Clade GR and clade GH isolates of SARS-CoV-2 in Asia show highest amount of SNPs

Sengupta, A. K.; Hassan, Sk. Sarif; Choudhury, Pabitra Pal

doi:10.1016/j.meegid.2021.104724

Cited by 29 publications

(24 citation statements)

References 46 publications

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“…We investigated the correlation between viral diversity and sequence variability using entropy and site selection analysis. Genomes from clade GH were found to have an overall higher pan-genomic entropy as well as higher evidence of pervasive selection as compared with clades GR and L. Increase site specific pressure and entropy, especially across Orf1ab and N regions in GH clade is consistent with the mutation data, and might suggest that the high selection pressure of GH clade is attributed to high transmission opportunities and/or dissemination into genetically diverse population observed in the transient phase of viral evolution before the virus adapts to the population/host selection pressures [ 48 ].…”

Section: Discussionsupporting

confidence: 61%

Higher entropy observed in SARS-CoV-2 genomes from the first COVID-19 wave in Pakistan

et al. 2021

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Background We investigated the genome diversity of SARS-CoV-2 associated with the early COVID-19 period to investigate evolution of the virus in Pakistan. Materials and methods We studied ninety SARS-CoV-2 strains isolated between March and October 2020. Whole genome sequences from our laboratory and available genomes were used to investigate phylogeny, genetic variantion and mutation rates of SARS-CoV-2 strains in Pakistan. Site specific entropy analysis compared mutation rates between strains isolated before and after June 2020. Results In March, strains belonging to L, S, V and GH clades were observed but by October, only L and GH strains were present. The highest diversity of clades was present in Sindh and Islamabad Capital Territory and the least in Punjab province. Initial introductions of SARS-CoV-2 GH (B.1.255, B.1) and S (A) clades were associated with overseas travelers. Additionally, GH (B.1.255, B.1, B.1.160, B.1.36), L (B, B.6, B.4), V (B.4) and S (A) clades were transmitted locally. SARS-CoV-2 genomes clustered with global strains except for ten which matched Pakistani isolates. RNA substitution rates were estimated at 5.86 x10−4. The most frequent mutations were 5’ UTR 241C > T, Spike glycoprotein D614G, RNA dependent RNA polymerase (RdRp) P4715L and Orf3a Q57H. Strains up until June 2020 exhibited an overall higher mean and site-specific entropy as compared with sequences after June. Relative entropy was higher across GH as compared with GR and L clades. More sites were under selection pressure in GH strains but this was not significant for any particular site. Conclusions The higher entropy and diversity observed in early pandemic as compared with later strains suggests increasing stability of the genomes in subsequent COVID-19 waves. This would likely lead to the selection of site-specific changes that are advantageous to the virus, as has been currently observed through the pandemic.

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Section: Discussionsupporting

confidence: 61%

Higher entropy observed in SARS-CoV-2 genomes from the first COVID-19 wave in Pakistan

et al. 2021

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“…Then, "G" was split into "GV", "GH", and "GR", due to the mutations NS3 W57H, S A222V, and N G204R, respectively. Clade "GRY" then emerged from clade "GR" in December 2020, because of a combination of ten marker mutations in S. To these eight clades, an "O" clade was added, which is a generic, less clearly defined group [12][13][14][15]. Amino acid changes, particularly in the structural proteins, can affect the infectivity of the strain as well as the severity of the symptoms.…”

Section: Introductionmentioning

confidence: 99%

SARS-CoV-2 Variants in Lebanon: Evolution and Current Situation

Fayad

Habib

Kandeil

et al. 2021

Biology

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The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has seen a worldwide spread since its emergence in 2019, including to Lebanon, where 534,968 confirmed cases (8% of the population) and 7569 deaths have been reported as of 14 May 2021. With the genome sequencing of strains from various countries, several classification systems were established via genome comparison. For instance, the GISAID clades classification highlights key mutations in the encoded proteins that could potentially affect the virus’ infectivity and transmission rates. In this study, 58 genomes of Lebanese SARS-CoV-2 strains were analyzed, 28 of which were sequenced for this study, and 30 retrieved from the GISAID and GenBank databases. We aimed to classify these strains, establish their phylogenetic relationships, and extract the mutations causing amino acid substitutions within, particularly, the structural proteins. The sequenced Lebanese SARS-COV-2 strains were classified into four GISAID clades and 11 Pango lineages. Moreover, 21 uncommon mutations in the structural proteins were found in the newly sequenced strains, underlining interesting combinations of mutations in the spike proteins. Hence, this study constitutes an observation and description of the current SARS-CoV-2 genetic and clade situation in Lebanon according to the available sequenced strains.

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“…The clade S, a subtype of SARS-CoV-2, was identified to possess the mutation L84S in the ORF8 protein sequence [25,26,27]. Presently, among many variants of SARS-CoV-2, the lineage B.1.1.7 carries a larger than usual number of genetic changes [28,29,30].…”

Section: Introductionmentioning

confidence: 99%

An Issue of Concern: Unique Truncated ORF8 Protein Variants of SARS-CoV-2

Hassan¹,

Kodakandla

et al. 2021

Preprint

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Open reading frame 8 (ORF8) protein is one of the most evolving accessory proteins in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19). It was previously reported that the ORF8 protein inhibits presentation of viral antigens by the major histocompatibility complex class I (MHC-I) and interacts with host factors involved in pulmonary inflammation. The ORF8 protein assists SARS-CoV-2 to evade immunity and replication. Among many contributing mutations, Q27STOP, a mutation in the ORF8 protein defines the B.1.1.7 lineage of SARS-CoV-2, which is engendering the second wave of COVID-19. In the present study, 47 unique truncated ORF8 proteins (T-ORF8) due to the Q27STOP mutations were identified among 49055 available B.1.1.7 SARS-CoV-2 sequences. The results show that only one of the 47 T-ORF8 variants spread to over 57 geo-locations in North America, and other continents which includes Africa, Asia, Europe and South America. Based on various quantitative features such as amino acid homology, polar/non-polar sequence homology, Shannon entropy conservation, and other physicochemical properties of all specific 47 T-ORF8 protein variants, a collection of nine possible T-ORF8 unique variants were defined. The question of whether T-ORF8 variants work similarly to ORF8 has yet to be investigated. A positive response to the question could exacerbate future COVID-19 waves, necessitating severe containment measures.

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Clade GR and clade GH isolates of SARS-CoV-2 in Asia show highest amount of SNPs

Cited by 29 publications

References 46 publications

Higher entropy observed in SARS-CoV-2 genomes from the first COVID-19 wave in Pakistan

Higher entropy observed in SARS-CoV-2 genomes from the first COVID-19 wave in Pakistan

SARS-CoV-2 Variants in Lebanon: Evolution and Current Situation

An Issue of Concern: Unique Truncated ORF8 Protein Variants of SARS-CoV-2

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