A phased bivalent Moderna mRNA-1273 vaccine reference sequence
Using plasmid contaminated patients to refine the Moderna vaccine sequence.
Abstract
The Moderna monovalent SARs-CoV-2 mRNA vaccine sequence is available from a UK filing. It is also independently sequenced by Jeong et al but is only available on GitHub. This Jeong et al sequence does not appear to be in NCBI which can lead to BLAST not finding it when searching for similar sequences. The Jeong et al sequence also did not disclose any raw sequencing reads eliminating the assessment of the plasmid backbone sequence. This is unusual as most sequencing papers demand raw reads be supplied. Its like providing the answer to a math problem with out showing your proof of work. Had these sequences been disclosed as is customary, the world would have known about the vaccine contamination nearly 2 years before McKernan et al published it.
McKernan et al however, sequenced the Moderna Bivalent vaccines but the assembly compressed 2 RNA sequences into 1 consensus sequence, leading to ambiguities where the 2 RNA sequences differ. This sequencing utilized RNA-seq which produces 100-1000X more coverage over the Spike region than the plasmid sequence. Many DNA assemblers rely on sequence read coverage to split contigs and organize their consensus. Polymorphisms combined with erradict coverage differences can cause some assemblers to create artifacts if the depth of coverage alters radically while the sequences diverge. Here we attempt to phase the bivalent Moderna vaccine sequences into two independent RNA sequences and note the 3’ UTRs are different.
Data sets
1)Medicinal Genomics RNAseq of Bivalent Moderna vaccines (Direct RNA-Seq of vials)
2)Krawcyzk Re-Adenylation data (RNA-seq of vaccinated mice)
3)UK Moderna Disclosure (Just Spike with UTR1)
4)Jeong-Fire (Just Spike with UTR1
5)Castruita et al (Just Spike)
The bivalent vaccines contain the original Alpha variant plasmid and a Omicron encoding plasmid.
Moderna_Alpha_UTR1 Variant
The below IGV window (Figure 3) displays the Bivalent Illumina reads from MGC RNAseq mapped back to the Moderna Alpha variant reference sequence described by Jeong-Fire and in the UK filing disclosure (Fire has no plasmid backbone sequence, Just Spike). You can see heterozygous SNPs that exist in the locations where Omicron is different from Alpha.
The below IGV track (Figure 4) has the bases changed to Omicron sequence and the RNAseq reads remapped to this Omicron adjusted reference and you can see the opposite pattern (C→G, G→C) as expected.
What stood out in this Phasing of the two plasmid sequences was that the 3’UTR in the Omicron plasmid was different.
>Moderna_WuhanSpike-UTR2 (No poly A)
CTAACATCCCTTCAGAGTCCCGGGTAGCATAACCCCTTGGGGCCTCTAAACGGGTCTTGA
GGGGTTTTTTGCGAGCTCGGTACCCAGCCCCGACGAGCTTCATGCCGTTAGTCGCACTGC
AAGGGGTGTTATGAGCCATATTCAGGTATAAATGGGCTCGCGATAATGTTCAGAATTGGT
TAATTGGTTGTAACACTGACCCCTATTTGTTTATTTTTCTAAATACATTCAAATATGTAT
CCGCTCATGAGACAATAACCCTGATAAATGCTTCAATAATATTGAAAAAGGAAGAATATG
AGCCATATTCAACGGGAAACGTCGAGGCCGCGATTAAATTCCAACATGGACGCTGATTTA
TATGGGTATAAATGGGCTCGCGATAATGTCGGGCAATCAGGTGCGACAATCTATCGCTTG
TATGGGAAGCCCGATGCGCCAGAGTTGTTTCTGAAACATGGCAAAGGTAGCGTTGCCAAT
GATGTTACAGATGAGATGGTCAGACTAAACTGGCTGACGGAATTTATGCCACTTCCGACC
ATCAAGCATTTTATCCGTACTCCTTATGATGCATGGTTACTCACCACTGCGATCCCCGGA
AAAACAGCGTTCCAGGTATTAGAAGAATATCCTGATTCAGGTGAAAATATTGTTGATGCG
CTGGCAGTGTTCCTGCGCCGGTTGCACTCGATTCCTGTTTGTAATTGTCCTTTTAACAGC
GATCGCGTCTTCCGTCTTGCACAAGCGCAATCACGAATGAATAACGGTTTGGTTGATGCG
AGTGATTTTGATGACGAGCGTAATGGCTGGCCTGTTGAACAAGTCTGGAAAGAAATGCAT
AAACTTTTGCCATTCTCACCGGATTCAGTCGTCACTCATGGTGATTTCTCACTTGATAAC
CTTATTTTTGACGAGGGGAAATTAATAGGTTGTATTGATGTTGGACGAGTCGGAATCGCA
GACCGATACCAGGATCTTGCCATTCTATGGAACTGCCTCGGTGAGTTTTCTCCTTCATTA
CAGAAACGGCTTTTTCAAAAATATGGTATTGATAATCCTGATATGAATAAATTGCAGTTT
CATTTGATGCTCGATGAGTTTTTCTAAGCAGAGCATTACGCTGACTTGACGGGACGGCGC
AAGCTCATGACCAAAATCCCTTAACGTGAGTTACGCGCGCGTCGTTCCACTGAGCGTCAG
ACCCCGTAGAAAAGATCAAAGGATCTTCTTGAGATCCTTTTTTTCTGCGCGTAATCTGCT
GCTTGCAAACAAAAAAACCACCGCTACCAGCGGTGGTTTGTTTGCCGGATCAAGAGCTAC
CAACTCTTTTTCCGAAGGTAACTGGCTTCAGCAGAGCGCAGATACCAAATACTGTTCTTC
TAGTGTAGCCGTAGTTAGCCCACCACTTCAAGAACTCTGTAGCACCGCCTACATACCTCG
CTCTGCTAATCCTGTTACCAGTGGCTGCTGCCAGTGGCGATAAGTCGTGTCTTACCGGGT
TGGACTCAAGACGATAGTTACCGGATAAGGCGCAGCGGTCGGGCTGAACGGGGGGTTCGT
GCACACAGCCCAGCTTGGAGCGAACGACCTACACCGAACTGAGATACCTACAGCGTGAGC
TATGAGAAAGCGCCACGCTTCCCGAAGGGAGAAAGGCGGACAGGTATCCGGTAAGCGGCA
GGGTCGGAACAGGAGAGCGCACGAGGGAGCTTCCAGGGGGAAACGCCTGGTATCTTTATA
GTCCTGTCGGGTTTCGCCACCTCTGACTTGAGCGTCGATTTTTGTGATGCTCGTCAGGGG
GGCGGAGCCTATGGAAAAACGCCAGCAACGCGGCCTTTTTACGGTTCCTGGCCTTTTGCT
GGCCTTTTGCTCACATGTTCTTTCCTGCGTTATCCCCTGATTCTGTGGATAACCGTATTA
CCGCCTGCTCGCCGCAGCCGAACGACCGAGCGCAGCGAGTCAGTGAGCGAGGAAGCGGAA
GGCGAGAGTAGGGAACTGCCAGGCATCAAACTAAGCAGAAGGCCCCTGACGCATGGCCTT
TTTGCGTTTCTACAAACTCTTTCTGTGTTGTAAAACGACGGCCAGTCTTAAGCTCGGGCC
CCTTTTCCGCCAGGGTTTTCCCAGTCACGACGAATTCGATCCGGCTCAAGCTTTTGGACC
CTCGTACAGAAGCTAATACGACTCACTATAGGGAAATAAGAGAGAAAAGAAGAGTAAGAA
GAAATATAAGACCCCGGCGCCGCCACCATGTTCGTGTTCCTGGTGCTGCTGCCCCTGGTG
AGCAGCCAGTGCGTGAACCTGACCACCCGGACCCAGCTGCCACCAGCCTACACCAACAGC
TTCACCCGGGGCGTCTACTACCCCGACAAGGTGTTCCGGAGCAGCGTCCTGCACAGCACC
CAGGACCTGTTCCTGCCCTTCTTCAGCAACGTGACCTGGTTCCACGCCATCCACGTGAGC
GGCACCAACGGCACCAAGCGGTTCGACAACCCCGTGCTGCCCTTCAACGACGGCGTGTAC
TTCGCCAGCACCGAGAAGAGCAACATCATCCGGGGCTGGATCTTCGGCACCACCCTGGAC
AGCAAGACCCAGAGCCTGCTGATCGTGAATAACGCCACCAACGTGGTGATCAAGGTGTGC
GAGTTCCAGTTCTGCAACGACCCCTTCCTGGGCGTGTACTACCACAAGAACAACAAGAGC
TGGATGGAGAGCGAGTTCCGGGTGTACAGCAGCGCCAACAACTGCACCTTCGAGTACGTG
AGCCAGCCCTTCCTGATGGACCTGGAGGGCAAGCAGGGCAACTTCAAGAACCTGCGGGAG
TTCGTGTTCAAGAACATCGACGGCTACTTCAAGATCTACAGCAAGCACACCCCAATCAAC
CTGGTGCGGGATCTGCCCCAGGGCTTCTCAGCCCTGGAGCCCCTGGTGGACCTGCCCATC
GGCATCAACATCACCCGGTTCCAGACCCTGCTGGCCCTGCACCGGAGCTACCTGACCCCA
GGCGACAGCAGCAGCGGGTGGACAGCAGGCGCGGCTGCTTACTACGTGGGCTACCTGCAG
CCCCGGACCTTCCTGCTGAAGTACAACGAGAACGGCACCATCACCGACGCCGTGGACTGC
GCCCTGGACCCTCTGAGCGAGACCAAGTGCACCCTGAAGAGCTTCACCGTGGAGAAGGGC
ATCTACCAGACCAGCAACTTCCGGGTGCAGCCCACCGAGAGCATCGTGCGGTTCCCCAAC
ATCACCAACCTGTGCCCCTTCGGCGAGGTGTTCAACGCCACCCGGTTCGCCAGCGTGTAC
GCCTGGAACCGGAAGCGGATCAGCAACTGCGTGGCCGACTACAGCGTGCTGTACAACAGC
GCCAGCTTCAGCACCTTCAAGTGCTACGGCGTGAGCCCCACCAAGCTGAACGACCTGTGC
TTCACCAACGTGTACGCCGACAGCTTCGTGATCCGTGGCGACGAGGTGCGGCAGATCGCA
CCCGGCCAGACAGGCAAGATCGCCGACTACAACTACAAGCTGCCCGACGACTTCACCGGC
TGCGTGATCGCCTGGAACAGCAACAACCTCGACAGCAAGGTGGGCGGCAACTACAACTAC
CTGTACCGGCTGTTCCGGAAGAGCAACCTGAAGCCCTTCGAGCGGGACATCAGCACCGAG
ATCTACCAAGCCGGCTCCACCCCTTGCAACGGCGTGGAGGGCTTCAACTGCTACTTCCCT
CTGCAGAGCTACGGCTTCCAGCCCACCAACGGCGTGGGCTACCAGCCCTACCGGGTGGTG
GTGCTGAGCTTCGAGCTGCTGCACGCCCCAGCCACCGTGTGTGGCCCCAAGAAGAGCACC
AACCTGGTGAAGAACAAGTGCGTGAACTTCAACTTCAACGGCCTTACCGGCACCGGCGTG
CTGACCGAGAGCAACAAGAAATTCCTGCCCTTTCAGCAGTTCGGCCGGGACATCGCCGAC
ACCACCGACGCTGTGCGGGATCCCCAGACCCTGGAGATCCTGGACATCACCCCTTGCAGC
TTCGGCGGCGTGAGCGTGATCACCCCAGGCACCAACACCAGCAACCAGGTGGCCGTGCTG
TACCAGGACGTGAACTGCACCGAGGTGCCCGTGGCCATCCACGCCGACCAGCTGACACCC
ACCTGGCGGGTCTACAGCACCGGCAGCAACGTGTTCCAGACCCGGGCCGGTTGCCTGATC
GGCGCCGAGCACGTGAACAACAGCTACGAGTGCGACATCCCCATCGGCGCCGGCATCTGT
GCCAGCTACCAGACCCAGACCAATTCACCCCGGAGGGCAAGGAGCGTGGCCAGCCAGAGC
ATCATCGCCTACACCATGAGCCTGGGCGCCGAGAACAGCGTGGCCTACAGCAACAACAGC
ATCGCCATCCCCACCAACTTCACCATCAGCGTGACCACCGAGATTCTGCCCGTGAGCATG
ACCAAGACCAGCGTGGACTGCACCATGTACATCTGCGGCGACAGCACCGAGTGCAGCAAC
CTGCTGCTGCAGTACGGCAGCTTCTGCACCCAGCTGAACCGGGCCCTGACCGGCATCGCC
GTGGAGCAGGACAAGAACACCCAGGAGGTGTTCGCCCAGGTGAAGCAGATCTACAAGACC
CCTCCCATCAAGGACTTCGGCGGCTTCAACTTCAGCCAGATCCTGCCCGACCCCAGCAAG
CCCAGCAAGCGGAGCTTCATCGAGGACCTGCTGTTCAACAAGGTGACCCTAGCCGACGCC
GGCTTCATCAAGCAGTACGGCGACTGCCTCGGCGACATAGCCGCCCGGGACCTGATCTGC
GCCCAGAAGTTCAACGGCCTGACCGTGCTGCCTCCCCTGCTGACCGACGAGATGATCGCC
CAGTACACCAGCGCCCTGTTAGCCGGAACCATCACCAGCGGCTGGACTTTCGGCGCTGGA
GCCGCTCTGCAGATCCCCTTCGCCATGCAGATGGCCTACCGGTTCAACGGCATCGGCGTG
ACCCAGAACGTGCTGTACGAGAACCAGAAGCTGATCGCCAACCAGTTCAACAGCGCCATC
GGCAAGATCCAGGACAGCCTGAGCAGCACCGCTAGCGCCCTGGGCAAGCTGCAGGACGTG
GTGAACCAGAACGCCCAGGCCCTGAACACCCTGGTGAAGCAGCTGAGCAGCAACTTCGGC
GCCATCAGCAGCGTGCTGAACGACATCCTGAGCCGGCTGGACCCTCCCGAGGCCGAGGTG
CAGATCGACCGGCTGATCACTGGCCGGCTGCAGAGCCTGCAGACCTACGTGACCCAGCAG
CTGATCCGGGCCGCCGAGATTCGGGCCAGCGCCAACCTGGCCGCCACCAAGATGAGCGAG
TGCGTGCTGGGCCAGAGCAAGCGGGTGGACTTCTGCGGCAAGGGCTACCACCTGATGAGC
TTTCCCCAGAGCGCACCCCACGGAGTGGTGTTCCTGCACGTGACCTACGTGCCCGCCCAG
GAGAAGAACTTCACCACCGCCCCAGCCATCTGCCACGACGGCAAGGCCCACTTTCCCCGG
GAGGGCGTGTTCGTGAGCAACGGCACCCACTGGTTCGTGACCCAGCGGAACTTCTACGAG
CCCCAGATCATCACCACCGACAACACCTTCGTGAGCGGCAACTGCGACGTGGTGATCGGC
ATCGTGAACAACACCGTGTACGATCCCCTGCAGCCCGAGCTGGACAGCTTCAAGGAGGAG
CTGGACAAGTACTTCAAGAATCACACCAGCCCCGACGTGGACCTGGGCGACATCAGCGGC
ATCAACGCCAGCGTGGTGAACATCCAGAAGGAGATCGATCGGCTGAACGAGGTGGCCAAG
AACCTGAACGAGAGCCTGATCGACCTGCAGGAGCTGGGCAAGTACGAGCAGTACATCAAG
TGGCCCTGGTACATCTGGCTGGGCTTCATCGCCGGCCTGATCGCCATCGTGATGGTGACC
ATCATGCTGTGCTGCATGACCAGCTGCTGCAGCTGCCTGAAGGGCTGTTGCAGCTGCGGC
AGCTGCTGCAAGTTCGACGAGGACGACAGCGAGCCCGTGCTGAAGGGCGTGAAGCTGCAC
TACACCTGATAATAGGCTGGAGCCTCGGTGGCCTAGCTTCTTGCCCCTTGGGCCTCCCCC
CAGCCCCTCCTCCCCTTCCTGCAGGAGAGATAGTGGAGTGGTCTTTGAATAAAGTCTGAG
TGGGCGGC
UTR2-Omicron: Moderna_Alpha_UTR1 (Above) BLAST’d against Omicron (below). 6149/6188 bases are identical (99%).
>Omicron_Spike_Hybrid4.1-UTR2 (6188 bp) No PolyA tail
CTAACATCCCTTCAGAGTCCCGGGTAGCATAACCCCTTGGGGCCTCTAAACGGGTCTTGA
GGGGTTTTTTGCGAGCTCGGTACCCAGCCCCGACGAGCTTCATGCCGTTAGTCGCACTGC
AAGGGGTGTTATGAGCCATATTCAGGTATAAATGGGCTCGCGATAATGTTCAGAATTGGT
TAATTGGTTGTAACACTGACCCCTATTTGTTTATTTTTCTAAATACATTCAAATATGTAT
CCGCTCATGAGACAATAACCCTGATAAATGCTTCAATAATATTGAAAAAGGAAGAATATG
AGCCATATTCAACGGGAAACGTCGAGGCCGCGATTAAATTCCAACATGGACGCTGATTTA
TATGGGTATAAATGGGCTCGCGATAATGTCGGGCAATCAGGTGCGACAATCTATCGCTTG
TATGGGAAGCCCGATGCGCCAGAGTTGTTTCTGAAACATGGCAAAGGTAGCGTTGCCAAT
GATGTTACAGATGAGATGGTCAGACTAAACTGGCTGACGGAATTTATGCCACTTCCGACC
ATCAAGCATTTTATCCGTACTCCTTATGATGCATGGTTACTCACCACTGCGATCCCCGGA
AAAACAGCGTTCCAGGTATTAGAAGAATATCCTGATTCAGGTGAAAATATTGTTGATGCG
CTGGCAGTGTTCCTGCGCCGGTTGCACTCGATTCCTGTTTGTAATTGTCCTTTTAACAGC
GATCGCGTCTTCCGTCTTGCACAAGCGCAATCACGAATGAATAACGGTTTGGTTGATGCG
AGTGATTTTGATGACGAGCGTAATGGCTGGCCTGTTGAACAAGTCTGGAAAGAAATGCAT
AAACTTTTGCCATTCTCACCGGATTCAGTCGTCACTCATGGTGATTTCTCACTTGATAAC
CTTATTTTTGACGAGGGGAAATTAATAGGTTGTATTGATGTTGGACGAGTCGGAATCGCA
GACCGATACCAGGATCTTGCCATTCTATGGAACTGCCTCGGTGAGTTTTCTCCTTCATTA
CAGAAACGGCTTTTTCAAAAATATGGTATTGATAATCCTGATATGAATAAATTGCAGTTT
CATTTGATGCTCGATGAGTTTTTCTAAGCAGAGCATTACGCTGACTTGACGGGACGGCGC
AAGCTCATGACCAAAATCCCTTAACGTGAGTTACGCGCGCGTCGTTCCACTGAGCGTCAG
ACCCCGTAGAAAAGATCAAAGGATCTTCTTGAGATCCTTTTTTTCTGCGCGTAATCTGCT
GCTTGCAAACAAAAAAACCACCGCTACCAGCGGTGGTTTGTTTGCCGGATCAAGAGCTAC
CAACTCTTTTTCCGAAGGTAACTGGCTTCAGCAGAGCGCAGATACCAAATACTGTTCTTC
TAGTGTAGCCGTAGTTAGCCCACCACTTCAAGAACTCTGTAGCACCGCCTACATACCTCG
CTCTGCTAATCCTGTTACCAGTGGCTGCTGCCAGTGGCGATAAGTCGTGTCTTACCGGGT
TGGACTCAAGACGATAGTTACCGGATAAGGCGCAGCGGTCGGGCTGAACGGGGGGTTCGT
GCACACAGCCCAGCTTGGAGCGAACGACCTACACCGAACTGAGATACCTACAGCGTGAGC
TATGAGAAAGCGCCACGCTTCCCGAAGGGAGAAAGGCGGACAGGTATCCGGTAAGCGGCA
GGGTCGGAACAGGAGAGCGCACGAGGGAGCTTCCAGGGGGAAACGCCTGGTATCTTTATA
GTCCTGTCGGGTTTCGCCACCTCTGACTTGAGCGTCGATTTTTGTGATGCTCGTCAGGGG
GGCGGAGCCTATGGAAAAACGCCAGCAACGCGGCCTTTTTACGGTTCCTGGCCTTTTGCT
GGCCTTTTGCTCACATGTTCTTTCCTGCGTTATCCCCTGATTCTGTGGATAACCGTATTA
CCGCCTGCTCGCCGCAGCCGAACGACCGAGCGCAGCGAGTCAGTGAGCGAGGAAGCGGAA
GGCGAGAGTAGGGAACTGCCAGGCATCAAACTAAGCAGAAGGCCCCTGACGCATGGCCTT
TTTGCGTTTCTACAAACTCTTTCTGTGTTGTAAAACGACGGCCAGTCTTAAGCTCGGGCC
CCTTTTCCGCCAGGGTTTTCCCAGTCACGACGAATTCGATCCGGCTCAAGCTTTTGGACC
CTCGTACAGAAGCTAATACGACTCACTATAGGGAAATAAGAGAGAAAAGAAGAGTAAGAA
GAAATATAAGACCCCGGCGCCGCCACCATGTTCGTGTTCCTGGTGCTGCTGCCCCTGGTG
AGCAGCCAGTGCGTGAACCTGATCACCCGGACCCAGCTGCCACCAGCCTACACCAACAGC
TTCACCCGGGGCGTCTACTACCCCGACAAGGTGTTCCGGAGCAGCGTCCTGCACAGCACC
CAGGACCTGTTCCTGCCCTTCTTCAGCAACGTGACCTGGTTCCACGCCATCCACGTGAGC
GGCACCAACGGCACCAAGCGGTTCGACAACCCCGTGCTGCCCTTCAACGACGGCGTGTAC
TTCGCCAGCACCGAGAAGAGCAACATCATCCGGGGCTGGATCTTCGGCACCACCCTGGAC
AGCAAGACCCAGAGCCTGCTGATCGTGAATAACGCCACCAACGTGGTGATCAAGGTGTGC
GAGTTCCAGTTCTGCAACGACCCCTTCCTGGACGTGTACTACCACAAGAACAACAAGAGC
TGGATGGAGAGCGAGTTCCGGGTGTACAGCAGCGCCAACAACTGCACCTTCGAGTACGTG
AGCCAGCCCTTCCTGATGGACCTGGAGGGCAAGCAGGGCAACTTCAAGAACCTGCGGGAG
TTCGTGTTCAAGAACATCGACGGCTACTTCAAGATCTACAGCAAGCACACCCCAATCAAC
CTGGGCCGGGATCTGCCCCAGGGCTTCTCAGCCCTGGAGCCCCTGGTGGACCTGCCCATC
GGCATCAACATCACCCGGTTCCAGACCCTGCTGGCCCTGCACCGGAGCTACCTGACCCCA
GGCGACAGCAGCAGCGGGTGGACAGCAGGCGCGGCTGCTTACTACGTGGGCTACCTGCAG
CCCCGGACCTTCCTGCTGAAGTACAACGAGAACGGCACCATCACCGACGCCGTGGACTGC
GCCCTGGACCCTCTGAGCGAGACCAAGTGCACCCTGAAGAGCTTCACCGTGGAGAAGGGC
ATCTACCAGACCAGCAACTTCCGGGTGCAGCCCACCGAGAGCATCGTGCGGTTCCCCAAC
ATCACCAACCTGTGCCCCTTCGACGAGGTGTTCAACGCCACCCGGTTCGCCAGCGTGTAC
GCCTGGAACCGGAAGCGGATCAGCAACTGCGTGGCCGACTACAGCGTGCTGTACAACTTC
GCCCCATTCTTCGCCTTCAAGTGCTACGGCGTGAGCCCCACCAAGCTGAACGACCTGTGC
TTCACCAACGTGTACGCCGACAGCTTCGTGATCCGTGGCAACGAGGTGAGCCAGATCGCA
CCCGGCCAGACAGGCAACATCGCCGACTACAACTACAAGCTGCCCGACGACTTCACCGGC
TGCGTGATCGCCTGGAACAGCAACAAGCTCGACAGCAAGGTGGGCGGCAACTACAACTAC
CGGTACCGGCTGTTCCGGAAGAGCAACCTGAAGCCCTTCGAGCGGGACATCAGCACCGAG
ATCTACCAAGCCGGCAACAAGCCTTGCAACGGCGTGGCCGGCGTGAACTGCTACTTCCCT
CTGCAGAGCTACGGCTTCCGGCCCACCTACGGCGTGGGCCACCAGCCCTACCGGGTGGTG
GTGCTGAGCTTCGAGCTGCTGCACGCCCCAGCCACCGTGTGTGGCCCCAAGAAGAGCACC
AACCTGGTGAAGAACAAGTGCGTGAACTTCAACTTCAACGGCCTTACCGGCACCGGCGTG
CTGACCGAGAGCAACAAGAAATTCCTGCCCTTTCAGCAGTTCGGCCGGGACATCGCCGAC
ACCACCGACGCTGTGCGGGATCCCCAGACCCTGGAGATCCTGGACATCACCCCTTGCAGC
TTCGGCGGCGTGAGCGTGATCACCCCAGGCACCAACACCAGCAACCAGGTGGCCGTGCTG
TACCAGGGTGTGAACTGCACCGAGGTGCCCGTGGCCATCCACGCCGACCAGCTGACACCC
ACCTGGCGGGTCTACAGCACCGGCAGCAACGTGTTCCAGACCCGGGCCGGTTGCCTGATC
GGCGCCGAGTACGTGAACAACAGCTACGAGTGCGACATCCCCATCGGCGCCGGCATCTGT
GCCAGCTACCAGACCCAGACCAAGTCACACCGGAGGGCAAGGAGCGTGGCCAGCCAGAGC
ATCATCGCCTACACCATGAGCCTGGGCGCCGAGAACAGCGTGGCCTACAGCAACAACAGC
ATCGCCATCCCCACCAACTTCACCATCAGCGTGACCACCGAGATTCTGCCCGTGAGCATG
ACCAAGACCAGCGTGGACTGCACCATGTACATCTGCGGCGACAGCACCGAGTGCAGCAAC
CTGCTGCTGCAGTACGGCAGCTTCTGCACCCAGCTGAAGCGGGCCCTGACCGGCATCGCC
GTGGAGCAGGACAAGAACACCCAGGAGGTGTTCGCCCAGGTGAAGCAGATCTACAAGACC
CCTCCCATCAAGTACTTCGGCGGCTTCAACTTCAGCCAGATCCTGCCCGACCCCAGCAAG
CCCAGCAAGCGGAGCTTCATCGAGGACCTGCTGTTCAACAAGGTGACCCTAGCCGACGCC
GGCTTCATCAAGCAGTACGGCGACTGCCTCGGCGACATAGCCGCCCGGGACCTGATCTGC
GCCCAGAAGTTCAACGGCCTGACCGTGCTGCCTCCCCTGCTGACCGACGAGATGATCGCC
CAGTACACCAGCGCCCTGTTAGCCGGAACCATCACCAGCGGCTGGACTTTCGGCGCTGGA
GCCGCTCTGCAGATCCCCTTCGCCATGCAGATGGCCTACCGGTTCAACGGCATCGGCGTG
ACCCAGAACGTGCTGTACGAGAACCAGAAGCTGATCGCCAACCAGTTCAACAGCGCCATC
GGCAAGATCCAGGACAGCCTGAGCAGCACCGCTAGCGCCCTGGGCAAGCTGCAGGACGTG
GTGAACCACAACGCCCAGGCCCTGAACACCCTGGTGAAGCAGCTGAGCAGCAAgTTCGGC
GCCATCAGCAGCGTGCTGAACGACATCCTGAGCCGGCTGGACCCTCCCGAGGCCGAGGTG
CAGATCGACCGGCTGATCACTGGCCGGCTGCAGAGCCTGCAGACCTACGTGACCCAGCAG
CTGATCCGGGCCGCCGAGATTCGGGCCAGCGCCAACCTGGCCGCCACCAAGATGAGCGAG
TGCGTGCTGGGCCAGAGCAAGCGGGTGGACTTCTGCGGCAAGGGCTACCACCTGATGAGC
TTTCCCCAGAGCGCACCCCACGGAGTGGTGTTCCTGCACGTGACCTACGTGCCCGCCCAG
GAGAAGAACTTCACCACCGCCCCAGCCATCTGCCACGACGGCAAGGCCCACTTTCCCCGG
GAGGGCGTGTTCGTGAGCAACGGCACCCACTGGTTCGTGACCCAGCGGAACTTCTACGAG
CCCCAGATCATCACCACCGACAACACCTTCGTGAGCGGCAACTGCGACGTGGTGATCGGC
ATCGTGAACAACACCGTGTACGATCCCCTGCAGCCCGAGCTGGACAGCTTCAAGGAGGAG
CTGGACAAGTACTTCAAGAATCACACCAGCCCCGACGTGGACCTGGGCGACATCAGCGGC
ATCAACGCCAGCGTGGTGAACATCCAGAAGGAGATCGATCGGCTGAACGAGGTGGCCAAG
AACCTGAACGAGAGCCTGATCGACCTGCAGGAGCTGGGCAAGTACGAGCAGTACATCAAG
TGGCCCTGGTACATCTGGCTGGGCTTCATCGCCGGCCTGATCGCCATCGTGATGGTGACC
ATCATGCTGTGCTGCATGACCAGCTGCTGCAGCTGCCTGAAGGGCTGTTGCAGCTGCGGC
AGCTGCTGCAAGTTCGACGAGGACGACAGCGAGCCCGTGCTGAAGGGCGTGAAGCTGCAC
TACACCTGATAATAGGCTGGAGCCTCGGTGGCCTAGCTTCTTGCCCCTTGGGCCTCCCCC
CAGCCCCTCCTCCCCTTCCTGCAGGAGAGATAGTGGAGTGGTCTTTGAATAAAGTCTGAG
TGGGCGGC
Moderna_Omicron_UTR2 BLAST’d against Jeong-Fire Moderna_Alpha-UTR1 without the Poly A tail and XbaI site.
There is a 14 base deletion that differs between the two 3 UTRs. These are not translated bases but may play a role in RNA expression or persistence.
>Moderna-Alpha_Spike_Jeong-Fire_UTR1 (no PolyA tail)
CTAACATCCCTTCAGAGTCCCGGGTAGCATAACCCCTTGGGGCCTCTAAACGGGTCTTGA
GGGGTTTTTTGCGAGCTCGGTACCCAGCCCCGACGAGCTTCATGCCGTTAGTCGCACTGC
AAGGGGTGTTATGAGCCATATTCAGGTATAAATGGGCTCGCGATAATGTTCAGAATTGGT
TAATTGGTTGTAACACTGACCCCTATTTGTTTATTTTTCTAAATACATTCAAATATGTAT
CCGCTCATGAGACAATAACCCTGATAAATGCTTCAATAATATTGAAAAAGGAAGAATATG
AGCCATATTCAACGGGAAACGTCGAGGCCGCGATTAAATTCCAACATGGACGCTGATTTA
TATGGGTATAAATGGGCTCGCGATAATGTCGGGCAATCAGGTGCGACAATCTATCGCTTG
TATGGGAAGCCCGATGCGCCAGAGTTGTTTCTGAAACATGGCAAAGGTAGCGTTGCCAAT
GATGTTACAGATGAGATGGTCAGACTAAACTGGCTGACGGAATTTATGCCACTTCCGACC
ATCAAGCATTTTATCCGTACTCCTTATGATGCATGGTTACTCACCACTGCGATCCCCGGA
AAAACAGCGTTCCAGGTATTAGAAGAATATCCTGATTCAGGTGAAAATATTGTTGATGCG
CTGGCAGTGTTCCTGCGCCGGTTGCACTCGATTCCTGTTTGTAATTGTCCTTTTAACAGC
GATCGCGTCTTCCGTCTTGCACAAGCGCAATCACGAATGAATAACGGTTTGGTTGATGCG
AGTGATTTTGATGACGAGCGTAATGGCTGGCCTGTTGAACAAGTCTGGAAAGAAATGCAT
AAACTTTTGCCATTCTCACCGGATTCAGTCGTCACTCATGGTGATTTCTCACTTGATAAC
CTTATTTTTGACGAGGGGAAATTAATAGGTTGTATTGATGTTGGACGAGTCGGAATCGCA
GACCGATACCAGGATCTTGCCATTCTATGGAACTGCCTCGGTGAGTTTTCTCCTTCATTA
CAGAAACGGCTTTTTCAAAAATATGGTATTGATAATCCTGATATGAATAAATTGCAGTTT
CATTTGATGCTCGATGAGTTTTTCTAAGCAGAGCATTACGCTGACTTGACGGGACGGCGC
AAGCTCATGACCAAAATCCCTTAACGTGAGTTACGCGCGCGTCGTTCCACTGAGCGTCAG
ACCCCGTAGAAAAGATCAAAGGATCTTCTTGAGATCCTTTTTTTCTGCGCGTAATCTGCT
GCTTGCAAACAAAAAAACCACCGCTACCAGCGGTGGTTTGTTTGCCGGATCAAGAGCTAC
CAACTCTTTTTCCGAAGGTAACTGGCTTCAGCAGAGCGCAGATACCAAATACTGTTCTTC
TAGTGTAGCCGTAGTTAGCCCACCACTTCAAGAACTCTGTAGCACCGCCTACATACCTCG
CTCTGCTAATCCTGTTACCAGTGGCTGCTGCCAGTGGCGATAAGTCGTGTCTTACCGGGT
TGGACTCAAGACGATAGTTACCGGATAAGGCGCAGCGGTCGGGCTGAACGGGGGGTTCGT
GCACACAGCCCAGCTTGGAGCGAACGACCTACACCGAACTGAGATACCTACAGCGTGAGC
TATGAGAAAGCGCCACGCTTCCCGAAGGGAGAAAGGCGGACAGGTATCCGGTAAGCGGCA
GGGTCGGAACAGGAGAGCGCACGAGGGAGCTTCCAGGGGGAAACGCCTGGTATCTTTATA
GTCCTGTCGGGTTTCGCCACCTCTGACTTGAGCGTCGATTTTTGTGATGCTCGTCAGGGG
GGCGGAGCCTATGGAAAAACGCCAGCAACGCGGCCTTTTTACGGTTCCTGGCCTTTTGCT
GGCCTTTTGCTCACATGTTCTTTCCTGCGTTATCCCCTGATTCTGTGGATAACCGTATTA
CCGCCTGCTCGCCGCAGCCGAACGACCGAGCGCAGCGAGTCAGTGAGCGAGGAAGCGGAA
GGCGAGAGTAGGGAACTGCCAGGCATCAAACTAAGCAGAAGGCCCCTGACGCATGGCCTT
TTTGCGTTTCTACAAACTCTTTCTGTGTTGTAAAACGACGGCCAGTCTTAAGCTCGGGCC
CCTTTTCCGCCAGGGTTTTCCCAGTCACGACGAATTCGATCCGGCTCAAGCTTTTGGACC
CTCGTACAGAAGCTAATACGACTCACTATAGGGAAATAAGAGAGAAAAGAAGAGTAAGAA
GAAATATAAGACCCCGGCGCCGCCACCATGTTCGTGTTCCTGGTGCTGCTGCCCCTGGTG
AGCAGCCAGTGCGTGAACCTGACCACCCGGACCCAGCTGCCACCAGCCTACACCAACAGC
TTCACCCGGGGCGTCTACTACCCCGACAAGGTGTTCCGGAGCAGCGTCCTGCACAGCACC
CAGGACCTGTTCCTGCCCTTCTTCAGCAACGTGACCTGGTTCCACGCCATCCACGTGAGC
GGCACCAACGGCACCAAGCGGTTCGACAACCCCGTGCTGCCCTTCAACGACGGCGTGTAC
TTCGCCAGCACCGAGAAGAGCAACATCATCCGGGGCTGGATCTTCGGCACCACCCTGGAC
AGCAAGACCCAGAGCCTGCTGATCGTGAATAACGCCACCAACGTGGTGATCAAGGTGTGC
GAGTTCCAGTTCTGCAACGACCCCTTCCTGGGCGTGTACTACCACAAGAACAACAAGAGC
TGGATGGAGAGCGAGTTCCGGGTGTACAGCAGCGCCAACAACTGCACCTTCGAGTACGTG
AGCCAGCCCTTCCTGATGGACCTGGAGGGCAAGCAGGGCAACTTCAAGAACCTGCGGGAG
TTCGTGTTCAAGAACATCGACGGCTACTTCAAGATCTACAGCAAGCACACCCCAATCAAC
CTGGTGCGGGATCTGCCCCAGGGCTTCTCAGCCCTGGAGCCCCTGGTGGACCTGCCCATC
GGCATCAACATCACCCGGTTCCAGACCCTGCTGGCCCTGCACCGGAGCTACCTGACCCCA
GGCGACAGCAGCAGCGGGTGGACAGCAGGCGCGGCTGCTTACTACGTGGGCTACCTGCAG
CCCCGGACCTTCCTGCTGAAGTACAACGAGAACGGCACCATCACCGACGCCGTGGACTGC
GCCCTGGACCCTCTGAGCGAGACCAAGTGCACCCTGAAGAGCTTCACCGTGGAGAAGGGC
ATCTACCAGACCAGCAACTTCCGGGTGCAGCCCACCGAGAGCATCGTGCGGTTCCCCAAC
ATCACCAACCTGTGCCCCTTCGGCGAGGTGTTCAACGCCACCCGGTTCGCCAGCGTGTAC
GCCTGGAACCGGAAGCGGATCAGCAACTGCGTGGCCGACTACAGCGTGCTGTACAACAGC
GCCAGCTTCAGCACCTTCAAGTGCTACGGCGTGAGCCCCACCAAGCTGAACGACCTGTGC
TTCACCAACGTGTACGCCGACAGCTTCGTGATCCGTGGCGACGAGGTGCGGCAGATCGCA
CCCGGCCAGACAGGCAAGATCGCCGACTACAACTACAAGCTGCCCGACGACTTCACCGGC
TGCGTGATCGCCTGGAACAGCAACAACCTCGACAGCAAGGTGGGCGGCAACTACAACTAC
CTGTACCGGCTGTTCCGGAAGAGCAACCTGAAGCCCTTCGAGCGGGACATCAGCACCGAG
ATCTACCAAGCCGGCTCCACCCCTTGCAACGGCGTGGAGGGCTTCAACTGCTACTTCCCT
CTGCAGAGCTACGGCTTCCAGCCCACCAACGGCGTGGGCTACCAGCCCTACCGGGTGGTG
GTGCTGAGCTTCGAGCTGCTGCACGCCCCAGCCACCGTGTGTGGCCCCAAGAAGAGCACC
AACCTGGTGAAGAACAAGTGCGTGAACTTCAACTTCAACGGCCTTACCGGCACCGGCGTG
CTGACCGAGAGCAACAAGAAATTCCTGCCCTTTCAGCAGTTCGGCCGGGACATCGCCGAC
ACCACCGACGCTGTGCGGGATCCCCAGACCCTGGAGATCCTGGACATCACCCCTTGCAGC
TTCGGCGGCGTGAGCGTGATCACCCCAGGCACCAACACCAGCAACCAGGTGGCCGTGCTG
TACCAGGACGTGAACTGCACCGAGGTGCCCGTGGCCATCCACGCCGACCAGCTGACACCC
ACCTGGCGGGTCTACAGCACCGGCAGCAACGTGTTCCAGACCCGGGCCGGTTGCCTGATC
GGCGCCGAGCACGTGAACAACAGCTACGAGTGCGACATCCCCATCGGCGCCGGCATCTGT
GCCAGCTACCAGACCCAGACCAATTCACCCCGGAGGGCAAGGAGCGTGGCCAGCCAGAGC
ATCATCGCCTACACCATGAGCCTGGGCGCCGAGAACAGCGTGGCCTACAGCAACAACAGC
ATCGCCATCCCCACCAACTTCACCATCAGCGTGACCACCGAGATTCTGCCCGTGAGCATG
ACCAAGACCAGCGTGGACTGCACCATGTACATCTGCGGCGACAGCACCGAGTGCAGCAAC
CTGCTGCTGCAGTACGGCAGCTTCTGCACCCAGCTGAACCGGGCCCTGACCGGCATCGCC
GTGGAGCAGGACAAGAACACCCAGGAGGTGTTCGCCCAGGTGAAGCAGATCTACAAGACC
CCTCCCATCAAGGACTTCGGCGGCTTCAACTTCAGCCAGATCCTGCCCGACCCCAGCAAG
CCCAGCAAGCGGAGCTTCATCGAGGACCTGCTGTTCAACAAGGTGACCCTAGCCGACGCC
GGCTTCATCAAGCAGTACGGCGACTGCCTCGGCGACATAGCCGCCCGGGACCTGATCTGC
GCCCAGAAGTTCAACGGCCTGACCGTGCTGCCTCCCCTGCTGACCGACGAGATGATCGCC
CAGTACACCAGCGCCCTGTTAGCCGGAACCATCACCAGCGGCTGGACTTTCGGCGCTGGA
GCCGCTCTGCAGATCCCCTTCGCCATGCAGATGGCCTACCGGTTCAACGGCATCGGCGTG
ACCCAGAACGTGCTGTACGAGAACCAGAAGCTGATCGCCAACCAGTTCAACAGCGCCATC
GGCAAGATCCAGGACAGCCTGAGCAGCACCGCTAGCGCCCTGGGCAAGCTGCAGGACGTG
GTGAACCAGAACGCCCAGGCCCTGAACACCCTGGTGAAGCAGCTGAGCAGCAACTTCGGC
GCCATCAGCAGCGTGCTGAACGACATCCTGAGCCGGCTGGACCCTCCCGAGGCCGAGGTG
CAGATCGACCGGCTGATCACTGGCCGGCTGCAGAGCCTGCAGACCTACGTGACCCAGCAG
CTGATCCGGGCCGCCGAGATTCGGGCCAGCGCCAACCTGGCCGCCACCAAGATGAGCGAG
TGCGTGCTGGGCCAGAGCAAGCGGGTGGACTTCTGCGGCAAGGGCTACCACCTGATGAGC
TTTCCCCAGAGCGCACCCCACGGAGTGGTGTTCCTGCACGTGACCTACGTGCCCGCCCAG
GAGAAGAACTTCACCACCGCCCCAGCCATCTGCCACGACGGCAAGGCCCACTTTCCCCGG
GAGGGCGTGTTCGTGAGCAACGGCACCCACTGGTTCGTGACCCAGCGGAACTTCTACGAG
CCCCAGATCATCACCACCGACAACACCTTCGTGAGCGGCAACTGCGACGTGGTGATCGGC
ATCGTGAACAACACCGTGTACGATCCCCTGCAGCCCGAGCTGGACAGCTTCAAGGAGGAG
CTGGACAAGTACTTCAAGAATCACACCAGCCCCGACGTGGACCTGGGCGACATCAGCGGC
ATCAACGCCAGCGTGGTGAACATCCAGAAGGAGATCGATCGGCTGAACGAGGTGGCCAAG
AACCTGAACGAGAGCCTGATCGACCTGCAGGAGCTGGGCAAGTACGAGCAGTACATCAAG
TGGCCCTGGTACATCTGGCTGGGCTTCATCGCCGGCCTGATCGCCATCGTGATGGTGACC
ATCATGCTGTGCTGCATGACCAGCTGCTGCAGCTGCCTGAAGGGCTGTTGCAGCTGCGGC
AGCTGCTGCAAGTTCGACGAGGACGACAGCGAGCCCGTGCTGAAGGGCGTGAAGCTGCAC
TACACCTGATAATAGGCTGGAGCCTCGGTGGCCTAGCTTCTTGCCCCTTGGGCCTCCCCC
CAGCCCCTCCTCCCCTTCCTGCACCCGTACCCCCGTGGTCTTTGAATAAAGTCTGAGTGG
GCGAAAAAAA
Bivalent MGC reads mapped against the Moderna_Omicron_UTR2 reference. Note the heterozygous SNPs. The spike region was downsampled (-s 0.01) with samtools due to IGV memory constraints. This is a much cleaner picture than what we started with.
Moderna Monovalent Filing can shed some light on what was disclosed. No information on the plasmid backbone but some discussion on 3’UTRs. Also note there is a 5bp XbaI site at the end of the polyA and there is no disclosure of an inverted Thymidine at the end. There is a Moderna powerpoint floating around that demonstrates they are playing around with this 3’ Cap as it has been shown to increase mRNA longevity but there is no disclosure of that in these documents so I am assuming its not there as it would add significant synthesis cost and purification to add it after the IVT reaction. This is not a base that the T7 polymerase can specifically add to the 3’ end without it also incorporating it internally so a terminal transferase or other enzymatic step plus additional purification would be required and those steps would be disclosed if they were part of the manufacturing process. There is disclosure of the 5’ cap and any 3’ cap would be discussed in these steps.
Text From UK Filing without 5’cap (no plasmid)
>Moderna_Alpha_UK_Disclosed_No_plasmid
GGAAAUAAGAGAGAAAAGAAGAGUAAGAAGAAAUAUAAGACCCCGGCGCCGCCACCAUGU
UCGUGUUCCUGGUGCUGCUGCCCCUGGUGAGCAGCCAGUGCGUGAACCUGACCACCCGGA
CCCAGCUGCCACCAGCCUACACCAACAGCUUCACCCGGGGCGUCUACUACCCCGACAAGG
UGUUCCGGAGCAGCGUCCUGCACAGCACCCAGGACCUGUUCCUGCCCUUCUUCAGCAACG
UGACCUGGUUCCACGCCAUCCACGUGAGCGGCACCAACGGCACCAAGCGGUUCGACAACC
CCGUGCUGCCCUUCAACGACGGCGUGUACUUCGCCAGCACCGAGAAGAGCAACAUCAUCC
GGGGCUGGAUCUUCGGCACCACCCUGGACAGCAAGACCCAGAGCCUGCUGAUCGUGAAUA
ACGCCACCAACGUGGUGAUCAAGGUGUGCGAGUUCCAGUUCUGCAACGACCCCUUCCUGG
GCGUGUACUACCACAAGAACAACAAGAGCUGGAUGGAGAGCGAGUUCCGGGUGUACAGCA
GCGCCAACAACUGCACCUUCGAGUACGUGAGCCAGCCCUUCCUGAUGGACCUGGAGGGCA
AGCAGGGCAACUUCAAGAACCUGCGGGAGUUCGUGUUCAAGAACAUCGACGGCUACUUCA
AGAUCUACAGCAAGCACACCCCAAUCAACCUGGUGCGGGAUCUGCCCCAGGGCUUCUCAG
CCCUGGAGCCCCUGGUGGACCUGCCCAUCGGCAUCAACAUCACCCGGUUCCAGACCCUGC
UGGCCCUGCACCGGAGCUACCUGACCCCAGGCGACAGCAGCAGCGGGUGGACAGCAGGCG
CGGCUGCUUACUACGUGGGCUACCUGCAGCCCCGGACCUUCCUGCUGAAGUACAACGAGA
ACGGCACCAUCACCGACGCCGUGGACUGCGCCCUGGACCCUCUGAGCGAGACCAAGUGCA
CCCUGAAGAGCUUCACCGUGGAGAAGGGCAUCUACCAGACCAGCAACUUCCGGGUGCAGC
CCACCGAGAGCAUCGUGCGGUUCCCCAACAUCACCAACCUGUGCCCCUUCGGCGAGGUGU
UCAACGCCACCCGGUUCGCCAGCGUGUACGCCUGGAACCGGAAGCGGAUCAGCAACUGCG
UGGCCGACUACAGCGUGCUGUACAACAGCGCCAGCUUCAGCACCUUCAAGUGCUACGGCG
UGAGCCCCACCAAGCUGAACGACCUGUGCUUCACCAACGUGUACGCCGACAGCUUCGUGA
UCCGUGGCGACGAGGUGCGGCAGAUCGCACCCGGCCAGACAGGCAAGAUCGCCGACUACA
ACUACAAGCUGCCCGACGACUUCACCGGCUGCGUGAUCGCCUGGAACAGCAACAACCUCG
ACAGCAAGGUGGGCGGCAACUACAACUACCUGUACCGGCUGUUCCGGAAGAGCAACCUGA
AGCCCUUCGAGCGGGACAUCAGCACCGAGAUCUACCAAGCCGGCUCCACCCCUUGCAACG
GCGUGGAGGGCUUCAACUGCUACUUCCCUCUGCAGAGCUACGGCUUCCAGCCCACCAACG
GCGUGGGCUACCAGCCCUACCGGGUGGUGGUGCUGAGCUUCGAGCUGCUGCACGCCCCAG
CCACCGUGUGUGGCCCCAAGAAGAGCACCAACCUGGUGAAGAACAAGUGCGUGAACUUCA
ACUUCAACGGCCUUACCGGCACCGGCGUGCUGACCGAGAGCAACAAGAAAUUCCUGCCCU
UUCAGCAGUUCGGCCGGGACAUCGCCGACACCACCGACGCUGUGCGGGAUCCCCAGACCC
UGGAGAUCCUGGACAUCACCCCUUGCAGCUUCGGCGGCGUGAGCGUGAUCACCCCAGGCA
CCAACACCAGCAACCAGGUGGCCGUGCUGUACCAGGACGUGAACUGCACCGAGGUGCCCG
UGGCCAUCCACGCCGACCAGCUGACACCCACCUGGCGGGUCUACAGCACCGGCAGCAACG
UGUUCCAGACCCGGGCCGGUUGCCUGAUCGGCGCCGAGCACGUGAACAACAGCUACGAGU
GCGACAUCCCCAUCGGCGCCGGCAUCUGUGCCAGCUACCAGACCCAGACCAAUUCACCCC
GGAGGGCAAGGAGCGUGGCCAGCCAGAGCAUCAUCGCCUACACCAUGAGCCUGGGCGCCG
AGAACAGCGUGGCCUACAGCAACAACAGCAUCGCCAUCCCCACCAACUUCACCAUCAGCG
UGACCACCGAGAUUCUGCCCGUGAGCAUGACCAAGACCAGCGUGGACUGCACCAUGUACA
UCUGCGGCGACAGCACCGAGUGCAGCAACCUGCUGCUGCAGUACGGCAGCUUCUGCACCC
AGCUGAACCGGGCCCUGACCGGCAUCGCCGUGGAGCAGGACAAGAACACCCAGGAGGUGU
UCGCCCAGGUGAAGCAGAUCUACAAGACCCCUCCCAUCAAGGACUUCGGCGGCUUCAACU
UCAGCCAGAUCCUGCCCGACCCCAGCAAGCCCAGCAAGCGGAGCUUCAUCGAGGACCUGC
UGUUCAACAAGGUGACCCUAGCCGACGCCGGCUUCAUCAAGCAGUACGGCGACUGCCUCG
GCGACAUAGCCGCCCGGGACCUGAUCUGCGCCCAGAAGUUCAACGGCCUGACCGUGCUGC
CUCCCCUGCUGACCGACGAGAUGAUCGCCCAGUACACCAGCGCCCUGUUAGCCGGAACCA
UCACCAGCGGCUGGACUUUCGGCGCUGGAGCCGCUCUGCAGAUCCCCUUCGCCAUGCAGA
UGGCCUACCGGUUCAACGGCAUCGGCGUGACCCAGAACGUGCUGUACGAGAACCAGAAGC
UGAUCGCCAACCAGUUCAACAGCGCCAUCGGCAAGAUCCAGGACAGCCUGAGCAGCACCG
CUAGCGCCCUGGGCAAGCUGCAGGACGUGGUGAACCAGAACGCCCAGGCCCUGAACACCC
UGGUGAAGCAGCUGAGCAGCAACUUCGGCGCCAUCAGCAGCGUGCUGAACGACAUCCUGA
GCCGGCUGGACCCUCCCGAGGCCGAGGUGCAGAUCGACCGGCUGAUCACUGGCCGGCUGC
AGAGCCUGCAGACCUACGUGACCCAGCAGCUGAUCCGGGCCGCCGAGAUUCGGGCCAGCG
CCAACCUGGCCGCCACCAAGAUGAGCGAGUGCGUGCUGGGCCAGAGCAAGCGGGUGGACU
UCUGCGGCAAGGGCUACCACCUGAUGAGCUUUCCCCAGAGCGCACCCCACGGAGUGGUGU
UCCUGCACGUGACCUACGUGCCCGCCCAGGAGAAGAACUUCACCACCGCCCCAGCCAUCU
GCCACGACGGCAAGGCCCACUUUCCCCGGGAGGGCGUGUUCGUGAGCAACGGCACCCACU
GGUUCGUGACCCAGCGGAACUUCUACGAGCCCCAGAUCAUCACCACCGACAACACCUUCG
UGAGCGGCAACUGCGACGUGGUGAUCGGCAUCGUGAACAACACCGUGUACGAUCCCCUGC
AGCCCGAGCUGGACAGCUUCAAGGAGGAGCUGGACAAGUACUUCAAGAAUCACACCAGCC
CCGACGUGGACCUGGGCGACAUCAGCGGCAUCAACGCCAGCGUGGUGAACAUCCAGAAGG
AGAUCGAUCGGCUGAACGAGGUGGCCAAGAACCUGAACGAGAGCCUGAUCGACCUGCAGG
AGCUGGGCAAGUACGAGCAGUACAUCAAGUGGCCCUGGUACAUCUGGCUGGGCUUCAUCG
CCGGCCUGAUCGCCAUCGUGAUGGUGACCAUCAUGCUGUGCUGCAUGACCAGCUGCUGCA
GCUGCCUGAAGGGCUGUUGCAGCUGCGGCAGCUGCUGCAAGUUCGACGAGGACGACAGCG
AGCCCGUGCUGAAGGGCGUGAAGCUGCACUACACCUGAUAAUAGGCUGGAGCCUCGGUGG
CCUAGCUUCUUGCCCCUUGGGCCUCCCCCCAGCCCCUCCUCCCCUUCCUGCACCCGUACC
CCCGUGGUCUUUGAAUAAAGUCUGAGUGGGCGGCAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAUCUAG
From Fire- Github (Spike only- No plasmid)
>Figure_2_32321_Spike-encoding_contig_assembled_from_Moderna_mRNA-1273_vaccine
GGGAAATAAGAGAGAAAAGAAGAGTAAGAAGAAATATAAGACCCCGGCGCCGCCACCATG
TTCGTGTTCCTGGTGCTGCTGCCCCTGGTGAGCAGCCAGTGCGTGAACCTGACCACCCGG
ACCCAGCTGCCACCAGCCTACACCAACAGCTTCACCCGGGGCGTCTACTACCCCGACAAG
GTGTTCCGGAGCAGCGTCCTGCACAGCACCCAGGACCTGTTCCTGCCCTTCTTCAGCAAC
GTGACCTGGTTCCACGCCATCCACGTGAGCGGCACCAACGGCACCAAGCGGTTCGACAAC
CCCGTGCTGCCCTTCAACGACGGCGTGTACTTCGCCAGCACCGAGAAGAGCAACATCATC
CGGGGCTGGATCTTCGGCACCACCCTGGACAGCAAGACCCAGAGCCTGCTGATCGTGAAT
AACGCCACCAACGTGGTGATCAAGGTGTGCGAGTTCCAGTTCTGCAACGACCCCTTCCTG
GGCGTGTACTACCACAAGAACAACAAGAGCTGGATGGAGAGCGAGTTCCGGGTGTACAGC
AGCGCCAACAACTGCACCTTCGAGTACGTGAGCCAGCCCTTCCTGATGGACCTGGAGGGC
AAGCAGGGCAACTTCAAGAACCTGCGGGAGTTCGTGTTCAAGAACATCGACGGCTACTTC
AAGATCTACAGCAAGCACACCCCAATCAACCTGGTGCGGGATCTGCCCCAGGGCTTCTCA
GCCCTGGAGCCCCTGGTGGACCTGCCCATCGGCATCAACATCACCCGGTTCCAGACCCTG
CTGGCCCTGCACCGGAGCTACCTGACCCCAGGCGACAGCAGCAGCGGGTGGACAGCAGGC
GCGGCTGCTTACTACGTGGGCTACCTGCAGCCCCGGACCTTCCTGCTGAAGTACAACGAG
AACGGCACCATCACCGACGCCGTGGACTGCGCCCTGGACCCTCTGAGCGAGACCAAGTGC
ACCCTGAAGAGCTTCACCGTGGAGAAGGGCATCTACCAGACCAGCAACTTCCGGGTGCAG
CCCACCGAGAGCATCGTGCGGTTCCCCAACATCACCAACCTGTGCCCCTTCGGCGAGGTG
TTCAACGCCACCCGGTTCGCCAGCGTGTACGCCTGGAACCGGAAGCGGATCAGCAACTGC
GTGGCCGACTACAGCGTGCTGTACAACAGCGCCAGCTTCAGCACCTTCAAGTGCTACGGC
GTGAGCCCCACCAAGCTGAACGACCTGTGCTTCACCAACGTGTACGCCGACAGCTTCGTG
ATCCGTGGCGACGAGGTGCGGCAGATCGCACCCGGCCAGACAGGCAAGATCGCCGACTAC
AACTACAAGCTGCCCGACGACTTCACCGGCTGCGTGATCGCCTGGAACAGCAACAACCTC
GACAGCAAGGTGGGCGGCAACTACAACTACCTGTACCGGCTGTTCCGGAAGAGCAACCTG
AAGCCCTTCGAGCGGGACATCAGCACCGAGATCTACCAAGCCGGCTCCACCCCTTGCAAC
GGCGTGGAGGGCTTCAACTGCTACTTCCCTCTGCAGAGCTACGGCTTCCAGCCCACCAAC
GGCGTGGGCTACCAGCCCTACCGGGTGGTGGTGCTGAGCTTCGAGCTGCTGCACGCCCCA
GCCACCGTGTGTGGCCCCAAGAAGAGCACCAACCTGGTGAAGAACAAGTGCGTGAACTTC
AACTTCAACGGCCTTACCGGCACCGGCGTGCTGACCGAGAGCAACAAGAAATTCCTGCCC
TTTCAGCAGTTCGGCCGGGACATCGCCGACACCACCGACGCTGTGCGGGATCCCCAGACC
CTGGAGATCCTGGACATCACCCCTTGCAGCTTCGGCGGCGTGAGCGTGATCACCCCAGGC
ACCAACACCAGCAACCAGGTGGCCGTGCTGTACCAGGACGTGAACTGCACCGAGGTGCCC
GTGGCCATCCACGCCGACCAGCTGACACCCACCTGGCGGGTCTACAGCACCGGCAGCAAC
GTGTTCCAGACCCGGGCCGGTTGCCTGATCGGCGCCGAGCACGTGAACAACAGCTACGAG
TGCGACATCCCCATCGGCGCCGGCATCTGTGCCAGCTACCAGACCCAGACCAATTCACCC
CGGAGGGCAAGGAGCGTGGCCAGCCAGAGCATCATCGCCTACACCATGAGCCTGGGCGCC
GAGAACAGCGTGGCCTACAGCAACAACAGCATCGCCATCCCCACCAACTTCACCATCAGC
GTGACCACCGAGATTCTGCCCGTGAGCATGACCAAGACCAGCGTGGACTGCACCATGTAC
ATCTGCGGCGACAGCACCGAGTGCAGCAACCTGCTGCTGCAGTACGGCAGCTTCTGCACC
CAGCTGAACCGGGCCCTGACCGGCATCGCCGTGGAGCAGGACAAGAACACCCAGGAGGTG
TTCGCCCAGGTGAAGCAGATCTACAAGACCCCTCCCATCAAGGACTTCGGCGGCTTCAAC
TTCAGCCAGATCCTGCCCGACCCCAGCAAGCCCAGCAAGCGGAGCTTCATCGAGGACCTG
CTGTTCAACAAGGTGACCCTAGCCGACGCCGGCTTCATCAAGCAGTACGGCGACTGCCTC
GGCGACATAGCCGCCCGGGACCTGATCTGCGCCCAGAAGTTCAACGGCCTGACCGTGCTG
CCTCCCCTGCTGACCGACGAGATGATCGCCCAGTACACCAGCGCCCTGTTAGCCGGAACC
ATCACCAGCGGCTGGACTTTCGGCGCTGGAGCCGCTCTGCAGATCCCCTTCGCCATGCAG
ATGGCCTACCGGTTCAACGGCATCGGCGTGACCCAGAACGTGCTGTACGAGAACCAGAAG
CTGATCGCCAACCAGTTCAACAGCGCCATCGGCAAGATCCAGGACAGCCTGAGCAGCACC
GCTAGCGCCCTGGGCAAGCTGCAGGACGTGGTGAACCAGAACGCCCAGGCCCTGAACACC
CTGGTGAAGCAGCTGAGCAGCAACTTCGGCGCCATCAGCAGCGTGCTGAACGACATCCTG
AGCCGGCTGGACCCTCCCGAGGCCGAGGTGCAGATCGACCGGCTGATCACTGGCCGGCTG
CAGAGCCTGCAGACCTACGTGACCCAGCAGCTGATCCGGGCCGCCGAGATTCGGGCCAGC
GCCAACCTGGCCGCCACCAAGATGAGCGAGTGCGTGCTGGGCCAGAGCAAGCGGGTGGAC
TTCTGCGGCAAGGGCTACCACCTGATGAGCTTTCCCCAGAGCGCACCCCACGGAGTGGTG
TTCCTGCACGTGACCTACGTGCCCGCCCAGGAGAAGAACTTCACCACCGCCCCAGCCATC
TGCCACGACGGCAAGGCCCACTTTCCCCGGGAGGGCGTGTTCGTGAGCAACGGCACCCAC
TGGTTCGTGACCCAGCGGAACTTCTACGAGCCCCAGATCATCACCACCGACAACACCTTC
GTGAGCGGCAACTGCGACGTGGTGATCGGCATCGTGAACAACACCGTGTACGATCCCCTG
CAGCCCGAGCTGGACAGCTTCAAGGAGGAGCTGGACAAGTACTTCAAGAATCACACCAGC
CCCGACGTGGACCTGGGCGACATCAGCGGCATCAACGCCAGCGTGGTGAACATCCAGAAG
GAGATCGATCGGCTGAACGAGGTGGCCAAGAACCTGAACGAGAGCCTGATCGACCTGCAG
GAGCTGGGCAAGTACGAGCAGTACATCAAGTGGCCCTGGTACATCTGGCTGGGCTTCATC
GCCGGCCTGATCGCCATCGTGATGGTGACCATCATGCTGTGCTGCATGACCAGCTGCTGC
AGCTGCCTGAAGGGCTGTTGCAGCTGCGGCAGCTGCTGCAAGTTCGACGAGGACGACAGC
GAGCCCGTGCTGAAGGGCGTGAAGCTGCACTACACCTGATAATAGGCTGGAGCCTCGGTG
GCCTAGCTTCTTGCCCCTTGGGCCTCCCCCCAGCCCCTCCTCCCCTTCCTGCACCCGTAC
CCCCGTGGTCTTTGAATAAAGTCTGAGTGGGCGGCAAAAAAAAA
If you take all of Krawczyk RNAseq data from vaccinated mice and map it to the Phased-Omicron_UTR2 sequence (Figure 7. Bottom track below). You will note the SNPs are now homozygous as expected.
Map MGC Bivalent data to the same Phased-Omicron-UTR2 reference and note the Heterozygous SNPs as expected (Top coverage tack below Figure 7.)
When you inspect the Bivalent reads mapped to either UTR1 or UTR2 references you will note these different 3’ UTRs. Top track (Figure 8) is monovalent sequence from Krawczyk. Bottom Track is MGC bivalent Moderna sequence where both UTRs are present. Bases are present when they differ from reference.
All Krawcyzk reads mapped to Jeong-Fire UTR1 is homozygous as expected (Figure 10.) The Coverage peak in the middle is T7 promoter which wasn’t downsampled (2300-6190)
So the new references are ~6294 bases and the older ones 6777bp. Where did 483bp go?
The initial assemblies duplicated a region of the plasmid near the 3’UTR and linearization loci and stitched them into a tandem repeat. We now know this is because the 3’UTRs in the two vaccines contain a 14bp in/del and with the Spike sequence being polymorphic and higher coverage than the plasmid backbone, the assembler saw these as unique sequences and split the two and smashed them together into 1 elongated reference (See Duplicated regions in Green)
This is now finished into the below Plasmid Map (Figure 13).
These 3’UTRs are used in other Moderna HIV vaccines and since Jeong et al isn’t in NCBI, the HIV hits are prioritized as the top hits in BLAST. Castruita et al also does not include the 3’ UTR.
If you take this Alpha UTR sequence
CAGCCCCTCCTCCCCTTCCTGCAGGAGAGATAGTGGAGTGGTCTTTGAATAAAGTCTGAG
TGGGCGGC
And BLAST it you get this HIT table.
The Top hit is this HIV vaccine from Fauci
Is this an undisclosed sequence and hence a contaminant as I originally posted? I don’t know? NCBI is bloated with SARs-CoV-2 sequence but has a shocking lack of Moderna Vaccine Sequence. Much of our focus has been on Pfizer largely because the EMA hack released Pfizer data which was a rich source of what was and was not disclosed to regulators. I have not seen the same disclosure information from Moderna on their Bivalent vaccines to determine if they disclosed these 3’UTR differences to the regulators. If anyone has such data, please link to it in the comments and I’ll dissect it accordingly.
Conclusions
We are now in a situation where Pharmaceutical companies can lobby for mandated injections of proprietary, potentially oncogenic gene therapies and the public is forced to decode these injections by scraping through the scraps of the Short Read Archive for evidence of what they have been mass injecting into the population. Fortunately, sequencing technology is very sensitive and inexpensive. This task can be done by anyone with the patience to search through published projects sequencing the vaccinated. There are now 5 peer reviewed papers that have sequenced the vaccinated that have evidence of vaccine plasmid DNA being found in vaccinated patients days to weeks after injection. This evidence is found despite all of these studies using DNaseI in their RNAseq to suppress the signal implying a very high initial dose of plasmid DNA. Some of these plasmids are now known to be used in HIV vaccines in development that have Fauci’s involvement.
Mandated injections from perpetually pardoned perpetrators.
Chakraborty et al (independent review of Ryan and Odak et al)
NCBI Accession >Moderna_Bivalent_UTR2_polyA #PV602126
NCBI Accession >Moderna_Alpha_UTR1_polyA #PV611495
Appendix
Krawczyk mapped against Moderna_Alpha_UTR1
Krawczyk_x_Moderna_Alpha_UTR1_PolyA.bam
Krawczyk_x_Moderna_Alpha_UTR1_PolyA.bam.bai
Downsampled with samtools view -s 0.001 -b
DS_Krawczyk_SRR24681517_v_Moderna.merge.bam
DS_Krawczyk_SRR24681517_v_Moderna.merge.bam.bai
MGC mapped against Moderna_Alpha_UTR1
MGC_x_Moderna_Alpha_UTR1_polyA.bam
MGC_x_Moderna_Alpha_UTR1_polyA.bam.bai
Downsampled with samtools view -s 0.001 -b
DS_MGC_x_Moderna_Alpha_UTR1_polyA.merge.bam
DS_MGC_x_Moderna_Alpha_UTR1_polyA.merge.bam.bai
Acknowledgements.
Jikky leaks and Scoops McGoo independently alerted me to some oddities in the original Moderna reference and motivated me to untangle to the 3’UTR.
It does hairpin and might cause cis-template switching
I understand just enough to be really pissed and also really thankful for the work you're doing.
Intense read for sure Dr Jessica Rose had to put on my glasses to read all this data. This is like a thriller crime scene sifting through all the elements. Colombo would’ve been extraordinarily amazed at your work Jessica 👍😊 and yes, Fauci signature with the HIV is all over this. The little shit !