SOME BASIC BIOLOGYTO HELP US UNDERSTAND
THE COVID-19 PANDEMIC
AND HELP YOU ANSWER MOST OF YOUR OWN QUESTIONSDICTIONARY
DiseaseImmune system

ProteinPopulation

Virus

Inflammation

CellSpecies

Bacteria

Antibody

Reproduce

Contamination

PathogenDNA

Public health

Pathogen hostRNA

Infectious disease

Infection

Cell membrane

Epidemiology

LET’S WARM UP

Please think for a minute: What questions do you have about COVID-19?
Please write your questions down. You will look at them again at the end of the lecture.

MAJOR QUESTIONS How was this coronavirus “born”? Where did it come from?
 Why people have different response to it? Why some get very sick and others - don’t? Is it REALLY that serious?
 Why the coronavirus changes over time? Is that normal?
 Why we don’t have a cure for coronavirus, a pill or sort?
 When can we finally travel again? Didn’t we have enough restrictions already?

What is a virus? What is bacteria?
Are all viruses/bacteria causing disease?
How do viruses/bacteria cause disease? Why do they cause disease?

LET’S START FROM THE BEGINNIGPATHOGENS
Virus: needs a host to reproduce

Bacterium: can reproduce by itself

genetic material

or DNA

protective cover

wikipedia

https://www.biologyonline.com/dictionary/bacteria

PATHOGENSCOVID-19 disease is caused by virus from the Coronavirus familywith “formal name” SARS-CoV-2
Coronavirus family has many other members,
many of them cause only light infections

PCR test
Looks directly for viral genetic material in the sample
If there is virus – there is viral genetic material
Shows that the virus is CURRENTLY present

Wikipedia

DISEASEWhen body functions are disrupted – we feel sick To cause a disease pathogens have to:Enter the body / enter individual cells

Kill cells

Disrupt body functions

Why viruses/bacteria want to invade animals (or plants)?
They want resources from us – food, shelter…
Sometimes getting what they want causes destruction(not very gentle invaders…)

Entering the host body is enough for most bacteria
BUT not for viruses – they need to get into cells!
Not all viruses or bacteria are pathogens – many do not cause disease at all, OR not in humans

HOW DO VIRUSES ENTER HOST?
VIRUSES NEED A CELL to reproduce

https://www.nature.com/articles/d41586-020-013157?utm_source=Nature+Briefing&utm_campaign=7f14edf8c1-briefing-wk20200507&utm_medium=email&utm_term=0_c9dfd39373-7f14edf8c1-42214427 2021/7/2

So they need to enter a cell…

How do viruses enter into cells?
By attaching to cell membrane structures!

Why do thesecell membrane structures exist…?
The cell needs them for its own functions!

wikipedia

WHAT HAPPENS AFTER VIRUSES ENTER HOST?
https://www.nature.com/articles/d41586-020-01221-y

Viruses enter a cell,use cell’s internal structures to reproduce
and when they leave, they often destroy the cell…

It takes time to invade a cell, reproduce, invade other cells,
reproduce…cause enough damage to be noticeable…

This time is called INCUBATION PERIODIn COVID-19 this is about 2 weeks

WHAT HAPPENS AFTER VIRUSES ENTER HOST?
Wikipedia

For a virus SPEED IS EVERYTHING:
making as many copies of itself as quickly as possible
before the immune system fights back!

PRECISION IS LESS IMPORTANT
Some virus copies might have small changes in the genetic code…
wikipedia

EPIDEMIOLOGY
We can look for these genetic changes!
And create a map of relationships

https://cen.acs.org/biological-chemistry/genomics/genomic-epidemiology-tracking-spread-COVID/98/i17

EPIDEMIOLOGY

https://nextstrain.org/ncov/global

EPIDEMIOLOGY

https://nextstrain.org/ncov/global
https://cen.acs.org/biological-chemistry/genomics/genomic-epidemiology-tracking-spread-COVID/98/i17

Some virus copies might have small changes in the genetic code…
some copies might have BIG changes…

Wikipedia

WHAT HAPPENS AFTER VIRUSES ENTER HOST?
wikipedia

JUMPING SPECIES
https://www.nature.com/articles/d41586-020-01315-7?utm_source=Nature+Briefing&utm_campaign=7f14edf8c1-briefing-wk20200507&utm_medium=email&utm_term=0_c9dfd39373-7f14edf8c1-42214427

Viral ATTACHMENT structures are made based on genetic instructions!
As the virus replicates very fast
- small – or big - changes in the genes happen (mutations)- small – or big - changes in the attachement structures may result!
These new MUTATIONS in the ATTACHEMENTS may lead to:- EASIER attachment – easier to enter host cells- more DIFFICULT attachment – more difficult to enter host cells- IMPOSSIBLE attachement – no longer can enter host cells
BUT ALSO may lead to new ability to attach to ANOTHER SPECIES!

JUMPING SPECIESNormal viral attachments
Fit perfectly
human cell
membrane structure

Mutated viral attachments
Don’t fit anymore
human cell
membrane structures

Invasion of human cells
Infection in humans

Invasion of anotheranimal cells
Infection in NEW SPECIES
Fit perfectly another species’s cell
membrane strcutures

JUMPING SPECIESThis is how viruses JUMP on to NEW SPECIES.
HOWEVER the virus with mutated attachements
HAS to MEET its NEW HOST.
IF they NEVER MEET – there will NEVER be an
infection in a new host.

https://www.nature.com/articles/d41586-020-03218-z?WT.ec_id=NATURE-20201119&utm_source=nature_etoc&utm_medium=email&utm_campaign=20201119&sap-outbound-id=FBA69AF14A8C2C4CD2B401B7452050B6ED15EF61

The new baby viruses are ready to look out for new host cells!

Wikipedia

WHAT HAPPENS AFTER VIRUSES ENTER HOST?
wikipedia

HOW DO PATHOGENS SPREAD BETWEEN INDIVIDUALS?
Major routes of infection transmission: Fecal-oral routecontaminated hands – to mouthcontaminated food Airborne routedroplets from cough of one - into nose of another

contaminated dust

 Direct contact route


sex



vector-borne: bite

Wikipedia

HOW DO PATHOGENS SPREAD BETWEEN INDIVIDUALS?
Let’s see the world from a pathogen’s point of view A few hosts living close by:A few chances to infect – a few chances to reproduce

Faster all hosts will become immune (or die) – SMALL DISTRIBUTION = SMALL RESULTS

 Many hosts living close by:Many chances to infect – many chances to reproduceLonger there will be new hosts to infect – BIG DISTRIBUTION = GREAT SUCCESS Many hosts traveling frequently and going to new places with many new hosts

Many new groups with new hosts to infect – even BIGGER DISTRIBUTION – GREATER SUCCESSEXAMPLE: THE “SPANISH” FLU

Wikipedia

Wikipedia

EPIDEMICS AND PUBLIC HEALTH
WHY we call some diseases epidemic - and some – we don’t care?
 Everyone has E.coli in their intestines – but this is not a pandemic?
 Imagine EBOLA was discovered in Nagoya – say, 10 cases…

we would probably be in lock down on the spot!
Pathogens differ in TWO main characteristsics:


How FAST they are – how fast they can be passed from one individual to another

How SERIOUS they are – how many infected hosts get severe disease – or die

If a virus is VERY SERIOUS, even if not very fast – many people will get very sickIf a virus causes severe infection/ kills a small number of hosts, but is VERY FAST – many people will get very sick

EPIDEMICS AND ECONOMICS
 Each city has X number of hospitals
 Each hospital has X number of beds for seriously ill patients
 These numbers are based on some general expectations:

how many people will PROBABLY get sick every day/every month

IF all of a sudden A LOT of people get seriously ill – there won’t be enough hospital beds, equipment andmedical personel to treat them
Simple economics

EPIDEMICS AND GAMES

https://www.engadget.com/plague-inc-the-cure-mode-now-available-233222554.html

For a virus SPEED IS EVERYTHING:
making as many copies of itself as quickly as possible

Wikipedia

BEFORE THE IMMUNE SYSTEM FIGHTS BACK!

WHAT HAPPENS AFTER VIRUSES ENTER HOST?
wikipedia

WHAT IS OUR BODY DOING ABOUT THIS?
STEP 1: INFLAMMATION:“INVADERS!” alarm
Always the same reaction to all pathogens
High temperature
Blood vessels enlarge: swelling, redness
Immune cells move into tissues from blood
Sometimes the ALARM ITSELF
is too long and too strong
can cause damage to body cells
and worsen the disease
THIS happens in worst COVID-19 cases

Wikipedia
Wikipedia

WHAT IS OUR BODY DOING ABOUT THIS?
STEP 2: The ADAPTIVE IMMUNE SYSTEM gets activatedhttps://www.nature.com/articles/d41586-020-01221-y

WHAT IS OUR BODY DOING ABOUT THIS?
ANTIBODIES:
Large proteinsthat can bind SPECIFICALLY
to surface structures on a pathogen
Produced by immune cells
AFTER EXPOSURE to a pathogen
which TAKES TIME
Producing cells increse in numbers:
SPECIFIC “MEMORY”
for fighting future infections by the same pathogen

https://www.nature.com/articles/d41586-020-01221-y

IMMUNITY
Some individuals get very sick – some a little - some not at all!
WHY?
 We are slightly GENETICALLY different

We are slightly different in HEALTH
We are slightly different in AGE

 We get exposed to different AMOUNT of the virus

The viruses land on different PLACES in our body

ALL of us, after recovering from infection, keep an IMMUNE MEMORY of it and are FAST TO FIGHT it the second time!

HERD IMMUNITY
Once majority of individuals in a population are immune against a pathogen – it has very little chance to invade
 “MAJORITY” – around 70% - is considered enough to protect the rest

 Japan is endemic to Japanese encephalitis

I’m not immune to it. But I am not worried.
WHY? Most Japanese nationals are VACCINATED against it.
 RABIES is an extremely deadly disease. We are not immune. But we are not worried.

WHY? Because all cats and dogs around us are VACCINATED multiple times (every year).

For all our scientific and medical advances why don’t we have a PILL or sort by now?

HOW CAN WE HELP?

HOW CAN WE HELP?

MEDICINES: pills and other fancy stuff
We have great arsenal against BACTERIA

We have very little against VIRUSES!

ANTIBIOTICS
target bacteria’s reproduction machinery
which is slightly different from ours

WHY?
Viruses use OUR reproduction machinery
Targeting them means targeting our own cells…

HOW CAN WE HELP?
VACCINES!
Teach the body immune system to recognize a pathogen BEFORE it meets it
Be ready and attack it FAST before it causes any damage.
For viruses, this is the only real strategy we have…

VACCINESClassics:

New gen:https://www.nature.com/articles/d41586-020-01221-y 2021/7/2

VACCINES
What it takes to develop a vaccine?
A lot!
You have to know WHAT you are fighting againstYou have to decide HOW to expose the immune system – trials in cells and labsYou have to check whether your mixture is NOT HARMFUL – safety trials on animals

You have to check whether your vaccine is actually EFFECTVE – efficacy trials – on animals and then on humans

 This usually takes decades!
 EBOLA vaccine took 5 years to first efficacy results! A record
 COVID-19 vaccine took less than an year to first efficacy results! This is a new record!

The discovery of the HIV virus won a Nobel Price not that long ago!

LET’S SUM UP

HOW DOES SCIENCE WORK?
Scientific research is a detective allowed to ask only YES/NO questions
Public question: What causes a disease?

Pregnancy test

 Science questions to answer the public questions:Is it a toxin? Yes/No

Is it a bacteria? Yes/No

Is it a virus? Yes/No

Is it virus X?

Is it virus Y?

Is it virus Z?

………

Answers exactly ONE question
YES or NO

PUBLIC HEALTH
Not all pathogens are serious enough to cause public health concerns. But some ARE serious enough.
First COVID-19 cases were identified in WINTER, amidst high influenza infections – which rarely cause pneumonia!
Prevention has TWO arms:
Remove chances of exposurePrepare the immune system

These principles are NOT ONLY for COVID-19!
There are many other diseases – including the common flu – that can be reduced by following public health practices.
We live in a world relatively free of serious infectious diseases because of PREVENTION – not because of treatments!

MAJOR QUESTIONS - REVISITED
Hopefully now you have the answers of the questions we asked in the beginning: How was this coronavirus “born”? Where did it come from?
 Why people have different response to it? Why some get very sick and others - don’t? Is it REALLY that serious?
 Why the coronavirus changes over time? Is that normal?
 Why we don’t have a cure for coronavirus, a pill or sort?
 When can we finally travel again? Didn’t we have enough restrictions already?

Take a minute to reflect on what you learned and answer these questions, and any other you might have noted down.

THANK YOU!