Mutational dynamics across VOCs in International travellers and Community transmission underscores importance of Spike-ACE2 interaction

Mehta, Priyanka; Ravi, Varsha; Devi, Priti; Maurya, Ranjeet; Parveen, Shaista; Mishra, Pallavi; Yadav, Aanchal; Swaminathan, Aparna; Saifi, Sheeba; Khare, Kriti; Chattopadhyay, Partha; Yadav, Monika; Chauhan, Nar Singh; Tarai, Bansidhar; Budhiraja, Sandeep; Shamim, Uzma; Pandey, Rajesh

doi:10.1016/j.micres.2022.127099

Cited by 6 publications

(5 citation statements)

References 30 publications

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“…These variations can affect diagnostic testing reliability, available treatment effectiveness, and vaccine efficacy [2,3]. Currently, the spike (S) protein is the region most affected by mutations, and the circulating SARS-CoV-2 variants are classified on the basis of variations in the S protein compared to the ancestral strain [4]. Among the growing number of SARS-CoV-2 variants documented worldwide during the pandemic, previously identified variants of concern (VOCs), such as Alpha (B.1.1.7/20I), Beta (B.1.351/20H), Gamma (B.1.1.28/P1), and Delta (B.1.617.2), have been associated with increased transmissibility, mortality, and decreased susceptibility to neutralising antibodies induced by vaccination or previous infection [2,3,[5][6][7][8].…”

Section: Introductionmentioning

confidence: 99%

Epidemiological and Clinical Features of SARS-CoV-2 Variants Circulating between April–December 2021 in Italy

Lai

Bergna

Ventura

et al. 2022

Viruses

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SARS-CoV-2 is constantly evolving, leading to new variants. We analysed data from 4400 SARS-CoV-2-positive samples in order to pursue epidemiological variant surveillance and to evaluate their impact on public health in Italy in the period of April–December 2021. The main circulating strain (76.2%) was the Delta variant, followed by the Alpha (13.3%), the Omicron (5.3%), and the Gamma variants (2.9%). The B.1.1 lineages, Eta, Beta, Iota, Mu, and Kappa variants, represented around 1% of cases. There were 48.2% of subjects who had not been vaccinated, and they had a lower median age compared to the vaccinated subjects (47 vs. 61 years). An increasing number of infections in the vaccinated subjects were observed over time, with the highest proportion in November (85.2%). The variants correlated with clinical status; the largest proportion of symptomatic patients (59.6%) was observed with the Delta variant, while subjects harbouring the Gamma variant showed the highest proportion of asymptomatic infection (21.6%), albeit also deaths (5.4%). The Omicron variant was only found in the vaccinated subjects, of which 47% had been hospitalised. The diffusivity and pathogenicity associated with the different SARS-CoV-2 variants are likely to have relevant public health implications, both at the national and international levels. Our study provides data on the rapid changes in the epidemiological landscape of the SARS-CoV-2 variants in Italy.

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Section: Introductionmentioning

confidence: 99%

Epidemiological and Clinical Features of SARS-CoV-2 Variants Circulating between April–December 2021 in Italy

Lai

Bergna

Ventura

et al. 2022

Viruses

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“…Moreover, the activity of QfeH toward AOPPs was positively related to the binding free energy and the dissociation constant. CFP binds most rapidly and tightly to QfeH, allowing enzymatic reactions to proceed faster than with other AOPP substrates. , These results could plausibly explain why QfeH exhibited different catalytic activities according to the kinetics results obtained for the AOPPs (CFP > FPE > CYB > QPE > HPM), which provides clarification on the biodegradation mechanisms of AOPPs.…”

Section: Resultsmentioning

confidence: 84%

Efficient Biodegradation of Multiple Aryloxyphenoxypropionate Herbicides by Corynebacterium sp. Z-1 and the Proposed Degradation Mechanism

Gao,

Guo,

Wang

et al. 2024

J. Agric. Food Chem.

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Esterases are crucial for aryloxyphenoxypropionate herbicide (AOPP) biodegradation. However, the underlying molecular mechanisms of AOPP biodegradation by esterases are poorly understood. In the current work, Corynebacterium sp. Z-1 was isolated and found to degrade multiple AOPPs, including quizalofop-p-ethyl (QPE), haloxyfop-p-methyl (HPM), fenoxaprop-p-ethyl (FPE), cyhalofop-butyl (CYB), and clodinafop-propargyl (CFP). A novel esterase, QfeH, which catalyzes the cleavage of ester bonds in AOPPs to form AOPP acids, was identified from strain Z-1. The catalytic activities of QfeH toward AOPPs decreased in the following order: CFP > FPE > CYB > QPE > HPM. Molecular docking, computational analyses, and site-directed mutagenesis indicated the catalytic mechanisms of QfeH-mediated degradation of different AOPPs. Notably, the key residue S159 is essential for the activity of QfeH. Moreover, V222Y, T227M, T227A, A271R, and M275K mutants, exhibiting 2.9–5.0 times greater activity than QfeH, were constructed. This study facilitates the mechanistic understanding of AOPPs bioremediation by esterases.

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“…No.20043675 and reference guide: 1000000126053 v04) and Oxford Nanopore Rapid barcoding kit (SQK-RBK110.96). The sequencing methodology and analysis pipeline of both platforms have been previously published ( 27 ).…”

Section: Methodsmentioning

confidence: 99%

Unraveling the genetic evolution of SARS-CoV-2 Recombinants using mutational dynamics across the different lineages

Ravi,

Shamim,

Khan

et al. 2024

Front. Med.

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IntroductionRecombination serves as a common strategy employed by RNA viruses for their genetic evolution. Extensive genomic surveillance during the COVID-19 pandemic has reported SARS-CoV-2 Recombinant strains indicating recombination events during the viral evolution. This study introspects the phenomenon of genome recombination by tracing the footprint of prominent lineages of SARS-CoV-2 at different time points in the context of on-going evolution and emergence of Recombinants.MethodWhole genome sequencing was carried out for 2,516 SARS-CoV-2 (discovery cohort) and 1,126 (validation cohort) using nasopharyngeal samples collected between the time period of March 2020 to August 2022, as part of the genomic surveillance program. The sequences were classified according to the different lineages of SARS-CoV-2 prevailing in India at respective time points.ResultsMutational diversity and abundance evaluation across the 12 lineages identified 58 Recombinant sequences as harboring the least number of mutations (n = 111), with 14 low-frequency unique mutations with major chunk of mutations coming from the BA.2. The spontaneously/dynamically increasing and decreasing trends of mutations highlight the loss of mutations in the Recombinants that were associated with the SARS-CoV-2 replication efficiency, infectivity, and disease severity, rendering them functionally with low infectivity and pathogenicity. Linkage disequilibrium (LD) analysis revealed that mutations comprising the LD blocks of BA.1, BA.2, and Recombinants were found as minor alleles or as low-frequency alleles in the LD blocks from the previous SARS-CoV-2 variant samples, especially Pre-VOC. Moreover, a dissipation in the size of LD blocks as well as LD decay along with a high negative regression coefficient (R squared) value was demonstrated in the Omicron and BA.1 and BA.2 lineages, which corroborated with the breakpoint analysis.ConclusionTogether, the findings help to understand the evolution and emergence of Recombinants after the Omicron lineages, for sustenance and adaptability, to maintain the epidemic spread of SARS-CoV-2 in the host population already high in immunity levels.

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Mutational dynamics across VOCs in International travellers and Community transmission underscores importance of Spike-ACE2 interaction

Cited by 6 publications

References 30 publications

Epidemiological and Clinical Features of SARS-CoV-2 Variants Circulating between April–December 2021 in Italy

Epidemiological and Clinical Features of SARS-CoV-2 Variants Circulating between April–December 2021 in Italy

Efficient Biodegradation of Multiple Aryloxyphenoxypropionate Herbicides by Corynebacterium sp. Z-1 and the Proposed Degradation Mechanism

Unraveling the genetic evolution of SARS-CoV-2 Recombinants using mutational dynamics across the different lineages

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