SARS-CoV-2 Omicron BA.1 and BA.2 are attenuated in rhesus macaques as compared to Delta

Science Advances, Journal Year: 2022, Volume and Issue: 8(46)

Published: Nov. 16, 2022

Since the emergence of SARS-CoV-2, five different variants concern (VOCs) have been identified: Alpha, Beta, Gamma, Delta, and Omicron. Because confounding factors in human population, such as preexisting immunity, comparing severity disease caused by VOCs is challenging. Here, we investigate progression rhesus macaque model upon inoculation with Omicron BA.1, BA.2 VOCs. Disease macaques inoculated BA.1 or was lower than those Delta resulted significantly viral loads nasal swabs, bronchial cytology brush samples, lung tissue macaques. Cytokines chemokines were up-regulated nasosorption samples animals compared to animals. Overall, these data suggest that, macaques, replicates levels VOC, resulting reduced clinical disease.

Language: Английский

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Analysis of SARS-CoV-2 genome evolutionary patterns

Microbiology Spectrum, Journal Year: 2024, Volume and Issue: 12(2)

Published: Jan. 10, 2024

ABSTRACT The spread of SARS-CoV-2 virus accompanied by public availability abundant sequence data provides a window for the determination viral evolutionary patterns. In this study, genome sequences were collected from seven countries in period January 2020–December 2022. classified into three phases, namely, pre-vaccination, post-vaccination, and recent period. Comparison was performed between these phases based on parameters like mutation rates, selection pressure (d N /d S ratio), transition to transversion ratios (T i /T v ). Similar comparisons among variants. Statistical significance tested using Graphpad unpaired t -test. analysis showed an increase percent genomic rates post-vaccination periods across all pre-vaccination sequences. Mutation highest NSP3, S, N, NSP12b before increased further after vaccination. NSP4 largest change d purifying that shifted toward neutral ORF8, ORF3a, ORF10 under positive Shift driven E, ORF7a vaccination set. sequences, observed NSP1, NSP13. T decreased with time. C→U G→U most frequent transitions transversions. However, U→G Omicron variant had while Delta ratio. Protein-wise ratio also seen vary different IMPORTANCE To best our knowledge, there exists no other large-scale study protein-wise patterns during time course evolution countries. Analyzing view varying spatial, temporal, biological signals is important diagnostics, therapeutics, pharmacovigilance SARS-CoV-2.

Language: Английский

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Autoimmunity and Immunodeficiency in Severe SARS-CoV-2 Infection and Prolonged COVID-19

Current Issues in Molecular Biology, Journal Year: 2022, Volume and Issue: 45(1), P. 33 - 50

Published: Dec. 21, 2022

SARS-CoV-2 causes the complex and heterogeneous illness known as COVID-19. The disease primarily affects respiratory system but can quickly become systemic, harming multiple organs leading to long-lasting sequelae in some patients. Most infected individuals are asymptomatic or present mild symptoms. Antibodies, complement, immune cells efficiently eliminate virus. However, 20% of develop severe organ failure. Virus replication has been described several patients who died from COVID-19, suggesting a compromised response. Immunodeficiency autoimmunity responsible for this impairment facilitate viral escape. Mutations IFN signal transduction T cell activation inadequate response young individuals. Autoantibodies accountable secondary immunodeficiency with infection prolonged Antibodies against cytokines (interferons α, γ ω, IL1β, IL6, IL10, IL-17, IL21), chemokines, nuclear proteins DNA, anticardiolipin, extracellular have reported. type titer autoantibodies depend on age gender. Organ-specific Their role is under study. Autoimmunity should be screened risk factors

Language: Английский

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Analysis of 3.5 million SARS-CoV-2 sequences reveals unique mutational trends with consistent nucleotide and codon frequencies

Virology Journal, Journal Year: 2023, Volume and Issue: 20(1)

Published: Feb. 17, 2023

Abstract Background Since the onset of SARS-CoV-2 pandemic, bioinformatic analyses have been performed to understand nucleotide and synonymous codon usage features mutational patterns virus. However, comparatively few attempted perform such on a considerably large cohort viral genomes while organizing plethora available sequence data for month-by-month analysis observe changes over time. Here, we aimed composition mutation SARS-CoV-2, separating sequences by gene, clade, timepoints, contrast profile other comparable RNA viruses. Methods Using cleaned, filtered, pre-aligned dataset 3.5 million downloaded from GISAID database, computed statistics, including calculation relative values. We then calculated adaptation index (CAI) nonsynonymous/synonymous ratio (dN/dS) time our dataset. Finally, compiled information types mutations occurring viruses, generated heatmaps showing at high entropy positions along Spike sequence. Results show that metrics remain relatively consistent 32-month span, though there are significant differences between clades within each gene various timepoints. CAI dN/dS values vary substantially different timepoints genes, with average both highest Mutational showed has higher proportion nonsynonymous than analogous genes in outnumbering ones up 20:1. several specific positions, were overwhelmingly predominant. Conclusions Our multifaceted covering signature gives valuable insight into frequency heterogeneity time, its unique compared

Language: Английский

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A comprehensive analysis of the mutational landscape of the newly emerging Omicron (B.1.1.529) variant and comparison of mutations with VOCs and VOIs

GeroScience, Journal Year: 2022, Volume and Issue: 44(5), P. 2393 - 2425

Published: Aug. 22, 2022

Language: Английский

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Heterogeneity and Risk of Bias in Studies Examining Risk Factors for Severe Illness and Death in COVID-19: A Systematic Review and Meta-Analysis

Pathogens, Journal Year: 2022, Volume and Issue: 11(5), P. 563 - 563

Published: May 10, 2022

This systematic review and meta-analysis synthesized the evidence on impacts of demographics comorbidities clinical outcomes COVID-19, as well sources heterogeneity publication bias relevant studies. Two authors independently searched literature from PubMed, Embase, Cochrane library, CINAHL 18 May 2021; removed duplicates; screened titles, abstracts, full texts by using criteria; extracted data eligible articles. The variations among studies were examined Cochrane, Q.; I

Language: Английский

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The Advantage of Using Immunoinformatic Tools on Vaccine Design and Development for Coronavirus

Vaccines, Journal Year: 2022, Volume and Issue: 10(11), P. 1844 - 1844

Published: Oct. 31, 2022

After the outbreak of SARS-CoV-2 by end 2019, vaccine development strategies became a worldwide priority. Furthermore, appearances novel variants challenge researchers to develop new pharmacological or preventive strategies. However, vaccines still represent an efficient way control pandemic worldwide. This review describes importance bioinformatic and immunoinformatic tools (in silico) for guide design. In silico permit identification epitopes (immunogenic peptides) which could be used as potential vaccines, well nonacarriers such as: vector viral based RNA-based dendrimers through immunoinformatics. Currently, nucleic acid protein sequential structural analyses allow us get immunogenic can induce immune response alone in complex with nanocarriers. One advantages techniques is that they facilitate epitopes, while accelerating process helping economize some stages safe vaccines.

Language: Английский

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Rapidly identifying new coronavirus mutations of potential concern in the Omicron variant using an unsupervised learning strategy

Scientific Reports, Journal Year: 2022, Volume and Issue: 12(1)

Published: Nov. 9, 2022

Extensive mutations in the Omicron spike protein appear to accelerate transmission of SARS-CoV-2, and rapid infections increase odds that additional mutants will emerge. To build an investigative framework, we have applied unsupervised machine learning approach 4296 viral genomes collected deposited GISAID as December 14, 2021, identified a core haplotype 28 polymutants (A67V, T95I, G339D, R346K, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, Y505H, T547K, D614G, H655Y, N679K, P681H, N764K, K796Y, N856K, Q954H, N69K, L981F) separate 17 non-spike genes: (K38, A1892) nsp3, T492 nsp4, (P132, V247, T280, S284) 3C-like proteinase, I189 nsp6, P323 RNA-dependent RNA polymerase, I42 Exonuclease, T9 envelope protein, (D3, Q19, A63) membrane glycoprotein, (P13, R203, G204) nucleocapsid phosphoprotein. Using these haplotypes reference, four newly emerging (R346, A701, I1081, N1192) (p value = 9.37*10-4, 1.0*10-15, 4.76*10-7 1.56*10-4, respectively), five genes (D343G phosphoprotein, V1069I V94A F694Y polymerase L106L/F ORF3a) exhibit significant increasing trajectories (all p values < 1.0*10-15). In absence relevant clinical data for mutations, it is important monitor them closely. Two may be particular concern: N1192S mutation locates extremely highly conserved region all human coronaviruses integral fusion process, induce conformational changes could impact remdesivir binding.

Language: Английский

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Genomic epidemiology of SARS-CoV-2 variants in South Korea between January 2020 and February 2023

Virology, Journal Year: 2023, Volume and Issue: 587, P. 109869 - 109869

Published: Aug. 26, 2023

The Korea Disease Control and Prevention Agency (KDCA) has been conducting national genomic surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-COV-2). To monitor characterize circulating SARS-CoV-2 variants in South Korea, 102,873 oropharyngeal/nasopharyngeal swab samples collected from patients with confirmed COVID-19 were sequenced, assigned lineages, phylogenetically analyzed. Each wave followed a pattern emerging first abroad then spreading domestically. In 2020, B.41 lineage led the wave, B.1.497 dominated second third waves. 2021, fourth was driven by Delta (AY.69 AY.122.5). 2022, fifth to seventh waves Omicron sub-lineages BA.1/BA.1.1 BA.2/BA.2.3, BA.5/BA.5.2, BN.1, sequentially. KDCA detected monitored increasing advance prior large-scale epidemics, but repeated emergence new could threaten public health again. Therefore, it is important continue through surveillance.

Language: Английский

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Real-World Effectiveness of the mRNA COVID-19 Vaccines in Japan: A Case–Control Study

Vaccines, Journal Year: 2022, Volume and Issue: 10(5), P. 779 - 779

Published: May 14, 2022

The real-world effectiveness of the coronavirus disease 2019 (COVID-19) vaccines in Japan remains unclear. This case-control study evaluated vaccine (VE) two doses mRNA vaccine, BNT162b2 or mRNA-1273, against delta (B.1.617.2) variant Japanese general population period June-September 2021. Individuals close contact with COVID-19 patients were tested using polymerase chain reaction (PCR). A self-administered questionnaire vaccination status, demographic data, underlying medical conditions, lifestyle, personal protective health behaviors, and living environment. Two reported by 11.6% cases (n = 389) 35.2% controls 179). Compared controls, younger had a lower proportion who always performed handwashing for ≥20 s, higher alcohol consumers, individuals single-family homes commuting family members. After adjusting these confounding factors day PCR testing multivariate logistic regression analysis, VE June-July (delta 45%) was 92% 79% August-September 89%). adjusted homestay, hotel-based isolation quarantine, hospitalization 78%, 77%, 97%, respectively. Despite declining slightly, remained robust ~3 months after second dose. Vaccination policymaking will require longer-term monitoring new variants.

Language: Английский

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