Coronaviruses have reached at Pre-elimination Stage with Nine Amino Acid Spike Deletions and Forty-nine Nucleotide 3’-UTR Deletions
Published on: 17th September, 2024
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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