Bio 171 Unit 1 Lecture 5: Viruses and Emerging Infectious Diseases

Antibodies:

Large specialied protein produced by B cells in immune system and bind to antigen molecules. Initiates destruction of pathogens.

Antigen:

Weakend/dead parts of pathogen containing proteins that stimulates immune system and leads to the production of antibodies.

Basic reproductive number (R0):

Basic reproductive # for an infectious disease. Measured as the expected # of secondary infections that result, on average, from a single infected individual entering a pop. of entirely vulnerable individuals (R0=CR*TE*IP).

B cells:

Immune system white blood cell that matures in the bone marrow of vertebrates and make antibodies.

Capsid:

Protein coat surrounding nucleic acid genome of virus.

COVID:

Zoonotic disease from SARSCOV2.

Disease:

Physical symptoms caused by pathogen.

Effective reproductive number [R (or Rt)]:

Real # of secondary infections that result, on average, from a single infected individual in a pop. that doesn’t need to be completely vulnerable. Never >R0.

Emerging infectious disease (EID):

Disease that has appeared recently/spread rapidly (incidence increased).

Endemic:

Disease persists at relatively stable level in host pop(s). In specific geographic area.

Epidemic:

Outbreak of an infectious disease that spreads rapidly and affects a large # of people in a larger region.

Herd immunity:

Majority of pop. is vaccinated breaks transmission chain and makes it unlikely for infected individual to contact vulnerable individual. R needs to be <1. p=1-(1/R0).

HIV & AIDS:

Retrovirus that causes AIDS (disease). Genome is made of RNA not DNA.

Immune system:

Complex response system that protects body from foreign substances.

Infectious period:

Length of time infected individual is infectious to other individuals.

Memory B cells:

Cells that recognize previous viral particles and initiate alarm to destroy them.

Pandemic:

Global/widespread epidemic.

Pathogen:

Organisms/agents (viruses) that cause disease.

Pre-exposure prophylaxis (PrEP):

Medication to prevent spread of HIV for people not yet exposed.

Reservoir:

Pop. of organsims or specific environment wher pathogen naturally lives and reproduces to survive.

Retrovirus:

Virus whose replication involves reverse transcriptase.

Reverse transcriptase:

RNA-dependent DNA polymerase enzyme that uses single-stranded RNA template to synthesize DNA, reversing the usual flow of information in cell.

Spillover:

Process of a disease moving from a host species to another.

Superspreading:

Event where infectious disease is spread much more than usual.

Vaccination:

Agent triggers primary immune response to specific pathogen, but doesn't cause disease, instead provides immunity against future infection by that specific pathogen.

Vector-borne disease:

Disease transmitted b/t hosts via vector (arthropod/insects).

Viral envelope:

Membrane derived from host cell membrane where virus reproduced and clocks capsid and encloses viral genome.

Virus:

An acellular small infectious agent that contains a linear/circular/segmented nucleic acid genome (DNA/RNA virus) in a capsid. Some have a phospholipid envelope. Recognize host cells w/ their unique cell surface glycoproteins uses their mechanisms to replicate. Type of obligate parasite.

Zoonosis:

Disease that moves b/t animals and humans.

Explain the factors that allow an infectious disease to (re)emerge.

Antibiotic-resistant strains of pathogens evolving. High rates of travel. Increased n, risky behaviors, urbanization. Contact w/ animal reservoirs. Reduced vaccination rates. Health inequalities. Environmental changes.

Explain the factors that affect the spread of an EID.

1. Frequency of contact b/t infected and vulnerable individuals (contact rate). 2.Efficiency with which the disease is transmitted from infected to susceptible individuals (transmission efficiency). 3. Infectious period.

Explain why Ro is important and how it can be used to inform vaccination programs

Shows the rate of increase and threat level that virus can have on pop.

Describe how mRNA vaccines produce protein antigens

mRNA directs virus cells to produce copies of protein on outside of virus. Piece of mRNA codes for antigen and fuses into virus.

Compare zoonotic diseases with vector-borne diseases.

Both come from non-humans. Vector-borne diseases can be zoonotic but zoonotic diseases can’t be vector borne.

Describe the structure of HIV's genome, explain how HIV enters its host cell, how it converts RNA into DNA and inserts its DNA into the host cell's genome, the types of cells it infects and how it attacks the immune system.

Retrovirus integrates genetic material into host cell’s DNA using the infected cell to release new virus particles. A specific protein on the surface of the HIV envelope binds to CD4 protein on the surface of some immune cells to interact w/ coreceptor CCR5 on T Cell.

Explain the evolutionary origins of HIV; be able to state the organisms in which HIV originated

HIV originated from at least 2 separate simian viruses in sooty mangebeys and chimpanzees that switched hosts to humans.

Describe the purpose of PrEP

HIV prevention drug taken daily for people w/ high risk/exposure to indiviual HIV+.

Describe the process by which viral DNA can become part of the human genome.

DNA copies of the viral genome are incorporated into the host genome (lysic/exocytosis) and passed through generations.

For measles, understand what has allowed it to reemerge in recent years, its effects on other infectious diseases, and the benefits of vaccination.

Reduced vaccinations and high rates of travel. Children who survive measles are more vulnerable to other diseeases. Benefits: eradication leads to immunity in pop.

Explain how R changes over the course of an epidemic.

Beginning of # of new cases: R=R0>1. Peak of epidemic: R=1. Afterwards: R<1.

Explain how SARS-CoV-2 relates to other coronaviruses that are known to infect people

All cause “common cold” symptoms however others are more virulent.

Describe the differing amount of transmission that can occur for pathogens that spillover from animals into humans

Stuttering transmission (R0<1) and sustained transmission (R0>1).

Compare growth of infections in the early part of an epidemic with exponential growth covered in the population biology lecture.

Exponential increase b/c a new disease can spread easier in a mostly susceptible pop.

Describe how public health measures like social distancing and wearing face masks can affect R0 (and R or Rt).

Social distancing decrerases CR and wearing masks decreases TE.

Explain how evolution is relevant to understanding the COVID pandemic

Tracking variants help understand outbreak origins.

How does R0 relate to the three key factors that whether a disease spreads in a population?

R0=CR*TE*IP.

In what sort of population do we define Ro?

Completely vulnerable populations.

What does Ro need to be for a disease to spread in a population? If Ro is relatively high, what does that mean for the speed at whiich a disease spreads through a population?

R0>1 for disease to spread. R0<1: disease transmitted to <1 person. Disease spreads faster to more people making to harder to control in outbreak.

What does it mean when R=1?

Diseases spread is constant one infected individuals can only affect one individual. Decreased transmission efficiency with less vulnerable people.

What are the two ways of gaining immunity and how do they work?

Natural: exposure to pathogen (get sick). Vaccination: Injection of antigens that stimulate immune response.

Is the antibody for one pathogen (e.g., measles) the same as the antibody for another pathogen (e.g., SARS-CoV-2)?

No. Each pathogen has a unique antigen that requires a unique antibody to attach and initiate destruction. Important if pathogen reappears so immune system remembers how to destroy.

What happens when an antigen from a pathogen is introduced into the body?

Immune system responds with antibodies to destroy pathogen.

What do the antigen presenting cells do?

Process and present cell antigens for recognition by T cells.

What happens once a pathogen is tagged for destruction?

Memory B cells are left behind to remember the pathogen and then white blood cells (macrophages) destroy the pathogen if it reappears.

When herd immunity is reached, what is R in the population?

R<1.

How do you calculate the fraction of individuals who need to be immune to disease (p) in order for a population to have herd immunity?

p=1-(1/R0).

What type of pathogen causes measles? What effect does it have on the immune system?

Virus. Serious health complications/severly weakened immune system.

How do the adverse effects of vaccines compare to the complications of a disease like measles?

Adverse effects of vaccines are significantly lower than complications of diseases.

What is the difference between enveloped and non-enveloped viruses? What advantages do enveloped viruses have?

Enveloped: Contains genome, capsid, and envelope phospholipid bilayer. Envelope makes it easier to avoid detection for some time from immune system due to host cell appearance. Non-enveloped: Only contain the genome and capsid.

What forms can viral genetic material take?

linear, circular, segmented, 1/2 strand, single/double helix, RNA/DNA

What are the steps in the generic replication cycle of a virus?

1. Virus attaches to receptor on cell surface. 2. Virus breaches cell membrane; injects nucleic acid into cell. 3. Viral nucleic acid replicates using host cell machinery then transcription and translation occur to make virus proteins. 4. Viral self assembly leads to new viral genome & proteins are packaged into particles & released.

What are the two ways that newly produced virus particles can exit a host cell?

1. Lysis: non-enveloped viruses burst out of cell. 2. Exocytosis: virus buds off w/ piece of host cell.

How is HIV transmitted?

Exchange of bodily fluids sexually b/t partners. From mother to fetus during pregnancy/birth. Blood in contaminated needles/blood products.

What are two recent innovations in HIV treatments that reduce the potential for people who are HIV+ to transmit the virus?

ART and PrEP.

Where in the world are HIV cases increasing, and what are some areas where HIV infections are decreasing?

Increasing: E. Europe & Central Asia. Decreasing: Americas & Africa.

Does contraception prevent against HIV infections?

Only condoms or barrier methods can protect against HIV.

Why doesn’t HIV have a place on the tree of life?

HIV isn’t a living organism because it doesn’t have ribosomes.

What is included in an HIV virus particle, and how does HIV replicate?

Genome made of single stranded RNA. Process using reverse transcriptase, capsid, and viral envelope.

What cell type is a main target for HIV, and how does the infection of that particular type of host cell affect the progression from initial infection to AIDS?

Helpter T cells which are important in immune response. When too many T cells are destroyed, immune system is extremely weakened and leads to AIDs.

What are the roles of HIV enzymes reverse transcriptase, integrase and protease?

Reverse transcriptase: converts HIV RNA into DNA. Integrase: Integrates HIV into host genome. Protease: Breaks up matured HIV chains into proteins that infect other cells.

What are some targets in the HIV replication cycle for drug therapy? Why can’t the transcription & translation step be effective drug targets?

Targets at fusion (prevent entry), reverse transcriptase (HIV conversion from RNA to DNA), integrase (block integration of HIV’s DNA into host’s DNA), protease (Prevent virus from assembling functional proteins). Can’t block transcription/translation b/c host cell machinery is involved.

Why has HIV historically been so difficult to treat, and why is there not yet an effective HIV vaccine?

The mutation rate of HIV is very high b/c of the high error rate assoc. w/ reverse transcriptase (doesn’t proofread bp nucleotides well) which leads to high genetic variability where the genome sequence of one virus is different from the next to evolve resistance to treatments. Also the cells attack T-cells that are important to body’s immune system.

Why does Anti-retroviral therapy (ART) work as an effective treatment for HIV infection?

The combination drug cocktails of reverse transcriptase, inteagrase, and protease inhibitors slow/stop viral replication.

Are there any options for people who are at high risk of contracting HIV? What about for someone who knows they have been exposed to HIV?

ART/Condoms/PrEP.

What is the difference between SARS-COV-2 and COVID-19?

SARS (virus) that caused COVID (disease).

What distinctive feature of coronaviruses lead to the "corona" in the name?

The spike studded phospholipid envelope appearance as a “crown” is the definition of corona.

What does it mean when we say SARS-CoV-2 is zoonotic?

Disease that moves b/t animals (bats/pigs) and humans.

Is SARS CoV-2 the only coronavirus that infects humans? Are all coronavirus infections as serious as SARS CoV-2?

Is 1 of 7 known to infect humans. Only 3.

Do we know the animal from which SARS-CoV-2 spilled over into humans? Do all spillovers result in sustained transmission in humans? Once SARS-CoV-2 moves into humans, can it move back to other animals?

Bats (unknown sequence). No some spillowvers can only lead to stuttered transmission among humans. Yes b/c of this their is concern for high mutations.

How easy is it to estimate R0 in human populations during an epidemic? What is the best estimate for R0 for SARS-CoV-2 when it first moved to human populations?

Very hard b/c it’s not constant. R0=3 or 2-4.

How do non-pharmaceutical interventions such as social distancing and wearing masks relate to R0? Is R0 for a particular virus variant fixed or can it be affected by behaviors?

It relates to 3 factors of R0. It can be affected by behaviors.

Would you expect the same number of genetic differences between the virus in one person who is infected with the “omicron” variant and a second person who is infected with the omicron variant, or between the virus in a person who is infected with omicron and someone who is infected with the delta variant?

No more differences w/ different variant.

What are three key Bio 171 topics that the COVID-19 pandemic relates to?

1. Exponential growth & pop. dynamics. 2. Vaccination. 3. Evolution.