Lecture 2 - Prokaryotes and Eukaryotes

Barriers to using plasma antibodies

- antibiotics work better - safety - availability of plasma FDA still approved this for emergency use in April and there have been promising results

Why do bats not have immune systems that overreact against viruses?

- high metabolic rate - produce A LOT of ROS and mediators to temper overreactions - have natural tolerance for persistent/latent infections with low-pathogenic viruses - live in highly balanced ecosystems - some bats have lost genes that cause cytokine storms and duplicated genes like interferons that help control viral invaders

Relevant information about bats?

- highly mobile, long-lived and ecologically active - mainly eat insects, which harbor many viruses - live in large, interactive and physically isolated populations - many other viruses have come from bats - host a higher proportion of ZOONOSES = disease transmitted from animals to humans than all other mammals

Why is pharmaceutical microbiology important?

- microbes infect and cause disease - our bodies and the pharmaceutical industry function to protect us from these diseases

What kind of drugs are being developed to treat COVID-19?

- prevent docking of SPIKE to ACE2 receptor - inhibit protease that cleaves to allow endocytosis - inhibit viral RNA polymerase that has a correcting function for a defective virus - shut down the virus to stop the proteins inside that cause the virus - stop immune cytokine response

How are microbes used in the pharmaceutical industry?

- produce intermediates and enzymes used for drugs - genetically engineered to serve as factories to producing a wide array of drugs - fecal transplants, oncolytic viruses and leeches used directly as therapeutic agents drugs from bugs and bugs as drugs!

What have we been doing to bats as humans that lead to COVID-19? Theory

- we invaded and destroyed bat ecosystems - captured bats as food and pets - therefore exposed to bats - sometimes the bat virus becomes infectious to human cells

What are COVID-19 risk factors?

1) Affects anyone 2) Certain populations are at higher risk

What populations are at higher risk of getting COVID-19?

1) Age 65 and up 2) Pre-existing conditions like diabetes, asthma, kidney, pulmonary or CV disease, obesity, metabolic syndrome, hematologic disorders 3) Immunocompromised - AIDS, cancer 4) People who are in close contact areas like nursing homes, plants, gyms, church?

Safe Virus

1) Alter virus so that genes that cause virus are replaced by genes that code for SPIKE 2) Inject into human so that the virus infects human cells and makes SPIKE but does NOT cause disease

Why do we think COVID-19 originated from bats ?

1) Bats show unusual inflammatory responses/immune reactions 2) Humans and other animals have intruded bat ecosystems

Theories of where COVID-19 came from?

1) Bats that have coronaviruses without pathogenic effects and was passed to humans from bats or through pangolins 2) Transfer to humans may have happens through contaminated surfaces 3) made in lab?

Pieces of Virus

1) Make a lot of virus and strip SPIKE protein off the membrane, purify it and isolate it 2) Inject pieces of SPIKE into humans

Who are the leading three pharmaceutical companies for COVID vaccines?

1) Moderna 2) AstraZeneca 3) Johnson and Johnson

How does COVID-19 enter the body?

1) Nasal/oral passages of respiratory tract 2) Conjunctiva of eyes passing through nasolacrimal duct 3) oral cavity/esophagus

Weakened Virus

1) Pass virus multiple times in animal or tissue to make the virus lose its ability to cause disease 2) Inject into humans. They won't get sick, but immune system will react against SPIKE

How can we use mAbs to treat COVID-19?

1) REGN-COV-2 = combo of 2 antibodies that bind to two points on SPIKE and prevent it from entering healthy cells - made in mice - currently in clinical trials 2) LY-CoV555 = isolated from recovered COVID-19 pt - undergoing trials - made in humans

How is COVID-19 spread?

1) Spread by people who are asymptomatic, presymptomatic or symptomatic 2) Aerosols and particulates expelled from breathing, coughing or sneezing 3) Contact with contaminated objects

DNA vaccine

1) Take DNA that codes for SPIKE and inject into people 2) DNA is transcribed and translated and makes SPIKE and body reacts to it 3) DNA will not cause disease

RNA Vaccine

1) Take RNA that codes for SPIKE and inject into people 2) RNA taken up by cells, muscle and is translated into SPIKE 3) RNA will not cause disease

Inactivated Virus

1) Treat virus with chemical radiation to destroy its ability to infect cells but still retain the antigenicity of the target protein 2) Inject into humans and body reacts

What are the two methods we can use to battle COVID-19?

1) Vaccines - prevent 2) Treatments - antiviral agents, anti-inflammatories and antibodies

What are three ways we can get the SPIKE protein into the human body to generate a human response, but NOT cause the disease?

1) Weakened virus 2) Inactivated Virus 3) Pieces of Virus

How is microbiology based on a paradox?

1) microbes have caused more deaths than any other medical area BUT 2) there have been the most important advances in human health in microbiology like vaccines, sanitation and antibiotics

When were coronaviruses first isolated? From what animal?

1930s in Chickens from North Dakota with severe respiratory infections

When were coronaviruses first isolated from humans?

1960s in children with common colds

What is the incubation time of COVID-19?

4-5 days range 2-14 days can detect virus through nasal swab because virus is shed by host cell in droplets

Which two companies have developed safe vaccines for ebola?

AstraZeneca and J&J

T/F: COVID-19 disappears from surfaces quickly so if you touch it, you won't get it.

FALSE - it stays on a surface for very long; hours.

T/F: ALL microbes are SMALL and grow autonomously.

FALSE!! some grow in clusters or communities some are over 400 tons and have many organs (helminths) and tissue systems some have complex life cycles

T/F: The speed of a pandemic eliminates important elements of developing a vaccine.

FALSE; IT COMPRESSES THEM.

T/F: We only need the adaptive immune system to battle COVID-19.

FALSE; both innate and adaptive are required to fight and recover from COVID-19.

T/F: COVID-19 is just a respiratory disease.

FALSE; it's pervasive and that's why it's infectious. multicellular tropism!

T/F: Viruses can replicate outside a cell.

FALSE; they are INTRACELLULAR PARASITES. Going INTO the cell is KEY to replication.

T/F: Emergent diseases still only happen in specific regions like East Asia.

FALSE; they can develop in hotspots ALL OVER THE WORLD

T/F: All microbes are living.

FALSE; viruses and prions are considered microbes but they're not alive.

What are the newer methods of making vaccines?

GENETICALLY DNA, RNA and SAFE VIRUS

What is the most common test for COVID-19?

Genomic - test for CURRENT INFECTION tests for presence of viral RNA using RT-PCR in swab/saliva sample

MERS-CoV

Middle East Respiratory Syndrome Coronavirus emerged in arabian peninsula in 2012 originated from camels isolation/quarantine contained it but remains public health concern

Can you use the antigen test to determine if a person is infected by COVID-19?

NO

If you have antibodies for COVID-19, does that mean you are immune to it now?

No, still unsure.

Rare cases of COVID-19 in children can progress to very a serious condition called?

Pediatric Inflammatory Multisystem Syndrome (PIMS) or Multisystem Inflammatory Syndrome in Children (MIS-C)

Advantages/Disadvantages of Genomic Test

Pros: accurate if taken 3+ days after exposure, sensitive, can be done at home Cons: may not catch early infection, takes couple days for results, rapid tests are often inaccurate

Advantages/Disadvantages of Antigen Test

Pros: results come out in few minutes, good screening tool Cons: not as accurate/sensitive as genomic test

Advantages/Disadvantages of Antibody test

Pros: tests are everywhere, scalable and automatable, cheap, sensitive and accurate Cons: only a few are approved by FDA, quality control issues

What is MIS-C?

Rare, terrible disease that is difficult to treat Symptoms include: fever, hypotension, rash, multiorgan involvement, and inflammation

What protein are we after when we're making vaccines against COVID-19?

SPIKE PROTEINS enables virus to bind to ACE2 receptor, get into cell and replicate to cause disease

What does SARS-CoV-2 stand for?

Severe Acute Respiratory Syndrome Coronavirus 2

What happens once COVID-19 enters your body?

Spike proteins bind to host cell receptors specially the ACE2 receptor - angiotensin-converting enzyme 2

Adaptive immune system

T, B cells and antibodies

T/F: Diseases are about individuals, whereas microbiology regarding infectious diseases is about community, population and the world.

TRUE

T/F: Just like COVID-19, symptoms of MIS-C (often no symptoms) are present weeks after exposure to virus.

TRUE

T/F: Most cases of COVID-19 are Stage 1 or Stage 2.

TRUE; about 80%. about 20% are stage 3.

T/F: Microbes are EVERYWHERE.

TRUE; human bodies contain more microbial cells than human cells (150 lb adult has 3-5 lbs of microbes) they are the first and most evolved organisms

T/F: Emergent diseases are slowly increasing.

TRUE; possibly due to climate change, ecological disruption, human interventions, wars and antibiotic overuse

How many pathogenic coronaviruses of animal origin have appeared in humans since 2000?

Three 1) SARS-CoV 2) MERS-CoV 3) COVID-19

Symptoms of MIS-C are similar to that of which diseases?

Toxic Shock Syndrome Kawasaki (inflammation of BV)

T/F: An overreaction of the immune system causes Stage 3 COVID.

True

Do children get infected by COVID-19?

Yes, infections are possible, some get seriously ill and some die. BUT, most children are asymptomatic and of the children who are symptomatic, the symptoms are mild like fever and cough. Most children are able to recover.

Are microbes harmful?

Yes, they can cause disease and kill people about 2000 microbes do this

What is unique about developing vaccines during a pandemic?

You start making them and producing them before they get approved so that if they do end up working, you already have a lot made to distribute right away.

Some examples of emergent diseases?

Zika Ebola Enterovirus D68 Acute Respiratory and Paralytic Disease H1N1 Influenza (swine flu) H5N1 Influenza (bird flu) MRSA (methicillin resistant S. aureus) VRSA (vancomycin resistant S. aureus) SARS (Severe acute respiratory syndrome) West Nile Disease (viral encephalitis) BSE (mad cow disease) CJD (human spongiform encephalopathy) Enterohaemorrhagic E. coli O157:H7 IGAS (flesh eating Streptococcus) Marburg virus hemorrhagic disease Cryptosporidiosis MERS (Middle East Respiratory Syndrome Coronavirus) HIV/AIDS

What are superspreaders?

a small proportion of individuals who account for most of the infections 10% account for 90% of infections

Which country globally has the most deaths and most cases of COVID-19?

america.

What is a coronavirus?

an enveloped RNA virus club-shaped spike proteins on outer surface like a "crown" genome contains large, SS, sense RNA (26-32kb) ribonucleic core cell membrane outside the core that resembles mammalian cells

Stage 2 - Upper Airway and Conducting Airway Response

battle begins cough, fever, SOB, chills, muscle pain, loss of taste/smell, sore throat, nausea and diarrhea

Why are organisms resistant to even last-resort antibiotics?

because new diseases keep emerging we use advances in science poorly

Why are children stronger against COVID-19 than adults?

because their adaptive immune system isn't as developed, they rely more on natural immunity so when they get infected, they produce more interferons and have more tempered inflammatory responses later than adults a THEORY

What is a potential danger of microbes in drugs?

contaminant major cause of iatrogenic and nosocomial morbidity

Stage 3 - hypoxia and ARDS

critical care/hospitalization 15% need oxygen and 5% need ventilation *pneumonia, can't breathe, chest pain/pressure, confusion, can't stay awake, bluish lips/skin *lungs fill with fluid, WBC, mucus and cellular debris as oxygen levels deplete

What is released from immune system in Stage 3 of COVID-19? What are the effects of this?

cytokines (cytokine storm) decreased BP, leaky BV, blood clots and organ failure

SARS-CoV

emerged in guangchung province, china 2002 originated in bats lots of quarantine but virus is not really contagious

COVID-19

emerged in wuhan, china originated with bats? still going pretty bad rn

What did Burnet win a Nobel Prize for?

figuring out basic immune reaction principles - that we are tolerant and don't react to our own antigens

Antibody Test

for people who were previously exposed to COVID-19 production of antibodies that usually appear 5+ days after exposure

How many low-pathogenic coronaviruses are regularly found in humans?

four

Stage 1 - Asymptomatic State of Covid-19

immune response initiated and virus propagates mild symptoms like stuffy nose can pass onto other people

What is the immune bystander effect?

immune system kills or harms normal organs occurs when immune system cannot be shut off bc of COVID-19

Where does most of the action of COVID-19 occur in stage 3 patients? Why?

in lungs, heart/BV, brain, eyes, nose, liver, kidneys and intestines. because many cells have ACE2 receptor! also COVID-19 has spread everywhere at this point because of cytokine storm

Who are the superspreaders of COVID-19 currently?

infected, asymptomatic in teens-40's

Innate immune system

interferons, cytokines, phagocytes

What are the physiological functions of ACE2 receptors?

lower BP control fluid balance regulate inflammatory response

Moderna's COVID Vaccine

mRNA based already showed safety and efficacy currently in Phase III

C.diff

present in our gut in small amounts but if taking immunosuppressants or antibiotics, these kill off the organisms that keep C.diff in balance as a result, we get infected antibiotic-resistant too

Microbes come from all phylogenetic kingdoms and include all ____ and ____.

prokaryotes (archaea) and many eukaryotes (planta, fungi, protists and animalia)

What are emergent diseases?

rare diseases that are unknown in humans or restricted to a particular region but suddenly appear and infect humans aka COVID lol a fundamental characteristic of infectious disease

Johnson and Johnson's/Beth Israel COVID Vaccine

recombinant adenovirus expressing SPIKE beginning phase III right now

AstraZeneca's Covid Vaccine

recombinant chimpmanzee adenovirus expressing SPIKE already showed safety and efficacy currently in Phase III

How do fecal transplants restore the balance of the microbiome?

restores the organisms in gut flora 70-90% effective but there have been deaths too

What are microbes?

small, autonomously growing, single cell organisms include: - bacteria, fungi (yeasts and molds), algae, protozoa, and viruses, prions

What is pharmaceutical microbiology?

study and management of medically important microbes and the diseases they cause

Why are microbes important?

they are mostly beneficial because they maintain ecological systems, involved in remediation/recycling, pest control, food and beverage production, fuel and chemical production

How do drugs like antibiotics and immunosuppressants cause the microbiome to go out of balance?

they cause the normally friendly microbiomes to cause disease

How many stages of disease does COVID-19 have?

three 1) Asymptomatic State 2) Upper airway response 3) Hypoxia and progression to acute respiratory distress syndrome within 8-12 days

Where are ACE2 receptors located?

tissues, lungs, kidneys, heart, arteries and GI tract

What is an example of engineering bacteria to treat a disease?

treat phenylketonuria (PKU) which is a mutation in gene for phenylalanine hydroxylase that metabolizes dietary phenylalanine so it doesn't build up if it builds up, it causes seizures, cardiac problems and even death can make bacteria to express enzymes to degrade PA still in clinical trials

What are fecal transplants?

use of feces or organisms in feces to treat disease

Antigen Test

uses antibody to detect presence of viral antigen (like a pregnancy test)

How can we use plasma containing antibodies to prevent/treat COVID-19?

using antibodies people already had that allowed them to fight off the virus and injecting their plasma into someone who can't fight off the virus

What happens after the SPIKE protein binds to ACE2 receptors?

viral endocytosis membrane fusion mRNA entry viral replication