SARS-CoV-2 Omicron variant: recent progress and future perspectives

Trends in Group A Streptococcus Pharyngitis and Co-Infection with Severe Acute Respiratory Syndrome Coronavirus 2: A Retrospective Observational Study

Background and Objectives: Group A Streptococcus (GAS) is a leading cause of acute pharyngitis with seasonal outbreaks. The coronavirus disease 2019 (COVID-19) pandemic significantly altered respiratory infection trends; however, its impact on GAS pharyngitis (GAS-P) incidence remains unclear. Additionally, data on co-infections with GAS and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are limited. In this study, temporal trends in GAS-P incidence and characteristics of GAS-SARS-CoV-2 co-infections in Japan were examined. Materials and Methods: In this observational study, data from patients who visited the Tokyo Shinagawa Hospital between January 2019 and December 2024 were retrospectively analyzed. Data on GAS and SARS-CoV-2 test results and patient demographics were extracted from medical records. The study period was categorized based on COVID-19-related public health measures as follows: pre-COVID-19 social period (January 2019-April 2020), restricted social period (May 2020-April 2023), and post-restriction period (May 2023-December 2024). GAS incidence stratified by sex, age, and period was calculated. Clinical characteristics of patients co-infected with GAS and SARS-CoV-2 were analyzed. Results: Among 4837 GAS tests, 463 (9.6%) were positive. GAS positivity rates varied significantly: 11.4% (pre-COVID-19), 7.1% (restricted social period), and 12.6% (post-restriction period; p < 0.001). The proportion of pediatric cases decreased significantly during the restricted social period (24.8-5.3%) before rising sharply in the post-restriction period (47.1%, p < 0.001). Among 151 patients tested for GAS and SARS-CoV-2, 14 (9.3%) had co-infections, which were identified exclusively after July 2022. Most patients exhibited mild symptoms, primarily fever and sore throat, with decreased lymphocyte counts despite normal white blood cell counts. Conclusions: In our cohort, the incidence of GAS pharyngitis temporarily declined during COVID-19-related public health measures and subsequently increased, particularly among children, after restrictions were lifted. Limited testing may contribute to the underdiagnosis of GAS-SARS-CoV-2 co-infections. Further large-scale studies are warranted to assess microbial interactions, disease severity, and long-term outcomes.

Perioperative SARS-CoV-2 infection and postoperative complications: a single-centre retrospective cohort study in China

OBJECTIVE

To explore the association between perioperative SARS-CoV-2 infection and the postoperative complications during the breakout of the Omicron epidemic wave.

DESIGN

Observational retrospective cohort study. Multivariable logistic regression was performed to explore the association between the duration from surgery to COVID-19 diagnosis and the likelihood of postoperative complications.

SETTING

A general hospital in China.

PARTICIPANTS

7927 patients aged 18 years and older who underwent surgical treatment between 1 December 2022 and 28 February 2023.

PRIMARY OUTCOME MEASURES

The outcome was a composite of postoperative adverse events that occurred within the initial 30 postoperative days.

RESULTS

Of all patients, 420 (11.76%) experienced postoperative complications. Compared with No COVID-19, preoperative COVID-19 within 1 week (pre-1w) exhibited a high risk of postoperative complications (adjusted OR (aOR), 2.67; 95% CI 1.50 to 4.78), followed by patients with pre-2w (aOR, 2.14; 95% CI 1.20 to 3.80). For patients with postoperative COVID-19 within 1 week (post-1w), the aOR was 2.48 (95% CI 1.48 to 4.13), followed by patients with post-2w (aOR 1.95; 95% CI 1.10 to 3.45), and those with post-3w (aOR 2.25; 95% CI 1.27 to 3.98). The risks of postoperative complications decreased roughly with the increase of the time interval between the surgery date and SARS-CoV-2 infection. Stratification analyses suggested that perioperative COVID-19 increased the risk of postoperative complications in older patients, smokers, those with comorbidities or experiencing moderate or severe COVID-19 symptoms.

CONCLUSIONS

Our findings reveal a significant time-dependent relationship between perioperative COVID-19 and postoperative complications, highlighting the importance of tailored preoperative risk evaluations, enhanced postoperative surveillance, and the implementation of effective postoperative COVID-19 prevention measures.

TRIAL REGISTRATION NUMBER

ChiCTR2300072473.

Virus-specific host responses and gene signatures following infection with major SARS-CoV-2 variants of concern: role of ZBP1 in viral clearance and lung inflammation

SARS-CoV-2 can cause severe lung damage due to uncontrolled viral replication or/and excessive inflammation. New variants of concern (VOCs) have raised additional concerns due to disparate pathogenicity and possible enhanced virulence. Herein, using RNA sequencing, we performed a comparative transcriptomic analysis following infection with major VOCs. We evaluated the transcriptional changes induced in the lungs of K18-hACE2 mice following infection with the ancestral B.1 lineage (Wuhan), B.1.1.7 (Alpha), B.1.351 (Beta), B.1.617.2 (Delta), B.1.1.529 (Omicron) variants or mouse-adapted SARS-CoV-2 (MA10). Our work reveals the molecular basis of pathological hallmarks in the lungs associated with SARS-CoV-2 infection. We report that infection with B.1, pre-Omicron VOCs, and MA10 induce similar molecular fingerprints of excessive lung inflammation and immune activation in K18-hACE2 mice. Analysis of differentially expressed genes revealed both shared and variant-specific responses, with key immune markers such as Cxcl10, Zbp1, Ifit3, Isg15, Rsad2, and Irf7 consistently upregulated across variants. Clustering of highly variable genes across samples revealed two variant groups distinguished by upregulation of antigen presentation and immune-related genes (e.g. Retnla, Saa3, Plac8, Ly6c2, H2-D1, and H2-K1). Delta, Beta, Alpha, and MA10 showed elevated expression, whereas Wuhan and Omicron exhibited attenuated responses. In addition, we show that Z-DNA-binding protein 1 (ZBP1) plays a role in viral clearance in the lungs after SARS-CoV-2 infection. ZBP1 deficiency resulted in reduced expression of cell death-associated markers and virus-induced cell death in the lungs following MA10 infection. Furthermore, the knockout of ZBP1 resulted in an attenuated inflammatory response with reduced production of proinflammatory cytokines and chemokines and decreased macrophage infiltration in the lungs. These results suggest that ZBP1 plays a role in viral clearance and in enhancing the inflammatory response and virus-induced cell death during SARS-CoV-2 infection. Altogether, our study provides insights into the pathogenesis of SARS-CoV-2 infection in mice, facilitating the identification of biomarkers and the development of potential therapeutic targets.

Rapid antigen test based on gold nanoparticles embedded with highly sensitive surface-enhanced Raman scattering probes for detecting antigen concentrations below the visual detection limit

The COVID-19 pandemic has proven that people expect medically high accuracy, sensitivity, and rapid testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection. These needs have led to developing various testing methods and platforms to replace reverse transcription polymerase chain reaction (RT-PCR), the golden standard in diagnostics. Rapid antigen testing (RAT) using gold nanoparticles (AuNPs) has been developed to compensate for the shortcomings of RT-PCR. However, RAT still shows less sensitive results because it is judged by sight only. Here, we applied gold-nanobridged nanogap particles (Au-NNPs) to conventional lateral flow assay (LFA) technology for high-sensitivity testing of samples containing antigen concentration below the visual detection limit through surface-enhanced Raman scattering (SERS) signal detection. By using Raman dye-embedded Au-NNPs showing susceptible Raman signals instead of simply using gold nanoparticles, the sensitivity of the conventional RAT has been significantly increased. Therefore, it was possible to increase the sensitivity of RAT combined with simplicity and rapidity of the approach. These developments will lead to characterization applications of bio-nanotechnology and nanoparticles for health and social issues.

Comprehensive preclinical characterization of IPB29, a pan-coronavirus fusion inhibitor under clinical trials

IPB29 is a lipopeptide-based coronavirus fusion inhibitor with the potent, broad-spectrum antiviral activity, and it has already been advanced to phase III clinical trials for the treatment of SARS-CoV-2 infection. We recently reported its design strategy and initial preclinical characterization; herein, we focused on characterizing its efficacies against newly-emerged Omicron variants, as well as its chronic general toxicity, toxicokinetics, immunogenicity, and reproductive toxicity in animal models. As anticipated, IPB29 demonstrated improved activity in inhibiting JN.1 and KP.2 variants, effectively blocking cell fusion and pseudovirus infections. Nebulized inhalation of IPB29 exhibited high therapeutic efficacy against live BA.5 and EG.5.1 infections in Syrian hamsters. The 26-week toxicity studies revealed that nebulized IPB29 has a favorable safety profile, with well-characterized toxicokinetics in SD rats and Beagle dogs. Notably, short-term nebulization of IPB29 did not elicit anti-drug antibody (ADA) responses in either species. However, IPB29-specific antibodies were detected after long-term administration. Finally, a three-stage reproductive toxicity study in SD rats indicated that IPB29 had no significant toxic effects on fertility, embryo-fetal development, or the development of offspring. In summary, our findings demonstrate that IPB29 is a safe and effective SARS-CoV-2 inhibitor with promising potential for clinical applications.

The COVID-19 Infection Did Not Aggravate the Mortality of Long-Term Care Facility Residents Under Strict Infection Control and with Immediate Anti-Viral Treatment: Real-World Analysis

BACKGROUND

Long-term care facilities (LTCFs) remain highly vulnerable to COVID-19. Despite reduced virulence, Omicron's high transmissibility poses ongoing risks. The effect of infection under strict control measures and early antiviral treatment remains unclear.

METHODS

We conducted a retrospective cohort study in a 450-bed LTCF, which implemented rigorous infection control and early antiviral use, evaluating survival outcomes during repeated Omicron outbreaks from January 2022 to December 2023 using Cox regression with time-dependent covariates, adjusted for age, sex, comorbidities, and vaccination status. Mortality trends were also compared across three periods: pre-COVID-19 (2018-2019), COVID-19 present in Japan but absent in our facility (2020-2021), and the Omicron outbreak period (2022-2023).

RESULTS

Among 623 residents, 253 were infected. Mortality was lower in the infected group than in the uninfected group (16% vs. 26%), and infection was not significantly associated with increased mortality (HR = 1.36; 95% CI: 0.91-2.04; p = 0.14). Although stratified analysis showed higher mortality among infected females, overall mortality during the outbreak period was unexpectedly lower than in prior periods.

CONCLUSIONS

In LTCFs with rigorous infection control and early antiviral use, Omicron infection did not raise mortality. Enhanced protocols may have improved survival, even among uninfected residents.

VCL/ICAM-1 pathway is associated with lung inflammatory damage in SARS-CoV-2 Omicron infection

SARS-CoV-2 variants present diverse clinical manifestations, necessitating deeper insights into their pathogenic effects. This study employs multi-omics approaches to investigate the molecular mechanisms underlying SARS-CoV-2 infection, focusing on vascular damage. Plasma proteomic analysis of unvaccinated participants infected with Omicron BA.2.76 or ancestral variants identifies key signaling pathways associated with endothelial dysfunction, with the vinculin (VCL) pathway emerging as a hallmark of Omicron infections, contributing to lung exudation. Metabolomic analysis of plasma samples from the same cohort reveals disruptions in immune function, cell membrane integrity, and metabolic processes, including altered tricarboxylic acid cycle and glycolysis pathways. An integrated analysis of proteomic and metabolomic data underscores the role of VCL in inflammation and extravasation, highlighting its interactions with adhesion molecules and inflammatory metabolites. A validation cohort of plasma samples from Omicron-infected participants confirms this association by replicating proteomic analysis, showing elevated VCL levels correlated with inflammatory markers. Functional studies in a male rat model of lung injury demonstrate that anti-VCL intervention reduces plasma VCL levels, mitigates alveolar edema, and restores alveolar-capillary barrier integrity, as assessed by histological staining and electron microscopy, thereby illustrating VCL modulation's impact on vascular leakage and extravasation. These findings establish VCL as a potential therapeutic target for mitigating vascular complications in SARS-CoV-2 infections.

Relationship between multimorbidity, SARS-COV-2 infection and long COVID: a cross-sectional population-based French survey

BACKGROUND

Understanding the risks of COVID-19-related consequences for vulnerable groups such as people with multimorbidity is crucial to better tailor health care and public health measures. The main objective of this study was to explore the association between multimorbidity and WHO-defined post-COVID condition (PCC), while also considering the association with SARS-COV-2 infection given that the infection is a prerequisite of PCC.

METHODS

This population-representative cross-sectional study was conducted in the general adult population in mainland France between 29 August and 31 December 2022 (N = 1813). The analyses of the association between multimorbidity (defined as disease count and most prevalent dyads/triads) and PCC or SAR-COV-2 infection were adjusted for age, sex, socioeconomic variables and number of infections (for PCC only) using adjusted Poisson regression with robust variance.

RESULTS

The study population had a mean age (SD) of 53 (± 18.5) years, while 53.6% were women. The likelihood of SARS-COV-2 infection increased with disease count but was only significant for ≥ 4 diseases. Five dyads and one triad presented a higher risk; almost all included anxiety. The likelihood of PCC increased with disease count, prevalence ratios (PRs) (95% CI) for 1, 2-3 and ≥ 4 diseases versus 0 were 1.90 (1.16-3.13), 3.32 (2.07-5.35) and 5.65 (3.41-9.38), respectively, and for 19 of 26 most prevalent dyads and the triad. The association was strongest for cardiac rhythm disorder and either low back pain (PR (95%CI) 4.17 (2.03-8.53)) or anxiety (PR (95%CI) 3.73 (1.98-7.01)).

CONCLUSIONS

Multimorbidity, most frequently in combination with anxiety or low back pain, presented a significant association with PCC beyond that of SARS-CoV-2 infection underscoring the importance of implementing strategies to prevent and manage persistent symptoms in vulnerable groups.

Long-term effects of SARS-CoV-2 infection on metal homeostasis

The outbreak of COVID-19 pandemic has caused substantial health loss worldwide, and the long-term sequelae of COVID, resulting from repeated coronavirus infection, have emerged as a new public health concern. We report the widespread presence of abnormal metallomic profiles in the sera of patients who have recovered from SARS-CoV-2 coronavirus infection, even after 6 months post-discharge from hospital. We measured the concentrations of Fe, Cu, Zn, Se, Cr, Mn, Ba, Ni, Pb, Ag, As, Cd, Co, and V in the sera of 25 recovered participants and 38 healthy controls in the cross-sectional study. Higher concentrations of Cu, Ag, As, Ba, Cd, Ni, Pb, Cr and V were observed in the recovered participants, whereas lower concentrations of Fe and Se were obtained in these participants. Except for Zn, Mn, and Co, all other elements showed significant differences (p < 0.05) between the two groups, with variations dependent on age and gender. Further correlation analysis between metallome and metabolome indicated that SARS-CoV-2 infection continues to disrupt metallic homeostasis and affect metabolic processes, such as lipid metabolism and cell respiration, as well as the functions of certain organs (e.g., liver, kidney, and heart), even after 6 months recovery. Our findings provide novel insights into the potential long-term effect of COVID-19 on the human body from a new perspective of metallomics.

Characteristics of Children Hospitalized for Acute COVID-19 in France From February 2020 to December 2023

We describe the characteristics of children hospitalized for coronavirus disease 2019 in France with a focus on the post-BA.1 Omicron period (February 2022-December 2023). We identified 3 main groups of children: those ≤90 days old (44.8%), older children with comorbidities (22.1%) and children with multisystem inflammatory syndrome (5.2%). Low vaccination coverage in these groups suggests that this burden could be alleviated with immunization.

Comparison of the pathogenicity and neutrophil and monocyte response between SARS-CoV-2 prototype and Omicron BA.1 in a lethal mouse model

BACKGROUND

SARS-CoV-2, first identified in late 2019, has given rise to numerous variants of concern (VOCs), posing a significant threat to human health. The emergence of Omicron BA.1.1 towards the end of 2021 led to a pandemic in early 2022. At present, the lethal mouse model for the study of SARS-CoV-2 needs supplementation, and the alterations in neutrophils and monocytes caused by different strains remain to be elucidated.

METHODS

Human ACE2 transgenic mice were inoculated with the SARS-CoV-2 prototype and Omicron BA.1, respectively. The pathogenicity of the two strains was evaluated by observing clinical symptoms, viral load and pathology. Complete blood count, immunohistochemistry and flow cytometry were performed to detect the alterations of neutrophils and monocytes caused by the two strains.

RESULTS

Our findings revealed that Omicron BA.1 exhibited significantly lower virulence compared to the SARS-CoV-2 prototype in the mouse model. Additionally, we observed a significant increase in the proportion of neutrophils late in infection with the SARS-CoV-2 prototype and Omicron BA.1. We found that the proportion of monocytes increased at first and then decreased. The trends in the changes in the proportions of neutrophils and monocytes induced by the two strains were similar.

CONCLUSION

Our study provides valuable insights into the utility of mouse models for simulating the severe disease of SARS-CoV-2 prototype infection and the milder manifestation associated with Omicron BA.1. SARS-CoV-2 prototype and Omicron BA.1 resulted in similar trends in the changes in neutrophils and monocytes.

The attitude of the unvaccinated children's parents toward pediatric COVID-19 vaccination in Tabriz, Iran

BACKGROUND

The COVID-19 vaccination has played a crucial role in combating the pandemic, yet vaccine hesitancy remains a significant barrier to achieving herd immunity. This challenge is particularly pronounced in specific cultural and geographic contexts. Understanding the reasons for parental reluctance to vaccinate their children is essential for developing effective public health strategies. This study aimed to assess the attitudes of parents with unvaccinated children aged 5-12 years toward COVID-19 vaccination and to explore their reasons for not vaccinating their children, despite having access to vaccination programs, in Tabriz, Iran.

METHOD

This cross-sectional study, conducted between March and August 2022 in Tabriz. A random sample of 400 parents was selected from five healthcare centers using a cluster sampling method in conjunction with the Iranian SIB system. To gather data, a questionnaire was developed based on a comprehensive literature review and interviews with local parents. The questionnaire's content validity was established through expert review, and its internal consistency reliability was assessed, yielding a Cronbach's alpha of 0.85, indicating good reliability. Statistical analysis was performed using one-way ANOVA, chi-square, and Fisher's exact tests to explore associations between demographic factors and vaccine hesitancy. Multiple logistic regression was employed to identify significant predictors of parents' reluctance to vaccinate their children. Additionally, the reasons for unwillingness were reported for hesitant and unwilling parents and compared using the chi-square test.

RESULT

Out of 400 parents of unvaccinated children, 263 parents (65.8%) were definitely unwilling, 21 (5.3%) were hesitant, and 116 (29.0%) were accepting to vaccinate their children against COVID-19. The analysis revealed that parents of children with underlying diseases were more hesitant or unwilling to vaccinate (OR = 1.77, (95% CI: (0.93, 3.42), P-value = 0.07). Additionally, mothers were more hesitant or unwilling than fathers (OR = 2.24, 95% CI: (1.42, 3.53), P-value = 0.001). The top three concerns among the unwilling and hesitant parents were the side effects of COVID-19 vaccination for children (reported by over 81.0%), the perception that vaccination could decrease the disease process (over 46.0%), and the lack of valid information about the side effects (above 42.9%). Furthermore, an important reason for unwillingness among unwilling parents was a lack of trust in the available vaccines (40.5%).

CONCLUSION

Parents' willingness to vaccinate their children against COVID-19 in Tabriz was low, primarily due to concerns about the potential side effects of the vaccine. To address this issue, culturally sensitive public health campaigns should be designed that specifically target these concerns and involve trusted community figures. These initiatives could help reduce vaccine hesitancy, particularly among mothers and parents of children with underlying health conditions.

Identification of aberrant interferon-stimulated gene associated host responses potentially linked to poor prognosis in COVID-19 during the Omicron wave

BACKGROUND

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron has demonstrated decreased pathogenicity, yet a few individuals suffer severe pneumonia from coronavirus disease 2019 (COVID-19) infection; the underlying mechanisms are unknown.

METHODS

The present work investigated the role of Interferon-stimulated genes (ISGs) in the occurrence and progression of severe Omicron infection. The expression and dynamic changes of ISGs were assessed using quantitative real-time polymerase chain reaction (qRT-PCR), and the anti-ISG15 autoantibody in infected patients was detected by ELISA. Moreover, we evaluated the correlation of ISGs with disease severity and outcomes by comparing expression of ISGs among each group.

RESULTS

Decreased expression of several ISGs such as IFI6 are potentially linked to increased severity or poor outcomes of Omicron infection. Longitudinal data also demonstrates that the dynamic variation of IFI6 in the Omicron infection phase may be linked to the prognosis of the disease. The increase of anti-ISG15 autoantibody potentially links to the disease progression and poor outcome of patients with high level of ISG15 expression.

CONCLUSIONS

These findings define aberrant Interferon-stimulated gene associated host responses and reveal potential mechanisms and therapeutic targets for Omicron or other viral infection.

Comparative spatial-temporal analysis of SARS-CoV-2 lineages B.1.1.33 and BQ.1.1 Omicron variant across pandemic phases

The evolution of COVID-19 pandemic has been characterized by the rapid emergence of new SARS-CoV-2 variants, each of which poses unique challenges to public health. This study analyzes the dispersion profiles during the Pre-Omicron and Post-Omicron phases in different epidemiological contexts. The Brazilian state of Espirito Santo, despite its low population density, plays a critical role as a commercial hub due to its intense port activity, which may have contributed to COVID-19 cases and mortality rates being higher than the national average. The state recorded 34,000 confirmed cases and 377 deaths per 100,000 inhabitants. Genomic surveillance revealed that the Pre-Omicron phase was dominated by the B.1.1.33 lineage, characterized by localized intraregional circulation. In contrast, the Post-Omicron phase, dominated by the BQ.1.1 lineage, exhibited greater diversity in circulating lineages, increased international interactions, and rapid viral dissemination, highlighting distinct transmission dynamics between such periods. This study highlights the need for adaptive public health strategies that account for both viral behavior and regional socioeconomic factors, while highlighting the strategic importance of Espirito Santo in monitoring SARS-CoV-2 evolution.

Postoperative cardiopulmonary complications in children with preoperative Omicron SARS-CoV-2 variants infection: a single-center retrospective cohort study

OBJECTIVE

The purpose of this study was to investigate: (1) the incidence of cardiopulmonary complications within 30 days after surgery in pediatric patients with preoperative Omicron variants infection, (2) the mortality, and (3) their possible risk factors.

METHODS

This retrospective study included a consecutive patient cohort who underwent elective non-cardiac surgery for any indication in the Pediatric Department of our hospital between November 2022 and February 2023. Cardiopulmonary complications and mortality within 30 days after surgery were compared between patients with pre-operative SARS-CoV-2 infection (Omicron variants infected group) and those without infection (the uninfected group) within 90-day before the surgery. The study evaluated the demographic data and related clinical factors of complications by analyzing their clinical records.

RESULTS

Our study included 502 patients, of which 194 (38.65%) had a pre-operative Omicron variants diagnosis. The mean duration between definite Omicron variants infection and surgery was 31.28 ± 10.19 days. In our study, the incidence of pulmonary complications was 1.59% (8/502 patients), no cardiac complication or mortality was found in the 30-day postoperative follow-up. The Omicron variants infected group had a significantly higher incidence of complications (7/194, 3.61%) compared to the uninfected group (1/308, 0.32%) (p = 0.006). After adjusted for other factors, it was found that the Omicron variants infection within 4 weeks before surgery (OR = 17.84, 95% CI: 1.25-255.35, p = 0.034), higher BMI (OR = 1.26, 95% CI: 1.02-1.55, p = 0.034), ASA physical status grade III-V (OR = 17.35, 95% CI: 1.19-253.80, p = 0.037), and abnormal preoperative chest radiograph (OR = 60.07, 95% CI: 1.92-1878.21, p = 0.020) were independent risk factors for postoperative pulmonary complications in patients within 30 days after the surgery.

CONCLUSIONS

Omicron infection may heighten the risk of pulmonary complications in children undergoing elective non-cardiac surgery. It is advisable to schedule elective surgery at least 4 weeks after infection of Omicron variants.

Diagnostic Efficiency of Tongue-Coating Microbiome in Patients With SARS-CoV-2 Omicron Variant Infection and Recovery

SARS-CoV-2 variants still pose threats to human public health. However, there has been little research regarding alterations in the tongue-coating microbiome in patients infected with the Omicron variant (PIOVs). Herein, we collected 963 tongue-coating samples prospectively, including 349 samples from PIOVs, 242 samples from recovered PIOVs, 300 samples from healthy controls (HCs) and 72 samples from patients infected with the original strain (PIOSs). We randomly selected tongue-coating samples from PIOVs and HCs as the discovery cohort and validation cohort. Tongue-coating microbiota was analyzed using Miseq sequencing. Our results showed that the tongue-coating microbial diversity of PIOVs was increased. We found that in PIOVs, the abundance was increased in 20 genera, including Prevonella and Atopobium, while the abundance was decreased in 23 genera, including Neisseria and Haemophilus. The classifier based on six optimal microbial markers had high diagnostic efficiency in the discovery cohort (area under the curve of 97.73%) and the validation cohort (area under the curve of 93.06%) between the PIOV and HC groups. Importantly, compared with PIOSs, PIOVs showed an increase in Fusobacterium. Recovery of patients was associated with the restoration of the tongue-coating microbiota. In conclusion, this study is the first to characterize the tongue-coating microbiota in PIOVs and to construct noninvasive diagnostic models, providing new strategies for the prevention and control of coronavirus variants.

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.

Risk factors for relapse and aggravation in membranous nephropathy after COVID-19 infection

BACKGROUND

Relapse of membranous nephropathy (MN) and other glomerular diseases has been observed after COVID-19 infection. The risk factors contributing to disease progression in MN patients after contracting COVID-19 remain unclear.

METHODS

This retrospective study included 656 consecutive patients with biopsy-proven primary MN who received treatment and were regularly followed up for over six months. Logistic regression analyses were conducted to identify risk factors for disease progression.

RESULTS

Among the cohort, 555 patients (84.6%) contracted COVID-19 from November 11th, 2022, to February 22nd, 2023. Of them, 112 patients (20.2%) experienced a > 50% increase in proteinuria, including 30 patients (5.4%) who experienced nephrotic syndrome relapse. Sixteen patients (2.9%) showed immune aggravation with elevated anti-PLA2R antibody levels, and five patients (0.9%) had immune relapse characterized by antibody reoccurrence. Kidney dysfunction, defined as an eGFR reduction > 30% from baseline, occurred in 10 patients (1.8%), with two patients (0.4%) progressing to ESKD. Four patients (0.7%) died of respiratory failure. Overall, 132 patients (24.0%) experienced disease progression after COVID-19 infection. Multivariate logistic regression identified longer fever duration (OR 1.118, 95% CI 1.029-1.356, P = 0.018), withdrawal of immunosuppressants and/or steroids (OR 2.571, 95% CI 1.377-4.799, P = 0.003) and extended drug cessation (OR 1.113, 95% CI 1.045-1.186, P = 0.001) as independent risk factors for MN progression.

CONCLUSIONS

These findings suggest prompt antiviral treatment and minimizing the duration of immunosuppressant withdrawal to optimize kidney outcomes in MN patients with COVID-19.

High-frequency PCR-testing as a powerful approach for SARS-CoV-2 surveillance in the field of critical infrastructure: A longitudinal, retrospective study in a German tertiary care hospital

A high number of SARS-CoV-2 infections are mild, often even asymptomatic. Because of high specificity and sensitivity, RT-PCR is considered the gold-standard for COVID-19 testing. The technology played a key role in detecting sources of infection at an early stage and therefore preventing larger outbreaks. This was especially important in case of critical infrastructure, such as hospitals. Until now, comprehensive studies concerning the impact of high-frequency PCR-testing in German tertiary care hospitals during the COVID-19 pandemic are lacking. We therefore analyzed about 285.000 oral swab probes of 3.421 healthcare-workers concerning SARS-CoV-2 RNA positivity between November 2020 and February 2023. Our data show that frequent PCR-testing is a useful tool concerning SARS-CoV-2 surveillance. Due to the longitudinal character of the study, we were able to observe SARS-CoV-2 variant-specific differences. For example, the omicron-variant led to high reinfection-rates as well as lower Ct-values. Nevertheless, reinfection rates in our hospital are much lower compared to other analyzed healthcare-worker cohorts described in the literature, which is again attributable to the frequent testing-regime implemented in the early phase of the pandemic. Our data further reveal a longer infection-duration in elderly compared to younger individuals.

Clinical characteristics, diagnosis and short-term outcomes of COVID-19-associated acute myocarditis in China

AIMS

Acute myocarditis (AM) has been recognized as a rare complication of coronavirus disease 2019 (COVID-19) infection. This study was conducted to present the clinical characteristics, disease courses and short-term prognoses of Omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) induced AM in China, which has been unavailable so far.

METHODS AND RESULTS

Data from 28 patients diagnosed with definite COVID-19-associated AM from 6 hospitals in China between 1 December 2022 and 30 June 2023 were collected and analysed. The diagnosis of AM was based on increased troponin level plus typical findings of AM on cardiac magnetic resonance (CMR) imaging and/or endomyocardial biopsy. Among 28 patients with definite COVID-19-related AM, median age was 37 years (Q1-Q3: 22-52) and 53.6% were men. Twenty-three patients occurred within 2 weeks of the onset of COVID-19 infection, 10 patients underwent endomyocardial biopsy and CMR was performed in all patients. Seven (25.0%) patients developed fulminant myocarditis that required inotropic agents or temporary mechanical circulatory support. Of the nine patients (32.1%) with left ventricular ejection fraction (LVEF) below 50% on admission, five had fully recovered LVEF and two demonstrated improvement but to levels below normal at discharge. The comparison of CMR parameters between the baseline and first follow-up showed that ECV was decreased at the first follow-up [28.95 (25.38, 32.55)% vs. 33.65 (31.58, 37.55)%, P = 0.028), while other CMR parameters had no significant changes. Eighteen patients (64.3%) were prescribed with corticosteroids, and seven patients (25.0%) underwent temporary mechanical circulatory support. Only two patients died during hospitalization.

CONCLUSIONS

The majority of COVID-19-associated AM occurred within 2 weeks of Omicron variant infection. Fulminant myocarditis complicated by hemodynamic instability requiring temporary mechanical circulatory support was not uncommon. However, short-term outcome was generally good and most AM patients fully recovered.

Safety and efficacy of oral administrated cepharanthine in non-hospitalized, asymptomatic or mild COVID-19 patients: a Double-blind, randomized, placebo-controlled trial : Author detials

Cepharanthine (CEP) is a natural remedy that potently inhibits SARS-CoV-2 activity both in vitro and in vivo. To evaluate the efficacy and safety of CEP compared with placebo in adults with asymptomatic or mild coronavirus disease 2019 (COVID-19), we conducted a proof-of-concept, double-blind, randomized, placebo-controlled trial. Patients were randomized to receive 120 mg/day of CEP, 60 mg/day CEP or placebo for 5 days. Main outcome was the time from randomization to negative nasopharyngeal swab and safety. Among 262 randomized participants, 188 completed the trial among group of 120 mg/day CEP (n = 65), 60 mg/day CEP (n = 68) and placebo (n = 55). Neither 120 mg/day or 60 mg/day CEP shortened the time to negative significantly compared with placebo. However, 60 mg/day CEP showed a slight trend (difference=-0.77 days, hazard ratio (HR) = 1.40, 95% CI 0.97-2.01, p = 0.072). In analysis of participants with good medication compliance, 60 mg/day CEP significantly shortened the time to negative (difference=-0.87 days, HR = 1.56, 95% CI 1.03-2.37, p = 0.035). Adverse events were not different among the three groups, and no serious adverse events occurred. In conclusion, treatment of asymptomatic or mild Covid-19 with 120 mg/day or 60 mg/day did not shorten the time to negative significantly. However, 60 mg/day CEP showed a slight trend which needs future confirmatory trials to validate. (NCT05398705).

Cryptic transmission of a SARS-CoV-2 variant detected by wastewater surveillance in Panama

The COVID-19 pandemic highlighted the critical role of viral genomic surveillance, prompting numerous countries to enhance their monitoring systems for acute respiratory infections (ARIs), especially influenza-like illnesses (ILIs). Given the significance of asymptomatic cases in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission, cases often undetected by the ILI surveillance, a more comprehensive approach was essential to track the circulation of SARS-CoV-2 variants in the population. In response, many countries swiftly adopted wastewater surveillance, which allowed the early detection of SARS-CoV-2 variants before they were identified through molecular characterization from confirmed clinical cases. In this report, we detail the implementation of SARS-CoV-2 wastewater genomic surveillance in Panama during the first half of 2024. Wastewater samples were collected monthly in duplicate at two collection points from three districts of Panama city metropolitan area for testing by SARS-CoV-2 RT-qPCR, and positive samples were analyzed by next-generation sequencing to identify sublineages. A total of 36 wastewater samples and 822 samples obtained through the clinical surveillance were analyzed for molecular detection and sequencing. Sublineages detected by wastewater surveillance were compared to those detected by clinical surveillance for the same period of time. Wastewater surveillance allowed the identification of the Omicron sublineage JN.1.16.1 in the capital city and its surroundings, which was not detected by the clinical surveillance in the country, despite its global circulation. This highlights the critical need to sustain both genomic surveillance programs beyond the pandemic in countries like Panama that serve as pivotal exchange hubs.

Fc-binding nanodisc restores antiviral efficacy of antibodies with reduced neutralizing effects against evolving SARS-CoV-2 variants

Passive antibody therapies, typically administered via parenteral routes, have played a crucial role in the initial response to the COVID-19 pandemic. However, the ongoing evolution of SARS-CoV-2 has revealed significant limitations of this approach, primarily due to mutational escape and the inadequate delivery of antibodies to the upper respiratory tract. To overcome these challenges, we propose a novel prophylactic strategy involving the intranasal delivery of an antibody in combination with an Fc-binding nanodisc. This nanodisc, engineered to specifically bind to the Fc regions of IgG antibodies, served two key functions: extending the antibody's half-life in the larynx and trachea, and enhancing its neutralization efficacy. Notably, Sotrovimab, an FDA-approved monoclonal antibody that has experienced a significant decline in neutralizing potency due to viral evolution, exhibited robust antiviral activity when complexed with the nanodisc against all tested Omicron variants. Furthermore, the Fc-binding nanodisc significantly boosted the antiviral efficacy of the soluble angiotensin-converting enzyme 2 (sACE2) Fc fusion protein, which possesses broad but modest antiviral activity. In ACE2 transgenic mice, the Fc-binding nanodisc protected better than sACE2-Fc alone with two more log reduction in lung viral titer. Therefore, the intranasal Fc-binding nanodisc offers a promising and powerful approach to counteract the diminished antiviral activity of neutralizing antibodies caused by mutational escape, effectively restoring antiviral efficacy against various evolving SARS-CoV-2 variants.

Discovery of a 2'-α-Fluoro-2'-β-C-(fluoromethyl) Purine Nucleotide Prodrug as a Potential Oral Anti-SARS-CoV-2 Agent

A novel 2'-α-fluoro-2'-β-C-(fluoromethyl) purine nucleoside phosphoramidate prodrug 15 has been designed and synthesized to treat SARS-CoV-2 infection. The SARS-CoV-2 central replication transcription complex (C-RTC, nsp12-nsp7-nsp82) catalyzed in vitro RNA synthesis was effectively inhibited by the corresponding bioactive nucleoside triphosphate (13-TP). The cryo-electron microscopy structure of the C-RTC:13-TP complex was also determined. Compound 15 exhibited potent in vitro antiviral activity against the SARS-CoV-2 20SF107 strain (EC50 = 0.56 ± 0.06 μM) and the Omicron BA.5 variant (EC50 = 0.96 ± 0.23 μM) with low cytotoxicity. Furthermore, it was well tolerated in rats at doses of up to 2000 mg/kg, and a single oral dose of this prodrug at 40 mg/kg led to high levels of 13-TP in the target organ lungs of rats with a long half-life. These findings support the further development of compound 15 as an orally available antiviral agent for the treatment of SARS-CoV-2 infection.

Potential associations of selected polymorphic genetic variants with COVID-19 disease susceptibility and severity

In this study, we analyzed the potential associations of selected laboratory and anamnestic parameters, as well as 12 genetic polymorphisms (SNPs), with clinical COVID-19 occurrence and severity in 869 hospitalized patients. The SNPs analyzed by qPCR were selected based on population-wide genetic (GWAS) data previously indicating association with the severity of COVID-19, and additional SNPs that have been shown to be important in cellular processes were also examined. We confirmed the associations of COVID-19 with pre-existing diabetes and found an unexpected association between less severe disease and the loss of smell and taste. Regarding the genetic polymorphisms, a higher allele frequency of the LZTFL1 and IFNAR2 minor variants significantly correlated with greater COVID-19 disease susceptibility (hospitalization) and severity, and a similar tendency was observed for the RAVER1 and the MUC5B variants. Interestingly, the ATP2B4 minor haplotype, protecting against malaria, correlated with an increased disease susceptibility, while in diabetic patients disease susceptibility was lower in the presence of a reduced-function ABCG2 transporter variant. Our current results, which should be reinforced by larger studies, indicate that together with laboratory and anamnestic parameters, genetic polymorphisms may have predictive value for the clinical occurrence and severity of COVID-19.

Impact of previous COVID-19 infection on postoperative complications and functional recovery: a 1-year follow-up ambispective cohort study

BACKGROUND

It's necessary to reassess the patients' short-term and long-term postoperative outcomes in the post-COVID-19 era. This study aims to provide more comprehensive evidence regarding the timing of surgery after COVID-19 infection among the vaccinated population upon Omicron variant, considering the duration after acute COVID-19 infection, the severity of COVID-19, patients' comorbidities, and the full course quality of postoperative recovery.

MATERIALS AND METHODS

This is a single-center cohort study. Patients diagnosed with preoperative COVID-19 infection were consecutively included before surgery. Patients' demographics, surgical characteristics, and COVID-19-related factors were documented. Exposure was the time interval from COVID-19 infection to surgery. The primary outcome was postoperative complications within 30 days. The secondary outcomes included postoperative mortality within 30 days, functional disability at 6 and 12 months after surgery.

RESULTS

A total of 4953 patients were included, and postoperative complications occurred in 353 patients (7.1%) within 30 days after surgery. Time interval from COVID-19 infection to surgery was associated with postoperative complications within 30 days after surgery [adjusted odds ratio (aOR) per day: 0.99; 95% CI, 0.99-1.00; P <0.01], as well as postoperative 6- and 12-month functional disability [(aOR): 1.00; 95% CI, 0.99-1.00; P <0.01; and (aOR) 0.99; 95% CI, 0.98-1.00; P =0.01, respectively). Delaying surgery beyond a time interval of 2 weeks was associated with reduced postoperative 30-day complications [(aOR): 0.63; 95% CI, 0.43-0.91; P =0.01] and mortality [(aOR): 0.07; 95% CI, 0.01-0.38; P <0.01]. Meanwhile, delaying surgery beyond a time interval of 7 weeks was associated with reduced functional disability at both 6-month [(aOR): 0.67; 95% CI, 0.58-0.79; P <0.01] and 12-month postoperatively [(aOR): 0.71; 95% CI, 0.53-0.95; P =0.02].

CONCLUSION

A 2 weeks delay after COVID-19 infection is necessary for decreasing short-term postoperative risks, and a longer waiting period could be beneficial for long-term functional recovery.

The molecular and metabolic landscape of ferroptosis in respiratory diseases: Pharmacological aspects

Ferroptosis is a form of cell death that occurs when there is an excess of reactive oxygen species (ROS), lipid peroxidation, and iron accumulation. The precise regulation of metabolic pathways, including iron, lipid, and amino acid metabolism, is crucial for cell survival. This type of cell death, which is associated with oxidative stress, is controlled by a complex network of signaling molecules and pathways. It is also implicated in various respiratory diseases such as asthma, chronic obstructive pulmonary disease (COPD), acute lung injury (ALI), lung cancer, pulmonary fibrosis (PF), and the coronavirus disease 2019 (COVID-19). To combat drug resistance, it is important to identify appropriate biological markers and treatment targets, as well as intervene in respiratory disorders to either induce or prevent ferroptosis. The focus is on the role of ferroptosis in the development of respiratory diseases and the potential of targeting ferroptosis for prevention and treatment. The review also explores the interaction between immune cell ferroptosis and inflammatory mediators in respiratory diseases, aiming to provide more effective strategies for managing cellular ferroptosis and respiratory disorders.

Humoral and cellular immune response to AZD1222 /Covishield and BV152/Covaxin COVID-19 vaccines among adults in India

Several COVID-19 vaccines were developed using different approaches to prevent both symptomatic COVID-19 cases and fatalities. The adults were vaccinated with two doses of AZD1222/Covishield (n = 77) [manufactured by Serum Institute of India Pvt Ltd] vaccine and BV152/Covaxin (n = 99) [manufactured by Bharat Biotech] vaccine. They were assessed for immune response at pre-vaccination, 1 month post first and 6 months post second dose for anti-SARS-CoV-2 IgG antibody, surrogate neutralizing antibody (NAbs), immune phenotypes, antigen specific NK, B and T cell response, their effector functionality by ELISPOT and plasma cytokine profile. Both vaccines elicited enhanced IgG antibody and Nab levels compared to the baseline. BV152/Covaxin, the whole virus inactivated vaccine exhibited higher IgG (70% vs 100%), Nab (90% vs 100%), and robust T cell (31% vs 96%) responses at 6 months post second dose compared to 1 month post first dose justifying the utility of the second dose. Detection of SARS-CoV-2 WV and S1 specific CD4+ central T cell memory response in AZD1222/Covishield vaccinee at 6 months post second dose and higher CD4+ and CD8+ naïve and central memory T cell response in BV152/Covaxin vaccinee at 1 month post first dose indicated the involvement of memory T cells. Persistent IgG and NAb responses along with IgG+B and IgG+memory B cells in AZD1222/Covishield recipients at 6 months post second dose indicated sustained immune memory response. Continued heightened IFN-γ secreting T cell response (ELISPOT) displayed by both the vaccine platforms could serve as a co correlate of protection, further to evaluation in follow up studies. Overall, our data suggest that coordinated functions of humoral and cellular branches of adaptive immunity may pave ways toward protective immunity against COVID-19.

FACTORS AFFECTING COVID-19 OUTCOMES IN PATIENTS WITH HEMATOLOGICAL MALIGNANCIES

BACKGROUND

Patients with hematological malignancies (HM) are considered to have a high risk of developing severe and life-threatening infections including COVID-19 because of immune deficiency and immunosuppressive treatments. Although the COVID pandemic spread worldwide, morbidity and mortality data varied from country to country. A more accurate identification of risk factors would allow the improvement of the clinical management of HM patients.

AIM

This study aimed to determine real-life data - the mortality rate, clinical outcomes, and risk factors affecting mortality in patients with HM and COVID-19 at the Riga East University Hospital (REUH) in Latvia.

MATERIALS AND METHODS

In this retrospective non-interventional cohort study, we included adult patients treated in REUH with ongoing HM and laboratory- confirmed COVID-19 observed between December 1st, 2020, and March 31st, 2023. All data were analyzed using descriptive statistics, binary logistic regression, univariable Cox regression model, and other methods.

RESULTS

We registered 156 patients with 11 different HMs. Multiple myeloma, non-Hodgkin lymphoma, and acute myeloid leukemia were the most common HM. COVID-19 mortality rate was 19.9% (31/156). Factors increasing the risk of death included the severity of COVID-19 (p < 0.001), the accession of bacterial infection (p < 0.001), longer hospital stay (p = 0.037), absolute neutrophil count (ANC) ≤ 0.5 × 109/mm3 (p = 0.014), fever (p = 0.039), and acute myeloid leukemia (p = 0.002). We also confirmed that the mortality in the third pandemic wave was significantly lower than in the second wave (p = 0.002). Although vaccination seemed to be a risk-mitigating factor (58.8% [10/17] of those who died from COVID-19 were not vaccinated), no statistically important correlation was found (p = 0.690).

CONCLUSION

This survey confirmed that the COVID-19 mortality rate was higher in patients with HM (19.9% [31/156]) than in the population. ANC, severity of COVID-19, accession of bacterial infection, hospital stay, fever, and acute myeloid leukemia were the factors that increased mortality in HM patients.

Study on the predictive value of laboratory inflammatory markers and blood count-derived inflammatory markers for disease severity and prognosis in COVID-19 patients: a study conducted at a university-affiliated infectious disease hospital

BACKGROUND

Since the outbreak of coronavirus disease 2019 (COVID-19), studies have found correlations between blood cell count-derived inflammatory markers (BCDIMs) and disease severity and prognosis in COVID-19 patients. However, there is currently a lack of systematic comparisons between procalcitonin (PCT), C-reactive protein (CRP), C-reactive protein-to-albumin ratio (CAR) and BCDIMs for assessing the severity and prognosis of COVID-19 patients.

METHODS

A total of 1040 COVID-19 patients were included in the study. Demographics, comorbidities and laboratory results were analysed. BCDIMs refer to the following ratios: neutrophil-to-lymphocyte ratio (NLR), monocyte-to-lymphocyte ratio (MLR), platelet-to-lymphocyte ratio (PLR), lymphocyte-to-C-reactive protein ratio (LCR), systemic inflammation response index (SIRI) and systemic inflammation index (SII). Disease severity and 28-day mortality are clinical outcomes of this study. Area under the curve (AUC) of receiver operating characteristic (ROC) curve was calculated for these markers, and DeLong's test compared their statistical differences. Cox regression analysis assessed their predictive value for the 28-day mortality rate.

RESULTS

Among the 1040 patients, 35.3% were severe/critical, 49.6% were moderate and 15.1% were mild cases. Within 28 days, 15.1% died. The NLR had the highest predictive value for disease severity (AUC: 0.790, 95% CI: 0.762-0.818). NLR differed significantly from other markers, except LCR. LCR best predicted 28-day mortality (AUC: 0.798, 95% CI: 0.766-0.829). Some markers showed significant differences in AUC with LCR. Multivariable Cox regression identified BCDIMs, PCT, CRP and CAR as significant risk factors for 28-day mortality.

CONCLUSIONS

PCT, CRP, CAR and BCDIMs, easily obtained in clinical settings, are valuable predictors of disease severity and the 28-day mortality in COVID-19 patients. The NLR is particularly effective for disease severity, while the LCR is highly predictive of 28-day mortality. These markers provide guidance for stratified management of COVID-19 patients.

Coronavirus S protein alters dsRNA accumulation and stress granule formation through regulation of ADAR1-p150 expression

The precise role of the highly variable coronavirus S protein in modulating innate immune responses remains unclear. In this study, we demonstrated that the mutant strain of swine coronavirus porcine enteric diarrhea virus induced significantly lower levels of double-stranded RNA (dsRNA) accumulation, inhibited protein kinase R (PKR) activation and suppressed stress granule (SG) formation compared with the classical strain. The 29th amino acid at N-terminus of S was identified as the key functional site for regulation of SG formation, and found that mutant S inhibited PKR phosphorylation and SG formation by upregulating adenosine deaminase acting on RNA 1 (ADAR1)-p150. Notably, the Zα domain of ADAR1-p150 was essential for inhibiting SG formation. Upregulation of ADAR1-p150 also reduced accumulation of dsRNA depending on its RNA editing function. Virus rescue confirmed that the mutant carrying a substitution at amino acid 29 failed to induce ADAR1-p150, leading to dsRNA accumulation, PKR activation and SG formation. Interestingly, the latest severe acute respiratory syndrome coronavirus-2 strains exhibit a novel 25PPA27 deletion at N-terminus of S that was also shown to lead to altered ADAR1-p150 expression and SG inhibition. The transcription factor TCF7L2 was identified as a player in S-mediated transcriptional enhancement of ADAR1-p150. This study is the first to clarify the crucial role of N-terminus of S in immune regulation of coronaviruses.

Exploring the Replication and Pathogenic Characteristics of Alpha, Delta, and Omicron Variants of SARS-CoV-2

The variants of concern (VOCs) of SARS-CoV-2 have exhibited different phenotypic characteristics in clinical settings which are yet to be fully explored. This study aimed to characterize the viral replication features of major VOCs of SARS-CoV-2 and their association with pathogenicity. The Alpha, Delta, and Omicron variants of SARS-CoV-2 isolated from the COVID-19 patients in Japan were propagated in VeroE6/TMPRSS2 cells. The viral replication and pathological features were evaluated by laser and electron microscopy at different time points. The results revealed that the Delta variant dominantly infected the VeroE6/TMPRSS2 cells and formed increased syncytia compared to the Alpha and Omicron variants. Relatively large numbers of virions and increased immunoreactivities of the SARS-CoV-2 N-protein were detected in the endoplasmic reticulum and intracellular vesicles of Delta-infected cells. Interestingly, the N-protein and virions were detected in the nucleus of Delta-infected cells, while such properties were not observed in the case of Alpha and Omicron variants. In addition, early nuclear membrane damage followed by severe cellular damage was prominent in Delta-infected cells. A unique mutation (G215C) in the N-protein of the Delta variant is thought to be associated with severe cell damage. In conclusion, this study highlights the distinct replicative and pathogenic characteristics of the Delta variant of SARS-CoV-2 compared to the Alpha and Omicron variants, shedding light on the potential mechanisms underlying its increased pathogenicity.

Clinical outcomes of Omicron infection and vaccine acceptance among pediatric liver transplant recipients: insights from a cross-sectional survey

OBJECTIVES

Our study aims to explore the clinical characteristics of Omicron infection in pediatric liver transplant recipients (PLTRs), after the national COVID-19 outbreak. Additionally, we will investigate changes in vaccine coverage and parental attitudes towards vaccinating their children after this current outbreak.

METHODS

We conducted a web-based questionnaire survey to gather information on Omicron infection, vaccination status, and guardian attitude among PLTRs. Besides, utilized valid questionnaire and long-term follow-up information processing techniques, and performed statistical analysis of relevant parameters.

RESULTS

528 valid questionnaires were collected, among which, 251 responses replied Omicron infection status. The Omicron infection rate in Chinese PLTRs was 56.2% (141/251), similar to the report in the normal population (around 60%). 99.3% of infected PLTRs presented mild symptoms, mostly with fever (78.0%), followed by Cough (76.6%), with a mean RTPCR conversion time of 7 days; the overall PLTRs' vaccination rate in this study was 13.3%, similar to that of our previous study (9.4%). Besides, we found no significant differences of either infection rate or clinical symptoms between the vaccinated and unvaccinated groups. Moreover, the study showed 61.6% of guardians supported COVID-19 inoculation despite the outbreak of Omicron status.

CONCLUSIONS

The symptoms of Omicron infection in Chinese PLTRs were relatively mild, vaccine immunization had a limited effect on PLTRs' defense against Omicron infection, besides, their guardians supported the inoculation policy with a caution.

CLINICAL TRIAL REGISTRATION

http://www.chictr.org.cn , identifier ChiCTR2200055968.

Efficacy of azvudine plus dexamethasone in severe hospitalized patients with Omicron infection: a prospective multicenter study

Background

Azvudine (AZV), the first Chinese oral anti-coronavirus disease 2019 (COVID-19) drug, has shown substantial clinical benefits to viral clearance and prognosis in patients with mild and common COVID-19. However, there is no evidence in severe hospitalized COVID-19 patients.

Methods

In this multicenter study, we analyzed 209 severe hospitalized COVID-19 patients in four hospitals. All the clinical data and the 28-day composite outcomes were recorded. All of the patients were categorized into two groups according to drug: the dexamethasone (DXM) group and the azvudine plus dexamethasone (AZV+DXM) group.

Results

There were no differences in sex, age, BMI, and underlying diseases between the two groups. The ratio of the 28-day composite outcome was lower for the AZV+DXM group than that for the DXM group (16.97% vs. 31.82%, p = 0.029). The viral clearance time was shorter in the AZV+DXM group than in the DXM group (7.32 ± 2.57 vs. 8.55 ± 2.34 days, p = 0.017). The PaO2/FiO2 levels on day 5 (258.89 ± 55.22 vs. 233.12 ± 60.51, p = 0.026) and day 10 (289.48 ± 44.09 vs. 261.52 ± 37.34, p = 0.015) were higher in the AZV+DXM group than the DXM group. However, data on the hospitalization duration of the two groups were similar. Cox analysis showed the benefit of AZV+DXM in the subgroups of ≥65 years old, multiple organ dysfunction syndrome (MODS), cerebrovascular disease, C-reactive protein (CRP) ≥70mg/L, and D-dimer ≥1 µg/L.

Conclusion

This study is the first to indicate that treatment with AZV+DXM might benefit severe Omicron-infected patients compared with DXM treatment alone. This finding demonstrates, at least partly, the necessity of antiviral treatment in severe patients.

Enhancing SARS-CoV-2 Lineage Surveillance through the Integration of a Simple and Direct qPCR-Based Protocol Adaptation with Established Machine Learning Algorithms

Emerging and evolving Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) lineages, adapted to changing epidemiological conditions, present unprecedented challenges to global public health systems. Here, we introduce an adapted analytical approach that complements genomic sequencing, applying a cost-effective quantitative polymerase chain reaction (qPCR)-based assay. Viral RNA samples from SARS-CoV-2 positive cases detected by diagnostic laboratories or public health network units in Ceará, Brazil, were tracked for genomic surveillance and analyzed by using paired-end sequencing combined with integrative genomic analysis. Validation of a key structural variation was conducted with gel electrophoresis for the presence of a specific open reading frame 7a(ORF7a) gene deletion within the "BE.9" lineages tracked. The analytical innovation of our method is the optimization of a simple intercalating dye-based qPCR assay through repositioning primers from the ARTIC v4.1 amplicon panel to detect large molecular patterns. This assay distinguishes between "BE.9" and "non-BE.9" lineages, particularly BQ.1, without the need for expensive probes or sequencing. The protocol was validated against lineage predictions from next-generation sequencing (NGS) using 525 paired samples, achieving 93.3% sensitivity, 95.1% specificity, and 92.4% agreement, as measured by Cohen's Kappa coefficient. Machine learning (ML) models were trained using the melting curves from intercalating dye-based qPCR of 1724 samples, enabling highly accurate lineage assignment. Among them, the support vector machine (SVM) model had the best performance and after fine-tuning showed ∼96.52% (333/345) accuracy in comparison to the test data set. Our integrated approach provides an adapted analytical method that is both cost-effective and scalable, suitable for rapid assessment of emerging variants, especially in resource-limited settings. In this work, the protocol is applied to improve the monitoring of SARS-CoV-2 sublineages but can be extended to track any key molecular signature, including large insertions and deletions (indels) commonly observed in pathogenic agent subtypes. By offering a complement to traditional sequencing methods and utilizing easily trainable machine learning algorithms, our methodology contributes to enhanced molecular surveillance strategies and supports global efforts in pandemic control.

Sustained applicability of SARS-CoV-2 variants identification by Sanger Sequencing Strategy on emerging various SARS-CoV-2 Omicron variants in Hiroshima, Japan

BACKGROUND

The evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) persists, giving rise to new variants characterized by mutations in the spike protein. However, public data regarding the virus's evolutionary trend is not widely available after the downgrade of coronavirus disease 2019(COVID-19). Therefore, this study aimed to investigate the applicability of an in-house Sanger-based method for identifying SARS-CoV-2 variants, particularly focusing on newly emerged Omicron variants, and updating the epidemiology of COVID-19 during the 8th wave in Hiroshima Prefecture.

RESULTS

A total of 639 saliva samples of individuals who had tested positive for COVID-19, received from Hiroshima City Medical Association Clinical Laboratory Center between February 01, 2023, and March 12, 2024, were included in the study. SARS-CoV-2 variants were identified in 69.3% (443/639) with the mean viral titer 2 × 106 copies/mL, and high viral titer in Omicron variant XBC.1.6* (5 × 108 copies/mL) using RT-qPCR. By partial Spike gene-based sequencing using the Sanger Sequencing strategy, Omicron sub-lineages XXB.1, BA.5, and EG.1 were identified during different periods. A comprehensive phylogenetic analysis of 7383 SARS-CoV-2 strains retrieved from GISAID, collected in Hiroshima from the onset of the COVID-19 pandemic in early 2020 until July 2024, revealed the dynamic evolution of SARS-CoV-2 variants over time. The study found a similar pattern of variant distribution between the full genomes from GISAID, and the partial genomes obtained from our screening strategy during the same period.

CONCLUSIONS

Our study revealed that all SARS-CoV-2 viruses circulated in Hiroshima were Omicron variants and their sub-lineages during the 8th wave outbreak in Hiroshima. Persistent molecular surveillance of SARS-CoV-2 is needed for the decision-making and strategic planning of the public promptly. Our study added evidence for the usefulness of SARS-CoV-2 spike gene partial sequencing-based SARS-CoV-2 variant identification strategy for mass screening and molecular surveillance even though the evolution of newly emerged various SARS-CoV-2 Omicron variants.

Evaluating male sexual function and reproductive health during Omicron outbreak in China

There are currently no studies exploring omicron infection and male sexual function and semen quality. Our aim was to estimate changes in sexual function and semen quality in men recovering from infection since the COVID-19 Omicron pandemic started in China in late 2022. We collected 1540 questionnaires and assessed male function before infection and acute phase after infection by using International Index of Erectile Function-5, Premature Ejaculation Diagnostic Tool, and Arizona Sexual Experience Scale. We also collected the before and after semen analysis results of 247 male patients. During the acute phase after infection, the proportion of erectile dysfunction was significantly higher than before infection, but ejaculatory function was not significantly altered; In addition, semen analysis showed significant difference in semen concentration, semen activity and PR a+b sperm forward movement after infection compared to pre-infection.: COVID-19 Omicron can affect erectile function as well as sexual experience in male patients in the acute phase. Decreased sexual function due to COVID-19 Omicron may be related to body temperature and anxiety during infection.

The optimal timing of breast cancer surgery after COVID-19 infection: an observational study

PURPOSE

It is controversial for the optimal time of breast cancer surgery after COVID-19 infection. Purpose was to assess the risk of postoperative complication in breast cancer patients with COVID-19 infection, in order to select optimal surgery timing after COVID-19 infection.

METHODS

Breast cancer patients infected with COVID-19 and performed surgery between December 20th, 2022 to March 20th, 2023 were included in this prospective study (n = 577). Patients performed surgery between May 1, 2019 to October 1, 2019 were listed as control group (n = 329). They had not been infected with COVID-19 before surgery. Patients were grouped by time of surgery relative to COVID-19 infection. Database was evaluated using logistic regression.

RESULTS

Patients infected with COVID-19 had a higher incidence of complications after surgery compared to that not-COVID-19 infection (6.59% vs. 3.04%). Multivariable logistic analysis demonstrated that timing of surgery was associated with complications (OR = 4.253; 95% CI: 0.855-21.153, P = 0.044). Patients performed surgery within 2 weeks after COVID-19 infection had the highest rates of complication (17.65%) when compared with other groups, while the incidence was decreased into 5.51% when surgery 2 weeks or more after COVID-19 infection. With a median follow-up was 10 months, all patients with complications were recovered without serious complications or death, which had no adverse effect on subsequent anti-tumor therapy.

CONCLUSIONS

It needs to be cautious when breast cancer surgery was performed within 2 weeks after COVID-19 infection. Although the incidence of complications in patients undergoing surgery 2 weeks after COVID-19 infection is still slightly high, surgery might be recommended considering urgency of treatment, good prognosis of complications and the lack of influence on subsequent adjuvant therapy.

Chemical Proteomics Approaches for Screening Small Molecule Inhibitors Covalently Binding to SARS-Cov-2

Although various strategies have been used to prevent and treat SARS-CoV-2, the spread and evolution of SARS-CoV-2 is still progressing rapidly. The emerging variants Omicron and its sublineage have a greater ability to spread and escape nearly all current monoclonal antibodies treatments, highlighting an urgent need to develop therapeutics targeting current and emerging Omicron variants or recombinants with breadth and potency. Here, some small molecule drugs are rapidly identified that could covalently binding to receptor binding domain (RBD) protein of Omicron through the combined application of artificial intelligence (AI) and activity-based protein profiling (ABPP) technology. The surface plasmon resonance (SPR) and pseudo-virus neutralization experiments further reveal that an FDA-approved drug gallic acid has robust neutralization potency against Omicron pseudo-virus with the IC50 values of 23.56 × 10-6 m. Taken together, a platform combining AI intelligence, biochemical, SPR, molecular docking, and pseudo-virus-based screening for rapid identification and evaluation of potential anti-SARS-CoV-2 small molecule drugs is established and the effectiveness of the platform is validated.

Effect of Chinese Medicine in Patients with COVID-19: A Multi-center Retrospective Cohort Study

OBJECTIVE

To evaluate the effectiveness and safety of Chinese medicine (CM) in the treatment of coronavirus disease 2019 (COVID-19) in China.

METHODS

A multi-center retrospective cohort study was carried out, with cumulative CM treatment period of ⩾3 days during hospitalization as exposure. Data came from consecutive inpatients from December 19, 2019 to May 16, 2020 in 4 medical centers in Wuhan, China. After data extraction, verification and cleaning, confounding factors were adjusted by inverse probability of treatment weighting (IPTW), and the Cox proportional hazards regression model was used for statistical analysis.

RESULTS

A total of 2,272 COVID-19 patients were included. There were 1,684 patients in the CM group and 588 patients in the control group. Compared with the control group, the hazard ratio (HR) for the deterioration rate in the CM group was 0.52 [95% confidence interval (CI): 0.41 to 0.64, P<0.001]. The results were consistent across patients of varying severity at admission, and the robustness of the results were confirmed by 3 sensitivity analyses. In addition, the HR for all-cause mortality in the CM group was 0.29 (95% CI: 0.19 to 0.44, P<0.001). Regarding of safety, the proportion of patients with abnormal liver function or renal function in the CM group was smaller.

CONCLUSION

This real-world study indicates that the combination of a full-course CM therapy on the basic conventional treatment, may safely reduce the deterioration rate and all-cause mortality of COVID-19 patients. This result can provide the new evidence to support the current treatment of COVID-19. Additional prospective clinical trial is needed to evaluate the efficacy and safety of specific CM interventions. (Registration No. ChiCTR2200062917).

Impact of genetic variations of gene involved in regulation of metabolism, inflammation and coagulation on pathogenesis of cardiac injuries associated with COVID-19

BACKGROUND

SARS-CoV-2 infection can result in long-term chronic cardiovascular (CV) damage after the acute phase of the illness. COVID-19 frequently causes active myocarditis, SARS-CoV-2 can directly infect and kill cardiac cells, causing severe pathology and dysfunction across the organs and cells. Till now, the pathogenesis of COVID-19-associated cardiac injuries has not been understood, but there are several factors that contribute to the progression of cardiac injuries, such as genetic, dietary, and environmental. Among them ranges of host genetic factor including metabolizing, inflammation, and coagulation related genes have a role to contribute the cardiac injuries induced by COVID-19. Hereditary DNA sequence variations contribute to the risk of illness in almost all of these diseases. Hence, we comprehended the occurrence of genetic variations of metabolizing, inflammation and coagulation-related genes in the general population, their expression in various diseases, and their impact on cardiac injuries induced by COVID-19.

METHOD

We utilized multiple databases, including PubMed (Medline), EMBASE, and Google Scholar, for literature searches.

DESCRIPTION

The genes involved in metabolism (APOE, MTHFR), coagulation (PAI-1, ACE2), and immune factors (CRP, ESR, and troponin I) may have a role in the progression of COVID-19-associated cardiac injuries. The risk factors for CVD are significantly varied between and within different regions. In healthy individuals, the ACE I allele is responsible for the predisposition to CAD, but the ACE D haplotype is responsible for susceptibility and severity, which ultimately leads to heart failure. Patients who carry the T allele of rs12329760 in the TMPRSS2 gene are at risk for developing the severe form of COVID-19. IL-6 (rs1800796/rs1800795) polymorphism is associated with an increased mortality rate and susceptibility to severe COVID-19 disease. While the putative role of IL-6 associated with chronic, inflammatory diseases like cardiac and cerebrovascular disease is well known.

CONCLUSION

The occurrence of genetic variations in the ACE-2, AGT, DPP-IV, TMPRSS2, FUIRN, IL-4, IL-6, IFN-γ, and CYP2D6 genes is varied among different populations. Examining the correlation between these variations and their protein levels and cardiac injuries induced by COVID-19 may provide valuable insights into the pathogenesis of cardiac injuries induced by COVID-19.

Homeopathic Medicines in Third (Omicron) Wave of COVID-19: Prognostic Factor Research

BACKGROUND

With the emergence of new variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus, such as the Omicron variant, during the third wave of the coronavirus disease 2019 (COVID-19) pandemic, there was a need to identify useful homeopathic medicines. This study aimed to identify such medicines and their indications using prognostic factor research (PFR).

METHODS

This was an open-label, multi-centred observational study conducted in January 2022, on confirmed COVID-19 cases. The data were collected from integrated COVID Care Centres in Delhi, India, where homeopathic medicines were prescribed along with conventional treatment. Only those cases that met a set of selection criteria were considered for analysis. The likelihood ratio (LR) was calculated for the frequently occurring symptoms of the frequently prescribed medicines. An LR of 1.3 or greater was considered meaningful.

RESULTS

Out of the 362 COVID-19 cases, 263 cases were selected for analysis after applying selection criteria. Common symptoms included fatigue, cough, sore throat, myalgia and headache. Twenty-one medicines were prescribed, of which nine medicines - Gelsemium sempervirens, Bryonia alba, Hepar sulphuris, Rhus toxicodendron, Pulsatilla nigricans, Arsenicum album, Belladonna, Nux vomica and Phosphorus - were frequently used. By calculating LRs, the study identified meaningful indications for these medicines.

CONCLUSION

Homeopathic medicines have shown promising results in the third wave of COVID-19 as an adjunct therapy. The medicines that were used in the first and second waves were found useful in the third wave also, and their indications were analogous to those found in the earlier waves. Certain new indications of some medicines were elicited in this wave, which warrant further research. However, it is important not to restrict to these medicines only and to continue data collection on COVID-19 in future waves for the improvement of the COVID-19 mini-repertory.

In vivo evaluation of Andrographis paniculata and Boesenbergia rotunda extract activity against SARS-CoV-2 Delta variant in Golden Syrian hamsters: Potential herbal alternative for COVID-19 treatment

The ongoing COVID-19 pandemic has triggered extensive research, mainly focused on identifying effective therapeutic agents, specifically those targeting highly pathogenic SARS-CoV-2 variants. This study aimed to investigate the in vivo antiviral efficacy and anti-inflammatory activity of herbal extracts derived from Andrographis paniculata and Boesenbergia rotunda, using a Golden Syrian hamster model infected with Delta, a representative variant associated with severe COVID-19. Hamsters were intranasally inoculated with the SARS-CoV-2 Delta variant and orally administered either vehicle control, B. rotunda, or A. paniculata extract at a dosage of 1000 mg/kg/day. Euthanasia was conducted on days 1, 3, and 7 post-inoculation, with 4 animals per group. The results demonstrated that oral administration of A. paniculata extract significantly alleviated both lethality and infection severity compared with the vehicle control and B. rotunda extract. However, neither extract exhibited direct antiviral activity in terms of reducing viral load in the lungs. Nonetheless, A. paniculata extract treatment significantly reduced IL-6 protein levels in the lung tissue (7278 ± 868.4 pg/g tissue) compared to the control (12,495 ± 1118 pg/g tissue), indicating there was a decrease in local inflammation. This finding is evidenced by the ability of A. paniculata extract to reduce histological lesions in the lungs of infected hamsters. Furthermore, both extracts significantly decreased IL-6 and IP-10 mRNA expression in peripheral blood mononuclear cells of infected hamsters compared to the control group, suggesting systemic anti-inflammatory effects occurred. In conclusion, A. paniculata extract's potential therapeutic application for SARS-CoV-2 arises from its observed capacity to lessen inflammatory cytokine concentrations and mitigate lung pathology.

Into the Cauldron of the Variant Soup: Insights into the Molecular Epidemiology and Transition to Endemicity of SARS-CoV-2 in Cyprus (November 2022-February 2024)

The coronavirus disease 2019 (COVID-19) pandemic, driven by the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has been characterized by the virus's ongoing evolution, leading to the appearance of more transmissible variants that have often triggered infection surges. In this study, we analyzed the SARS-CoV-2 epidemic in Cyprus, utilizing 1627 viral sequences from infected individuals between November 2022 and February 2024. Over this period, 251 distinct lineages and sublineages were identified, predominantly categorized into three groups: Omicron 5, XBB, and JN.1 (parental lineage BA.2.86), all of which harbor S protein mutations linked to enhanced transmissibility and immune escape. Despite the relatively low numbers of new infections during this period, and the lack of any major waves, unlike earlier phases of the pandemic, these lineages demonstrated varying periods of dominance, with Omicron 5 prevailing from November 2022 to February 2023, XBB variants leading from March to November 2023, and JN.1 generating a wavelet from December 2023 to February 2024. These findings suggest that the SARS-CoV-2 epidemic in Cyprus has reached endemicity, with new variants gradually replacing previously circulating variants irrespective of seasonal patterns. This study highlights the critical importance of ongoing surveillance of SARS-CoV-2 evolution in Cyprus and emphasizes the role of preventive measures in limiting virus transmission, providing valuable insights for safeguarding public health.

Immunogenicity and Protectivity of Sputnik V Vaccine in hACE2-Transgenic Mice against Homologous and Heterologous SARS-CoV-2 Lineages Including Far-Distanced Omicron BA.5

BACKGROUND

The SARS-CoV-2 virus continuously acquires mutations, leading to the emergence of new variants. Notably, the effectiveness of global vaccination efforts has significantly declined with the rise and spread of the B.1.1.529 (Omicron) variant.

METHODS

The study used virological, immunological and histological research methods, as well as methods of working with laboratory animals. In this study, we evaluated the Gam-COVID-Vac (Sputnik V), an adenoviral vaccine developed by the N.F. Gamaleya National Research Center for Epidemiology and Microbiology, and conducted experiments on hemizygous K18-ACE2-transgenic F1 mice. The variants studied included B.1.1.1, B.1.1.7, B.1.351, B.1.1.28/P.1, B.1.617.2, and B.1.1.529 BA.5.

RESULTS

Our findings demonstrate that the Sputnik V vaccine elicits a robust humoral and cellular immune response, effectively protecting vaccinated animals from challenges posed by various SARS-CoV-2 variants. However, we observed a notable reduction in vaccine efficacy against the B.1.1.529 (Omicron BA.5) variant.

CONCLUSIONS

Our results indicate that ongoing monitoring of emerging mutations is crucial to assess vaccine efficacy against new SARS-CoV-2 variants to identify those with pandemic potential. If protective efficacy declines, it will be imperative to develop new vaccines tailored to current variants of the virus.

Omicron XBB.1.5 subvariant causes severe pulmonary disease in K18-hACE-2 mice

Owing to their continuous evolution, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) display disparate pathogenicity in mouse models. Omicron and its sublineages have been dominant worldwide. Compared to pre-Omicron VOCs, early Omicron subvariants reportedly cause attenuated disease in human ACE-2-expressing mice (K18-hACE-2). In late 2022, the frequency of Omicron subvariant XBB.1.5 rapidly increased and it progressively replaced other circulating strains. The emergence of new strains requires current SARS-CoV-2 clinical animal model re-evaluation. In this study, we aim to characterize XBB.1.5 pathogenesis in K18-hACE-2. Herein, we demonstrated that XBB.1.5 infection is associated with significant weight loss, severe lung pathology, and substantial mortality. Intranasal XBB.1.5 infection resulted in 100% mortality in K18-hACE2 mice. High virus titers were detected in the lungs on days 3 and 5 after infection. Moreover, XBB.1.5 productively infected the cells within the nasal turbinate, olfactory bulb, intestines, and kidneys. In addition, in a subset of infected mice, we detected high virus titers in the brain. Consistently, we detected high viral antigen expression in the lungs. Furthermore, we observed severe lung injury hallmarks (e.g., immune cell infiltration, perivascular cuffing, and alveolar consolidation). Using immunofluorescence labeling and cytometric analysis, we revealed that XBB.1.5 infection leads to CD45+ cell influx into the lung parenchyma. We further demonstrated that most immune infiltrates are CD11b+ CD11c+ dendritic cells. Additionally, we detected significant induction of proinflammatory cytokines and chemokines in infected lungs. Taken together, our data show that Omicron subvariant XBB.1.5 is highly pathogenic in K18-hACE2 mice.

A COVID-19 outbreak with a high attack rate among inpatients in a psychiatric hospital in Wenzhou, China

Background

Since the emergence of COVID-19, China has taken strict prevention and control measures against the disease. At the end of 2022, when the government optimized and relaxed the COVID-19 prevention and control policy, a new wave of the epidemic appeared. This paper reports an outbreak of COVID-19 among inpatients in a psychiatric hospital in Wenzhou, China.

Methods

The case definition of COVID-19 was established. Throat swab specimens were collected and examined by RT-PCT. Questionnaires were distributed to hospitalized patients. Survey data were collected and analyzed.

Results

Of 902 inpatients in our hospital, 762 became infected with COVID-19, an attack rate of 84.5%. The outbreak occurred from 10 December, 2022 to January 18, 2023. Twenty patients died, yielding a case fatality rate of 2.6%. Most of the dead were among elderly people with underlying diseases, and 19 of the deceased were over 65 years old.

Conclusion

Our investigation showed that the outbreak of COVID-19 among hospitalized patients had the characteristics of high incidence, strong infectivity, and rapid transmission. Infectious sources were introduced into the hospital from the community and spread within the hospital, resulting in an outbreak. In addition, special attention should be paid to elderly people with underlying diseases when treating patients with COVID-19 in the future.

The new pattern for dual NOTCH pathway involving nuclear transcription and mitochondrial regulation supports therapeutic mechanism of 4-butyl benzophenone derivatives against SIRS

The systemic inflammatory response syndrome (SIRS) represents a self-amplifying cascade of inflammatory reactions and pathophysiological states triggered by infectious or non-infectious factors. The identification of disease targets and differential proteins in the liver (the unique and important immune organ) of SIRS mice treated with the lead compound D1 was conducted using the Genecards database and proteomic analysis, respectively. Subsequently, NOTCH1 was identified as the potential hub target via an intersection analysis between the aforementioned differentially expressed proteins and disease targets. Based on our previous research on the structure-activity relationship, we designed and synthesized a series of SIRS-related derivatives, wherein butyl, halogen, and ester groups were incorporated into benzophenone, aiming at exploring the anti-inflammatory protective action from the perspective of macrophage polarization. Notably, these derivatives exhibited a direct binding capability to the O-glucosylation site (SER496) or its vicinities (such as SER492, VAL485) of NOTCH1 using docking, SPR, DARTS, and CETSA techniques. Mechanistically, derivative D6 exerted anti-inflammatory effects via the dual NOTCH pathway. Firstly, it could inhibit NOTCH1 nuclear transcriptional activity, attenuate the interaction between NICD and RBPJK, concurrently suppress NF-κB and NLRP3 inflammasome (NLRP3, ASC, and cleaved CASP1) activation, and promote NICD (NOTCH1 active fragments) ubiquitination metabolism (the nuclear transcriptional pathway). Secondly, it might possess the ability to increase PGC1α level, subsequently, enhance ATP and MMP levels, mitigate ROS production, increase mitochondrial numbers, and ameliorate mitochondrial inflammatory damage (the mitochondrial pathway). Importantly, the activator Jagged1 could effectively reverse the aforementioned effects, while the inhibitor DAPT exhibited a synergistic effect, suggesting that the nuclear transcriptional regulation and mitochondrial regulation were both in a NOTCH1-dependent manner. Subsequently, it effectively alleviated the inflammatory response and preserved organ function as evidenced by up-regulating M2-type macrophage-related anti-inflammatory cytokines (IL10, TGFβ, CD206, and ARG1) and down-regulating M1-type macrophage-related pro-inflammatory cytokines (NO, IL6, IL18, iNOS, TNFα, CD86, and IL1β). In a word, derivative D6 modulated macrophage polarization and effectively mitigated SIRS by targeting inhibition of the dual NOTCH pathway.

Insights into the Replication Kinetics Profiles of Malaysian SARS-CoV-2 Variant Alpha, Beta, Delta, and Omicron in Vero E6 Cell Line

Comprehending the replication kinetics of SARS-CoV-2 variants helps explain why certain variants spread more easily, are more contagious, and pose a significant health menace to global populations. The replication kinetics of the Malaysian isolates of Alpha, Beta, Delta, and Omicron variants were studied in the Vero E6 cell line. Their replication kinetics were determined using the plaque assay, quantitative real-time PCR (qRT-PCR), and the viral growth curve. The Beta variant exhibited the highest replication rate at 24 h post-infection (h.p.i), as evidenced by the highest viral titers and lowest viral RNA multiplication threshold. The plaque phenotypes also varied among the variants, in which the Beta and Omicron variants formed the largest and smallest plaques, respectively. All studied variants showed strong cytopathic effects after 48 h.p.i. The whole-genome sequencing highlighted cell-culture adaptation, where the Beta, Delta, and Omicron variants acquired mutations at the multibasic cleavage site after three cycles of passaging. The findings suggest a strong link between the replication rates and their respective transmissibility and pathogenicity. This is essential in predicting the impacts of the upcoming variants on the local and global populations and is useful in designing preventive measures to curb virus outbreaks.