UNIT 3 DAY 4 - THE COVID VIRUS KEEPS EVOLVING

Question 1

coronavirus

Answer 1

covered with spikes

Question 2

virus process

Answer 2

• virus enter through nose, sometimes through eyes and mouth
• once inside, virus invades cells in nasal cavity and trachea –> can travel deeper into lungs
• virus enters, attaches to cells in airway that produces proteins called ACE-2
• virus infects cell –> fuses its oily membrane to cell membrane –> once inside, coronavirus releases snippet of genetic material (RNA)
• infected cell reads RNA, begin to make proteins, keeping immune system at bay, assemble new copies

Question 3

antibiotics

Answer 3

• kill bacteria, don’t work against viruses

Question 4

infection progresses

Answer 4

• new spikes and other proteins form new copies of coronavirus –> carried to outer-edge of cell
• each infected cell releases millions of copies of virus before cells dies

Question 5

coughing and sneezing

Answer 5

expel virus-laden droplets

Question 6

virus transmission occurs by 2 routes

Answer 6

1. relatively large airborne droplets falling within 5 seconds and contaminating surfaces
2. tiny aerosols remain airborne for hours, accumulate in poorly ventilated spaces (IMPORTANT)

Question 7

factors affecting airborne transmission

Answer 7

1. distance –> droplets travel less than 6 feet, aerosols disperse over distance, concentrating diminishing exponentially with distance
2. duration
3. ventilation
4. intensity of inhalation and/or exhalation

Question 8

soap

Answer 8

• destroys virus as soap molecules wedge themselves into the lipid membrame

Question 9

viral envelope

Answer 9

protein encapsulates genetic material

Question 10

spike protein

Answer 10

used by virus to gain entry to human cells –> attaches to ACE-2

Question 11

ACE-2

Answer 11

attaches protein early

Question 12

endocytosis

Answer 12

human cells ingests virus

Question 13

exocytosis

Answer 13

virus carried by golgi bodies out of cell

Question 14

hijacks

Answer 14

takes DNA and mutates it

Question 15

mRNA

Answer 15

• single-stranded RNA involved in protein synthesis
• role = carry protein information from DNA In nucleus to cytoplasm
• translation of mRNA into protein places of ribosomes

Question 16

endoplasmic reticulum

Answer 16

• network of membrane inside a cell through which proteins and other molecules move
• ribosomes attach to endoplasmic reticulum

Question 17

apoptosis

Answer 17

• cell death
• stress of viral production on endoplasmic reticulum leads to apoptosis

Question 18

why did SARS-CoV-2 evolve

Answer 18

• it acquired mutations, fast replication, slight genetic change and huge populations

Question 19

mutations

Answer 19

• mutations accumulate, work together to elicit changes and enhanced traits
• one mutation, might not increase transmissibility of virus alone

Question 20

characteristics of disease-causing virus

Answer 20

1. transmissibility –> capacity to infect people
2. virulence –> severity of symptoms
3. immune escape –> ability to invade immune protections

Question 21

can viruses become VERY contagious and VERY deadly?

Answer 21

• no, as they would burn themselves out

Question 22

commensal bacteria

Answer 22

• not harmful, may be beneficial

Question 23

Lenksi experiment

Answer 23

• population of E. Coli into 12 flasks (37 degrees c), feed on water, glucose and other nutrients
• when bacteria replicated (each day) –> transferred some drops of food mixture into new flaks

Question 24

Evolution experiment

Answer 24

• how quickly, effectively, creatively and consistently microorganisms improve their reproductive fitness
• evolutionary biologists defined fitness as reproductive success: the number of offsprings that survive/number of grandchildren
• since bacteria don’t have children (they just divide), Lenski measures fitness and how fast one of his evolved population divides and multiplies in direct competition with its start-of-the-experiment ancestor

Question 25

Why did Lenski expect to see a significant change in the 12 populations?

Answer 25

• by forcing his 12 populations to subsist only on glucose, instead of the rich mix of nutrients they find in their usual environment (the human intestine)
• Lenski had placed them in a state of maladaption (trait more harmful than helpful) relative to their intestine-living ancestor
  -He wanted to see how quickly they would evolve to be better at coping with their new environment

Question 26

Lenski’s first finding

Answer 26

• diminishing returns to mutations over time –> bacteria made many of their most reproductively advantageous moves early on

Question 27

Lenski’s first finding explanation

Answer 27

• if a population starts out poorly adapted, mutations of relatively large effects can be advantageous early on
• mutations of large effects that help more than they hurt will be extremely rare
• huge size and short generation time of bacteria populations means that huge numbers of mutations will be generated, increasing the odds that a beneficial mutation of large effect eventually appears
• population rapidly increases in fitness due to the initial accumulation of mutations of large effects
• increases in fitness more slowly, as only mutations of small effects are viable

Question 28

How does Lenski’s thoughts differ from Darwin and Fisher?

Answer 28

• Both Darwin and Fisher imagined that evolution by natural selection proceeds in numerous tiny steps
• Fisher reasoned that only mutations of tiny effect could yield improvements without damaging side effects
• If Darwin and Fisher are right, a population encountering a new environment, to which it is poorly adapted, would evolve

Question 29

Lenski’s 2nd finding

Answer 29

• bacteria never stopped getting fitter
• 70,000 generations in and still finding new ways to improve
• at the start, there will be mutations with large effects but as generations pass, the effects will be smaller

Question 30

Lenski’s 3rd finding

Answer 30

• rare mutations have potential to explode in growth
  –> large jumps are proceeded by small gradual mutations that set the stage for bigger changes

Question 31

lineages

Answer 31

• most lineages have gone extinct but 2 persist in the present:
  –> Cit+ = specialises on eating citrate
  –> Cit- = can’t eat citrate and is better at eating glucose

Question 32

SARS-CoV-2

Answer 32

• 1 citrate moment: when it evolved the ability to leap into humans
• since then, virus accumulated innumerable mutations, allow to generate copies of itself more efficiently –> alters how it binds to our cells

Question 33

COVID vaccines

Answer 33

• developed and deployed vaccines in real time

Question 34

immunised

Answer 34

• exert selective pressure for virus to find new, more efficient replication strategies

Question 35

Fear there will be a 2nd mutate moment

Answer 35

• viruses are able to circumvent our vaccines
• prospect of a variant that is vastly more contagious or deadly

Question 36

why do viruses evolve?

Answer 36

• viruses evolved to fit environment strains from different locations move apart at thriving in that specific locations –> changing environment for virus to exceed –> strong selection pressure

Question 37

what is Dr. Burtoni’s three potential futures for the coronavirus?

Answer 37

1. virus can’t evolve its way around vaccines
2. virus partially evade our vaccine-generated immune defences –> became less infectious or lethal
3. virus could accumulate mutations that allow it to circumvent immunity without suffering a major reduction in transmissibility of lethality

Question 38

What is the key difference between Lenski’s experiment and the situation in which the SARS-CoV-2 is evolving?

Answer 38

• most fundamental difference between Lenski’s experiment and our reality
• Lenski’s environment kept constant, COVID Is ever changing as vaccines develop, behaviour changes

Question 39

How can “peak fitness” differ in different environments?

Answer 39

• highest number of cases per day depends on many factors: population size, vaccination rates, climates

Question 40

Why did Beta and Gamma variants evolve in areas with high levels of prior infection, whereas the delta variant evolved in India?

Answer 40

• beta and gamma variants evolve in high levels of prior infection –> settled on mutations that offered them gains of immune escape but not transmissibility
• delta variant –> emerged in India, low vaccination rates, goal was to spread as fast and as far as possible, somewhat more immune-evasive and lethal

Question 40

how could the virus evolve in ways that allow it to escape our immune response?

Answer 40

• virus alters the way it enters the body so antibodies can prevent it
• coronavirus = generalist … can bind to many receptor sites, capacity for innovative mutations, many mutations at once, BUT human immune system complex, very effective against previously encountered pathogens
• convergent evolution –> many variants share similar mutations despite evolving separately

Question 41

On the flip side of the virus’s ability to evolve is our immune system’s ability to respond: What lesson does human immunity to H1N1 and SARS-CoV-1 offer for being optimistic about our immune system’s ability to respond to continually evolving SARS-CoV-2?

Answer 41

• In 2009, when the H1N1 influenza strain emerged, it had a curious feature: it caused more severe illness in younger people than older people
• It turned out that many older people had likely been exposed to relative of the strain decades ago-and that their immune systems, remembering that fight, were prepared for the next one
  -The blood of COVID-19 survivors has the potential to neutralise the 2003 strain
  -The vaccines appear to generate huge numbers of antibodies that work against SARS-CoV-1 in those who have also been infected with COVID-19
  -Same antibodies bind to both of them
  -Scientist don’t think that their will every be a variant that completely escapes our immune systems