Circulation and Evolution of SARS-CoV-2 in India: Let the Data Speak

Limaye, Sanket; Kasibhatla, Sunitha Manjari; Ramtirthkar, Mukund; Kinikar, Meenal; Kale, Mohan; Kulkarni‐Kale, Urmila

doi:10.3390/v13112238

Cited by 13 publications

(6 citation statements)

References 80 publications

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“…Also, the mutation S194L found in the Nucleocapsid gene was a highly significant mutation observed across our cohort and is also associated with mortality. Several other studies have also reported that this mutation is deleterious and correlated with fatal outcomes ( Limaye et al., 2021 ; Mehta et al., 2021 ; SeyedAlinaghi et al., 2021 ). This could possibly indicate their crucial role in elevating the pathogenicity of the virus, thereby contributing to increased disease severity and clinical outcome.…”

Section: Discussionmentioning

confidence: 84%

SARS-CoV-2 Mutations and COVID-19 Clinical Outcome: Mutation Global Frequency Dynamics and Structural Modulation Hold the Key

Maurya

Mishra

Swaminathan

et al. 2022

Front. Cell. Infect. Microbiol.

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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has had an enormous burden on the healthcare system worldwide as a consequence of its new emerging variants of concern (VOCs) since late 2019. Elucidating viral genome characteristics and its influence on disease severity and clinical outcome has been one of the crucial aspects toward pandemic management. Genomic surveillance holds the key to identify the spectrum of mutations vis-à-vis disease outcome. Here, in our study, we performed a comprehensive analysis of the mutation distribution among the coronavirus disease 2019 (COVID-19) recovered and mortality patients. In addition to the clinical data analysis, the significant mutations within the two groups were analyzed for their global presence in an effort to understand the temporal dynamics of the mutations globally in comparison with our cohort. Interestingly, we found that all the mutations within the recovered patients showed significantly low global presence, indicating the possibility of regional pool of mutations and the absence of preferential selection by the virus during the course of the pandemic. In addition, we found the mutation S194L to have the most significant occurrence in the mortality group, suggesting its role toward a severe disease progression. Also, we discovered three mutations within the mortality patients with a high cohort and global distribution, which later became a part of variants of interest (VOIs)/VOCs, suggesting its significant role in enhancing viral characteristics. To understand the possible mechanism, we performed molecular dynamics (MD) simulations of nucleocapsid mutations, S194L and S194*, from the mortality and recovered patients, respectively, to examine its impacts on protein structure and stability. Importantly, we observed the mutation S194* within the recovered to be comparatively unstable, hence showing a low global frequency, as we observed. Thus, our study provides integrative insights about the clinical features, mutations significantly associated with the two different clinical outcomes, its global presence, and its possible effects at the structural level to understand the role of mutations in driving the COVID-19 pandemic.

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Section: Discussionmentioning

confidence: 84%

SARS-CoV-2 Mutations and COVID-19 Clinical Outcome: Mutation Global Frequency Dynamics and Structural Modulation Hold the Key

Maurya

Mishra

Swaminathan

et al. 2022

Front. Cell. Infect. Microbiol.

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“…Her group has developed novel algorithms for epitope predictions [57], alignment-free phylogeny and designed servers for virus tying [58][59][60]. She has active collaborations with national and international virologists and has worked towards investigating virus outbreaks and pandemics including COVID-19 [61][62][63]. With a focus on translation, Urmila has contributed to computational vaccine design (JEV, HPV16), to explain the escape of viruses from vaccine-induced neutralization (Mumps) and to understand potential impact of virus-host variations on efficacy of vaccine (COVID- 19).…”

Section: Dr Urmila Kulkarni-kale: Virus Evolution Diversification And...mentioning

confidence: 99%

Women in the European Virus Bioinformatics Center

Hufsky

Abecasis

Patrícia

et al. 2022

Viruses

Self Cite

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Viruses are the cause of a considerable burden to human, animal and plant health, while on the other hand playing an important role in regulating entire ecosystems. The power of new sequencing technologies combined with new tools for processing “Big Data” offers unprecedented opportunities to answer fundamental questions in virology. Virologists have an urgent need for virus-specific bioinformatics tools. These developments have led to the formation of the European Virus Bioinformatics Center, a network of experts in virology and bioinformatics who are joining forces to enable extensive exchange and collaboration between these research areas. The EVBC strives to provide talented researchers with a supportive environment free of gender bias, but the gender gap in science, especially in math-intensive fields such as computer science, persists. To bring more talented women into research and keep them there, we need to highlight role models to spark their interest, and we need to ensure that female scientists are not kept at lower levels but are given the opportunity to lead the field. Here we showcase the work of the EVBC and highlight the achievements of some outstanding women experts in virology and viral bioinformatics.

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“…A possible reason why the Indian subcontinent was so dramatically affected may have been the high prevalence of the A97V (SNP: C13730T) and P323L (SNP: C14408T) mutations in the RNA-dependent RNA polymerase (NSP12) on the subcontinent [39]. Both substitutions correlate with an approximately 100-fold higher evolution rate in India (6,73 x 10 -2 substitutions/site/year) compared to the global average (6,50 x 10 -4 substitutions/site/year) [41].…”

Section: Dominant Lineages With Fixed Snpsmentioning

confidence: 99%

From Minor Mutant to Dominance, the Evolution of SARS-CoV-2 Variants

Caspari¹

2022

Preprint

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The successive waves of the Covid-19 pandemic are driven by SARS-CoV-2 variants that reached critical detection levels in different parts of the world. But how evolved the Wuhan virus since its detection in December 2019 into the Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Delta (B.1.617.2) and Omicron (B.1.1.529) variants of concern? This is a story of mice and men, of up to 1,000,000 infected cells in one person, where each cell produces between 105 and 106 viral RNAs, of immune-compromised patients, the digestive tract and viral recombination.

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Circulation and Evolution of SARS-CoV-2 in India: Let the Data Speak

Cited by 13 publications

References 80 publications

SARS-CoV-2 Mutations and COVID-19 Clinical Outcome: Mutation Global Frequency Dynamics and Structural Modulation Hold the Key

SARS-CoV-2 Mutations and COVID-19 Clinical Outcome: Mutation Global Frequency Dynamics and Structural Modulation Hold the Key

Women in the European Virus Bioinformatics Center

From Minor Mutant to Dominance, the Evolution of SARS-CoV-2 Variants

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