Mutational characterization of Omicron SARS-CoV-2 lineages circulating in Chhattisgarh, a central state of India

Singh, Pushpendra; Sharma, Kuldeep; Shaw, Dipika; Bhargava, Anudita; Negi, Sanjay Singh

doi:10.3389/fmed.2022.1082846

Cited by 6 publications

(5 citation statements)

References 29 publications

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“…Between August and September 2021, the prevalence of BA.5 increased from 27.84 to 34.05%. The spike gene mutations in Omicron variant are A67V, Δ69-70, T95I, G142D/Δ143-145, Δ211/L212I, ins214EPE, V213G, L212I, G339D, S371L, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, G446S, S477N, T478K, L452R/L452Q, E484A, F486V, Q493R, G496S, Q498R, N501Y, Y505H, T547K, D614G, H655Y, N679K, P681H, S704L, N764K, D796Y, N856K, A879V, Q954H, N969K, and L981F ( Muik et al, 2022 ; Shanmugaraj et al, 2022 ; Singh et al, 2022a ; Takashita et al, 2022 ; Yoshida et al, 2022 ). In this study, Omicron variant (OP763688 and OP763695) has an additional spike L179P and Q271R mutations, which are present in 0.02 and 0.002% of strains deposited in the GISAID database, as of May 2023 ( Table 2 ).…”

Section: Resultsmentioning

confidence: 99%

Genomic surveillance of genes encoding the SARS-CoV-2 spike protein to monitor for emerging variants on Jeju Island, Republic of Korea

Kim

Park

et al. 2023

Front. Microbiol.

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IntroductionThe severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has been fueled by new variants emerging from circulating strains. Here, we report results from a genomic surveillance study of SARS-CoV-2 on Jeju Island, Republic of Korea, from February 2021 to September 2022.MethodsA total of 3,585 SARS-CoV-2 positive samples were analyzed by Sanger sequencing of the gene encoding the spike protein before performing phylogenetic analyses.ResultsWe found that the Alpha variant (B.1.1.7) was dominant in May 2021 before being replaced by the Delta variant (B.1.617.2) in July 2021, which was dominant until December 2021 before being replaced by the Omicron variant. Mutations in the spike protein, including N440K and G446S, have been proposed to contribute to immune evasion, accelerating the spread of Omicron variants.DiscussionOur results from Juju Island, Republic of Korea, are consistent with and contribute to global surveillance efforts crucial for identifying new variants of concern of SARS-CoV-2 and for monitoring the transmission dynamics and characteristics of known strains.

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Section: Resultsmentioning

confidence: 99%

Genomic surveillance of genes encoding the SARS-CoV-2 spike protein to monitor for emerging variants on Jeju Island, Republic of Korea

Kim

Park

et al. 2023

Front. Microbiol.

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“…VIR-7831) against group E epitopes with omicron spike is significantly hampered by the G339D mutation ( 10 ). Mutation of G339D to G339H inflicts fusogenicity and thus enhances the infection rate to 44-fold ( 33 ). It also permits BA.2.75 to escape the host’s effective neutralizing antibody response generated against different RBD epitopes.…”

Section: Discussionmentioning

confidence: 99%

Section: Sn Positionmentioning

confidence: 99%

Genome sequencing of SARS-CoV-2 omicron variants in Delhi reveals alterations in immunogenic regions in spike glycoprotein

Shikha,

Jogi,

Jha

et al. 2023

Front. Immunol.

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The SARS-CoV-2 omicron variants keep accumulating a large number of mutations in the spike (S) protein, which contributes to greater transmissibility and a rapid rise to dominance within populations. The identification of mutations and their affinity to the cellular angiotensin-converting enzyme-2 (ACE-2) receptor and immune evasion in the Delhi NCR region was under-acknowledged. The study identifies some mutations (Y505 reversion, G339H, and R346T/N) in genomes from Delhi, India, and their probable implications for altering the immune response and binding affinity for ACE-2. The spike mutations have influenced the neutralizing activity of antibodies against the omicron variant, which shows partial immune escape. However, researchers are currently exploring various mitigation strategies to tackle the potential decline in efficacy or effectiveness against existing and future variants of SARS-CoV-2. These strategies include modifying vaccines to target specific variants, such as the omicron variant, developing multivalent vaccine formulations, and exploring alternative delivery methods. To address this, it is also necessary to understand the impact of these mutations from a different perspective, especially in terms of alterations in antigenic determinants. In this study, we have done whole genome sequencing (WGS) of SARS-CoV-2 in COVID-19 samples from Delhi, NCR, and analyzed the spike’s mutation with an emphasis on antigenic alterations. The impact of mutation in terms of epitope formation, loss/gain of efficiency, and interaction of epitopes with antibodies has been studied. Some of the mutations or variant genomes seem to be the progenitors of the upcoming variants in India. Our analyses suggested that weakening interactions with antibodies may lead to immune resistance in the circulating genomes.

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“…The BA.2 strain exhibits unique mutations in ORF1a, S protein, and ORF6, specifically L3201F, Q493R, and D61L. Notably, the Q493R mutation has the potential to facilitate interspecies transmission and requires vigilance 29 . On the other hand, the BA.5.1.3 strain carries distinct mutations, D3N and L37F, in the M protein and ORF10, respectively.…”

Section: Experiments and Analysesmentioning

confidence: 99%

Clustering analysis for the evolutionary relationships of SARS-CoV-2 strains

Chen,

Wang,

Liu

et al. 2024

Sci Rep

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To explore the differences and relationships between the available SARS-CoV-2 strains and predict the potential evolutionary direction of these strains, we employ the hierarchical clustering analysis to investigate the evolutionary relationships between the SARS-CoV-2 strains utilizing the genomic sequences collected in China till January 7, 2023. We encode the sequences of the existing SARS-CoV-2 strains into numerical data through k-mer algorithm, then propose four methods to select the representative sample from each type of strains to comprise the dataset for clustering analysis. Three hierarchical clustering algorithms named Ward-Euclidean, Ward-Jaccard, and Average-Euclidean are introduced through combing the Euclidean and Jaccard distance with the Ward and Average linkage clustering algorithms embedded in the OriginPro software. Experimental results reveal that BF.28, BE.1.1.1, BA.5.3, and BA.5.6.4 strains exhibit distinct characteristics which are not observed in other types of SARS-CoV-2 strains, suggesting their being the majority potential sources which the future SARS-CoV-2 strains’ evolution from. Moreover, BA.2.75, CH.1.1, BA.2, BA.5.1.3, BF.7, and B.1.1.214 strains demonstrate enhanced abilities in terms of immune evasion, transmissibility, and pathogenicity. Hence, closely monitoring the evolutionary trends of these strains is crucial to mitigate their impact on public health and society as far as possible.

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Mutational characterization of Omicron SARS-CoV-2 lineages circulating in Chhattisgarh, a central state of India

Cited by 6 publications

References 29 publications

Genomic surveillance of genes encoding the SARS-CoV-2 spike protein to monitor for emerging variants on Jeju Island, Republic of Korea

Genomic surveillance of genes encoding the SARS-CoV-2 spike protein to monitor for emerging variants on Jeju Island, Republic of Korea

Genome sequencing of SARS-CoV-2 omicron variants in Delhi reveals alterations in immunogenic regions in spike glycoprotein

Clustering analysis for the evolutionary relationships of SARS-CoV-2 strains

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