Some Basic Biology about mRNA
There are many reasons why someone might fail to learn this basic biology in 7th grade science class. If you are out sick with a virus, you might not learn about how viruses work!
So a bit of remediation, so you can understand this tweet.
But I’ll take you beyond the stuff I learned in 7th grade, and look at exactly what mRNA is in the vaccines and the SARS-CoV-2 virus.
The vax has mRNA for one protein.
— Bob (Moderna #4) Kerns (@BobKerns) June 12, 2022
The virus has mRNA for that one + 28 more.
The vax mRNA is quickly destroyed by the body.
The virus keeps making more complete copies of itself.
This discussion is about the mRNA vaccines. There are other types of vaccine, which I will not discuss further here.
- Protein-based vaccines contain viral proteins for the immune system to recognize.
- Killed-virus vaccines contain the whole virus, killed. These contains the complete set of proteins.
- Attenuated-virus vaccines contain live virus that has been weakened so it does not cause disease. The virus triggers your cells to produce enough viral proteins to trigger immunity.
- Viral vector vaccines contain a live non-disease-causing virus which contains genes for viral proteins from the disease-causing virus. The virus triggers your cells to produce enough viral proteins to trigger immunity.
The mRNA vaccines differ from these in that they contain mRNA for a single protein, which your cell then produces, until the mRNA is destroyed by the cell.
What is a protein?
Proteins are long molecules made up of sequences of amino acids. Proteins are produced in the cells in the ribosomes, according to directions originating in the cell’s DNA.
But the DNA lives in the cell nucleus, and is big and complex and contains many genes. The ribosomes are in the cytoplasm (the stuff inside the cell but outside the nucleus), the cells have a mechanism to copy the information from the DNA, which is then used by the ribosomes.
What is mRNA?
mRNA (Messenger RNA) is the link between a cell’s DNA and creating proteins.
DNA consists of sequences of 4 subunits, abbreviated G, T, A, and C. DNA has two paired strands. If one strand has a G, the other has a T, and vise versa. Likewise for A and C. These make up the “alphabet” of genetics. They function in groups of three; each group of 3 codes for a specific amino acid to be used in constructing the protein.
RNA usually consists of one strand (mRNA always does). Rather than T, RNA uses U, but otherwise it functions the same, in groups of three.
To construct a protein, the first step is to transcribe the DNA into RNA, so G becomes U, T becomes G, A becomes C, and C becomes A in the RNA.
After a bit of editing, this is transported to the ribosomes—the protein factories of the cell. This is the mRNA.
Each mRNA has some extra stuff at the begining and end that I’ll skip to keep things simple. I’m also going to skip to the amino acids coded by each group of 3. This makes the sequences $\frac{1}{3}$ as long. The letters for the amino acids are:
A R N D B C Q E Z G H I L K M F P S T W Y V
Or you can see this textual table.
How does a virus work?
A virus is a small particle containing some genetic material, some structural proteins, and some lipids (oils). It gains entry to cells, where the genetic material and the initial proteins work together with the cell’s own machinery to make new copies of the virus.
There are different types of virus, using different types of genetic matieral—single or double stranded, DNA or RNA.
The RNA viruses can be positive sense or negative sense. Positive sense viruses have RNA that directly codes for proteins, as mRNA. Negative sense viruses have RNA that has to be re-transcribed to positive sense mRNA to function.
SARS-Cov-2 (the virus for COVID-19) is a positive-sense virus.
The genetic material codes the additional proteins the virus needs, both as part of the virus particles and to replicate. The newly-formed virus particles then escape from the cell, usually killing the cell in the process. SARS-Cov-2, however, does not kill the cell, but rather emits viruses by budding them off through the cell membrane.
In the case of positive-sense RNA viruses, the genetic material from the virus cannot become part of the host cell genome, as can happen with some DNA viruses.
So what is in the mRNA vaccines
I’ve taken the data from here. These were sequenced by people outside the companies (and in the case of the BioNTech/Pfizer vaccine, confirmed by the company).
Here’s the amino acid sequence for the BioNTech/Pfizer BNT-162b2 vaccine
MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHS
TQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNI
IRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNK
SWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGY
FKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLT
PGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETK
CTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASV
YAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSF
VIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYN
YLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPT
NGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTG
VLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITP
GTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCL
IGAEHVNNSYECDIPIGAGICASYQTQTNSPRRARSVASQSIIAYTMSLG
AENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECS
NLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGF
NFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLI
CAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAM
QMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQD
VVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGR
LQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLM
SFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGT
HWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKE
ELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDL
QELGKYEQYIKWPWYIWLGFIAGLIAIVMVTIMLCCMTSCCSCLKGCCSC
GSCCKFDEDDSEPVLKGVKLHYT
Here it is for the Moderna mRNA-1273 vaccine
MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHS
TQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNI
IRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNK
SWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGY
FKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLT
PGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETK
CTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASV
YAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSF
VIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYN
YLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPT
NGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTG
VLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITP
GTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCL
IGAEHVNNSYECDIPIGAGICASYQTQTNSPRRARSVASQSIIAYTMSLG
AENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECS
NLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGF
NFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLI
CAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAM
QMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQD
VVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGR
LQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLM
SFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGT
HWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKE
ELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDL
QELGKYEQYIKWPWYIWLGFIAGLIAIVMVTIMLCCMTSCCSCLKGCCSC
GSCCKFDEDDSEPVLKGVKLHYT
Both are 1273 amino acids long—the Moderna vaccine is named for the length.
Both are exactly the same proteins.
What mRNA is in the virus?
There are a total of 10 genes that code a total of 29 different proteins. Of these 29 proteins, four are structural, making up part of the virus particles themselves. These are:
- Envelope (E)
- Membrane (M)
- Nucleocapsid (N)
- Spike (S)
The other proteins are needed for replication and interaction with the host cell, but do not become part of the virus.
Here is the spike protein from the final version of the virus collected in December 2019 and first sequenced in January of 2020 (2nd update):
MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHS
TQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNI
IRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNK
SWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGY
FKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLT
PGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETK
CTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASV
YAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSF
VIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYN
YLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPT
NGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTG
VLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITP
GTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCL
IGAEHVNNSYECDIPIGAGICASYQTQTNSPRRARSVASQSIIAYTMSLG
AENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECS
NLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGF
NFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLI
CAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAM
QMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQD
VVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDKVEAEVQIDRLITGR
LQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLM
SFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGT
HWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKE
ELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDL
QELGKYEQYIKWPWYIWLGFIAGLIAIVMVTIMLCCMTSCCSCLKGCCSC
GSCCKFDEDDSEPVLKGVKLHYT
Individual variants have mutations that can make alter how well the spike protein works to enter cells. Despite small differences, these are variants of the same virus.
Here’s a map of where the proteins are coded:
Here’s a more detailed view:
How long does mRNA persist?
In mammalian cells, between hours and days. Longer-lived mRNA can be transcribed into more protein molecules, but is slower to turn on and off.
It is important that mRNA be destroyed, so genes can be turned on and off to maintain the correct level of each protein.
Since mRNA is continuously created by active genes, it would otherwise accumulate. Life would be impossible.
mRNA vaccines begin producing protein shortly after injection. This production quicly declines as the mRNA is destroyed. The viral proteins produced then activate the immune system, before they, too, are destroyed.
How long does a virus produce viruses and virus proteins?
Each virus, once it gains entry to a cell, produces multiple copies. If it produces 10 on average, after one generation we’d have 10, after 2, 100, and so on. 6 generations would give 1,000,000 virus particles.
The number of viruses each infected cell produces is referred to as the burst size (because most viruses release them all at once when the cell dies). For SARS-CoV-2, the effective burst size (even though it doesn’t kill the cell) is estimated to be at least 10.
This obviously cannot continue forever. One of two things happens:
- The host organism dies.
- The immune system gets ramped up and starts killing viruses and infected cells.
If the second, the viral growth is stopped or slowed. For most viruses, the virus can be completely eliminated, but there are many which persist and even become lifelong.
But without having seen the viral proteins before, it takes considerable time for the immune system to ramp up, and so the first phase of an infection is characterized by exponential growth of the viral population.
More details
If you are interested, here are more details:
How do the vaccine proteins differ from the original virus?
Both vaccines code for the same protein. This substitutes for two Prolines (see just before 990) to lock the Receptor Binding Domain (RBD) in the active position, to ensure the immune system can see it.
The colons indicate matches.
10 20 30 40 50 60 70 80 90 100 110 120
Vax MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIV
::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
Virus MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIV
10 20 30 40 50 60 70 80 90 100 110 120
130 140 150 160 170 180 190 200 210 220 230 240
Vax NNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQT
::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
Virus NNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQT
130 140 150 160 170 180 190 200 210 220 230 240
250 260 270 280 290 300 310 320 330 340 350 360
Vax LLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISN
::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
Virus LLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISN
250 260 270 280 290 300 310 320 330 340 350 360
370 380 390 400 410 420 430 440 450 460 470 480
Vax CVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPC
::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
Virus CVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPC
370 380 390 400 410 420 430 440 450 460 470 480
490 500 510 520 530 540 550 560 570 580 590 600
Vax NGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITP
::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
Virus NGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITP
490 500 510 520 530 540 550 560 570 580 590 600
610 620 630 640 650 660 670 680 690 700 710 720
Vax GTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPRRARSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTI
::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
Virus GTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPRRARSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTI
610 620 630 640 650 660 670 680 690 700 710 720
730 740 750 760 770 780 790 800 810 820 830 840
Vax SVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDC
::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
Virus SVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDC
730 740 750 760 770 780 790 800 810 820 830 840
850 860 870 880 890 900 910 920 930 940 950 960
Vax LGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALN
::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
Virus LGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALN
850 860 870 880 890 900 910 920 930 940 950 960
970 980 990 1000 1010 1020 1030 1040 1050 1060 1070 1080
Vax TLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPA
::::::::::::::::::::::::: :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
Virus TLVKQLSSNFGAISSVLNDILSRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPA
970 980 990 1000 1010 1020 1030 1040 1050 1060 1070 1080
1090 1100 1110 1120 1130 1140 1150 1160 1170 1180 1190 1200
Vax ICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDL
::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
Virus ICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDL
1090 1100 1110 1120 1130 1140 1150 1160 1170 1180 1190 1200
1210 1220 1230 1240 1250 1260 1270
Vax QELGKYEQYIKWPWYIWLGFIAGLIAIVMVTIMLCCMTSCCSCLKGCCSCGSCCKFDEDDSEPVLKGVKLHYT
:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
Virus QELGKYEQYIKWPWYIWLGFIAGLIAIVMVTIMLCCMTSCCSCLKGCCSCGSCCKFDEDDSEPVLKGVKLHYT
1210 1220 1230 1240 1250 1260 1270
How do the vaccines differ?
Both vaccines code for the same S-Protein. However, their mRNA sequences are different. Each is tuned to work best with their delivery method—they use different techniques to preserve the mRNA and get it into the cells.
Their mRNA differ both in the begin/end parts outside the region that codes for the protein, and in exactly which 3-letter RNA codes are used to code for each amino acid in the protein. (Many amino acids can be coded by more than one sequence.)
Here is just the portion that codes for the protein:
Modern ATGTTCGTGTTCCTGGTGCTGCTGCCCCTGGTGAGCAGCCAGTGCGTGAACCTGACCACCCGGACCCAGCTGCCACCAGCCTACACCAACAGCTTCACCCGGGGCGTCTACTACCCCGAC
:::::::::::::::::::::::::: :::::: ::::::::: ::::::::::::::: : :: :::::::: :::::::::::::::::::: ::: : ::::: ::::::::::::
Pfizer ATGTTCGTGTTCCTGGTGCTGCTGCCTCTGGTGTCCAGCCAGTGTGTGAACCTGACCACCAGAACACAGCTGCCTCCAGCCTACACCAACAGCTTTACCAGAGGCGTGTACTACCCCGAC
10 20 30 40 50 60 70 80 90 100 110 120
130 140 150 160 170 180 190 200 210 220 230 240
Modern AAGGTGTTCCGGAGCAGCGTCCTGCACAGCACCCAGGACCTGTTCCTGCCCTTCTTCAGCAACGTGACCTGGTTCCACGCCATCCACGTGAGCGGCACCAACGGCACCAAGCGGTTCGAC
::::::::: : :::::: :::::: :::::::::::::::::::: ::::::::::::::::::::::::::::::::::::::: ::::::::: ::::::::: : ::::::
Pfizer AAGGTGTTCAGATCCAGCGTGCTGCACTCTACCCAGGACCTGTTCCTGCCTTTCTTCAGCAACGTGACCTGGTTCCACGCCATCCACGTGTCCGGCACCAATGGCACCAAGAGATTCGAC
130 140 150 160 170 180 190 200 210 220 230 240
250 260 270 280 290 300 310 320 330 340 350 360
Modern AACCCCGTGCTGCCCTTCAACGACGGCGTGTACTTCGCCAGCACCGAGAAGAGCAACATCATCCGGGGCTGGATCTTCGGCACCACCCTGGACAGCAAGACCCAGAGCCTGCTGATCGTG
:::::::::::::::::::::::::: :::::::: ::::::::::::::: :::::::::: : :::::::::::::::::::: :::::::::::::::::::::::::::::::::
Pfizer AACCCCGTGCTGCCCTTCAACGACGGGGTGTACTTTGCCAGCACCGAGAAGTCCAACATCATCAGAGGCTGGATCTTCGGCACCACACTGGACAGCAAGACCCAGAGCCTGCTGATCGTG
250 260 270 280 290 300 310 320 330 340 350 360
370 380 390 400 410 420 430 440 450 460 470 480
Modern AATAACGCCACCAACGTGGTGATCAAGGTGTGCGAGTTCCAGTTCTGCAACGACCCCTTCCTGGGCGTGTACTACCACAAGAACAACAAGAGCTGGATGGAGAGCGAGTTCCGGGTGTAC
:: ::::::::::::::::: ::::: ::::::::::::::::::::::::::::::::::::::::: :::::::::::::::::::::::::::::::: ::::::::::::::::::
Pfizer AACAACGCCACCAACGTGGTCATCAAAGTGTGCGAGTTCCAGTTCTGCAACGACCCCTTCCTGGGCGTCTACTACCACAAGAACAACAAGAGCTGGATGGAAAGCGAGTTCCGGGTGTAC
370 380 390 400 410 420 430 440 450 460 470 480
490 500 510 520 530 540 550 560 570 580 590 600
Modern AGCAGCGCCAACAACTGCACCTTCGAGTACGTGAGCCAGCCCTTCCTGATGGACCTGGAGGGCAAGCAGGGCAACTTCAAGAACCTGCGGGAGTTCGTGTTCAAGAACATCGACGGCTAC
::::::::::::::::::::::::::::::::: :::::: ::::::::::::::::: ::::::::::::::::::::::::::::: ::::::::::: ::::::::::::::::::
Pfizer AGCAGCGCCAACAACTGCACCTTCGAGTACGTGTCCCAGCCTTTCCTGATGGACCTGGAAGGCAAGCAGGGCAACTTCAAGAACCTGCGCGAGTTCGTGTTTAAGAACATCGACGGCTAC
490 500 510 520 530 540 550 560 570 580 590 600
610 620 630 640 650 660 670 680 690 700 710 720
Modern TTCAAGATCTACAGCAAGCACACCCCAATCAACCTGGTGCGGGATCTGCCCCAGGGCTTCTCAGCCCTGGAGCCCCTGGTGGACCTGCCCATCGGCATCAACATCACCCGGTTCCAGACC
:::::::::::::::::::::::::: :::::::: :::::::::::::: ::::::::::: :: ::::: ::::::::::: ::::::::::::::::::::::::::::: :::::
Pfizer TTCAAGATCTACAGCAAGCACACCCCTATCAACCTCGTGCGGGATCTGCCTCAGGGCTTCTCTGCTCTGGAACCCCTGGTGGATCTGCCCATCGGCATCAACATCACCCGGTTTCAGACA
610 620 630 640 650 660 670 680 690 700 710 720
730 740 750 760 770 780 790 800 810 820 830 840
Modern CTGCTGGCCCTGCACCGGAGCTACCTGACCCCAGGCGACAGCAGCAGCGGGTGGACAGCAGGCGCGGCTGCTTACTACGTGGGCTACCTGCAGCCCCGGACCTTCCTGCTGAAGTACAAC
::::::::::::::: : ::::::::::: :: ::::: ::::::::::: :::::::: :: :: :: :::::::: ::::::::::::::::: : :::::::::::::::::::::
Pfizer CTGCTGGCCCTGCACAGAAGCTACCTGACACCTGGCGATAGCAGCAGCGGATGGACAGCTGGTGCCGCCGCTTACTATGTGGGCTACCTGCAGCCTAGAACCTTCCTGCTGAAGTACAAC
730 740 750 760 770 780 790 800 810 820 830 840
850 860 870 880 890 900 910 920 930 940 950 960
Modern GAGAACGGCACCATCACCGACGCCGTGGACTGCGCCCTGGACCCTCTGAGCGAGACCAAGTGCACCCTGAAGAGCTTCACCGTGGAGAAGGGCATCTACCAGACCAGCAACTTCCGGGTG
::::::::::::::::::::::::::::: :: :: ::::: :::::::::::::: ::::::::::::::: :::::::::::: :::::::::::::::::::::::::::::::::
Pfizer GAGAACGGCACCATCACCGACGCCGTGGATTGTGCTCTGGATCCTCTGAGCGAGACAAAGTGCACCCTGAAGTCCTTCACCGTGGAAAAGGGCATCTACCAGACCAGCAACTTCCGGGTG
850 860 870 880 890 900 910 920 930 940 950 960
970 980 990 1000 1010 1020 1030 1040 1050 1060 1070 1080
Modern CAGCCCACCGAGAGCATCGTGCGGTTCCCCAACATCACCAACCTGTGCCCCTTCGGCGAGGTGTTCAACGCCACCCGGTTCGCCAGCGTGTACGCCTGGAACCGGAAGCGGATCAGCAAC
::::::::::: :::::::::::::::::: :::::::: :::::::::::::::::::::::::: :::::: : :::::: ::::::::::::::::::::::::::::::::
Pfizer CAGCCCACCGAATCCATCGTGCGGTTCCCCAATATCACCAATCTGTGCCCCTTCGGCGAGGTGTTCAATGCCACCAGATTCGCCTCTGTGTACGCCTGGAACCGGAAGCGGATCAGCAAT
970 980 990 1000 1010 1020 1030 1040 1050 1060 1070 1080
1090 1100 1110 1120 1130 1140 1150 1160 1170 1180 1190 1200
Modern TGCGTGGCCGACTACAGCGTGCTGTACAACAGCGCCAGCTTCAGCACCTTCAAGTGCTACGGCGTGAGCCCCACCAAGCTGAACGACCTGTGCTTCACCAACGTGTACGCCGACAGCTTC
::::::::::::::: ::::::::::::: :::::::::::::::::::::::::::::::::: ::: :::::::::::::::::::::::::: :::::::::::::::::::::
Pfizer TGCGTGGCCGACTACTCCGTGCTGTACAACTCCGCCAGCTTCAGCACCTTCAAGTGCTACGGCGTGTCCCCTACCAAGCTGAACGACCTGTGCTTCACAAACGTGTACGCCGACAGCTTC
1090 1100 1110 1120 1130 1140 1150 1160 1170 1180 1190 1200
1210 1220 1230 1240 1250 1260 1270 1280 1290 1300 1310 1320
Modern GTGATCCGTGGCGACGAGGTGCGGCAGATCGCACCCGGCCAGACAGGCAAGATCGCCGACTACAACTACAAGCTGCCCGACGACTTCACCGGCTGCGTGATCGCCTGGAACAGCAACAAC
:::::::: :: :: :: ::::::::::: :: :: :: :::::::::::::::::::::::::::::::::::::::::::::::::::::::: ::::: ::::::::::::::::::
Pfizer GTGATCCGGGGAGATGAAGTGCGGCAGATTGCCCCTGGACAGACAGGCAAGATCGCCGACTACAACTACAAGCTGCCCGACGACTTCACCGGCTGTGTGATTGCCTGGAACAGCAACAAC
1210 1220 1230 1240 1250 1260 1270 1280 1290 1300 1310 1320
1330 1340 1350 1360 1370 1380 1390 1400 1410 1420 1430 1440
Modern CTCGACAGCAAGGTGGGCGGCAACTACAACTACCTGTACCGGCTGTTCCGGAAGAGCAACCTGAAGCCCTTCGAGCGGGACATCAGCACCGAGATCTACCAAGCCGGCTCCACCCCTTGC
:: ::: ::: :: :::::::::::::: :::::::::::::::::::::::: ::: :::::::::::::::::::::::: :::::::::::: :: :::::: :::::::::
Pfizer CTGGACTCCAAAGTCGGCGGCAACTACAATTACCTGTACCGGCTGTTCCGGAAGTCCAATCTGAAGCCCTTCGAGCGGGACATCTCCACCGAGATCTATCAGGCCGGCAGCACCCCTTGT
1330 1340 1350 1360 1370 1380 1390 1400 1410 1420 1430 1440
1450 1460 1470 1480 1490 1500 1510 1520 1530 1540 1550 1560
Modern AACGGCGTGGAGGGCTTCAACTGCTACTTCCCTCTGCAGAGCTACGGCTTCCAGCCCACCAACGGCGTGGGCTACCAGCCCTACCGGGTGGTGGTGCTGAGCTTCGAGCTGCTGCACGCC
::::::::::: :::::::::::::::::::: :::::: ::::::::: :::::::: :: ::::::::::: ::::::::: : :::::::::::::::::::: :::::::: :::
Pfizer AACGGCGTGGAAGGCTTCAACTGCTACTTCCCACTGCAGTCCTACGGCTTTCAGCCCACAAATGGCGTGGGCTATCAGCCCTACAGAGTGGTGGTGCTGAGCTTCGAACTGCTGCATGCC
1450 1460 1470 1480 1490 1500 1510 1520 1530 1540 1550 1560
1570 1580 1590 1600 1610 1620 1630 1640 1650 1660 1670 1680
Modern CCAGCCACCGTGTGTGGCCCCAAGAAGAGCACCAACCTGGTGAAGAACAAGTGCGTGAACTTCAACTTCAACGGCCTTACCGGCACCGGCGTGCTGACCGAGAGCAACAAGAAATTCCTG
:: ::::: ::::: ::::: ::::: :::::::: :: ::::::::::: :::::::::::::::::::::::::: :::::::::::::::::::: :::::::::::::: ::::::
Pfizer CCTGCCACAGTGTGCGGCCCTAAGAAAAGCACCAATCTCGTGAAGAACAAATGCGTGAACTTCAACTTCAACGGCCTGACCGGCACCGGCGTGCTGACAGAGAGCAACAAGAAGTTCCTG
1570 1580 1590 1600 1610 1620 1630 1640 1650 1660 1670 1680
1690 1700 1710 1720 1730 1740 1750 1760 1770 1780 1790 1800
Modern CCCTTTCAGCAGTTCGGCCGGGACATCGCCGACACCACCGACGCTGTGCGGGATCCCCAGACCCTGGAGATCCTGGACATCACCCCTTGCAGCTTCGGCGGCGTGAGCGTGATCACCCCA
:: :: :::::::: :::::::: :::::::: ::::: ::::: :: : ::::::::::: ::::: :::::::::::::::::::::::::::::::: ::: :::::::::::
Pfizer CCATTCCAGCAGTTTGGCCGGGATATCGCCGATACCACAGACGCCGTTAGAGATCCCCAGACACTGGAAATCCTGGACATCACCCCTTGCAGCTTCGGCGGAGTGTCTGTGATCACCCCT
1690 1700 1710 1720 1730 1740 1750 1760 1770 1780 1790 1800
1810 1820 1830 1840 1850 1860 1870 1880 1890 1900 1910 1920
Modern GGCACCAACACCAGCAACCAGGTGGCCGTGCTGTACCAGGACGTGAACTGCACCGAGGTGCCCGTGGCCATCCACGCCGACCAGCTGACACCCACCTGGCGGGTCTACAGCACCGGCAGC
::::::::::::::::: :::::::: ::::::::::::::::::::::: ::::: :::::::::::::: :::::::: ::::::::::: :: :::::::: ::: ::::::::::
Pfizer GGCACCAACACCAGCAATCAGGTGGCAGTGCTGTACCAGGACGTGAACTGTACCGAAGTGCCCGTGGCCATTCACGCCGATCAGCTGACACCTACATGGCGGGTGTACTCCACCGGCAGC
1810 1820 1830 1840 1850 1860 1870 1880 1890 1900 1910 1920
1930 1940 1950 1960 1970 1980 1990 2000 2010 2020 2030 2040
Modern AACGTGTTCCAGACCCGGGCCGGTTGCCTGATCGGCGCCGAGCACGTGAACAACAGCTACGAGTGCGACATCCCCATCGGCGCCGGCATCTGTGCCAGCTACCAGACCCAGACCAATTCA
:: ::::: :::::: : ::::: :: :::::::: ::::::::::::::::: ::::::::::::::::::::::::::::: :: ::::: :::::::::::::: ::::: ::
Pfizer AATGTGTTTCAGACCAGAGCCGGCTGTCTGATCGGAGCCGAGCACGTGAACAATAGCTACGAGTGCGACATCCCCATCGGCGCTGGAATCTGCGCCAGCTACCAGACACAGACAAACAGC
1930 1940 1950 1960 1970 1980 1990 2000 2010 2020 2030 2040
2050 2060 2070 2080 2090 2100 2110 2120 2130 2140 2150 2160
Modern CCCCGGAGGGCAAGGAGCGTGGCCAGCCAGAGCATCATCGCCTACACCATGAGCCTGGGCGCCGAGAACAGCGTGGCCTACAGCAACAACAGCATCGCCATCCCCACCAACTTCACCATC
:: ::::: :: :: ::::::::::::::::::::::: :::::::: ::: ::::::::::::::::::::::::::: ::::::: ::::: :::::::::::::::::::::
Pfizer CCTCGGAGAGCCAGAAGCGTGGCCAGCCAGAGCATCATTGCCTACACAATGTCTCTGGGCGCCGAGAACAGCGTGGCCTACTCCAACAACTCTATCGCTATCCCCACCAACTTCACCATC
2050 2060 2070 2080 2090 2100 2110 2120 2130 2140 2150 2160
2170 2180 2190 2200 2210 2220 2230 2240 2250 2260 2270 2280
Modern AGCGTGACCACCGAGATTCTGCCCGTGAGCATGACCAAGACCAGCGTGGACTGCACCATGTACATCTGCGGCGACAGCACCGAGTGCAGCAACCTGCTGCTGCAGTACGGCAGCTTCTGC
::::::::::: ::::: ::::: ::: ::::::::::::::::::::::::::::::::::::::::::::: :::::::::: :::::::::::::::::::::::::::::::
Pfizer AGCGTGACCACAGAGATCCTGCCTGTGTCCATGACCAAGACCAGCGTGGACTGCACCATGTACATCTGCGGCGATTCCACCGAGTGCTCCAACCTGCTGCTGCAGTACGGCAGCTTCTGC
2170 2180 2190 2200 2210 2220 2230 2240 2250 2260 2270 2280
2290 2300 2310 2320 2330 2340 2350 2360 2370 2380 2390 2400
Modern ACCCAGCTGAACCGGGCCCTGACCGGCATCGCCGTGGAGCAGGACAAGAACACCCAGGAGGTGTTCGCCCAGGTGAAGCAGATCTACAAGACCCCTCCCATCAAGGACTTCGGCGGCTTC
::::::::::: : :::::::: :: ::::::::::: ::::::::::::::::: :::::::::::::: :::::::::::::::::::::::::: :::::::::::::::::::::
Pfizer ACCCAGCTGAATAGAGCCCTGACAGGGATCGCCGTGGAACAGGACAAGAACACCCAAGAGGTGTTCGCCCAAGTGAAGCAGATCTACAAGACCCCTCCTATCAAGGACTTCGGCGGCTTC
2290 2300 2310 2320 2330 2340 2350 2360 2370 2380 2390 2400
2410 2420 2430 2440 2450 2460 2470 2480 2490 2500 2510 2520
Modern AACTTCAGCCAGATCCTGCCCGACCCCAGCAAGCCCAGCAAGCGGAGCTTCATCGAGGACCTGCTGTTCAACAAGGTGACCCTAGCCGACGCCGGCTTCATCAAGCAGTACGGCGACTGC
:: ::::::::::: :::::::: :: ::::::::::::::::::::::::::::::::::::::::::::::: ::::: :: :::::::::::::::::::::::::: ::::: ::
Pfizer AATTTCAGCCAGATTCTGCCCGATCCTAGCAAGCCCAGCAAGCGGAGCTTCATCGAGGACCTGCTGTTCAACAAAGTGACACTGGCCGACGCCGGCTTCATCAAGCAGTATGGCGATTGT
2410 2420 2430 2440 2450 2460 2470 2480 2490 2500 2510 2520
2530 2540 2550 2560 2570 2580 2590 2600 2610 2620 2630 2640
Modern CTCGGCGACATAGCCGCCCGGGACCTGATCTGCGCCCAGAAGTTCAACGGCCTGACCGTGCTGCCTCCCCTGCTGACCGACGAGATGATCGCCCAGTACACCAGCGCCCTGTTAGCCGGA
:: :::::::: :::::: :::: ::::: :::::::::::::: ::::: ::::: ::::::::::: ::::::::::: :::::::::::::::::::: :::::: : :::::
Pfizer CTGGGCGACATTGCCGCCAGGGATCTGATTTGCGCCCAGAAGTTTAACGGACTGACAGTGCTGCCTCCTCTGCTGACCGATGAGATGATCGCCCAGTACACATCTGCCCTGCTGGCCGGC
2530 2540 2550 2560 2570 2580 2590 2600 2610 2620 2630 2640
2650 2660 2670 2680 2690 2700 2710 2720 2730 2740 2750 2760
Modern ACCATCACCAGCGGCTGGACTTTCGGCGCTGGAGCCGCTCTGCAGATCCCCTTCGCCATGCAGATGGCCTACCGGTTCAACGGCATCGGCGTGACCCAGAACGTGCTGTACGAGAACCAG
:: ::::: ::::::::::: :: :: :: :: :::::::::::::::::::: :: :::::::::::::::::::::::::::::::: ::::::::::: ::::::::::::::::::
Pfizer ACAATCACAAGCGGCTGGACATTTGGAGCAGGCGCCGCTCTGCAGATCCCCTTTGCTATGCAGATGGCCTACCGGTTCAACGGCATCGGAGTGACCCAGAATGTGCTGTACGAGAACCAG
2650 2660 2670 2680 2690 2700 2710 2720 2730 2740 2750 2760
2770 2780 2790 2800 2810 2820 2830 2840 2850 2860 2870 2880
Modern AAGCTGATCGCCAACCAGTTCAACAGCGCCATCGGCAAGATCCAGGACAGCCTGAGCAGCACCGCTAGCGCCCTGGGCAAGCTGCAGGACGTGGTGAACCAGAACGCCCAGGCCCTGAAC
:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: :: ::::::::::: ::::::::::::::::: :::::::: :::::::: ::::::
Pfizer AAGCTGATCGCCAACCAGTTCAACAGCGCCATCGGCAAGATCCAGGACAGCCTGAGCAGCACAGCAAGCGCCCTGGGAAAGCTGCAGGACGTGGTCAACCAGAATGCCCAGGCACTGAAC
2770 2780 2790 2800 2810 2820 2830 2840 2850 2860 2870 2880
2890 2900 2910 2920 2930 2940 2950 2960 2970 2980 2990 3000
Modern ACCCTGGTGAAGCAGCTGAGCAGCAACTTCGGCGCCATCAGCAGCGTGCTGAACGACATCCTGAGCCGGCTGGACCCTCCCGAGGCCGAGGTGCAGATCGACCGGCTGATCACTGGCCGG
:::::::: ::::::::: : ::::::::::::::::::: ::::::::::: ::::::::: : ::::::::::: ::::::::::::::::::::: : :::::::: ::: :
Pfizer ACCCTGGTCAAGCAGCTGTCCTCCAACTTCGGCGCCATCAGCTCTGTGCTGAACGATATCCTGAGCAGACTGGACCCTCCTGAGGCCGAGGTGCAGATCGACAGACTGATCACAGGCAGA
2890 2900 2910 2920 2930 2940 2950 2960 2970 2980 2990 3000
3010 3020 3030 3040 3050 3060 3070 3080 3090 3100 3110 3120
Modern CTGCAGAGCCTGCAGACCTACGTGACCCAGCAGCTGATCCGGGCCGCCGAGATTCGGGCCAGCGCCAACCTGGCCGCCACCAAGATGAGCGAGTGCGTGCTGGGCCAGAGCAAGCGGGTG
::::::::::: ::::: ::::::::::::::::::::: : :::::::::::: : ::: ::::: :::::::::::::::::: ::::: :::::::::::::::::: : :::
Pfizer CTGCAGAGCCTCCAGACATACGTGACCCAGCAGCTGATCAGAGCCGCCGAGATTAGAGCCTCTGCCAATCTGGCCGCCACCAAGATGTCTGAGTGTGTGCTGGGCCAGAGCAAGAGAGTG
3010 3020 3030 3040 3050 3060 3070 3080 3090 3100 3110 3120
3130 3140 3150 3160 3170 3180 3190 3200 3210 3220 3230 3240
Modern GACTTCTGCGGCAAGGGCTACCACCTGATGAGCTTTCCCCAGAGCGCACCCCACGGAGTGGTGTTCCTGCACGTGACCTACGTGCCCGCCCAGGAGAAGAACTTCACCACCGCCCCAGCC
::::: ::::::::::::::::::::::::::::: :: ::: :: :: ::::: :::::::: ::::::::::: :: :::::::: :: :::::::: ::::::::::: ::::::
Pfizer GACTTTTGCGGCAAGGGCTACCACCTGATGAGCTTCCCTCAGTCTGCCCCTCACGGCGTGGTGTTTCTGCACGTGACATATGTGCCCGCTCAAGAGAAGAATTTCACCACCGCTCCAGCC
3130 3140 3150 3160 3170 3180 3190 3200 3210 3220 3230 3240
3250 3260 3270 3280 3290 3300 3310 3320 3330 3340 3350 3360
Modern ATCTGCCACGACGGCAAGGCCCACTTTCCCCGGGAGGGCGTGTTCGTGAGCAACGGCACCCACTGGTTCGTGACCCAGCGGAACTTCTACGAGCCCCAGATCATCACCACCGACAACACC
::::::::::::::::: ::::::::::: : :: :::::::::::: :::::::::::: ::::::::::: :::::::::::::::::::::::::::::::::::::::::::::
Pfizer ATCTGCCACGACGGCAAAGCCCACTTTCCTAGAGAAGGCGTGTTCGTGTCCAACGGCACCCATTGGTTCGTGACACAGCGGAACTTCTACGAGCCCCAGATCATCACCACCGACAACACC
3250 3260 3270 3280 3290 3300 3310 3320 3330 3340 3350 3360
3370 3380 3390 3400 3410 3420 3430 3440 3450 3460 3470 3480
Modern TTCGTGAGCGGCAACTGCGACGTGGTGATCGGCATCGTGAACAACACCGTGTACGATCCCCTGCAGCCCGAGCTGGACAGCTTCAAGGAGGAGCTGGACAAGTACTTCAAGAATCACACC
:::::: :::::::::::::: ::::::::::: :::::::: ::::::::::: :: :::::::::::::::::::::::::: ::::: :::::::::::::: ::::: :::::
Pfizer TTCGTGTCTGGCAACTGCGACGTCGTGATCGGCATTGTGAACAATACCGTGTACGACCCTCTGCAGCCCGAGCTGGACAGCTTCAAAGAGGAACTGGACAAGTACTTTAAGAACCACACA
3370 3380 3390 3400 3410 3420 3430 3440 3450 3460 3470 3480
3490 3500 3510 3520 3530 3540 3550 3560 3570 3580 3590 3600
Modern AGCCCCGACGTGGACCTGGGCGACATCAGCGGCATCAACGCCAGCGTGGTGAACATCCAGAAGGAGATCGATCGGCTGAACGAGGTGGCCAAGAACCTGAACGAGAGCCTGATCGACCTG
::::::::::::::::::::::: :::::::: ::::: :::::::: :::::::::::::: :::::::: ::::::::::::::::::::::: ::::::::::::::::::::::::
Pfizer AGCCCCGACGTGGACCTGGGCGATATCAGCGGAATCAATGCCAGCGTCGTGAACATCCAGAAAGAGATCGACCGGCTGAACGAGGTGGCCAAGAATCTGAACGAGAGCCTGATCGACCTG
3490 3500 3510 3520 3530 3540 3550 3560 3570 3580 3590 3600
3610 3620 3630 3640 3650 3660 3670 3680 3690 3700 3710 3720
Modern CAGGAGCTGGGCAAGTACGAGCAGTACATCAAGTGGCCCTGGTACATCTGGCTGGGCTTCATCGCCGGCCTGATCGCCATCGTGATGGTGACCATCATGCTGTGCTGCATGACCAGCTGC
:: :: ::::: ::::::::::::::::::::::::::::::::::::::::::::::: :::::::: ::::: :::::::::::::: :: ::::::::::: :::::::::::::::
Pfizer CAAGAACTGGGGAAGTACGAGCAGTACATCAAGTGGCCCTGGTACATCTGGCTGGGCTTTATCGCCGGACTGATTGCCATCGTGATGGTCACAATCATGCTGTGTTGCATGACCAGCTGC
3610 3620 3630 3640 3650 3660 3670 3680 3690 3700 3710 3720
3730 3740 3750 3760 3770 3780 3790 3800 3810 3820
Modern TGCAGCTGCCTGAAGGGCTGTTGCAGCTGCGGCAGCTGCTGCAAGTTCGACGAGGACGACAGCGAGCCCGTGCTGAAGGGCGTGAAGCTGCACTACACCTGATAA
:: :::::::::::::::::::: ::::: ::::::::::::::::::::::::::::: ::::::::::::::::::::::: ::::::::::: :::: :
Pfizer TGTAGCTGCCTGAAGGGCTGTTGTAGCTGTGGCAGCTGCTGCAAGTTCGACGAGGACGATTCTGAGCCCGTGCTGAAGGGCGTGAAACTGCACTACACATGATGA
So the vaccines are a bit different from the virus?
Not nearly as different as the virus is from itself!
Here’s the Spike protein from one from January 2022. This is an Omicron / BA.1.1 variant collected in Upper Austria.
10 20 30 40 50 60 70 80 90 100 110
202201 MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHVI--SGTNGTKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLLIV
::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::.: :::::::::::::::::::::::: :::::::::::::::::::::::::
Origin MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIV
10 20 30 40 50 60 70 80 90 100 110 120
120 130 140 150 160 170 180 190 200 210 220 230
202201 NNATNVVIKVCEFQFCNDPFLD---HKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPI-IVREPEDLPQGFSALEPLVDLPIGINITR
::::::::::::::::::::: ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: .:: :::::::::::::::::::::::
Origin NNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVR---DLPQGFSALEPLVDLPIGINITR
130 140 150 160 170 180 190 200 210 220 230
240 250 260 270 280 290 300 310 320 330 340 350
202201 FQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFDEVFNATKFASVYAWNRKR
::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: ::::::.:::::::::::
Origin FQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKR
240 250 260 270 280 290 300 310 320 330 340 350
360 370 380 390 400 410 420 430 440 450 460 470
202201 ISNCVADYSVLYNLAPFFTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVSGNYNYLYRLFRKSNLKPFERDISTEIYQAGN
::::::::::::: : : :::::::::::::::::::::::::::::::::::::::::.::::::::::::::::::::::.:::::.::::::::::::::::::::::::::::::.
Origin ISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGS
360 370 380 390 400 410 420 430 440 450 460 470
480 490 500 510 520 530 540 550 560 570 580 590
202201 KPCNGVAGFNCYFPLRSYSFRPTYGVGHQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLKGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSV
::::: ::::::::.::.:.:: :::.::::::::::::::::::::::::::::::::::::::::: ::::::::::::::::::::::::::::::::::::::::::::::::::
Origin TPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSV
480 490 500 510 520 530 540 550 560 570 580 590
600 610 620 630 640 650 660 670 680 690 700 710
202201 ITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEYVNNSYECDIPIGAGICASYQTQTKSHRRARSVASQSIIAYTMSLGAENSVAYSNNSIAIPTN
:::::::::::::::: ::::::::::::::::::::::::::::::::::::::::.:::::::::::::::::::::::.: ::::::::::::::::::::::::::::::::::::
Origin ITPGTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPRRARSVASQSIIAYTMSLGAENSVAYSNNSIAIPTN
600 610 620 630 640 650 660 670 680 690 700 710
720 730 740 750 760 770 780 790 800 810 820 830
202201 FTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLKRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKYFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQY
::::::::::::::::::::::::::::::::::::::::::::::.::::::::::::::::::::::::::::::: :::::::::::::::::::::::::::::::::::::::::
Origin FTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQY
720 730 740 750 760 770 780 790 800 810 820 830
840 850 860 870 880 890 900 910 920 930 940 950
202201 GDCLGDIAARDLICAQKFKGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNHNAQ
::::::::::::::::::.:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::.:::
Origin GDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQ
840 850 860 870 880 890 900 910 920 930 940 950
960 970 980 990 1000 1010 1020 1030 1040 1050 1060 1070
202201 ALNTLVKQLSSKFGAISSVLNDIFSRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTT
:::::::::::.:::::::::::.::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
Origin ALNTLVKQLSSNFGAISSVLNDILSRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTT
960 970 980 990 1000 1010 1020 1030 1040 1050 1060 1070
1080 1090 1100 1110 1120 1130 1140 1150 1160 1170 1180 1190
202201 APAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESL
::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
Origin APAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESL
1080 1090 1100 1110 1120 1130 1140 1150 1160 1170 1180 1190
1200 1210 1220 1230 1240 1250 1260 1270
202201 IDLQELGKYEQYIKWPWYIWLGFIAGLIAIVMVTIMLCCMTSCCSCLKGCCSCGSCCKFDEDDSEPVLKGVKLHYT
::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
Origin IDLQELGKYEQYIKWPWYIWLGFIAGLIAIVMVTIMLCCMTSCCSCLKGCCSCGSCCKFDEDDSEPVLKGVKLHYT
1200 1210 1220 1230 1240 1250 1260 1270
Where there is a ‘.’ instead of a ‘:’, the sequence may be similar but not identical.
As you can see, this variant is far more different than the vaccines are from the first virus sample or each other. It’s still close enough for the immune system to recognize it, but with reduced effectiveness. It is still a SARS-Cov-2 virus.
Where did you get your virus info?
For Omicron, I just searched for complete genomes of Omicron variants in GeneBank and picked one.
For the original Wuhan-Hu-1 isolate, I’ve had that bookmarked since it was first published.
How did you do the comparisons?
To get the vaccine protein sequences I used Expasy to translate the RNA sequence to a protein sequence. Use the Forward direction, and select the Compact format, and select the first M of the first Open Reading Frame to get the protein sequence.
I used this online FASTA tool to do the comparisons, selecting FASTA: DNA:DNA for RNA sequences (this works for either DNA or RNA) and FASTA: protein:protein to compare protein sequences.