Next generation sequencing shows diversity of Omicron sub-lineages of SARS-COV2 circulating in Jeddah, Saudi Arabia DOI Creative Commons
Ahmed Bouna, Ahmed Atef, Hadiah Bassam Al Mahdi

et al.

Journal of King Saud University - Science, Journal Year: 2023, Volume and Issue: 36(2), P. 103081 - 103081

Published: Dec. 26, 2023

The ever-evolving Omicron variant of the SARS-CoV-2 and its sub-lineages have prompted Saudi Arabia to continuously track circulating lineages. We focused on presence diverse circulation in presented whole genome sequencing study 94 positive specimens procured between February April 2022 city Jeddah, Arabia. Following whole-genome sequencing, bioinformatics analysis was undertaken. clades 21K 21L constituted entirety sequenced specimens, belonging BA.2 (n=56) BA.1.1 (n=20), respectively, low-frequency were BA.2.3 (n=6), BA.1 (n=4), BA.2.40.1 (n=2), BA.1.14 (n=1), BA.2.10 BA2.32 BA.2.57 BA2.64 BA2.5 (n=1). Mutational patterns identified, as well possible consequences for spread virus. Comparative molecular docking Omicron-specific Nucleocapsid protein harboring mutations P13L, R203K, G204R, S413R, deletions E31-, R32-, S33- showed reduced interaction with human RIG-I 8 interacting amino acid residues 10 polar interactions, while exhibited 15 26 interactions. Ongoing monitoring is essential assessing genomic epidemiological tourist travel pilgrimage Jeddah across Arabia, prompt identification emerging variants further investigation.

Language: Английский

A systems approach evaluating the impact of SARS-CoV-2 variant of concern mutations on CD8+ T cell responses DOI Creative Commons
Paul Buckley, Chloe H. Lee, Agne Antanaviciute

et al.

Immunotherapy Advances, Journal Year: 2023, Volume and Issue: 3(1)

Published: Jan. 1, 2023

T cell recognition of SARS-CoV-2 antigens after vaccination and/or natural infection has played a central role in resolving infections and generating adaptive immune memory. However, the clinical impact SARS-CoV-2-specific responses is variable mechanisms underlying interaction with target are not fully understood. This especially true given virus' rapid evolution, which leads to new variants escape capacity. In this study, we used Omicron variant as model organism took systems approach evaluate mutations on CD8+ immunogenicity. We computed an immunogenicity potential score for each peptide antigen from ancestral strain Omicron, capturing both presentation probabilities. By comparing vs. scores, reveal divergent heterogeneous landscape mutated targets variants. While peptides broadly preserved, observed deteriorated that may assist breakthrough some individuals. then combined our scoring scheme

Language: Английский

Citations

3
The humoral and cellular immune response of a third dose adenoviral-based vectored vaccine after a single or 2 shots of inactivated COVID-19 vaccine in healthy adults DOI Creative Commons
Supaporn Suparak, Kobkaew Bumroongthai, Danai Jantapalaboon

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2022, Volume and Issue: unknown

Published: Oct. 19, 2022

Abstract The coronavirus pandemic is a severe infectious respiratory disease which caused massive loss worldwide. Thailand was affected by the wild-type, and Delta variant started in mid-2021. Due to shortage of effective vaccines, ministry public health suggested heterologous vaccine scheme, comprises inactivated COVID-19 (CoronaVac) an adenoviral-based vectored (ChAdOx1). However, data on humoral cellular immune responses single or 2 shots followed are very limited. In this current study, sera from participants who received either CoronaVac ChAdOx1 were evaluated for SARS-CoV-2 spike receptor-binding-domain (RBD) IgG. cytokine level also assessed using Luminex immunoassay. PBMC collected evaluate spike-specific T-cell B-cell responses. Participants possessed significantly ( P <0.0001) higher levels RBD-specific They exhibited CD4+T-cell IFN-gamma than those only 1 shot vaccine. volunteers two had p <0.01) marginal response against wild-type S peptides one ChAdOx1. Surprisingly, class switch CoronaVac. TNF-alpha IL-6. This study indicated that boosting as third dose after completing induced strong

Language: Английский

Citations

1
A systems approach evaluating the impact of SARS-CoV-2 variant of concern mutations on CD8+ T cell responses DOI Creative Commons
Paul Buckley, Chloe H. Lee, Agne Antanaviciute

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2022, Volume and Issue: unknown

Published: Oct. 21, 2022

Abstract T cell recognition of SARS-CoV-2 antigens after vaccination and/or natural infection has played a central role in resolving infections and generating adaptive immune memory. However, the clinical impact SARS-CoV-2-specific responses is variable mechanisms underlying interaction with target are not fully understood. This especially true given virus’ rapid evolution, which leads to new variants escape capacity. In this study, we used Omicron variant as model organism took systems approach evaluate mutations on CD8+ immunogenicity. We computed an ‘immunogenicity potential’ score for each peptide antigen from ancestral strain Omicron, capturing both presentation probabilities. By comparing vs. immunogenicity scores, reveal divergent heterogeneous landscape mutated targets variants. While peptides broadly preserved, observed deteriorated that may assist breakthrough some individuals. then combined our scoring scheme in-silico mutagenesis, characterise position- residue-specific theoretical mutational predict many trajectories substitutions, study suggests epitopes did develop under cell-mediated pressure. Our provides generalisable platform fostering deeper understanding existing novel antigen-specific vaccine- infection-induced immunity.

Language: Английский

Citations

1
Next generation sequencing shows diversity of Omicron sub-lineages of SARS-COV2 circulating in Jeddah, Saudi Arabia DOI Creative Commons
Ahmed Bouna, Ahmed Atef, Hadiah Bassam Al Mahdi

et al.

Journal of King Saud University - Science, Journal Year: 2023, Volume and Issue: 36(2), P. 103081 - 103081

Published: Dec. 26, 2023

The ever-evolving Omicron variant of the SARS-CoV-2 and its sub-lineages have prompted Saudi Arabia to continuously track circulating lineages. We focused on presence diverse circulation in presented whole genome sequencing study 94 positive specimens procured between February April 2022 city Jeddah, Arabia. Following whole-genome sequencing, bioinformatics analysis was undertaken. clades 21K 21L constituted entirety sequenced specimens, belonging BA.2 (n=56) BA.1.1 (n=20), respectively, low-frequency were BA.2.3 (n=6), BA.1 (n=4), BA.2.40.1 (n=2), BA.1.14 (n=1), BA.2.10 BA2.32 BA.2.57 BA2.64 BA2.5 (n=1). Mutational patterns identified, as well possible consequences for spread virus. Comparative molecular docking Omicron-specific Nucleocapsid protein harboring mutations P13L, R203K, G204R, S413R, deletions E31-, R32-, S33- showed reduced interaction with human RIG-I 8 interacting amino acid residues 10 polar interactions, while exhibited 15 26 interactions. Ongoing monitoring is essential assessing genomic epidemiological tourist travel pilgrimage Jeddah across Arabia, prompt identification emerging variants further investigation.

Language: Английский

Citations

0