The recently emerged BA.4 and BA.5 lineages of Omicron and their global health concerns amid the ongoing wave of COVID-19 pandemic - Correspondence

Recent SARS-CoV-2 evolution trajectories indicate the emergence of Omicron's several subvariants and the current rise of KP.3.1.1 and XEC

The recent COVID-19 pandemic is one of the quickest-evolving pandemics in the world history. Therefore, the evolution of SARS-CoV-2 needs to be tracked consistently. Various VOIs, VOCs, and recent subvariants of Omicron have emerged from the dynamically evolving SARS-CoV-2. Various offspring of the Omicron subvariants have emerged since its origin, including lineages such as BA, BQ, and XBB, as well as more recent subvariants like BA.2.86, JN.1, JN.11.1, KP.3, KP.3.1.1, and XEC. The study evaluated the overall and one year evolutionary patterns, genome diversity, divergence event, transmission and geographical distributions, circulating frequency, entropy diversity, mutational diversity, risk mutations in S-protein and mutational fitness of the subvariants. The study estimated the substitution rate of all variants and subvariants of SARS-CoV-2 since its origin (32.001 × 10-4 subs/year). The geographical distributions of the recent KP.3.1.1 and XEC subvariant indicated its distribution in North America, South America, Europe, and Southeast Asia. Simultaneously, genome mutational landscapes were noted, including Spike and RBD mutations. We found that JN.1, JN.1.11.1, KP.3, KP.3.1.1 and XEC subvariants have gained the highest mutational fitness in Europe and North America. Our study indicates that the rapid evolution and highest frequency of mutational fitness have created a variety of subvariants from Omicron. It also indicates a shift from waves to mini-waves. Finally, our possible explanation is that mutation-driven divergent evolution contributes to the emergence of recent subvariants.

Vaccination burnout impedes the compliance with multiple-dose administration of vaccines

Timely and complete administration of multiple-dose vaccines is essential to guarantee the efficacy. Our study aimed to investigate how people's vaccination attitudes changed over the course of the multi-dose vaccination schedule and comprehensively reported a phenomenon of vaccination burnout. The participants' vaccination burnout levels were quantified by our designed vaccination burnout scale. This study is a retrospective cross-sectional study. Among 3068 valid participants, 2991 had finished the routine two shots of COVID-19 vaccine, and 2367 had a positive attitude towards the primary doses of vaccination. Notably, 232 participants who previously had a positive attitude towards primary doses of vaccination refused to take additional multiple shots, and another 83 had changed their positive attitudes to negative, despite having taken the third shot. Participants whose attitudes or behaviors had changed had higher scores of vaccination burnout than those who still maintained a positive attitude (Z=-8.491, P < .001). The frequency of actively paying attention to the related disease news, occupation, monthly income, and residence of the participants were key factors associated with the vaccination burnout. Interventions should be implemented to alleviate the exhausted attitudes and improve people's compliance with vaccination schedules against the future pandemic.

Impact of African-Specific ACE2 Polymorphisms on Omicron BA.4/5 RBD Binding and Allosteric Communication Within the ACE2-RBD Protein Complex

Severe acute respiratory symptom coronavirus 2 (SARS-CoV-2) infection occurs via the attachment of the spike (S) protein's receptor binding domain (RBD) to human ACE2 (hACE2). Natural polymorphisms in hACE2, particularly at the interface, may alter RBD-hACE2 interactions, potentially affecting viral infectivity across populations. This study identified the effects of six naturally occurring hACE2 polymorphisms with high allele frequency in the African population (S19P, K26R, M82I, K341R, N546D and D597Q) on the interaction with the S protein RBD of the BA.4/5 Omicron sub-lineage through post-molecular dynamics (MD), inter-protein interaction and dynamic residue network (DRN) analyses. Inter-protein interaction analysis suggested that the K26R variation, with the highest interactions, aligns with reports of enhanced RBD binding and increased SARS-CoV-2 susceptibility. Conversely, S19P, showing the fewest interactions and largest inter-protein distances, agrees with studies indicating it hinders RBD binding. The hACE2 M82I substitution destabilized RBD-hACE2 interactions, reducing contact frequency from 92 (WT) to 27. The K341R hACE2 variant, located distally, had allosteric effects that increased RBD-hACE2 contacts compared to WThACE2. This polymorphism has been linked to enhanced affinity for Alpha, Beta and Delta lineages. DRN analyses revealed that hACE2 polymorphisms may alter the interaction networks, especially in key residues involved in enzyme activity and RBD binding. Notably, S19P may weaken hACE2-RBD interactions, while M82I showed reduced centrality of zinc and chloride-coordinating residues, hinting at impaired communication pathways. Overall, our findings show that hACE2 polymorphisms affect S BA.4/5 RBD stability and modulate spike RBD-hACE2 interactions, potentially influencing SARS-CoV-2 infectivity-key insights for vaccine and therapeutic development.

Clinical characteristics and prognostic factors of COVID-19 in rheumatic patients and their family members: a retrospective study

Background

Patients with rheumatic diseases who receive long-term treatment with steroids, immunosuppressants, or biologics are more susceptible to infection with pathogens than the general population. In order to explore the differences in clinical features and prognosis of Corona Virus Disease 2019 (COVID-19) infection between patients with rheumatic diseases and the general population (family members), a retrospective investigative study was used to analyze the differences between the two populations.

Methods

The study was conducted in 13 Grade A Tertiary hospitals in China to investigate the clinical symptoms and prognostic factors of patients with rheumatic diseases who were infected with COVID-19 for the first time and their families.

Results

A total of 2,889 participants were included in this study, including 1,530 patients with rheumatic diseases and 1,359 family members. In terms of clinical symptoms, the complete recovery time from COVID-19 for patients with rheumatic disease patients was 13 days (8.00, 18.00), which was shorter than that of family members (16 days, 11.00, 20.00). The risk of developing moderate to severe cases of COVID-19 was lower in patients with rheumatic disease than in their family members (OR=0.511, P=0.0026). Compared with non-use of non-steroidal anti-inflammatory drugs (NSAIDs), the risk of developing mild cases of COVID-19 was 0.595 times greater with pre-infection use of NSAIDs (P = 0.0003). The use of glucocorticoids and Chinese herbal decoctions before infection increased the probability of developing mild cases of COVID-19 (OR=1.537, 1.773, P<0.05). The risk of developing moderate to severe cases with disease-modifying anti-rheumatic drugs (DMARDs) used before infection was 0.350 times that without such drugs (P<0.001). In terms of prognosis, compared with family members, the complete recovery time of patients with rheumatic diseases was reduced by 2.241 days on average (P<0.001), and the complete recovery time of patients with mild rheumatism was reduced by 4.178 days on average (P<0.001). There was no significant difference in the complete recovery time from COVID-19 in patients with severe rheumatism compared with their family members (P=0.1672). The use of NSAIDs, glucocorticoids, DMARDs, biologics, Chinese patent medicine, and Chinese herbal decoctions during the infection period could shorten the recovery time of COVID-19 symptoms (P<0.05).

Conclusions

Compared with their family members, patients with rheumatic diseases had milder symptoms after infection with COVID-19, which was related to the use of glucocorticoids, DMARDs, and Chinese herbal decoctions before infection. During the COVID-19 infection phase, the use of NSAIDs, glucocorticoids, DMARDs, biologics, Chinese patent medicine, and Chinese herbal decoctions might shorten the recovery time from symptoms of COVID-19.

Chinese clinical trial registry

ChiCTR2300072679.

Genomic Evolution of the SARS-CoV-2 Omicron Variant in Córdoba, Argentina (2021-2022): Analysis of Uncommon and Prevalent Spike Mutations

Understanding the evolutionary patterns and geographic spread of SARS-CoV-2 variants, particularly Omicron, is essential for effective public health responses. This study focused on the genomic analysis of the Omicron variant in Cordoba, Argentina from 2021 to 2022. Phylogenetic analysis revealed the dominant presence of BA.1 and BA.2 lineages, with BA.5 emerging earlier than BA.4, aligning with observations from other regions. Haplotype network analysis showed significant genetic divergence within Omicron samples, forming distinct clusters. In comparison to global datasets, we identified mutations in the Omicron genomes (A27S, Y145D, and L212I) situated within the NTD region of the Spike protein. These mutations, while not widespread globally, showed higher prevalence in our region. Of particular interest were the Y145D and L212I substitutions, previously unreported in Argentina. In silico analysis revealed that both mutations impact the binding affinity of T-cell epitopes to HLA type I and II alleles. Notably, these alleles are among the most common in the Argentinian population, with some associated with protection against and others with susceptibility to SARS-CoV-2 infection. These findings strongly suggest that these prevalent mutations likely influence the immunogenicity of the Spike protein and contribute to immune evasion mechanisms. This study provides valuable insights into the genomic dynamics of the Omicron variant in Cordoba, Argentina and highlights unique mutations with potential implications for COVID-19 vaccines.

Cross-Section of Neurological Manifestations Among SARS-CoV-2 Omicron Subvariants-Single-Center Study

Background/Objectives: The Omicron variant of SARS-CoV-2 is undergoing constant mutation. New strains vary in neuropathogenicity and the neurological spectrum of disease. The aim of this study was to assess the frequency and clinical characteristics of neurological manifestations during the Omicron dominance among hospitalized patients, including the differences between three subsequent periods. Methods: This retrospective single-center study included 426 hospitalized adults with confirmed COVID-19 divided into three periods (O1, O2, and O3) dependent on the dominance of Omicron subvariants in Poland. Demographic and clinical data, in particular neurological manifestations, were collected and compared. Results: The median age of the group was 74, older in subsequent (later) periods. The number of patients with a history of previous SARS-CoV-2 infection or vaccination increased with the duration of the pandemic. The severity of COVID-19 became lower in successive periods. Neurological manifestations were observed in 55.4% of patients, and the most frequent were delirium, headache, myalgia, dizziness, cerebrovascular diseases, and encephalopathy. In subsequent periods of Omicron dominance, a higher frequency of neurological manifestations such as delirium, transient ischemic attack (TIA), and encephalopathy was observed. Headache or myalgia was related to a shorter hospitalization while delirium, cerebrovascular diseases, and ischemic stroke were linked with an increased risk of death. Conclusions: The Omicron variant of SARS-CoV-2 presents a wide spectrum of neurological manifestations. Although there is an improvement in the survival rate of patients with COVID-19, the frequency of neurological manifestations increases. The occurrence of delirium, cerebrovascular diseases, and ischemic stroke results in higher mortality.

Characterization of the viral genome of Omicron variants of SARS-CoV-2 circulating in Tripura, a remote frontier state in Northeastern India

INTRODUCTION

From 2020, with advent of COVID-19 pandemic, Tripura has experienced SARS-CoV-2 viral evolution in accordance with other parts of India. Since January 2022, the Omicron variant of SARS-CoV-2 virus became the predominant lineage circulating in India and neighboring countries. This study characterizes the viral genome of the omicron variant circulating in the state since its inception to June, 2023.

METHODS AND RESULTS

The current study was performed on nasopharyngeal and oropharyngeal samples received from the various departments of AGMC, as well as eight district hospitals from Tripura. The positive samples with a cycle threshold value of 25 or less for the E and/or N gene were considered for whole genome sequencing using Illumina Miseq NGS platform. Majority of the sequences belonged to Clade 21 L, with BA.5.2 being the major sub variant detected during the study period. Majority of the mutations were detected in the Spike protein region, including L24-, P25-, P26-, V213G, G339D, S371F, S373P, S375F, T376A, D405N, R408S, K417N, S477N, T478K, Q498R, Y505H, Q954H and N969K. All the sequences uniquely showed the mutations A27S and G142D in N terminal domain in Spike protein, not being reported from other Indian sequences like BA.5 variants. T9I, A63T and P13L were major substitutions in E, M and N protein regions respectively. Escape of mutants from vaccine induced immunity was mostly observed in BA.2 sub variants, majority endowed with the triplet mutation of K417N + E484K + N501Y.

CONCLUSION

The current study indicates that Omicron variants circulating in the state of Tripura is comparable to other regions of India and the neighbouring country of Bangladesh. Genetic mutations increasing viral transmissibility have been identified in the circulating viral genomes.

Science-based exit from stringent countermeasures against COVID-19: Mortality prediction using immune landscape between 2021 and 2022 in Japan

Background

Stringent public health and social measures against COVID-19 infection were implemented to avoid an overwhelming hospital caseload and excessive number of deaths, especially among elderly people. We analyzed population-level immunity and predicted mortality, calculated as the potential number of deaths on a given calendar date in Japan, to develop a science-based exit strategy from stringent control measures.

Methods

Immune proportions were inferred by age group using vaccination coverage data and the estimated number of naturally infected individuals. Immunity against symptomatic illness and death were estimated separately, allowing for inference of the immune fraction that was protected against either COVID-19-related symptomatic infection or death. By multiplying the infection fatality risk by age group for the immune fraction, the potential number of deaths was obtained.

Results

Accounting for a second and third dose of messenger RNA vaccine in the present-day population, approximately 155,000 potential deaths would be expected among people aged ≥ 60 years if all individuals were infected at the very end of 2022. A fourth dose (i.e., second booster) with a coverage identical to that of the third dose could reduce mortality by 60%. In all examined settings, the largest number of deaths occurred among people aged 80 years and older.

Conclusions

Our estimates can help policymakers understand the mortality impact of the COVID-19 epidemic in a quantitative manner and the critical importance of timely immunization so as to assist in decision making.

Molecular characterization, phylogenetic and variation analyses of SARS-CoV-2 strains in India

In the wake of the havoc caused by the COVID-19 pandemic, it is imperative to use the available genomic sequence data to gain insight into the mutational and genomic diversity of SARS-CoV-2. Here we have performed comparative phylogenetic, mutational and genetic diversity analysis on 1962 SARS-CoV-2 genome sequences from seven worst hit Indian states during the third Covid-19 wave, to determine the SARS-CoV-2 strains and mutations in circulation during the third wave and the transmission pattern and disease epidemiology across the states and gain valuable insight into the viral evolution. 6083 Single nucleotide polymorphisms (SNPs) were discovered in the analysis with 93 SNPs common to all states. The genetic relatedness among the statewise multilocus genotypes was visualized by plotting a minimum spanning tree based on Bruvo's distance framework. The phylogenetic tree based on Nei's genetic distance showed distinct clades. The AMOVA results indicated that large proportion of the total genetic variation is distributed within the samples, rather than between the samples within each population and between the populations. Our findings provide insight into the SARS-CoV-2 variants and mutations which dominated the third COVID-19 wave in India and thus provide a basis to monitor and further assess these variants and their sub lineages and mutations for their clinical impact and reaction to existing and newly designed drugs and vaccines. The genetic diversity analysis helps in comprehending the viral transmission scenarios across the Indian states so as to enable the State government and researchers in developing state specific prevention measures for future.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13337-024-00878-7.

SARS-CoV-2 journey: from alpha variant to omicron and its sub-variants

The COVID-19 pandemic has affected hundreds of millions of individuals and caused more than six million deaths. The prolonged pandemic duration and the continual inter-individual transmissibility have contributed to the emergence of a wide variety of SARS-CoV-2 variants. Genomic surveillance and phylogenetic studies have shown that substantial mutations in crucial supersites of spike glycoprotein modulate the binding affinity of the evolved SARS-COV-2 lineages to ACE2 receptors and modify the binding of spike protein with neutralizing antibodies. The immunological spike mutations have been associated with differential transmissibility, infectivity, and therapeutic efficacy of the vaccines and the immunological therapies among the new variants. This review highlights the diverse genetic mutations assimilated in various SARS-CoV-2 variants. The implications of the acquired mutations related to viral transmission, infectivity, and COVID-19 severity are discussed. This review also addresses the effectiveness of human neutralizing antibodies induced by SARS-CoV-2 infection or immunization and the therapeutic antibodies against the ascended variants.

Mutational dynamics of SARS-CoV-2: Impact on future COVID-19 vaccine strategies

The rapid emergence of multiple strains of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) has sparked profound concerns regarding the ongoing evolution of the virus and its potential impact on global health. Classified by the World Health Organization (WHO) as variants of concern (VOC), these strains exhibit heightened transmissibility and pathogenicity, posing significant challenges to existing vaccine strategies. Despite widespread vaccination efforts, the continual evolution of SARS-CoV-2 variants presents a formidable obstacle to achieving herd immunity. Of particular concern is the coronavirus spike (S) protein, a pivotal viral surface protein crucial for host cell entry and infectivity. Mutations within the S protein have been shown to enhance transmissibility and confer resistance to antibody-mediated neutralization, undermining the efficacy of traditional vaccine platforms. Moreover, the S protein undergoes rapid molecular evolution under selective immune pressure, leading to the emergence of diverse variants with distinct mutation profiles. This review underscores the urgent need for vigilance and adaptation in vaccine development efforts to combat the evolving landscape of SARS-CoV-2 mutations and ensure the long-term effectiveness of global immunization campaigns.

Reverse Zoonotic Transmission of SARS-CoV-2 and Monkeypox Virus: A Comprehensive Review

Reverse zoonosis reveals the process of transmission of a pathogen through the human-animal interface and the spillback of the zoonotic pathogen. In this article, we methodically demonstrate various aspects of reverse zoonosis, with a comprehensive discussion of SARS-CoV-2 and MPXV reverse zoonosis. First, different components of reverse zoonosis, such as humans, different pathogens, and numerous animals (poultry, livestock, pets, wild animals, and zoo animals), have been demonstrated. Second, it explains the present status of reverse zoonosis with different pathogens during previous occurrences of various outbreaks, epidemics, and pandemics. Here, we present 25 examples from literature. Third, using several examples, we comprehensively illustrate the present status of the reverse zoonosis of SARS-CoV-2 and MPXV. Here, we have provided 17 examples of SARS-CoV-2 reverse zoonosis and two examples of MPXV reverse zoonosis. Fourth, we have described two significant aspects of reverse zoonosis: understanding the fundamental aspects of spillback and awareness. These two aspects are required to prevent reverse zoonosis from the current infection with two significant viruses. Finally, the One Health approach was discussed vividly, where we urge scientists from different areas to work collaboratively to solve the issue of reverse zoonosis.

SARS-CoV-2 Omicron (BA.4, BA.5) variant: Lessons learned from a new variant during the COVID-19 pandemic

Background and Aim

In late 2021, the world faced the rapid spread of the SARS-CoV-2 Omicron variant, which quickly became the variant of concern. In April 2022, two new lineages of Omicron (BA.4/BA.5) emerged from Africa, where they caused the fifth wave of infection.

Method

We searched PubMed, Google Scholar, and Scopus online databases up to December 2023 for founding relevant studies.

Results

BA.4 and BA.5 subgroups, with changes in the spike protein, have a greater ability to escape from the immune system, which was possible with the help of L452R and F486V mutations. Epidemiologically, these evolving subtypes show similarities to seasonal influenza but with higher mortality rates. The symptoms of these subgroups are different from the previous types in the form of upper respiratory symptoms. Antiviral treatments, the use of antibodies such as bebtelovimab, and the development of vaccines are promising.

Conclusion

Consequently, we must continue to be vigilant in our joint surveillance efforts against COVID-19 in diagnosis and treatment.

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.

Chemical and spectroscopic characterization of (Artemisinin/Querctin/ Zinc) novel mixed ligand complex with assessment of its potent high antiviral activity against SARS-CoV-2 and antioxidant capacity against toxicity induced by acrylamide in male rats

A novel Artemisinin/Quercetin/Zinc (Art/Q/Zn) mixed ligand complex was synthesized, tested for its antiviral activity against coronavirus (SARS-CoV-2), and investigated for its effect against toxicity and oxidative stress induced by acrylamide (Acy), which develops upon cooking starchy foods at high temperatures. The synthesized complex was chemically characterized by performing elemental analysis, conductance measurements, FT-IR, UV, magnetic measurements, and XRD. The morphological surface of the complex Art/Q/Zn was investigated using scanning and transmission electron microscopy (SEM and TEM) and energy dispersive X-ray analysis (XRD). The in vitro antiviral activity of the complex Art/Q/Zn against SARS-CoV-2 and its in vivo activity against Acy-induced toxicity in hepatic and pulmonary tissues were analyzed. An experimental model was used to evaluate the beneficial effects of the novel Art/Q/Zn novel complex on lung and liver toxicities of Acy. Forty male rats were randomly divided into four groups: control, Acy (500 mg/Kg), Art/Q/Zn (30 mg/kg), and a combination of Acy and Art/Q/Zn. The complex was orally administered for 30 days. Hepatic function and inflammation marker (CRP), tumor necrosis factor, interleukin-6 (IL-6), antioxidant enzyme (CAT, SOD, and GPx), marker of oxidative stress (MDA), and blood pressure levels were investigated. Histological and ultrastructure alterations and caspase-3 variations (immunological marker) were also investigated. FT-IR spectra revealed that Zn (II) is able to chelate through C=O and C-OH (Ring II) which are the carbonyl oxygen atoms of the quercetin ligand and carbonyl oxygen atom C=O of the Art ligand, forming Art/Q/Zn complex with the chemical formula [Zn(Q)(Art)(Cl)(H2O)2]⋅3H2O. The novel complex exhibited a potent anti-SARS-CoV-2 activity even at a low concentration (IC50 = 10.14 µg/ml) and was not cytotoxic to the cellular host (CC50 = 208.5 µg/ml). Art/Q/Zn may inhibit the viral replication and binding to the angiotensin-converting enzyme-2 (ACE2) receptor and the main protease inhibitor (MPro), thereby inhibiting the activity of SARS-CoV-2 and this proved by the molecular dynamics simulation. It alleviated Acy hepatic and pulmonary toxicity by improving all biochemical markers. Therefore, it can be concluded that the novel formula Art/Q/Zn complex is an effective antioxidant agent against the oxidative stress series, and it has high inhibitory effect against SARS-CoV-2.

Assessing the Burden of COVID-19 among Children Aged 6-14 Years in Karnataka, India: A Cross-sectional Survey

Background

India experienced three coronavirus disease (COVID-19) waves, with the third attributed to the highly contagious Omicron variant. Before the national vaccination rollout for children above 6, understanding severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) immunoglobulin G (IgG) positivity in the pediatric population was essential. This study aims to assess the burden of Covid-19 infection and to estimate the seroprevalence in children aged 6 to 14 years in the state of Karnataka.

Material and Methods

We surveyed 5,358 children aged 6-14 across Karnataka using 232 health facilities, from June 6 to 14, 2022. We determined the sample size using the PPS (Population Proportional to Size) technique and employed cluster sampling. We tested all participants for SARS-CoV-2 IgG with an enzyme-linked immunosorbent assay (ELISA) kit and SARS-CoV-2 RNA with reverse transcription-polymerase chain reaction (RT-PCR). We sequenced samples with a cycle threshold (CT) value below 25 using whole genomic sequencing (WGS).

Result

We found an adjusted seroprevalence of IgG at 75.38% statewide, and we found 0.04% of children RT-PCR positive for COVID-19. We determined a case-to-infection ratio of 1:37 and identified the SARS-CoV-2 strains as Omicron, BA.5, and BA.2.10.

Conclusion

The study showed a high seroprevalence of IgG among children with low active infection. Omicron, BA. 5, and BA. 2.10 variants were detected through WGS.

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

The rapid evolution of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has led to the emergence of new variants with different genetic profiles, with important implications for public health. The continued emergence of new variants with unique genetic features and potential changes in biological properties poses significant challenges to public health strategies, vaccine development, and therapeutic interventions. Omicron variants have attracted particular attention due to their rapid spread and numerous mutations in key viral proteins. This review aims to provide an updated and comprehensive assessment of the epidemiological characteristics, immune escape potential, and therapeutic advances of the SARS-CoV-2 Omicron XBB.1.5 variant, as well as other variants.

An expanded RT-PCR melting temperature coding assay to rapidly identify all known SARS-CoV-2 variants and sub-variants of concern

The continued emergence of vaccine-resistant SARS-CoV-2 variants of concern (VOC) requires specific identification of each VOC as it arises. Here, we report an expanded version of our previously described sloppy molecular beacon (SMB) melting temperature (Tm) signature-based assay for VOCs, now modified to include detection of Delta (B.1.617.2) and Omicron (B.1.1.529) sub-variants. The SMB-VOC assay targets the signature codons 501, 484 and 452 in the SARS-CoV-2 spike protein which we show can specifically detect and differentiate all known VOCs including the Omicron subvariants (BA.1, BA.2, BA.2.12.1, BA.4/BA.5). The limit of detection (LOD) of the assay was 20, 22 and 36 genomic equivalents (GE) per reaction with the Delta, Omicron BA.1 and BA.2 respectively. Clinical validation of the 3-codon assay in the LC480 instrument showed the assay detected 94% (81/86) of the specimens as WT or VOCs and 6% (5/86) of the tests producing indeterminate results compared to sequencing. Sanger sequencing also failed for four samples. None of the specimens were incorrectly identified as WT or as a different VOC by our assay. Thus, excluding specimens with indeterminant results, the assay was 100% sensitive and 100% specific compared to Sanger sequencing for variant identification. This new assay concept can be easily expanded to add newer variants and can serve as a robust diagnostic tool for selecting appropriate monoclonal antibody therapy and rapid VOC surveillance.

The Suitability of RNA from Positive SARS-CoV-2 Rapid Antigen Tests for Whole Virus Genome Sequencing and Variant Identification to Maintain Genomic Surveillance

The COVID-19 pandemic has transformed laboratory management, with a surge in demand for diagnostic tests prompting the adoption of new diagnostic assays and the spread of variant surveillance tools. Rapid antigen tests (RATs) were initially used only for screening and later as suitable infection assessment tools. This study explores the feasibility of sequencing the SARS-CoV-2 genome from the residue of the nasopharyngeal swab extraction buffers of rapid antigen tests (RATs) to identify different COVID-19 lineages and sub-lineages.

METHODS

Viral RNA was extracted from the residue of the nasopharyngeal swab extraction buffers of RATs and, after a confirmation of positivity through a reaction of RT-PCR, viral genome sequencing was performed.

RESULTS

Overall, the quality of the sequences obtained from the RNA extracted from the residue of the nasopharyngeal swab extraction buffers of RATs was adequate and allowed us to identify the SARS-CoV-2 variants' circulation and distribution in a period when the use of molecular swabs had been drastically reduced.

CONCLUSIONS

This study demonstrates the potential for genomic surveillance by sequencing SARS-CoV-2 from the residue of the nasopharyngeal swab extraction buffers of RATs, highlighting alternative possibilities for tracking variants.

SARS-CoV-2 reinfections in the pediatric cohort-a single-center experience

BACKGROUND

This study focused on timelines of infection episodes and dominant variants and aims to determine disease severity and outcome of pediatric patients with reinfection.

MATERIALS AND METHODS

This study retrospectively evaluated the medical records of the hospitalized patients and/or outpatients aged 0-18 with a positive severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) polymerase chain reaction between March 2020 and September 2022 at Ege University Children's Hospital.

RESULTS

Ninety-one pediatric patients reinfected with SARS-CoV-2 were included in the study. There was an underlying disease in 26.4% of the patients. The median time between the two infection episodes was 184 (90-662) days. There were 24 patients (26.3%) with the first infection in pre-Delta period; 17 (18.6%) of them were reinfected in Omicron BA.1 period, while 7 (7.6%) in Omicron BA.4/BA.5 period. Forty-five patients (49.4%) were infected initially in the Delta period; 35 patients (38.4%) were reinfected in the Omicron BA.1 period, while 10 patients (10.9%) were reinfected in the Omicron BA.4/BA.5 period. Twenty-two patients (24.1%) had the first infection in the Omicron BA.1 period and then reinfected in the Omicron BA.4/BA.5 period. Patients with reinfection more frequently displayed a symptom (84.6% vs. 94.5%, p = 0.03). The hospitalization rate significantly declined in reinfection (15.3% vs. 7.6%, p = 0.03). Severe disease, treatment needs and steroid use were decreased in reinfections without a significant difference (p > 0.05). Intensive care unit admission was not altered.

CONCLUSION

This study revealed that reinfections frequently develop in previously healthy children but do not cause more severe outcomes. The risk of symptomatic reinfections is still high due to the effect of the Omicron variant.

Heterologous booster vaccines reduce severity and mortality in COVID-19 during BA.2 and BA.4/BA.5 omicron predominance in Thailand

BACKGROUND

The COVID-19 pandemic has evolved quickly, with variants of concern resulting in the need to offer booster vaccinations. Unfortunately, the booster uptake has been slow and vaccine response has shown to wane over time. Therefore, it's critical to evaluate the role of vaccinations on outcomes with newer sub-lineages of omicron.

METHODS

Utilising a Hospital Information System established in Chiang Mai, Thailand, we conducted a cohort study by linking patient-level data of laboratory-confirmed COVID-19 cases to the national immunization records, during BA.2 and BA.4/BA.5 predominance.

RESULTS

In adjusted cox-proportional hazard models, BA.4/BA.5 was not associated with more severe COVID-19 outcomes or deaths as compared to BA.2. Risk of severe outcomes and deaths were significantly reduced with third (87% and 95%) and fourth (88% and 95%) dose vaccination, while events were not observed with a fifth dose. Across the regimens, vaccination within 14-90 days prior showed the highest level of protection. All the vaccine types used for boosting in Thailand offered similar protection against severe COVID-19.

CONCLUSIONS

Boosters provide high level of protection against severe COVID-19 outcomes and deaths with newer omicron sub-lineages. Booster campaigns should focus on improving coverage utilising all available vaccines to ensure optimal protection.

Antibody evasion associated with the RBD significant mutations in several emerging SARS-CoV-2 variants and its subvariants

Since the origin of the wild strain of SARS-CoV-2, several variants have emerged, which were designated as VOC, VOI, and VUM from time to time. The Omicron variant is noted as the recent VOC. After the origin of the Omicron variant on November 2021, several subvariants of Omicron have originated subsequently, like BA.1/2, BA.2.75/2.75.2, BA.4/5, BF.7, BQ.1/1.1, XBB.1/1.5, etc. which are circulated throughout the globe. Scientists reported that antibody escape is a common phenomenon observed in all the previous VOCs, VOIs, including Omicron and its subvariants. The mutations in the NTD (N-terminal domain) and RBD (Receptor-binding domain) of the spike of these variants and subvariants are responsible for antibody escape. At the same time, it has been noted that spike RBD mutations have been increasing in the last few months. This review illustrates significant RBD mutations namely R346T, K417N/T, L452R, N460K E484A/K/Q, and N501Y found in the previous emerging SARS-CoV-2 variants, including Omicron and its subvariants in high frequency and their role in antibody evasion and immune evasion. The review also describes the different classes of nAb responsible for antibody escape in SARS-CoV-2 variants and the molecular perspective of the mutation in nAb escape. It will help the future researchers to develop efficient vaccines which can finally prevent the pandemic.

Delineating the Structure-Dynamics-Binding Differences among BA.1, BA.4/5, and BF.7 SARS-CoV-2 Variants through Atomistic Simulations: Correlation with Structural and Epidemiological Features

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an RNA virus possessing a spike (S) protein that facilitates the entry of the virus into human cells. The emergence of highly transmissible and fit SARS-CoV-2 variants has been driven by the positive selection of mutations within the S-protein. Notable among these variants are alpha, beta, gamma, delta, and omicron (BA.1), with the latter contributing to significant global health challenges and impacting populations worldwide. Recently, a novel subvariant of BA.1, named BF.7, has surfaced, purportedly exhibiting elevated transmissibility and infectivity rates. In order to comprehend and compare the transmissibility and disease progression characteristics of distinct SARS-CoV-2 variants, we performed an extensive comparative analysis utilizing all-atom molecular dynamics (MD) simulations (in triplicate) to investigate the structural, dynamic, and binding features of BA.1, BA.4/5, and BF.7. Our simulation findings, energetic analysis, and assessment of physicochemical properties collectively illuminate the dominance of the BA.1 variant over the others, a trend that is further substantiated by the sustained global prevalence of BA.1 relative to BA.4/5 and BF.7. Additionally, our simulation results align well with the reported cryoelectron microscopy (cryo-EM) structural data and epidemiological characteristics obtained from the Global Initiative on Sharing All Influenza Data (GISAID). This study presents a comprehensive comparative elucidation of the critical structural, dynamic, and binding attributes of these variants, providing insights into the predominance of BA.1 and its propensity to continuously generate numerous novel subvariants.

Molecular epidemiology of SARS-CoV-2 variants in circulation in the state of Maranhão, Brazil

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a coronavirus belonging to the beta CoV genus, responsible for SARS in humans, which became known as COVID-19. The emergence of variants of this virus is related to the presence of cases of reinfection, reduced vaccine effectiveness and greater transmission of the virus. Objective: In this study, we evaluated the molecular epidemiology of SARS-CoV-2 lineages circulating in the state of Maranhão. This is a cross-sectional and retrospective epidemiological study of genomic surveillance of SARS-CoV-2. The study comprised of 338 genomes sequenced by the Next Generation Sequencing technique on Illumina's Miseq equipment, submitted to Global Initiative on Sharing Avian Influenza Data, 190 (56.2%) are from samples of female and 148 (43.8%) from male patients. Sequencing performed covered samples of patients aged between 1 and 108 years, with emphasis on the age groups from 30 to 39 years with 15.0% of sequenced genomes and 20 to 29 years with 12.4%. As for the distribution of sequenced genomes by health macro-regions, 285 (84.3%) are from cities in the northern macro-region. We evidenced the circulation of 29 lineages and sub-lineages, four of which belonging to the Delta variant (AY.43, AY.99.1, AY.99.2 and AY.101 responsible for 4.5% of the genomes) and the others belonging to the Omicron variant, with emphasis on: BA.1 and sub-lineages (42.8%); BA.4, BA.5 and sub-lineages (5.3% and 41.1%); the sub-lineages DL.1 and BQ.1 (5% and 2%). A strong genomic surveillance system allows the study of the natural history of the disease, when there is a resurgence of SARS-CoV-2 cases.

Efficacy of novel SARS-CoV-2 rapid antigen tests in the era of omicron outbreak

Following the outbreak of Omicron and its subvariants, many of the currently available rapid Ag tests (RATs) showed a decrease in clinical performance. In this study, we evaluated the clinical sensitivity of the SARS-CoV-2 Rapid Antigen Test 2.0 for nasopharyngeal swabs and SARS-CoV-2 Rapid Antigen Test 2.0 Nasal for nasal swabs in 56 symptomatic individuals by comparing the results between RATs, RT-PCR, Omicron RT-PCR, and whole-genome sequencing (WGS). Furthermore, sequences of the Omicron subvariants' spike proteins were subjected to phylogenetic analysis. Both novel RATs demonstrated a high sensitivity of up to 92.86%, (95% CI 82.71%- 98.02%), 94.23%, (95% CI 83.07%- 98.49%), and 97.95% (95% CI 87.76%- 99.89%) compared to the RT-PCR, Omicron RT-PCR, and WGS, respectively. The clinical sensitivity of RATs was at its highest when the Ct value was restricted to 15≤Ct<25, with a sensitivity of 97.05% for RdRp genes. The Omicron RT-PCR analysis revealed subvariants BA.4 or BA.5 (76.8%) and BA.2.75 (16.1%). Subsequently, the WGS analysis identified BA.5 (65.5%) as the dominant subvariant. Phylogenetic analysis of the spike protein of Omicron's subvariants showed a close relationship between BA.4, BA.5, and BA.2.75. These results demonstrated that SARS-CoV-2 Rapid Antigen Test 2.0 and SARS-CoV-2 Rapid Antigen Test 2.0 Nasal are considered useful and efficient RATs for the detection of SARS-CoV-2, particularly during the current Omicron subvariants wave.

Clinical characteristics of COVID-19 patients infected by the Omicron variants in Macao, China: A cross-sectional study

Background and Aims

The evolving mutants of SARS-CoV-2 have made the COVID-19 pandemic sustained for over 3 years. In 2022, BA.4 and BA.5 were the Omicron variants dominating the spread globally. Although COVID-19 was no longer a Public Health Emergency of International Concern (PHEIC) as announced by WHO, the SARS-CoV-2 variants remain a challenge to global healthcare under the circumstances of withdrawal and loosening of personal protective behavior in the post-quarantine era. This study aims to acknowledge the clinical characteristics caused by Omicron BA.4/BA.5 in COVID-19 naive people and analyze possible factors affecting disease severities.

Methods

In this retrospective study, we report and analyze the clinical features of 1820 COVID-19 patients infected with the BA.4/BA.5 Omicron variants of SARS-CoV-2 during a local outbreak that occurred in Macao SAR, China, from June to July 2022.

Results

A total of 83.5% of patients were symptomatic eventually. The most common symptoms were fever, cough, and sore throat. Hypertension, dyslipidemia, and diabetes mellitus were the leading comorbidities. There were significantly more elderly patients (p < 0.001), more patients with comorbidity (p < 0.001) and more patients without vaccination or not completing the series (p < 0.001) in the "Severe to Critical" group. All deceased patients were elderly with at least three comorbidities and were partial to totally dependent in their daily lives.

Conclusion

Our data are consistent with a milder disease caused by BA.4/5 Omicron variants in the general population, while patients with old age and comorbidities have developed severe to critical diseases. Complete vaccination series and booster doses are effective strategies to reinforce protection against severe diseases and avoid mortality.

Omicron subvariant BA.5 efficiently infects lung cells

The SARS-CoV-2 Omicron subvariants BA.1 and BA.2 exhibit reduced lung cell infection relative to previously circulating SARS-CoV-2 variants, which may account for their reduced pathogenicity. However, it is unclear whether lung cell infection by BA.5, which displaced these variants, remains attenuated. Here, we show that the spike (S) protein of BA.5 exhibits increased cleavage at the S1/S2 site and drives cell-cell fusion and lung cell entry with higher efficiency than its counterparts from BA.1 and BA.2. Increased lung cell entry depends on mutation H69Δ/V70Δ and is associated with efficient replication of BA.5 in cultured lung cells. Further, BA.5 replicates in the lungs of female Balb/c mice and the nasal cavity of female ferrets with much higher efficiency than BA.1. These results suggest that BA.5 has acquired the ability to efficiently infect lung cells, a prerequisite for causing severe disease, suggesting that evolution of Omicron subvariants can result in partial loss of attenuation.

Effect of vaccine dosing intervals on Omicron surrogate neutralization after three doses of BNT162b2

Background

Increasing the interval between the first and second SARS-CoV-2 vaccine doses enhances vaccine immunogenicity, however the optimal timing of the third vaccine is unknown. In this study, we investigated how the time interval between the first and second (V1-V2), or second and third (V2-V3) doses affects immunogenicity after three doses of the BNT162b2 (Comirnaty, Pfizer-BioNTech) vaccine.

Methods

This is an observational cohort consisting of 360 participants enrolled in the COVID-19 Occupational Risks, Seroprevalence, and Immunity among Paramedics in Canada (CORSIP) study. Immune responses to BA.1 and other variants were measured from serum using an ACE2 competitive binding assay for surrogate SARS-CoV-2 neutralization. We fit a multiple linear regression model to estimate the independent association between both the V1-V2 and V2-V3 intervals and serum SARS-CoV-2 neutralization, while adjusting for age, sex, and the V3-to-blood collection interval. We examined vaccine dosing intervals as continuous variables and categorized them into quartiles.

Results

The mean age was 40 years, 45% were female sex (at birth), and the median BA.1 surrogate neutralization was 61% (IQR 38-77%). The multivariate analysis indicated that longer V1-V2 (β = 0.1292, 95% CI: 0.04807-0.2104) and V2-V3 (β = 0.2653, 95% CI: 0.2291-0.3015) intervals were associated with increased surrogate neutralization of BA.1. These results were consistent when examining responses against Spike from other SARS-CoV-2 strains. When categorized into V2-V3 quartiles, the first (56-231 days), and second (231-266 days) quartiles demonstrated decreased BA.1 surrogate neutralization compared to the longest V2-V3 quartile (282-329 days). There was no significant difference in surrogate neutralization between the long (266-282 days) and longest (282-329 days) V2-V3 intervals.

Conclusion

Longer intervals between first, second and third doses are independently associated with increased immunogenicity for all tested SARS-CoV-2 strains. Increasing the intervals between the second and third vaccine doses up to 8.9 months provided additive benefits increasing the immunogenicity of BNT162b2 vaccine schedules.

Safety and Immunogenicity of the Inactivated COVID-19 Vaccine Booster in People Living with HIV in China

Current knowledge regarding the long-term humoral response of people infected with human immunodeficiency virus to the third dose of inactivated coronavirus disease (COVID-19) vaccine is incomplete. As a result, concerns remain about the safety and efficacy of the vaccination. To improve our understanding of the safety and immunogenicity of the COVID-19 inactivated vaccine booster in people living with HIV (PLWH), a prospective study was conducted on participants who had not yet received a third dose of the COVID-19 inactivated vaccine, had no history of SARS-CoV-2 infection, and had received a second dose of the vaccine more than six months prior. The primary safety outcomes included the incidence of adverse reactions, changes in CD4⁺ T-cell count, viral load, blood routine examination, liver and kidney function examination, blood sugar, and blood lipid examination. The pseudovirus-neutralizing antibody responses to the D614G variant, Delta variant, and Omicron variants BA.5 and BF.7 were evaluated before vaccination, 14 days, 28 days, 3 months, and 6 months after vaccination to evaluate the immune response of PLWH to the injection of inactivated vaccine booster and the safety of the vaccine. In conclusion, COVID-19 vaccine booster shots were effective in PLWH, resulting in an increase in the number of CD4⁺ T-cells, neutralizing antibodies that lasted up to six months, and higher levels of neutralizing antibodies lasting approximately 3 months. However, the vaccine protection against the two variants of BA.5 and BF.7 was significantly lower than that of D614G and Delta.

On-admission and dynamic trend of laboratory profiles as prognostic biomarkers in COVID-19 inpatients

This large-scale study aimed to investigate the trend of laboratory tests of patients with COVID-19. Hospitalized confirmed and probable COVID-19 patients in three general hospitals were examined from March 20, 2020, to June 18, 2021. The confirmed and probable COVID-19 patients with known outcomes and valid laboratory results were included. The least absolute shrinkage and selection operator (LASSO) and Cox regression were used to select admittance prognostic features. Parallel Pairwise Comparison of mortality versus survival was used to examine the trend of markers. In the final cohort, 11,944 patients were enrolled, with an in-hospital mortality rate of 21.8%, mean age of 59.4 ± 18.0, and a male-to-female ratio of 1.3. Abnormal admittance level of white blood cells, neutrophils, lymphocytes, mean cellular volume, urea, creatinine, bilirubin, creatine kinase-myoglobin binding, lactate dehydrogenase (LDH), Troponin, c-reactive protein (CRP), potassium, and creatinine phosphokinase reduced the survival of COVID-19 inpatients. Moreover, the trend analysis showed lymphocytes, platelet, urea, CRP, alanine transaminase (ALT), and LDH have a dissimilar trend in non-survivors compared to survived patients. This study proposed a novel approach to find serial laboratory markers. Serial examination of platelet count, creatinine, CRP, LDH, and ALT can guide healthcare professionals in finding patients at risk of deterioration.

Impact of COVID-19 pandemic on business operations of Taiwan High Speed Rail and 7-Eleven stores

Governmental non-pharmaceutical interventions (NPIs) and concerns regarding COVID-19 infection greatly affected population mobility during the COVID-19 pandemic. This study analyzed the effect of the COVID-19 pandemic on the business operations of Taiwan High Speed Rail (THSR) and 7-Eleven stores in Taiwan. We collected data from COVID-19 Mobility Reports published by Google, the Our World in Data website, and the monthly financial reports of THSR and 7-Eleven stores. The findings revealed that the mean population mobility at transit stations decreased by over 50% during the pandemic. Changes in population mobility were significantly associated with the reproduction rate (7-day rolling average) and with the daily number of new confirmed cases per million people (7-day rolling average). The operating income of THSR was significantly associated with the decrease in population mobility at transit stations. The monthly and annual operating income of THSR in 2020, 2021, and 2022 (during the pandemic) were significantly lower than those in 2019 (before the pandemic). THSR's monthly operating income was lowest compared with the 2019 value during the Alpha variant period (89.89% lower). No significant correlation was noted between the operating income of 7-Eleven stores and population mobility. Moreover, no significant differences were discovered between the monthly and annual operating incomes of 7-Eleven stores in 2019 and those in 2020, 2021, and 2022. Implementation of the policy of coexistence with the virus by the Taiwanese government began in May 2022, and from May 2022 to October 2022, the monthly income of 7-Eleven stores was higher than that in 2019 whereas the monthly income of THSR began lower than and then slowly increased to the level in 2019. In conclusion, the operating performance of THSR was closely related to population mobility and government NPIs, whereas the operating performance of 7-Eleven stores was less strongly affected by NPIs. These stores increased their operating income by providing e-commerce and delivery services; they thus remained popular in the community.

SARS-CoV-2 Vaccines, Vaccine Development Technologies, and Significant Efforts in Vaccine Development during the Pandemic: The Lessons Learned Might Help to Fight against the Next Pandemic

We are currently approaching three years since the beginning of the coronavirus disease 2019 (COVID-19) pandemic. SARS-CoV-2 has caused extensive disruptions in everyday life, public health, and the global economy. Thus far, the vaccine has worked better than expected against the virus. During the pandemic, we experienced several things, such as the virus and its pathogenesis, clinical manifestations, and treatments; emerging variants; different vaccines; and the vaccine development processes. This review describes how each vaccine has been developed and approved with the help of modern technology. We also discuss critical milestones during the vaccine development process. Several lessons were learned from different countries during the two years of vaccine research, development, clinical trials, and vaccination. The lessons learned during the vaccine development process will help to fight the next pandemic.

Curcumin for the treatment of COVID-19 patients: A meta-analysis of randomized controlled trials

Curcumin is a low-cost and easily accessible therapeutic option for COVID-19 patients. We aimed to conduct a meta-analysis to assess the effect of curcumin on clinical outcomes in COVID-19 patients. Various databases, including PubMed, the Cochrane Library and Embase were searched from inception until October 2022 for randomized controlled trials (RCTs) evaluating curcumin use in COVID-19 patients. Results from 13 RCTs were pooled using R software version 4.1.0. Curcumin reduced the risk of all-cause mortality (RR 0.38; 95% CI: 0.20-0.72; moderate certainty of evidence), and patients with no recovery status (RR 0.54; 95% CI: 0.42-0.70; moderate certainty of evidence) but had no effect on the incidence of mechanical ventilation and hospitalization, and the rate of a positive viral PCR test. The results of subgroup analysis suggested a higher benefit with early administration of curcumin (within 5 days of onset of symptoms) and with the use of combination regimens. Curcumin is likely to be of benefit in mild-to-moderate COVID-19 patients, but large-scale RCTs are needed to confirm these findings. The limitations of our meta-analysis include the small sample sizes of the included RCTs and the variable formulations of curcumin used across the studies.

Intrinsic D614G and P681R/H mutations in SARS-CoV-2 VoCs Alpha, Delta, Omicron and viruses with D614G plus key signature mutations in spike protein alters fusogenicity and infectivity

The SARS-CoV-2 virus has been rapidly evolving over the time and the genetic variation has led to the generation of Variants of Concerns (VoC), which have shown increased fitness. These VoC viruses contain the key mutations in the spike protein which have allowed better survival and evasion of host defense mechanisms. The D614G mutation in the spike domain is found in the majority of VoC; additionally, the P681R/H mutation at the S1/S2 furin cleavage site junction is also found to be highly conserved in major VoCs; Alpha, Delta, Omicron, and its' current variants. The impact of these genetic alterations of the SARS-CoV-2 VoCs on the host cell entry, transmissibility, and infectivity has not been clearly identified. In our study, Delta and D614G + P681R synthetic double mutant pseudoviruses showed a significant increase in the cell entry, cell-to-cell fusion and infectivity. In contrast, the Omicron and P681H synthetic single mutant pseudoviruses showed TMPRSS2 independent cell entry, less fusion and infectivity as compared to Delta and D614G + P681R double mutants. Addition of exogenous trypsin further enhanced fusion in Delta viruses as compared to Omicron. Furthermore, Delta viruses showed susceptibility to both E64d and Camostat mesylate inhibitors suggesting, that the Delta virus could exploit both endosomal and TMPRSS2 dependent entry pathways as compared to the Omicron virus. Taken together, these results indicate that the D614G and P681R/H mutations in the spike protein are pivotal which might be favoring the VoC replication in different host compartments, and thus allowing a balance of mutation vs selection for better long-term adaptation.

Outcomes of laboratory-confirmed SARS-CoV-2 infection during resurgence driven by Omicron lineages BA.4 and BA.5 compared with previous waves in the Western Cape Province, South Africa

OBJECTIVES

We aimed to compare the clinical severity of Omicron BA.4/BA.5 infection with BA.1 and earlier variant infections among laboratory-confirmed SARS-CoV-2 cases in the Western Cape, South Africa, using timing of infection to infer the lineage/variant causing infection.

METHODS

We included public sector patients aged ≥20 years with laboratory-confirmed COVID-19 between May 01-May 21, 2022 (BA.4/BA.5 wave) and equivalent previous wave periods. We compared the risk between waves of (i) death and (ii) severe hospitalization/death (all within 21 days of diagnosis) using Cox regression adjusted for demographics, comorbidities, admission pressure, vaccination, and previous infection.

RESULTS

Among 3793 patients from the BA.4/BA.5 wave and 190,836 patients from previous waves, the risk of severe hospitalization/death was similar in the BA.4/BA.5 and BA.1 waves (adjusted hazard ratio [aHR] 1.12; 95% confidence interval [CI] 0.93; 1.34). Both Omicron waves had a lower risk of severe outcomes than previous waves. Previous infection (aHR 0.29, 95% CI 0.24; 0.36) and vaccination (aHR 0.17; 95% CI 0.07; 0.40 for at least three doses vs no vaccine) were protective.

CONCLUSION

Disease severity was similar among diagnosed COVID-19 cases in the BA.4/BA.5 and BA.1 periods in the context of growing immunity against SARS-CoV-2 due to previous infection and vaccination, both of which were strongly protective.

Spike recognition and neutralization of SARS-CoV-2 Omicron subvariants elicited after the third dose of mRNA vaccine

Several severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron subvariants have recently emerged, becoming the dominant circulating strains in many countries. These variants contain a large number of mutations in their spike glycoprotein, raising concerns about vaccine efficacy. In this study, we evaluate the ability of plasma from a cohort of individuals that received three doses of mRNA vaccine to recognize and neutralize these Omicron subvariant spikes. We observed that BA.4/5 and BQ.1.1 spikes are markedly less recognized and neutralized compared with the D614G and other Omicron subvariant spikes tested. Also, individuals who have been infected before or after vaccination present better humoral responses than SARS-CoV-2-naive vaccinated individuals, thus indicating that hybrid immunity generates better humoral responses against these subvariants.

Mutational characterization of Omicron SARS-CoV-2 lineages circulating in Chhattisgarh, a central state of India

Introduction

The emergence of the Omicron SARS-CoV-2 variant from various states of India in early 2022 has caused fear of its rapid spread. The lack of such reports from Chhattisgarh (CG), a central state in India, has prompted us to identify the Omicron circulating lineages and their mutational dynamics.

Materials and methods

Whole-genome sequencing (WGS) of SARS-CoV-2 was performed in 108 SARS-CoV-2 positive combined samples of nasopharyngeal and oropharyngeal swabs obtained from an equal number of patients.

Results

All 108 SARS-CoV-2 sequences belonged to Omicron of clade 21L (84%), 22B (11%), and 22D (5%). BA.2 and its sub-lineages were predominantly found in 93.5% of patients, BA.5.2 and its sub-lineage BA.5.2.1 in 4.6% of patients, and B.1.1.529 in 2% of patients. Various BA.2 sub-lineages identified were BA.2 (38%), BA.2.38 (32%), BA.2.75 (9.25%), BA.2.56, BA.2.76, and BA.5.2.1 (5% each), BA.2.74 (4.6%), BA.5.2.1 (3.7%), BA.2.43 and B.1.1.529 (1.8% each), and BA.5.2 (0.9%). Maximum mutations were noticed in the spike (46), followed by the nucleocapsid (5), membrane (3), and envelope (2) genes. Mutations detected in the spike gene of different Omicron variants were BA.1.1.529 (32), BA.2 (44), BA.2.38 (37), BA.2.43 (38), BA.2.56 (30), BA.2.74 (31), BA.2.75 (37), BA.2.76 (32), BA.5.2, and BA.5.2.1 (38 similar mutations). The spike gene showed the signature mutations of T19I and V213G in the N-terminal domain (NTD), S373P, S375F, T376A, and D405N in receptor-binding domain (RBD), D614G, H655Y, N679K, and P681H at the furin cleavage site, N764K and D796K in fusion peptide, and Q954H and N969K in heptapeptide repeat sequence (HR)1. Notably, BA.2.43 exhibited a novel mutation of E1202Q in the C terminal. Other sites included ORF1a harboring 13 mutations followed by ORF1b (6), ORF3a (2), and ORF6 and ORF8 (1 mutation each).

Conclusion

BA.2 followed by BA.2.38 was the predominant Omicron lineage circulating in Chhattisgarh. BA.2.75 could supersede other Omicron due to its mutational consortium advantage. The periodical genomic monitoring of Omicron variants is thus required for real-time assessment of circulating strains and their mutational-induced severity.

Monitoring algorithm of hospitalized patients in a medical center with SARS-CoV-2 (Omicron variant) infection: clinical epidemiological surveillance and immunological assessment

Purpose

Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a major healthcare threat worldwide. Since it was first identified in November 2021, the Omicron (B.1.1.529) variant of SARS-CoV-2 has evolved into several lineages, including BA.1, BA.2-BA.4, and BA.5. SARS-CoV-2 variants might increase transmissibility, pathogenicity, and resistance to vaccine-induced immunity. Thus, the epidemiological surveillance of circulating lineages using variant phenotyping is essential. The aim of the current study was to characterize the clinical outcome of Omicron BA.2 infections among hospitalized COVID-19 patients and to perform an immunological assessment of such cases against SARS-CoV-2.

Patients and Methods

We evaluated the analytical and clinical performance of the BioIC SARS-CoV-2 immunoglobulin (Ig)M/IgG detection kit, which was used for detecting antibodies against SARS-CoV-2 in 257 patients infected with the Omicron variant.

Results

Poor prognosis was noted in 38 patients, including eight deaths in patients characterized by comorbidities predisposing them to severe COVID-19. The variant-of-concern (VOC) typing and serological analysis identified time-dependent epidemic trends of BA.2 variants emerging in the outbreak of the fourth wave in Taiwan. Of the 257 specimens analyzed, 108 (42%) and 24 (9.3%) were positive for anti-N IgM and IgG respectively.

Conclusion

The VOC typing of these samples allowed for the identification of epidemic trends by time intervals, including the B.1.1.529 variant replacing the B.1.617.2 variant. Moreover, antibody testing might serve as a complementary method for COVID-19 diagnosis. The combination of serological testing results with the reverse transcription-polymerase chain reaction cycle threshold value has potential value in disease prognosis, thereby aiding in epidemic investigations conducted by clinicians or the healthcare department.

Omicron subvariant BA.5 is highly contagious but containable: Successful experience from Macau

Introduction

Due to its high transmissibility and immune escape, Omicron subvariant BA.5 has become the dominant strain of the SARS-CoV-2 virus and led to escalating COVID-19 cases, how to cope with it becomes an urgent issue. A BA.5 infection surge burst out on 18 June 2022 and brought an unprecedented challenge to Macau, the most densely populated region worldwide. This study aimed to analyze the characteristics of this outbreak and summarize the useful anti-epidemic measures and experiences during this outbreak.

Methods

All data were obtained from the Government Portal of Macao SAR (https://www.gov.mo), and the Special Webpage Against Epidemics, the Macao Health Bureau (www.ssm.gov.mo). An epidemiologic study was performed to analyze epidemic outcomes, including the infection rate, the proportion of symptomatic cases, the case fatality ratio (CFR), etc. Data were analyzed using SPSS Version 20. A p-value <0.05 was considered statistically significant. The anti-epidemic measures and experience were reviewed and summarized.

Results

The BA.5 outbreak resulted in 1,821 new cases, which was significantly more than the cumulative cases of the previous variants of COVID-19 in Macau. The symptomatic cases accounted for 38.71% of the total cases, which was higher than that of the previous variants. After 6-week concerted efforts, Macau effectively controlled the outbreak, with an infection rate of 0.27%, which was much lower than many BA.5-attacked regions. The CFR was approximately 0.86%, which was not statistically different from that of previous variants. Six victims were chronically ill senior elders and their vaccination rate was much lower than the average level. Macau took a comprehensive anti-epidemic strategy to win a quick victory against BA.5, especially the "relatively static" strategy that was first formulated and applied by Macau for the management of the COVID-19 pandemic. Successful experience showed that although BA.5 was highly contagious, it could be contained by comprehensive anti-epidemic measures, including adequate anti-epidemic preparation, herd immunity through vaccination, repeated mass nucleic acid tests and rapid antigen tests, KN-95 mask mandate, the "relatively static" strategy, precise prevention and control, epidemiological investigation and tracing, and traditional Chinese medicine treatment, etc.

Discussion

In Macau, compared with the previous subvariants, BA.5 is associated with increased transmissibility and a higher proportion of symptomatic cases, however, the risk of death remains similar, and the infection rate is much lower than that in many other BA.5-attacked regions. BA.5 is highly contagious but still containable, Macau's experience may offer hints for the regions experiencing the BA.5 waves to choose or adjust a more rational anti-epidemic strategy.

A Detailed Overview of SARS-CoV-2 Omicron: Its Sub-Variants, Mutations and Pathophysiology, Clinical Characteristics, Immunological Landscape, Immune Escape, and Therapies

The COVID-19 pandemic has created significant concern for everyone. Recent data from many worldwide reports suggest that most infections are caused by the Omicron variant and its sub-lineages, dominating all the previously emerged variants. The numerous mutations in Omicron's viral genome and its sub-lineages attribute it a larger amount of viral fitness, owing to the alteration of the transmission and pathophysiology of the virus. With a rapid change to the viral structure, Omicron and its sub-variants, namely BA.1, BA.2, BA.3, BA.4, and BA.5, dominate the community with an ability to escape the neutralization efficiency induced by prior vaccination or infections. Similarly, several recombinant sub-variants of Omicron, namely XBB, XBD, and XBF, etc., have emerged, which a better understanding. This review mainly entails the changes to Omicron and its sub-lineages due to it having a higher number of mutations. The binding affinity, cellular entry, disease severity, infection rates, and most importantly, the immune evading potential of them are discussed in this review. A comparative analysis of the Delta variant and the other dominating variants that evolved before Omicron gives the readers an in-depth understanding of the landscape of Omicron's transmission and infection. Furthermore, this review discusses the range of neutralization abilities possessed by several approved antiviral therapeutic molecules and neutralizing antibodies which are functional against Omicron and its sub-variants. The rapid evolution of the sub-variants is causing infections, but the broader aspect of their transmission and neutralization has not been explored. Thus, the scientific community should adopt an elucidative approach to obtain a clear idea about the recently emerged sub-variants, including the recombinant variants, so that effective neutralization with vaccines and drugs can be achieved. This, in turn, will lead to a drop in the number of cases and, finally, an end to the pandemic.

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

Several nations have recently begun to relax their public health protocols, particularly regarding the use of face masks when engaging in outdoor activities. This is because there has been a general trend towards fewer cases of coronavirus disease 2019 (COVID-19). However, new Omicron sub-variants (designated BA.4 and BA.5) have recently emerged. These two subvariants are thought to be the cause of an increase in COVID-19 cases in South Africa, the United States, and Europe. They have also begun to spread throughout Asia. They evolved from the Omicron lineage with characteristics that make them even more contagious and which allow them to circumvent immunity from a previous infection or vaccination. This article reviews a number of scientific considerations about these new variants, including their apparently reduced clinical severity.

Association between vaccination status and COVID-19-related health outcomes among community-dwelling COVID-19 patients in Nara, Japan

BACKGROUND

Many previous studies have reported COVID-19 vaccine effectiveness, but there are few studies in Japan. This community-based, retrospective observational study investigated the association between vaccination status and COVID-19-related health outcomes in COVID-19 patients by SARS-CoV-2 variant type.

METHODS

The study participants were 24,314 COVID-19 patients aged 12 or older whose diagnoses were reported to the Nara Prefecture Chuwa Public Health Center from April 2021 to March 2022, during periods when the alpha, delta, and omicron variants of COVID-19 were predominant. The outcome variables were severe health consequences (SHC) (i.e., ICU admission and COVID-19-related death), hospitalization, and extension of recovery period. The explanatory variable was vaccination status at least 14 days prior to infection. Covariates included gender, age, population size, the number of risk factors for aggravation, and the number of symptoms at diagnosis. The generalized estimating equations of the multivariable Poisson regression models were used to estimate the adjusted incidence proportion (AIP) and 95% confidence interval (CI) for each health outcome. We performed stratified analyses by SARS-CoV-2 variant type, but the association between vaccination status and COVID-19-related health outcomes was stratified only for the delta and omicron variants due to the small number of vaccinated patients during the alpha variant.

RESULTS

Of the 24,314 participants, 255 (1.0%) had SHC; of the 24,059 participants without SHC, 2,102 (8.7%) were hospitalized; and of the 19,603 participants without SHC, hospitalization, and missing data on recovery period, 2,960 (15.1%) had extension of recovery period. Multivariable Poisson regression models showed that regardless of SARS-CoV-2 variant type or health outcome, those who received two or more vaccine doses had significantly lower risk of health outcomes than those who did not receive the vaccine, and there was a dose-response relationship in which the AIP for health outcomes decreased with an increased number of vaccinations.

CONCLUSION

A higher number of vaccinations were associated with lower risk of COVID-19-related health outcomes, not only in the delta variant but also in the omicron variant. Our findings suggest that increasing the number of COVID-19 vaccine doses can prevent severe disease and lead to early recovery of patients not requiring hospitalization.

SARS-CoV-2 emerging Omicron subvariants with a special focus on BF.7 and XBB.1.5 recently posing fears of rising cases amid ongoing COVID-19 pandemic

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron versions have been the sole one circulating for quite some time. Subvariants BA.1, BA.2, BA.3, BA.4, and BA.5 of the Omicron emerged over time and through mutation, with BA.1 responsible for the most severe global pandemic between December 2021 and January 2022. Other Omicron subvariants such as BQ.1, BQ.1.1, BA.4.6, BF.7, BA.2.75.2, XBB.1 appeared recently and could cause a new wave of increased cases amid the ongoing COVID-19 pandemic. There is evidence that certain Omicron subvariants have increased transmissibility, extra spike mutations, and ability to overcome protective effects of COVID-19 neutralizing antibodies through immunological evasion. In recent months, the Omicron BF.7 subvariant has been in the news due to its spread in China and a small number of other countries, raising concerns about a possible rebound in COVID-19 cases. More recently, the Omicron XBB.1.5 subvariant has captured international attention due to an increase in cases in the United States. As a highly transmissible sublineage of Omicron BA.5, as well as having a shorter incubation time and the potential to reinfect or infect immune population, BF.7 has stronger infection ability. It appears that the regional immunological landscape is affected by the amount and timing of previous Omicron waves, as well as the COVID-19 vaccination coverage, which in turn determines whether the increased immune escape of BF.7 and XBB.1.5 subvariants is sufficient to drive new infection waves. Expanding our understanding of the transmission and efficacy of vaccines, immunotherapeutics, and antiviral drugs against newly emerging Omicron subvariants and lineages, as well as bolstering genomic facilities for tracking their spread and maintaining a constant vigilance, and shedding more light on their evolution and mutational events, would help in the development of effective mitigation strategies. Importantly, reducing the occurrence of mutations and recombination in the virus can be aided by bolstering One health approach and emphasizing its significance in combating zoonosis and reversal zoonosis linked with COVID-19. This article provides a brief overview on Omicron variant, its recently emerging lineages and subvairants with a special focus on BF.7 and XBB.1.5 as much more infectious and highly transmissible variations that may once again threaten a sharp increase in COVID-19 cases globally amid the currently ongoing pandemic, along with presenting salient mitigation measures.

Reproduction numbers of SARS-CoV-2 Omicron subvariants

Estimating the effective reproduction number of Omicron subvariants is crucial for evaluating the effectiveness of control measures, and adjusting control measures promptly. We conducted a systematic review to synthesize the evidence from estimates of the reproduction numbers for Omicron subvariants, and estimated their effective reproduction number.

Acceptance of the COVID-19 vaccine booster dose and associated factors among the elderly in China based on the health belief model (HBM): A national cross-sectional study

BACKGROUND

The reluctance of individuals to obtain solid vaccine-induced immunity represents a fundamental challenge to containing the spread of SARS-CoV-2, including its highly mutated variants. We aimed to assess vaccination acceptance and associated factors for the COVID-19 vaccine booster dose among elderly people (≥60 years old) in China, providing a theoretical and practical reference for universal vaccination policy.

METHODS

A national anonymous survey was conducted in mainland China from May 25 to June 8, 2022, using a stratified random sampling method. Individuals 60 years of age and above were the target population. A chi-squared test and Cochran-Armitage test for trend were used to compare and examine vaccine acceptance rates by characteristics. Via a backward stepwise method, multivariable logistic regression models were established to assess factors associated with booster dose acceptance. Two-sided P < 0.05 was considered statistically significant.

RESULTS

Of 3,321 eligible participants, 82.8% (95% CI: 81.5-84.1%) were willing to receive COVID-19 vaccine booster shots. Concerns about contraindications (38.3%), vaccine safety (32.0%), and limited movement (28.0%) were the main reasons for vaccine hesitancy. Nearly one-third still believed that the booster dose was unnecessary after receiving the initial vaccination. Older adults with a low level of perceived barriers (aOR = 1.86, 95% CI, 1.03-3.38), a high level of perceived benefit (aOR = 2.31, 95% CI, 1.38-3.87), and higher cues to action (moderate, aOR = 2.22, 95% CI, 1.39-3.56; high, aOR = 5.46, 95% CI: 3.44-8.67) were more likely to accept the booster dose. Other major factors affecting the booster dose acceptance rate were occupation, time spent on social media, vaccination history, and a high knowledge score for COVID-19 and vaccines. In addition, for those over 70 years of age, rising awareness of susceptibility could be a better gateway for improving their willingness to get vaccinated.

CONCLUSIONS

A total of 82.8% of recruited older adults were willing to receive the booster dose. Acceptance behaviors were closely related to occupation, time spent on social media, vaccination history, knowledge factors, perception of barriers, and benefit, as well as action cues. Targeted public health measures are a priority for improving the vaccination coverage of valid immunity among the elderly population, not only to prevent infection and poor prognosis caused by emerging variants but also to reduce the huge disease and economic burden caused by the long-term sequelae after SARS-CoV-2 infection.

Bayesian Molecular Dating Analyses Combined with Mutational Profiling Suggest an Independent Origin and Evolution of SARS-CoV-2 Omicron BA.1 and BA.2 Sub-Lineages

The ongoing evolution of severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) has resulted in the recent emergence of a highly divergent variant of concern (VOC) defined as Omicron or B.1.1.529. This VOC is of particular concern because it has the potential to evade most therapeutic antibodies and has undergone a sustained genetic evolution, resulting in the emergence of five distinct sub-lineages. However, the evolutionary dynamics of the initially identified Omicron BA.1 and BA.2 sub-lineages remain poorly understood. Herein, we combined Bayesian phylogenetic analysis, mutational profiling, and selection pressure analysis to track the virus's genetic changes that drive the early evolutionary dynamics of the Omicron. Based on the Omicron dataset chosen for the improved temporal signals and sampled globally between November 2021 and January 2022, the most recent common ancestor (tMRCA) and substitution rates for BA.1 were estimated to be that of 18 September 2021 (95% highest posterior density (HPD), 4 August-22 October 2021) and 1.435 × 10-3 (95% HPD  =  1.021 × 10-3 - 1.869 × 10-3) substitution/site/year, respectively, whereas 3 November 2021 (95% highest posterior density (HPD) 26 September-28 November 2021) and 1.074 × 10-3 (95% HPD  =  6.444 × 10-4 - 1.586 × 10-3) substitution/site/year were estimated for the BA.2 sub-lineage. The findings of this study suggest that the Omicron BA.1 and BA.2 sub-lineages originated independently and evolved over time. Furthermore, we identified multiple sites in the spike protein undergoing continued diversifying selection that may alter the neutralization profile of BA.1. This study sheds light on the ongoing global genomic surveillance and Bayesian molecular dating analyses to better understand the evolutionary dynamics of the virus and, as a result, mitigate the impact of emerging variants on public health.

Omicron variant: Current insights and future directions

The global COVID-19 outbreak has returned with the identification of the SARS-CoV-2 Omicron variant (B.1.1.529) after appearing to be persistently spreading for the more than past two years. In comparison to prior SARS-CoV-2 variants, this new variant revealed a significant amount of mutation. This novel variety may have a greater rate of transmissibility which might impede the effectiveness of current diagnostic equipment as well as vaccination efficacy and also impede immunotherapies (Antibody / monoclonal antibody based). WHO designated B.1.1.529 as a variant of concern on November 26, 2021, identified as Omicron. The Omicron variant transmission method and severity, on the other hand, are well defined. The global spread of Omicron, which has now seized many nations, has resulted in numerous speculations regarding its origin and degree of infectivity. The following sections will go over its potential for transmission, omicron structure, and impact on COVID-19 vaccines, how it is different from delta variant and diagnostics.