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

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

doi:10.21203/rs.3.rs-2400971/v1

Cited by 2 publications

(2 citation statements)

References 25 publications

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“…Previous observation is valid that Delta variant has unique deletions and substitutions in many gene coding region. We observed almost all data of Delta variant dataset in this study has deletion at Del22005-22010 and Del27055-27067, as well as substitution compared to Wuhan-Hu-1 strain at T19R, E157G, F158Del, F159Del, and T482K in spike gene, D63G, R203M and D377Y in NP, G5063S and P5401L in ORF1AB, V82A and T120I in ORF7A, as well as D119Del and F120Del in ORF8 as earlier described as unique Delta variant markers (Suardana et al 2023;Suharsono et al 2023). The evolutionary history was inferred by using the Maximum Likelihood method and Kimura 2-parameter model (Kimura 1980).…”

Section: Discussionmentioning

confidence: 50%

Surveillance for Genetic Markers of Adaptation of SARS-CoV-2 in Dogs and Cats

2024

Int J Vet Sci

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Surveillance for genetic markers of adaptation of SARS-CoV-2 in dogs and cats could help to predict the risk of variant emergence, that resulted from virus adaptation to the new host. The Delta variant of SARS-CoV-2 collected from dog and cat is of high interest, since this variant caused global major cases and fatality during the pandemic. All complete and high coverage sequence data of Delta variant of dog and cat origin, as well as samples of human origin SARS-CoV-1 were downloaded. All selected sequence data were subjected to Clustal Omega alignment. The evolutionary history was inferred by using the Maximum Likelihood method using Mega11. Species-specific marker indicating a probable species adaptation of the pandemic SARS-CoV-2 in dog and cat could not be identified. The markers found in many dog and cat samples is confirmed to be location specific markers that occurred in human origin virus.

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Section: Discussionmentioning

confidence: 50%

Surveillance for Genetic Markers of Adaptation of SARS-CoV-2 in Dogs and Cats

2024

Int J Vet Sci

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“…Perhaps most strikingly we observed a 9bp nucleotide deletion immediately prior to the start of the C-terminal domain of the nucleocapsid in the disordered linker region responsible for RNA binding and oligomerisation (65, 66) in the last timepoint of our chronically infected NL63 patient. This had parallels in SARS-CoV-2, with a 3 AA nucleocapsid deletion relative to the ancestral Wuhan strain a feature of the Omicron lineage, albeit in the N terminal domain (67). The recent spillover of a novel canine coronavirus in Malaysia also reported a larger 12 AA deletion in the middle of the N protein, hypothesised to be associated with adaptation to a new host (68), similar to previously reported nucleocapsid deletions (and insertions) found to determine nuclear localization in MERS and SARS-CoV-1 infections (69).…”

Section: Discussionmentioning

confidence: 98%

‘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.

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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 25 publications

Surveillance for Genetic Markers of Adaptation of SARS-CoV-2 in Dogs and Cats

Surveillance for Genetic Markers of Adaptation of SARS-CoV-2 in Dogs and Cats

‘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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