Biochemical characterization of naturally occurring mutations in SARS-CoV-2 RNA-dependent RNA polymerase DOI Creative Commons
Matěj Danda, Anna Klimešová,

Klára Kušková

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Feb. 26, 2024

Abstract Since the emergence of SARS-CoV-2, mutations in all subunits RNA-dependent RNA polymerase (RdRp) virus have been repeatedly reported. Although RdRp represents a primary target for antiviral drugs, experimental studies exploring phenotypic effect these limited. This study focuses on effects substitutions three subunits: nsp7, nsp8, and nsp12, selected based their occurrence rate potential impact. We employed nano-differential scanning fluorimetry microscale thermophoresis to examine impact protein stability complex assembly. observed diverse impacts; notably, single mutation nsp8 significantly increased its as evidenced by 13 °C increase melting temperature, whereas certain nsp7 reduced binding affinity nsp12 during formation. Using fluorometric enzymatic assay, we assessed overall activity. found that most examined altered activity, often direct result changes or other components complex. Intriguingly, combination A21V P323L resulted 50% Additionally, some notably influenced sensitivity Remdesivir®, highlighting implications therapeutic strategies. To our knowledge, this is first biochemical demonstrate amino acid across constituting emerging SARS-CoV-2 subvariants. Significance statement While spike has extensively explored, understanding within (RdRp), crucial viral replication key antivirals like Remdesivir, remains limited with conducted solely silico . focused identified from December 2019 June 2022, assessing enzyme stability, assembly, Advanced analyses reveal how can alter functionality, providing insights into evolution resistance mechanisms. study, pioneering mutations, provides invaluable roles resistance, hereby opening new pathways developing therapies against continuously evolving variants.

Language: Английский

Differential beta‐coronavirus infection dynamics in human bronchial epithelial organoids DOI Creative Commons
Dongbin Park, Se‐Mi Kim, Ho Bin Jang

et al.

Journal of Medical Virology, Journal Year: 2024, Volume and Issue: 96(4)

Published: April 1, 2024

Abstract The lower respiratory system serves as the target and barrier for beta‐coronavirus (beta‐CoV) infections. In this study, we explored beta‐CoV infection dynamics in human bronchial epithelial (HBE) organoids, focusing on HCoV‐OC43, SARS‐CoV, MERS‐CoV, SARS‐CoV‐2. Utilizing advanced organoid culture techniques, observed robust replication all beta‐CoVs, particularly noting that SARS‐CoV‐2 reached peak viral RNA levels at 72 h postinfection. Through comprehensive transcriptomic analysis, identified significant shifts cell population dynamics, marked by an increase goblet cells a concurrent decrease ciliated cells. Furthermore, our tropism analysis unveiled distinct preferences targeting: HCoV‐OC43 predominantly infected club cells, while SARS‐CoV had dual contrast, primarily MERS‐CoV showed affinity Host factor revealed upregulation of genes encoding receptors proteases. Notably, induced unfolded protein response pathway, which may facilitate replication. Our study also reveals complex interplay between inflammatory pathways suppression interferon responses during These findings provide insights into host‐virus interactions antiviral defense mechanisms, contributing to understanding infections tract.

Language: Английский

Citations

0
No evidence for enhanced disease with human polyclonal SARS-CoV-2 antibody in the ferret model DOI Creative Commons
Douglas S. Reed, Anita K. McElroy, Dominique J. Barbeau

et al.

PLoS ONE, Journal Year: 2024, Volume and Issue: 19(6), P. e0290909 - e0290909

Published: June 20, 2024

Since SARS-CoV-2 emerged in late 2019, it spread from China to the rest of world. An initial concern was potential for vaccine- or antibody-dependent enhancement (ADE) disease as had been reported with other coronaviruses. To evaluate this, we first developed a ferret model by exposing ferrets either mucosal inoculation (intranasal/oral/ocular) inhalation using small particle aerosol. Mucosal caused mild fever and weight loss that resolved quickly; via route resulted virus shedding detected nares, throat, rectum 7–10 days post-infection. ADE, then inoculated groups intravenously 0.1, 0.5, 1 mg/kg doses human polyclonal anti-SARS-CoV-2 IgG hyper-immunized transchromosomic bovines (SAB-185). Twelve hours later, were challenged SARS-CoV-2. We found no significant differences fever, loss, viral after infection between three antibody controls. Signs pathology lungs noted infected but control groups. The results this study indicate healthy, young adult both sexes are suitable COVID-19 low specific SAB-185 unlikely enhance

Language: Английский

Citations

0
Mutational and evolutionary dynamics of non-structural and spike proteins from variants of concern (VOC) of SARS-CoV-2 in India DOI

A. Chaudhuri,

Subhrangshu Das,

Saikat Chakrabarti

et al.

International Journal of Biological Macromolecules, Journal Year: 2024, Volume and Issue: unknown, P. 137154 - 137154

Published: Oct. 1, 2024

Language: Английский

Citations

0
Enhanced Detection and Molecular Modeling of Adaptive Mutations in SARS-CoV-2 Coding and Non-Coding Regions Using the c/µ Test DOI Creative Commons
Nicholas J. Paradis, Chun Wu

Virus Evolution, Journal Year: 2024, Volume and Issue: 10(1)

Published: Jan. 1, 2024

Accurately identifying mutations under beneficial selection in viral genomes is crucial for understanding their molecular evolution and pathogenicity. Traditional methods like the Ka/Ks test, which assesses non-synonymous (Ka) versus synonymous (Ks) substitution rates, assume that substitutions at sites are neutral thus equal to mutation rate (µ). Yet, evidence suggests translated regions (TRs) untranslated (UTRs) can be strong (Ks > µ) strongly conserved ≈ 0), leading false predictions of adaptive from codon-by-codon analysis. Our previous work used a relative test (c/µ, c: UTR/TR, µ: rate) identify SARS-CoV-2 genome without neutrality assumption sites. This study refines c/µ by optimizing µ value, smaller set nucleotide amino acid both UTR (11 with 3) TR (69 nonsynonymous sites: 3 2.5; 107 Ks/µ 3). Encouragingly, top two 70% had reported or predicted effects literature. Molecular modeling some critical proteins (S, NSP11, NSP5) was carried out elucidate possible mechanism adaptivity.

Language: Английский

Citations

0
Biochemical characterization of naturally occurring mutations in SARS-CoV-2 RNA-dependent RNA polymerase DOI Creative Commons
Matěj Danda, Anna Klimešová,

Klára Kušková

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Feb. 26, 2024

Abstract Since the emergence of SARS-CoV-2, mutations in all subunits RNA-dependent RNA polymerase (RdRp) virus have been repeatedly reported. Although RdRp represents a primary target for antiviral drugs, experimental studies exploring phenotypic effect these limited. This study focuses on effects substitutions three subunits: nsp7, nsp8, and nsp12, selected based their occurrence rate potential impact. We employed nano-differential scanning fluorimetry microscale thermophoresis to examine impact protein stability complex assembly. observed diverse impacts; notably, single mutation nsp8 significantly increased its as evidenced by 13 °C increase melting temperature, whereas certain nsp7 reduced binding affinity nsp12 during formation. Using fluorometric enzymatic assay, we assessed overall activity. found that most examined altered activity, often direct result changes or other components complex. Intriguingly, combination A21V P323L resulted 50% Additionally, some notably influenced sensitivity Remdesivir®, highlighting implications therapeutic strategies. To our knowledge, this is first biochemical demonstrate amino acid across constituting emerging SARS-CoV-2 subvariants. Significance statement While spike has extensively explored, understanding within (RdRp), crucial viral replication key antivirals like Remdesivir, remains limited with conducted solely silico . focused identified from December 2019 June 2022, assessing enzyme stability, assembly, Advanced analyses reveal how can alter functionality, providing insights into evolution resistance mechanisms. study, pioneering mutations, provides invaluable roles resistance, hereby opening new pathways developing therapies against continuously evolving variants.

Language: Английский

Citations

0