- Hi everyone.
Welcome to BIEB 152.
This is lecture number two.
Okay.
So each lecture, I wanna start
by taking the temperature of the epidemic.
So this is where I go over a few slides
updating you on how it's proceeding,
whether or not our interventions are working,
whether or not there's hopeful news
or maybe bad news,
and so we'll do that,
and then we'll move on to the actual course content.
Okay, I wasn't gonna,
this is an update of the data that I showed you last time.
I wasn't gonna show this,
because it's just gonna look more of the same.
This phylogeny here, this evolutionary relationship
of SARS-CoV-2,
it's gonna probably remain very robust.
There's so much data that's put into this phylogeny,
that I don't anticipate that the patterns
will change much,
and certainly the patterns to right
of the spread of the disease around the world.
You know, it's spread, it's everywhere now.
It's sort of mounting,
and endemic infections in each of the countries.
But I did wanna go back to this data,
because I got an email asking about this idea that,
UCSD, it appears,
hasn't been hit as hard as other places,
and people are wondering that they had
a really bad cold in the fall,
and was that actually some sort of precursor
to the current strain of SARS,
and did that give them immunity to SARS-CoV-2?
And I wanna say that I don't believe in that theory.
And that it is hopeful that this idea
that maybe somehow in San Diego,
we were pre-exposed to this pathogen,
and we've developed immunity,
and why I'm worried about that kind of thinking spreading,
is it's good to be hopeful,
but not so hopeful that we begin
to influence our own behaviors,
and stop doing things like social distancing.
And so the reason why I don't think
that theory holds is this data here.
And so if you see on this x-axis here,
this is, these are gates
in which certain strains were isolated in sequence,
and then they're using evolutionary biology
and phylogenetic reconstruction
to be able to predict when the strain probably emerged
from bats to humans,
and it certainly emerged,
or all of the data suggests
that emerged in early December,
and that was in Wuhan.
So it was confined to a region of the world,
and then from there, it spread out.
And we have so much data now that suggests that,
that I just don't think that that's actually gonna change.
So, there's also a lot of theories about,
was this in Italy first?
No, the data does not suggest that.
Other theories are that this was a lab strain.
The data we'll look at later in this lecture
and later in the course,
suggests that this is certainly not a lab strain,
that this looks like an actual variant
that's very similar to variants
that we've seen in bats,
in sampled a couple years ago.
So it's not a lab strain.
It emerged in Wuhan, and spread around the world,
after that.
Okay, I'm gonna keep moving.
So, this is more about checking the temperature,
of what's going on.
So, this is a plot that I showed you last time,
and I had fit this little curve here, optimistically,
hoping that we were no longer
in the exponential increase phase of spread
within the United States,
but when we look at the...
Sorry I have to move the window.
When we look at the data from two days ago
and from today, we find that my fit to that curve
was overly optimistic.
The rate of increase of the spread
within the United States, is still increasing.
It does appear to be slowing down,
but of course, just a few data points
don't really make a trend.
We have to see more data and see how this unfolds.
Certainly the CDC is predicting
that in the next couple weeks, nationwide,
that's when it's gonna be the worst
for the United States,
but remember we're states,
and we all have different behaviors in each state,
and different economies and different cultures,
and so, and different times
in which we got the disease,
and so it's probably a state-by-state basis,
in which you're gonna see this sort of peak,
and then hopefully dropping back down.
It looks that that is what happened already
in Washington.
I would say New York is probably at the peak stage now,
will be dropping,
and then in the future,
it'll sort of cycle through other states as well.
So remember to remain social distancing.
It's the best thing that we can do right now.
Okay, and I showed you this confusing plot last time,
and I wasn't gonna show it again,
because these lines are all over the place.
That y-axis is complicated.
That y-axis, I will explain the math behind it,
in three lectures when we talk about natural selection,
and I go over exponential growth.
For now, just know that higher values are bad.
Lower values are good,
and that if you have a flat line,
in this graph, that means that you're still
in exponential expansion of the disease.
And so what's kind of good news for the world
is that in all of these different countries,
the trajectory is downwards,
rather than flat,
and that means that,
they're leaving the exponential expansion phase
of the disease, and it's hopefully grinding down.
It won't be as big of a problem in the near future,
but the U.S., you can see is kind of
all over the place.
This is 'cause we're a giant country,
and there's probably different kinds of dynamics
happening within each state,
and so it's hard to just look at this
sort of combined data,
but it also reminds us,
and we're barely deviating at all
from exponential growth,
and so it reminds us that we have to remain vigilant
on social distancing and other practices.
The CDC is contemplating uses masks,
face masks now for the general public,
as a precaution,
and as a way to limit the spread,
and I would say don't use masks
that are the ones that should be used in the hospital.
We should give them to the people in the hospital.
But there are lots of ways
to make your own mask at home
that are relatively effective.
And so, I do suggest doing that.
I haven't actually worn a mask outside yet,
but I think we should sort of break the kind
of social barrier and acceptability
of wearing masks in the United States,
and maybe start doing that.
Okay, and this data that I showed last time,
but this is an update on it.
And what we can see here
is that this is the,
this temperature data,
from the smart thermometers
that are spread throughout the United States,
by Kinsa Healthcare.
And here are some plots,
and they just show that COVID-19
was causing these atypical patterns,
and now that, once we started social distancing,
now we've actually dropped below
what they expected would be the normal level
of sick people, based on temperature
across the United States.
So social distancing is having a real effect.
This is the data that shows it,
and so we just need to keep on social distancing.
Okay.
So, let's keep moving forward.
So, you know, the other data I showed
is kinda bad data.
It seems that we're still
in the exponential expansion phase
in the United States,
in most of the states.
But, so I wanted to share some good information,
and this a little bit old,
compared to a lot of the information
that I've been sharing,
but basically the NIH has started
a clinical trial of a COVID-19 vaccine.
All over the world,
people are coming together
to develop these vaccines.
There's trials either starting or have started
in other countries in the world,
but this is very promising,
and hopefully we can have a vaccine,
and just sort of forget about SARS-CoV-2.
I have this picture here.
That's just a model of the virus itself,
and then it has these red protrusions,
and that's this,
this structure, this protein here,
are those red protrusions.
That's the S-protein.
That's the host recognition protein,
and this is highlighted,
because this is likely the feature
that they're using to,
to put in the vaccine to elicit immunological response
from our own bodies
to become immune from this viral particle.
The vaccine is being carried out
by this collaborative effort,
which is amazing.
I can't even imagine putting all
of these pieces together.
But you have Kaiser Healthcare.
They have hospitals,
and all over the west coast, especially,
but in Washington, where they're doing
this clinical trial.
You have the NIH, through one of their,
the NIAID, funding the science,
and also scientists that are associated with them,
doing the research.
You have Moderna, which is a company in Massachusetts,
in Cambridge,
and they're helping the development
with their scientists,
and then you have this Coalition
for Epidemic Preparedness Innovations in Norway,
that's actually manufacturing some of the,
sorry, the vaccine.
So it is, it's this collaborative effort,
but I have to say that it's more
than just this one group and this one collaboration.
In the "New York Times," just yesterday,
they're pointing out
that scientists are working together
across the world,
whether they're in the public sector like I am,
or in the private sector at places
like Moderna.
They're working together, sharing data,
and it's a great thing.
There was news that Trump tried to buy a,
or get a company from Germany to move over here,
so that we would have the rights, I guess,
to the vaccine, or maybe not the rights,
but control over the vaccine,
and China also proposed a similar kind of deal
with another company in Germany.
And so it seems that our politicians
are sort of gonna fight over this vaccine,
but at least the scientists
are not engaged in that.
So, hopefully they'll be enough for everybody,
and we'll get over this soon.
What's the timeline for vaccine testing?
At least a year, so it's gonna take a long time.
We have to continue social distancing
and other practices.