Microbial Exam 3

the host range of a virus can refer to

the specific organism the virus can infect, the specific cell type the virus can infect

which of the following viruses has the largest genome?

Megavirus chilensis

all viruses can be described as which of the following

genetic elements that can multiply only inside host cells

Baltimore Class III viruses have genomes that are immediately targeted for degradation in the host cell if not contained within the capsid. these viruses can also be referred to as

dsRNA viruses

a viral infection that results in the slow production of viral particles without destroying the host cell is called

a persistent infection

a disease whose incidence has increased in the past twenty years is known as a(n)

emerging infectious disease

Norovirus and polio virus share all but which of the following characteristics in common

presence of only one open reading frame

who created the first successful vaccine?

Peter Plett

when an infection spreads from a localized population to multiple continents, we consider it a(n)

pandemic

the R0 of a pathogen can best be described as

the infectivity rate of a pathogen that does not consider natural or artificial immunity

the shift in pandemic frequency following the industrial revolution can be attributed to which of the following?

greater ease of global travel

this monstrous microbe is transmitted through a bite and causes a crippling fear of water

Rabies lyssavirus

this form of vaccine utilizes a weakened form of the pathogen and can be seen in examples such as the cholera vaccine

attenuated pathogen vaccine

are vaccines safe and effective?

yes

which of the following is true regarding both West Nile virus and Dengue virus?

a single polyprotein is produced and later cleaved apart

most soilborne viruses are RNA viruses that affect which type of eukaryote?

plants

which of the following groups of people would most likely not be recommended for prophylactic rabies vaccines?

pet owners

we generally categorize influenza based on which two proteins?

hemagglutinin and neuraminidase

transmission of the flu can be traced to which of the following routes?

direct person-to-person contact; indirect contact with bodily fluids; aerosols, respiratory droplets, and fomites

is there a human vaccine against West Nile virus?

no, no vaccines have made it past phase II clinical trials

the spike protein of the rabies lyssavirus is generally found on all but which region of the viral capsid?

the planar end of the capsid

where did the Sin Nombre virus get its name?

local population objected to the previously proposed names and so virologist named it such out of fustration

Dengue fever is colloquially known by which other name?

break-bone fever

what are viruses?

-a genetic element that can multiply only inside a living cell
--obligate intracellular pathogens
-not found on the tree of life, but can infect all three main branches
---viruses rely on the host cell for energy, metabolic intermediates, and protein synthesis
---viruses possess their own nucleic acid genomes and are independent of the host's genome
---viruses infect cells in all three domains of life

viral evolution

-since viruses can replicate only within cells, they probably evolved as bits of cellular nucleic acid
-candidates for the source of viral genomes
--plasmids and transposons
---all mobile genetic elements
----viruses do not fit our definition of living organisms

discovery of the virus

late 1800s:
-researchers hypothesized that unusually small bacteria might be causing tobacco mosaic disease
1935:
-Wendell Stanley crystallized the infectious particle tobacco mosaic virus (TMV)
--viruses were detected indirectly long before they were actually seen
---tobacco mosaic disease stunts growth of tobacco plants and gives their leaves a mosaic coloration
---later work suggested that the infectious agent did not share features with bacteria

viral size

-the largest virus yet discovered is the size of a small bacterium
--its genome encodes proteins involved in translation, DNA repair, protein folding, and polysaccharide synthesis
--there is controversy about whether this virus evolved before or after cells
-Pithovirus sibericum: 1500 nm x 500nm (Yellow inset, 1000nm bar)
-E. coli: ~2000nm x 500nm when not dividing (1000nm bar)

viral structure

-viruses are not cells
-nucleic acid enclosed in a protein coat (capsid)
-may or not be enclosed in a membranous envelope

viral genomes

-viral genomes may consist of either:
--double- or single-stranded DNA
--double- or single-stranded RNA
-the genome is either a single linear or circular molecule of the nucleic acid
-viruses have between three and 2000 genes in their genomes
---influenza has only seven genes

viral capsids

protein shell that encloses the nucleic acid

the capsomere

individual protein molecules that comprise the capsid
-arranged in a precise and highly repetitive pattern around the nucleic acid
-capsomere shape and arrangement dictates capsid structure
-some viruses only have one capsomere protein
--TMV only has one capsomere protein

capsid arrangement

-some capsomere proteins will self-arrange into a capsid
--others require host chaperone proteins to direct assembly
-capsids are often highly symmetrical

bacteriophages

-viruses that attack only bacteria
--commonly referred to simply as "phages"
-phages posses several distinct capsid "subunits"
--head
--collar
--tail
----a protein tail piece attaches the phage to the host and injects the phage DNA inside
---base plate
---tail fibers
---tail pins

naked viruses

-comprise only the nucleocapsid
--nucleic acid
--capsid
-typically, plant viruses or bacteriophages

enveloped viruses

-the nuclear envelope is a phospholipid bilayer that surrounds the nucleocapsid
--viral envelope is comprised of host membrane
-animal viruses and some others are enveloped viruses
---viral envelopes contains a combination of viral and host cell molecules
---some viruses have accessory structures that help them infect hosts
----influenza/coronavirus are good examples
-in contrast to bacteriophages, the entire virion of enveloped viruses enters the host cell

Retroviruses

-the broadest variety of RNA genomes is found in viruses that infect animals
-retroviruses use reverse transcriptase to copy their RNA genome into DNA

virus classification

-viruses are usually classified by their genetic material: DNA or RNA
-infectious particles that are not quite viruses:
--viroids
--prions

viroids

-viroids are infectious RNA molecules that lack a protein component
--small
--circular
--single-stranded
-the smallest known pathogens
--all known viroids affect flowering plants

prions

-prion proteins are incorrectly folded, infectious proteins
--can be transmitted in food
--slow acting
--virtually indestructable
--affect normal, healthy proteins
-appear to cause degenerative brain diseases in animals
--scrapie (sheep)
--bovine spongiform encephalopathy/mad cow disease (bovines)
--creutzfedlt-jakob disease and kuru (humans)

DNA viruses

-most viruses that infect prokaryotes are DNA viruses
-split into two groups
--Baltimore Class I- dsDNA viruses
--Baltimore Class II-ssDNA viruses
---Baltimore classification is a system used to classify viruses based on their manner of messenger RNA (mRNA) synthesis
----named after virologist David Baltimore
----group=class, names are interchangeable
---Orthopoxvirus: genus of viruses that includes smallpox, monkeypox, cowpox

double-stranded DNA viruses

-Baltimore Class I viruses
-dsDNA phages are some of the most well-studied viruses
--T4 phage
--T7 phage
--λ-phage
---lambda phage on E. coli

single-stranded DNA viruses

-Baltimore Class II viruses
-affect animals, plants, and bacteria
-some possess overlapping genes
--phage ΦX174
-typically possess a circular genome
-upon entering a host cell, the genome is synthesized into dsDNA
--rolling circle replication
--rolling hairpin replication
---canine parvovirus

RNA viruses

split into three groups:
-Baltimore Class III-dsRNA viruses
-Baltimore Class IV- (+) sense ssRNA viruses
-Baltimore Class V-(-) sense ssRNA viruses

double-stranded RNA viruses

-Baltimore Class III viruses
-dsRNA is very rare inside cells and is immediately targeted for degradation
-to combat this the genome replicates inside the capsid
--mRNA is forced out of the capsid in order to be translated
---rotavirus- diarrheal illness

positive sense ssRNA viruses

-Baltimore Class IV viruses
-the genome also functions as mRNA
--no transcription is required for translation
--these viruses do use a dsRNA genome intermediate
---COVID

negative sense ssRNA viruses

-Baltimore Class IV viruses
-"Negarnaviricota"
-the genome acts as the complementary strand from which the mRNA is synthesized
-many are arthropod vector-borne pathogens
--ebolavirus
--sin nombre virus (a hantavirus)
--hendra virus
--rhabdovirus
--measles virus

viral replication

five basic steps:
1. attachment (adsorption) of the virion to the host cell
2. penetration (entry, injection) of the virion nucleic acid into the host cell
3. synthesis of virus nucleic acid and protein by host cell machinery as redirected by the virus
4. assembly of capsids and packaging of viral genomes into new virions
5. release of new virions from the cell

bacteriophage receptors

different viruses have different receptors that they will bind to

genome insertion: T4 phage

-attachment induces changes to both the host cell surface and virus
-tailed phages have the most intricate penetration method
--similar to the T3SS

virulent phage reproduction: lytic cycle

-a phage replicative cycle that culminates in the death of the host cell
-a phage that reproduces only by the lytic cycle is called a virulent phage
--produces new phages and lyses (breaks open) the host's cell wall, releasing the progeny viruses

phage reproduction: lysogenic cycle

-replicates the phage genome without destroying the host
-viral DNA molecule is incorporated into the host cell's chromosome(s)
-this state is called lysogeny- very few viral particles are produced

lysogenic cycle: the prophage

-viral DNA that integrates into the genome
-every time the host divides, it copies the phage DNA and passes the copies to daughter cells
-an environmental signal can trigger the virus genome to exit the bacterial chromosome and switch to the lytic mode

temperate phage reproduction

some double stranded DNA bacterial viruses capable of the virulent cycle, can also infect their host and establish a long-term stable lysogenic relationships
-these viruses are called temperate viruses

viral infection of animal cells

-unlike phages that inject DNA, animal viruses often fuse with the cell membrane to trigger entry (endocytosis)
-animal viruses can trigger one of four different outcomes:
1. lytic infection (same as bacteriophage lytic cycle)
2. latent infection via a provirus stage- can be triggered to initiate lytic infection
3. persistent infection: slow production of viral particles
4. tumor initiation (transformation)
--HPV- cervical cancers

viral infection of plant cells

-plants are protected by the cell wall, preventing endocytosis
-many have broad host ranges
--cucumber mosaic virus can infect 1200 plant species
-viral entry is typically through a wound or by a vector
-some viruses possess movement proteins to traverse plant plasmodesmata

largest and smallest viral genomes

-largest (*):
--Megavirus chilensis: dsDNA
---1,259,197bp (1.26Mbp), 1120 protein coding genes
-smallest (‡):
--Circovirus SFBeef: ssDNA
---859bp, 1 protein-coding gene (726/859bps)
----Megavirus chilensis and a circoviridae (not specifically SFBeef)

single-stranded DNA viruses

prior to transcription, ssDNA serves as a template for dsDNA
-replicative form
--canine parvovirus

rolling hairpin replication

-identical hairpins at both ends
--produces both positive and negative strands
--adeno-associated virus
-dissimilar hairpins
--produces primarily negative strands
--minute virus of mice

double-stranded DNA viruses

DNA replication is identical to eukaryotic DNA replication
-leading strand
--single continuous
-lagging strand
--Okazaki fragments

example: Lambda Phage

-lambda DNA integrates at specific attachment (att) sites on both the host and phage genomes
-dark green strand is rolled out and:
--serves as a template for synthesis of the complementary strand
--is replicated at its opposite end
---A: transmission electron micrograph of phage lambda virions. the head of each virion is about 65 nm in diameter and contains linear dsDNA
---b: lambda integrase is required, and specific pairing of the complementary ends results in integration of lambda DNA
---C: during rolling circle replication

double-stranded RNA viruses

-the 5' may be naked, capped, or covalently linked to a viral protein
-genomic dsRNA is transcribed into viral mRNA
--serves as a template for both translation and genome replication
--occurs primarily within the capsid
---translation generates proteins required for replication and viral encapsidation

positive sense ssRNA viruses

the genome also functions as mRNA
-no transcription is required for translation
-do use a dsRNA genome intermediate for transcription

example: MS2 phage

gene overlap:
-lysis protein gene overlaps with both the coat protein and replicase genes
--A: transmission electron micrograph of the pilus of a cell of Escherichia coli showing virions of phage MS2 attached
--B: genetic map of mS2. the numbers refer to the nucleotide positions on the RNA, the entire genome being 3569 nucleotides in length
--C: flow of events during MS2 replication

negative sense ssRNA viruses

(-) ssRNA is transcribed into mRNA and translated into proteins
(-) ssRNA is generates a (+) ssRNA complement
(+) ssRNA acts as the template for replication

example: Rhabdovirus

viral-encoded RNA replicase is necessary for:
-formation of mRNA
-formation of (+) ssRNA complement
-duplication of (-) ssRNA genome
--Rhabdoviruses are viruses of plants, fish, and humans. includes Rabies lyssavirus

frequency of emerging infectious diseases (EIDs)

an infectious disease whose incidence has increased recently (in the past 20 years), and could increase in the near future
-the disease can be disseminated from a small, isolated human population and can eventually spread around the world
-RNA viruses have an unusually high rate of mutation
-about 75% of new human diseases originate by zooinotic transmission

contributing factors to EIDs

-microbial adaption and change
-human susceptibility to infection
-climate and weather
-changing ecosystems
-human demographics and behavior
-economic development and land use
-international travel and commerce
-technology and industry
-breakdown of public health measures
-poverty and social inequality
-war and famine
-lack of political will
-intent to harm

epidemic vs. pandemic

epidemic:
-an outbreak of disease that attacks many people at about the same time and may spread through one or more communities
pandemic:
-an epidemic that spreads through multiple continents or the entire world

epidemics and pandemics throughout history

there have been over 250 recorded epi- or pandemics across human history
-more may exist but were not recorded due to poor record keeping or destruction of entire populations
-only ~20 have reached "pandemic" status

why do we see a shift in pandemic frequency?

1st shift:
-(late) industrial revolution
--easier global travel
--no real improvements to sanitation or hygiene
2nd shift:
-antibiotic era (WWII-present)
--better medical treatment
--most pandemics are viral in nature
--antivax movements and vaccine hesitancy

epidemics and pandemics throughout history

second plague pandemic (Black Death) continued until 1813 with sporadic epidemics across Europe, Asia, N. Africa, and the Middle East
-HIV (1981-)
-SARS-CoV-1 (2002-4)
-H1N1 Swine Flu (2009)
-Zika (2015-6)
-SARS-CoV-2 (2019-)
-Hepatitis of unknown origin in children (2022-)

vaccines

-a biological preparation that provides active, acquired immunity to a particular disease
-vaccines can prevent certain illnesses
-typically contains an agent that resembles a disease-causing microbe
--weakened (attenuated form of the pathogen (Anthrax*, cholera, etc vaccines))
--inactivated (killed) pathogen (rabies, influenza, J&J covid, etc vaccines)
--toxoids (Anthrax*, DPTǂ, etc vaccines)
---toxoid=inactivated bacterial or viral toxins
--viral subunits (SARS-CoV-2 mRNA vaccine)
DTwP (pertussis whole cell) and TDaP (pertussis antigen) are mixed toxoid and "other type" vaccines

history of vaccines

-pre 1760s (pre-vaccine era): variolation (smallpox)
--Variola major and Variola minor
-Edward Jenner (1760s-1798):
--first vaccine (1796): infected people with cowpox to prevent smallpox
---Variolae vaccinae/Vaccinia Virus
-Jenner was actually not the first
--Peter Plett inoculated three children 1790
---Peter Plett=German teacher/professor received little credit for his findings and was often dismissed by his peers

safety of vaccines

-vaccines are safe
--immunocompromised individuals should consult their doctor about live-virus (attenuated) vaccines
--rarely, allergic reactions may occur
--very rare occurrence of Guillain-Barré syndrome (0.0001-0.0002%)
-vaccines DO NOT cause autism
--MMR vaccine reduced the rate of autism by 7% (in Denmark)

rabies (Rabies lyssavirus)

-transmitted primarily through a bite
-symptom stages:
--early:
---fever and headaches
--mid-stage
---partial paralysis, anxiety, insomnia, confusion, agitation, paranoia, hallucinations, and hydrophobia
--end-stage
---delirium, coma, and death
----once symptoms occur, the disease is fatal
----the vaccine is effective post-exposure

how do we name viruses?

-unlike prokaryotes and eukaryotes, virus naming conventions are not standardized
--some have "genus and species" names
---Variola major
--most do not
---tobacco mosaic virus
---West Nile virus
---SARS-CoV-2
-novel viruses were often named after where they were isolated or where major outbreaks occurred
--virologists have been trying to rectify this with novel viruses
--stigmatized the area

how infectious is a pathogen?

basic reproductive rate (R0)- "R naught"
-the expected number of cases directly generated by one case in a population where all individuals are susceptible to infection
-does not take into account natural immunity or vaccination

R0 of various pathogens

-influenza 1.3-2
-COVID-19: 2.4-9.5
--ancestral (hypothesized): 2.4-3.4
--alpha: 4-5
--delta: 5.1
--omicron: 9.5
-monkeypox: 1.5-2.7
-ebola: 1.4-1.8
-HIV: 2-5
-smallpox: 3.5-6
-polio: 5-7
-measles: 12-18
-RSV: 2.3-2.8

herd immunity and R0

-herd immunity:
--occurs when the majority of a population is immune to a disease
-the larger the R0, the greater the percentage the population must be immune to achieve herd immunity

pathogen #1: Norovirus

-#1 foodborne viral pathogen in the US
-BSL-2
-causative agent of "Winter Vomiting Disease"
--also known as Norwalk virus, or as a general stomach bug
--initially isolated in Norwalk, Ohio
---R0 of 1.1 to 7.2

Norovirus characteristics

-(+) strand ssRNA virus with no envelope
-the genome is linear, about 7.5 kbp in size, and covalently bound to a protein (VPg)
--encodes 3 open reading frames (ORFs)
---sometimes there is a loss of taste, general lethargy, weakness, muscle aches, headache, cough, and/or low-grade fever
---can establish a long term infection in people who are immunocompromised

Norovirus ORFs

-ORF1: a large polyprotein that is cleaved by a protease (NS6)
-ORF2: Viral Protein 1 (VP1): major capsid protein
-ORF3: Viral Protein 2 (VP2): minor capsid protein
--NS1/2 (p48): replication complex formation
-NS3: Putative NTPase/RNA helicase
--NS4 (p22): replication complex formation
--NS5 (VPg): covalently binds the genome
--NS6 (pro): virus-encoded protease
--NS7 (pol): viral RNA-dependent RNA poymerase

Norovirus: route of infection

-Norovirus is a common food and water contaminant
-mechanisms of spread:
--the fecal-route
--may spread person-to-person
--can spread by contaminated surfaces
--can spread as an aerosol from the vomit of an infected individual
---in one incident, a person who vomited spread infection across a restaurant, suggesting that many unexplained cases of food poisoning may have their source in vomit

Norovirus: pathopysiology

-the virus replicates primarily in the small intestine and causes symptoms within 12 to 48 hours
-symptoms include:
--nausea
--forceful vomiting
--watery diarrhea
--abdominal pain
-symptoms may last 24 to 72 hours

Norovirus: prophylaxis/treatments

-there is no vaccine
-alcohol-based disinfectant/sanitizers are ineffective
-handwashing and proper food and surface sterilization helps limit the spread
-treatment is typically only to address potential dehydration

pathogen #2: Poliovirus

-#1 foodborne viral pathogen in the US
-BSL-2
-causative agent of polio (poliomyelitis)
-R0 of 1.1 to 7.2

Poliovirus characteristics

-(+) strand ssRNA virus with no envelope (just like norovirus)
-the genome is linear, about 7.5 kbp in size, and covalently bound to a protein (VPg)- sound familiar?
--encodes one large polyprotein that is autocleaved by internal proteases
---results in about 10 individual viral proteins

Poliovirus: route of infection

-poliovirus only affects humans
--wild poliovirus can quickly infect an entire population
-mechanisms of spread:
--the fecal-oral route
--the oral-oral route
-viral particles continue to be excreted for several weeks following infection
---it is seasonal in temperate climates, with peak transmission occurring in summer and autumn. these seasonal differences are far less pronounced in tropical areas

Poliovirus pathology

-initial infection occurs in pharynx and intestinal mucosa but symptoms do no appear for 3-35 days
-sever symptoms include:
--partial or permanent paralysis
--wasting of limbs, especially the legs
--respiratory failure
--death
---6-20 days is most common for onset of symptoms
---many show no symptoms or mild symptoms (headache, neck stiffness, paresthesia, abnormal skin sensations)
---1950s iron lung

Poliovirus: prophylaxis

-there are vaccines against polio
--Sabin and Salk vaccines
---Albert Sabin and Jonas Salk
-Salk vaccine (1952-1955):
--inactivated virus, injected
-Sabin vaccine (1957-1962)
--live virus, oral
--can lead to vaccine-derived poliovirus (cVDPV)
---a prototype vaccine was developed by Hilary Koprowski, but was outcompeted by Sabin
----Sabin's vaccine was the predominant vaccine, many countries have switched back to inactivated vaccines to combat cVDPV

Poliovirus: treatments

-there is no cure for poliovirus
-modern treatments focus on providing relief of symptoms, speeding recovery and preventing complications
-physical therapy is used to help with paralytic polio

soilborne viral pathogens

-compared to prokaryotes, viruses are less common in the soil
-most viruses in the soil are plant pathogens or mycoviruses
--these are often RNA viruses
-recent evidence suggests these viruses help with carbon cycling in the soil

impact of phytopathogens

-damage natural and cultivated plants
--especially problematic in staple food crops
-constitute over 50% of all emerging and reemerging plant diseases worldwide
-plant viruses have an estimated impact of >$30,000,000,000.00 per year
---curly top vines- one of the pathogens behind the great potato famine in Ireland

top 10 plants viruses

-surveyed all plant virologists with an association with Molecular Plant Pathology (a scientific journal)
1. tobacco mosaic tobamovirus (TMV)
2. tomato spotted wilt tospovirus (TSWV)
3. tomato yellow leaf curl begomovirus (TYLCV)
4. cucumber mosaic cucmovirus (CMV)
5. potato virus Y (potyvirus, PVY)
6. cauliflower mosaic caulmovirus (CaMV)
7. African cassava mosaic begomovirus (ACMV)
8. plum pox potyvirus (PPV)
9. brome mosaic bromovirus (BMV)
10. potato virus X (potexvirus, PVX)
--perceived importance, scientifically or economically

prevalence of human pathogens in soil

-soil is generally not a great environment for the survival of human-pathogenic viruses
--most viruses cannot survive in soil for extended periods of time
---a few hours
---two days at most*
--viruses capable of short-term survival in soil:
---poliovirus* and other enteroviruses*
----enteroviruses can survive for up to 170 days in loamy sandy-loamy soils
----poliovirus can survive in most soils for 80-96 days
---rhinovirus and parainfluenza virus
----parainfluenza virus- common cold and croup (swelling of trachea and barking cough)

human pathogen #1: Hantavirus

-also called "Orthohantavirus"
-BSL-4
-causative agent of either "hantavirus pulmonary syndrome" (HPS) or "hemorrhagic fever with renal syndrome" (HFRS)
--formerly referred to as "Korean hemorrhagic disease"
---first outbreak occurred during the Korean War
----named after the Hantan River in Korea

Hantavirus characteristics

-(-) strand ssRNA virus with an envelope
-typically causes symptomatic infections in rodents
--can be transmitted to humans through their feces
--human to human transmission has recently been observed

Hantavirus genome

-comprised of a small, medium, and large segment
--small segment:
---1-3 kbp, encodes the nucleocapsid protein
--medium segment:
---3.2-4.9 kbp, encodes glycoproteins as a polyprotein that is cleaved apart
---these glycoproteins bind to sugars on the envelope
--large segment:
---6.8-12 kbp, encodes the RNA-dependent RNA polymerase
----N proteins help stabilize the RNA

Hantavirus: route of infection

-Hantavirus is spread primarily through contact with deer mouse droppings
-mechanisms of spread:
--inhalation of aerosolized droppings or contaminated soils
--direct transmission between humans has been demonstrated
---in one incident, a person who vomited spread infection across a restaurant, suggesting that many unexplained cases of food poisoning may have been their source in vomit

Hantavirus pathophysiology

-the specific pathophysiology is unclear
-mouse models for studying the infection are ineffective
--rodents do not show sever disease symptoms
---sometimes there is a loss of taste, general lethargy, weakness, muscle aches, headache, cough, and/or low-grade fever
---can establish a long term infection in people who are immunocompromised