SARS-CoV-2: analysis of the effects of mutations in non-structural proteins

Senthilazhagan, Kavya; Sakthimani, Seshagiri; Kallanja, Deepthi; Venkataraman, Sangita

doi:10.1007/s00705-023-05818-2

Cited by 4 publications

(2 citation statements)

References 88 publications

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“…However, we observed that S26F and M129I had no significant effect on either complex formation or catalytic activity. In contrast, T141M substitution in nsp8 was predicted to destabilize the RdRp complex by Senthilazhagan et al, 2023 21 , which was confirmed by our data. Both mentioned studies suggested that substituting S25 in nsp7 per leucine could stabilize the RdRp, but our results showed the opposite (Fig 3, E, Fig 4, C).…”

Section: Discussionsupporting

confidence: 90%

“…Previous research on SARS-CoV-2 RdRp mutations has been focused mainly on nsp12 19,20 , although Subissi et al, 2014 11 demonstrated that mutations in accessory subunits, nsp7 and nsp8, can significantly influence virus fitness. Some of the polymorphisms of both nsp7 and nsp8 have been explored in silico, to predict their potential impact on the RdRp complex 21,22 . Despite the key role of RdRp in the virus life cycle, its significance in the development of drugs against COVID-19 23,24 and recognizing the potential for amino acid changes in viral enzymes to induce drug resistance [25][26][27] , our knowledge of polymorphisms in the RdRp proteins remains rather limited.…”

Section: Introductionmentioning

confidence: 99%

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

Danda,

Klimešová,

Kušková

et al. 2024

Preprint

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Since the emergence of SARS-CoV-2, mutations in all subunits of the RNA-dependent RNA polymerase (RdRp) of the virus have been repeatedly reported. Although RdRp represents a primary target for antiviral drugs, experimental studies exploring the phenotypic effect of these mutations have been limited. This study focuses on the phenotypic effects of substitutions in the three RdRp subunits: nsp7, nsp8, and nsp12, selected based on their occurrence rate and potential impact. We employed nano-differential scanning fluorimetry and microscale thermophoresis to examine the impact of these mutations on protein stability and RdRp complex assembly. We observed diverse impacts; notably, a single mutation in nsp8 significantly increased its stability as evidenced by a 13 [deg]C increase in melting temperature, whereas certain mutations in nsp7 and nsp8 reduced their binding affinity to nsp12 during RdRp complex formation. Using a fluorometric enzymatic assay, we assessed the overall effect on RNA polymerase activity. We found that most of the examined mutations altered the polymerase activity, often as a direct result of changes in stability or affinity to the other components of the RdRp complex. Intriguingly, a combination of nsp8 A21V and nsp12 P323L mutations resulted in a 50% increase in polymerase activity. Additionally, some of the examined substitutions in the RdRp subunits notably influenced the sensitivity of RdRp to Remdesivir, highlighting their potential implications for therapeutic strategies. To our knowledge, this is the first biochemical study to demonstrate the impact of amino acid mutations across all components constituting the RdRp complex in emerging SARS-CoV-2 subvariants.

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Section: Discussionsupporting

confidence: 90%

Section: Introductionmentioning

confidence: 99%

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

Danda,

Klimešová,

Kušková

et al. 2024

Preprint

View full text Add to dashboard Cite

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

Danda,

Klimešová,

Kušková

et al. 2024

Protein Science

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Since the emergence of SARS‐CoV‐2, mutations in all subunits of the RNA‐dependent RNA polymerase (RdRp) of the virus have been repeatedly reported. Although RdRp represents a primary target for antiviral drugs, experimental studies exploring the phenotypic effect of these mutations have been limited. This study focuses on the phenotypic effects of substitutions in the three RdRp subunits: nsp7, nsp8, and nsp12, selected based on their occurrence rate and potential impact. We employed nano‐differential scanning fluorimetry and microscale thermophoresis to examine the impact of these mutations on protein stability and RdRp complex assembly. We observed diverse impacts; notably, a single mutation in nsp8 significantly increased its stability as evidenced by a 13°C increase in melting temperature, whereas certain mutations in nsp7 and nsp8 reduced their binding affinity to nsp12 during RdRp complex formation. Using a fluorometric enzymatic assay, we assessed the overall effect on RNA polymerase activity. We found that most of the examined mutations altered the polymerase activity, often as a direct result of changes in stability or affinity to the other components of the RdRp complex. Intriguingly, a combination of nsp8 A21V and nsp12 P323L mutations resulted in a 50% increase in polymerase activity. To our knowledge, this is the first biochemical study to demonstrate the impact of amino acid mutations across all components constituting the RdRp complex in emerging SARS‐CoV‐2 subvariants.

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Pandemic potential of the Nipah virus and public health strategies adopted during outbreaks: Lessons from Kerala, India

Anish,

Aravind,

Radhakrishnan

et al. 2024

PLOS Glob Public Health

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Kerala, a south Indian state witnessed several outbreaks of Nipah encephalitis since 2018, a zoonotic viral disease with significant pandemic potential. This review highlights the relevance of surveillance and health system preparedness, infection control, early diagnosis and treatment with broad-spectrum antivirals, environmental conservation, and community engagement in mitigating Nipah outbreaks. Additionally, it emphasises the importance of developing new biologicals and anti-viral drugs to combat the disease. The article discusses the available evidence on the spillover mechanisms, genetic attributes of the circulating virus, ecological factors, risk of hospital-based superspreading, treatment outcomes and successful strategies employed in Kerala in response to the recurrent Nipah outbreaks.

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SARS-CoV-2: analysis of the effects of mutations in non-structural proteins

Cited by 4 publications

References 88 publications

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

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

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

Pandemic potential of the Nipah virus and public health strategies adopted during outbreaks: Lessons from Kerala, India

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