In silico analysis of non-structural protein 12 sequences from SARS-COV-2 found in Manaus, Amazonas, Brazil, reveals mutations linked to higher transmissibility

Anais da Academia Brasileira de Ciências, Год журнала: 2024, Номер 96(2)

Опубликована: Янв. 1, 2024

The disease coronavirus COVID-19 has been the cause of millions deaths worldwide. Among proteins SARS-CoV-2, non-structural protein 12 (NSP12) plays a key role during COVID infection and is part RNA-dependent RNA polymerase complex. monitoring NSP12 polymorphisms extremely important for design new antiviral drugs viral evolution. This study analyzed mutations detected in circulating SARS-CoV-2 years 2020 to 2022 population city Manaus, Amazonas, Brazil. most frequent found were P323L G671S. Reports literature indicate that these are related transmissibility efficiency, which may have contributed high numbers cases this location. In addition, two described here (E796D R914K) close RMSD similar M794V N911K, as influential on performance enzyme. These data demonstrate need monitor emergence order better understand their consequences treatments currently used drugs.

Язык: Английский

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Point mutations at specific sites of the nsp12–nsp8 interface dramatically affect the RNA polymerization activity of SARS-CoV-2

Proceedings of the National Academy of Sciences, Год журнала: 2024, Номер 121(29)

Опубликована: Июль 11, 2024

In a recent characterization of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) variability present in 30 diagnostic samples from patients first COVID-19 pandemic wave, 41 amino acid substitutions were documented RNA-dependent RNA polymerase (RdRp) nsp12. Eight selected this work to determine whether they had an impact on RdRp activity SARS-CoV-2 nsp12–nsp8–nsp7 replication complex. Three these found around central cavity, template entry channel (D499G and M668V), within motif B (V560A), showed polymerization rates similar wild type RdRp. The remaining five mutations (P323L, L372F, L372P, V373A, L527H) placed near nsp12–nsp8 F contact surface; residues L372, V373, L527 participated large hydrophobic cluster involving contacts between two helices nsp12 fingers long α-helix nsp8 . presence any resulted important alterations activity. Comparative primer elongation assays different behavior depending hydrophobicity their side chains. substitution L by bulkier chain at position 372 slightly promoted However, was dramatically reduced with L527H mutations, lesser extent all which weaken interactions cluster. Additional specifically designed disrupt (nsp12-V330S, nsp12-V341S, nsp8-R111A/D112A), also impaired activity, further illustrating importance interface regulation synthesis.

Язык: Английский

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Comparative Atlas of SARS-CoV-2 Substitution Mutations: A Focus on Iranian Strains Amidst Global Trends

Viruses, Год журнала: 2024, Номер 16(8), С. 1331 - 1331

Опубликована: Авг. 20, 2024

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a new emerging that caused disease 2019 (COVID-19). Whole-genome tracking of SARS-CoV-2 enhanced our understanding the mechanism disease, control, and prevention COVID-19.

Язык: Английский

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Antiviral susceptibility of SARS-CoV-2 and influenza viruses from 3 co-infected pediatric patients

International Journal of Infectious Diseases, Год журнала: 2024, Номер 146, С. 107134 - 107134

Опубликована: Июнь 27, 2024

Язык: Английский

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Biochemical characterization of naturally occurring mutations in SARS‐CoV‐2 RNA‐dependent RNA polymerase

Protein Science, Год журнала: 2024, Номер 33(9)

Опубликована: Авг. 15, 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% To our knowledge, this is first biochemical demonstrate amino acid across constituting emerging SARS‐CoV‐2 subvariants.

Язык: Английский

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The host protease KLK5 primes and activates spike proteins to promote human betacoronavirus replication and lung inflammation

Science Signaling, Год журнала: 2024, Номер 17(850)

Опубликована: Авг. 20, 2024

Coronaviruses rely on host proteases to activate the viral spike protein, which facilitates fusion with cell membrane and release of genomic RNAs into cytoplasm. The distribution specific in determines host, tissue, cellular tropism these viruses. Here, we identified kallikrein (KLK) family member KLK5 as a major protease secreted by human airway cells exploited multiple betacoronaviruses. cleaved both priming (S1/S2) activation (S2') sites proteins from various betacoronaviruses vitro. In contrast, KLK12 KLK13 displayed preferences for either S2' or S1/S2 site, respectively. Whereas worked concert SARS-CoV-2 MERS-CoV proteins, itself efficiently activated several betacoronaviruses, including SARS-CoV-2. Infection differentiated bronchial epithelial (HBECs) induced an increase that promoted virus replication. Furthermore, ursolic acid other related plant-derived triterpenoids inhibit effectively suppressed replication SARS-CoV, MERS-CoV, HBECs mitigated lung inflammation mice infected We propose is pancoronavirus factor promising therapeutic target current future coronavirus-induced diseases.

Язык: Английский

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Enhanced Detection and Molecular Modeling of Adaptive Mutations in SARS-CoV-2 Coding and Non-Coding Regions Using the c/µ Test

Virus Evolution, Год журнала: 2024, Номер 10(1)

Опубликована: Янв. 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.

Язык: Английский

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COVID-19 Genomic Surveillance in Bangui (Central African Republic) Reveals a Landscape of Circulating Variants Linked to Validated Antiviral Targets of SARS-CoV-2 Proteome

Viruses, Год журнала: 2023, Номер 15(12), С. 2309 - 2309

Опубликована: Ноя. 24, 2023

Since its outbreak, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) spread rapidly, causing the Disease 19 (COVID-19) pandemic. Even with vaccines’ administration, virus continued to circulate due inequal access prevention and therapeutic measures in African countries. Information about COVID-19 Africa has been limited contradictory, thus regional studies are important. On this premise, we conducted a genomic surveillance study lineages circulating Bangui, Central Republic (CAR). We collected 2687 nasopharyngeal samples at four checkpoints Bangui from 22 July 2021. Fifty-three tested positive for SARS-CoV-2, viral genomes were sequenced look presence of different strains. performed phylogenetic analysis described lineage landscape SARS-CoV-2 CAR along 15 months pandemics during period, finding Delta variant as predominant Variant Concern (VoC). The deduced aminoacidic sequences structural non-structural genes determined compared reference reported isolates Africa. Despite number obtained, provides valuable information evolution level allows better understanding circulation CAR.

Язык: Английский

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Assessing Genomic Mutations in SARS-CoV-2: Potential Resistance to Antiviral Drugs in Viral Populations from Untreated COVID-19 Patients

Microorganisms, Год журнала: 2023, Номер 12(1), С. 2 - 2

Опубликована: Дек. 19, 2023

Naturally occurring SARS-CoV-2 variants mutated in genomic regions targeted by antiviral drugs have not been extensively studied. This study investigated the potential of RNA-dependent RNA polymerase (RdRp) complex subunits and non-structural protein (Nsp)5 severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) to accumulate natural mutations that could affect efficacy drugs. To this aim, sequences isolated from 4155 drug-naive individuals southern Italy were analyzed using Illumina MiSeq platform. Sequencing samples showed following viral variant distribution: 71.2% Delta, 22.2% Omicron, 6.4% Alpha. In Nsp12 sequences, we found 84 amino acid substitutions. The most common one was P323L, detected 3777/4155 (91%) samples, with 2906/3777 (69.9%) also showing G671S substitution combination. Additionally, identified 28, 14, 24 different substitutions Nsp5, Nsp7, Nsp8 regions, respectively. Of note, V186F A191V substitutions, affecting residues adjacent active site Nsp5 (the target drug Paxlovid), 157/4155 (3.8%) 3/4155 (0.07%) conclusion, RdRp region exhibit susceptibility accumulating mutations. poses a risk drugs, as these may compromise ability inhibit replication

Язык: Английский

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SARS-CoV-2 Aerosol and Intranasal Exposure Models in Ferrets

Viruses, Год журнала: 2023, Номер 15(12), С. 2341 - 2341

Опубликована: Ноя. 29, 2023

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of worldwide COVID-19 pandemic. Animal models are extremely helpful for testing vaccines and therapeutics dissecting viral host factors that contribute to disease severity transmissibility. Here, we report assessment comparison intranasal small particle (~3 µm) aerosol SARS-CoV-2 exposure in ferrets. The primary endpoints analysis were clinical signs disease, recovery virus upper tract, damage within tract. This work demonstrated ferrets productively infected with following either or exposure. infection resulted an asymptomatic course exposure, no signs, significant weight loss, fever. In both ferret models, replication, genomes, antigens detected little material lungs. exhibited a specific IgG immune response full spike protein. Mild pathological findings included inflammation, necrosis, edema nasal turbinates, which correlated positive immunohistochemical staining virus. Environmental sampling was performed ferrets, genomic on feeders nesting areas from days 2–10 post-exposure. We conclude displayed measurable parameters could be utilized future studies, including transmission studies therapeutics.

Язык: Английский

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