Molecular insight into the genomic variation of SARS-CoV-2 strains from current outbreak

Das, Avizit; Khurshid, Sarah; Ferdausi, Aleya; Nipu, Eshita Sadhak; Das, Amit Kumar; Ahmed, Fee Faysal

doi:10.1016/j.compbiolchem.2021.107533

Cited by 3 publications

(3 citation statements)

References 42 publications

(61 reference statements)

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“…To date, a large number of single nucleotide polymorphisms (SNPs) in the SARS-CoV-2 genome have been identified by high-throughput sequencing [43] , [44] . However, the functions of these SNPs remain elusive.…”

Section: Resultsmentioning

confidence: 99%

A DNA-based non-infectious replicon system to study SARS-CoV-2 RNA synthesis

Feng

Zhang²,

Jiang³

et al. 2022

Computational and Structural Biotechnology Journal

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Section: Resultsmentioning

confidence: 99%

A DNA-based non-infectious replicon system to study SARS-CoV-2 RNA synthesis

Feng

Zhang²,

Jiang³

et al. 2022

Computational and Structural Biotechnology Journal

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“…The extensive genomic surveillance of SARS CoV-2 viral isolates in Bangladesh throughout the pandemic is motivated by the urgency to identify the next strains of SARS CoV-2 carrying S-protein mutations or other genetic changes [25][26][27][28][29][30][31][32][33][34]. In the first and second pandemic waves in Bangladesh, the alpha and beta variants of the B.1.1.7 and B.1.351 lineages were associated with an Ro of approximately 1.2 [27].…”

Section: Discussionmentioning

confidence: 99%

“…The Q677H is positioned adjacent to the S1/S2 cleavage site. Its effect on cell tropism and transmissibility is predicted by molecular modeling [34,35]. So far, there is no evidence that Q677H is dangerous in terms of conferring increased SARS-CoV-2 viral pathogenicity or COVID-19 disease severity [36,37].…”

Section: Discussionmentioning

confidence: 99%

Molecular and Serological Characterization of the SARS-CoV-2 Delta Variant in Bangladesh in 2021

Ghosh

Kaiser

Molla

et al. 2021

Viruses

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Novel SARS-CoV-2 variants are emerging at an alarming rate. The delta variant and other variants of concern (VoC) carry spike (S)-protein mutations, which have the potential to evade protective immunity, to trigger break-through infections after COVID-19 vaccination, and to propagate future waves of COVID-19 pandemic. To identify SARS CoV-2 variants in Bangladesh, patients who are RT-PCR-positive for COVID-19 infections in Dhaka were screened by a RT-PCR melting curve analysis for spike protein mutations. To assess the anti-SARS CoV-2 antibody responses, the levels of the anti-S -proteins IgA and IgG and the anti-N-protein IgG were measured by ELISA. Of a total of 36 RT-PCR positive samples (75%), 27 were identified as delta variants, with one carrying an additional Q677H mutation and two with single nucleotide substitutions at position 23029 (compared to Wuhan-Hu-1 reference NC 045512) in the genome sequence. Three (8.3%) were identified as beta variants, two (5.5%) were identified as alpha variants, three (8.3%) were identified as having a B.1.1.318 lineage, and one sample was identified as an eta variant (B.1.525) carrying an additional V687L mutation. The trend of higher viral load (lower Cp values) among delta variants than in the alpha and beta variants was of borderline statistical significance (p = 0.045). Prospective studies with larger Bangladeshi cohorts are warranted to confirm the emergence of S-protein mutations and their association with antibody response in natural infection and potential breakthrough in vaccinated subjects.

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Genome Analysis of 10K SARS-COV-2 Sequences to Identify the Presence of Single-Nucleotide Polymorphisms

Nugrahapraja,

Hasna Syahira,

Fauzi

2023

BIO Web Conf.

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A new type of coronavirus was identified in Wuhan, China, in December 2019, which was named SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus-2). The high mutation rate of SARS-CoV2 makes it challenging to develop effective vaccines for all variants. Substitution is the most common type of mutation that occurs in SARS-CoV-2. This research was conducted to identify the genetic variability of mutations in SNP of SARS-CoV-2 and analyse the impact. About 15,000 sequences of SARS-CoV-2 were downloaded from GISAID, which were isolated from 33 different countries around the world from February 2020 to July 2021. Sequence analysis was done using the MAFFT and the Nextclade. The results of this study are expected to help identify conserved regions in SARS-CoV-2 which can be used as probes for the virus identification process and can be used as target areas in vaccine development. Furthermore the results showed that the most common variants were variants 20B, 20A, and 20I (Alpha), with a population percentage of 32.12%, 23.95% and 17.39% of the total population, respectively. Furthermore, SNPs were called in the samples using the SNP-sites and extracted using Excel. Of the 10,107 sequences of SARSCoV-2 studied, 154 SNPs were found with the highest number of SNPs in the spike, nsp3 and nucleocapsid genes. The ratio of the number of mutations to the most extensive sequence length was in the ORF8, ORF7a, and ORF7b genes with respective values of 0.537, 0.474, and 0.419.

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Molecular insight into the genomic variation of SARS-CoV-2 strains from current outbreak

Abstract: Graphical abstract

Cited by 3 publications

References 42 publications

A DNA-based non-infectious replicon system to study SARS-CoV-2 RNA synthesis

A DNA-based non-infectious replicon system to study SARS-CoV-2 RNA synthesis

Molecular and Serological Characterization of the SARS-CoV-2 Delta Variant in Bangladesh in 2021

Genome Analysis of 10K SARS-COV-2 Sequences to Identify the Presence of Single-Nucleotide Polymorphisms

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