Mutational Analysis of SARS-CoV-2. ORF8 and the Evolution of the Delta and Omicron Variants

Trieu, Gopika; Ng, Kevin Tak‐Pan; Trieu, Vuong

doi:10.2139/ssrn.4056882

Cited by 2 publications

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“…In consistent with our findings many other authors have reported an ongoing divergence in the genome of SARS-CoV-2, owing to its continuous and rapid evolution, compared with its reference genome (Wuhan-Hu-1) [12,[21][22][23][24][25][26]. These findings are further corroborated with the emergence of many new variants of this virus, accumulating a large number of mutations which have enhanced their fitness, transmission and pathogenicity [27][28][29][30]. Out of the 899 missense variants, 537 were found in ORF1ab, which transcribe into 16…”

Section: Discussionsupporting

confidence: 92%

Genomic landscape of alpha-variant of SARS-CoV-2 circulated in Pakistan

et al. 2022

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In this study, we investigated the genomic variability of alpha-VOC of SARS-CoV-2 in Pakistan, in context of the global population of this variant. A set of 461 whole-genome sequences of Pakistani samples of alpha-variant, retrieved from GISAID, were aligned in MAFFT and used as an input to the Coronapp web-application. Phylogenetic tree was constructed through maximum-likelihood method by downloading the 100 whole-genome sequences of alpha-variant for each of the 12 countries having the largest number of Pakistani diasporas. We detected 1725 mutations, which were further categorized into 899 missense mutations, 654 silent mutations, 52 mutations in non-coding regions, 25 in-frame deletions, 01 in-frame insertion, 51 frameshift deletions, 21 frameshift insertions, 21 stop-gained variants, and 1 stop-gained deletion. We found NSP3 and Spike as the most variable proteins with 355 and 233 mutations respectively. However, some characteristic mutations like Δ144(S), G204R(N), and T1001I, I2230T, del3675–3677(ORF1ab) were missing in the Pakistani population of alpha-variant. Likewise, R1518K(NSP3), P83L(NSP9), and A52V, H164Y(NSP13) were found for the first time in this study. Interestingly, Y145 deletion(S) had 99% prevalence in Pakistan but globally it was just 4.2% prevalent. Likewise, R68S substitution (ORF3a), F120 frameshift deletion, L120 insertion, L118V substitution (ORF8), and N280Y(NSP2) had 20.4%, 14.3%, 14.8%, 9.1%, 13.9% prevalence locally but globally they were just 0.1%, 0.2%, 0.04%, 1.5%, and 2.4% prevalent respectively. The phylogeny analysis revealed that majority of Pakistani samples were grouped together in the same clusters with Italian, and Spanish samples suggesting the transmission of alpha-variant to Pakistan from these western European countries.

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Section: Discussionsupporting

confidence: 92%

Genomic landscape of alpha-variant of SARS-CoV-2 circulated in Pakistan

et al. 2022

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“…On the other hand, Orf9c expression impaired interferon signaling, antigen processing and presentation, complement signaling, and induced IL-6 signaling (45). Our study reports that the T60A mutation, which is correlated to Orf9b, is the more frequent mutation found in France, although Gopika et al found this mutation in Thailand as well (46). Gupta S et al, concluded that in the Orf3a protein, Serine to Leucine conversion occurred at position 171 in India.…”

Section: Discussionmentioning

confidence: 48%

The First Geographic Identification by Country of Sustainable Mutations of SARS-COV2 Sequence Samples: Worldwide Natural Selection Trends

Mahmanzar

Houseini

Rahimian

et al. 2022

Preprint

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The high mutation rates of RNA viruses, coupled with short generation times and large population sizes, allow viruses to evolve rapidly and adapt to the host environment. The rapidity of viral mutation also causes problems in developing successful vaccines and antiviral drugs. With the spread of SARS-CoV-2 worldwide, thousands of mutations have been identified, some of which have relatively high incidences, but their potential impacts on virus characteristics remain unknown. The present study analyzed mutation patterns, SARS-CoV-2 AASs retrieved from the GISAID database containing 10,500,000 samples. Python 3.8.0 programming language was utilized to pre-process FASTA data, align to the reference sequence, and analyze the sequences. Upon completion, all mutations discovered were categorized based on geographical regions and dates. The most stable mutations were found in nsp1(8% S135R), nsp12(99.3% P323L), nsp16 (1.2% R216C), envelope (30.6% T9I), spike (97.6% D614G), and Orf8 (3.5% S24L), and were identified in the United States on April 3, 2020, and England, Gibraltar, and, New Zealand, on January 1, 2020, respectively. The study of mutations is the key to improving understanding of the function of the SARS-CoV-2, and recent information on mutations helps provide strategic planning for the prevention and treatment of this disease. Viral mutation studies could improve the development of vaccines, antiviral drugs, and diagnostic assays designed with high accuracy, specifically useful during pandemics. This knowledge helps to be one step ahead of new emergence variants.

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Mutational Analysis of SARS-CoV-2. ORF8 and the Evolution of the Delta and Omicron Variants

Cited by 2 publications

References 0 publications

Genomic landscape of alpha-variant of SARS-CoV-2 circulated in Pakistan

Genomic landscape of alpha-variant of SARS-CoV-2 circulated in Pakistan

The First Geographic Identification by Country of Sustainable Mutations of SARS-COV2 Sequence Samples: Worldwide Natural Selection Trends

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