Genomic Surveillance and Phylodynamic Analyses Reveal the Emergence of Novel Mutations and Co-mutation Patterns Within SARS-CoV-2 Variants Prevalent in India

Biswas, Nupur; Mallick, Priyanka; Maity, Sujay Krishna; Bhowmik, Debaleena; Mitra, Arpita; Saha, Soumen; Roy, Aviral; Chakrabarti, Partha; Paul, Sandip; Chakrabarti, Saikat

doi:10.3389/fmicb.2021.703933

Cited by 11 publications

(5 citation statements)

References 39 publications

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“…In an analysis of the original variant, this lineage revealed 23 substitutions, most of which are discrete mutations ( Silva et al., 2021 ; Korber et al., 2020 ). Lineage B.1.618 was discovered for the first time in October of 2020, this variant contained E484K mutation with many other variations and showed substantial development in West Bengal, India, in April 2021 ( Biswas et al., 2021 ). On 23 April 2021, The PANGOLIN analysis identified 135 sequences in India ( Singh et al., 2021 ).…”

Section: Sars-cov-2 Vaccine and Variantsmentioning

confidence: 99%

SARS-CoV-2: Emergence of New Variants and Effectiveness of Vaccines

Singh

Parveen

Yadav

2021

Front. Cell. Infect. Microbiol.

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The emergence of SARS-CoV-2 variants may cause resistance at the immunity level against current vaccines. Some emergent new variants have increased transmissibility, infectivity, hospitalization, and mortality. Since the administration of the first SARS-CoV-2 vaccine to a human in March 2020, there is an ongoing global race against SARS-CoV-2 to control the current pandemic situation. Spike (S) glycoprotein of SARS-CoV-2 is the main target for current vaccine development, which can neutralize the infection. Companies and academic institutions have developed vaccines based on the S glycoprotein, as well as its antigenic domains and epitopes, which have been proven effective in generating neutralizing antibodies. The effectiveness of SARS-CoV-2 vaccines and other therapeutics developments are limited by the new emergent variants at the global level. We have discussed the emergent variants of SARS-CoV-2 on the efficacy of developed vaccines. Presently, most of the vaccines have been tremendously effective in severe diseases. However, there are still noteworthy challenges in certifying impartial vaccines; the stories of re-infections are generating more stressful conditions, and this needs further clinical evaluation.

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Section: Sars-cov-2 Vaccine and Variantsmentioning

confidence: 99%

SARS-CoV-2: Emergence of New Variants and Effectiveness of Vaccines

Singh

Parveen

Yadav

2021

Front. Cell. Infect. Microbiol.

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“…The region-specific co-mutations in the three countries with high vaccine coverage were linked steadily all through time, with the frequencies in Israel and the USA increasing over time. This phenomenon indicated that the mutation patterns may be associated with the genetic background of the populations, or may be correlated to some feature change of the virus, e.g., infectivity, transmissibility and disease severity, just as a previous study demonstrated the possible association of co-mutations with the infection outcomes manifested in Indian patients [ 36 ]. As none of the linked sites were in the RBD, or even in the S gene, it was speculated that they may not be related to immune evasion.…”

Section: Discussionmentioning

confidence: 89%

Evolutionary Pattern Comparisons of the SARS-CoV-2 Delta Variant in Countries/Regions with High and Low Vaccine Coverage

Zhang

Fan

et al. 2022

Viruses

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It has been argued that vaccine-breakthrough infections of SARS-CoV-2 would likely accelerate the emergence of novel variants with immune evasion. This study explored the evolutionary patterns of the Delta variant in countries/regions with relatively high and low vaccine coverage based on large-scale sequences. Our results showed that (i) the sequences were grouped into two clusters (L and R); the R cluster was dominant, its proportion increased over time and was higher in the high-vaccine-coverage areas; (ii) genetic diversities in the countries/regions with low vaccine coverage were higher than those in the ones with high vaccine coverage; (iii) unique mutations and co-mutations were detected in different countries/regions; in particular, common co-mutations were exhibited in highly occurring frequencies in the areas with high vaccine coverage and presented in increasing frequencies over time in the areas with low vaccine coverage; (iv) five sites on the S protein were under strong positive selection in different countries/regions, with three in non-C to U sites (I95T, G142D and T950N), and the occurring frequencies of I95T in high vaccine coverage areas were higher, while G142D and T950N were potentially immune-pressure-selected sites; and (v) mutation at the N6-methyladenosine site 4 on ORF7a (C27527T, P45L) was detected and might be caused by immune pressure. Our study suggested that certain variation differences existed between countries/regions with high and low vaccine coverage, but they were not likely caused by host immune pressure. We inferred that no extra immune pressures on SARS-CoV-2 were generated with high vaccine coverage, and we suggest promoting and strengthening the uptake of the COVID-19 vaccine worldwide, especially in less developed areas.

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“… 7 In the second wave, several deaths in India occurred due to “cytokine storm” in adults, while many children contracted the disease with mild to severe symptoms. 8 , 9 , 10 Whether this differential clinical outcome was due to host specific immunity alone or also due to viral genomic mutations, remains to be investigated.…”

Section: Introductionmentioning

confidence: 99%

“…Two possibilities behind these variable symptoms are the virus genotype and the unique host genetic make‐up orchestrating their immune responses 7 . In the second wave, several deaths in India occurred due to “cytokine storm” in adults, while many children contracted the disease with mild to severe symptoms 8–10 . Whether this differential clinical outcome was due to host specific immunity alone or also due to viral genomic mutations, remains to be investigated.…”

Section: Introductionmentioning

confidence: 99%

Emergence of a unique SARS‐CoV‐2 Delta sub‐cluster harboring a constellation of co‐appearing non‐Spike mutations

Banerjee

Mazumder

Roy

et al. 2023

Journal of Medical Virology

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Accumulation of diverse mutations across the structural and nonstructural genes is leading to rapid evolution of SARS‐CoV‐2, altering its pathogenicity. We performed whole genome sequencing of 239 SARS‐CoV‐2 RNA samples collected from both adult and pediatric patients across eastern India (West Bengal), during the second pandemic wave in India (April–May 2021). In addition to several common spike mutations within the Delta variant, a unique constellation of eight co‐appearing non‐Spike mutations was identified, which revealed a high degree of positive mutual correlation. Our results also demonstrated the dynamics of SARS‐CoV‐2 variants among unvaccinated pediatric patients. 41.4% of our studied Delta strains harbored this signature set of eight co‐appearing non‐Spike mutations and phylogenetically out‐clustered other Delta sub‐lineages like 21J, 21A, or 21I. This is the first report from eastern India that portrayed a landscape of co‐appearing mutations in the non‐Spike proteins, which might have led to the evolution of a distinct Delta subcluster. Accumulation of such mutations in SARS‐CoV‐2 may lead to the emergence of “vaccine‐evading variants.” Hence, monitoring of such non‐Spike mutations will be significant in the formulation of any future vaccines against those SARS‐CoV‐2 variants that might evade the current vaccine‐induced immunity, among both the pediatric and adult populations.

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Genomic Surveillance and Phylodynamic Analyses Reveal the Emergence of Novel Mutations and Co-mutation Patterns Within SARS-CoV-2 Variants Prevalent in India

Cited by 11 publications

References 39 publications

SARS-CoV-2: Emergence of New Variants and Effectiveness of Vaccines

SARS-CoV-2: Emergence of New Variants and Effectiveness of Vaccines

Evolutionary Pattern Comparisons of the SARS-CoV-2 Delta Variant in Countries/Regions with High and Low Vaccine Coverage

Emergence of a unique SARS‐CoV‐2 Delta sub‐cluster harboring a constellation of co‐appearing non‐Spike mutations

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