Chapter 6 - Viruses and Prions PDF

Chapter 6 - Viruses and Prions Viruses are Nonliving Pathogens Viruses are: ○ Extremely small but various in sizes (30-1000 nm) ○ Acellular ○ Obligate intracellular pathogens (microbes that are unable to live outside of a host cell) 70% of viruses...

Chapter 6 - Viruses and Prions Viruses are Nonliving Pathogens Viruses are: ○ Extremely small but various in sizes (30-1000 nm) ○ Acellular ○ Obligate intracellular pathogens (microbes that are unable to live outside of a host cell) 70% of viruses that infect humans tend to be harbored in other animals – zoonosis Viruses Exhibit Diverse Structual and Genomic Features Viruses can infect every branch in the tree of life Animal viruses: ○ viruses that infect animals and humans Virion: ○ Single, infectious virus particle, ○ Have an exterior protective protein capsid ○ Contain genetic material (DNA or RNA) Viral Capsids Capsid ○ Protein shell that packages and protects the genome ○ Makes up most of virion’s mass ○ Made of capsomere subunits Most animal viruses have either helical or icosahedral capsids ○ Helical capsids look like a hollow tube ○ Icosahedral capsids look like 3D polygons Deviations from these 2 include complex capsids How are capsid protein shells held together? ○ Protein-protein interactions based on hydrophobic binding, van der Waals forces and salt bridges Bacteriophages exhibit a complex capsid structure ○ Usually have capsids with icosahedral symmetry Viral Envelopes Enveloped viruses have a lipid based envelope (phospholipid bilayer) that surrounds the capsid ○ Virus coats itself in envelope when it arises out from plasma membrane Naked/nonenveloped viruses don’t have envelope  ○ Bacterialphages Viral Spikes (Peplomers) Many viruses have spikes (peplomers) that protude from capsid or envelope Only bind to specific factors in a host cells Narrow tropism: ○ HIV ○ Needs few specific receptors Broad tropism: ○ Ebola ○ Infects a lot of diff cell types Influenza does not have specific receptors → very infectious + high mutation rate ○ HA – Hemagglutinin ○ NA – Neuraminidase Make up subtype of influenza variants (H1N1, H7N9) Viral Genomes Viral genes encode: ○ Capsomere proteins ○ Enzymes needed for viral replication ○ Structual factors Viral genomes can be either: ○ RNA or DNA ○ Single or double stranded ○ Single or segmented sections ○ Circular or linear Viruses need to hijack/invade host cells → HIV DNA viral genomes ○ Circular or linear ○ Often double stranded RNA viral genomes ○ Linear or segmented ○ Often single stranded  Double-stranded DNA virus (dsDNA) ○ Viral DNA is transcribed using host RNA polymerases ○ mRNA is then translated into protein Single-stranded DNA virus (ssDNA) ○ Converted to a double stranded form before transcription Single-stranded positive RNA (ssRNA+) ○ Directly translated by host cell ribosomes Single-stranded negative RNA (ssRNA-) ○ Transcribed into mRNA by RNA-dependent RNA polymerases (RdRPs) Single stranded retroviruses ○ RNA genome is made into DNA by reverse transriptase ○ Requires RNA-dependent RNA polymerases Viral Genomes Change Over Time Viruses exhibit a faster rate, of genomic change than do living infectious agents because ○ Quick replication time ○ Large quantity of virions are produced ○ RNA genomes mutate more than DNA DNA polymerases have proofreading capabilities RNA polymerases lack proofreading  Mutations can have neutral, beneficial, or deleterious effects Viral Genomes Change Over Time Genetic changes that limit infectivity to attenuated strains ○ Attenuated: knocked down in virulence/ damage done ○ Used in vaccines Beneficial mutations allow the virus to: ○ Escape host immune system detection ○ Broaden host range ○ Expand tropism ○ Increase infectivity Leads to new viral strains Antigenic Drift Frequent minor changes to the HA and NA spikes RNA polymerase is error prone ○ No proofreading → mistakes are maintained Influenza only affects humans ○ Very infectious because it constantly mutates Antigenic Shift Sometimes major changes to genetic reassortment ○ RNA genome is 8 segments occurs when two or more different strains of a virus combine to create a new subtype with a combination of surface antigens from the original strains ○ Animal virus + influenza or influenza strain + influenza strain Naming Viruses The International Committee on Taxonmy of Viruses (ICTV) ○ Develop criteria for naming ○ Refine naming conventions for virsuses Responsible for ‘SARS-CoV-2’ Viruses are now grouped by these properties: ○ Type of nucleic acid present (DNA or RNA) ○ Capsid symmetry (helical, icosahedral or complex) ○ Presence or absence of an envelope ○ Genome architecture (ssDNA, ssRNA, etc.) Medically Important DNA + RNA Families DNA dsDNA circular ○ Papillomaviridae Human papilloma viruses (warts, cervial cancer) dsDNA linear ○ Herpesviridae Herpes Varicella-zoster virus/chickenpox ○ Poxviridae Smallpox RNA ssRNA+ nonsegmented ○ Coronaviridae SARS SARS-CoV-2 Common colds ○ Noreverse transcriptase Flaviviridae Hepatitis C virus West Nile Virus Dengue fever virus ○ Reverse transcriptase Retroviridae HIV(AIDS) ssRNA- ○ Nonsegmented Parmyxoviridae Measles + mumps (airborne) ○ Segmented Orthomyxoviridae Influenza Animal Virus Replication 1. Attachment a. Nonenveloped viruses attach to host cell membranes thru capsid proteins binding to receptor  b. Other viruses (nonenveloped or enveloped) use spikes 2. Penetration a. Nonenveloped viruses enter thru endocytosis b. Enveloped viruses enter thru endocytosis or membrane fusion 3. Uncoating a. Capsid comes apart and digested in cytoplasm/nucleus/endocytic vesicle 4. Replication a. Genome is replicated and viral proteins are made 5. Assembly a. New virions are formed 6. Release a. Enveloped viruses → budding b. Nonenveloped → kill the host cell Acute infections ○ Viruses infect a host cell and new virions are IMMEDIATELY made Persistent Infections ○ Viruses have replication strats that help them avoid immune system clearance ○ Chronic Persistent Infection Continous release of virions over time Slow progression EBV (Herpes) ~90%, HIV ~1% ○ Latent Persistent Infections Flare-ups with intermittent periods of dormancy (latency) During flare ups: Virions are shed Person experiences symptoms Flare-ups are triggered by stress Hepesviridae is very common latent infection  HSV-1: cold sores HSV-2: genital herpes Varicella-zoster virus (HHV-3): chickenpox-shingles Growing/Propagating Animal Viruses Animal viruses are more difficult to cultivate than bacteriophages Most animal viruses are grown using tissue culture technique Live animal hosts (mice,rats.guinea pigs) and fertilized eggs may be required to support growth of some viruses Testing Specificity – test only detects virus(es) of interest → no false positives Sensitivity – test detects low levels of the target → no false negatives Agglutination ○ Purified antibodies linked to tiny latex beads ○ Antibodies bind the viral antigen ○ Beads agglutinate (stick together) Latex Agglutination ○ Viral antigens linked to tiny latex beads ○ Patient antibodies bind the viral antigen ○ Beads agglutinate Enzyme-Linked Immunosorbent Assay (ELISA) Limitations ○ Sample must be a liquid ○ Antigens must be fairly well known ○ Viruses can undergo antigenic shift ○ Seroconversion window → when initially infected, dont have antibodies for up to 12 days Detecting Viral Genetic Material Detecting viral nucic acid is growing trend Nucleic acid detection techinques are very sensitve and sometimes more rapid To perform the test: ○ Clinical sample (blood/tissue/cerebrospinal fluid) is collected ○ DNA + RNA is extracted ○ Very specific segments of viral nucleic acid are detected by: Fluorescent-labeled probes PCR (polymerase chain reaction) RT-qPCR Viral genome is first made into complementary DNA (cDNA) by the viral HIV enzyme reverse transcriptase (RT). The DNA is then put through the polymerase chain reaction ○ Fluorescence is obtained after a certain # of cycles Results are often reported as ‘Cycle Threshold) ○ High concentrations are less cycles  ○ Low concentrations are more cycles Antiviral Drugs Treat Infections, but Don’t Typically Cure Them Any step in viral replication pathways is a potential drug target Antiviral drugs only limit infections Difficulties when designing antiviral drugs: ○ Viruses are obligate intracellular pathogens (bacteria that can’t live outside of cells) ○ Antivirals should be selectively toxic Few effective antiviral agents Drugs that Block Viral Attachment, Penetration and Uncoating Postexposure and prophylaxis ○ Used to treat rabies ○ Used shortly after suspected exposure ○ Lab prepped mixture of injectable antibodies prevents viruses from binding and entering host cells Nucleoside analogs (block enzymes) ○ Block replication ○ Activated into compounds that mimic normal nucelotides (adenine, guanine, cytosine, thymine and uracil) ○ Ex; Acyclovir Inhibits DNA replication Effective against HHV-1, HHV-2 or varicella-zoster virus Ribavirin  Targets RNA polymerases Effective against respiratory virus and hepatitis C Nuceloside Reverse Transcriptase Inhibitors (NTRIs) Target reverse transcriptase enzymes Azidothymidine (AZT) Interferons ○ Naturally occurring substances released by cells in response to viral infections ○ Signal the presence of a virus ○ Makes neighboring cells defensive Oseltamivir (Tamiflu) and Zanamivir (Relenza) ○ Prevent influenza A and influenza B virions from budding off the host cell surface Influenza binds to sialic acid (on proteins on the surface of cells) Influenza has no specific binding → very contagious Prions are Infectious Proteins Prions ○ Infectious proteins; no genetic material ○ Do NOT replicate ○ Cause transmissible spongiform encephalopathies (TSEs): Gerstmann-Straussler-Schienker Syndrome Fatal familial insomnia Cruezfeldt-Jakob Disease (CJD or Mad Cow Disease) Acquired ○ If eaten → causes normal folded proteins to change conformational state → cell death Misfolded proteins are associated with neurodegenerative diseases ○ Alzheimers Disease (AD) ○ Parkinson’s disease (PD) ○ Amyotrophic lateral sclerosis (ALS) Chapter 11 – Innate Immunitiy Immune Response Classification Immune ○ Specific protection by adaptability Susceptible ○ Not immune to a given pathogen → may cause infection Our immune system includes 2 branches: innate + adaptive immunity ○ Common features:  Recongize diverse pathogens Eliminate identified invaders Discriminate between self and foreign antigens Innate Immunity Ancient protection in all eukarytic organisms No specificity and memory Generalized Adaptive Immunity Only in vertebraes Matures over time and very tailored/specific Requires 4-7 days to fully activate Exhbits memory ○ Important for vaccines Normal Microbiota Has Role in Shaping Immune Responses Hygiene hypothesis ○ Proposes a decrease in diversity and levels of microbes in our normal microbiota may negatively affect immune responses Microbe-free environments lead to underdeveloped immune systems Normal microbiota havea direct role in immune system development Mechanical Barriers Rinse, flush or trap pathogens to limit spread ○ Tears wetting eyes, urine flushing microbes out, saliva limits what microbes adhere, mucus membranes trap microbes (line all body entrances such as stomach, intestines, lungs and bladder), mucociliar escalator sweeps away from the lungs and toward mouth Chemical Barriers May directly attack invaders or establish environments that limit pathogen survival in or on a specific tissue ○ Lysozome – found in secretions (tears/breastmilk) and breaks down bacterial cell walls and chews up proteins (does nothing against viruses or fungi ○ Hydrochlric acid in the stomach ○ Skin is relatively dry, salty, slightly acidic ○ Fatty acid in sweat and earwax  Antimicrobial Peptides (AMPs) ○ Proteins that destroy a wide spectrum of viruses, parasites, bacteria and fungi ○ Rare for microbes to develop resistance against AMPs 1. Stimulate leukocytes a. Modulate inflammation b. Clear pathogens by phagocytosis 2. Directly target pathogens a. Disrupt plasma membrane and/or cell wall b. Target intracellular components and/or processes c. Group of them are called Defensins → important class of AMPS that rapidly kill invaders by inserting themselves into target cell membranes Physical Barriers Epithelial tissue is main physical barrier ○ Lines every body cavity and body entrance Skin is very important Epidermis is made up of tightly compacted dead epithelial cells When 1st barrier is breached → 2nd barrier consists of molecular factors (proteins) and leukocytes (white blood cells) Lymphoid Tissues Primary Site of production and maturation of leukocytes Thymus (T cells) and bone marrow (B cells) Secondary Filter lymph Sample body sites for antigens Lymph nodes, spleen and mucosa-assocated lymphoid tissue (MALT) Thymus Site of T cell maturation Bone Marrow Site for red and white blood cell production  Site of B cell maturation Lymph Nodes Humans have 500-700 lymph nodes In neck, underarm, and groin Filters and screens for lymph Upon detecting an invading microbe: ○ Nodes become swollen ○ Swollen nodes are indicator of infections Spleen Place where leukocytes look for invaders Filters blood rather than lymph Damaged erthrocytes removed MALT Diffuse system of lymphoid tissue Found in all mucosal linings ○ Play key role in finding and fighting harmful microbes ○ Tonsils, appendix, peyer’s patches MALT is often more specifically named based on its location in the body: ○ GALT – gut associated lymphoid tissue Leukocytes Granulocytes – cells with granules in their cytoplasm that are visible when stained Agranulocytes – lack granules in cytoplasm →innate immunitity Differential White Blood Cell Count ○ Rapid + inexpensive test ○ Determines if any leukocytes are over/under represented in patient’s blood ○ Leukocytosis – increase in leukocytes After leukocyte activation, active molecules are released into local environment These molecules have diverse functions:  ○ Recruiting other leukocytes ○ Restricting pathogen growth ○ Triggering fever Neutrophils Most abundant white blood cells Contain multilobed segmented nucleus – makes it easier to squeeze thru into tissues out of the bloodstream Release AMPs Phagocytize foreign cells and viruses Neutropenia – low neutrophil count ○ Caused by certain viral infections Eosinophils – fight parasites or causes allergies