodies followed the first vaccination dose; however, there was a minimal increase in the anti-S1 IgGs and neutralizing antibody titers after administration of the second dose of the vaccine. Furthermore, neutralizing antibodies elicited by the wild-type virus alone were largely ineffective against emerging variants of concern in our natural infection-only cohort, in contrast to a much broader and more robust neutralization profile observed in individuals who achieved hybrid immunity. Our findings emphasize the need for global SARS-CoV-2 vaccination efforts to further sustain protective immune responses required to minimize viral spread and disease severity in the population. As SARS-CoV-2 variants continue to emerge, understanding the interplay between previous infections, vaccine durability, and virus evolution will be critical for guiding ongoing vaccination strategies.

IMPORTANCE

A major challenge with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), has been assessing the intensity, dynamics, and determinants of the antibody response after infection and/or vaccination. Our paper addresses this in a large Canadian cohort with antibody responses that were generated by natural infection as well as vaccine in some persons studied.

Effect of SARS-CoV-2 infection on sperm telomere length

PURPOSE

The repercussions and outcomes of the coronavirus disease 2019 (COVID-19) pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has raised concerns about potential adverse effects on the male reproductive system. Telomeres are crucial in maintaining the integrity and stability of genomic DNA, and viral infections can induce changes in telomere biology. In this study, the repercussions of SARS-CoV-2 infection in male reproductive health were analyzed.

METHODS

This case-control study enrolled subjects who donated blood and semen samples. Fifty-six men with and 56 without prior COVID-19 infection, ages 18-45 years, were included. Semen analysis and hormonal levels were evaluated. The presence of SARS-CoV-2 RNA in semen and the sperm telomere length were assessed by quantitative polymerase chain reaction and associated with clinical and laboratory data. To reduce interference factors, known variables that influence telomere length were analyzed independently.

RESULTS

Sperm telomere length was significantly diminished in the COVID-19 positive group with a mean difference of 0.635 compared to the negative group (p = 0.041). Most individuals in the COVID-19 positive group were clinically classified as asymptomatic/mild illness, and all samples were collected more than 90 days after recovery. No statistically significant differences were observed between the groups in terms of clinical data, semen parameters, and serum levels of follicle-stimulation hormone, estradiol, and testosterone. Persistent or subgenomic SARS-CoV-2 RNA was not detected in the semen samples.

CONCLUSION

This study revealed that SARS-CoV-2 infection reduced sperm telomere length without alterations in semen parameters or hormonal levels. These results provide further evidence that SARS-CoV-2 infection can induce genomic alterations in human sperm.

RBD-depleted SARS-CoV-2 spike generates protective immunity in cynomolgus macaques

The SARS-CoV-2 pandemic revealed the rapid evolution of circulating strains. This led to new variants carrying mostly mutations within the receptor binding domain, which is immunodominant upon immunization and infection. In order to steer the immune response away from RBD epitopes to more conserved domains, we generated S glycoprotein trimers without RBD and stabilized them by formaldehyde cross-linking. The cryoEM structure demonstrated that SΔRBD folds into the native prefusion conformation, stabilized by one specific cross-link between S2 protomers. SΔRBD was coated onto lipid vesicles, to produce synthetic virus-like particles, SΔRBD-LV, which were utilized in a heterologous prime-boost strategy. Immunization of cynomolgus macaques either three times with the mRNA Comirnaty vaccine or two times followed by SΔRBD-LV showed that the SΔRBD-LV boost induced similar antibody titers and neutralization of different variants, including omicron. Upon challenge with omicron XBB.3, both the Comirnaty only and Comirnaty/SΔRBD-LV vaccination schemes conferred similar overall protection from infection for both the Comirnaty only and Comirnaty/SΔRBD-LV vaccination schemes. However, the SΔRBD-LV boost indicated better protection against lung infection than the Comirnaty strategy alone. Together our findings indicate that SΔRBD is highly immunogenic and provides improved protection compared to a third mRNA boost indicative of superior antibody-based protection.

On the adjuvanticity of hyaluronan: The case of a SARS-CoV-2 vaccine

Vaccines based on mRNA have been fundamental in facing the COVID-19 pandemic, however, they still raise concerns about stability and long-term efficacy. Thus, protein-based vaccines remain valid options and hence the study of effective adjuvants is crucial. Here, we developed a COVID-19 vaccine based on the receptor-binding domain (RBD) of SARS-CoV-2 Spike protein, which is covalently conjugated to the natural polymer hyaluronan (HA) that acts as an immunological adjuvant. Vaccination of K18-hACE2 mice with HA-RBD was well tolerated, and elicited high and sustained titres of RBD-binding antibodies and SARS-CoV-2-neutralizing antibodies, without the addition of other immunostimulatory compounds. Most importantly, HA-RBD vaccination conferred long-term protection to K18-hACE2 mice after challenge with SARS-CoV-2, also in the case of two consequent infections driven by different variants. These findings demonstrate the efficacy of HA-based vaccination against COVID-19 disease, and support the promising use of HA as an efficient and well tolerated adjuvant.

Aging shapes infection profiles of influenza A virus and SARS-CoV-2 in human precision-cut lung slices

BACKGROUND

The coronavirus disease 2019 (COVID-19) outbreak revealed the susceptibility of elderly patients to respiratory virus infections, showing cell senescence or subclinical persistent inflammatory profiles and favoring the development of severe pneumonia.

METHODS

In our study, we evaluated the potential influence of lung aging on the efficiency of replication of influenza A virus (IAV) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), as well as determining the pro-inflammatory and antiviral responses of the distal lung tissue.

RESULTS

Using precision-cut lung slices (PCLS) from donors of different ages, we found that pandemic H1N1 and avian H5N1 IAV replicated in the lung parenchyma with high efficacy. In contrast to these IAV strains, SARS-CoV-2 Early isolate and Delta variant of concern (VOC) replicated less efficiently in PCLS. Interestingly, both viruses showed reduced replication in PCLS from older compared to younger donors, suggesting that aged lung tissue represents a suboptimal environment for viral replication. Regardless of the age-dependent viral loads, PCLS responded to H5N1 IAV infection by an induction of IL-6 and IP10/CXCL10, both at the mRNA and protein levels, and to H1N1 IAV infection by induction of IP10/CXCL10 mRNA. Finally, while SARS-CoV-2 and H1N1 IAV infection were not causing detectable cell death, H5N1 IAV infection led to more cytotoxicity and induced significant early interferon responses.

CONCLUSIONS

In summary, our findings suggest that aged lung tissue might not favor viral dissemination, pointing to a determinant role of dysregulated immune mechanisms in the development of severe disease.

Assessment of mortality due to severe SARS-CoV-2 infection in public and private intensive care units in Brazil: a multicenter retrospective cohort study

BACKGROUND

This retrospective multicenter cohort study compared characteristics and outcomes of 5,790 critically ill patients with COVID-19 in Brazil's public and private intensive care units. Patients in public intensive care units exhibited greater disease severity, more frequent use of organ support, and higher mortality rates compared to those in private intensive care units. The risk of in-hospital death was more than twice as high in public intensive care units. ■ Public intensive care unit COVID-19 patients presented with more comorbidities and higher severity at admission. ■ Public intensive care units required more invasive organ support (e.g., mechanical ventilation, vasopressors, and renal replacement therapy) but less non-invasive ventilation and high-flow nasal cannula than private intensive care units. ■ In-hospital mortality was higher in public intensive care units, with an increased risk of death even after adjusting for patient characteristics and illness severity at intensive care unit admission.

OBJECTIVE

To compare the clinical characteristics, use of organ support, and outcomes of critically ill patients with COVID-19 admitted to public and private intensive care units.

METHODS

This multicenter retrospective cohort study included patients admitted to four intensive care units from March 1, 2020, to December 31, 2021. Patients with COVID-19 admitted to public and private intensive care units were compared. The primary outcome of interest, in-hospital mortality, was assessed using a hierarchical logistic regression (multilevel) model adjusted for study site and patient characteristics.

RESULTS

A total of 5,790 patients with COVID-19 were admitted to the participating intensive care units, with 3,321 (57.3%) admitted to private hospitals and 2,469 (42.6%) admitted to public hospitals. Patients in public intensive care units were less likely to be male and had higher median SAPS III scores, Charlson Comorbidity Index values, and SOFA scores. They also required mechanical ventilation (53.1% versus 40.0%, p<0.001), vasopressors (43.1% versus 33.9%, p<0.001), and renal replacement therapy (20.3% versus. 14.5%, p<0.001) more frequently than those in private intensive care units. In contrast, patients in private intensive care units were more frequently managed with non-invasive ventilation (38.0% versus 66.8%; p<0.001) and high-flow nasal cannulas (18.3% versus 48.1%; p<0.001). The in-hospital mortality rate was significantly higher in public intensive care units (40.3%) compared to private intensive care units (16.4%) (adjusted OR=2.96; 95%CI=1.94-4.51; p<0.001).

CONCLUSION

We observed significant differences in resource utilization and mortality rates between patients with COVID-19 admitted to public and private intensive care units. Patients with COVID-19 in public care units face a higher risk of in-hospital mortality compared to those in private care units.

In Silico and In Vitro development of novel small interfering RNAs (siRNAs) to inhibit SARS-CoV-2

SARS-CoV-2 is causing severe to moderate respiratory tract infections, posing global health, social life, and economic threats. Our design strategy for siRNAs differs from existing studies through a step-by-step filtration process utilizing integrative bioinformatics protocols and web tools. Stage one: Multiple Sequence Alignment was employed to identify the most conserved areas. Stage two involves using various online tools, among the most reputable tools for building siRNA. The first filtration step of siRNA uses the Huesken dataset, estimating a 90 % experimental inhibition. The second filtration stage involves choosing the most suitable and targeted siRNA by utilizing thermodynamics and Target Accessibility of siRNAs. The final filtration step is off-target filtration using BLAST with specific parameters. Four of the 258 siRNAs were chosen for their potency and specificity, targeting conserved regions (NSP8, NSP12, and NSP14) with minimal human transcripts off-targets. We conducted in-vitro experiments, including cytotoxicity, TCID50, and RT-PCR assays. When tested on the SARS-CoV-2 strain hCoV-19/Egypt/NRC-03/2020 at 100 nM, none showed cellular toxicity. The TCID50 assay confirmed viral replication reduction at 12 h.p.i; the efficacy of the four siRNAs and their P value were highly significant. siRNA2 maintaining efficacy at 24, 36, and 48 h.p.i, while siRNA4 had a significant P value (≤0.0001) at 48 h.p.i. At 24 h.p.i, siRNA2 and siRNA4 showed statistical significance in viral knockdown of the virus's S gene and ORF1b gene by 95 %, 89 %, and 96 %, 97 %, respectively. Our computational method and experimental assessment of specific siRNAs have led us to conclude that siRNA2 and siRNA4 could be promising new therapies for SARS-CoV-2 that need further development.

Antiviral Activity of Halogenated Compounds Derived from L-Tyrosine Against SARS-CoV-2

INTRODUCTION

Currently, there are no effective medications for treating all the clinical conditions of patients with COVID-19. We aimed to evaluate the antiviral activity of compounds derived from L-tyrosine against the B.1 lineage of SARS-CoV-2 in vitro and in silico.

METHODOLOGY

The cytotoxicities of 15 halogenated compounds derived from L-tyrosine were evaluated in Vero-E6 cells by the MTT assay. The antiviral activity of the compounds was evaluated using four strategies, and viral quantification was performed by a plaque assay and qRT-PCR. The toxicity of the compounds was evaluated by ADMET predictor software. The affinity of these compounds for viral or cellular proteins and the stability of their conformations were determined by docking and molecular dynamics, respectively.

RESULTS

TODC-3M, TODI-2M, and YODC-3M reduced the viral titer >40% and inhibited the replication of viral RNA without significant cytotoxicity. In silico analyses revealed that these compounds presented low toxicity and binding energies between -4.3 and -5.2 Kcal/mol for three viral proteins (spike, Mpro, and RdRp). TODC-3M and YODC-3M presented the most stable conformations with the evaluated proteins.

CONCLUSIONS

The most promising compounds were TODC-3M, TODI-2M, and YODC-3M, which presented low in vitro and in silico toxicity, antiviral potential through different strategies, and favorable affinities for viral targets. Therefore, they are candidates for in vivo studies.

Enhanced and long-lasting SARS-CoV-2 immune memory in individuals with common cold coronavirus cross-reactive T cell immunity

With the continuous emergence of novel SARS-CoV-2 variants, long-lasting and broadly reactive cellular and humoral immunity is critical for durable protection from COVID-19. We investigated SARS-CoV-2-specific T cell immunity in relation to antibodies, infection outcome and disease severity and assessed its durability in a longitudinal cohort over a three-year time course. We identified pre-existing T cells reactive to the seasonal coronavirus (CoV) OC43 that cross-react with the conserved SARS-CoV-2 spike S813-829 peptide. These cross-reactive T cells increased in frequency following SARS-CoV-2 infection or vaccination and correlated with enhanced spike-specific T cell responses and significantly reduced viral loads. Furthermore, our data revealed that CoV-cross-reactive T cells were maintained as part of the long-lasting memory response, contributing to increased T cell frequencies against omicron variants. These findings suggest a functional role of CoV-cross-reactive T cells that extends beyond the initial SARS-CoV-2 exposure, contributing to enhanced immunity against highly mutated SARS-CoV-2 variants.

Differential efficacy of first licensed western vaccines protecting without immunopathogenesis Wuhan-1-challenged hamsters from severe COVID-19

Four COVID-19 vaccines were developed, tested, and authorized early in Europe and the US. Comirnaty and Spikevax are mRNA-based, whereas Jcovden and Vaxzevria utilize adenoviral vectors (AdV). We described a hamster model of COVID-19 utilizing Wuhan-1 strain SARS-CoV-2, in which vaccine-associated immunopathogenesis can be induced by Alum-adjuvanted Spike protein (Alum+S). Such animals were vaccinated with the authorized vaccines or Alum+S, challenged, and examined. All vaccinated hamsters produced antibodies targeting S. Neutralizing antibodies (nAb) were induced only by authorized vaccines. While nAbs were present after one vaccination with AdV-vaccines, mRNA vaccines needed a boost immunization. Upon challenge, all authorized vaccines protected from severe disease. Less tissue damage and no live virus (one exception) were detectable in the lungs. In contrast, Alum+S immunized hamsters developed VAERD. Our data reveal the absence of induction of VAERD by early commercial vaccines in hamsters, while animals´ immune responses and protection seem to match the clinical vaccine efficacy.

Prevalence of EBV, HHV6, HCMV, HAdV, SARS-CoV-2, and Autoantibodies to Type I Interferon in Sputum from Myalgic Encephalomyelitis/Chronic Fatigue Syndrome Patients

An exhausted antiviral immune response is observed in myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) and post-SARS-CoV-2 syndrome, also termed long COVID. In this study, potential mechanisms behind this exhaustion were investigated. First, the viral load of Epstein-Barr virus (EBV), human adenovirus (HAdV), human cytomegalovirus (HCMV), human herpesvirus 6 (HHV6), and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was determined in sputum samples (n = 29) derived from ME/CFS patients (n = 13), healthy controls (n = 10), elderly healthy controls (n = 4), and immunosuppressed controls (n = 2). Secondly, autoantibodies (autoAbs) to type I interferon (IFN-I) in sputum were analyzed to possibly explain impaired viral immunity. We found that ME/CFS patients released EBV at a significantly higher level compared to controls (p = 0.0256). HHV6 was present in ~50% of all participants at the same level. HAdV was detected in two cases with immunosuppression and severe ME/CFS, respectively. HCMV and SARS-CoV-2 were found only in immunosuppressed controls. Notably, anti-IFN-I autoAbs in ME/CFS and controls did not differ, except in a severe ME/CFS case showing an increased level. We conclude that ME/CFS patients, compared to controls, have a significantly higher load of EBV. IFN-I autoAbs cannot explain IFN-I dysfunction, with the possible exception of severe cases, also reported in severe SARS-CoV-2. We forward that additional mechanisms, such as the viral evasion of IFN-I effect via the degradation of IFN-receptors, may be present in ME/CFS, which demands further studies.

GM-CBAM-ResNet: A Lightweight Deep Learning Network for Diagnosis of COVID-19

COVID-19 can cause acute infectious diseases of the respiratory system, and may probably lead to heart damage, which will seriously threaten human health. Electrocardiograms (ECGs) have the advantages of being low cost, non-invasive, and radiation free, and is widely used for evaluating heart health status. In this work, a lightweight deep learning network named GM-CBAM-ResNet is proposed for diagnosing COVID-19 based on ECG images. GM-CBAM-ResNet is constructed by replacing the convolution module with the Ghost module (GM) and adding the convolutional block attention module (CBAM) in the residual module of ResNet. To reveal the superiority of GM-CBAM-ResNet, the other three methods (ResNet, GM-ResNet, and CBAM-ResNet) are also analyzed from the following aspects: model performance, complexity, and interpretability. The model performance is evaluated by using the open 'ECG Images dataset of Cardiac and COVID-19 Patients'. The complexity is reflected by comparing the number of model parameters. The interpretability is analyzed by utilizing Gradient-weighted Class Activation Mapping (Grad-CAM). Parameter statistics indicate that, on the basis of ResNet19, the number of model parameters of GM-CBAM-ResNet19 is reduced by 45.4%. Experimental results show that, under less model complexity, GM-CBAM-ResNet19 improves the diagnostic accuracy by approximately 5% in comparison with ResNet19. Additionally, the interpretability analysis shows that CBAM can suppress the interference of grid backgrounds and ensure higher diagnostic accuracy under lower model complexity. This work provides a lightweight solution for the rapid and accurate diagnosing of COVD-19 based on ECG images, which holds significant practical deployment value.

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.

Surveillance of SARS-CoV-2 in Pets of Harris County, Texas, Revealed More Common Pet Infections in Households With Human COVID-19 Cases

Local health departments can play a critical role in zoonoses surveillance at the human-domestic animal interface, especially when existing public health services and close relationships with community groups can be leveraged. Investigators at Harris County Veterinary Public Health employed a community-based surveillance tool for identifying severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections in dogs and cats in June--December 2021. Diagnosis was made using both RT-qPCR testing of oral and nasal swabs and plaque reduction neutralization testing of serum samples. Recruitment for this free companion animal surveillance program occurred through the following two streams: case-based and event-based. The case-based stream recruited companion animals of confirmed human COVID-19 cases through the Harris County Public Health case investigations platform and used the information from epidemiological investigations of the owners to conduct further investigations of their pet(s). The event-based stream recruited companion animals participating in free or low-cost spay/neuter events at Harris County Pets Resource Center (HCPRC). A total of 97 animals were tested, with the case-based and event-based streams accounting for 36 and 61, respectively. A total of 13 animals (13.4%) tested seropositive including one that also had positive RT-qPCR swabs. Of the positives, 11 (84.6%) were associated with a confirmed human case of SARS-CoV-2 living in the same household including one household with four out of the seven animals positive for SARS-CoV-2 neutralizing antibodies. These two surveillance methods employed at the local level emphasize the importance of the One Health approach and provide a model for future zoonoses surveillance systems.

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.

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).

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.

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.

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.

Phenol-free in-house kit for RNA extraction with applicability to SARS-CoV-2 genomic sequencing studies: A contribution to biotechnological sovereignty in Colombia

During the COVID-19 pandemic, reagents for SARS-CoV-2 detection were scarce or sold at high prices, particularly in Latin America. In this study, a significant step towards self-sufficiency was achieved through the development of an in-house extraction kit for detecting SARS-CoV-2 from nasopharyngeal swab samples. The purity and concentration of the RNA extracted using the in-house kit were compared to those obtained using the GeneJET RNA Purification Kit (Thermo-Scientific®) as a reference. The applicability of the RNA extracted using the kit was evaluated using four samples positive for SARS-CoV-2 by NGS sequencing with Illumina®. There were no significant differences between the results obtained with the in-house kit and those obtained with the commercial kit. These findings confirm that the in-house protocol demonstrated satisfactory diagnostic accuracy for detecting the virus in patients with COVID-19. The in-house extraction kit works effectively, providing optimal RNA extraction for genomic characterization and lineage assignment of SARS-CoV-2 within the four positive samples analyzed. This phenol-free kit represents a local design and production achievement, offering an effective solution for RNA extraction and detection and sequencing of SARS-CoV-2 from nasopharyngeal swabs. The data highlight the essential contribution of this study to health and biotechnological sovereignty in Colombia.

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.

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.

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.

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.