An updated review of epidemiological characteristics, immune escape, and therapeutic advances of SARS-CoV-2 Omicron XBB.1.5 and other mutants

Comparison of the pathogenicity of multiple SARS-CoV-2 variants in mouse models

BACKGROUND

New variants of severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)continue to drive global epidemics and pose significant health risks. The pathogenicity of these variants evolves under immune pressure and host factors. Understanding these changes is crucial for epidemic control and variant research.

METHODS

Human angiotensin-converting enzyme 2(hACE2) transgenic mice were intranasally challenged with the original strain WH-09 and the variants Delta, Beta, and Omicron BA.1, while BALB/c mice were challenged with Omicron subvariants BA.5, BF.7, and XBB.1. To compare the pathogenicity differences among variants, we conducted a comprehensive analysis that included clinical symptom observation, measurement of viral loads in the trachea and lungs, evaluation of pulmonary pathology, analysis of immune cell infiltration, and quantification of cytokine levels.

RESULTS

In hACE2 mice, the Beta variant caused significant weight loss, severe lung inflammation, increased inflammatory and chemotactic factor secretion, greater macrophage and neutrophil infiltration in the lungs, and higher viral loads with prolonged shedding duration. In contrast, BA.1 showed a significant reduction in pathogenicity. The BA.5, BF.7, and XBB.1 variants were less pathogenic than the WH-09, Beta, and Delta variants when infected in BALB/c mice. This was evidenced by reduced weight loss, diminished pulmonary pathology, decreased secretion of inflammatory factors and chemokines, reduced macrophage and neutrophil infiltration, as well as lower viral loads in both the trachea and lungs.

CONCLUSION

In hACE2 mice, the Omicron variant demonstrated the lowest pathogenicity, while the Beta variant exhibited the highest. Pathogenicity of the Delta variant was comparable to the original WH-09 strain. Among BALB/c mice, Omicron subvariants BA.5, BF.7, and XBB.1 showed no statistically significant differences in virulence.

Rapid Detection of Spike Protein Receptor Binding Region of SARS-CoV-2 and Its Variants Using a Nanosheet Probe

Strategies for the rapid detection of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) are critically needed due to conventional methods' limitations: narrow range, virus mutation-induced failure, time-consuming, and complex operations. Herein, we propose a method utilizing CuInP2S6 nanosheet probes and Bio-Layer Interferometry (BLI) technology for the rapid (5-10 min), noninvasive, and broad-spectrum detection of the SARS-CoV-2 spike receptor binding domain (RBD) in human saliva. The nanoprobe exhibits a higher binding affinity to the RBD compared to most saliva proteins, allowing it to be immobilized on BLI sensors for easier detection of protein binding and elution. An eluent buffer containing Tween-20 and salts was employed to separate salivary proteins while retaining the RBD on the probes. This system can detect the RBD across a broad spectrum and a low limit of 25 ng/mL (S/N = 3) in less than 10 min. To validate this system, experiments with pseudoviruses showed accurate identification and binding of the RBD. Molecular dynamics simulations elucidated the mechanism for selective binding of probes to RBD. In conclusion, we propose a conceptual study based on an in situ strategy with inorganic nanoprobes alongside BLI techniques for convenient, noninvasive, and rapid detection of SARS-CoV-2 and its variants. This strategy is anticipated to inspire the design and implementation of nanoprobes for the rapid and selective detection of pathogens in the future.

Clinical Characteristics of Hospitalized Children With Coronavirus Disease 2019 After the Spread of the BA.5 Omicron Variants in Japan

BACKGROUND

The spread of the BA.5 Omicron variant of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has increased the number of hospitalized children. However, the impact of the spread of new omicron subvariants in children remains poorly described.

METHODS

This prospective observational study evaluated the clinical characteristics of children hospitalized with coronavirus disease 2019 (COVID-19) in 13 hospitals in Niigata, Japan, during September 2022-February 2024. The data were divided and compared across 3 periods based on the dominant subvariants: BA.5/BF.5/BF.7 period (September 2022-April 2023), XBB/EG.5 period (May-December 2023) and BA.2.86/JN.1 periods (January-February 2024). In addition, the COVID-19 vaccination rates in hospitalized patients were compared with those in the general population.

RESULTS

In total, 298 children with COVID-19 were hospitalized during the study period. The patients' median ages were 4.7 years during the BA.5/BF.5/BF.7 period, 1.2 years during the XBB/EG.5 period and 2.4 years during the BA.2.86/JN.1 period. The peak monthly number of admissions decreased over time, with 44, 32, 19 cases/mo during the BA.5/BF.5/BF.7 period, the XBB/EG.5 period and the BA.2.86/JN.1 period, respectively. Dehydration/oral intake failure (37.2%, 111/298) and febrile seizures (16.8%, 50/298) were the predominant reasons for hospitalization. The COVID-19 vaccination rates in hospitalized children 5-11 years of age (11.1%) and 12-15 years of age (38.9%) were significantly lower than those in the general population (41.5% and 71.0%).

CONCLUSIONS

Although the clinical impact of the Omicron subvariants in children diminished over time, they continued to pose a risk. Continued efforts are needed to protect children from this evolving virus.

Impact of Vaccination Status on COVID-19 Severity and Pulmonary Involvement

Background and Objectives: The COVID-19 pandemic has had a significant impact on global health, with serious outcomes, such as lung damage, being major determinants of patient morbidity and mortality. Immunization has been essential in attenuating these outcomes. This study aimed to evaluate the impact of COVID-19 vaccination on disease severity, particularly focusing on pulmonary involvement, among hospitalized patients. Materials and Methods: A retrospective cohort study was conducted at Victor Babes Hospital, Timisoara, involving 3005 patients diagnosed with COVID-19 between December 2020 and March 2022. Patients were stratified into vaccinated and unvaccinated groups. Results: The study found that vaccinated patients had significantly lower rates of severe pulmonary involvement compared to unvaccinated patients. Specifically, only 24.24% of vaccinated patients experienced severe lung involvement, compared to 35.64% in the unvaccinated group (p < 0.001). Vaccinated individuals had shorter hospital stays (8.96 ± 6.40 days vs. 10.70 ± 6.29 days), but this difference was not statistically significant (p = 0.219). Additionally, chronic pulmonary diseases and stroke were less prevalent among vaccinated patients, highlighting the protective effect of vaccination. Conclusions: COVID-19 vaccination significantly reduces the severity of disease, particularly in preventing severe pulmonary involvement, which is a major determinant of patient outcomes. These findings underscore the importance of ongoing vaccination efforts and the need for booster doses to maintain immunity, especially as new variants emerge. The study supports the continued prioritization of vaccination in public health strategies to mitigate the long-term impact of COVID-19.

Genetic diversity and genomic epidemiology of SARS-CoV-2 during the first 3 years of the pandemic in Morocco: comprehensive sequence analysis, including the unique lineage B.1.528 in Morocco

During the 3 years following the emergence of the COVID-19 pandemic, the African continent, like other regions of the world, was substantially impacted by COVID-19. In Morocco, the COVID-19 pandemic has been marked by the emergence and spread of several SARS-CoV-2 variants, leading to a substantial increase in the incidence of infections and deaths. Nevertheless, the comprehensive understanding of the genetic diversity, evolution, and epidemiology of several viral lineages remained limited in Morocco. This study sought to deepen the understanding of the genomic epidemiology of SARS-CoV-2 through a retrospective analysis. The main objective of this study was to analyse the genetic diversity of SARS-CoV-2 and identify distinct lineages, as well as assess their evolution during the pandemic in Morocco, using genomic epidemiology approaches. Furthermore, several key mutations in the functional proteins across different viral lineages were highlighted along with an analysis of the genetic relationships amongst these strains to better understand their evolutionary pathways. A total of 2274 genomic sequences of SARS-CoV-2 isolated in Morocco during the period of 2020 to 2023, were extracted from the GISAID EpiCoV database and subjected to analysis. Lineages and clades were classified according to the nomenclature of GISAID, Nextstrain, and Pangolin. The study was conducted and reported in accordance with STROBE (Strengthening the Reporting of Observational Studies in Epidemiology) guidelines. An exhaustive analysis of 2274 genomic sequences led to the identification of 157 PANGO lineages, including notable lineages such as B.1, B.1.1, B.1.528, and B.1.177, as well as variants such as B.1.1.7, B.1.621, B.1.525, B.1.351, B.1.617.1, B.1.617.2, and its notable sublineages AY.33, AY.72, AY.112, AY.121 that evolved over time before being supplanted by Omicron in December 2021. Among the 2274 sequences analysed, Omicron and its subvariants had a prevalence of 59.5%. The most predominant clades were 21K, 21L, and 22B, which are respectively related phylogenetically to BA.1, BA.2, and BA.5. In June 2022, Morocco rapidly observed a recrudescence of cases of infection, with the emergence and concurrent coexistence of subvariants from clade 22B such as BA.5.2.20, BA.5, BA.5.1, BA.5.2.1, and BF.5, supplanting the subvariants BA.1 (clade display 21K) and BA.2 (clade display 21L), which became marginal. However, XBB (clade 22F) and its progeny such XBB.1.5(23A), XBB.1.16(23B), CH.1.1(23C), XBB.1.9(23D), XBB.2.3(23E), EG.5.1(23F), and XBB.1.5.70(23G) have evolved sporadically. Furthermore, several notable mutations, such as H69del/V70del, G142D, K417N, T478K, E484K, E484A, L452R, F486P, N501Y, Q613H, D614G, and P681H/R, have been identified. Some of these SARS-CoV-2 mutations are known to be involved in increasing transmissibility, virulence, and antibody escape. This study has identified several distinct lineages and mutations involved in the genetic diversity of Moroccan isolates, as well as the analysis of their evolutionary trends. These findings provide a robust basis for better understanding the distinct mutations and their roles in the variation of transmissibility, pathogenicity, and antigenicity (immune evasion/reinfection). Furthermore, the noteworthy number of distinct lineages identified in Morocco highlights the importance of maintaining continuous surveillance of COVID-19. Moreover, expanding vaccination coverage would also help protect patients against more severe clinical disease.

Interplay between Comorbidities and Long COVID: Challenges and Multidisciplinary Approaches

Long COVID, a name often given to the persistent symptoms following acute SARS-CoV-2 infection, poses a multifaceted challenge for health. This review explores the intrinsic relationship between comorbidities and autoimmune responses in shaping the trajectory of long COVID. Autoantibodies have emerged as significant players in COVID-19 pathophysiology, with implications for disease severity and progression. Studies show immune dysregulation persisting months after infection, marked by activated innate immune cells and high cytokine levels. The presence of autoantibodies against various autoantigens suggests their potential as comorbid factors in long COVID. Additionally, the formation of immune complexes may lead to severe disease progression, highlighting the urgency for early detection and intervention. Furthermore, long COVID is highly linked to cardiovascular complications and neurological symptoms, posing challenges in diagnosis and management. Multidisciplinary approaches, including vaccination, tailored rehabilitation, and pharmacological interventions, are used for mitigating long COVID's burden. However, numerous challenges persist, from evolving diagnostic criteria to addressing the psychosocial impact and predicting disease outcomes. Leveraging AI-based applications holds promise in enhancing patient management and improving our understanding of long COVID. As research continues to unfold, unravelling the complexities of long COVID remains paramount for effective intervention and patient care.

Performance evaluation of a newly developed 2019-nCoV nucleic acid detection kit based on Ion Proton sequencing platform and its comparison with the MGI Tech (DNBSEQ-G99) platform

PURPOSE

To evaluate the performance of a newly developed 2019-nCoV nucleic acid detection kit based on Ion Proton sequencing platform and make comparation with MGI Tech (DNBSEQ-G99) platform.

METHODS

References and clinical samples were used to evaluate the precision, agreement rate, limit of detection (LOD), anti-interference ability and analytical specificity. Twenty-seven clinical specimens were used to make comparison between two platforms.

RESULTS

The kit showed good intra-assay, inter-assay, inter-day precision between different operators and laboratories, fine agreement rate with references, a relatively low LOD of 1 × 103 copies/ml, anti-interference capability of 5 % whole blood and 1mg/ml mucin and no cross reaction with twenty-nine common clinical pathogens. Consistency of variant classification was observed between two platforms. The WGS from Ion Proton tended to have higher coverage and less missing data.

CONCLUSIONS

The newly developed kit has shown satisfactory performances and excellent consistency with DNBSEQ-G99, making it a good alternative choice clinically.

Potential immune evasion of the severe acute respiratory syndrome coronavirus 2 Omicron variants

Coronavirus disease 2019 (COVID-19), which is caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has caused a global pandemic. The Omicron variant (B.1.1.529) was first discovered in November 2021 in specimens collected from Botswana, South Africa. Omicron has become the dominant variant worldwide, and several sublineages or subvariants have been identified recently. Compared to those of other mutants, the Omicron variant has the most highly expressed amino acid mutations, with almost 60 mutations throughout the genome, most of which are in the spike (S) protein, especially in the receptor-binding domain (RBD). These mutations increase the binding affinity of Omicron variants for the ACE2 receptor, and Omicron variants may also lead to immune escape. Despite causing milder symptoms, epidemiological evidence suggests that Omicron variants have exceptionally higher transmissibility, higher rates of reinfection and greater spread than the prototype strain as well as other preceding variants. Additionally, overwhelming amounts of data suggest that the levels of specific neutralization antibodies against Omicron variants decrease in most vaccinated populations, although CD4+ and CD8+ T-cell responses are maintained. Therefore, the mechanisms underlying Omicron variant evasion are still unclear. In this review, we surveyed the current epidemic status and potential immune escape mechanisms of Omicron variants. Especially, we focused on the potential roles of viral epitope mutations, antigenic drift, hybrid immunity, and "original antigenic sin" in mediating immune evasion. These insights might supply more valuable concise information for us to understand the spreading of Omicron variants.