Update on the omicron sub-variants BA.4 and BA.5

Virological and Mitochondriopathogical Characteristics of the SARS-CoV-2 Omicron XBB.1.16 Spike

The emergence of XBB.1.16 has gained rapid global prominence. Previous studies have elucidated that the infection of SARS-CoV-2 induces alterations in the mitochondrial integrity of host cells, subsequently influencing the cellular response to infection. In this study, we compared the differences in infectivity and pathogenicity between XBB.1.16 and the parental Omicron sublineages BA.1 and BA.2 and assessed their impact on host mitochondria. Our findings suggest that, in comparison with BA.1 and BA.2, XBB.1.16 exhibits more efficient spike protein cleavage, more efficient mediating syncytia formation, mild mitochondriopathy, and less pathogenicity. Altogether, our investigations suggest that, based on the mutation of key sites, XBB.1.16 exhibited enhanced infectivity but lower pathogenicity. This will help us to further investigate the biological functions of key mutation sites.

SARS-CoV-2 Seroepidemiology and Antibody Levels in Children during BA.5 Predominance Period

This is a SARS-CoV-2 seroepidemiological study in a pediatric population (0-16 years) during the BA.5 Omicron predominance period in the Athens metropolitan area. Serum samples were tested for SARS-CoV-2 nucleocapsid antibodies (Abs-N), representing natural infection during three periods of BA.5 predominance: 1 May 2022-31 August 2022 (period A), 1 September 2022-31 December 2022 (period B), and July 2023 (period C). Εpidemiological data were also collected. Additionally, in period C, Abs-N-seronegative samples were tested for SARS-CoV-2 spike antibodies (Abs-S). A total of 878 children were tested (males: 52.6%), with a median age (IQR) of 96 (36-156) months; the number of cases of seropositivity during the three periods were as follows: A: 292/417 (70%), B: 288/356 (80.9%), and C: 89/105 (84.8%), with p < 0.001. SARS-CoV-2 seropositivity increased from period A to C for children 0-1 year (p = 0.044), >1-4 years (p = 0.028), and >6-12 years (p = 0.003). Children > 6-12 years had the highest seropositivity rates in all periods (A: 77.3%, B: 91.4%, and C: 95.8%). A significant correlation of monthly median Abs-N titers with monthly seropositivity rates was detected (rs: 0.812, p = 0.008). During period C, 12/105 (11.4%) Abs-S-seropositive and Abs-N-seronegative samples were detected and total seropositivity was estimated at 96.2% (101/105). The findings of this study indicate a high SARS-CoV-2 exposure rate of children during the BA.5 predominance period and suggest that in future seroepidemiological studies, both antibodies should be tested in Abs-N-seronegative populations.

SARS-CoV-2 Omicron: Viral Evolution, Immune Evasion, and Alternative Durable Therapeutic Strategies

Since the SARS-CoV-2 Omicron virus has gained dominance worldwide, its continual evolution with unpredictable mutations and patterns has revoked all authorized immunotherapeutics. Rapid viral evolution has also necessitated several rounds of vaccine updates in order to provide adequate immune protection. It remains imperative to understand how Omicron evolves into different subvariants and causes immune escape as this could help reevaluate the current intervention strategies mostly implemented in the clinics as emergency measures to counter the pandemic and, importantly, develop new solutions. Here, we provide a review focusing on the major events of Omicron viral evolution, including the features of spike mutation that lead to immune evasion against monoclonal antibody (mAb) therapy and vaccination, and suggest alternative durable options such as the ACE2-based experimental therapies superior to mAbs to address this unprecedented evolution of Omicron virus. In addition, this type of unique ACE2-based virus-trapping molecules can counter all zoonotic SARS coronaviruses, either from unknown animal hosts or from established wild-life reservoirs of SARS-CoV-2, and even seasonal alpha coronavirus NL63 that depends on human ACE2 for infection.

Emergent emm4 group A Streptococcus evidences a survival strategy during interaction with immune effector cells

The major gram-positive pathogen group A Streptococcus (GAS) is a model organism for studying microbial epidemics as it causes waves of infections. Since 1980, several GAS epidemics have been ascribed to the emergence of clones producing increased amounts of key virulence factors such as streptolysin O (SLO). Herein, we sought to identify mechanisms underlying our recently identified temporal clonal emergence amongst emm4 GAS, given that emergent strains did not produce augmented levels of virulence factors relative to historic isolates. Through the creation and analysis of isoallelic strains, we determined that a conserved mutation in a previously undescribed gene encoding a putative carbonic anhydrase was responsible for the defective in vitro growth observed in the emergent strains. We also identified that the emergent strains survived better inside macrophages and killed macrophages at lower rates relative to the historic strains. Via creation of isogenic mutant strains, we linked the emergent strain "survival" phenotype to the downregulation of the SLO encoding gene and upregulation of the msrAB operon which encodes proteins involved in defense against extracellular oxidative stress. Our findings are in accord with recent surveillance studies which found high ratio of mucosal (i.e., pharyngeal) relative to invasive infections amongst emm4 GAS. Inasmuch as ever-increasing virulence is unlikely to be evolutionary advantageous for a microbial pathogen, our data furthers understanding of the well described oscillating patterns of virulent GAS infections by demonstrating mechanisms by which emergent strains adapt a "survival" strategy to outcompete previously circulating isolates.

Current Progress, Challenges and Prospects in the Development of COVID-19 Vaccines

The COVID-19 pandemic has resulted in over 772 million confirmed cases, including nearly 7 million deaths, according to the World Health Organization (WHO). Leveraging rapid development, accelerated vaccine approval processes, and large-scale production of various COVID-19 vaccines using different technical platforms, the WHO declared an end to the global health emergency of COVID-19 on May 5, 2023. Current COVID-19 vaccines encompass inactivated, live attenuated, viral vector, protein subunit, nucleic acid (DNA and RNA), and virus-like particle (VLP) vaccines. However, the efficacy of these vaccines is diminishing due to the constant mutation of SARS-CoV-2 and the heightened immune evasion abilities of emerging variants. This review examines the impact of the COVID-19 pandemic, the biological characteristics of the virus, and its diverse variants. Moreover, the review underscores the effectiveness, advantages, and disadvantages of authorized COVID-19 vaccines. Additionally, it analyzes the challenges, strategies, and future prospects of developing a safe, broad-spectrum vaccine that confers sufficient and sustainable immune protection against new variants of SARS-CoV-2. These discussions not only offer insight for the development of next-generation COVID-19 vaccines but also summarize experiences for combating future emerging viruses.

Feature selection for effective prediction of SARS-COV-2 using machine learning

BACKGROUND

With rise in variants of SARS-CoV-2, it is necessary to classify the emerging SARS-CoV-2 for early detection and thereby reduce human transmission. Genomic and proteomic information have less frequently been used for classifying in a machine learning (ML) approach for detection of SARS-CoV-2.

OBJECTIVE

With this aim we used nucleoprotein and viral proteomic evolutionary information of SARS-CoV-2 along with the charge and basicity distribution of amino acids from various strains of SARS-CoV-2 to generate a disease severity model based on ML.

METHODS

All sequence and clinical data were obtained from GISAID. Proteomic level calculations were added to comprise the dataset. The training set was used for feature selection. Select K- Best feature selection method was employed which was cross validated with testing set and performance evaluated. Delong's test was also done. We also employed BIRCH clustering on SARS-CoV-2 for clustering the strains.

RESULTS

Out of six ML models four were successful in training and testing. Extra Trees algorithm generated a micro-averaged F1-score of 74.2% and a weighted averaged area under the receiver operating characteristic curve (AUC-ROC) score of 73.7% with multi-class option. The feature selection set to 5, enhanced the ROC AUC from 73.7 to 76.4%. Accuracy of the selected model of 86.9% was achieved.

CONCLUSION

The unique features identified in the ML approach was able to classify disease severity into classes and had potential for predicting risk in newer variants.

Impact of vaccination on morbidity and mortality in adults hospitalized with COVID-19 during the omicron wave in the Jazan Region, Saudi Arabia

OBJECTIVES

To evaluate the impact of coronavirus disease-19 (COVID-19) vaccination on morbidity and mortality in adults hospitalized with COVID-19 during the omicron wave in the Jazan Region, Saudi Arabia.

METHODS

A 6-month record-based historical prospective study enrolled COVID-19 adult patients admitted between January and June 2022. Individuals were classified into 3 groups according to their immunity status (immunized, partially immunized, and not immunized). Death, intensive care unit (ICU) admission, and mechanical ventilation were identified as the primary outcomes, collectively referred to as "serious outcomes". On the other hand, the length of hospital stays longer than 5 days was categorized as a secondary outcome. Multiple logistic regression analysis was used to evaluate independent factors and the relationship between the outcomes and vaccination status.

RESULTS

Among the 634 COVID-19 patients admitted to Jazan hospitals, 46.4% were fully immunized, 19.7% were partially immunized, and 33.9% were not immunized. Not being immunized was significantly associated with ICU admission (odds ratio [OR]=1.91, 95% confidence interval [CI]: [1.17-3.11]; p=0.009), mechanical ventilation (OR=2.11, 95% CI: [1.25-3.56]; p=0.005), increased length of hospital stays (OR=1.79, 95% CI: [1.24-2.59]; p=0.002), and death (OR=3.03, 95% CI: [1.85-4.98]; p<0.001).

CONCLUSION

Our study underscores the importance of a comprehensive approach for managing COVID-19 patients that includes vaccination against the disease.

Seizures in hospitalised paediatric patients with SARS-CoV-2 and comparison of severity with seizures in hospitalised paediatric patients with other respiratory viruses during the COVID-19 pandemic: a population-based cohort study

OBJECTIVE

To study seizures in patients hospitalised due to SARS-CoV-2 infection, and compare their severity with seizures in patients hospitalised due to other viral respiratory tract infections (RTIs).

DESIGN

Observational population-based cohort study.

SETTING

Northern Stockholm.

PATIENTS

Patients aged 1 month-18 years hospitalised due to SARS-CoV-2 with and without seizures, and patients of the same age hospitalised due to other viral RTIs with seizures, between 1 March 2020 and 30 June 2022.

MAIN OUTCOME MEASURES

The prevalence of seizures in hospitalised patients due to SARS-CoV-2, the evaluation of assumed predictors of seizures and the comparison of severity markers in patients with SARS-CoV-2 versus other RTIs.

RESULTS

32 of 239 included patients (13.4%) admitted due to SARS-CoV-2 infection had seizures. Central nervous system (CNS) disease and the omicron period had significantly increased OR for seizures (OR: 5.12; CI: 2.06 to 12.72 and OR: 3.01; CI: 1.15 to 7.88, respectively). Seizures in patients with SARS-CoV-2 were more common in children older than 5 years (p=0.001), even in the absence of fever (p=0.007), as compared with other viral RTIs. The duration of hospitalisation was longer in patients with seizures due to other viral RTIs (p=0.023). There was no significant difference regarding severity markers of seizures between the two groups.

CONCLUSIONS

CNS disease and the omicron period were risk factors for seizures in patients with SARS-CoV-2, who were older than patients with other RTIs. The severity of seizures was comparable between the two groups; hospitalisation was however longer in patients with other RTIs.

Zoonosis and zooanthroponosis of emerging respiratory viruses

Lung infections in Influenza-Like Illness (ILI) are triggered by a variety of respiratory viruses. All human pandemics have been caused by the members of two major virus families, namely Orthomyxoviridae (influenza A viruses (IAVs); subtypes H1N1, H2N2, and H3N2) and Coronaviridae (severe acute respiratory syndrome coronavirus 2, SARS-CoV-2). These viruses acquired some adaptive changes in a known intermediate host including domestic birds (IAVs) or unknown intermediate host (SARS-CoV-2) following transmission from their natural reservoirs (e.g. migratory birds or bats, respectively). Verily, these acquired adaptive substitutions facilitated crossing species barriers by these viruses to infect humans in a phenomenon that is known as zoonosis. Besides, these adaptive substitutions aided the variant strain to transmit horizontally to other contact non-human animal species including pets and wild animals (zooanthroponosis). Herein we discuss the main zoonotic and reverse-zoonosis events that occurred during the last two pandemics of influenza A/H1N1 and SARS-CoV-2. We also highlight the impact of interspecies transmission of these pandemic viruses on virus evolution and possible prophylactic and therapeutic interventions. Based on information available and presented in this review article, it is important to close monitoring viral zoonosis and viral reverse zoonosis of pandemic strains within a One-Health and One-World approach to mitigate their unforeseen risks, such as virus evolution and resistance to limited prophylactic and therapeutic interventions.

Adjuvant activities of immunostimulating natural products: Astragalus membranaceus (Fisch.) Bge. and Coriolus versicolor in BNT162b2 vaccination against COVID-19 infection

The global pandemic of COVID-19, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been developing all over the world for more than 3 years. In late 2020, several variants of concern of SARS-CoV-2 virus emerged, with increased viral fitness and transmissibility by mutations of the spike proteins of the viral particle, denting hopes of the use of early-generation vaccines for a widespread protective immunity against viral infection. The use of adjuvants may enhance the immune responses of the conventional application of the COVID-19 vaccine. We have shown that the water extract of 2 β-glucan-enriched immunostimulating natural products, Astragalus membranaceus (Fisch.) Bge. (AM) and Coriolus versicolor (CV), could induce innate immunity-related cytokines from human monocytes (CCL5, interleukin [IL]-6, IL-10, and tumor necrosis factor α) and monocyte-derived dendritic cells (IL-1β, IL-10, IL-12, and tumor necrosis factor α). Using BALB/c mice, orally administrated AM and CV (1,384 and 742 mg/kg/d) for 4 d after vaccination, respectively, could enhance (1) the immunoglobulin G binding activities of BNT162b2 vaccination against ancestral and Delta SARS-CoV-2 spike proteins by 5.8- and 4.3-fold, respectively; (2) the immunoglobulin G3 subclass production of BNT162b2 vaccination against ancestral and variant SARS-CoV-2 spike proteins; and (3) the in vitro antibody-neutralizing activities of BNT162b2 vaccinated mice. In conclusion, combining AM and CV was effective in acting as an oral adjuvant with the messenger RNA vaccine BNT162b2 to improve the antigen binding activities against SARS-CoV-2 ancestral and variant SARS-CoV-2 spike proteins, probably via trained immunity of macrophages and dendritic cells.

From Archipelago to Pandemic Battleground: Unveiling Indonesia's COVID-19 Crisis

The coronavirus disease 2019 (COVID-19) pandemic has posed unprecedented challenges to countries worldwide, including Indonesia. With its unique archipelagic geography consisting of more than 17,000 thousand islands, Indonesia faces unique complexities in managing the spread of the virus. Based on existing literature, this review article elaborates on key issues that have shaped Indonesia's COVID-19 response. The article begins by examining the early stages of the COVID-19 pandemic in Indonesia, along with the implementation of various preventive measures and the impact of the virus on public health. This article examines how Indonesia's socio-economic factors have generally influenced its healthcare system and further delves into the COVID-19 response strategies implemented by the Indonesian government and public health authorities as well as overall crisis preparedness. It discusses the actions taken to control the spread of the virus, including testing strategies and vaccination efforts. The difficulties encountered in implementing these measures are presented. In conclusion, this review article provides a comprehensive understanding of the COVID-19 crisis in Indonesia, covering facts on multiple dimensions ranging from the timeline of the pandemic to vaccination efforts, epidemiology, socio-economic implications, testing strategies, mobility patterns, public holidays, the impact of working from home, and the utilization of complementary and alternative medicine in addition to the standard of care for COVID-19. The insights gained from this article can complement future strategies for pandemic management and response in Indonesia and other countries facing similar challenges.

Comparative Computational Analysis of Spike Protein Structural Stability in SARS-CoV-2 Omicron Subvariants

The continuous emergence of new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with multiple spike (S) protein mutations pose serious threats to current coronavirus disease 2019 (COVID-19) therapies. A comprehensive understanding of the structural stability of SARS-CoV-2 variants is vital for the development of effective therapeutic strategies as it can offer valuable insights into their potential impact on viral infectivity. S protein mediates a virus' attachment to host cells by binding to angiotensin-converting enzyme 2 (ACE2) through its receptor-binding domain (RBD), and mutations in this protein can affect its stability and binding affinity. We analyzed S protein structural stability in various Omicron subvariants computationally. Notably, the S protein sequences analyzed in this work were obtained directly from our own sample collection. We evaluated the binding free energy between S protein and ACE2 in several complex forms. Additionally, we measured distances between the RBD of each chain in S protein to analyze conformational changes. Unlike most of the prior studies, we analyzed full-length S protein-ACE2 complexes instead of only RBD-ACE2 complexes. Omicron subvariants including BA.1, BA.2, BA.2.12.1, BA.4/BA.5, BA.2.75, BA.2.75_K147E, BA.4.6 and BA.4.6_N658S showed enhanced stability compared to wild type, potentially due to distinct S protein mutations. Among them, BA.2.75 and BA.4.6_N658S exhibited the highest and lowest level of stability, respectively.

Antibody response to inactivated COVID-19 vaccine in patients with type 2 diabetes mellitus after the booster immunization

BACKGROUND

The immunogenicity of booster inactivated COVID-19 vaccines in patients with type 2 diabetes mellitus (T2DM) has remained unclear. Our study aims to investigate the antibody response to inactivated COVID-19 vaccine following booster vaccination in patients with T2DM.

METHODS

A total of 201 patients with T2DM and 102 healthy controls (HCs) were enrolled. The levels of anti-SARS-CoV-2 total antibodies, anti-receptor-binding domain (RBD)-specific IgG, neutralizing antibody (NAb) toward SARS-CoV-2 wild type (WT), and NAb toward SARS-CoV-2 Omicron BA.4/5 subvariant were measured to evaluate the vaccine-induced immunological responses.

RESULTS

The titers of anti-RBD-specific IgG (p = 0.018) and inhibition rates of NAb toward WT (p = 0.007) were significantly decreased in patients with T2DM compared to HCs after booster vaccination for more than 6 months. Both HCs and patients with T2DM showed poor resistance against BA.4/5 due to the detected inhibition rates being lower than the positive threshold. The levels of anti-RBD-specific IgG were positively associated with the proportions of CD3+ CD4- CD8- T cells (p = 0.045), and patients with T2DM who had anti-RBD-specific IgG positivity showed higher proportions of CD3+ CD4- CD8- T cells compared to those negative (p = 0.005).

CONCLUSIONS

Patients with T2DM showed impaired antibody responses after booster vaccination for more than 6 months. Decreased anti-BA.4/5 responses give rise to the possibility of breakthrough infections for both patients with T2DM and HCs.

First identification of the SARS-COV-2/XBB.1.5 sublineage among indigenous COVID-19 cases through the influenza sentinel surveillance system in Niger

The emergence of the Omicron variant in November 2021, has caused panic worldwide due to the rapid evolution and the ability of the virus to escape the immune system. Since, several Omicron sublineages (BA.1 to BA.5) and their descendent recombinant lineages have been circulating worldwide. Furthermore, in December 2022, a new Omicron subvariant XBB.1.5 characterized by an unusual mutation in the spike protein evolved in the United States and rapidly spread to the other continents. Our study reports on the first cases of XBB.1.5 sublineage among indigenous Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-COV-2) positive cases detected through the influenza sentinel surveillance system in Niger. All influenza suspected cases were tested for both influenza and SARS-COV-2 using the Centre for Disease Control and prevention (CDC) Influenza SARS-COV-2 Multiplex quantitative Reverse-Transcription Polymerase Chain Reaction (qRT-PCR) Assay. SARS-COV-2 positive samples with cycle threshold ≤28 were selected for whole genome sequencing subsequently using the Oxford Nanopore Midnight protocol with rapid barcoding on a MinIon MK1B device. A total of 51 SARS-COV-2 positive samples were confirmed between December 2022 and March 2023. We successfully obtained 19 sequences with a predominance of the XBB.1/XBB.1.5 sublineages (73.7 %). In addition, a recombinant XBD sequence was also first-ever identified in early March 2023. Our findings support the need to strengthen the influenza sentinel surveillance for routine Coronavirus Disease 2019 (COVID-19) surveillance and SARS-COV-2 variants monitoring in Niger.

Editorial: A Rapid Global Increase in COVID-19 is Due to the Emergence of the EG.5 (Eris) Subvariant of Omicron SARS-CoV-2

A new variant of SARS-CoV-2 has currently achieved global domination. EG.5 (Eris) was first reported by the World Health Organization (WHO) on February 17, 2023, and designated as a variant under monitoring (VUM) on July 19, 2023. EG.5 (Eris), and its sublineages, EG.5.1, EG.5.1.1, and EG.5.2, is a descendent lineage of XBB.1.9.2, which has the same spike amino acid profile as XBB.1.5 (Kraken). However, EG.5 (Eris) has an additional F456L amino acid mutation in the spike protein compared to these parent subvariants, and the subvariant EG.5.1 has another spike mutation, Q52H. Following risk evaluation by the WHO, EG.5 (Eris) and its sublineages were designated as a variant of interest (VOI) on August 8, 2023. In the US, the Centers for Disease Control and Prevention (CDC) provides two-weekly monitoring data on the incidence and mortality from COVID-19 and SARS-CoV-2 variants. The most recent CDC data for August 19, 2023, showed an increase in cases in the past two weeks, with hospitalizations for COVID-19 increasing by 14.3% and mortality from COVID-19 rising by 8.3%. In the US, the most common COVID-19 cases have been due to three new SARS-CoV-2 Omicron variants: EG.5 (Eris) (20.6%); FL.1.5.1 (Fornax) (13.3%); and XBB.1.16 (Arcturus) (10.7%). This Editorial aims to highlight the importance of rapid virus genomic sequencing and continued global SARS-CoV-2 surveillance to identify rapidly emerging SARS-CoV-2 Omicron variants, such as EG.5 (Eris).

Novel receptor, mutation, vaccine, and establishment of coping mode for SARS-CoV-2: current status and future

Since the outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its resultant pneumonia in December 2019, the cumulative number of infected people worldwide has exceeded 670 million, with over 6.8 million deaths. Despite the marketing of multiple series of vaccines and the implementation of strict prevention and control measures in many countries, the spread and prevalence of SARS-CoV-2 have not been completely and effectively controlled. The latest research shows that in addition to angiotensin converting enzyme II (ACE2), dozens of protein molecules, including AXL, can act as host receptors for SARS-CoV-2 infecting human cells, and virus mutation and immune evasion never seem to stop. To sum up, this review summarizes and organizes the latest relevant literature, comprehensively reviews the genome characteristics of SARS-CoV-2 as well as receptor-based pathogenesis (including ACE2 and other new receptors), mutation and immune evasion, vaccine development and other aspects, and proposes a series of prevention and treatment opinions. It is expected to provide a theoretical basis for an in-depth understanding of the pathogenic mechanism of SARS-CoV-2 along with a research basis and new ideas for the diagnosis and classification, of COVID-19-related disease and for drug and vaccine research and development.

Detection of SARS-CoV-2 Based on Nucleic Acid Amplification Tests (NAATs) and Its Integration into Nanomedicine and Microfluidic Devices as Point-of-Care Testing (POCT)

The coronavirus SARS-CoV-2 has highlighted the criticality of an accurate and rapid diagnosis in order to contain the spread of the virus. Knowledge of the viral structure and its genome is essential for diagnosis development. The virus is still quickly evolving and the global scenario could easily change. Thus, a greater range of diagnostic options is essential to face this threat to public health. In response to the global demand, there has been a rapid advancement in the understanding of current diagnostic methods. In fact, innovative approaches have emerged, leveraging the benefits of nanomedicine and microfluidic technologies. Although this development has been incredibly fast, several key areas require further investigation and optimization, such as sample collection and preparation, assay optimization and sensitivity, cost effectiveness, scalability device miniaturization, and portability and integration with smartphones. Addressing these gaps in the knowledge and these technological challenges will contribute to the development of reliable, sensitive, and user-friendly NAAT-based POCTs for the diagnosis of SARS-CoV-2 and other infectious diseases, facilitating rapid and effective patient management. This review aims to provide an overview of current SARS-CoV-2 detection methods based on nucleic acid detection tests (NAATs). Additionally, it explores promising approaches that combine nanomedicine and microfluidic devices with high sensitivity and relatively fast 'time to answer' for integration into point-of-care testing (POCT).

Detection of SARS-CoV-2 Variants via Different Diagnostics Assays Based on Single-Nucleotide Polymorphism Analysis

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is characterized by fast evolution with the appearance of several variants. Next-Generation Sequencing (NGS) technology is considered the gold standard for monitoring known and new SARS-CoV-2 variants. However, the complexity of this technology renders this approach impracticable in laboratories located in areas with limited resources. We analyzed the capability of the ThermoFisher TaqPath COVID-19 RT-PCR (TaqPath) and the Seegene Novaplex SARS-CoV-2 Variant assay (Novaplex) to detect Omicron variants; the Allplex VariantII (Allplex) was also evaluated for Delta variants. Sanger sequencing (SaS) was the reference method. The results obtained with n = 355 nasopharyngeal samples were: negative with TaqPath, although positive with other qualitative molecular assays (n = 35); undetermined (n = 40) with both the assays; negative for the ∆69/70 mutation and confirmed as the Delta variant via SaS (n = 100); positive for ∆69/70 and confirmed as Omicron BA.1 via SaS (n = 80); negative for ∆69/70 and typed as Omicron BA.2 via SaS (n = 80). Novaplex typed 27.5% of samples as undetermined with TaqPath, 11.4% of samples as negative with TaqPath, and confirmed 100% of samples were Omicron subtypes. In total, 99/100 samples were confirmed as the Delta variant with Allplex with a positive per cent agreement (PPA) of 98% compared to SaS. As undermined samples with Novaplex showed RdRp median Ct values (Ct = 35.4) statistically higher than those of typed samples (median Ct value = 22.0; p < 0.0001, Mann-Whitney test), the inability to establish SARS-CoV-2 variants was probably linked to the low viral load. No amplification was obtained with SaS among all 35 negative TaqPath samples. Overall, 20% of samples which were typed as negative or undetermined with TaqPath, and among them, twelve were not typed even by SaS, but they were instead correctly identified with Novaplex. Although full-genome sequencing remains the elected method to characterize new strains, our data show the high ability of a SNP-based assay to identify VOCs, also resolving samples typed as undetermined with TaqPath.

Peculiar weather patterns effects on air pollution and COVID-19 spread in Tokyo metropolis

As a pandemic hotspot in Japan, between March 1, 2020-October 1, 2022, Tokyo metropolis experienced seven COVID-19 waves. Motivated by the high rate of COVID-19 incidence and mortality during the seventh wave, and environmental/health challenges we conducted a time-series analysis to investigate the long-term interaction of air quality and climate variability with viral pandemic in Tokyo. Through daily time series geospatial and observational air pollution/climate data, and COVID-19 incidence and death cases, this study compared the environmental conditions during COVID-19 multiwaves. In spite of five State of Emergency (SOEs) restrictions associated with COVID-19 pandemic, during (2020-2022) period air quality recorded low improvements relative to (2015-2019) average annual values, namely: Aerosol Optical Depth increased by 9.13% in 2020 year, and declined by 6.64% in 2021, and 12.03% in 2022; particulate matter PM2.5 and PM10 decreased during 2020, 2021, and 2022 years by 10.22%, 62.26%, 0.39%, and respectively by 4.42%, 3.95%, 5.76%. For (2021-2022) period the average ratio of PM2.5/PM10 was (0.319 ± 0.1640), showing a higher contribution to aerosol loading of traffic-related coarse particles in comparison with fine particles. The highest rates of the daily recorded COVID-19 incidence and death cases in Tokyo during the seventh COVID-19 wave (1 July 2022-1 October 2022) may be attributed to accumulation near the ground of high levels of air pollutants and viral pathogens due to: 1) peculiar persistent atmospheric anticyclonic circulation with strong positive anomalies of geopotential height at 500 hPa; 2) lower levels of Planetary Boundary Layer (PBL) heights; 3) high daily maximum air temperature and land surface temperature due to the prolonged heat waves (HWs) in summer 2022; 4) no imposed restrictions. Such findings can guide public decision-makers to design proper strategies to curb pandemics under persistent stable anticyclonic weather conditions and summer HWs in large metropolitan areas.

Next-generation nanophotonic-enabled biosensors for intelligent diagnosis of SARS-CoV-2 variants

Constantly mutating SARS-CoV-2 is a global concern resulting in COVID-19 infectious waves from time to time in different regions, challenging present-day diagnostics and therapeutics. Early-stage point-of-care diagnostic (POC) biosensors are a crucial vector for the timely management of morbidity and mortalities caused due to COVID-19. The state-of-the-art SARS-CoV-2 biosensors depend upon developing a single platform for its diverse variants/biomarkers, enabling precise detection and monitoring. Nanophotonic-enabled biosensors have emerged as 'one platform' to diagnose COVID-19, addressing the concern of constant viral mutation. This review assesses the evolution of current and future variants of the SARS-CoV-2 and critically summarizes the current state of biosensor approaches for detecting SARS-CoV-2 variants/biomarkers employing nanophotonic-enabled diagnostics. It discusses the integration of modern-age technologies, including artificial intelligence, machine learning and 5G communication with nanophotonic biosensors for intelligent COVID-19 monitoring and management. It also highlights the challenges and potential opportunities for developing intelligent biosensors for diagnosing future SARS-CoV-2 variants. This review will guide future research and development on nano-enabled intelligent photonic-biosensor strategies for early-stage diagnosing of highly infectious diseases to prevent repeated outbreaks and save associated human mortalities.

Systematic Guidelines for Effective Utilization of COVID-19 Databases in Genomic, Epidemiologic, and Clinical Research

The pandemic has led to the production and accumulation of various types of data related to coronavirus disease 2019 (COVID-19). To understand the features and characteristics of COVID-19 data, we summarized representative databases and determined the data types, purpose, and utilization details of each database. In addition, we categorized COVID-19 associated databases into epidemiological data, genome and protein data, and drug and target data. We found that the data present in each of these databases have nine separate purposes (clade/variant/lineage, genome browser, protein structure, epidemiological data, visualization, data analysis tool, treatment, literature, and immunity) according to the types of data. Utilizing the databases we investigated, we created four queries as integrative analysis methods that aimed to answer important scientific questions related to COVID-19. Our queries can make effective use of multiple databases to produce valuable results that can reveal novel findings through comprehensive analysis. This allows clinical researchers, epidemiologists, and clinicians to have easy access to COVID-19 data without requiring expert knowledge in computing or data science. We expect that users will be able to reference our examples to construct their own integrative analysis methods, which will act as a basis for further scientific inquiry and data searching.

Monitoring and immunogenicity of SARS-CoV-2 vaccination of laboratory rhesus monkeys (Macaca mulatta)

The availability of effective vaccines and a high vaccination rate allowed the recent mitigation, or even withdrawal, of many protective measures for containing the SARS CoV-2 pandemic. At the same time, new and highly mutated variants of the virus are found to have significantly higher transmissibility and reduced vaccine efficacy, thus causing high infection rates during the third year of the pandemic. The combination of reduced measures and increased infectivity poses a particular risk for unvaccinated individuals, including animals susceptible to the virus. Among the latter, non-human primates (NHPs) are particularly vulnerable. They serve as important models in various fields of biomedical research and because of their cognitive capabilities, they receive particular attention in animal welfare regulations around the world. Yet, although they played an extraordinarily important role for developing and testing vaccines against SARS-CoV-2, the protection of captive rhesus monkeys against Covid-19 has rarely been discussed. We here report upon twofold mRNA vaccination of a cohort of 19 elderly rhesus monkeys (Macaca mulatta) against infection by SARS-CoV-2. All animals were closely monitored on possible side effects of vaccination, and were tested for neutralising antibodies against the virus. The data show that vaccination of rhesus monkeys is a safe and reliable measure to protect these animals against SARS-CoV-2.

Infection Control in Dental Practice during the COVID-19 Pandemic: What Is Changed?

The COVID-19 pandemic has profoundly changed our lives. Since the SARS-CoV-2 was discovered, many studies have been done on the transmission mode, its replication within humans, and its survival even in the outside environment and on inanimate surfaces. Undoubtedly, health care workers have faced the greatest risks because of their close contact with potentially infected patients. Of these, dental health care professionals are certainly among the most vulnerable categories, precisely because infection occurs with the airborne virus. The treatment of patients within the dental office has changed profoundly, respecting all preventive measures towards the patient and the practitioners themselves. The aim of this paper is to understand whether the protocols changed for the prevention of SARS-CoV-2 infection among dentists remained even after the most acute phase of the pandemic. In particular, this study analyzed habits, protocols, preventive measures, and any costs incurred in the COVID-19 era for the prevention of SARS-CoV-2 infection among dental workers and patients.

BA.1, BA.2 and BA.2.75 variants show comparable replication kinetics, reduced impact on epithelial barrier and elicit cross-neutralizing antibodies

The Omicron variant of SARS-CoV-2 is capable of infecting unvaccinated, vaccinated and previously-infected individuals due to its ability to evade neutralization by antibodies. With multiple sub-lineages of Omicron emerging in the last 12 months, there is inadequate information on the quantitative antibody response generated upon natural infection with Omicron variant and whether these antibodies offer cross-protection against other sub-lineages of Omicron variant. In this study, we characterized the growth kinetics of Kappa, Delta and Omicron variants of SARS-CoV-2 in Calu-3 cells. Relatively higher amounts infectious virus titers, cytopathic effect and disruption of epithelial barrier functions was observed with Delta variant whereas infection with Omicron sub-lineages led to a more robust induction of interferon pathway, lower level of virus replication and mild effect on epithelial barrier. The replication kinetics of BA.1, BA.2 and BA.2.75 sub-lineages of the Omicron variant were comparable in cell culture and natural infection in a subset of individuals led to a significant increase in binding and neutralizing antibodies to the Delta variant and all the three sub-lineages of Omicron but the level of neutralizing antibodies were lowest against the BA.2.75 variant. Finally, we show that Cu2+, Zn2+ and Fe2+ salts inhibited in vitro RdRp activity but only Cu2+ and Fe2+ inhibited both the Delta and Omicron variants in cell culture. Thus, our results suggest that high levels of interferons induced upon infection with Omicron variant may counter virus replication and spread. Waning neutralizing antibody titers rendered subjects susceptible to infection by Omicron variants and natural Omicron infection elicits neutralizing antibodies that can cross-react with other sub-lineages of Omicron and other variants of concern.

Safety and immunogenicity of a mosaic vaccine booster against Omicron and other SARS-CoV-2 variants: a randomized phase 2 trial

An ongoing randomized, double-blind, controlled phase 2 trial was conducted to evaluate the safety and immunogenicity of a mosaic-type recombinant vaccine candidate, named NVSI-06-09, as a booster dose in subjects aged 18 years and older from the United Arab Emirates (UAE), who had administered two or three doses of inactivated vaccine BBIBP-CorV at least 6 months prior to enrollment. The participants were randomly assigned with 1:1 to receive a booster dose of NVSI-06-09 or BBIBP-CorV. The primary outcomes were immunogenicity and safety against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant, and the exploratory outcome was cross-immunogenicity against other circulating strains. Between May 25 and 30, 2022, 516 adults received booster vaccination with 260 in NVSI-06-09 group and 256 in BBIBP-CorV group. Interim results showed a similar safety profile between two booster groups, with low incidence of adverse reactions of grade 1 or 2. For immunogenicity, by day 14 post-booster, the fold rises in neutralizing antibody geometric mean titers (GMTs) from baseline elicited by NVSI-06-09 were remarkably higher than those by BBIBP-CorV against the prototype strain (19.67 vs 4.47-fold), Omicron BA.1.1 (42.35 vs 3.78-fold), BA.2 (25.09 vs 2.91-fold), BA.4 (22.42 vs 2.69-fold), and BA.5 variants (27.06 vs 4.73-fold). Similarly, the neutralizing GMTs boosted by NVSI-06-09 against Beta and Delta variants were also 6.60-fold and 7.17-fold higher than those by BBIBP-CorV. Our findings indicated that a booster dose of NVSI-06-09 was well-tolerated and elicited broad-spectrum neutralizing responses against divergent SARS-CoV-2 variants, including Omicron and its sub-lineages.

Chronobiological Efficacy of Combined Therapy of Pelargonium Sidoides and Melatonin in Acute and Persistent Cases of COVID-19: A Hypothetical Approach

Since the outbreak of the first SARS-CoV-2 epidemic in China, pharmacists have rapidly engaged and developed strategies for pharmaceutical care and supply. According to the guidelines of the International Pharmaceutical Federation (FIP), clinical pharmacists/hospital pharmacists, as members of care teams, play one of the most important roles in the pharmaceutical care of patients with COVID-19. During this pandemic, many immuno-enhancing adjuvant agents have become critical in addition to antivirals and vaccines in order to overcome the disease more easily. The liquid extract obtained from the Pelargonium sidoides plant is used for many indications such as colds, coughs, upper respiratory tract infections, sore throat, and acute bronchitis. The extract obtained from the roots of the plant has been observed to have antiviral and immunomodulatory activity. In addition to its anti-inflammatory and antioxidant effects, melatonin plays a role in suppressing the cytokine storm that can develop during COVID-19 infection. Knowing that the severity and duration of COVID-19 symptoms vary within 24 hours and/or in different time periods indicates that COVID-19 requires a chronotherapeutic approach. Our goal in the management of acute and long COVID is to synchronize the medication regimen with the patient's biological rhythm. This chapter provides a comprehensive review of the existing and emerging literature on the chronobiological use of Pelargonium sidoides and melatonin during acute and prolonged COVID-19 episodes.

Mapping the Early Dispersal Patterns of SARS-CoV-2 Omicron BA.4 and BA.5 Subvariants in the Absence of Travel Restrictions and Testing at the Borders in Europe

The circulation of SARS-CoV-2 omicron BA.4 and BA.5 subvariants with enhanced transmissibility and capacity for immune evasion resulted in a recent pandemic wave that began in April-May of 2022. We performed a statistical phylogeographic study that aimed to define the cross-border transmission patterns of BA.4 and BA.5 at the earliest stages of virus dispersal. Our sample included all BA.4 and BA.5 sequences that were publicly available in the GISAID database through mid-May 2022. Viral dispersal patterns were inferred using maximum likelihood phylogenetic trees with bootstrap support. We identified South Africa as the major source of both BA.4 and BA.5 that migrated to other continents. By contrast, we detected no significant export of these subvariants from Europe. Belgium was identified as a major hub for BA.4 transmission within Europe, while Portugal and Israel were identified as major sources of BA.5. Western and Northern European countries exhibited the highest rates of cross-border transmission, as did several popular tourist destinations in Southern and Central/Western Europe. Our study provides a detailed map of the early dispersal patterns of two highly transmissible SARS-CoV-2 omicron subvariants at a time when there was an overall relaxation of public health measures in Europe.

An average of nearly 200,000 new infections per day over a six-week period: What is the impact of such a severe COVID-19 pandemic on the healthcare system in Japan?

During a six-week period from July 20 to August 31, 2022, Japan experienced its highest level of COVID-19 infection ever, with an average of nearly 200,000 new infections per day nationwide. Cases requiring inpatient care peaked at 1,993,062. Twenty-seven prefectures (out of 47 prefectures) had an average hospital bed occupancy of 50% or higher, and bed occupancy in Kanagawa in particular reached 98% in mid-August. In Tokyo, bed occupancy by patients with severe COVID-19 reached 57% and peaked at 64% in mid-August. Although the number of new infections per day has decreased since September, hospital bed occupancy, the number of severe cases, and deaths remain high nationwide. Efforts including vaccination campaigns, domestic surveillance, and routine infection control measures based on the varied knowledge that the Japanese public already has should be thoroughly implemented to reduce the number of the infected in order to avoid an increase the number of serious cases and deaths.