Manually converted sequencing doc to markdown. Markdown will facilitate easier diffing of files for collaborative work, although I had to manually insert sequence coloring information using HTML.
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# Assemblies of putative SARS-CoV2-spike-encoding mRNA sequences for
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vaccines BNT-162b2 and mRNA-1273.
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### (version 0.1.1Beta 03/23/21)
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Dae Eun Jeong, Matthew McCoy, Karen Artiles, OrkanIlbay, Andrew Fire*, Kari Nadeau,
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Helen Park, Brooke Betts, Scott Boyd, Ramona Hoh, and Massa Shoura*
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Departments of Pathology, Genetics, Pediatrics, and Medicine, Stanford University School of
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Medicine and Veterans Affairs Palo Alto Medical Center
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*Correspondence: [afire@stanford.edu](afire@stanford.edu) and/or [massa86@stanford.edu](massa86@stanford.edu)
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RNA vaccines have become a key tool in moving forward through the challenges raised both
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in the current pandemic and in numerous other publichealth and medical challenges. With
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the rollout of vaccines for COVID-19, these synthetic mRNAs have become broadly
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distributed RNA species in numerous human populations. Despite their ubiquity, sequences
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are not always available for such RNAs. Standard methods facilitate such sequencing. In this
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note, we provide experimental sequence informationfor the RNA components of the initial
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[Moderna](https://pubmed.ncbi.nlm.nih.gov/32756549/)and [Pfizer/BioNTech](https://pubmed.ncbi.nlm.nih.gov/33301246/)
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COVID-19 vaccines, allowing a working assembly of the former and a confirmation of previously
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reported sequence information for the latter RNA.
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Sharing of sequence information for broadly used therapeutics has the benefit of allowing any
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researchers or clinicians using sequencing approaches to rapidly identify such sequences as
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therapeutic-derived rather than host or infectious in origin.
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For this work, RNAs were obtained as discards from the small portions of vaccine doses that
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remained in vials after immunization; such portions would have been required to be
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otherwise discarded and were analyzed under FDA authorization for research use. To obtain
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the small amounts of RNA needed for characterization,vaccine remnants were
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phenol-chloroform extracted using TRIzol Reagent (Invitrogen), with intactness assessed by
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Agilent 2100 Bioanalyzer before and after extraction.
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Although our analysis mainly focused on RNAs obtained as soon as possible following
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discard, we also analyzed samples which had been refrigerated (~4 °C) for up to 42 days with
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and without the addition of EDTA. Interestingly a substantial fraction of the RNA remained
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intact in these preparations. We note that the formulation of the vaccines includes numerous
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key chemical components which are quite possibly unstable under these conditions-- so these
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data certainly do not suggest that the vaccine as a biological agent is stable. But it is of
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interest that chemical stability of RNA itself is not sufficient to preclude eventual
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development of vaccines with a much less involved cold-chain storage and transportation.
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For further analysis, the initial RNAs were fragmentedby heating to 94°C, primed with a
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random hexamer-tailed adaptor, amplified through atemplate-switch protocol (Takara
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SMARTerer Stranded RNA-seq kit), and sequenced usinga MiSeq instrument (Illumina) with
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paired end 78-per end sequencing. As a reference material in specific assays, we included
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RNA of known concentration and sequence (from bacteriophage MS2).
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From these data, we obtained partial information on strandedness and a set of segments that
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could be used for assembly. This was particularly useful for the Moderna vaccine, for which
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the original vaccine RNA sequence was not available at the time our study was carried out.
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Contigs encoding full-length spikes were assembled from the Moderna and Pfizer datasets.
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The Pfizer/BioNTech data [Figure 1] verified the [reported sequence for that vaccine](https://berthub.eu/articles/posts/reverse-engineering-source-code-of-the-biontech-pfizer-vaccine/), while
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the Moderna sequence [Figure 2] could not be checked against a published reference.
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RNA preparations lacking dsRNA are desirable in generating vaccine formulations as these
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will minimize an otherwise dramatic biological (and non-specific) response that vertebrates
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have to double stranded character in RNA (https://www.nature.com/articles/nrd.2017.243).
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In the sequence data that we analyzed, we found that the vast majority of reads were from the
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expected sense strand. In addition, the minorityof antisense reads appeared different from
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sense reads in lacking the characteristic extensions expected from the template switching
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protocol. Examining only the reads with an evident template switch (as an indicator for
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strand-of-origin), we observed that both vaccines overwhelmingly yielded sense reads
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(>99.99%). Independent sequencing assays and otherexperimental measurements are
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ongoing and will be needed to determine whether this template-switched sense read fraction
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in the SmarterSeq protocol indeed represents the actual dsRNA content in the original
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material.
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This work provides an initial assessment of two RNAs that are now a part of the human
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ecosystem and that are likely to appear in numerous other high throughput RNA-seq studies
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in which a fraction of the individuals may have previously been vaccinated.
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ProtoAcknowledgements: Thanks to our colleagues for help and suggestions (Nimit Jain,
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Emily Greenwald, Lamia Wahba, William Wang, Amisha Kumar, Sameer Sundrani, David
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Lipman, Marc Salit, Bijoyita Roy).
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### Figure 1: Spike-encoding contig assembled from BioNTech/PfizerBNT-162b
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vaccine.
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Although the full coding region is included,the nature of the methodology used for
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sequencing and assembly is such that the assembled contig could lack some sequence from
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the ends of the RNA. Within the assembled sequence, this hypothetical sequence shows a
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perfect match to the corresponding sequence from documents available online derived from
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manufacturer communications with the World Health Organization [as reported by
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https://berthub.eu/articles/posts/reverse-engineering-source-code-of-the-biontech-pfizer-vaccine/]. The 5’ end for
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the assembly matches the start site noted in these documents, while the read-based assembly
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lacks an interrupted polyA tail (A30(GCATATGACT)A70) that is expected to be present in the
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mRNA.
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### Figure 2: Spike-encoding contig assembled from Moderna mRNA-1273 vaccine.**
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This is a partial sequence of the vaccine RNA. Although the full coding region is included, the
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assembled contig could lack some sequence from the ends of the RNA.
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**Figure 1: Spike-encoding contig assembled from BioNTech/PfizerBNT-162b vaccine.**
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<span style="background-color:cyan">GAGAATAAACTAGTATTCTTCTGGTCCCCACAGACTCAGAGAGAACCCGCCACC</span><span style="background-color: green">ATG</span><span style="background-color:yellow">TTCGTGTTCCTGGTGCTGCTGCCTCTGGTGTCCAGCCAGTGTGTG</span><span style="background-color:orange">AACCTGACCACCAGAACACAGCTGCCTCCAGCCTACACCAACAGCTTTACCAGAGGCGTGTACTACCCCGACAAGGTGTT
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CAGATCCAGCGTGCTGCACTCTACCCAGGACCTGTTCCTGCCTTTCTTCAGCAACGTGACCTGGTTCCACGCCATCCACGTGTCCGGCACC
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AATGGCACCAAGAGATTCGACAACCCCGTGCTGCCCTTCAACGACGGGGTGTACTTTGCCAGCACCGAGAAGTCCAACATCATCAGAGGCT
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GGATCTTCGGCACCACACTGGACAGCAAGACCCAGAGCCTGCTGATCGTGAACAACGCCACCAACGTGGTCATCAAAGTGTGCGAGTTCCA
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GTTCTGCAACGACCCCTTCCTGGGCGTCTACTACCACAAGAACAACAAGAGCTGGATGGAAAGCGAGTTCCGGGTGTACAGCAGCGCCAAC
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AACTGCACCTTCGAGTACGTGTCCCAGCCTTTCCTGATGGACCTGGAAGGCAAGCAGGGCAACTTCAAGAACCTGCGCGAGTTCGTGTTTA
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AGAACATCGACGGCTACTTCAAGATCTACAGCAAGCACACCCCTATCAACCTCGTGCGGGATCTGCCTCAGGGCTTCTCTGCTCTGGAACC
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CCTGGTGGATCTGCCCATCGGCATCAACATCACCCGGTTTCAGACACTGCTGGCCCTGCACAGAAGCTACCTGACACCTGGCGATAGCAGC
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AGCGGATGGACAGCTGGTGCCGCCGCTTACTATGTGGGCTACCTGCAGCCTAGAACCTTCCTGCTGAAGTACAACGAGAACGGCACCATCA
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CCGACGCCGTGGATTGTGCTCTGGATCCTCTGAGCGAGACAAAGTGCACCCTGAAGTCCTTCACCGTGGAAAAGGGCATCTACCAGACCAG
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CAACTTCCGGGTGCAGCCCACCGAATCCATCGTGCGGTTCCCCAATATCACCAATCTGTGCCCCTTCGGCGAGGTGTTCAATGCCACCAGA
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TTCGCCTCTGTGTACGCCTGGAACCGGAAGCGGATCAGCAATTGCGTGGCCGACTACTCCGTGCTGTACAACTCCGCCAGCTTCAGCACCT
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TCAAGTGCTACGGCGTGTCCCCTACCAAGCTGAACGACCTGTGCTTCACAAACGTGTACGCCGACAGCTTCGTGATCCGGGGAGATGAAGT
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GCGGCAGATTGCCCCTGGACAGACAGGCAAGATCGCCGACTACAACTACAAGCTGCCCGACGACTTCACCGGCTGTGTGATTGCCTGGAAC
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AGCAACAACCTGGACTCCAAAGTCGGCGGCAACTACAATTACCTGTACCGGCTGTTCCGGAAGTCCAATCTGAAGCCCTTCGAGCGGGACA
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TCTCCACCGAGATCTATCAGGCCGGCAGCACCCCTTGTAACGGCGTGGAAGGCTTCAACTGCTACTTCCCACTGCAGTCCTACGGCTTTCA
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GCCCACAAATGGCGTGGGCTATCAGCCCTACAGAGTGGTGGTGCTGAGCTTCGAACTGCTGCATGCCCCTGCCACAGTGTGCGGCCCTAAG
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AAAAGCACCAATCTCGTGAAGAACAAATGCGTGAACTTCAACTTCAACGGCCTGACCGGCACCGGCGTGCTGACAGAGAGCAACAAGAAGT
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TCCTGCCATTCCAGCAGTTTGGCCGGGATATCGCCGATACCACAGACGCCGTTAGAGATCCCCAGACACTGGAAATCCTGGACATCACCCC
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TTGCAGCTTCGGCGGAGTGTCTGTGATCACCCCTGGCACCAACACCAGCAATCAGGTGGCAGTGCTGTACCAGGACGTGAACTGTACCGAA
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GTGCCCGTGGCCATTCACGCCGATCAGCTGACACCTACATGGCGGGTGTACTCCACCGGCAGCAATGTGTTTCAGACCAGAGCCGGCTGTC
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TGATCGGAGCCGAGCACGTGAACAATAGCTACGAGTGCGACATCCCCATCGGCGCTGGAATCTGCGCCAGCTACCAGACACAGACAAACAG
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CCCTCGGAGAGCCAGAAGCGTGGCCAGCCAGAGCATCATTGCCTACACAATGTCTCTGGGCGCCGAGAACAGCGTGGCCTACTCCAACAAC
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TCTATCGCTATCCCCACCAACTTCACCATCAGCGTGACCACAGAGATCCTGCCTGTGTCCATGACCAAGACCAGCGTGGACTGCACCATGT
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ACATCTGCGGCGATTCCACCGAGTGCTCCAACCTGCTGCTGCAGTACGGCAGCTTCTGCACCCAGCTGAATAGAGCCCTGACAGGGATCGC
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CGTGGAACAGGACAAGAACACCCAAGAGGTGTTCGCCCAAGTGAAGCAGATCTACAAGACCCCTCCTATCAAGGACTTCGGCGGCTTCAAT
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TTCAGCCAGATTCTGCCCGATCCTAGCAAGCCCAGCAAGCGGAGCTTCATCGAGGACCTGCTGTTCAACAAAGTGACACTGGCCGACGCCG
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GCTTCATCAAGCAGTATGGCGATTGTCTGGGCGACATTGCCGCCAGGGATCTGATTTGCGCCCAGAAGTTTAACGGACTGACAGTGCTGCC
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TCCTCTGCTGACCGATGAGATGATCGCCCAGTACACATCTGCCCTGCTGGCCGGCACAATCACAAGCGGCTGGACATTTGGAGCAGGCGCC
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GCTCTGCAGATCCCCTTTGCTATGCAGATGGCCTACCGGTTCAACGGCATCGGAGTGACCCAGAATGTGCTGTACGAGAACCAGAAGCTGA
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TCGCCAACCAGTTCAACAGCGCCATCGGCAAGATCCAGGACAGCCTGAGCAGCACAGCAAGCGCCCTGGGAAAGCTGCAGGACGTGGTCAA
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CCAGAATGCCCAGGCACTGAACACCCTGGTCAAGCAGCTGTCCTCCAACTTCGGCGCCATCAGCTCTGTGCTGAACGATATCCTGAGCAGA
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CTGGACCCTCCTGAGGCCGAGGTGCAGATCGACAGACTGATCACAGGCAGACTGCAGAGCCTCCAGACATACGTGACCCAGCAGCTGATCA
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GAGCCGCCGAGATTAGAGCCTCTGCCAATCTGGCCGCCACCAAGATGTCTGAGTGTGTGCTGGGCCAGAGCAAGAGAGTGGACTTTTGCGG
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CAAGGGCTACCACC</span><span style="background-color: red">TGATGA</span><span style="background-color: magenta">CTCGAGCTGGTACTGCATGCACGCAATGCTAGCTGCCCCTTTCCCGTCCTGGGTACCCCGAGTCTCCCCCGACCTCGGGTCCCAGGTATGCTCCCACCTCCACCTGCCCCACTCACCACCTCTGCTAGTTCCAGACACCTCCCAAGCACGCAGCAATGCAGCTCAAAACGCTTAGCCTAGCCACACCCCCACGGGAAACAGCAGTGATTAACCTTTAGCAATAAACGAAAGTTTAACTAAGCTATACTAACCCCAGGGTTGGTCAATTTCGTGCCAGCCACACCCTGGAGCTAGC</span><span style="background-color:blue">A</blue>
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<span style="background-color: cyan">Cyan: Putative 5’ UTR</span>
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<span style="background-color: green">Green: Start Codon</span>
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<span style="background-color: yellow">Yellow: Signal Peptide</span>
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<span style="background-color: orange">Orange: Spike encoding region</span>
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<span style="background-color: red">Red: Stop codon(s)</span>
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<span style="background-color: magenta">Purple: 3’ UTR</span>
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<span style="background-color: blue">Blue: Start of polyA region (incomplete)</span>
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**Figure 2: Spike-encoding contig assembled from Moderna mRNA-1273 vaccine.**
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<span style="background-color: cyan">GGGAAATAAGAGAGAAAAGAAGAGTAAGAAGAAATATAAGACCCCGGCGCCGCCACC</span><span style="background-color: green">ATG</span><span style="background-color: yellow">TTCGTGTTCCTGGTGCTGCTGCCCCTGGTGAGCAGCCAGTGCGTG</span><span style="background-color: orange">AACCTGACCACCCGGACCCAGCTGCCACCAGCCTACACCAACAGCTTCACCCGGGGCGTCTACTACCCCGACAAGGT
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GTTCCGGAGCAGCGTCCTGCACAGCACCCAGGACCTGTTCCTGCCCTTCTTCAGCAACGTGACCTGGTTCCACGCCATCCACGTGAGCGGC
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ACCAACGGCACCAAGCGGTTCGACAACCCCGTGCTGCCCTTCAACGACGGCGTGTACTTCGCCAGCACCGAGAAGAGCAACATCATCCGGG
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GCTGGATCTTCGGCACCACCCTGGACAGCAAGACCCAGAGCCTGCTGATCGTGAATAACGCCACCAACGTGGTGATCAAGGTGTGCGAGTT
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CCAGTTCTGCAACGACCCCTTCCTGGGCGTGTACTACCACAAGAACAACAAGAGCTGGATGGAGAGCGAGTTCCGGGTGTACAGCAGCGCC
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AACAACTGCACCTTCGAGTACGTGAGCCAGCCCTTCCTGATGGACCTGGAGGGCAAGCAGGGCAACTTCAAGAACCTGCGGGAGTTCGTGT
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TCAAGAACATCGACGGCTACTTCAAGATCTACAGCAAGCACACCCCAATCAACCTGGTGCGGGATCTGCCCCAGGGCTTCTCAGCCCTGGA
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GCCCCTGGTGGACCTGCCCATCGGCATCAACATCACCCGGTTCCAGACCCTGCTGGCCCTGCACCGGAGCTACCTGACCCCAGGCGACAGC
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AGCAGCGGGTGGACAGCAGGCGCGGCTGCTTACTACGTGGGCTACCTGCAGCCCCGGACCTTCCTGCTGAAGTACAACGAGAACGGCACCA
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TCACCGACGCCGTGGACTGCGCCCTGGACCCTCTGAGCGAGACCAAGTGCACCCTGAAGAGCTTCACCGTGGAGAAGGGCATCTACCAGAC
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CAGCAACTTCCGGGTGCAGCCCACCGAGAGCATCGTGCGGTTCCCCAACATCACCAACCTGTGCCCCTTCGGCGAGGTGTTCAACGCCACC
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CGGTTCGCCAGCGTGTACGCCTGGAACCGGAAGCGGATCAGCAACTGCGTGGCCGACTACAGCGTGCTGTACAACAGCGCCAGCTTCAGCA
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CCTTCAAGTGCTACGGCGTGAGCCCCACCAAGCTGAACGACCTGTGCTTCACCAACGTGTACGCCGACAGCTTCGTGATCCGTGGCGACGA
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GGTGCGGCAGATCGCACCCGGCCAGACAGGCAAGATCGCCGACTACAACTACAAGCTGCCCGACGACTTCACCGGCTGCGTGATCGCCTGG
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AACAGCAACAACCTCGACAGCAAGGTGGGCGGCAACTACAACTACCTGTACCGGCTGTTCCGGAAGAGCAACCTGAAGCCCTTCGAGCGGG
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ACATCAGCACCGAGATCTACCAAGCCGGCTCCACCCCTTGCAACGGCGTGGAGGGCTTCAACTGCTACTTCCCTCTGCAGAGCTACGGCTT
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CCAGCCCACCAACGGCGTGGGCTACCAGCCCTACCGGGTGGTGGTGCTGAGCTTCGAGCTGCTGCACGCCCCAGCCACCGTGTGTGGCCCC
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AAGAAGAGCACCAACCTGGTGAAGAACAAGTGCGTGAACTTCAACTTCAACGGCCTTACCGGCACCGGCGTGCTGACCGAGAGCAACAAGA
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AATTCCTGCCCTTTCAGCAGTTCGGCCGGGACATCGCCGACACCACCGACGCTGTGCGGGATCCCCAGACCCTGGAGATCCTGGACATCAC
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CCCTTGCAGCTTCGGCGGCGTGAGCGTGATCACCCCAGGCACCAACACCAGCAACCAGGTGGCCGTGCTGTACCAGGACGTGAACTGCACC
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GAGGTGCCCGTGGCCATCCACGCCGACCAGCTGACACCCACCTGGCGGGTCTACAGCACCGGCAGCAACGTGTTCCAGACCCGGGCCGGTT
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GCCTGATCGGCGCCGAGCACGTGAACAACAGCTACGAGTGCGACATCCCCATCGGCGCCGGCATCTGTGCCAGCTACCAGACCCAGACCAA
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TTCACCCCGGAGGGCAAGGAGCGTGGCCAGCCAGAGCATCATCGCCTACACCATGAGCCTGGGCGCCGAGAACAGCGTGGCCTACAGCAAC
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AACAGCATCGCCATCCCCACCAACTTCACCATCAGCGTGACCACCGAGATTCTGCCCGTGAGCATGACCAAGACCAGCGTGGACTGCACCA
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TGTACATCTGCGGCGACAGCACCGAGTGCAGCAACCTGCTGCTGCAGTACGGCAGCTTCTGCACCCAGCTGAACCGGGCCCTGACCGGCAT
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CGCCGTGGAGCAGGACAAGAACACCCAGGAGGTGTTCGCCCAGGTGAAGCAGATCTACAAGACCCCTCCCATCAAGGACTTCGGCGGCTTC
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AACTTCAGCCAGATCCTGCCCGACCCCAGCAAGCCCAGCAAGCGGAGCTTCATCGAGGACCTGCTGTTCAACAAGGTGACCCTAGCCGACG
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CCGGCTTCATCAAGCAGTACGGCGACTGCCTCGGCGACATAGCCGCCCGGGACCTGATCTGCGCCCAGAAGTTCAACGGCCTGACCGTGCT
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GCCTCCCCTGCTGACCGACGAGATGATCGCCCAGTACACCAGCGCCCTGTTAGCCGGAACCATCACCAGCGGCTGGACTTTCGGCGCTGGA
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GCCGCTCTGCAGATCCCCTTCGCCATGCAGATGGCCTACCGGTTCAACGGCATCGGCGTGACCCAGAACGTGCTGTACGAGAACCAGAAGC
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TGATCGCCAACCAGTTCAACAGCGCCATCGGCAAGATCCAGGACAGCCTGAGCAGCACCGCTAGCGCCCTGGGCAAGCTGCAGGACGTGGT
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GAACCAGAACGCCCAGGCCCTGAACACCCTGGTGAAGCAGCTGAGCAGCAACTTCGGCGCCATCAGCAGCGTGCTGAACGACATCCTGAGC
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CGGCTGGACCCTCCCGAGGCCGAGGTGCAGATCGACCGGCTGATCACTGGCCGGCTGCAGAGCCTGCAGACCTACGTGACCCAGCAGCTGA
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TCCGGGCCGCCGAGATTCGGGCCAGCGCCAACCTGGCCGCCACCAAGATGAGCGAGTGCGTGCTGGGCCAGAGCAAGCGGGTGGACTTCTG
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CGGCAAGGGCTACCACCTGATGAGCTTTCCCCAGAGCGCACCCCACGGAGTGGTGTTCCTGCACGTGACCTACGTGCCCGCCCAGGAGAAG
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AACTTCACCACCGCCCCAGCCATCTGCCACGACGGCAAGGCCCACTTTCCCCGGGAGGGCGTGTTCGTGAGCAACGGCACCCACTGGTTCG
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TGACCCAGCGGAACTTCTACGAGCCCCAGATCATCACCACCGACAACACCTTCGTGAGCGGCAACTGCGACGTGGTGATCGGCATCGTGAA
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CAACACCGTGTACGATCCCCTGCAGCCCGAGCTGGACAGCTTCAAGGAGGAGCTGGACAAGTACTTCAAGAATCACACCAGCCCCGACGTG
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GACCTGGGCGACATCAGCGGCATCAACGCCAGCGTGGTGAACATCCAGAAGGAGATCGATCGGCTGAACGAGGTGGCCAAGAACCTGAACG
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AGAGCCTGATCGACCTGCAGGAGCTGGGCAAGTACGAGCAGTACATCAAGTGGCCCTGGTACATCTGGCTGGGCTTCATCGCCGGCCTGAT
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CGCCATCGTGATGGTGACCATCATGCTGTGCTGCATGACCAGCTGCTGCAGCTGCCTGAAGGGCTGTTGCAGCTGCGGCAGCTGCTGCAAG
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TTCGACGAGGACGACAGCGAGCCCGTGCTGAAGGGCGTGAAGCTGCACTACACC</span><span style="background-color: red">TGATAATAG</span><span style="background-color: magenta">GCTGGAGCCTCGGTGGCCTAGCTTCTTGCCCCTTGGGCCTCCCCCCAGCCCCTCCTCCCCTTCCTGCACCCGTACCCCCGTGGTCTTTGAATAAAGTCTGAGTGGGCGGCA</span><span style="background-color: blue">AAAAAAAA</span>
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<span style="background-color: cyan">Cyan: Putative 5’ UTR</span>
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<span style="background-color: green">Green: Start Codon</span>
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<span style="background-color: yellow">Yellow: Signal Peptide</span>
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<span style="background-color: orange">Orange: Spike encoding region</span>
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<span style="background-color: red">Red: Stop codon(s)</span>
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<span style="background-color: magenta">Purple: 3’ UTR</span>
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<span style="background-color: blue">Blue: Start of polyA region (incomplete)</span>
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