A Novel Coronavirus from Patients with Pneumonia in China, 2019

Hypophysitis after COVID-19 vaccination in a patient with Rathke's cleft cyst: A case report

With the widespread vaccination of COVID-19 vaccine, a few cases have been reported that COVID-19 vaccine may cause endocrine disorders. A 59-y-old man presented with a loss of appetite after the first COVID-19 vaccination, which resolved spontaneously after 3 d. After the second COVID-19 vaccination, the symptoms including the loss of appetite, nausea, and vomiting reappeared and worsened along with loss of vision. He was found to have severe hyponatremia, and further investigations revealed secondary adrenal insufficiency, secondary hypothyroidism and Rathke's cleft cyst. The patient responded well to glucocorticoid and levothyroxine supplementation, and at 1-y follow-up the patient developed hypogonadism. We hypothesize that hypophysitis is probably induced by COVID-19 vaccine and report the rare but serious adverse reactions for early recognition and intervention.

COVID-19 vaccines: Immune correlates and clinical outcomes

Severe disease due to COVID-19 has declined dramatically as a result of widespread vaccination and natural immunity in the population. With the emergence of SARS-CoV-2 variants that largely escape vaccine-elicited neutralizing antibody responses, the efficacy of the original vaccines has waned and has required vaccine updating and boosting. Nevertheless, hospitalizations and deaths due to COVID-19 have remained low. In this review, we summarize current knowledge of immune responses that contribute to population immunity and the mechanisms how vaccines attenuate COVID-19 disease severity.

Harnessing traditional Chinese medicine polysaccharides for combatting COVID-19

With the global spread of COVID-19 posing ongoing challenges to public health systems, there is an ever-increasing demand for effective therapeutics that can mitigate both viral transmission and disease severity. This review surveys the landscape of polysaccharides derived from traditional Chinese medicine, acclaimed for their medicinal properties and potential to contribute to the COVID-19 response. We specifically focus on the capability of these polysaccharides to thwart SARS-CoV-2 entry into host cells, a pivotal step in the viral life cycle that informs transmission and pathogenicity. Moreover, we delve into the concept of trained immunity, an innate immune system feature that polysaccharides may potentiate, offering an avenue for a more moderated yet efficacious immune response against various pathogens, including SARS-CoV-2. Our comprehensive overview aims to bolster understanding of the possible integration of these substances within anti-COVID-19 measures, emphasizing the need for rigorous investigation into their potential applications and underlying mechanisms. The insights provided here strongly support ongoing investigations into the adjunctive use of polysaccharides in the management of COVID-19, with the anticipation that such findings could lead to a deeper appreciation and clearer elucidation of the antiviral potentials inherent in complex Chinese herbal remedies.

Inhibition of SARS-CoV-2 growth in the lungs of mice by a peptide-conjugated morpholino oligomer targeting viral RNA

Further development of direct-acting antiviral agents against human SARS-CoV-2 infections remains a public health priority. Here, we report that an antisense peptide-conjugated morpholino oligomer (PPMO) named 5'END-2, targeting a highly conserved sequence in the 5' UTR of SARS-CoV-2 genomic RNA, potently suppressed SARS-CoV-2 growth in vitro and in vivo. In HeLa-ACE 2 cells, 5'END-2 produced IC50 values of between 40 nM and 1.15 μM in challenges using six genetically disparate strains of SARS-CoV-2, including JN.1. In vivo, using K18-hACE2 mice and the WA-1/2020 virus isolate, two doses of 5'END-2 at 10 mg/kg, administered intranasally on the day before and the day after infection, produced approximately 1.4 log10 virus titer reduction in lung tissue at 3 days post-infection. Under a similar dosing schedule, intratracheal administration of 1.0-2.0 mg/kg 5'END-2 produced over 3.5 log10 virus growth suppression in mouse lungs. Electrophoretic mobility shift assays characterized specific binding of 5'END-2 to its complementary target RNA. Furthermore, using reporter constructs containing SARS-CoV-2 5' UTR leader sequence, in an in-cell system, we observed that 5'END-2 could interfere with translation in a sequence-specific manner. The results demonstrate that direct pulmonary delivery of 5'END-2 PPMO is a promising antiviral strategy against SARS-CoV-2 infections and warrants further development.

Intelligent mobile robot for contagious disease treatments in hospitals

This paper provides a novel and applicable work that builds a real system for disinfecting the air and surfaces of the environment in a hospital room, with a non-contact measurement system for supporting contagious disease treatments in hospitals. The system is built on an intelligent mobile robot system that operates autonomously in a simulated real treatment room. The research team uses a new positioning algorithm. It is a combination of data from the Lidar sensor, encoder, and Extended Kalman filter. The program that applies segmentation and image feature extraction algorithms is developed to meet requirements of real-time environment mapping in the room. Control algorithms for moving and avoiding obstacles are also proposed. Next, techniques for collecting health data including patient identification, body temperature, and blood oxygen index via wireless sensor network are also mentioned in the article. Analysis and experimental results show qualified outcomes and promise. The main contribution of the paper can be listed as follows.•Design and build a new CEE-IMR, an intelligent mobile robot that can regconize patients, guide and lead them walking in hospitals, especially keep a safe distance avoiding contagious deseases.•A novel framework for controlling the robot is proposed. The robot can move flexible, avoid obstacles, etc. based on advanced control algorithms. A new control mechanism is also proposed.•Methods of collecting data and processing medical data to support either patients or doctors to improve the effecency in hospitals in contagious disease management.

Waste management and disease spread potential: A case study of SARS-CoV-2 in garbage dumping sites in Bangkok and its vicinity

During the coronavirus disease 2019 (COVID-19) pandemic, hospitals and households have used personal protective equipment (PPE), such as masks and gloves. Some of these potentially infectious materials were discarded with other household wastes in garbage dumping sites. Thus, this study aimed to detect the presence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in contaminated wastes, environments, and mammals scavenging around these sites. From September to October 2022, we visited three garbage dumping sites located in Bangkok, Nakhon Pathom, and Nonthaburi provinces of Thailand. Oral, nasal, rectal swabs, and blood samples were collected from small mammals, stray dogs, and cats. Masks, gloves, soil, and water samples from the sites were additionally collected. Of the 582 samples collected from 238 animals, none tested positive for SARS-CoV-2 in the virus isolation, real-time reverse-transcription polymerase chain reaction, and neutralizing antibody detection. However, one sample (1.18 %; 1/85) from a rat (Rattus spp.) captured in Nonthaburi was serologically positive in the indirect enzyme-linked immunosorbent assay. The surveillance of coronaviruses in rats is strongly encouraged because rats may harbor different zoonotic pathogens, including unknown potentially zoonotic coronaviruses. Moreover, two face mask samples (4.65 %; 2/43) collected from the dumping site in Nakhon Pathom tested positive for SARS-CoV-2 by real-time RT-PCR. To reduce environmental contamination, detecting the SARS-CoV-2 viral genome in contaminated face masks highlights the critical need for proper waste management in households and communities in Thailand. Thus, to minimize exposure and prevent onward transmission, waste management personnel, including garbage dump staff and waste pickers, should be equipped with appropriate PPE and receive regular training on safe handling and disposal.

SARS-CoV-2 infection induces adaptive NK cell responses by spike protein-mediated induction of HLA-E expression

HLA-E expression plays a central role for modulation of NK cell function by interaction with inhibitory NKG2A and stimulatory NKG2C receptors on canonical and adaptive NK cells, respectively. Here, we demonstrate that infection of human primary lung tissue with SARS-CoV-2 leads to increased HLA-E expression and show that processing of the peptide YLQPRTFLL from the spike protein is primarily responsible for the strong, dose-dependent increase of HLA-E. Targeting the peptide site within the spike protein revealed that a single point mutation was sufficient to abrogate the increase in HLA-E expression. Spike-mediated induction of HLA-E differentially affected NK cell function: whereas degranulation, IFN-γ production, and target cell cytotoxicity were enhanced in NKG2C+ adaptive NK cells, effector functions were inhibited in NKG2A+ canonical NK cells. Analysis of a cohort of COVID-19 patients in the acute phase of infection revealed that adaptive NK cells were induced irrespective of the HCMV status, challenging the paradigm that adaptive NK cells are only generated during HCMV infection. During the first week of hospitalization, patients exhibited a selective increase of early NKG2C+CD57- adaptive NK cells whereas mature NKG2C+CD57+ cells remained unchanged. Further analysis of recovered patients suggested that the adaptive NK cell response is primarily driven by a wave of early adaptive NK cells during acute infection that wanes once the infection is cleared. Together, this study suggests that NK cell responses to SARS-CoV-2 infection are majorly influenced by the balance between canonical and adaptive NK cells via the HLA-E/NKG2A/C axis.

Binding affinity between coronavirus spike protein and human ACE2 receptor

Coronaviruses (CoVs) pose a major risk to global public health due to their ability to infect diverse animal species and potential for emergence in humans. The CoV spike protein mediates viral entry into the cell and plays a crucial role in determining the binding affinity to host cell receptors. With particular emphasis on α- and β-coronaviruses that infect humans and domestic animals, current research on CoV receptor use suggests that the exploitation of the angiotensin-converting enzyme 2 (ACE2) receptor poses a significant threat for viral emergence with pandemic potential. This review summarizes the approaches used to study binding interactions between CoV spike proteins and the human ACE2 (hACE2) receptor. Solid-phase enzyme immunoassays and cell binding assays allow qualitative assessment of binding but lack quantitative evaluation of affinity. Surface plasmon resonance, Bio-layer interferometry, and Microscale Thermophoresis on the other hand, provide accurate affinity measurement through equilibrium dissociation constants (KD). In silico modeling predicts affinity through binding structure modeling, protein-protein docking simulations, and binding energy calculations but reveals inconsistent results due to the lack of a standardized approach. Machine learning and deep learning models utilize simulated and experimental protein-protein interaction data to elucidate the critical residues associated with CoV binding affinity to hACE2. Further optimization and standardization of existing approaches for studying binding affinity could aid pandemic preparedness. Specifically, prioritizing surveillance of CoVs that can bind to human receptors stands to mitigate the risk of zoonotic spillover.

The lethal K18-hACE2 knock-in mouse model mimicking the severe pneumonia of COVID-19 is practicable for antiviral development

Animal models of COVID-19 facilitate the development of vaccines and antivirals against SARS-CoV-2. The efficacy of antivirals or vaccines may differ in different animal models with varied degrees of disease. Here, we introduce a mouse model expressing human angiotensin-converting enzyme 2 (ACE2). In this model, ACE2 with the human cytokeratin 18 promoter was knocked into the Hipp11 locus of C57BL/6J mouse by CRISPR - Cas9 (K18-hACE2 KI). Upon intranasal inoculation with high (3 × 105 PFU) or low (2.5 × 102 PFU) dose of SARS-CoV-2 wildtype (WT), Delta, Omicron BA.1, or Omicron BA.2 variants, all mice showed obvious infection symptoms, including weight loss, high viral loads in the lung, and interstitial pneumonia. 100% lethality was observed in K18-hACE2 KI mice infected by variants with a delay of endpoint for Delta and BA.1, and a significantly attenuated pathogenicity was observed for BA.2. The pneumonia of infected mice was accompanied by the infiltration of neutrophils and pulmonary fibrosis in the lung. Compared with K18-hACE2 Tg mice and HFH4-hACE2 Tg mice, K18-hACE2 KI mice are more susceptible to SARS-CoV-2. In the antivirals test, REGN10933 and Remdesivir had limited antiviral efficacies in K18-hACE2 KI mice upon the challenge of SARS-CoV-2 infections, while Nirmatrelvir, monoclonal antibody 4G4, and mRNA vaccines potently protected the mice from death. Our results suggest that the K18-hACE2 KI mouse model is lethal and stable for SARS-CoV-2 infection, and is practicable and stringent to antiviral development.

Concomitant administration of seasonal influenza and COVID-19 mRNA vaccines

Current clinical guidelines support the concomitant administration of seasonal influenza vaccines and COVID-19 mRNA boosters vaccine. Whether dual vaccination may impact vaccine immunogenicity due to an interference between influenza or SARS-CoV-2 antigens is unknown. We aimed to understand the impact of mRNA COVID-19 vaccines administered concomitantly on the immune response to influenza vaccines. For this, 128 volunteers were vaccinated during the 22-23 influenza season. Three groups of vaccination were assembled: FLU vaccine only (46, 35%) versus volunteers that received the mRNA bivalent COVID-19 vaccines concomitantly to seasonal influenza vaccines, FluCOVID vaccine in the same arm (42, 33%) or different arm (40, 31%), respectively. Sera and whole blood were obtained the day of vaccination, +7, and +28 days after for antibody and T cells response quantification. As expected, side effects were increased in individuals who received the FluCOVID vaccine as compared to FLU vaccine only based on the known reactogenicity of mRNA vaccines. In general, antibody levels were high at 4 weeks post-vaccination and differences were found only for the H3N2 virus when administered in different arms compared to the other groups at day 28 post-vaccination. Additionally, our data showed that subjects that received the FluCOVID vaccine in different arm tended to have better antibody induction than those receiving FLU vaccines for H3N2 virus in the absence of pre-existing immunity. Furthermore, no notable differences in the influenza-specific cellular immune response were found for any of the vaccination groups. Our data supports the concomitant administration of seasonal influenza and mRNA COVID-19 vaccines.

Climate change, its impact on emerging infectious diseases and new technologies to combat the challenge

ABSTRACTImproved sanitation, increased access to health care, and advances in preventive and clinical medicine have reduced the mortality and morbidity rates of several infectious diseases. However, recent outbreaks of several emerging infectious diseases (EIDs) have caused substantial mortality and morbidity, and the frequency of these outbreaks is likely to increase due to pathogen, environmental, and population effects driven by climate change. Extreme or persistent changes in temperature, precipitation, humidity, and air pollution associated with climate change can, for example, expand the size of EID reservoirs, increase host-pathogen and cross-species host contacts to promote transmission or spillover events, and degrade the overall health of susceptible host populations leading to new EID outbreaks. It is therefore vital to establish global strategies to track and model potential responses of candidate EIDs to project their future behaviour and guide research efforts on early detection and diagnosis technologies and vaccine development efforts for these targets. Multi-disciplinary collaborations are demanding to develop effective inter-continental surveillance and modelling platforms that employ artificial intelligence to mitigate climate change effects on EID outbreaks. In this review, we discuss how climate change has increased the risk of EIDs and describe novel approaches to improve surveillance of emerging pathogens that pose the risk for EID outbreaks, new and existing measures that could be used to contain or reduce the risk of future EID outbreaks, and new methods to improve EID tracking during further outbreaks to limit disease transmission.

Antibiotics daptomycin interacts with S protein of SARS-CoV-2 to promote cell invasion of Omicron (B1.1.529) pseudovirus

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has posed enormous challenges to global public health. The use of antibiotics has greatly increased during the SARS-CoV-2 epidemic owing to the presence of bacterial co-infection and secondary bacterial infections. The antibiotics daptomycin (DAP) is widely used in the treatment of infectious diseases caused by gram-positive bacteria owing to its highly efficient antibacterial activity. It is pivotal to study the antibiotics usage options for patients of coronavirus infectious disease (COVID-19) with pneumonia those need admission to receive antibiotics treatment for bacterial co-infection in managing COVID-19 disease. Herein, we have revealed the interactions of DAP with the S protein of SARS-CoV-2 and the variant Omicron (B1.1.529) using the molecular docking approach and Omicron (B1.1.529) pseudovirus (PsV) mimic invasion. Molecular docking analysis shows that DAP has a certain degree of binding ability to the S protein of SARS-CoV-2 and several derived virus variants, and co-incubation of 1-100 μM DAP with cells promotes the entry of the PsV into human angiotensin-converting enzyme 2 (hACE2)-expressing HEK-293T cells (HEK-293T-hACE2), and this effect is related to the concentration of extracellular calcium ions (Ca2+). The PsV invasion rate in the HEK-293T-hACE2 cells concurrently with DAP incubation was 1.7 times of PsV infection alone. In general, our findings demonstrate that DAP promotes the infection of PsV into cells, which provides certain reference of antibiotics selection and usage optimization for clinicians to treat bacterial coinfection or secondary infection during SARS-CoV-2 infection.

Human monoclonal antibody F61 nasal spray effectively protected high-risk populations from SARS-CoV-2 variants during the COVID-19 pandemic from late 2022 to early 2023 in China

Following the national dynamic zero-COVID strategy adjustment, the utilization of broad-spectrum nasal neutralizing antibodies may offer an alternative approach to controlling the outbreak of Omicron variants between late 2022 and early 2023 in China. This study involved an investigator-initiated trial (IIT) to assess the pharmacokinetic, safety and efficacy of the F61 nasal spray. A total of 2,008 participants were randomly assigned to receive F61 nasal spray (24 mg/0.8 mL/dose) or normal saline (0.8 mL/dose) and 1336 completed the follow-up in the IIT. Minimal absorption of F61 antibody into the bloodstream was detected in individuals receiving F61 nasal spray for seven consecutive days. No treatment-emergent adverse reactions of grade 3 severity or higher were reported. In the one-dose cohort, the 7-day cumulative SARS-CoV-2 infection rate was 79.0% in the F61 group and 82.6% in the placebo group, whereas, in the multiple-dose (once daily for 7 consecutive days) cohort, the rates were 6.55% in the F61 group and 23.83% in the placebo group. The laboratory-confirmed efficacy of F61 was 3.78% (-3.74%-10.75%) in the one-dose cohort and 72.19% (57.33%-81.87%) in the multiple-dose cohort. In the real-world study, 60,225 volunteers in four different regions were administered the F61 nasal spray based on the subject's wishes, over 90% efficacy rate was observed against different Omicron variants. The F61 nasal spray, with its favourable safety profile, could be a promising prophylactic monoclonal antibody against SARS-CoV-2 VOCs.

Safety and immunogenicity of CoronaVac in healthy adults: A prospective observational multicenter real-world study in Henan Province, China

Vaccination has emerged as the primar approach for managing the COVID-19 pandemic. Despite certain clinical trials reporting the safety and immunogenicity of CoronaVac, additional multicenter real-world studies are still necessary. In this study, we recruited 506 healthy volunteers who were not infected with COVID-19 or vaccinated. Each participant provided peripheral blood samples three times: prior to the first dose of vaccine, prior to the second dose, and 8 weeks following the second dose. Ultimately, 388 participants completed the entire follow-up process. No serious adverse events were observed among any of the participants. Within 1 week of vaccination, 13.4% of participants experienced systemic adverse reactions, with fatigue (5.93%) and dizziness (3.35%) being the most frequent. Although some clinical indicators, including creatinine, significantly changed after vaccination (p < 0.05), the mean of all altered indicators remained within the normal range. The positive rates of neutralizing antibodies (NAb), IgG, and IgM were 12.3%, 18.85%, and 5.24% prior to the second dose, respectively; and 57.99%, 86.34%, and 2.32% at 8 weeks following the second dose, respectively. Additionally, seven indicators, such as sex, age, and BMI, were significantly correlated with NAb (p < 0.05). Finally, a prediction model was developed based on age, monocytes, and alanine aminotransferase (ALT) with an AUC value of 87.56% in the train set and 80.71% in the test set. This study demonstrated that safety and immunogenicity of CoronaVac were good. The prediction model based on the baseline clinical characteristics prior to vaccination can help to develop more suitable vaccination strategies.

Exploring of N-phthalimide-linked 1,2,3-triazole analogues with promising -anti-SARS-CoV-2 activity: synthesis, biological screening, and molecular modelling studies

In this study, a library of phthalimide Schiff base linked to 1,4-disubstituted-1,2,3-triazoles was designed, synthesised, and characterised by different spectral analyses. All analogues have been introduced for in vitro assay of their antiviral activity against COVID-19 virus using Vero cell as incubator with different concentrations. The data revealed most of these derivatives showed potent cellular anti-COVID-19 activity and prevent viral growth by more than 90% at two different concentrations with no or weak cytotoxic effect on Vero cells. Furthermore, in vitro assay was done against this enzyme for all analogues and the results showed two of them have IC50 data by 90 µM inhibitory activity. An extensive molecular docking simulation was run to analyse their antiviral mechanism that found the proper non-covalent interaction within the Mpro protease enzyme. Finally, we profiled two reversible inhibitors, COOH and F substituted analogues that might be promising drug candidates for further development have been discovered.

Antidepressants and COVID-19: Increased use, occurrence in water and effects and consequences on aquatic environment. A review

The COVID-19 pandemic changed the consumption of many drugs, among which antidepressants stand out. This review evaluated the frequency of antidepressant use before and after COVID-19. Once the most consumed antidepressants were identified, detecting a variation in the frequency of consumption on the different continents, an overview of their life cycle was carried out, specifying which antidepressants are mostly detected and the places where there is a greater concentration. In addition, the main metabolites of the most used antidepressants were also investigated. A correlation between the most consumed drugs and the most detected was made, emphasizing the lack of information on the occurrence of some of the most consumed antidepressants. Subsequently, studies on the effects on aquatic life were also reviewed, evaluated through different living beings (fish, crustaceans, molluscs, planktonic crustaceans and algae). Likewise, many of the most used antidepressants lack studies on potential adverse effects on aquatic living beings. This review underscores the need for further research, particularly focusing on the life cycle of the most prescribed antidepressants. In particular, it is a priority to know the occurrence and adverse effects in the aquatic environment of the most used antidepressants after the pandemic.

Preconcentration and detection of SARS-CoV-2 in wastewater: A comprehensive review

Severe acute respiratory syndrome coronaviruses 2 (SARS-CoV-2) causing coronavirus disease 2019 (COVID-19) affected the health of human beings and the global economy. The patients with SARS-CoV-2 infection had viral RNA or live infectious viruses in feces. Thus, the possible transmission of SARS-CoV-2 through wastewater received great attentions. Moreover, SARS-CoV-2 in wastewater can serve as an early indicator of the infection within communities. We summarized the preconcentration and detection technology of SARS-CoV-2 in wastewater aiming at the complex matrices of wastewater and low virus concentration and compared their performance characteristics. We described the emerging tests that would be possible to realize the rapid detection of SARS-CoV-2 in fields and encourage academics to advance their technologies beyond conception. We concluded with a brief discussion on the outlook for integrating preconcentration and the detection of SARS-CoV-2 with emerging technologies.

Comparative Analysis of Characteristics of Patients Who Visited the Emergency Department due to Suicide Attempts During Coronavirus Disease-2019 Pandemic

The coronavirus infection 2019 (COVID-19) pandemic has affected on mental health and contributed to increased depression and anxiety. We assessed the impact of the COVID-19 pandemic on suicide-related the emergency department (ED) visits. We compared the characteristics of suicide-related patients who visited the ED between the "COVID-19 period" and the "pre-COVID-19 period". The mean age of patients was younger after COVID-19 pandemic. In comparison by age group, the proportion of patients during the COVID-19 period increased in their teens and 20s, and the rest of the age groups decreased. The proportion of patients who requested help was higher during the COVID-19. The authenticity of suicide attempts showed a higher proportion of patients during the pre-COVID-19. Therefore, during the pandemic, attention should be paid to worsening mental health problems, such as anxiety or depression, rather than the lethality of suicide attempts.

Deciphering inhibitory activity of marine algae Ecklonia cava phlorotannins against SARS CoV-2 main protease: A coupled in-silico docking and molecular dynamics simulation study

The onset of COVID-19 due to the SARS CoV-2 virus has spurred an urgent need for potent therapeutics and vaccines to combat this global pandemic. The main protease (Mpro) of the virus, crucial in its replication, has become a focal point in developing anti-COVID-19 drugs. The cysteine protease Mpro in SARS CoV-2 bears a significant resemblance to the same protease found in SARS CoV-1. Previous research highlighted phlorotannins derived from Ecklonia cava, an edible marine algae, as inhibitors of SARS CoV-1 Mpro activity. However, it remains unclear whether these marine-derived phlorotannins also exert a similar inhibitory effect on SARS CoV-2 Mpro. To unravel this, our study utilized diverse in-silico methodologies. We explored the pharmacological potential of various phlorotannins (phloroglucinol, triphloretol-A, eckol, 2-phloroeckol, 7-phloroeckol, fucodiphloroethol G, dieckol, and phlorofucofuroeckol-A) and assessed their binding efficacies alongside established Mpro inhibitors (N3 and lopinavir) through molecular docking studies. Among these compounds, five phlorotannins (eckol, 2-phloroeckol, 7-phloroeckol, dieckol, and phlorofucofuroeckol-A) exhibited potent binding affinities comparable to or surpassing N3 and lopinavir, interacting especially with the catalytic residues His41 and Cys145 of Mpro. Moreover, molecular dynamics simulations revealed that these five Mpro-phlorotannin complexes displayed enhanced stability and maintained comparable or slightly reduced compactness. They exhibited reduced conformational changes and increased expansion relative to the Mpro-N3 and/or Mpro-lopinavir complex. Our MM-GBSA analysis further supported these findings. Overall, our investigation highlights the potential of these five phlorotannins in inhibiting the proteolytic function of SARS CoV-2 Mpro, offering promise for anti-COVID-19 drug development.

Rapid and specific detection of nanoparticles and viruses one at a time using microfluidic laminar flow and confocal fluorescence microscopy

Mainstream virus detection relies on the specific amplification of nucleic acids via polymerase chain reaction, a process that is slow and requires extensive laboratory expertise and equipment. Other modalities, such as antigen-based tests, allow much faster virus detection but have reduced sensitivity. In this study, we introduce an approach for rapid and specific detection of single nanoparticles using a confocal-based flow virometer. The combination of laminar flow in a microfluidic channel and correlated fluorescence signals emerging from both free dyes and fluorescently labeled primary antibodies provide insights into nanoparticle volumes and specificities. We evaluate and validate the assay using fluorescent beads and viruses, including SARS-CoV-2 with fluorescently labeled primary antibodies. Additionally, we demonstrate how hydrodynamic focusing enhances the assay sensitivity for detecting viruses at relevant loads. Based on our results, we envision the future use of this technology for clinically relevant bio-nanoparticles, supported by the implementation of the assay in a portable and user-friendly setup.

Multi-scenario surveillance of respiratory viruses in aerosols with sub-single-copy spatial resolution

Highly sensitive airborne virus monitoring is critical for preventing and containing epidemics. However, the detection of airborne viruses at ultra-low concentrations remains challenging due to the lack of ultra-sensitive methods and easy-to-deployment equipment. Here, we present an integrated microfluidic cartridge that can accurately detect SARS-COV-2, Influenza A, B, and respiratory syncytial virus with a sensitivity of 10 copies/mL. When integrated with a high-flow aerosol sampler, our microdevice can achieve a sub-single-copy spatial resolution of 0.83 copies/m3 for airborne virus surveillance with an air flow rate of 400 L/min and a sampling time of 30 minutes. We then designed a series of virus-in-aerosols monitoring systems (RIAMs), including versions of a multi-site sampling RIAMs (M-RIAMs), a stationary real-time RIAMs (S-RIAMs), and a roaming real-time RIAMs (R-RIAMs) for different application scenarios. Using M-RIAMs, we performed a comprehensive evaluation of 210 environmental samples from COVID-19 patient wards, including 30 aerosol samples. The highest positive detection rate of aerosol samples (60%) proved the aerosol-based SARS-CoV-2 monitoring represents an effective method for spatial risk assessment. The detection of 78 aerosol samples in real-world settings via S-RIAMs confirmed its reliability for ultra-sensitive and continuous airborne virus monitoring. Therefore, RIAMs shows the potential as an effective solution for mitigating the risk of airborne virus transmission.

Associations between clinical data, vaccination status, antibody responses, and post-COVID-19 symptoms in Thais infected with SARS-CoV-2 Delta and Omicron variants: a 1-year follow-up study

BACKGROUND

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes coronavirus disease 2019 (COVID-19), led to a global pandemic from 2020. In Thailand, five waves of outbreaks were recorded, with the fourth and fifth waves driven by the Delta and Omicron variants, resulting in over 20,000 new confirmed cases daily at their peaks.

METHODS

This cross-sectional study investigated the associations between clinical symptoms, vaccination status, antibody responses, and post-COVID-19 sequelae in COVID-19 patients. Plasma samples and clinical data were collected from participants admitted to hospitals in Thailand between July 2021 and August 2022, with follow-ups conducted for one year. The study included 110 participants infected with either the Delta (n = 46) or Omicron (n = 64) variants. Virus genotypes were confirmed by RT-PCR of nasal swab RNA and partial nucleotide sequencing of the S gene. IgG and IgA antibody levels against the receptor-binding domain (RBD) of SARS-CoV-2 Delta and Omicron variants were measured in plasma samples using ELISA.

RESULTS

Pneumonia was found to be associated with Delta variant infections, while sore throat, congestion or runny nose, and headache were linked to Omicron infections. Vaccination with fewer than two doses and diabetes mellitus were significantly associated with higher disease severity. Specific IgG and IgA antibodies against the RBD of the Delta variant generally rose by day 14 and were maintained for up to two months, whereas the pattern of antibody response to the Omicron variant was less clear. Antibody risings were found to be positively associated with pneumonia, certain underlying conditions (obesity, hypertension, dyslipidemia, and diabetes mellitus), and age ≥ 60 years. Delta variant infections were associated with forgetfulness, hair loss, and headache during the 1-year post-infection period. Females were more likely to experience hair loss, forgetfulness, and joint pain, while older age was associated with joint pain.

CONCLUSIONS

This study enhances our understanding of SARS-CoV-2 infections in Thais, particularly concerning the Delta and Omicron variants. The findings can inform public health planning and response strategies for future outbreaks of SARS-CoV-2 or other emerging viral diseases.

The epithelial barrier theory and its associated diseases

The prevalence of many chronic noncommunicable diseases has been steadily rising over the past six decades. During this time, over 350,000 new chemical substances have been introduced to the lives of humans. In recent years, the epithelial barrier theory came to light explaining the growing prevalence and exacerbations of these diseases worldwide. It attributes their onset to a functionally impaired epithelial barrier triggered by the toxicity of the exposed substances, associated with microbial dysbiosis, immune system activation, and inflammation. Diseases encompassed by the epithelial barrier theory share common features such as an increased prevalence after the 1960s or 2000s that cannot (solely) be accounted for by the emergence of improved diagnostic methods. Other common traits include epithelial barrier defects, microbial dysbiosis with loss of commensals and colonization of opportunistic pathogens, and circulating inflammatory cells and cytokines. In addition, practically unrelated diseases that fulfill these criteria have started to emerge as multimorbidities during the last decades. Here, we provide a comprehensive overview of diseases encompassed by the epithelial barrier theory and discuss evidence and similarities for their epidemiology, genetic susceptibility, epithelial barrier dysfunction, microbial dysbiosis, and tissue inflammation.

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

BACKGROUND

During the coronavirus disease 19 (COVID-19) pandemic, diagnostic testing of the general population proved challenging due to limitations of the gold-standard diagnostic procedure using reverse transcription real-time polymerase chain reaction (RT-qPCR) for large-scale testing on the centralised model, especially in low-resource areas.

OBJECTIVES

To address this, a point-of-care (PoC) diagnostic protocol for COVID-19 was developed, providing fast, reliable, and affordable testing, particularly for low-mid develop areas.

METHODS

The PoC diagnostic process combines a simple paper-based RNA extraction method housed within a 3D-printed plastic device with a colorimetric reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay. Nasopharyngeal/oropharyngeal swabs (NOS) and saliva samples were tested between 2020 and 2021, with the assistance of Santa Catarina's State Health Secretary, Brazil.

FINDINGS

The developed diagnostic protocol showed a limit of detection of 9,900 copies and an overall diagnostic specificity of 98% for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from 1,348 clinical analysed samples. The diagnostic sensitivity was 95% for NOS samples, 85% for early morning saliva, and 69% for indiscriminate saliva.

MAIN CONCLUSIONS

In conclusion, the developed device successfully extracted SARS-CoV-2 viral RNA from swabs and saliva clinical samples. When combined with colorimetric RT-LAMP, it provides results within 45 min using minimal resources, thus delivering a diagnostic kit protocol that is applicable in large-scale sampling.

Pulmonary fibrosis followed by severe pneumonia in patients with COVID-19 infection requiring mechanical ventilation: a prospective multicentre study

BACKGROUNDS

The management of lung complications, especially fibrosis, after COVID-19 pneumonia, is an important issue in the COVID-19 post-pandemic era. We aimed to investigate risk factors for pulmonary fibrosis development in patients with severe COVID-19 pneumonia.

METHODS

Clinical and radiological data were prospectively collected from 64 patients who required mechanical ventilation due to COVID-19 pneumonia and were enrolled from eight hospitals in South Korea. Fibrotic changes on chest CT were evaluated by visual assessment, and extent of fibrosis (mixed disease score) was measured using automatic quantification system.

RESULTS

64 patients were enrolled, and their mean age was 58.2 years (64.1% were males). On chest CT (median interval: 60 days [IQR; 41-78 days] from enrolment), 35 (54.7%) patients showed ≥3 fibrotic lesions. The most frequent fibrotic change was traction bronchiectasis (47 patients, 73.4 %). Median extent of fibrosis measured by automatic quantification was 10.6% (IQR, 3.8-40.7%). In a multivariable Cox proportional hazard model, which included nine variables with a p value of <0.10 in an unadjusted analysis as well as age, sex and Body Mass Index, male sex (HR, 3.01; 95% CI, 1.27 to 7.11) and higher initial Sequential Organ Failure Assessment (SOFA) score (HR, 1.18; 95% CI, 1.02 to 1.37) were independently associated with pulmonary fibrosis (≥3 fibrotic lesions).

CONCLUSION

Our data suggests that male gender and higher SOFA score at intensive care unit admission were associated with pulmonary fibrosis in patients with severe COVID-19 pneumonia requiring mechanical ventilation.

The SARS-CoV-2 spike protein contains a furin cleavage site located in a short loop between antiparallel β-strands

The furin cleavage site (FCS) of the SARS-CoV-2 spike protein, which connects the S1/S2 junction, is essential for facilitating fusion with host cells. The wild-type (Wt) SARS-CoV-2 spike protein, PDB ID: 6yvb, lacks a sequence of amino acid residues, including the FCS that links the S1/S2 junction. For the first time, we demonstrated that a stretch of 14 amino acid residues (677QTNSPRRARSVASQ689) forms an antiparallel β-sheet and contains the PRRAR sequence in the FCS within a short loop. Upon comparing the loop content of the S1/S2 junction with that of Wt SARS-CoV-2 containing PRRAR in the FCS, we observed a decrease in antiparallel β-sheet content and an increase in loop content in the B.1.1.7 variant with HRRAR in the FCS. This short loop within an antiparallel β-sheet can serve as a docking site for various proteases, including TMPRSS2 and α1AT. We conducted a 300-ns simulation of the SARS-CoV-2 receptor binding domain (RBD) using several antibacterial and antiviral ligands commonly used to treat various infections. Our findings indicate that the receptor binding domain (RBD) comprising the receptor binding motif (RBM) utilizes β6 and a significant portion of the loop to bind with ligands, suggesting its potential for treating SARS-CoV-2 infections.

HLA-G neo-expression modifies genetic programs governing tumor cell lines

The development of immunotherapies has proved to be clinically encouraging to re-establish the immune function modified by the expression of immune inhibitory molecules in tumors. However, there are still patients with poor survival rates following treatment. The elucidation of molecular mechanisms triggered by the neo-expression of particular IC in tumors would constitute a major step toward better understanding tumor evolution and would help to design future clinical protocols. To this end, we investigate the modifications triggered by the neo-expression of the immune checkpoints HLA-G in ccRCC tumor cells. We demonstrate, for the first time, that HLA-G modifies key genes implicated mainly in tumor development, angiogenesis, calcium flow and mitochondria dynamics. The involvement of HLA-G on the expression of genes belonging to these pathways such as ADAM-12, NCAM1 and NRP1 was confirmed by the CRISPR/Cas9-mediated edition of HLA-G. The data reveal multifaceted roles of HLA-G in tumor cells which are far beyond the well-known function of HLA-G in the immune anti-tumor response. This warrants further investigation of HLA-G and these new partners in tumors of different origin so as to propose future new treatments to improve health patient's outcome.

Admission and outcomes of COVID-19 among chronic obstructive pulmonary diseases patients in Africa: protocol for a systematic review and meta-analysis

When the coronavirus case was originally reported in Wuhan, China, in December 2019, it quickly spread throughout the world and became a global public health problem. Evidence of the admission and outcomes of coronavirus disease among patients with chronic obstructive pulmonary disease (COPD) has not been reported in Africa. Consequently, this research protocol uses a systematic review and meta-analysis of the admission and outcomes of COVID-19 in patients with COPD in Africa. All observational studies published in the English language and reporting on the prevalence, admission and outcomes of COVID-19 among patients with COPD in Africa will be included. A search strategy will be implemented using electronic databases and the Preferred Reporting Items for Systematic Reviews and Meta-Analysis Protocol recommendations. The findings of this review will be reported to health program designers, decision-makers and healthcare providers.

An interlaboratory proficiency test using metagenomic sequencing as a diagnostic tool for the detection of RNA viruses in swine fecal material

Metagenomic shotgun sequencing (mNGS) can serve as a generic molecular diagnostic tool. An mNGS proficiency test (PT) was performed in six European veterinary and public health laboratories to detect porcine astroviruses in fecal material and the extracted RNA. While different mNGS workflows for the generation of mNGS data were used in the different laboratories, the bioinformatic analysis was standardized using a metagenomic read classifier as well as read mapping to selected astroviral reference genomes to assess the semiquantitative representation of astrovirus species mixtures. All participants successfully identified and classified most of the viral reads to the two dominant species. The normalized read counts obtained by aligning reads to astrovirus reference genomes by Bowtie2 were in line with Kraken read classification counts. Moreover, participants performed well in terms of repeatability when the fecal sample was tested in duplicate. However, the normalized read counts per detected astrovirus species differed substantially between participants, which was related to the different laboratory methods used for data generation. Further modeling of the mNGS data indicated the importance of selecting appropriate reference data for mNGS read classification. As virus- or sample-specific biases may apply, caution is needed when extrapolating this swine feces-based PT for the detection of other RNA viruses or using different sample types. The suitability of experimental design to a given pathogen/sample matrix combination, quality assurance, interpretation, and follow-up investigation remain critical factors for the diagnostic interpretation of mNGS results.

IMPORTANCE

Metagenomic shotgun sequencing (mNGS) is a generic molecular diagnostic method, involving laboratory preparation of samples, sequencing, bioinformatic analysis of millions of short sequences, and interpretation of the results. In this paper, we investigated the performance of mNGS on the detection of porcine astroviruses, a model for RNA viruses in a pig fecal material, among six European veterinary and public health laboratories. We showed that different methods for data generation affect mNGS performance among participants and that the selection of reference genomes is crucial for read classification. Follow-up investigation remains a critical factor for the diagnostic interpretation of mNGS results. The paper contributes to potential improvements of mNGS as a diagnostic tool in clinical settings.

Nationwide epidemiology and health resource use among children with COVID-19 in Japan

BACKGROUND

The COVID-19 pandemic posed substantial challenges to healthcare systems. Understanding the responses of pediatric health services is crucial for future pandemic planning and preparedness, yet such data remains limited.

METHODS

In this retrospective cohort study, we analyzed data from administrative databases developed by Japan Medical Data Center and DeSC Healthcare Inc. The dataset comprised records of 2,612,511 children, totaling 60,224,888 person-months, from January 2020 to May 2022. Multivariate generalized estimation equations were used to examine the incidence rates of COVID-19 and associated health resource use.

RESULTS

Our analysis revealed that the incidence rates of COVID-19 gradually increased from Wave I (2.2 cases per 100,000 person-months) to Wave V (177.8cases per 100,000 person-months), with a notable elevation during Wave VI (2367.7 cases per 100,000 person-months). While nucleic acid amplification tests were primarily used during Waves I-V, the use of rapid antigen tests markedly increased in Wave VI. The hospitalization rates increased gradually from 0.2 in Wave I to 10.2 events per 100,000 person-months in Wave VI, and the case-hospitalization risk decreased from 14.9% in Wave II to 0.7% in Wave VI. Additionally, we observed decreasing trends in the use of antibiotics (Wave I, 31.8%; Wave VI, 9.0%), whereas antipyretic use rose from Wave I (56.1%) to Wave VI (86.6%).

CONCLUSIONS

Our study highlighted essential changes in the nationwide pediatric healthcare system's response to the COVID-19 pandemic. These findings provide valuable insights into the future pandemic planning and preparedness.

SARS-CoV-2 replication and drug discovery

The coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has killed millions of people and continues to wreak havoc across the globe. This sudden and deadly pandemic emphasizes the necessity for anti-viral drug development that can be rapidly administered to reduce morbidity, mortality, and virus propagation. Thus, lacking efficient anti-COVID-19 treatment, and especially given the lengthy drug development process as well as the critical death tool that has been associated with SARS-CoV-2 since its outbreak, drug repurposing (or repositioning) constitutes so far, the ideal and ready-to-go best approach in mitigating viral spread, containing the infection, and reducing the COVID-19-associated death rate. Indeed, based on the molecular similarity approach of SARS-CoV-2 with previous coronaviruses (CoVs), repurposed drugs have been reported to hamper SARS-CoV-2 replication. Therefore, understanding the inhibition mechanisms of viral replication by repurposed anti-viral drugs and chemicals known to block CoV and SARS-CoV-2 multiplication is crucial, and it opens the way for particular treatment options and COVID-19 therapeutics. In this review, we highlighted molecular basics underlying drug-repurposing strategies against SARS-CoV-2. Notably, we discussed inhibition mechanisms of viral replication, involving and including inhibition of SARS-CoV-2 proteases (3C-like protease, 3CLpro or Papain-like protease, PLpro) by protease inhibitors such as Carmofur, Ebselen, and GRL017, polymerases (RNA-dependent RNA-polymerase, RdRp) by drugs like Suramin, Remdesivir, or Favipiravir, and proteins/peptides inhibiting virus-cell fusion and host cell replication pathways, such as Disulfiram, GC376, and Molnupiravir. When applicable, comparisons with SARS-CoV inhibitors approved for clinical use were made to provide further insights to understand molecular basics in inhibiting SARS-CoV-2 replication and draw conclusions for future drug discovery research.

Malnutrition independently predicts mortality at 18 months in patients hospitalised for severe acute respiratory syndrome corona virus 2 (SARS-coV-2)

RATIONALE

To investigate the association between malnutrition and patient outcome following hospitalisation for Corona Virus Disease 2019 (COVID-19).

METHODS

In April 2020, 268 adult patients (235 included in the follow-up) hospitalised for COVID-19 infection were evaluated for malnutrition risk and diagnosis using modified Nutritional Risk Screening 2002 and modified Global Leadership Initiative on Malnutrition criteria (GLIM), respectively. An 18-month follow-up was carried out to assess the incidence and the associated risk factors for death and re-hospitalization.

RESULTS

The outcome was unknown for 33 patients. Death occurred in 39% of the 235 patients included in the follow-up. The risk of death was independently associated with malnutrition risk or diagnosis of malnutrition, whereas the male sex showed a protective association. The Kaplan-Meier survival curves showed that patients with diagnosis of malnutrition had lower survival rate. The re-hospitalization rate was 31% and was negatively associated with BMI≥25, and positively associated with length of hospitalisation for COVID-19 and with cancer comorbidity.

CONCLUSIONS

In hospitalized patients for SARS-CoV-2 disease, both malnutrition risk (p = 0.050) and diagnosis of malnutrition (p = 0.047 with modified GLIM and C-reactive protein >0.5 mg/dL; p = 0.024 with modified GLIM and C-reactive protein >5 mg/dL) were predictive risk factors for mortality, whereas male sex was associated with lower risk of death. Overweight at time of hospitalization and the length of hospitalisation were respectively protective and risk factor for re-hospitalization after discharge.

Clinician Wellbeing and Mental Health Assessment Across Two Acute Care Hospitals During the COVID-19 Pandemic

OBJECTIVE

The purposes of this study were to determine whether positive work environments affect clinician wellbeing and mental health, and to identify participants' priority interventions to improve clinician wellbeing. This study was designed to determine the potential benefit of modifying the aforementioned factors for clinicians and hospitals to impact positive patient outcomes.

BACKGROUND

The SARS-CoV-2 virus pandemic has become one of the leading causes of death in the United States and worldwide, and has exacerbated widespread burnout among health care professionals. This has resulted in negative collateral implications for the stability of the clinician workforce. A Clinician Wellbeing study (CWS) was launched in two Magnet®-designated hospitals in the southeast. The CWS was part of a multi-site collaborative research project led by the Center for Health Outcomes and Policy Research (CHOPR) at the University of Pennsylvania School of Nursing.

METHOD

A cross-sectional observational study design was implemented. Data were collected through anonymous surveys of 708 registered nurses (RNs) and advanced practice providers (APPs) working in two Magnet hospitals in the southeastern United States. Each participant completed 8 surveys.

RESULTS

Clinicians' self-reported level of burnout was higher for both RNs and APPs at Emory University Hospital than Emory Saint Joseph's Hospital including intent to leave and dissatisfaction with their jobs. RNs and APPs self-reported their overall health to be good or excellent and they reported sleep quality as fair. Both groups in both hospitals indicated that they experienced anxiety, depression, and stress. The APPs reported a higher percent that their work did not leave enough time for personal and family life. Data also indicated that the primary work environment concern was related to inadequate nurse staffing.

CONCLUSIONS

The data illuminated opportunities for the two hospitals to employ continuous improvement interventions to positively transform the work environment.

COVID-19 Vaccination in Liver Cirrhosis: Safety and Immune and Clinical Responses

Introduction

Three years after the beginning of the SARS-CoV-2 pandemic, the safety and efficacy of COVID-19 vaccination in liver cirrhosis (LC) patients remain controversial. We aimed to study the safety, immunological, and clinical responses of LC patients to COVID-19 vaccination.

Methods

Prospective multicentric study in adults with LC eligible for COVID-19 vaccination, without prior known infection. Patients were followed up until the timing of a booster dose, SARS-CoV-2 infection, or death. Spike-protein immunoglobulin G antibody titers for SARS-CoV-2 at 2 weeks, 3 months, and 6 months postvaccination were assessed. Antibody titers <33.8 binding antibody units (BAU)/mL were considered seronegative and <200 BAU/mL suboptimal. Postvaccination infection and its severity were registered.

Results

We included 124 LC patients, 81% males, mean aged 61 ± 10 years, with a mean follow-up of 221 ± 26 days. Alcohol was the most common (61%) cause of cirrhosis, and 7% were under immunosuppressants for autoimmune hepatitis; 69% had portal hypertension, 42% had a previous decompensation, and 21% had a Child-Pugh-Turcotte score of B/C. The type of vaccine administrated was BNT162b2 (n = 59, 48%), ChAdOx1nCoV-19 (n = 45, 36%), mRNA-1273 (n = 14, 11%), and Ad26.COV2.S (n = 6, 5%). Eighteen percent of the patients reported adverse events after vaccination, none serious. Median [Q1; Q3] antibody titers were 1,185 [280; 2,080] BAU/mL at 2 weeks, 301 [72; 1,175] BAU/mL at 3 months, and 192 [49; 656] BAU/mL at 6 months. There were seronegative and suboptimal antibody responses in 8% and 23% of the patients at 2 weeks, 16% and 38% at 3 months, and 22% and 48% at 6 months. Older age and adenovirus vector vaccines were the only factors associated with seronegative and suboptimal responses at 2 weeks and 3 months (p < 0.05) in a multivariable logistic regression analysis. Eleven patients (9%) were infected with SARS-CoV-2 during follow-up (3.8-6.6 months postvaccination), all with mild disease. There were no differences regarding the type of vaccine, and 73% had antibody titers >200 BAU/mL at 3 months.

Conclusion

COVID-19 vaccines in patients with LC were safe, without serious adverse events. The humoral and clinical responses were similar to the reported for the general population. Humoral response was adversely impacted by older age and adenovirus vector vaccines and unrelated to the liver disease severity.

Developing a mouse model of human coronavirus NL63 infection: comparison with rhinovirus-A1B and effects of prior rhinovirus infection

Human coronavirus (HCoV)-NL63 causes respiratory tract infections in humans and uses angiotensin-converting enzyme 2 (ACE2) as a receptor. We sought to establish a mouse model of HCoV-NL63 and determine whether prior rhinovirus (RV)-A1B infection affected HCoV-NL63 replication. HCoV-NL63 was propagated in LLC-MK2 cells expressing human ACE2. RV-A1B was grown in HeLa-H1 cells. C57BL6/J or transgenic mice expressing human ACE2 were infected intranasally with sham LLC-MK2 cell supernatant or 1 × 105 tissue culture infectious dose (TCID50) units HCoV-NL63. Wild-type mice were infected with 1 × 106 plaque-forming units (PFU) RV-A1B. Lungs were assessed for vRNA, bronchoalveolar lavage (BAL) cells, histology, HCoV-NL63 nonstructural protein 3 (nsp3), and host gene expression by next-generation sequencing and qPCR. To evaluate sequential infections, mice were infected with RV-A1B followed by HCoV-NL63 infection 4 days later. We report that hACE2 mice infected with HCoV-NL63 showed evidence of replicative infection with increased levels of vRNA, BAL neutrophils and lymphocytes, peribronchial and perivascular infiltrates, and expression of nsp3. Viral replication peaked 3 days after infection and inflammation persisted 6 days after infection. HCoV-NL63-infected hACE2 mice showed increased mRNA expression of IFNs, IFN-stimulated proteins, and proinflammatory cytokines. Infection with RV-A1B 4 days before HCoV-NL63 significantly decreased both HCoV-NL63 vRNA levels and airway inflammation. Mice infected with RV-A1B prior to HCoV-NL63 showed increased expression of antiviral proteins compared with sham-treated mice. In conclusion, we established a mouse model of HCoV-NL63 replicative infection characterized by relatively persistent viral replication and inflammation. Prior infection with RV-A1B reduced HCoV-NL63 replication and airway inflammation, indicative of viral interference.NEW & NOTEWORTHY We describe a mouse model of human coronavirus (HCoV) infection. Infection of transgenic mice expressing human angiotensin-converting enzyme 2 (ACE2) with HCoV-NL63 produced a replicative infection with peribronchial inflammation and nonstructural protein 3 expression. Mice infected with RV-A1B 4 days before HCoV-NL63 showed decreased HCoV-NL63 replication and airway inflammation and increased expression of antiviral proteins compared with sham-treated mice. This research may shed light on human coronavirus infections, viral interference, and viral-induced asthma exacerbations.

Coronavirus disease 2019 vaccination effectiveness based on the 2021 Japanese dialysis registry

AIM

The effectiveness of the coronavirus disease (COVID-19) vaccine in Japanese patients undergoing haemodialysis has previously not been evaluated on a large scale. We analyzed data from the Japanese Society for Dialysis Therapy Renal Data Registry (JRDR), covering nearly all Japanese patients undergoing dialysis (~95% coverage), to examine the association between COVID-19 vaccination and infection or mortality.

METHODS

We used data from the JRDR end-of-year surveys conducted in 2020 and 2021, including information on the COVID-19 vaccination and infection months. COVID-19 infection incidence and its associated mortality rates based on vaccination status (time updated) and odds ratio (OR) (vaccinated vs. unvaccinated) were estimated monthly from April 2021, when vaccination commenced in Japan.

RESULTS

COVID-19 infection analysis included 228 865 patients (215 941 vaccinated and 12 924 unvaccinated patients at the end of 2021). The age- and sex-adjusted ORs (aORs) were significantly lower in August, September, October and November 2021, especially in September (aOR [95% confidence interval (CI)]: 0.25 [0.18-0.36]). Additional adjustments for past medical history and laboratory results rarely affected these results. Similarly, in the COVID-19-related mortality analysis with 228 731 patients, including 216 781 vaccinated and 11 950 unvaccinated at the end of 2021, COVID-19-related mortality risk was significantly lower in the vaccinated group in August, September, October and November (aOR [95% CI]: August, 0.32 [0.12-0.84], September, 0.04 [0.01-0.11]; October, 0.10 [0.01-0.81]; November, 0.05 [0.00-0.79]).

CONCLUSION

In Japanese patients undergoing haemodialysis, the first or second COVID-19 vaccine dose was significantly associated with decreased COVID-19 infection and mortality rates, suggesting its effectiveness in this population.

Influenza, SARS-CoV-2, and Their Impact on Chronic Lung Diseases and Fibrosis: Exploring Therapeutic Options

Respiratory tract infections represent a significant global public health concern, disproportionately affecting vulnerable populations such as children, the elderly, and immunocompromised individuals. RNA viruses, particularly influenza viruses and coronaviruses, significantly contribute to respiratory illnesses, especially in immunosuppressed and elderly individuals. Influenza A viruses (IAVs) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continue to pose global health threats due to their capacity to cause annual epidemics, with profound implications for public health. In addition, the increase in global life expectancy is influencing the dynamics and outcomes of respiratory viral infections. Understanding the molecular mechanisms by which IAVs and SARS-CoV-2 contribute to lung disease progression is therefore crucial. The aim of this review is to comprehensively explore the impact of IAVs and SARS-CoV-2 on chronic lung diseases, with a specific focus on pulmonary fibrosis in the elderly. It also outlines potential preventive and therapeutic strategies and suggests directions for future research.

Rapid response to a COVID-19 outbreak at a nightclub in Kagoshima prefecture, Japan, in the early phase of the COVID-19 pandemic, June and July 2020: A descriptive epidemiological study

INTRODUCTION

During COVID-19 pandemic in Japan, nightclubs were identified as high-risk locations for COVID-19 outbreaks, but an outbreak investigation in this setting is challenging because of the anonymous and opportunistic nature of interactions.

METHODS

The joint rapid response team collected epidemiological data, conducted descriptive epidemiology to determine the characteristics of cases associated with the nightclub, and implemented countermeasures. Polymerase chain reaction (PCR) tests were performed by the Local Institute of Public Health, Kagoshima University, and several commercial laboratories.

RESULTS

Between June 15 and July 20, 2020, 121 individuals tested positive for SARS-CoV-2 (59 confirmed and 62 asymptomatic) of whom 8 were nightclub staff who had no travel history of outside Kagoshima, 66 were guests, and 47 were subsequent contacts. The median age was 32 years (interquartile range: 24-43 years). One individual showed severe symptoms but there were no fatal. The epidemic curve showed one peak on June 30 and July 1 with a limited number of cases subsequently. Of the 121 cases, 116 and 5 were in individuals living in and outside Kagoshima Prefecture, respectively. Haplotype network analysis showed 5 genome-wide single-nucleotide variants between the isolates before and during this outbreak.

CONCLUSIONS

There is a possibility that unidentified guests from outside Kagoshima Prefecture could infect staff who could subsequently spread the virus to guests and other staff, who were mainly a younger population. The rapid outbreak response enabled onward transmission in the community to be minimized. This outbreak investigation could provide insights for effective responses to challenging situations in future pandemic.

Cardiovascular disease and covid-19: A systematic review

Background

Cardiovascular complications of COVID-19 are numerous and aspects of this phenomenon are not well known. The main objective of this manuscript is a systematic review of the acute and chronic cardiovascular complications secondary to COVID-19.

Methods

A systematic review of the literature through Medline via PubMed was conducted (2020-2024).

Results

There is a plethora of effects of COVID-19 on the heart in the acute setting. Here we discuss pathophysiology, myocardial infarctions, heart failure, Takotsubo Cardiomyopathy, myocardial injury, myocarditis and arrhythmias that are caused by COVID-19. Additionally, these cardiovascular injuries can linger and may be an underlying cause of some Long COVID symptoms.

Conclusions

Cardiovascular complications of COVID-19 are numerous and life-threatening. Long COVID can affect cardiovascular health. Microclotting induced by SARS-CoV-2 infection could be a therapeutic target for some aspects of Long Covid.

Exhaled Volatile Organic Compounds Detection in Pneumonia Screening: A Comprehensive Meta-analysis

BACKGROUND

Pneumonia is a common lower respiratory tract infection, and early diagnosis is crucial for timely treatment and improved prognosis. Traditional diagnostic methods for pneumonia, such as chest imaging and microbiological examinations, have certain limitations. Exhaled volatile organic compounds (VOCs) detection, as an emerging non-invasive diagnostic technique, has shown potential application value in pneumonia screening.

METHOD

A systematic search was conducted on PubMed, Embase, Cochrane Library, and Web of Science, with the retrieval time up to March 2024. The inclusion criteria were diagnostic studies evaluating exhaled VOCs detection for the diagnosis of pneumonia, regardless of the trial design type. A meta-analysis was performed using a bivariate model for sensitivity and specificity.

RESULTS

A total of 14 diagnostic studies were included in this meta-analysis. The pooled results demonstrated that exhaled VOCs detection had a combined sensitivity of 0.94 (95% CI: 0.92-0.95) and a combined specificity of 0.83 (95% CI: 0.81-0.84) in pneumonia screening, with an area under the summary receiver operating characteristic (SROC) curve (AUC) of 0.96. The pooled diagnostic odds ratio (DOR) was 104.37 (95% CI: 27.93-390.03), and the pooled positive and negative likelihood ratios (LR) were 8.98 (95% CI: 3.88-20.80) and 0.11 (95% CI: 0.05-0.22), indicating a high diagnostic performance.

CONCLUSION

This study highlights the potential of exhaled VOCs detection as an effective, non-invasive screening method for pneumonia, which could facilitate future diagnosis in pneumonia. Further high-quality, large-scale studies are required to confirm the clinical utility of exhaled VOCs detection in pneumonia screening.

STUDY REGISTRATION

PROSPERO, Review no. CRD42024520498.

The role and therapeutic potential of itaconate in lung disease

Lung diseases triggered by endogenous or exogenous factors have become a major concern, with high morbidity and mortality rates, especially after the coronavirus disease 2019 (COVID-19) pandemic. Inflammation and an over-activated immune system can lead to a cytokine cascade, resulting in lung dysfunction and injury. Itaconate, a metabolite produced by macrophages, has been reported as an effective anti-inflammatory and anti-oxidative stress agent with significant potential in regulating immunometabolism. As a naturally occurring metabolite in immune cells, itaconate has been identified as a potential therapeutic target in lung diseases through its role in regulating inflammation and immunometabolism. This review focuses on the origin, regulation, and function of itaconate in lung diseases, and briefly discusses its therapeutic potential.

Evaluating the Impact of Different Education Methods on Cleft Lip and Palate Anatomy Training

OBJECTIVE

To compare the effects of different educational methods on short and long-term learning outcomes and to investigate the satisfaction and perception of cleft lip and palate (CLP) education among dental students.

DESIGN

The theoretical exam on CLP to determine their baseline level of knowledge was taken by the participants(T0). After the exam, the students were randomly divided into three groups and all students attended a lecture-based traditional education on CLP. Students in the first group (n = 40) received no additional teaching (Group A). Students in the second group (n = 38) received model teaching with 3D-printed models (Group B). The third group (n = 39) was trained in e-learning-supported education (Group C). The theoretical exam was repeated immediately after the education (T1/short-term learning), one week later (T2/early long-term learning), and one month later (T3/late long-term learning), and the effect of the education methods on information level was assessed. In addition, a post-training satisfaction questionnaire was administered to participants of Group B and Group C.

RESULTS

Both 3D model-based and e-learning-supported approaches significantly improved immediate knowledge of CLP. However, no significant differences were found in knowledge retention over time between the all methods. A majority of students favored the incorporation of both methods in orthodontic education.

CONCLUSIONS

While both 3D models and e-learning effectively enhance short-term CLP knowledge among dental students, their long-term educational impacts are comparable. However, student preferences indicated that the use of 3D-printed models and e-learning strategies may be useful augmentations to traditional lecture education.

The collateral effects of COVID-19 on coastal and marine environments

The COVID-19 pandemic has generated a global health and economic crisis, significantly impacting coastal and marine environments. Lockdowns and restrictions, while necessary for public health, led to both positive and negative environmental consequences. Reduced human activity resulted in decreased pollution and habitat disruption, allowing for ecosystem recovery and improved water quality. However, the surge in single-use plastics and personal protective equipment (PPE) during the pandemic exacerbated plastic pollution. Additionally, the economic downturn severely affected coastal communities reliant on tourism and fisheries, highlighting the need for sustainable recovery strategies. This Special Issue explores these collateral effects, emphasizing the importance of adaptive management and resilient governance in safeguarding coastal and marine ecosystems against future crises.

Metabolic changes assessed by 1H MR spectroscopy in the corpus callosum of post-COVID patients

OBJECTIVE

Many patients with long COVID experience neurological and psychological symptoms. Signal abnormalities on MR images in the corpus callosum have been reported. Knowledge about the metabolic profile in the splenium of the corpus callosum (CCS) may contribute to a better understanding of the pathophysiology of long COVID.

MATERIALS AND METHODS

Eighty-one subjects underwent proton MR spectroscopy examination. The metabolic concentrations of total N-acetylaspartate (NAA), choline-containing compounds (Cho), total creatine (Cr), myo-inositol (mI), and NAA/Cho in the CCS were statistically compared in the group of patients containing 58 subjects with positive IgG COVID-19 antibodies or positive SARS-CoV-2 qPCR test at least two months before the MR and the group of healthy controls containing 23 subjects with negative IgG antibodies.

RESULTS

An age-dependent effect of SARS-CoV-2 on Cho concentrations in the CCS has been observed. Considering the subjective threshold of age = 40 years, older patients showed significantly increased Cho concentrations in the CCS than older healthy controls (p = 0.02). NAA, Cr, and mI were unchanged. All metabolite concentrations in the CCS of younger post-COVID-19 patients remained unaffected by SARS-CoV-2. Cho did not show any difference between symptomatic and asymptomatic patients (p = 0.91).

DISCUSSION

Our results suggest that SARS-CoV-2 disproportionately increases Cho concentration in the CCS among older post-COVID-19 patients compared to younger ones. The observed changes in Cho may be related to the microstructural reorganization in the CCS also reported in diffusion measurements rather than increased membrane turnover. These changes do not seem to be related to neuropsychological problems of the post-COVID-19 patients. Further metabolic studies are recommended to confirm these observations.

Application of the second-generation sequencing technology of metagenomics in the detection of pathogens in respiratory patients

OBJECTIVE

To explore the application value of the second-generation metagenomic next-generation sequencing (mNGS) in the detection of pathogens in patients with pulmonary infection.

METHODS

We conducted a retrospective analysis of 65 pulmonary infection cases treated at our institution and the Fifth People's Hospital of Shanghai between January 2021 and May 2023. All subjects were subjected to mNGS, targeted next-generation sequencing (tNGS), and conventional microbiological culture. A comparative analysis was performed to evaluate the diversity and quantity of pathogens identified by these methodologies and to appraise their respective diagnostic capabilities in pulmonary infection diagnostics.

RESULTS

The mNGS successfully identified etiological agents in 60 of the 65 cases, compared to tNGS, which yielded positive results in 42 cases, and conventional laboratory cultures, which detected pathogens in 24 cases. At the bacterial genus level, mNGS discerned 9 genera, 11 species, and 92 isolates of pathogenic bacteria, whereas tNGS identified 8 genera, 8 species, and 71 isolates. Conventional methods were less sensitive, detecting only 6 genera, 7 species, and 33 isolates. In terms of fungal detection, mNGS identified 4 fungal species, tNGS detected 4 isolates of the Candida genus, and conventional methods identified 2 isolates of the same genus. Viral detection at the species level revealed 10 species and 46 isolates by mNGS, whereas tNGS detected only 3 species and 7 isolates. The area under the receiver operating characteristic curve (AUC) with 95% confidence intervals for diagnosing pulmonary infections was 0.818 (0.671 to 0.966) for mNGS, 0.668 (0.475 to 0.860) for tNGS, and 0.721 (0.545 to 0.897) for conventional culture.The mNGS demonstrates superior diagnostic efficacy and pathogen detection breadth in critically ill patients with respiratory infections, offering a significant advantage by reducing the time to diagnosis. The enhanced sensitivity and comprehensive pathogen profiling of mNGS underscore its potential as a leading diagnostic tool in clinical microbiology.

Programmable and ultra-efficient Argonaute protein-mediated nucleic acid tests: A review

With the attributes of high sensitivity, single-base resolution, multiplex detection capability, and programmability upon nucleic acid recognition, Argonaute (Ago)-based biosensing assays are increasingly recognized as one of the most promising tools for precise identification and quantification of target analytes. Employed as highly specific sequence recognition elements of these robust diagnostic methods, Agos are revolutionizing how nucleic acid targets are detected. A systematic and comprehensive summary of this emerging and rapid-advancing technology is necessary to give play to the potential of Ago-based biosensing assays. The structure and function of Agos were briefly overviewed at the beginning of the work, followed by a review of the recent advancements in employing Agos sensing for detecting various targets with a comprehensive analysis such as viruses, tumor biomarkers, pathogens, mycoplasma, and parasite. The significance and benefits of these platforms were then deliberated. In addition, the authors shared subjective viewpoints on the existing challenges and offered relevant guidance for the future progress of Agos assays. Finally, the future research outlook regarding Ago-based sensing in this field was also outlined. As such, this review is expected to offer valuable information and fresh perspectives for a broader group of researchers.

An IGHG1 variant exhibits polarized prevalence and confers enhanced IgG1 antibody responses against life-threatening organisms

Evolutionary pressures sculpt population genetics, whereas immune adaptation fortifies humans against life-threatening organisms. How the evolution of selective genetic variation in adaptive immune receptors orchestrates the adaptation of human populations to contextual perturbations remains elusive. Here, we show that the G396R coding variant within the human immunoglobulin G1 (IgG1) heavy chain presents a concentrated prevalence in Southeast Asian populations. We uncovered a 190-kb genomic linkage disequilibrium block peaked in close proximity to this variant, suggestive of potential Darwinian selection. This variant confers heightened immune resilience against various pathogens and viper toxins in mice. Mechanistic studies involving severe acute respiratory syndrome coronavirus 2 infection and vaccinated individuals reveal that this variant enhances pathogen-specific IgG1+ memory B cell activation and antibody production. This G396R variant may have arisen on a Neanderthal haplotype background. These findings underscore the importance of an IGHG1 variant in reinforcing IgG1 antibody responses against life-threatening organisms, unraveling the intricate interplay between human evolution and immune adaptation.