corona.txt

UNIT 8B: Coronavirus

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EXTRA

Done in great haste; should add simple models of human response to pathogen damage, among other things

Make it all more actionable

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SEC Initial projections

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REPSLIDE Flattening the curve

FIG dd/flatSimPlots.Rout-0.pdf

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REPSLIDE Flattening the curve

FIG dd/flatSimPlots.Rout-1.pdf

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REPSLIDE Flattening the curve

FIG dd/flatSimPlots.Rout-2.pdf

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REPSLIDE Flattening the curve

FIG dd/flatSimPlots.Rout-3.pdf

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What happens when we flatten?

BCC

PIC CFIG dd/flatSimPlots.Rout-3.pdf

NCC

	POLL Which scenario has the lowest total number of cases shown (area under
	the curve)? | Which scenario has the fewest total cases? No control; 20%;
	40%; all the same

EC

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REPSLIDE Flattening the curve

FIG dd/flatResponsePlots.Rout.pdf

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Flattening the curve

DOUBLEFIG dd/flatSimPlots.Rout-3.pdf dd/flatResponsePlots.Rout.pdf

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Flattening the curve

	More flattening than reduction in total

		ANS As long as \Ro\ is medium-to-large we expect almost everyone to get
		infected in a simple model

		ANS Changes in \Ro\ don't affect area under the curve

		ANS But they can have big effects on the peak

	What are some benefits of just flattening?

		ANS Less peak demand

		ANS More time to find solutions:

			ANS Better treatments

			ANS Vaccines

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Behaviour and policy change

	Why were our early models so wrong?

		ANS People and governments changed behaviour much more than we expected

			ANS Fear of overflowing hospitals and chaos in general

		ANS Population heterogeneity

			ANS Not everyone mixes the same, or at the same time

			ANS A less important effect so far

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TSEC Endemic coronavirus

	POLL What does it mean for \scv\ to become ``endemic'' | What do we mean by endemic?

		ANS Not going extinct

		ANS Not \emph{too} much variation in annual incidence

	What it doesn't mean:

		ANS Not fluctuating

		ANS Not dangerous

	COMMENT A lot of double negatives, make sure you're clear!

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Disease burnout

	A disease that has a big epidemic and leaves very few susceptibles
	behind can go locally or globally extinct -- we call this burnout

	Lots of evidence for influenza or measles burning out in isolated
	areas during less global times

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REPSLIDE Disease burnout

FIG sims/recurrent.plots.Rout.pdf

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REPSLIDE Disease burnout

FIG sims/recurrent.newplots.Rout.pdf

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Disease burnout

DOUBLEFIG sims/recurrent.plots.Rout.pdf sims/recurrent.newplots.Rout.pdf

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Adaptive responses

	How do people respond to fear of \cnv?

		ANS Masking, distancing, booster shots

		ANS Mandates, lockdowns

	What effects do we expect if people's worry levels about \scv\
	fluctuate with virus levels?

		ANS Will increase spread when levels are high (or growing)

		ANS Tendency to stabilize the dynamics

			ANS Smaller outbreaks, less chance of random extinction

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Burnout and \scv

	Burnout seems very rare in the global era

	Adaptive responses work against burnout

		When things are bad, people are more careful: less overshoot

		When things are good, people are less careful: less chance to
		keep the virus down

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TSEC Pathogen aggressiveness

	POLL Should viruses evolve to become more or less dangerous? more; less; it depends

		ANS It depends

		ANS The virus evolves in the way that's best for the virus

		ANS Host death and host recovery are equally bad!

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REPSLIDE Tradeoffs

FIG life_history/frontier.Rout-2.pdf

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Which strain will win?

	If the competing strains produce similar immune responses, this is
	exactly like equal competition: infections are competing for a
	single resource:

		ANS Susceptible humans

	The winner will be the strain that has the highest ``carrying
	capacity'':

		ANS Removes the largest number from susceptible pool

		ANS Highest \Ro

		ANS This could be more or less deadly

		ANS Removal by killing and removal by recovery have similar
		effects on the virus

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REPSLIDE Pathogen aggressiveness

FIG life_history/aggressionPlots.Rout-0.pdf

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REPSLIDE Pathogen aggressiveness

FIG life_history/aggressionPlots.Rout-1.pdf

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REPSLIDE Pathogen aggressiveness

FIG life_history/aggressionPlots.Rout-2.pdf

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Pathogen aggressiveness

BC

CFIG life_history/aggressionPlots.Rout-2.pdf

NC

	Pathogen will evolve to maximize \Ro.

	Is not affected by whether duration $D$ is ended by host death, or by immune
	system clearing the pathogen

EC

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Human evolution

	We have evolved very good immune systems, but we can't always stay ahead of
	the viruses

	Should people evolve to favor the spread of more or less dangerous viruses?

		ANS Less dangerous!

		ANS Viruses that do well in the upper respiratory tract may spread better

		ANS Viruses that do well in the lower respiratory tract are more dangerous

		ANS Have we evolved to make this a tradeoff for viruses?

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Omicron example

	Omicron spreads \emph{much} better than earlier \scv\ viruses

	It does less well in the lungs and better in the upper airways

	\scv\ \emph{may} be evolving in a less dangerous direction

		There is no guarantee

		Delta spread better and was \emph{more} dangerous than previous 

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SEC The future of \scv

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What is different about \scv?

	What is the main difference between \scv\ and other colds and flus?

		ANS There was almost no immunity before 2020

		ANS It is still adapting to humans

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Human immunity

	The immune system is very complicated and very effective

		T cells and B cells recognize different parts of the
		\textbf{pathogen}

		Even partial recognition often protects people against severe
		outcomes

	Vaccines

		Also likely to protect against severe outcomes

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Immunity and the virus

	Our immune systems may see different variants of the virus
	differently:

		Cross-immunity to a different strain might be less effective than
		direct immunity to the strain I was infected with

	How will this change our picture of competition?

		ANS It makes it easier for different strains to co-exist

		ANS We don't know yet how much easier. Some viruses (HPV) have
		dozens of co-existing strains. Others (influenza A) have limited
		cross-immunity, but strong population-level competition

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Herd immunity

	POLL What is meant by herd immunity?

		ANS A level of immunity in the population that interferes with
		\emph{the spread of the pathogen}

			ANS In particular, the phenomenon of immune people protecting
			others by reducing population-level spread

		ANS May or may not mean that the pathogen cannot survive

	How much herd immunity do we need?

		ANS About $1-1/\Ro$ for $\Reff\approx1$

		ANS In the long run, we expect to see about the right number of
		susceptibles to keep the infectious individuals in balance

		ANS If we can get above this level through vaccination, there is
		a chance to drive the pathogen extinct, in theory

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Can herd immunity drive \scv\ extinct?

	What extinct viruses do we know about? How did they get there?

		ANS Smallpox and rinderpest

		ANS Vaccination!

			ANS Herd immunity by vaccination is the only realistic hope for
			driving \scv\ extinct

			ANS Burnout did not work!

		ANS What about our luck with measles, mumps, polio, influenza,
		etc?

			ANS \scv\ is mutating more effectively than most of these!

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Levels of disease

	In the long run, how long we go between \cnv\ infections will likely
	depend mostly on how long our immunity lasts, or else on

		ANS how often we get vaccine boosters

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PRESLIDE Terminology

FIG webpix/giantSpider.png

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Just another seasonal coronavirus (JASC)

	This is a \emph{theory} that lack of population immunity is the
	\emph{only} difference between \scv\ and other viruses that cause
	common colds

		Some versions of the theory account for \scv\ continuing to
		evolve in that direction

	POLL What do you think of this theory?

		ANS We all had versions of the common cold viruses as young
		children

		ANS The common cold viruses face a high level of population
		immunity and can't have big outbreaks the way \scv\ does.

			ANS Smaller doses may be correlated with less-severe cases

		ANS It's good to hope, but we shouldn't count on it

		ANS We don't know how \scv\ is going to evolve

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Moving forward

	We need to pay attention and figure out how strongly to prioritize
	\scv\ control

	We also need to be thinking about detecting and responding to the
	next pandemic!

		ANS Better surveillance

		ANS Routine monitoring of viruses from patient samples