Rapid worldwide spread of 17MPLF spike insertion mutants (JN.1-JN.1.25, KP.1, KP.2, KQ.1, KR.1, XDD, XDP, XDK, XDQ subvariants) of omicron coronaviruses and spike gene 5’-end sequencing problem

Chakraborty, Asit Kumar

doi:10.21203/rs.3.rs-4741070/v1

Cited by 2 publications

References 26 publications

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Coronaviruses have Reached at Pre-Elimination Stage with nine amino acids spike deletions and forty-nine nucleotides 3’-UTR deletion

Chakraborty

2024

Preprint

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Human 30kb coronaviruses entered through the ACE-2 receptors causing fibrosis of lungs and claimed six million deaths worldwide. Here, we investigated the mutations, deletions and insertions of the recent JN.1 omicron coronaviruses. The 49nt deletions in the 3’-UTR was found in 4997 JN.1 sequences although 26nt deletion was initiated previously in JN.1 as well as BA.5, BF.7, BQ.1 and XBB.1.5 omicron viruses. The 31S spike deletion was initiated lately apart from 24LPP, 69HV, 145Y, 211N and 483V deletions. The important 17MPLF spike insertion was found although few scientists claimed there was no such insertion. we first to compare 3-D structures of spike proteins with or without 17MPLF four amino acids insertion and nine amino acids deletions using SWISS MODELLING. The JN.1 viruses caused a more stable trimeric spike involving Thr342, Lys436, Lys440, His441, Ser442, Gly443, Tyr445, Lys479, Ser489, Tyr490, Arg493, Pro494, Thr495, and Gln501 amino acids to interact with ACE-2 receptors. The cytokine storm was reduced in patients with increased immune evasion due to L455S, F456L and R346T spike mutations in KP.2 variants. The JN.1 8th codon GGA = TGA termination codon mutation was initiated which was demonstrated previously in XBB.1.5 lineages. We also detected few small deletions in the ORF8 gene near termination codon with the formation of few amino acids extended ORF8 protein. We claimed that pre-death changes were initiated in JN.1 COVID-19 lineages and computer-simulation showed that Howard-spike with 17MPLF spike insertion appeared more stable than Oppentron-spike without 17MPLF insertion.

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Coronaviruses have Reached at Pre-Elimination Stage with nine amino acids spike deletions and forty-nine nucleotides 3’-UTR deletion

Chakraborty

2024

Preprint

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Coronaviruses have reached at Pre-elimination Stage with Nine Amino Acid Spike Deletions and Forty-nine Nucleotide 3’-UTR Deletions

Asit Kumar

2024

Int J Clin Virol

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Background: Human 30kb coronaviruses entered through the ACE-2 receptors causing fibrosis of the lungs and causing six million deaths worldwide. Here, we have investigated the mutations, deletions and insertions of the recent JN.1 omicron coronaviruses to demonstrate that coronaviruses have reached the pre-elimination stage. Methods: We multi-aligned the genomes of recent JN.1 variants using NCBI Virus Portal and CLUSTAL-Omega. The spike proteins are multi-aligned using MultAlin software and CLUSTAL-Omega. Results: The 17MPLF spike insertion was confirmed to compensate 24LPP, 31S, 69HV, 145Y, 211N and 483V deletions. The 49nt deletions in the 3’-UTR were found in 4997 JN.1 sequences although 26nt deletion was initiated previously in JN.1 as well as BA.5, BF.7, BQ.1 and XBB.1.5 omicron viruses. We first compare 3-D structures of spike proteins with or without 17MPLF four amino acids insertion and nine amino acids deletions using SWISS MODELLING. The JN.1 viruses caused a more stable trimeric spike involving Thr342, Lys436, Lys440, His441, Ser442, Gly443, Tyr445, Lys479, Ser489, Tyr490, Arg493, Pro494, Thr495, and Gln501 amino acids to interact with ACE-2 receptors. The FLiRT spike mutations were found in most KP.2 variants and other changes occurred at the NH2 terminus. Conclusion: We claimed that pre-death changes were initiated in JN.1 COVID-19 lineages and computer simulation showed that the Howard spike with 17MPLF spike insertion appeared more stable than the Oppentrons-spike without 17MPLF insertion. Surely, conflicts of COVID-19 spike sequences must be resolved.

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Rapid worldwide spread of 17MPLF spike insertion mutants (JN.1-JN.1.25, KP.1, KP.2, KQ.1, KR.1, XDD, XDP, XDK, XDQ subvariants) of omicron coronaviruses and spike gene 5’-end sequencing problem

Cited by 2 publications

References 26 publications

Coronaviruses have Reached at Pre-Elimination Stage with nine amino acids spike deletions and forty-nine nucleotides 3’-UTR deletion

Coronaviruses have Reached at Pre-Elimination Stage with nine amino acids spike deletions and forty-nine nucleotides 3’-UTR deletion

Coronaviruses have reached at Pre-elimination Stage with Nine Amino Acid Spike Deletions and Forty-nine Nucleotide 3’-UTR Deletions

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