Shared 6mer Peptides of Human and Omicron (21K and 21L) at SARS-CoV-2 Mutation Sites DOI Creative Commons
Yekbun Adıgüzel, Yehuda Shoenfeld

Antibodies, Journal Year: 2022, Volume and Issue: 11(4), P. 68 - 68

Published: Oct. 25, 2022

We investigated the short sequences involving Omicron 21K and 21L variants to reveal any possible molecular mimicry-associated autoimmunity risks changes in those. first identified common 6mers of viral human protein present for both mutant (Omicron) nonmutant (SARS-CoV-2) versions same sequence then predicted binding affinities those HLA supertype representatives. evaluated change potential risk, through comparative assessment their similar peptides with allele. This is lost new, or de novo, associated mutations variants. Accordingly, e.g., affinity virus-similar Ig heavy chain junction regions shifted from HLA-B*15:01 HLA-A*01:01 allele at sequences. Additionally, different proteins sharing SARS-CoV-2 mutation sites interest HLA-B*07:02 allele, such as respective sequences, were lost. Among all, novel risk appeared be prominent HLA-A*24:02 HLA-B*27:05 serotypes upon infection 21L. Associated disease, pathway, tissue expression data supported new serotypes, while could have been diminished, HLA-A*03:01 retained, individuals infected under study. These are likely affect complications related cross-reactions influencing relevant

Language: Английский

Emerging Omicron subvariants evade neutralizing immunity elicited by vaccine or BA.1/BA.2 infection DOI
Zehui Chen, Jiaming Li, Jing Zheng

et al.

Journal of Medical Virology, Journal Year: 2023, Volume and Issue: 95(2)

Published: Jan. 31, 2023

The newly emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron BA.2.75 and BA.2.76 subvariants contained 35 29 additional mutations in its spike (S) protein compared with the reference SARS-CoV-2 genome, respectively. Here, we measured evasion degree of BA.1, BA.2, BA.4, BA.5, BA.2.75, from neutralizing immunity people previously infected BA.1 determined effect vaccination on immune evasion, titers antibodies serums between infection convalescence. Results showed that neutralization patients different statuses BA.1/BA.2 breakthrough decreased evolution to BA.2.76. This study also indicated existing vaccines could no longer provide effective protection, especially for subvariants. Therefore, against epidemic strains should be designed specifically. In future, can not only focus current strains, but predict design new potential mutant strains. At same time, combine virus strains' characteristics develop protective measures colonization areas, such as nasal protection spray. Besides, further studies Y248N mutation subvariant were necessary explore contribution enhanced ability.

Language: Английский

Citations

8
Immune Dysregulation in SARS-CoV-2 patients coinfected with Mycobacterium tuberculosis (Mtb) or HIV in China DOI Creative Commons
Lei Li, Jianxiang Zhang, Ranran Sun

et al.

BMC Public Health, Journal Year: 2024, Volume and Issue: 24(1)

Published: Feb. 22, 2024

Abstract Background SARS-CoV-2 infections usually cause immune dysregulation in the human body. Studies of immunological changes resulting from coinfections with Mycobacterium tuberculosis ( Mtb ) or HIV are limited. Methods We conducted a retrospective study focusing on patients COVID-19. A total 550 infected were enrolled our and categorized into four groups based presence coinfections; 166 Delta-infected patients, among whom 103 had no coinfections, 52 who coinfected , 11 HIV, 384 Omicron-infected patients. By collecting data epidemiologic information, laboratory findings, treatments, clinical outcomes, we analyzed compared characteristics. Results Compared those Delta group, median white blood cell, CD4 + T-cell B-cell counts lower group group. Except for Omicron more than half three abnormal chest CT findings. Among groups, there significant differences any cytokines. disease duration LOS longer For unvaccinated number B cells T was that difference duration. In (6%) presented greater months decreased lymphocyte IL17A counts, possibly due to double lungs caused by M. tuberculosis. Conclusions found exhibited LOS, decrease cells, suggesting these related function. Changes cytokine levels suggest coinfection does not result response. Importantly, discovered chronic course involving infection.

Language: Английский

Citations

2
SARS-CoV-2 within-host diversity of human hosts and its implications for viral immune evasion DOI Creative Commons
Binbin Xi, Xi Zeng, Zixi Chen

et al.

mBio, Journal Year: 2023, Volume and Issue: unknown

Published: June 5, 2023

ABSTRACT Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is continuously evolving, bringing great challenges to the control of virus. In present study, we investigated characteristics SARS-CoV-2 within-host diversity human hosts and its implications for immune evasion using about 2,00,000 high-depth next-generation genome sequencing data SARS-CoV-2. A total 44% samples showed variations (iSNVs), average number iSNVs in with iSNV was 1.90. C-to-U dominant substitution pattern iSNVs. C-to-U/G-to-A A-to-G/U-to-C preferentially occur 5′-CG-3′ 5′-AU-3′ motifs, respectively. addition, found that are under negative selection. About 15.6% had an impact on content CpG dinucleotide (CpG) genomes. We detected signatures faster loss CpG-gaining iSNVs, possibly resulting from zinc-finger antiviral protein-mediated activities targeting CpG, which could be major reason depletion consensus The non-synonymous S gene can largely alter protein’s antigenic features, many these distributed amino-terminal domain (NTD) receptor-binding (RBD). These results suggest interacts actively attempts take different evolutionary strategies escape innate adaptive immunity. new findings further deepen widen our understanding features IMPORTANCE (SARS-CoV-2), causative pathogen disease 2019, has evolved rapidly since it discovered. Recent studies have pointed out some mutations protein confer ability evade system. observed sequences decreased over time, reflecting adaptation host. significance research revealing hosts, identifying causes genomes, exploring potential impacts escape,

Language: Английский

Citations

5
The Rise and Fall of Omicron BA.1 Variant as Seen in Wastewater Supports Epidemiological Model Predictions DOI Creative Commons
Michal Liddor Naim, Yu Fu,

Marilou Shagan

et al.

Viruses, Journal Year: 2023, Volume and Issue: 15(9), P. 1862 - 1862

Published: Aug. 31, 2023

The COVID-19 pandemic caused by the SARS-CoV-2 virus has inflicted significant mortality and morbidity worldwide. Continuous mutations have led to emergence of new variants. Omicron BA.1 sub-lineage prevailed as dominant variant globally at beginning 2022 but was subsequently replaced BA.2 in numerous countries. Wastewater-based epidemiology (WBE) offers an efficient tool for capturing viral shedding from infected individuals, enabling early detection potential outbreaks without relying solely on community cooperation clinical testing resources. This study integrated RT-qPCR assays detecting general its variants levels wastewater into a modified triple susceptible-infected-recovered-susceptible (SIRS) model. observed, replacing presence predecessor, Delta variant. Comparative analysis between data SIRS model effectively described subsequent waves, with decline aligning diminished below threshold wastewater. demonstrates WBE valuable future pandemics. Furthermore, analyzing sensitivity different parameters, we are able deduce real-life values cross-variant immunity probabilities, emphasizing asymmetry their strength.

Language: Английский

Citations

5
Revealing patterns of SARS-CoV-2 variant emergence and evolution using RBD amplicon sequencing of wastewater DOI Creative Commons
Xingwen Chen,

John Balliew,

Cici Bauer

et al.

Journal of Infection, Journal Year: 2024, Volume and Issue: 89(5), P. 106284 - 106284

Published: Sept. 26, 2024

Rapid evolution of SARS-CoV-2 has resulted in the emergence numerous variants, posing significant challenges to public health surveillance. Clinical genome sequencing, while valuable, limitations capturing full epidemiological dynamics circulating variants general population. This study aimed monitor variant community and using receptor-binding domain (RBD) amplicon sequencing wastewater samples.

Language: Английский

Citations

1
Evaluation of Immunoassay Based Biosensor Platforms for SARS-CoV-2 Detection Using Highly Specific Monoclonal Antibodies DOI

Göknur Gizem Dinç,

Ebru Saatçi,

İlkay Göksu Polat

et al.

Diagnostic Microbiology and Infectious Disease, Journal Year: 2024, Volume and Issue: 111(3), P. 116644 - 116644

Published: Dec. 3, 2024

Language: Английский

Citations

1
The Rise and Fall of Omicron BA.1 Variant as Seen in Wastewater Supports Epidemiological Model Predictions DOI Open Access
Michal Liddor Naim, Yu Fu,

Marilou Shagan

et al.

Published: July 20, 2023

The COVID-19 pandemic caused by the SARS-CoV-2 virus has inflicted significant mortality and morbidity worldwide. Continuous mutations have led to emergence of new variants. Omicron BA.1 sub-lineage prevailed as dominant variant globally at beginning 2022 but was subsequently replaced BA.2 in numerous countries. Wastewater-based epidemiology (WBE) offers an efficient tool for capturing viral shedding from infected individuals, enabling early detection potential outbreaks without relying solely on community cooperation clinical testing resources. This study integrated RT-qPCR assays detecting general its variants levels wastewater into a modified triple susceptible-infected-recovered-susceptible (SIRS) model. Omicron-BA.1 observed, replacing presence predecessor, Delta variant. Comparative analysis between data SIRS model effectively described subsequent waves, with decline aligning diminished below threshold wastewater. demonstrates WBE valuable future pandemics. Furthermore, analyzing sensitivity different parameters, we are able deduce real-life values cross-variant immunity probabilities, emphasizing asymmetry their strength.

Language: Английский

Citations

3
A novel mAb broadly neutralizes SARS‐CoV‐2 VOCs in vitro and in vivo, including the Omicron variants DOI
Qiuqi Kan, Xian Lin, Tuofan Li

et al.

Journal of Medical Virology, Journal Year: 2023, Volume and Issue: 95(3)

Published: March 1, 2023

Abstract Novel immune escape variants have emerged as severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) continues to spread worldwide. Many of the cause breakthrough infections in vaccinated populations, posing great challenges current antiviral strategies targeting immunodominance receptor‐binding domain within spike protein. Here, we found that a novel broadly neutralizing monoclonal antibody (mAb), G5, provided efficient protection against SARS‐CoV‐2 concern (VOCs) vitro and vivo. A single dose mAb G5 could significantly inhibit viral burden mice challenged with mouse‐adapted or Omicron BA.1 variant, well body weight loss cytokine release induced by SARS‐CoV‐2. The refined epitope recognized was identified 1148 FKEELDKYF 1156 stem helix subunit S2. In addition, human−mouse chimeric generated based on variable region heavy chain VL genes G5. Our study provides broad drug candidate VOCs reveals target for developing pan‐SARS‐CoV‐2 vaccines.

Language: Английский

Citations

2
Current Progress in Genomic and Genetic Research on Human Viral Diseases DOI Open Access
Binhua Liang, Birte Möhlendick, Hezhao Ji

et al.

Frontiers research topics, Journal Year: 2024, Volume and Issue: unknown

Published: Jan. 1, 2024

it is a pioneering approach to the world of academia, radically improving way scholarly research managed.The grand vision Frontiers where all people have an equal opportunity seek, share and generate knowledge.Frontiers provides immediate permanent online open access its publications, but this alone not enough realize our goals. journal seriesThe series multi-tier interdisciplinary set openaccess, journals, promising paradigm shift from current review, selection dissemination processes in academic publishing.All journals are driven by researchers for researchers; therefore, they constitute service community.At same time, operates on revolutionary invention, tiered publishing system, initially addressing specific communities scholars, gradually climbing up broader public understanding, thus serving interests lay society, too. Dedication qualityEach article landmark highest quality, thanks genuinely collaborative interactions between authors review editors, who include some world's best academicians.Research must be certified peers before entering stream knowledge that may eventually reach -and shape society; only applies most rigorous unbiased reviews.Frontiers revolutionizes freely delivering outstanding research, evaluated with no bias both social point view.By applying advanced information technologies, catapulting into new generation.

Language: Английский

Citations

0
The SARS-CoV-2 ORF6 protein inhibits nuclear export of mRNA and spliceosomal U snRNA DOI Creative Commons
Ichiro Taniguchi

PLoS ONE, Journal Year: 2024, Volume and Issue: 19(10), P. e0312098 - e0312098

Published: Oct. 31, 2024

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of disease 19 (COVID-19). SARS-CoV-2 infection suppresses host innate immunity and impairs cell viability. Among viral proteins, ORF6 exhibits potent interferon (IFN) antagonistic activity cellular toxicity. It also interacts with RNA export factor RAE1, which bridges nuclear pore complex receptors, suggesting an effect on export. Using Xenopus oocyte microinjection system, I found that blocked not only mRNA but spliceosomal U snRNA. further demonstrated affects interaction between RAE1 receptors inhibits binding RAE1. These effects may cumulatively block several classes RNA. binds forms oligomers. findings provide insights into suppression immune responses reduction in viability caused by infection, contributing to development antiviral drugs targeting ORF6.

Language: Английский

Citations

0