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Assemblies-of-putative-SARS-CoV2-spike-encoding-mRNA-sequences-for-vaccines-BNT-162b2-and-mRNA-1273
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Larry Du 2021-03-30 10:24:48 -07:00
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36
sequenced.md
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@ -15,8 +15,7 @@ the rollout of vaccines for COVID-19, these synthetic mRNAs have become broadly
distributed RNA species in numerous human populations. Despite their ubiquity, sequences
are not always available for such RNAs. Standard methods facilitate such sequencing. In this
note, we provide experimental sequence informationfor the RNA components of the initial
[Moderna](https://pubmed.ncbi.nlm.nih.gov/32756549/)and [Pfizer/BioNTech](https://pubmed.ncbi.nlm.nih.gov/33301246/)
COVID-19 vaccines, allowing a working assembly of the former and a confirmation of previously
[Moderna](https://pubmed.ncbi.nlm.nih.gov/32756549/)and [Pfizer/BioNTech](https://pubmed.ncbi.nlm.nih.gov/33301246/) COVID-19 vaccines, allowing a working assembly of the former and a confirmation of previously
reported sequence information for the latter RNA.
Sharing of sequence information for broadly used therapeutics has the benefit of allowing any
@ -74,9 +73,8 @@ ProtoAcknowledgements: Thanks to our colleagues for help and suggestions (Nimit
Emily Greenwald, Lamia Wahba, William Wang, Amisha Kumar, Sameer Sundrani, David
Lipman, Marc Salit, Bijoyita Roy).
### Figure 1: Spike-encoding contig assembled from BioNTech/PfizerBNT-162b
vaccine.
Although the full coding region is included,the nature of the methodology used for
### Figure 1: Spike-encoding contig assembled from BioNTech/PfizerBNT-162b vaccine.
Although the full coding region is included,the nature of the methodology used for
sequencing and assembly is such that the assembled contig could lack some sequence from
the ends of the RNA. Within the assembled sequence, this hypothetical sequence shows a
perfect match to the corresponding sequence from documents available online derived from
@ -91,9 +89,11 @@ This is a partial sequence of the vaccine RNA. Although the full coding region i
assembled contig could lack some sequence from the ends of the RNA.
**Figure 1: Spike-encoding contig assembled from BioNTech/PfizerBNT-162b vaccine.**
<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
<span style="background-color:cyan">GAGAATAAACTAGTATTCTTCTGGTCCCCACAGACTCAGAGAGAACCCGCCACC</span><span style="background-color: green">ATG</span><span style="background-color:yellow">TTCGTGTTCCTGGTGCTGCTGCCTCTGGTGTCCA
GCCAGTGTGTG</span><span style="background-color:orange">AACCTGACCACCAGAACACAGCTGCCTCCAGCCTACACCAACAGCTTTACCAGAGGCGTGTACTACCCCGACAAGGTGTT
CAGATCCAGCGTGCTGCACTCTACCCAGGACCTGTTCCTGCCTTTCTTCAGCAACGTGACCTGGTTCCACGCCATCCACGTGTCCGGCACC
AATGGCACCAAGAGATTCGACAACCCCGTGCTGCCCTTCAACGACGGGGTGTACTTTGCCAGCACCGAGAAGTCCAACATCATCAGAGGCT
GGATCTTCGGCACCACACTGGACAGCAAGACCCAGAGCCTGCTGATCGTGAACAACGCCACCAACGTGGTCATCAAAGTGTGCGAGTTCCA
@ -127,21 +127,32 @@ TCGCCAACCAGTTCAACAGCGCCATCGGCAAGATCCAGGACAGCCTGAGCAGCACAGCAAGCGCCCTGGGAAAGCTGCAG
CCAGAATGCCCAGGCACTGAACACCCTGGTCAAGCAGCTGTCCTCCAACTTCGGCGCCATCAGCTCTGTGCTGAACGATATCCTGAGCAGA
CTGGACCCTCCTGAGGCCGAGGTGCAGATCGACAGACTGATCACAGGCAGACTGCAGAGCCTCCAGACATACGTGACCCAGCAGCTGATCA
GAGCCGCCGAGATTAGAGCCTCTGCCAATCTGGCCGCCACCAAGATGTCTGAGTGTGTGCTGGGCCAGAGCAAGAGAGTGGACTTTTGCGG
CAAGGGCTACCACC</span><span style="background-color: red">TGATGA</span><span style="background-color: magenta">CTCGAGCTGGTACTGCATGCACGCAATGCTAGCTGCCCCTTTCCCGTCCTGGGTACCCCGAGTCTCCCCCGACCTCGGGTCCCAGGTATGCTCCCACCTCCACCTGCCCCACTCACCACCTCTGCTAGTTCCAGACACCTCCCAAGCACGCAGCAATGCAGCTCAAAACGCTTAGCCTAGCCACACCCCCACGGGAAACAGCAGTGATTAACCTTTAGCAATAAACGAAAGTTTAACTAAGCTATACTAACCCCAGGGTTGGTCAATTTCGTGCCAGCCACACCCTGGAGCTAGC</span><span style="background-color:blue">A</blue>
CAAGGGCTACCACC</span><span style="background-color: red">TGATGA</span><span style="background-color: magenta">CTCGAGCTGGTACTGCATGCACGCAATGCTAGCTGCCCCTTTCCCGTCC
TGGGTACCCCGAGTCTCCCCCGAC
CTCGGGTCCCAGGTATGCTCCCACCTCCACCTGCCCCACTCACCACCTCTGCTAGTTCCAGACACCTCCCAAGCACGCAGCAATGCAGCTCAA
AACGCTTAGCCTAGCCACACCCCCACGGGAAACAGCAGTGATTAACCTTTAGCAATAAACGAAAGTTTAACTAAGCTATACTAACCCCAGGGTTGGTCAATTTCGTGCCAGCCACACCCTGGAGCTAGC</span><span style="background-color:blue">A</blue>
<span style="background-color: cyan">Cyan: Putative 5’ UTR</span>
<span style="background-color: green">Green: Start Codon</span>
<span style="background-color: yellow">Yellow: Signal Peptide</span>
<span style="background-color: orange">Orange: Spike encoding region</span>
<span style="background-color: red">Red: Stop codon(s)</span>
<span style="background-color: magenta">Purple: 3’ UTR</span>
<span style="background-color: blue">Blue: Start of polyA region (incomplete)</span>
**Figure 2: Spike-encoding contig assembled from Moderna mRNA-1273 vaccine.**
<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
<span style="background-color: cyan">GGGAAATAAGAGAGAAAAGAAGAGTAAGAAGAAATATAAGACCCCGGCGCCGCCACC</span><span style="background-color: green">ATG</span><span style="background-color: yellow">TTCGTGTTCCTGGTGCTGCTGCCCCTGGTGA
GCAGCCAGTGCGTG</span><span style="background-color: orange">AACCTGACCACCCGGACCCAGCTGCCACCAGCCTACACCAACAGCTTCACCCGGGGCGTCTACTACCCCGACAAGGT
GTTCCGGAGCAGCGTCCTGCACAGCACCCAGGACCTGTTCCTGCCCTTCTTCAGCAACGTGACCTGGTTCCACGCCATCCACGTGAGCGGC
ACCAACGGCACCAAGCGGTTCGACAACCCCGTGCTGCCCTTCAACGACGGCGTGTACTTCGCCAGCACCGAGAAGAGCAACATCATCCGGG
GCTGGATCTTCGGCACCACCCTGGACAGCAAGACCCAGAGCCTGCTGATCGTGAATAACGCCACCAACGTGGTGATCAAGGTGTGCGAGTT
@ -182,13 +193,20 @@ CAACACCGTGTACGATCCCCTGCAGCCCGAGCTGGACAGCTTCAAGGAGGAGCTGGACAAGTACTTCAAGAATCACACCA
GACCTGGGCGACATCAGCGGCATCAACGCCAGCGTGGTGAACATCCAGAAGGAGATCGATCGGCTGAACGAGGTGGCCAAGAACCTGAACG
AGAGCCTGATCGACCTGCAGGAGCTGGGCAAGTACGAGCAGTACATCAAGTGGCCCTGGTACATCTGGCTGGGCTTCATCGCCGGCCTGAT
CGCCATCGTGATGGTGACCATCATGCTGTGCTGCATGACCAGCTGCTGCAGCTGCCTGAAGGGCTGTTGCAGCTGCGGCAGCTGCTGCAAG
TTCGACGAGGACGACAGCGAGCCCGTGCTGAAGGGCGTGAAGCTGCACTACACC</span><span style="background-color: red">TGATAATAG</span><span style="background-color: magenta">GCTGGAGCCTCGGTGGCCTAGCTTCTTGCCCCTTGGGCCTCCCCCCAGCCCCTCCTCCCCTTCCTGCACCCGTACCCCCGTGGTCTTTGAATAAAGTCTGAGTGGGCGGCA</span><span style="background-color: blue">AAAAAAAA</span>
TTCGACGAGGACGACAGCGAGCCCGTGCTGAAGGGCGTGAAGCTGCACTACACC</span><span style="background-color: red">TGATAATAG</span><span style="background-color: magenta">GCTGGAGCCTCGGTGGCCTAGCTTCTTGCCC
CTTGGGCCTCCCCCCAGCCCCTCCTCCCCTTCCTGCACCCGTACCCCCGTGGTCTTTGAATAAAGTCTGAGTGGGCGGCA</span><span style="background-color: blue">AAAAAAAA</span>
<span style="background-color: cyan">Cyan: Putative 5’ UTR</span>
<span style="background-color: green">Green: Start Codon</span>
<span style="background-color: yellow">Yellow: Signal Peptide</span>
<span style="background-color: orange">Orange: Spike encoding region</span>
<span style="background-color: red">Red: Stop codon(s)</span>
<span style="background-color: magenta">Purple: 3’ UTR</span>
<span style="background-color: blue">Blue: Start of polyA region (incomplete)</span>

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style.css
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@ -1,120 +1,3 @@
/*
* CSS for making a resume with pandoc. Inspired by moderncv.
*
* This CSS document is delivered to you under the CC BY-SA 3.0 License.
* https://creativecommons.org/licenses/by-sa/3.0/deed.en_US
*/
/* Whole document */
body {
font-family: "Helvetica Neue", Helvetica, Arial, sans-serif;
width: 800px;
margin: auto;
background: #FFFFFF;
padding: 9px 9px 9px 9px;
font-size: 12px;
}
/* Title of the resume */
h1 {
font-size: 40px;
color: #446fff;
text-align:center;
margin-top: 4px;
margin-bottom:8px;
}
h1:hover {
color: #094fff;
text-shadow: 1px 1px 1px #333;
}
/* Titles of categories */
h2 {
color: #000000;
margin-bottom:3px;
}
h2:hover {
color: #094fff;
text-shadow: 1px 1px 1px #333;
}
/* There is a bar just before each category */
h2:before {
content: "";
display: inline-block;
margin-right:1%;
width: 10%;
height: 10px;
background-color: #0936ff;
}
h3 {
color: #000000;
margin-bottom: 3px;
}
h4 {
margin-bottom: 2px;
}
h5{
color: #989898;
margin-top: 2px;
margin-botton: 3px;
padding: 0px;
}
/* Definitions */
dl{
margin-top: 5px;
margin-bottom: 10px;
}
dt {
float: left;
clear: left;
width: 17%;
margin-bottom: 25px; /*Space out these sections*/
/*font-weight: bold;*/
}
dd {
margin-left: 20%;
}
p {
margin-top:0;
margin-bottom:3px;
}
/* Blockquotes */
blockquote {
margin-top: 2px;
margin-bottom: 2px;
padding: 3px;
text-align: center;
}
ul{
padding-top: 1px;
padding-bottom: 1px;
margin-top: 0px;
padding-left: 4px;
}
li{
margin-top: 2px;
}
/* Links */
a {
text-decoration: none;
color: #001488;
}
a:hover, a:active {
background-color: #0084ff;
color: #FFFFFF;
text-decoration: none;
text-shadow: 1px 1px 1px #333;
}
/* Horizontal separators */
hr {
color: #A6A6A6;
}
* Replace this with a stylesheet to change the appearance of the document
/