Consensus insertion/deletions and amino acid variations of all coding and noncoding regions of the SARS-CoV-2 Omicron clades, including the XBB and BQ.1 lineages

Suharsono, Hamong; Mahardika, Bayu K.; Sudipa, Putu Henrywaesa; Sari, Tri Komala; Suardana, Ida Bagus Kade; Mahardika, Gusti Ngurah

doi:10.1007/s00705-023-05787-6

Cited by 2 publications

(1 citation statement)

References 28 publications

(32 reference statements)

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“…The 5'-UTR of SARS-CoV-2 forms ve hairpin structures and nsp1 protein bound to rst stem and loop structure helping transport of nsp1 to ribosome (Vora SM et al 2022). Thus, 26nt 3'-UTR (29534-29870nt) S2M long stem-loop structure implicated in replication and other function in the coronavirus biology (Zhao J et al 2020;Suharsono, H et al 2023). The size of the genome has been changed from 29903nt to 29782nt (Farkas C et al 2021;Patarca & Hasltine, 2023).…”

Section: Resultsmentioning

confidence: 99%

Highly infectious, less pathogenic and antibody resistant Omicron XBB.1, XBB.1.5 and XBB.1.5.1-XBB.1.5.39 subvariant Coronaviruses do not produce ORF8 protein due to 8th codon GGA=TGA Termination Codon Mutation

Chakraborty

2023

Preprint

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RNA viruses are very mutation prone. We recently reported SARS-CoV-2 ORF8 gene CAA = TAA and AAA = TAA Termination Codon Mutations in B.1.1.7 variants with no production of viable ORF8 protein. We described here another GGA = TGA termination codon in the 8th codon of ORF8 gene located exclusively in XBB.1 (XBB.1.16 and XBB.1.22) and XBB.1.5 subvariants (XBB.1.5.1 to XBB.1.5.39) but not in XBB.2 variant or Alpha, Beta, Gamma, Delta and Omicron BA.1, BA.2, BA.4, BA.5, BF.7 and BQ.1 subvariants. However, G > T mutation at 27915 also created an alternate ATG codon but the protein product was short due to preceding TAG and TGA termination codons. The originally located following ATG codons were there but in alternate reading frames and ultimately no ORF8 protein was formed in XBB.1.5 subvariants which were spreading highly now over BA.2.75, BA.4.6, BA.5.2.1, BF.7 and BQ.1.1 subvariants. This is a vivid example of three termination codon mutations in the coronavirus ORF8 protein which was implicated as target for many human proteins regulating interferon production, chromosome instability, antibody production, pathogenicity and virus clearance. The 30nt deletion in the 3’-UTR, including 24LPP, and 145Y deletions in Spike protein as well as N-protein 31ERS and ORF1ab polyprotein 3675SGF deletions made XBB.1.5 Omicron coronavirus weak and less pathogenic so that WHO declared coronaviruses as non-emergency pathogen.

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Section: Resultsmentioning

confidence: 99%

Highly infectious, less pathogenic and antibody resistant Omicron XBB.1, XBB.1.5 and XBB.1.5.1-XBB.1.5.39 subvariant Coronaviruses do not produce ORF8 protein due to 8th codon GGA=TGA Termination Codon Mutation

Chakraborty

2023

Preprint

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‘Vivaldi’: An amplicon-based whole genome sequencing method for the four seasonal human coronaviruses 229E, NL63, OC43 & HKU1, alongside SARS-CoV-2’

McClure,

Tsoleridis,

Holmes

et al. 2024

Preprint

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Prior to the emergence of SARS-CoV-2 in 2019, Alphacoronaviruses 229E and NL63 and Betacoronaviruses OC43 and HKU1 were already established endemic ‘common cold’ viral infections. Despite their collective contribution towards global respiratory morbidity and mortality and potential to inform the future trajectory of SARS-CoV-2 endemicity, they are infrequently sequenced. We therefore developed a 1200bp amplicon-based whole genome sequencing scheme targeting all four seasonal coronaviruses and SARS-CoV-2.The ‘Vivaldi’ method was applied retrospectively and prospectively using Oxford Nanopore Technology to approximately 400 seasonal coronavirus infections diagnosed in Nottingham, UK, from February 2016 to July 2023. We demonstrate that the amplicon multiplex strategy can be applied agnostically to determine complete genomes of five different species from two coronaviral genera. 304 unique seasonal coronavirus genomes of greater than 95% coverage were achieved: 64 for 229E, 85 for NL63, 128 for OC43 and 27 for HKU1. They collectively indicated a dynamic seasonal coronavirus genomic landscape, with co-circulation of multiple variants emerging and declining over the UK winter respiratory infection season, with further geographical distinction when compared to a global dataset. Prolonged infection with concomitant intra-host evolution was also observed for both Alpha-(NL63) and Betacoronaviruses (OC43).This data represents the largest single cohort of seasonal coronavirus genomes to date and also a novel amplicon scheme for their future global surveillance suitable for widespread and easy adoption in the post-SARS-CoV-2 era of viral genomics.

show abstract

Consensus insertion/deletions and amino acid variations of all coding and noncoding regions of the SARS-CoV-2 Omicron clades, including the XBB and BQ.1 lineages

Cited by 2 publications

References 28 publications

Highly infectious, less pathogenic and antibody resistant Omicron XBB.1, XBB.1.5 and XBB.1.5.1-XBB.1.5.39 subvariant Coronaviruses do not produce ORF8 protein due to 8th codon GGA=TGA Termination Codon Mutation

Highly infectious, less pathogenic and antibody resistant Omicron XBB.1, XBB.1.5 and XBB.1.5.1-XBB.1.5.39 subvariant Coronaviruses do not produce ORF8 protein due to 8th codon GGA=TGA Termination Codon Mutation

‘Vivaldi’: An amplicon-based whole genome sequencing method for the four seasonal human coronaviruses 229E, NL63, OC43 & HKU1, alongside SARS-CoV-2’

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