So what is a coronavirus you can go to Wikipedia. And you can look at these viruses. These are, This is an electron micrograph of a number of coronaviruses. There are about 80 or 90 nanometers in diameter, so they're a tenth micron. They're about a hundred the width of a speck of dust.
so you can't see them. They are so like that they float in air China knew that they reported that to us in March of 2,020, and unfortunately. I'll just say people in our leadership did not take that seriously, and didn't understand the importance of masking
these little spikes here on the outer edge. This is how they attach to our to ourselves person deep in our lung. And now in the nasal cavities, coronaviruses
we're discovered in 1960, Ish.
and one of the first ones Oc. 43 was discovered.
and then to some genetic sequencing and some pathological data clinical data, it's
surmise that O. C. 43 was actually what we thought was a Russian influenza, a Russian blue pandemic in 1,890. If we go back and look at the symptoms. It seems more like it could have been a Coronavirus.
and in addition to that.
it it could genetically, over a period of about 70 years migrate into a cold virus. So coronaviruses are always on the move. There are 4 of these that are known in humans to circulate and cause common colds about one out of 5, one out of 6 common calls.
and then we have Sars. Cov. One, which is in 2,003. That was significant. If that had been as contagious as Sars Cov. 2, I think the world would have been a different place.
There's Mars, which is Middle Eastern respiratory syndrome which, in fact, camels
and among camel workers in the Middle East 50 will show antibodies, tumors. So it's still out there and still circulating. And then, of course, COVID-19.
If you ask, where do coronaviruses live? If you would ask, where does influenza live? Influenza lives in birds, mostly in birds, and why, while file, it also is able to.
In fact, pigs
and pigs are a particularly dangerous mixing vessel for influenza, because they can be infected by bird by avian influenza, and they, of course, have a million influenza. So that's likely where we get some really bad recombination. But beta coronaviruses tends to live in bats and rodents.
And so, if you have never been told this, if you are going through a garage, if you're going through the storage area, you start to find rodent down the inside boxes. Get a mask on immediately.
because it's really getting to risk.
So the start, this is a little nerve model of a Sars. Cov. 2 viral particle e, there are different proteins, ease and envelope protein. It sits on the outside of the membrane Ms, a membrane. Protein and S is the spike protein. The spike protein is what attaches to our cells, and this is where genetically all of the action is.
and it is where we are going to do our genetic, genomic, pairwise alignment, analysis. and look for a putative ancestor. But the word put it, it, means to be asserted, but not with a penalty.
So this is a diagram of the Coronavirus genome. If you're new to viruses, and and I'm going to assume that you guys don't know a whole ton about viruses, but viruses can be Rna. They can be DNA.
This letter here has 30,000 letters of Rna. And over this genome. By the way, HIV. Human immuno virus deficiency, syndrome.
as well as simian immunovirus, deficiency, syndrome, also 30,000 letters also containing most of these proteins, but they do different things. So viruses. If you look at their genetic chassis, they have a lot of similarities, and if you go into microbiology. You'll study all of this. We have an excellent microbiology program at Foot Hill College.
The programs that are the sorry, the programs, the genes that are called orphs are like zip files, open reading brain, and they unzip into multiple proteins. We come here to this bread section. And this is by protein.
So we're gonna look at Sars and Mers at the Covid genome.
And this is just letting you see over 30,000 letters span. Where do these genes live. So the open reading frame, one and open reading frame to an open reading frame begins with the methigning amino acid. It begins with atg, and the sequence. Reading will run with
The Rna brought the case
until you hit a stop code on, and then you stop, go and stop translation.
The protein that we're looking at here. The spike protein can be broken down into a couple of areas, the ones that you guys maybe may read about in the future Rvd is receptor binding domain that attaches to a cell. So this is really important.
Viruses don't know what animal
that they're attached to. They're just attaching to a protein. So Rvd attaches to a protein. And among other important areas here, if we look at a spike protein I'm trying to look for.
Oh, gosh! I think it's right here around. It's right here. So I apologize. It says, S. One subunit, and then there's an arrow in a in a bar, and then S. 2 subunit. These 2 subunits in this protein and the spike protein have to split. It's a process called cleavage, and they have to split so that Mrna can be injected inside of us.
and that Rna then is attached to our
sorry. My brain just stopped. There is a a unit within a cell that does all the transcription and at that point of injection you have to cleavage here. Cleavage takes a long time. unless there's an enzyme that can do that for us. And that's what we're gonna look at today where that enzyme came from.
So this is a slide that shows what happens when they when a virus comes. And if we're looking at a membrane, if we're looking at the 2 different pieces of our and below protein and our spike protein. The spike protein attaches here to an ace 2
and this is a Angio tense and conversion. Enzyme. This is present in our kidneys and in our lungs. It allows our body to quickly create an enzyme that allows our blood pressure to go up and constrict for fighter flight. So it's a very fast conversion.
and these cells exist everywhere. But this is what the Sars Covid, by protein, was able to
attached to. Initially. There's something called Tmp, which is a transmembrane of protease, and this is super important, because these 2 have to attach at the same time, and then cleavage occurs.
So a virus attaching to us is kind of a complicated process. It's a docking procedure you have to do, and then a hatch has to open, but there's a cleavid step before that.
and this slide here shows the fusion event here. It's a virus coming in, and the spike protein dots first with ace 2,
and then you have the subunit to which cleves from the subunit one. When that happens, then you get injection membrane fusion. So there's an initial docking event. Then there's proteolytic activation. That is the cleavage between S. One s. 2,
a subunit, one subunit 2. And that's where the magic is, and then the membrane fusion is boom. The rna is injected to us, and then we are infected.
So what's really important? Here is the spike protein is activated and cleaved at the S. One s. 2 level.
user avatar
Justin Tu
00:15:35
I have a quick question. You mentioned earlier. That cleavage is usually a
user avatar
Robert Cormia
00:15:41
long passes. How fast, how much faster is it with the
I want to say, it's a thousand times more efficient. Yeah. So I don't want to say faster because efficiency and speed are not quite the same thing. I don't. I do not have microbiology training right here, but my background. If I didn't share with you. I taught bioinformatics at Foothills College, 20 years ago I got a certificate at Uc. Santa Cruz
extension, and that allowed me to actually develop a program and teach a course in it.
If there's a question in the chat, I can't see it, but Adrian, perhaps can read it so you can look at.
user avatar
Adrienne Nguyen
00:16:32
Oh, sorry we did a lab in Bio to track this. It's so much faster with an enzyme present.
user avatar
Robert Cormia
00:16:49
And so I'm glad someone has seen that. So you can look at the structure of these spike proteins. And this is called Ncb. I, pdd, Pv. Stands for protein Data bank and 6 v. Atx is an accession number.
An accession number is a primary key in the database. It's like the license plate on your car. and so it attaches to a file. And this file happens to be a structure file for Covid.
and you can go here, and Cbi is free and freely available. So if you look at here, you can almost read this. This is out of our Csv.
but this is our csv.org slash structure. Slash 6 Dxx. All you need to do to find this is probably Google, our Csb, which is a data bank of genetic structure information. And then the accession number, which is 6. Vxx.
No, I'm not gonna touch on this a lot because this gets into chemistry biochemistry that you guys may do in D, you go on. You may do what's called the 5 Si angle, but the fi Si angle is like a second Level genetic code, where amino acids next to each other have different rotations and scare of hindrance. Derek. Hindrance is the bulkiness of what you are doing, colliding with a partner.
and so these.
a sequence of amino acids and their rotations and their confirmation that they eventually end up their shape right? And they charge is what allows them to fold and attach to things, and do what enzymes do and do what proteins do. So all the flexibility and all the shape is determined by the by side angle.
which is why you, an amino acid substitution can make a protein more effective at a certain place, or it can make it ineffective.
And again, this is. If you look at by side angles, you look at a rotation around the nitrogen atom and the carbon atom, and then a carbon nitrogen bond.
So the spike protein is key to vaccine development. That's why the sequencing of protein structure is so very important. If we didn't have that ability we couldn't quickly, rapidly, scramble and take a sequence and develop a vaccine for it.
The Mrna vaccines that we'll see, and a lot of people early on. We're concerned because they thought, how could we trust the vaccine that was developed in a year? Well, the quick answer to that was, it took 25 years to become that overnight sensation. And so there is 25 years, a long, painful development, 5 generations of scientific leadership.
all of them taking like a relay race, taking the baton a little further, but not closing in on it, and we were just gosh! Our lucky that in the year 2,000 that we had 2 companies, moderna
and Pfizer that we're able to scramble on this.
So the spite protein, this is a trimer. And so the there are 3 identical proteins that come together, and when you go to a protein databank you can see where the amino acids change, and you can see the Rvd is the receptor binding domain
we're gonna compare here. And this is you know, I read a number of papers early on sars cov 2, and that our atg. 1, 3. That's how you spell it. The car capital, R. Little, a, T, T. 1, 3
half. The signs I read was out of China, and all of it was outstanding.
And so early on, a lot of scientific prowess emerged from China to understand what's going on here, because obviously this was a pandemic. So this was a virus that had a lot of firepower in terms of being able to be contagious and and do some damage at the same time.
So there's a comparison, and Sars Cov. 2 and a bat virus in particular places. And so what you do is you look at these residues and compare them for similarity. And if they're not an identical residue, you compare them for their shape. So they're not. They don't need to be the same amino acid as long as they're from the same family, and when they fit in the same by side angle.
So all of this molecular modeling is done in the computer. It's very, very extensive. It requires just a lot of time.
So early on thanks to just a good journalism. New York Times. Ran an article and shows the spike, protein and amino acid compensation.
When I first read this article and saw a Pdv. 6 Vxx. I thought, well, heck! I can take these letters 1,270 odd letters, or brown there, and paste them into and Cbi. Blast and blast the protein sequence, and see where this came from.
They looked at this, and then they ran the article about the B 1, 1, 7 variance. So I think that this was some time around spring, mid spring, maybe Mayish, maybe about 3 years ago, when this article in in 2,021. I apologize 2 years ago, and came out and looked at
how the virus shape initially emerged, and then how mutations change the shape and the foldability of it. So one of the things and we'll look at this with the B 111 variant
was the point of mutations, and so scientists can very quickly from a sequence, and they look at the genetic sequence and translate to proteins. And so what they found in the B 1, 1 7 lineage is that there were 2 deletions. These 2 little dots mean that 2 amino acids disappeared. So that means that 6 nucleotides we're no longer there and did not cause a frame shift.
And then you have 1, 2, 3, 4, 5, 6 other key mutations and spots.
And so these are hotspots in the spike protein, where genetic changes that results in a different amino acid raise, then it can for much greater activity, much greater virulence.
And that's what this virus obviously wants to do.
Now I want to point out. And this is, I don't wanna get into the conspiracy re reg regime. But when you are, when you have these viruses and you're working in a lab. not just the Lab and Wuhan Institute of Virology, but all across the globe, and including the Us. Is at scientists by
biologists are able to move these things around. And so it is not implausible that the spike protein of one virus could be attached to pieces of another, or that
key features of one virus could be inserted.
And it's a matter of just changing the genetic code.
So, looking at this in more detail, there are 2 deletions. This is one at 69 and 70. So 870. There is a deletion, and why? 144, 145, also a deletion. And so those amino acids are no longer there.
and then, if we look at positions 501570. So this is long. A 1,270 is string amino acid string at these positions
amino acid, and there are 21 amino acids. When you go on to biology you'll probably have to memorize this I did in biochemistry. I can't remember most of them but and shifts to why, a shifts to the at position 6 81 P. Shifts to H.
7, 1 6 T. Shifts to I. And then at 9 82 s. Becomes A, and then 1, 1, 1 8 d. Becomes age. So there are couple of things going on here that aren't one is that are not immediately obvious. Not only does this confer greater or for virulent.
but if you guys know sports, you're familiar with what an all-star team is, and then all start. Team is when you have the best athletes at a particular position, and I want you to think of that metaphor and apply it to the sequence of amino acids and realize that these are an all star team. And once you get a good team member at one of these positions. It's awfully hard to replace that one because they're working well with their other team members.
I would make a basketball matter for right, but not everyone has the same basketball favorite that's involved in.
So what I did was New York Times again. This was super simple and great the way they did it. They published this sequence, and they wrote deletion here, deletion here and then I highlighted in red letters where there was a change of amino acid. So I literally went back to the first sequence of letters.
and then I copied this in. It's a little painstaking because you cannot make a mistake with a character, and then blast this in is you can. You can make a lot of big errors. But I was able to get all of these letters in. And so this is where I got the Wuhan sequence.
and then the B 1 1 7 variant. I then spent a lot of time plentying down other variants. it's not as simple as going to Google.
So what I want to show you is there about a dozen positions where amino acids have occurred. And some of these when we got to Delta K. 4, 1, 7, and E. 40,
4, 84 K. And 501, why.
They clustered together, and these 3 would appear in a lot of variance. This is your all-star team. There's a word for these 3 things, and this is just my my brain getting old and stressed.
there's a work for how amino acid mutations function together as a team, and then it becomes difficult to replace any one of them, because you're essentially replacing the entire team.
If these are what happens, you can have a virus more effective infected. You can also have a mean escape. so infection is attachment to us. An immune escape is avoiding the attachment of our antibodies to it, either through a vaccination or a natural infection
user avatar
Justin Tu
00:27:08
so early on one more question. So go back at the other side again. You mentioned Sorry. Not that one the one we were talking about the st stabilizing mutations and the infectivity genomes. I think it was. Go forward one more side
user avatar
Robert Cormia
00:27:26
here
user avatar
Justin Tu
00:27:28
one more by you.
Okay, so I think you said it briefly. But these stabilizing mutations that basically means these, all star members are not going away. They're gonna stay there through all of the.
It's always covid to mutations.
user avatar
Robert Cormia
00:27:46
Probably remember that there is probably so. We. We had a massive change between Delta and Omega.
and the exact origin of all, Macron is not understood, but there are assertions that are reasonable, that
what happened
with all Macron is that you had an infected patient who was amino compromised, and that could be any one of a number of things. So it's just choose cancer. And so they don't have a strong immune system. They're infected with Covid, and they're in a hospital for, and their studies done up to 100 days before they either lived or died, and Most of them would pass away.
but or a significant fraction of them. But during that 100 days their blood was sampled every 10 days.
and genetic analysis was done of the virus inside of this body, and it was found that giving a virus free run of an amino compromise patient means that
your immune system is gonna just stand up and try to knock down any new virus. But if your immune system isn't strong, then the virus is sort of gonna have their way with you, and they're going to explore a lot of different confirmational spaces with mutations and over time probably develop something that can be really, really different and really novel, because they're not fighting against a very strong partner.
This is. This is one of the theories of Omicron. And so when Omar Kron came out. And you'll see, Justin later that you can tear into these sequences and actually look point by point where these mutations occurred. And if you have a molecular modeling tool. I never took the molecular modeling tools that far within Cbi, because 20 years ago they were a little painful to make a point mutation. But today I think you may have access to free
modeling tools where you can make point mutations and see how this affects the shape.
I don't know if that answers your question.
that was more info than I was expecting. But I'm I'm going to do the best to sort of read into where all of this is right. And so this is all Delta. Once I'm a chron here. Omicron, I remember quite well, was Thanksgiving right of 2,000, 22,020, right going into 2, no, 2,021 going into 22.
I remember quite well, because, we were all you know, going into winter quarter, and at the end of Fall quarter, and yours truly stood up and asked, you know
we're looking at a doubling rate. This this virus is doubling every 2 days.
and You know it was a tsunami that came over the top of us. We were vaccinated right, but it sure got a lot of people sick
what I might, and still does. What I want to show you is a couple of things these proteins have. They're known as a trimer, a protom, or a proteom, or b protom, or C hemoglobin in your body are also Those are diners. Those are 2 subunits that come together there for proteins, and you get 2, one protein sub protein and 2 of another.
And so these sub proteins come together and they build these shapes. And here, in these low colors.
user avatar
Unknown Speaker
00:31:13
you can see.
user avatar
Robert Cormia
00:31:14
So within the 1,270 amino acids, this cleavid site. Here
is where where the fear and
this is where the fear and Cleveland site is inserted. When I I I want to be super careful in my language. Here.
This is where, when you compare 2 sequences of. and the Wuhan a two-one.
That was the the buyer. That was the sequence that China, released in the first week of January, that the fewer and Cleveland site appears here right there between S. One s. 2, and that's what confers its ability to be much more infected.
So here we have. S. One I'm going to show you 2 different slides. This is what this is more firepower than you'll probably have access to in a free modeling tool. But scientists, microbiologists and biologists
are able to take and model. Say, this is S. One Rvd. On the left hand side. This is the spike protein of the Coronavirus that is attaching to us, and on the right hand side. This is our ace, 2
cell on our body. So this would be deep inside our lungs. And this is why so many people got sick and died. Is that an infection deep inside your lungs is a big deal versus one in your nasal cavity is going to be more like a cold right? And so that's why this symptoms change so significantly.
Omega is so much more effective than Delta that it just displaced it. Delta couldn't compete with it.
So this
piece here when we have when we have a change in a mutation is detected, or we have a new variant. The first thing we do is, we ask, does it have better attachment, capability? And they actually scientists look at the energetics, the interaction between an amino acid and the shape of our protein. So our proteins don't change because of what we're born with, and they're what we have for our lifetime.
But this virus is gonna change, and it can be more able to attach to a particular type of cell. Or we can model an entirely different type of cell, say, in our nasal cavity.
And so literally, we look at these point mutations.
the. And again, the the Pdf that I sent out to you guys should contain presenter notes, and if I did my job well or half well, there should be references to where these came from.
The second thing, a microbial. This will be a viral. Just, we'll look at the change in a mutation pattern in the new variant and our immune system.
So this is called infectivity, and this is a mean escape. So you have 2 ways that you're gonna overrun, that mutations are going to be successful. One is to be more effective, and the other is to avoid the immune system.
And so scientists, again, can look at the docking
of this. All right, we're gonna have some fun.
So question number one in your assignment. And you know, you guys have 5 or 6 questions. If you don't get the questions perfect it it it doesn't matter so much. One of the
the pattern of questions that I'm asking you is what is a Geno general next portal one is one is Ncbi, one is our Csv. But then Cbi is the National Center for Biotechnology information. It's part of the National Institute of Health National Library and Medicine.
This was the class that I taught going on almost 20 years ago. I taught it, I think, in all 4 I was teaching it when Sars Cov one came out.
and so you can go to. And Cdi, what I'm gonna do is I'm gonna go. I should have to this up earlier. So hang on, guys. As I mentioned earlier. I have a little hiccup with my computer. Adrian is my co-host and so
pay me if I have
problem, what I'm gonna do. I'm gonna type in. I'd like you to open up
3 tabs.
Okay, one at a time and in your tab in your browser. What I would like you to do is to type in for Google. I'd like you to type in N. Cbi.
The reason that I don't pass out the URL is it's just really really complicated and hang on. I'm having a thought. Nothing is happening.
Adrian, are we looking at a slide that says Google and Cbi for the page? It says, yeah, and Cbi National Center for biotechnology information.
We there's not a lot of Urls and clicking to do. But I'll tell you. I thought dozens and dozens and dozens of sessions, and it's super easy to get lost. And so I don't want to get too far ahead of you. Maybe what we can do, Adrian, if I were clever
with the A big if is, I'm going to pay this in chat.
Oh, there's is there anyone in the waiting room right now, said Waiting room participants. Maybe that's just my chat. So I just paste it inside chat, for everyone
is to go to Ncbi. Okay? And so, Adrian, you can see that there.
Yeah. So how you you did a lab in Bio to track this. So that's that's great. How did you do a pairwise alignment in your class?
If not so, there's an answer in chat.
We use potato start. Okay? So this is all. This is all done with the computer. And this is the the fun part about what we're doing is that you can
anywhere in the world that you can have access to this portal. And so what I want you to think about is way back in the day. because I taught Internet technology, 1990,
5 ish. there was a new portal call Yahoo right? And so Yahoo was a directory. It was a catalog search, and you had entries for news and sports and health and medicine and friends and then search right in movies, and you name it in commerce. And it was there.
And Cbi is a genomics portal.
And it has basically 2 things there. 3 things. It has tools. it has data. and it has literature.
So the tools is what I use to teach tools that you could download. And you could then analyze genetic information.
And I'm going to slow down here. The genomic information
is comprises, probably. Oh, I'm gonna just throw this out and say half a dozen different categories. So category one would be viruses. Category 2 would be bacteria category. 3 would be mammals and us.
And then you're going to have
protein data.
You're going to have DNA data. Those can intersect these other categories.
You can also have structure data which is the shape of a data safe of a protein, or you can have snaps. so sniffs are single nucleotide polymorphisms if you haven't heard the term. but you've heard of 23 and me 23, and me as a company.
It'll they send you a spit, kit, and you just spit in it and It'll look at your genome, and it'll categorize
thousands of snips. And a snip is a place along our genome where every 6, 5, 6, 700 spaces in our genome, there is a point of variance. And so we are 99.9% the same. I wouldn't go 99.9, but it's 99, plus.
But every 6 or 700 spots there's this place where, a single nucleotide for us, that's DNA is going to be different.
And so it's usually one or 2 different things. It could be A or T, it could be G or C. I want you to think of it as simply chocolate or vanilla, and that that space you are either in in the Pr in the majority category or the minority category and majority minority doesn't mean anything. It just means. What is the dominant sniff, and what is the what is the balance of it? So if it'd be 60, 40, it could be 80, 20, it would be 70 30. But at that position there are 2 choices.
and then you run down the genome and other 1,000 spaces, and then there's another snip, and another snip, and another snip.
and so a pattern of snips is called the haplotype for any of you who play music and know what a chord is on a say guitar. So you have multiple notes that come together. I might either think of a half what type is multiple notes that come together, and so sniffs is why we are not identical. Right? Bacteria can be identical.
But in certain clones of other species can be identical. For very good reasons we are not identical. and these haplo types are what have blended when we have meiosis, which is our reproductive process. Right?
So
the snip database and and Cbi is particularly important, because over time we put in more variant data. And so then, 23 and me uses this, and they use snip data and use the literature data
to let you know if your genome matches data that's been in a particular study.
So spoiler, alert, we all have things that are going to end up costing us trouble. When you get older I'll just say as European being white European, there is a one third chance that you will develop cardiovascular disease.
hypertension, cholesterol. What is it called colesthemia? So high cholesterol and some other heart disease? It's like bang right? Or you may have certain in inbred allergies to things, or you may be prone to a particular type of cancer by not having the strongest immune response to a particular whatever.
So we all have something, we have multiple, something, because for good reason, we don't.
Or you hope that you
because at a certain point life catches up with you. And so all these resources pup. That is where you can go and download literature. This called pubnet Central, which is everything is free.
There's a book. So that's part of that of men. Central, everything is free. Blast is what we're going to do. We're going to do a local alignment search technique and be stands for basic. There's for you to hide data. There's protein data that's genes. Pub, can. So I just give you tons of information for your quit. First question, what is N. Cbi? It's a gen on this portal where you have tools, you have genomic data. And you have literature.
Okay?
So let's go and give me just a second here, because I haven't done this in a little while.
Close this. And then I'm gonna go back to.
I'm gonna ask Adrian, we're looking at the
I just switch to databases. Correct? Right? So this is your database information. And again, since you guys, you know, the phrase must be present to when you can go ask 5 pad points on this activity. And you can say I went to Genbank right, or I went to
of that central. I went to Dv. Snp. And lo and behold, I started to find all this information. You can always please me by saying, I always wondered what 23 and me was, so I ordered a kit.
It's fun, I mean, it's it's you can actually find out that your lineage is exactly what your parents told you it was. I found out that my paternal.
genetic flank is indeed a hundred percent branch.
So nucleotide databases. These get into the leads into some of the information. As I said, you have bacteria, you have
viruses, you have ways of doing vectors and for microbiologists. This is where you get some of your primers. I will go into what a primer is
because you're gonna do that in biology.
Some of the information that's also coded by whether it's new or old. one of my
hugeest frustrations in life is that
all the search capability that you have with Google does not exist in the genomics databases. They are literal literal string. That which means, if you misspell a character.
it ain't gonna find what you want. It's not gonna find it, it can't do it. And so when you go to Ncbi and search, and you're looking for, say, any of these sequences. It is painful. I find the sequences through literature, and then I get an accession number, and then I use the accession number, which is a primary key, and database is like a license plate. I use that to down information.
Alright. So this is where Adrian says Mr. Cormia, can we just do something fun.
Let's do it all right. So, guys, we are going to go to.
I'm gonna ask, are you looking at a screen that says Ncbi. Library of medicine and here.
But to get to this to get to this string, I'm gonna put this into chat. I don't know.
The fastest way to get here is just to type in. So I'll type in Google. And I'll type in Ncbi, and this will get you to this page. Google and Cbi blast.
And last is a central page where you're going to look at the various tools. So this is one of your 2, 5, 2 of your 5 questions, what is blast? It's where you do a search with a string of letters to see. Is there any other string of letters in the world
in these databases that matches ours. I didn't mention this, but half the genomics data in the world exist at Ncbi. The other half is private, so people will take, you know, tons of resources, and come up with their own sequence of a particular animal, a particular gene, and then they'll put it in a private database.
So, Adrian, we're looking at the page that says newly type last.
user avatar
Adrienne Nguyen
00:46:04
this is this is searching for against letters for nucleotide. Protein blast is searching for letters that are amino acids.
user avatar
Robert Cormia
00:46:12
Blast X is a translated. It'll take your nucleotide letters turn them into a protein inserts against a protein database.
and the last
T. Plus 10 is where you take your protein sequence and you translate it into potential nucleotides and search against a nucleotide database. I'm not going to go into what translated glass are.
20 years ago it took me a month to of a hard study to where I thought I could explain it to a class. But translation allows you to move between these 2 worlds of nucleotides and proteins and either discover proteins or discovered genes.
What I'm gonna have you do now is I'm gonna have you click on protein blast.
And then, Adrian, you're gonna tell us. Tell me if we're looking at a screen that says
yes, your screen may not look quite identical to my
that will say, Ni National National Library of Medicine, and the Blue Tab is highlighted last. P.
This is where I'm gonna I'm gonna pause and wait. And I need all of you guys to be in the same place. You have to be in the same place, otherwise you're left behind.
I don't want to.
If you're watching this on replay, just go to blast pleat last P. And I did send out a step by step. I did done on Friday. I hope it actually works.
But I want you to see this box here that says, align 2 or more sequences. When you come to this page, your box isn't checked right. My box was checked because I did an alignment on Friday.
and the cookie for this page left it in the checked position. Alright. So when you come here.
it's say, enter it. Session number.
and I want you to click on this one with this box. And then Adrian and Company, I'm gonna ask
you guys have 2 boxes here.
so I'm just gonna be good. I'm gonna look at and just call out, people, are you able to get 2 boxes?
Let's see here, Liz, are you able to get 2 boxes on your protein glass page?
user avatar
Elizabeth McGee
00:48:36
All right. Great, thank you, Holly. You probably done this before. Have you done a blast holly
user avatar
Robert Cormia
00:48:45
just in Justin? You have 2 boxes counter in
I got 2 boxes
and excellent, and then you to.
We've got a whole bunch of people from that a diversity.
This is the biggest group I've ever taken in, but it's not too big to manage, almost too big, but not too big to manage. All right, and in the chat everyone says so. No May or holly. No, no worries at all. You can communicate to Adrian.
Alright. So we have 2 boxes. So what we're gonna do. You are a guy, you guys are 5 min from being a spike protein. you. I'll just say that you've gone down the road that very few people have gone down
all right. What I want to do now is I'm gonna do a new share. And it's super important.
You need to have the Covid biomatic spike protein sequences file open.
You can scrape these letters out of the message that I sent out.
But it's probably easier to copy them from this file. So I'm gonna do one more time, and then I paste in here
a file.
And I'm gonna put the Covid by bioinformatics sequences. Okay? And then I'm going to hit return.
and so, if you joined us a little late, we may not have seen this file, but it is now in the it's now in the that all right.
And I'm getting something in the chat that says Stacy says, great. Okay? So Adrian, we're looking at a page that says, Covid bioinformatics, protein, spike sequences
perfect. All right, you guys, this is the carrot, right? And so this is the header.
once upon a time, actually, I can't remember what the name of this is, but this carrot, followed by sequence of letters that are text readable, but are not amino acids.
It is stripped out of the paste, and so you don't need to remove this. But for this exercise I want you to just copy your letters all right. You gotta copy your letters perfectly here.
and I don't need to say that in a denigrative way
I want you to highlight starting with I, T. 1, 3, and I'm going to highlight all the way down
through the last letter I'm going to control. C. I'm going to copy that
all right. And then I'm gonna go back to
my blast P. Page. And then, Adrian, I'm gonna ask, are you guys looking at my blast? P.
user avatar
Adrienne Nguyen
00:51:40
Yes, all right, great.
user avatar
Robert Cormia
00:51:43
4 or 3 min from 3 or 4 min away, so you'll notice that I copied and pasted my that virus up top.
Try to keep track of what you're doing here. Because if you lose track of what you're pasting, you're going to get a different result. I'm gonna go back to my
last, my sequence page. And I want you to look down to Wuhan. 81 sars. Cov. 2. Okay.
And then we're going to highlight all of this and come down to the letter T.
And so you notice we start with them. Which is Mac, I mean, that's a start. That's your start.
protein.
right? And at the atg, as your start code on.
I'm going to come back to
you. Want to come back to?
Here's my paste.
all right. So rat R, a. T. G. 1, 3, not a rat. It's about our it. G. 1, 3 is up top, Wuhan. 81 is on the bottom. Now, if you can remember this, it's it's helpful.
I'm gonna come down. And Adrian, did you see what I just did? I copied? I'd I'd already done this, but I brought in, and I wrote that rat. G, 1, 3 versus Wuhan, a 2, one. And I put that in my job title
right? All right. Can you quickly, guys just let Adrian know in chat.
Excuse me if you guys have 2 sequences, and because once I do my next activity. you really can't go back. hey?
And are you guys all pasted in 2 sequences.
All right. Now, you can show results in a new window. I typically don't do this because I've got on there already. Got a dozen times open. So when I click last, we're going to take these 2 sequences of letters. They're going to be sent to Virginia.
where their Server Farm is for Ncbi, and they're going to do pairwise. Alignment of these 2. You can do a single blast of one if you uncheck this box and you can search as a bunch of letters that can take over a minute to return, because there's
hundreds of thousands of people that are hitting these servers all at once. Right? So we're gonna do this all right. You guys ready 2 sequences.
I've got my mouse over blast. I've got a line 2, and I'm gonna do 3, 2, one
last. Okay?
Right? And then this will. This result will come back really fast, because it's just a pairwise alignment of 2 sequences. And what it's gonna do is look for similarities and do differences.
And so, Adrian, you're looking at our page now that says.
yes, okay. Once you guys to note here it says our Id. That's your request. Id. What the pros do is that they'll save this request. Id, so that they can come back to it. If your blast took you minutes to search a database, you don't want to do that over and over and over and over, so you can return to a save search.
Alright, we're gonna come down. And I want you guys to look at these tabs. Be really careful here, because if you click the wrong tab and then the back button. You may have to re
search, realign your sequences alright. So, Adrian. Descriptions, graphics, summary alignments, and dot plot. Alright, I want you guys to click on alignments.
Alright. And guess what?
30 of you have just become
bioinformatics searchers.
Okay. yeah. So
what the pros do I? I've already created a second tab and a third tab for my protein blast.
What we're gonna do at least 3 blasts. I want you to do at least 3 blast to get your 5 points, if you do more than that, and if you describe more than that, and if you really impress me with how much
effort and interest you put into this. I will say you can get more than 5 points.
and then 8 point. That's the credit is not unheard of. Alright. I'm going to highlight this. And
we're gonna look at this. I apologize before I go even further. We're going to look at
your identity, your positives and your gaps. So your identity set. there are 1,240 exact matches out of 1,273. That's 97%.
Okay.
there are 1, 252
of 1,273 that are positive. The difference between an identity and a positive is you send your partner into the grocery store and ask them to pick up an item right? And then you give them the brand. If they come back with the exact item. That's an identity. If they don't get the exact item. But they still get you catch up or they still get. You may names, or they still get you milk, or whatever you're looking for.
That's a positive so positive means you're in the same family. But it wasn't the same identical amino acid. You may have the same 5 Si angle or close enough. Right?
That's a 98% match. You now have gaps. And so when we have gaps, we're going to talk about indels in indels and insertion and deletion depending on your direction of time.
So in everything that we're going to do today? So query one on top is our atg. 1, 3.
Subject, one on the bottom is Wuhan, 81 H. Wuhan Wu Wuhan. 81. I'm sorry.
all right. What I want you to see is as we're going to go 60 letters at a time. There's a space here, but that space means is that you didn't have an identical match, and you didn't have a positive
if you don't have an identical match. But you have a plus. So if you look down here, you don't have an identical match, but you have a plus that's a positive. So you didn't get the same amino acid. But you got one in the same family.
The families are basic acidic polar non-polar, and the fifth is special. You don't have to memorize that for today. But this is a mutation space. This is a mutation space. All of those are identical.
If you look at position 61 to 120, they are identical, 121 to 180. They're identical.
You've got a mutation here. So again, you can go into a modeling program, and you can figure out what that difference means, and I want to quote a gentleman. He was my instructor.
He was, He was a charming man, and he was very humble. as a scientist and the biologists and computers.
he said, I'm not an expert, but I'll teach you some things, and he said it takes a difference to make a difference, and what that means is that if you have a different
insertion, if you have a different identity, then you can get different properties out of that. G,
so you make it.
you know, in case of a virus better infection, I mean escape. It takes a difference to make a difference. If you guys put that in and put a star by, it must be present to when
you'll get a point.
Okay, I can't remember his name. He's a charming
alright. So we come down here and you're looking. Okay.
Yeah, there appears to be quite a little bit of difference going on here. I wonder what that is. All right.
This is a bat virus on top. This is a human virus on the bottom ourselves are not different. Or excuse me, our cells are not the same. We are different animals, right? And so it could be that.
And I'm going to be extremely careful with what I say here. It could be that if it was this fat virus by protein that it infected a human, then these were the adjustments that were made during the first 6, 8 weeks before we actually saw the virus. If you do your literature, search in your homework.
This virus is likely circulating in early November, unbeknownst to people.
Certainly in December, unbeknownst to people, the stats are somewhere around 5, 6, 700 people cases putative cases.
What I want you to come down here. because this is where you're going to get some credit. You see these dashes. So, Adrian, we've got 4 dashes on top.
and we've got 4 letters down here. Right?
Yeah, I want, yeah. So now I'm gonna explain what last is doing. Last is saying letter for letter. I'm gonna compare these 2 sequences. And so we get to 6 6 one. And it's like, everything's great. We're identical. Everything's great. We're identical oops.
I see. On the other side of this ravine. Everything is identical, everything is identical. Right? So the middle band is is what your what your comparison is.
But you have a gap.
So, as I said, I'm time when I do this, I do, old on top.
new on the bottom. So we know that this bat virus on top. It's 2,013. That was its presence in the database was 2,013, and when it's Friday's were found in the dust on this cave
the Florida is Kate. This would be a deletion if it were newer.
because this is the younger virus. This is called an insertion. So if you are missing amino acids, as I've shown in that one. We'll look at it with the B 111. That's a deletion.
This is an insertion. And this spot, what? This is your s. One s. 2 cleavage site. And this is a poly basic p, r, a.
I want to say, prolene.
Okay, I mean.
I don't know. Pr, a. I'm sorry.
but this is a poly basic site. And so poly basic site allows the fear and enzyme. So the you're an enzyme exists in us. The virus says, if I expose the pure and enzyme to this poly basic sequence of letters, I'm going to trick you into cleaning me, and you're going to split these 2 pieces apart.
So this is the fear. And F. U. R. I, n, and it's capital F.
You're in Cleveland's site. Cleavage is C. L. E. A. V. A. T- to split right?
So this is
a deletion. If you were going forwards in time. But it's an insertion here. So what this means, guys, is that our at G. 1 3 did not contain. If you're in Cleveland site.
But Wuhan at you.
Wuhan, H. One which is extremely similar to our it. G. 1, 3 does contain the fewer and Cleveland site.
And so now you guys have seen what most mortals have not
is this is evidence, but
many people. And I'm sort of in that camp. This is the this, the telltale symptom of potential mischief.
Right? If you're looking for what's called gain of function work is, if you take a bad virus and ask, how do I make it more effective, I would put a cleavid site in it. No Cleveland sites can move. If you have these 2 viruses inside, inside a person
at the inside a mammal or any animal, the pure cleavit site can move from one virus to the other, so it is not necessarily evidence of human insertion. But this is definitely. If you compare 2 sequences.
it says how they're different.
Now, when you go to the rest of the genome. The rest of these amino acids, I think, from here on, in right, from here on in
these are identical. I don't think that there's a single difference.
And so you get to 1,269 for our atg. 1, 3. You get to 1,273 for the Wuhan, and this is the insertion of 4 amino acids.
Alright. So that was a long, long description and analysis, right?
Of 2
amino acids and the pairwise sequence alignment.
Okay.
alright. How do you guys, are you guys ready to do our next one? We're gonna do 3. Okay, you can do all 5. But we're gonna do 3. Adriene, are we ready to do another set?
user avatar
Adrienne Nguyen
01:05:06
Yes, alright.
user avatar
Robert Cormia
01:05:08
When I say, Are you guys ready? You'll learn. Yeah, always reply. I was born ready.
Okay, so here we go. Are we looking at? Take the blast survey today? And
on my screen
I change screens.
Oops, Adrian, or are you still there? Perfect? I'm sorry. So you'll notice that I didn't click align 2 or more sequences, did I?
user avatar
Adrienne Nguyen
01:05:41
So now I have my 2 boxes right?
user avatar
Robert Cormia
01:05:44
Alright. What I want you guys to do now is, I want you to go back to your sequences.
Yeah. And I want you to take
with them and compare 2 different ones. We're going to go to the consensus sequence. So consensus says.
after a bunch of time, scientists agree that this sequence is what we're going to call our standard sequence. Things change. But this is going to be our sequence, right?
And so I highlighted. I'm gonna copy. I moved down to
spike protein, right? This is a consensus sequence. It's different by one amino acid from all on one.
So we're going to take the consensus sequence. And then I'm going to go back to
my last P. All I did to get to blast P. Was I typed into N. Cb, I blast P.
Or if I started ahead of time I would open up 3 or 4 tabs, and I would to them on into the last P. Right? Okay. So now I'm going to go back to.
I'm gonna go back to my amino acids and I'm scrolling down. So, Adrian, you can see B 1, 1 7 alpha variant.
user avatar
Adrienne Nguyen
01:07:02
So I'm going to highlight all of the alpha variant.
user avatar
Robert Cormia
01:07:07
And then I'm going to come back here and I'm gonna go back to New share. And I'm gonna come back here.
And what are we looking at? So you can see that it says
I've got my sequence on top sequence on my bottom. And so now, what I'm gonna type in is this one is a little different. So I'm gonna pay paste in part of what I had here before.
But this is alpha variant.
So get out of there. And what we're gonna do is we're going to compare the consensus sequence against the Alpha variant. You could compare Wuhan one against Alpha Variant. That's perfectly fine.
You're only different by one amino acid. What you want to have. What you want to do is after we do 3. Is you want to have the courage to do a few more on your own, and you realize, gosh! If I can copy and paste and keep track of my tabs.
I can do this
user avatar
Adrienne Nguyen
01:08:02
alright. So, Adrian, we're ready. We're ready set and ready to blast again.
user avatar
Robert Cormia
01:08:09
Here we go, all right, blast away!
And so again this is pretty fast we come back. If the reason it's fast is the pairwise alignment doesn't take a whole lot of
computational power.
And I scroll down. And here's descriptions, graphics, summary. And I'm going to click on alignments.
And our alignments say.
now, remember, these are going to be very, very close, because consensus sequences. This is now Coronavirus. This is COVID-19. Right on top is a consensus sequence.
the Alpha variant.
and I cannot remember now when the also varying came out.
But the the New York Times did that analysis of it. And what I want to show you guys is
again, you're looking at 1,264, 1,273, 99% positive. That's what you expect.
a 99% identity. Your positives obviously are going to be one more than that, and then gaps are 3. So gaps mean you've got indels. You've got either a deletion or an insertion.
I want you to look in our first row. Everything is identical in our second row. What we see is the consensus sequence has H. And B in those positions, and that's 69, and 70, and you have 2 dashes.
So, Adrian, the the one on the bottom is my newer sequence, right? The one on the top is my older sequence. That's a deletion.
Okay, I come down here and you'd be hard pressed unless you've got a really good eye.
There is a mutation spot. Right?
Here's a mutation spot.
and there are total of 7 of these, right?
And I'm looking around and to see where most of these are, and I'm coming up with, here's one right here. It takes a good eye to see these.
But this is how you track mutations.
All right. How did you guys do on that.
So the big in terms of the big things that I want you to see is the first is our at G. 1, 3 versus Wuhan, which I think is not coincidental.
And then the second is, when we look at the Alpha variant versus consensus. All right.
Okay, we're gonna do one more. So I'm going to go to my tab right? And I shifted my tab. And so I'm going to show you exactly how I do this I type in blast.
T. Alright, I type in.
and then I go to
and Cpi. So this is how I get to blast. P.
If I forget. All I have to do is type in the last, all uppercase, and then P. Lowercase. Not that it matters when I get here, Adrian, what's the first thing I have to remember to do
the line 2 or more sequences right?
You don't want to stand there that page and go what the heck is wrong. Why don't I have to?
You have to align 2 or more sequences. All right.
Okay, we are now going to go back, and we're gonna go to our that to our
sequences, and I'd like you to take Spike protein again. We're going to do Sars Kobe, too. So we're going to take that one again.
And then I'm gonna put this one on top. So I'm going back to new share.
And I put that on top. So I'm sars, Cov 2 consensus.
Or you may see Covid consensus.
And then I'm gonna go back to
fine
letters, and I'm gonna go to Omaha.
Now, if you guys are feeling like you want to be. sequence a.
user avatar
Unknown Speaker
01:12:15
since you can do all 5 and impress me.
user avatar
Robert Cormia
01:12:18
and I can be impressed.
And now I'm back to
and back to my blast bait. So, Adrian, we're looking at blast again, right? And I'm going to type in. So
my job title here, as far as Cov. 2 versus on the ground. So if you can do 3 pair wise alignments, you're you're golden, and and if you can describe what you saw for those you're you're 5 plus already.
I can't remember what I told you. I'd give you an extra point, for. Oh, it takes a difference to make a difference. There we go
right, because that's not in the other instructions. Okay, Adrian, we're ready for our last blast.
user avatar
Adrienne Nguyen
01:13:04
Yes, we are.
user avatar
Robert Cormia
01:13:08
And sorry is Kobe, too. Now
try not to close your other tabs. Try not to forget what your other tabs are.
Try to go left to right. Sorry! That's a bias against left handed people.
But if you go left to right in your tabs and time, you can keep track of this. Most people I know have a scratch pad, and they're writing down what they're doing on each tab, because if they have a feeble memory like mine, I'll never remember, and then you'll get lost, especially if you forgot your job. Id.
All right, we're going to click on alignments. And now what we're looking at, what I want you guys to see and appreciate is we're looking at the consensus sequence. So what is consensus? You know? February, March 2,020.
And what is Omicron? Omar Kron was a horse of a different color. Right? So a lot of things changed. And the reason is is, we don't know.
But one of the suspicions is inside a patient. you know. Compromised is that the virus is given time to explore new structural patterns
and long, the whole one of which was to move up into being able to infect nasal cavity. which, if you think about the difference between a deep lung infection and a common call boom!
Oh, Macron, is this, and practices measles? So it's got an are not of 1516. This is in that. This is me.
Okay.
so what do we see, we've got mutations up here. And now what do we have?
We've got a deletion down here. So this deletion was probably inherited from what this deletion was probably inherited from B. 101 7.
But this deletion right here. I believe this new
right? So this is a deletion.
And then what do we have? Okay, what do we have down here on 1, 7, 6. Do you see the Epe?
All right. This is an insertion because you're older on top. You're younger on the bottom. So this is an insertion in time. Okay? And
scientists took P. You'll say you think, well, what's so special about Epe. Those 3 amino acids next to each other in a coronavirus, as it turns out, are not that common except guess where they were found?
So scientists go into a database. They blast this sequence of letters near this position. And what do you think they found? A cold virus?
So this omicron here in other theory could be. You have Coronavirus circulating with a cold virus. And the same time it's like, boy, and that's in your bad luck, right? You're infected with
a you're infected with Coronavirus, and you're infected with a cold virus. Well, another
another possible idea, for on the Chron is that boom
these viruses are just copying
in all of your cells right? And so genetic materials all mixed up, and the Epe jumps from the cold virus into the for excuse me, jumps from the cold virus into another Coronavirus, and then on the crime. Right?
So if you, if you were to go with that, what would you look for, you'd look for another sign that these other differences. which go much deeper into the genetic chassis of the spine protein they go is that they could be part of a cold virus.
So scientists couldn't have a lot of fun
doing this research. And what I want you guys to understand here is that you don't need a license to be a bioinformatics person.
You don't need a special membership. You don't need a special computer, and you don't need access to too many special databases, because that's what Ncbi is. That's your tax dollars at work.
So all 30 of you from today going on forward can be a bioinformatics researcher of site of types, right? You can think, call it citizen science. But you're just
scouring databases and looking for patterns and coming up with hypotheses and all this stuff, and you can do it on all on your own. Okay.
what I'd like to suggest. It's 1017. I'd like you guys to take a
one or 2 min break. And I'm going to queue up
a video. I'm gonna take my headphone off because I'm not smart enough to know how to play the audio of this video while I'm also
talking
right? And so I want to have the audio from my tablet go into the microphone. So go get a cup of coffee, or whatever you need to do. Take a break, and when you come back I'm going to put the S notorious link in here.
and
and Adrian, I'll get it to the
I'm not quite getting it. So, Mrna vaccines. I did put it into our our
instructions.
and I'm pretty sure that this is right. But let me make sure it's right before I actually put it in chat. Here we go.
Okay? And then, Adrian, I'm gonna ask a favor that you also queue of this video. And if I stumble on my side, you can take over as co-host.
user avatar
Adrienne Nguyen
01:19:13
But I I'm going to try to pull this off. I've done this a number of times. It's never
user avatar
Robert Cormia
01:19:19
any other.
And then what I'm gonna do is, I'm gonna get it for quickly, and we'll come back in in a minute.
I'm gonna have a tangerine.
Are they still on the top side? Yeah.
yeah.
alright
for it.
All right. Is everyone back? We're gonna do this adren, are we ready?
user avatar
Adrienne Nguyen
01:20:38
Yes. so
user avatar
Robert Cormia
01:20:42
I don't know how this is gonna work. You can just put in chat if you can hear it. But once I start the video.
I'm gonna go and
in trouble. So I'm going to do this in 2 steps. I'm going to go full screen. And then I'm going to launch the video.
user avatar
Unknown Speaker
01:21:07
There are many kinds of vaccines and many ways to manufacture them
user avatar
Robert Cormia
01:21:12
vaccines take an average of 10 years from research in the lab to administering them in a doctor's office. This timeline must be shortened if we want to be prepared for pandemics or novel diseases as they emerge.
Why do traditional vaccines take so long? Well, it's the process for developing and testing them
all pathogens that cause infectious diseases, like viruses of an associated Antigen.
This Antigen activates our immune system. To fight that virus scientists must identify the right antigen, find a way to produce mass quantities of it and then integrate it into a vaccine. It's a long process.
Antigens are usually proteins, and human cells are constantly making proteins as building blocks to maintain our bodies. So scientists asked the question, What if we could program our own cells to make these antigens and trigger the same immune response as traditional vaccines. This is the goal of Mrna vaccines.
Mrna, or messenger Rna is the code that tells ourselves which protein to make.
and, thanks to recent advances in DNA, sequencing scientists can quickly identify the code. To make the Antigen protein is specific to the disease. We want to find and build the Mrna in the lab at
the Mrna vaccine delivers this code, not a form of the pathogen or antigen to tell our cells to produce the Antigen. Once the Antigen is present in our bodies, it initiates an immune response, just as a traditional vaccine word.
The good news is that Mrna are much simpler to produce in the lab than proteins to create the synthesized Mrna. Scientists insert the sequence corresponding to the Mrna into a plasmid, a small DNA molecule within a cell that can replicate itself. This plasmid is put into a reactor where an enzymatic reaction treats the synthesis of the Mrna.
The synthesized Mrna is then purified and encapsulated in a lipid nanoparticle. The lipid coating enables the Mrna to reach our cells where protein production takes place, triggering the immune response.
This process could be used to produce many different Mrna, but just changing the sequence inserted in the DNA plasmid.
Scientists have great confidence in the potential of Mrna vaccines, not just for the prevention of infectious diseases, but also in the treatment of cancer, and perhaps even allergies.
To summarize Mrna vaccines will offer many benefits over traditional vaccine manufacturing speed. They don't require the slow process of producing antigens by cell culture or bacterial fermentation in a lab. They simply signal our bodies to produce the antigen ourselves.
Savings. The same production set up can be used for multiple vaccines, reducing costs significantly unlike traditional vaccines which require dedicated facilities for each kind of vaccine.
Mrna vaccines are not common today, but have tremendous potential and could alter how we think about vaccine development in the future to learn more about the different vaccine development and manufacturing processes. Visit sororious.com forward slash vaccines.
Okay, we did it.
Now, I have to get my computer back. It's not all right. Okay.
so let's go ahead, then a second. Here, Adrian, I'm goofed.
Okay, so are we looking back at? a page that says, blast look, alignment search. Okay, great. So you guys have this handout. If for any reason
you can't find it, just email, me and I'm happy to attach it. It's also in your canvas messages. These are the different types of last programs.
And the translated last again, back in the day, I was comfortable enough to explain this, but without a whiteboard I wouldn't even try. It's actually the on the complicated side.
the open reading frame. This is just some of your biology. If you're interested in in how we get the orphs.
and then the blast, step by step, right? What you guys have done, you can go to a database called unipr if you want, and you can also look up some of these files. The Unipro is a protein.
it's a genomics portal. It's in the Uk. It's a collaboration with another bioinformatics with another university, I think.
and they have tons of protein information much more detailed. and Cbi has covid resources. And this is the Cartorus video that you guys just saw if you want to play it again.
This is just a diagram of what happens with the injection. Remember, you're being injected with a sequence of letters. You're not being injected with the pathogen, your body. The ribosome will replicate that the cell says, I don't recognize you, tears it into pieces.
expresses it, on the outside membrane of the cell, and then that's where your immune system, picks it up and says, Okay, it goes into our database. That's why that seems give you
a faster response, because you've seen it before. So it's The virus doesn't have as much time to build up that viral mode and make you terribly sickly for you mean system, Hicks, and that's the plan. And also you have a more targeted response.
So bringing this to a conclusion way back in, I think, 2,021. When I started doing this activity.
we were looking at a time where we didn't have enough vaccine to get around the world. We're in a better strategy. We're in a better situation. Now.
staying ahead of that, making sure that we can get boosters. And again, I'll sort of nudge you guys if you haven't gotten your on the ground variant, which would have been as early as last September.
please go out and get that I'm already vaccinated. On the second. I have a boost on that, because I'm over. So I was able to get that. Our strategy is now probably every 6 months. If you want to stay up with this.
and so that'll be an Mr. An injection every 6 months. I wouldn't let it go a year, because I think your vaccine strength Will Will Lane.
The surveillance is antibody testing. Originally I thought we should be doing that in people, but then we realized that we can do that through sewage and through water treatment we can see if there's If there's that, if there's virus out there, it's important as, and with any new infection to figure out. Let's sequence it.
and then let's get on top of building in an Mrna vaccine. If we have to do this, this isn't just for Covid, this is not our last pandemic. I don't think I told you guys this story, but my maternal grandmother, my
my mother's grandmother, died in 1919 in the third way. what was called then Spanish influenza. Don't ask why it was Spain. Spain was the only country that reported on it. It's it's a crazy story because of the only country in World War one that was reporting news.
So
it's basically the influenza epidemic of 1918 which started in 1,917. The first wave, and my maternal grandmother died in 1,919,
so I never stop hearing about that. This is not our last pandemic. If you you don't have to look much further than Africa to realize that we've got some stuff out there, Ebola that would make Covid seem like nothing, and we, in my opinion, should be doing more aggressive work with vaccine development and getting ring inoculation. All of that. But the good news is we're in much better shape than we were 20 years ago.
We've also got great therapeutics. If you get sick. An older person in your also get sick.
Please get them packs a little bit. Get them in antiviral. That'll keep that viral load down so that their immune system can come back faster, and the last I'll just end common sense health measures. That's why I make you guys wear a mask and lab in lecture. Not so much, but I know that we have good that good ventilation.
I would just advise you that when you go into a building space and then closed area. Count the number of people you're in a building or an enclosed area with more than 100 people. I'd immediately try to figure out what the ventilation in that building is, and if it's not good, I would really think twice about being in there.
That's just me. There's some other follow up articles that you can download in what the waves of what we thought 2 years ago, what the waves of this pandemic might look like, and instead of Macron just came and said, We're just here, and we're just here all the time. I can tell you this, that the number of reported incidents among students, because I thought that I have to get a positive report.
Really, I'd say it's half of what it was 3 months ago. So I'm encouraged. But I'll simply say, don't let your card down.
Okay. So in summary genomics is pivotal to fighting Coronavirus, we went from the sequence, allows us to figure out what mutations are going on. The sequence allows us to develop an Mrna vaccine. We don't know where Coronavirus came from. There is still a lot of research going on. Some of it is obviously politically charged, because, You don't certainly want to to be digging up.
digging up evidence that could point to to opportunities messed. I'll just leave it at that. But you have seen, certainly that there's a putative ancestor. I think that our Atg, 103 is obviously an ancestor in my mind, is a putative ancestor to the Wuhan sequence, and what happened between 2,013, and where it is right now remains a mystery. My opinion.
How can bioinformatics and form therapeutics? Well, if you, if your spike protein is changing, you might have to change the shape of some of your.
and I'm not in therapeutics, and many of the, if you guys remember.
then President Donald Trump was infected in November of 2,020,
and he got a model from the antibody. They're no longer as effective because we've had other sequences that come out, but that could have saved his life.
How do we develop so? Surveillance tools just by being on top of it in China did an extraordinary job staying on top of surveillance for years and years and years, and just doing nasal swaps and just figuring out where people were sick.
And and that was important in and really keeping that down.
So where is the next covid likely to strike? We don't know.
but certainly being on top of having a a solid world health or plan right, having countries that are allies and not adversaries would help, certainly, and then working, in my opinion, working collaboratively
to move as quickly as we can to respond with vaccines and treatments.
All right. So that's where we are. And then, Adrian, do you have the question list?
user avatar
Adrienne Nguyen
01:32:50
We're right at 1030. So I didn't do too badly.
user avatar
Robert Cormia
01:32:55
So right at 1030 we've covered what is N Cbi? It's a bioinformatics portal. What kind of data is there all kinds of genomics data. So sequence data proteins,
obviously amino acids, nucleotides snip data, which is your variant variance data.
you have tools that you can use. You have organisms, everything, from viruses to bacteria, to insects, to plants, to mammals, or it's all there.
And I think this is so, I'm sort of getting further and further away from my area of I don't want to even say expertise familiarity.
But I'm hopeful that over time that we're going to be able to get sequence data from.
we have humans that have been frozen. And I right for thousands and thousands of years, and to be able to recover that DNA and understand what pathogens that they have to fight.
There is literature, data. And Ncbi, it's really important.
user avatar
Unknown Speaker
01:33:58
how does genomics data inform Mrna development? We have to have a target string.
user avatar
Robert Cormia
01:34:04
And every time, like with the on the Chron, I think we've waited way too long to get an overcome back scene out. We could have done it earlier.
Now you have a by Valent next, so you have the consensus sequence in that vaccine, which is the you you guys have have seen the consensus sequence. So it's one amino acid different than move on.
And then you have the
the over.
It is amazing. But the Mrna vaccines they didn't come out of nowhere. There was a 25 to 30 year development. People spent their careers painstakingly.
making advantage advances to get to where we were able to do this. We had an injectable vaccine inside a human, and I believe that person she was at Kaiser in Santa Clara within a hundred days.
so Moderna really came forward with it. The Us. Government worked hard.
user avatar
Unknown Speaker
01:34:57
What other questions are there.
user avatar
Robert Cormia
01:35:01
and I cover most of them.
Oh, important! How will you use? Everyone forgets this.
How will you use genomics data?
You could use it to tell the story right to to inform people about what you've learned. Tell me what you learned and how you might use it, that I was.
Please let me. Okay.
So how are we doing? What questions do you guys have? I have absolutely nowhere to go this morning. I'm not driving.
So if you have any questions in bioinformatics
user avatar
Unknown Speaker
01:35:35
and try to do my best with Covid. I'm not a microbiologist for all of this.
user avatar
Robert Cormia
01:35:40
Let's see, Holly. she was there earlier. I don't know if it is still there. Only did you learn anything today? You can put that in chat.
She took biology 40 or something
for the O 102 group you'll be. There's a bioinformatics assignment.
that you can upload to. I'm encouraging you to get that done by Sunday. There's an except until that goes past that date.
And for the 304 group I've set the assignment date as one week from today, and it will close on the following Sunday.
So you've got some time. Do at least a page of work for 5 points.
and if you do twice as much you'll probably get 50% more.
Liz, did you learn something new today? In Bella?
user avatar
Elizabeth McGee
01:36:54
I learned a lot new today.
user avatar
Robert Cormia
01:37:02
I always ask you, you know your trading time, your training time for experience.
user avatar
Elizabeth McGee
01:37:08
Yeah, it was interesting.
user avatar
Robert Cormia
01:37:10
There's the what I like about this topic is, it's approachable. You guys are, you know, you're smart. You're smart cookies to be in in 38, doing as well as you are, so if you can copy and paste it, just exploring a portal.
you can have tons of fun at N. Cbi. If you ever need to do a literature search of a human malady, go to Omem, the online Mendelian inheritance of man. As I said it at a certain point in our lives we will all be struck down with an inherited disease. That's how we're designed
and it's a great place to look things up.
if you've never. if you've ever had a curiosity about your own genetic makeup, get a 23 and me test their loads of fun.
All right, I'm gonna go ahead. Are there any questions on the assignment? If there are none, I'm going to stop recording?
user avatar
Justin Tu
01:38:09
I have something I don't. It's only a question, but more like
So bioinformatics they've been using that for.
I don't know how to put. I guess generations to study how viruses have been changing over the decades.
user avatar
Robert Cormia
01:38:27
So genetic information sequencing goes back to.
We had a code on lookup table in the late sixties.
and so probably 50 years of being able to use sequencing techniques. We didn't have sequencing machines like we like we have now.
And so companies like celera. What was cel around? I can't remember who their CEO was.
but we sequence the first human in 2,000. Who was that?
I don't remember his name.
He's a famous scientist. He, arrogant, is now but extremely brilliant. He grew up in San Mateo.
He actually went to
but he held it started to sell or see developed sequencing machines. So I would say, we've been using sequence data fast and hard for at least a couple of decades.
and where it's very, very important, is.
among other things, a test that I did a couple of years ago was looking at the Allele for dementia. As you get older, you know you'll be curious. Do I have an allele? For there, you know you'll have 2 different alleles.
and one can be fast and slow in terms of processing a protein. and that can be, you know, related. It's not strongly correlated. right? But it will give you some idea of your future.
I believe that it will it it. Our genetics helps us with
targeted
treatments in terms of medication. A lot of medicines will have an adverse effect depending on one genotype. So if you're of a particular Gina type, if there are 2 genotypes in your one where you have an adverse response, then your pharmacist probably doesn't want to, you know. Have that in your hand
versus another therapeutic that could be very effective against another population, and you just have to keep them separated. So that's another place where it is certainly targeting your cancer. If you have any form of cancer. So just in one area that it genomics is exceedingly important
when I studied this 20 years ago is in child leukemia. And so in childhood leukemia, you you do what's called tumor typing. And so you pull the tumor out right away and figure out from the sequence what type of tumor is, and then you go into a database and ask what therapeutics really work when we tried treating this leukemia
and patience so for a medication.
I I don't think that genomics will ever be used to discriminate against people. Because I will say this very strongly, we all have multiple ways that will undo us as we get older. And so, if you want to look for points of defects they're simply built in.
It's that's what inherent it is it about. So there's no point in discriminating. And there's a lot of point and trying to figure out if I've inherited a certain haplo type, a certain tendency, what can I do in my life that I change my diet right?
That is always important. no particular exercise, or the things that I should avoid.
But to, you know, to say that there is a gene for cancer. There are multiple genes that will allow you to be more susceptible to cancer, less able to fight it.
and we know those those are. Say, break a one break to 2 jeans, but that doesn't. That's not a best sentence. You know. Genetics is just one piece of it. You have something called your transcript on.
and that's where you influence your life and your genetics to your life habit.
This is where, I'll say, did you know that studying hard and doing math leads to longevity.
user avatar
Justin Tu
01:42:19
If Nope.
user avatar
Robert Cormia
01:42:21
you know what I know, I asked these things. No one's ever heard of that.
We'll see if it works all right. Is this a good place to leave it?
Yes, thank you very much.

Bioinformatics activity - Zoom replay link: Sp23 CHEM F030A SURVEY OF INORGANIC/ORGANIC CH 03, 04 Cormia 40393, 40073

 

https://fhda-edu.zoom.us/rec/play/5IVYlA_rYiEk90EsaA-OXlhStGn9HW6sZVBE6hZlAuEODeByLIrtSPgBYi8su03O0sc3xuri8HdQZnCw.Ek09ESZXanZuzxTe?canPlayFromShare=true&from=share_recording_detail&continueMode=true&componentName=rec-play&originRequestUrl=https%3A%2F%2Ffhda-edu.zoom.us%2Frec%2Fshare%2Fdzko4sDFoPKsp4KsbmZzdAjBrtXFg8jyEjjdZbYmjXKOA1PQnaaIg7NtZmPadf6D.7310zSe1inlrV3I6  

COVID Bioinformatics Spike Protein Sequences

>Bat coronavirus RaTG13 Spike Protein 

MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSSTRGVYYPDKVFRSSVLHLTQDLFLPFFSNVTWFHAIHVSGTNGIKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPPGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTDSIVRFPNITNLCPFGEVFNATTFASVYAWNRKRISNCVADYSVLYNSTSFSTFKCYGVSPTKLNDLCFTNVYADSFVITGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSKHIDAKEGGNFNYLYRLFRKANLKPFERDISTEIYQAGSKPCNGQTGLNCYYPLYRYGFYPTDGVGHQPYRVVVLSFELLNAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNASNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSRSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGSCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWPWYIWLGFIAGLIAIIMVTIMLCCMTSCCSCLKGCCSCGSCCKFDEDDSEPVLKGVKLHYT


>Wuhan-Hu-1 SARS-CoV-2 Spike Protein 

MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPRRARSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWPWYIWLGFIAGLIAIVMVTIMLCCMTSCCSCLKGCCSCGSCCKFDEDDSEPVLKGVKLHYT

>SARS CoV-2 Spike Protein

MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPRRARSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWPWYIWLGFIAGLIAIVMVTIMLCCMTSCCSCLKGCCSCGSCCKFDEDDSEPVLKGVKLHYT

>B.117 Alpha Variant Spike Protein with deletion and mutations (NY Times article) 

MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAISGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTYGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIDDTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSHRRARSVASQSIIAYTMSLGAENSVAYSNNSIAIPINFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILA]RLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTHNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWPWYIWLGFIAGLIAIVMVTIMLCCMTSCCSCLKGCCSCGSCCKFDEDDSEPVLKGVKLHYT

>SARS-CoV-2 Delta Variant Spike Protein 

MFVFLVLLPLVSSQCVNLRTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDVYYHKNNKSWMESGVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYRYRLFRKSNLKPFERDISTEIYQAGSKPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSRRRARSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQNVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWPWYIWLGFIAGLIAIVMVTIMLCCMTSCCSCLKGFCSCGSCCKFDEDDSEPVLKGVKLHYT

>SARS-CoV-2 Omicron Variant Spike Protein (OSF.io)

MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHVISGTNGTKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPIIVREPEDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFDEVFNATRFASVYAWNRKRISNCVADYSVLYNLAPFFTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVSGNYNYLYRLFRKSNLKPFERDISTEIYQAGNKPCNGVAGFNCYFPLKSYSFRPTYGVGHQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLKGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEYVNNSYECDIPIGAGICASYQTQTKSHRRARSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLKRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKYFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFKGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNHNAQALNTLVKQLSSKFGAISSVLNDIFSRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWPWYIWLGFIAGLIAIVMVTIMLCCMTSCCSCLKGCCSCGSCCKFDEDDSEPVLKGVKLHYT

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