MICR2000 - All Modules

What is this

Coccus (cocci) - sphere

What is this

Rod shaped

What is this

Spirillum (spirilla)

What is this

Spirochete

What is this

Budding and appendaged

What is this

Filamentous

Robert Hooke

First description of microbes

fruiting structures of molds

Antoni Van Leeuwenhoek

First to describe bacteria

Louis Pasteur

Showed microbes responsible for fermentation

Disproved theory of spontaneous generation (microbes appear from thin air)

Koch’s postulates

used to establish causal relationship btwn microbe and disease

1. The suspected pathogen must be present in all cases of disease and absent from healthy animals

2. Suspected pathogen must be grown on pure cultures

3. Cells from a pure culture must cause disease in a healthy animal

4. The suspected pathogen must be reisolated and shown to be the same as the originals

Cytoplasmic membrane structure and function

Phospholipid bilayer with embedded proteins

Functions as highly selectively permeable barrier

Bacterial vs Archaeal Cytoplasmic Membranes

both phospholipids

Bacteria

• fatty acids joined to glycerol through ester linkages

Archaea

• isoprene units joined to glycerol via ether linkages

Gram +ve vs Gram -ve cell walls

Both

• peptidoglycan - rigidity

  • composed of G + M

  • peptide crosslinking provides strength in X and Y direction

Gram +ve

• 90% peptidoglycan

• peptidoglycan above cytoplasmic membrane

  • crosslinking via peptide interbridge

• teichoic acids (embedded) and lipoteichoic (teichoic acids covalently bonded to lipids) acids in cell wall

Gram -ve

• 10% peptidoglycan

• peptidoglycan sandwiched btwn outer and inter membranes

  • crosslinking via NH2 group of DAP and COOH of D-alanine link

• Periplasm

  • gel-like compartment containing proteins btwn outer and cytoplasmic (inner) membranes

• Lipopolysaccharides embedded in outer membrane

  • Lipid A (endotoxin) buried in membrane - highly toxic

  • core polysaccharide and lipid A conserved

  • O-antigen (sticking out) varies

Gram staining

Process

• add crystal violet

  • crystal violet makes cells purple but will wash out unless u cross link with iodine

• add iodine

  • iodine only cross links with crystal violet in peptidoglycan - only g+ve have peptidoglycan exposed

• wash with alcohol 

  • washes off crystal violet on gram -ve cells

• counterstain with saffranin

  • stains g-ve pink

Acid fast bacteria

E.g., Mycobacterium

Waxy lipid mycolic acid makes cell impermeable to gram stain components

Able to be stained red using acid fast stain

Cell walls of Archaea

S layer

• interlocking protein and glycoprotein arranged in paracrystalline surface structure

• no peptidoglycan or outer membrane

Some archaea contain pseudomurein - similar to peptidoglycan

Capsules of bacteria

Polysaccharide layers

• assist in attachment and biofilm formation

• aid in evading immune system

• resist desiccation

Fimbriae

Filamentous bacterial appendages involved in adhesion

Different fimbriae can be expressed to allow adhesion in different environments

Flagella (arrangements, structure, biosynthesis)

3 arrangements

• peritrichous

  • spread evenly around cell

• polar

  • one flagella

• lophotrichous

  • multiple flagella concentrated on one end

Structure

• filament

  • composed of flagellin

• hook

  • connects filament to motor

• mot proteins

  • motor

  • anchored to cytoplasmic membrane and cell wall

• fli proteins

  • motor switch

  • reverses rotation of flagella in response to intracellular signals

Biosynthesis

• requires many genes

• flagellin synthesised in cytoplasm, moved through filament to build (filament core is hollow)

Types of flagella movement

Polar

• move forwards and backwards

• can reorient to move forwards/backwards in different heading

Peritrichous or lophotrichous

• can bundle flagella to move like polar cells

• tumble and run

  • flagella pushed apart to tumble

  • bundled to run

Gliding motility

Flagella independent motility - very slow

• slime

  • shoot slime for propulsion

• type IV pili

  • attach to surface and twitch

• specific proteins

  • membrane fluidity - proteins move along cell membrane and push against a surface

Microbial taxes

Chemotaxis

• moving up a gradient of attractant chemicals

• increased tumble and run

• chemoreceptors

• measured using capillary tube assay if run and tumble behaviour not observed)

  • things attracted or repelled by tube

Cell inclusions

Aggregate of a molecule

• lipid or glycogen storage for extra energy

• accumulate inorganic compounds 

• magnetosomes

  • magnetite, orient bacteria in magnetic field

Gas vesicles

spindle shaped gas filled protein structrues

buoyancy

optimise position in water column

Endospores

Dormant bacteria resistant to extreme conditions

ideal for dispersion in harsh environments e.g., wind, water, gut

only in some g+ve

Germinate to produce mature spore (sporulation)

Structure

• exosporium = outermost protein coat

• spore coats = more layers made of peptidoglycan or carbohydrates

• cortex = peptidoglycan

• core = cellular components surroudned by core wall

Generation time/doubling time

Interval for formation of two cells (from one cell)

Batch culture

Closed system microbial culture of fixed volume

Phases of growth curve

Lag phase

• period before growth begins at maximal rate

• cells adapted to stationary phase have to adapt to fresh medium (adapt for growth) or adapt to different medium (e.g., minimal) by producing new enzymes

Exponential phase

• doubling/generation time (g) constant

• N = N0×2^n

• n = number of generations

• t = incubation time (time)

• g=t/n

• mean growth rate constant (k) = n/t

Stationary phase

• no net increase in cell number

• something limiting growth - nutrient or inhibitory products

• adaptation to stationary phase - specific genes

  • RpoS (RNA polymerase sigma factor)

    • directs RNA polymerase to transcribe stationary phase adaptation genes

Death phase

• cells die

• associated with lysis

Total cell count

counting cells in square and extrapolating

rapid but imprecise, hard to see small cells, can’t distinguish live from dead

Viable cell count

serial dilutions until little enough cells to count, then use dilution factor

Turbidimetric measurements

measures turbidity - how much light is scatterede by density of culture

optical density (OD)

Primary vs secondary metabolites in microbial growth

Primary

• made during exponential growth

Secondary

• produced during stationary phase

• not essential for growth

• overproduced

Biofilms

community of bacterial cells enclosed in self produced matrix (polysaccharide, protein, extracellular DNA) and adhered to surface

Model of biofilm development

Reversible attachment - bacteria contact surface with flagella

Irreversible attachment - fimbriae/pili attach to surface, adhesins

Microcolony formations

• matrix of polysaccharide, protein, DNA surrounds colony and holds it together

• quorum sensing

  • bacteria communicate with homoserine lactone (HSL)

  • cells start communicating when quorum achieved (minimum conc of HSL for comms)

    • regulate gene expression, control cell density, change behaviours

Metabolic interactions

Dispersal of bacteria

Why do bacteria form biofilms?

Self defense (physical forces, phagocytosis, antibiotics)

Colonise favourable niches (remain attached to nutrient rich areas)

Enable bacteria to live together (quorum sensing, genetic exchange)

Survival strategy when nutrients limited

Why are biofilms antibiotic resistant?

Slow penetration of antibiotic

Inner layers have more time to adapt to antibiotic

Cells in nutrient low zones inactive and thus antibiotics may not act on them - persister cells are in dormancy

Antimicrobial depletion due to adsorption

Sterilisation

killing or removal of all viable organisms within a growth medium

Inhibition

Effectively limiting microbial growth

Decontamination

Treatment of an object to make it safe to handle

Disinfection

Directly targets removal of all pathogens, not necessarily all microbes

Microbial growth control

Heat sterilisation

• endospores can survive heat that would kill vegetative cells

• decimal reduction time = time req for 10 fold reduction in viability

• thermal death time = time to kill all cells at given temp

• autoclave - uses steam under pressure

Pasteurisation

• precise heat to reduce microbial load, controls pathogens not killing all

Radiation sterilisation

• ionising radiation can also produce reactive molecular species

Filter sterilisation

• filter organisms out

Antimicrobial agent classification

Bacteriostatic

• stops growth of bacteria but doesn’t kill them

Bacteriocidal

• kills but doesn’t lyse cells - viable cell count decreases

Bacteriolytic

• kills and lyses bacteria

Measuring antimicrobial activity

Minimum Inhibitory Concentration

• smallest amount of agent req to inhibit growth of microbe

Disk diffusion assay

Microbial community vs population

Community = multiple interacting populations

Population = one species

Classes of antimicrobials

Synthetic

• growth factor analogues - man made

Semi synthetic

• microbially produced and chemically modified

How are drugs that block the synthesis of folic acid able to maintain
selective toxicity?

humans acquire folic acid from diet while bacteria synthesis it themselves

Beta lactam antibiotics

Beta lactam ring

incl penicillins

inhibit cell wall synthesis by binding to penicillin binding proteins (PBPs) and preventing cross linking

cell wall synthesis continues but weakened

Penicillin-PBP complex stimulates release of autolysins, which degrade the cell wall (normally used for cell division)

AMR mechanisms

resistant organisms can:

• lack structure antibiotics inhibit

• impermeable to antibiotic

• inactivate antibiotics

• modify target of antibiotic

• resistant biochemical pathways (take up folic acid instead of secreting)

• efflux of antibiotic

Vancomycin resistance

Vancomycin = last line antibiotic

Resistant S. aureus replaces components of cell wall with different ones still recognised by PBPs for cross linking but no by vancomycin

Conjugation

Conjugative R plasmid

DNA transfer from one cell to another

• Attach two cells via pilus

• transfer one strand of plasmid to recipient cell

• synthesis of complementary strands in both cells

• cells separate

Can carry AMR genes

Transposable elements

DNA sequences that can move positions within or between DNA strands

Two types:

• Insertion sequences (IS)

  • smallest, encode transposase (endonuclease and integrase activities)

    • this cuts it out and puts it in somewhere else

    • IS does not encode any other genes

  • flanked by inverted repeat (IR) that is recognised by transposase

• Transposons

  • contain transposase and IR as well as non transposition related genes - often AMR

  • often contain integrons

    • contain promotor and attachment site for gene cassettes (free floating DNA)

      • cassettes encoding gene followed by integrase specific recombination site - 59 base element recognised by integrase

    • integrase integrates cassettes to attachment site and promoter tests what they do

    • cassettes excised and transferred btwn integrons

Transposition methods

Conservative - cut and paste

• transposase cuts target DNA (staggered nick)

• IS integrates

Replicative - copy and paste

• TnpA gene transcribed to make transposase

• transposase binds to IR and initiates transposition

  • cuts donor plasmid at ends and makes staggered nicks on target plasmid

• ligation of transposon to target ends

  • 3’ ends replicate through DNA polymerase, replicating the carried genes of the transposon

  • this forms a cointegrate - a single molecule of DNA between the donor and target plasmid (looks like 8)

    • contains 2x copies of transferred DNA

• Resolvase binds to ‘res’ regions on transposon

  • cuts and recombines forming 2x plasmids with the transposon

How to stop spread of AMR

stop inappropriate use of antibiotics to reduce selective pressure

remove ineffective antibiotics from use

monitoring, isolation and treatment programs to prevent establishment and spread of multiple resistant pathogens

Normal flora

microbes that live on and in our body without causing infection under healthy conditions

• balance btwn enough for microbes to survive and not enough to cause infection

• pathogens can be transient members of normal flora

Virulence factors

Bacterial product or strategy contributing to virulence or pathogenicity

• colonisation of host

• evade immune system

• damage host

6 categories

• motility

  • motile bacteria can target host cells in dynamic environments like mucosal environments

  • ability to contact host cells

• adhere to host cells and resist physical removal

  • pili/fimbriae and adhesins

• invade host cells

  • invasins allow penetration

  • inside the cell access to nuritents, hide from immune system, divide and multiply

• resist phagocytosis and complement

  • capsules hard for macrophages to attach and engulf, biofilms

• evade immune defenses

  • phase variation of surface

    • vary surface structures to evade detection

  • capsules can resemble human tissue

  • don’t evade - KILL

    • endotoxin

      • lipid A in gram -ve outer membrane

      • released when bacteria attacked (membrane breached) and can be secreted

    • exotoxin

      • soluble excreted toxins

      • toxin genes spread on plasmids

      • cytotoxins kill or inhibit cells

      • neurotoxins interfere with nerves

      • enterotoxins affect epithelial cells of GI tract

    • requires production of antitoxins

• ability to compete for nutrients

  • compete with host tissue and normal flora for limited nutrients

Staphylococcus aureus virulence factors

g+ve cocci

adhesins - adhere to host cells

secrete exotoxins that kill host cells

secrete enzymes that deteriorate red blood cells and immune system enzymes

neutralise hydrogen peroxide from macrophages - resist phagocytosis

protein a - evade immune system

capsule - resist phagocytosis

coagulase - slow down immune system through blood clot

Helicobacter pylori and virulence factors

Host adapted pathogen that colonises human stomach and duodenum - inhabits mucosal layer )noninvasive) so not cleared by immune response (persistent infection), can be treated by antibiotics

symptomatic or asymptomatic infection - virulent strains have cag a pathogenicity island

Virulence factors:

Urease

• bacteria imports urea from gastric juice (through porin to periplasm, UreI to cytoplasm) 

• urease in cytoplasm catalyses urea → ammonia reaction

• ammonia makes gastric acid more basic allowing H pylori to survive

Flagella

• motility

• lophotrichous arrangement

• move in mucosal lining

Adhesins

• BabA and SabA allow adherence to gastric epithelium

Mucinase

• degrades gastric mucus locally for easier motility

CagA - cagA pathogenicity island confers high virulence

• CagA protein and type IV secretory system transcribed and translated

• injected into host cells via type IV secretory system (syringe) to release pro-inflammatory cytokines

• increases acid which wears away mucous

Testing for H. pylori

Rapid urease test

• pH test for urease catalysing ammonia production

Treatment and prevention of H. pylori infection

Acid lowering drugs

Antibiotics

Group A Streptococcus (Streptococcus pyogenes) diseases, location

Location

• skin and throat

Range of diseases

• sore throat

• localised common infections

  • cellulitis

  • impetigo (skin infection)

• less common invasive infections

  • bacteraemia

  • toxic shock systems

  • necrotising fascilitis

• post streptococcal sequelae - diseases after repeated infection with GAS

  • kidney failure and acute rheumatic fever (heart failure)

  • immune sequelae

    • GAS makes M protein which has anti phagocytic activity

    • similar to heart myosin - autoimmunity against heart myosin causing rheumatic heart disease

How do GAS infections align/misalign with Koch’s old postulates?

1 - Bacteria present in every case of disease and absent in healthy animals (NO FIT)

• GAS present in normal flora

2 - Bacteria must be isolated from host with disease and grown in pure culture (FITS)

• GAS can be cultured

3 - Specific disease must be reproduced when pure culture of bacteria is inoculated into a healthy susceptible host (NO FIT)

• bacteria absent from post streptococcal sequelae so this doesn’t hold

• different strains produce different things

4 - Bacteria must be recoverable from experimentally infected host and found to be same as original (NO FIT)

• different strains of GAS

Koch’s molecular postulates

Identifying the gene or gene product responsible for virulence rather than the pathogen

Postulates

• shows gene present in strains of bacteria that cause disease and not present in avirulent strains

• disrupting the gene reduces virulence and reintroduction restores virulence

• introduction of cloned gene into avirulent strain congers virulence

• gene is expressed (not methylated)

• specific immune response to gene protects against virulence 

Is HtrA involved in GAS virulence?

thought HtrA involved in protecting GAS proteins during thermal stress

did test and found virulence disappeared when DNA added but didn’t return when it was returned to normal.

• polar effect - DNA downstream affected (frame shift)

double crossover recombination

• keeps reading frame the same

• deleted mutant had no effect on virulence

Therefore HtrA doesn’t affect virulence

GAS virulence factors

M protein

• helps resist phagocytosis

• similar to heart myosin - immune sequelae

Fibronectin binding proteins (FBP)

• allows GAS to bind to fibronectin in ECM of tissues and colonise that tissue

• Phase variation

  • swap out FBPs

  • different combinations can contribute to different tissue binding - tissue tropisms

  • redundancy in FBPs allows infection of more than one tissue

What is a virus?

Structure evolved to transfer nucleic acid from one cell to another

obligate, intracellular parasites

• cannot replicate outside host cell

possess one kind of nucleic acid (DNA or RNA)

limited genetic material

no ribosomes

viral nucleic acid and protein synthesis occur separately and come together

lipids and carbohydrates acquired from host cell

Origins of viruses

Pre LUCA (RNA world)

May have invented DNA

• RNA viruses infected RNA cells

• sensing of RNA evolved to combat viruses

• viruses evolved DNA to counter

• DNA from viruses integrated into cell genomes, more stable thus eventually takes over as genomic repository

Types of viral proteins

proteins are encoded in genome or acquired from host through budding

Structural

• make up viral particle (virion)

• involved in cell attachment and penetration

• viral assembly and release

• protect nucleic acid which is sensitive to restriction enzymes

Non-structural

• not part of virion

• involved in viral replication

  • e.g., polymerases, helicases

• involved in virus assembly

Virus composition

Nucleocapsid

• protein shell that surrounds viral genome

• capsomers (structural protein subunits) in icosahedral or helical symmetry

  • icosahedral

    • capsomers form equilateral triangular faces (n-fold symmetry)

  • helical

    • capsomers wrapped around central genome core in helical pattern, tend to be rod shaped

Naked vs enveloped viruses

• naked

  • only nucleic acid and protein

• enveloped

  • acquire lipid membrane as they bud through membranes (ER or cell membrane often)

  • susceptible to inactivation from e.g., detergents

  • membranes have been transformed by virus proteins which were synthesised inside the cell, thus have these viral proteins

    • peplomers - spike proteins

  • helical nucleocapsids have flexible structure, can coil up to be

    • spherical/icosehedral

    • pleomorphic

    • filamentous

  • other shapes

    • rod (bacilform)

    • bullet

Complex viruses

neither helical or icosehedral

e.g., poxviruses

complex assembly processes

mulberry (multiple balls) or ball of yarn shapes

T - even bacteriophage

• icosahedral head w genetic material

• contractile tail/sheath

• base plate

• tail fibres

  • bind to receptor

  • pulls down and base plate goes into cell

  • tail contracts and genetic material injected

mimivirus - giant DNA virus

pandoravirus

Two main symmetries viruses use and examples, examples of enveloped and naked viruses

helical

• orthomyxoviruses

  • influenza

• paramyxoviruses

  • measles, mumps, hendra

• filoviruses

  • marburg, ebola

icosahedral

• togaviruses

  • ross river

  • rubella

• flaviviruses

  • dengue

  • yellow fever

• herpesviruses

  • chicken pox

  • herpes simplex

enveloped

• influenza

• COVID

• HIV

naked

• plant and bacteria viruses

• polio

• FDMV

Structure of virus determined by

size and coding capacity of genome

• must fit inside nucleocapsid

• most economic nucleocapsid symmetry

• number of structural proteins available

functional requirements

• protection of genome from environment (water vs air)

• mode of attachment and cell entry

• mode of replication

• mode of virion assembly and release

  • burst or budding

Structural analysis of viruses

Electron microscopy

• virus ID, cellular location

• low res

X-ray crystallography

• high resolution structure

• virus/receptor interactions

• identification of precise targets for antivirals

Virus vs Bacteria

Stages of viral infection

attachment

penetration

uncoating

transcription/translation (protein synthesis)

genome replication

assembly

release

Viral attachment

brownian (random) motion until collision w cell receptors which allows attachment

Virus attachment sites

• enveloped viruses

  • spikes/peplomers

• naked viruses

  • anywhere on virus surface

Cell receptors (attachment site on cells)

• cell surface molecules

• e.g., CCR5 binds to HIV peplomers, CD4 coreceptor pulls HIV towards membrane

Specific interaction

• physical complementarity req for attachment

• most viruses interact with specific receptors (only certain cell types)

  • host and tissue specificity

Virus entry/penetration methods

Endocytosis

• virus engulfed into cytoplasmic vacuole

• for enveloped viruses

  • virus endocytosed after binding to receptors

  • envelope fuses with endosome (vacuole) membrane

  • release of nucleic acid into cytoplasm

Membrane fusion (enveloped viruses)

• envelope fuses with cell membrane

• only nucleocapsid enters cell (envelope fuses)

Direct entry (some naked viruses)

• capsid undergoes molecular rearrangement

• whole virus or only genome enters

Exosomes (naked viruses)

• membrane bound particles cells excrete as waste

• naked viruses travel in these and enter new cells

Viral uncoating

Often spontaneous release of nucleic acid

carried out by host cell or viral enzymes (protease, lipases, etc)

Viral synthesis of proteins and nucleic acid

DNA viruses replicate in cell nucleus (except pox viruses which are too large to fit and carry their own replicative material)

RNA viruses generally replicate in cytoplasm, encode their own RNA dependent RNA polymerase

• need ribosomes

• need host cell enzymes e.g., to cleave polyproteins into individual proteins

How do viruses deal with competition?

Take over ribosomes to synthesis ONLY viral proteins

downregulate receptors so other viruses can’t enter

Baltimore classes of viruses

I = dsDNA

II = ssDNA

III = dsRNA

IV = ssRNA +ve sense

V = ssRNA -ve sense

VI = +ssRNA replicates w DNA intermediate

VII = dsDNA replicates w RNA intermediate

DNA viruses synthesis of viral proteins

dsDNA (I, VII)

• direct transcription of mRNA

ssDNA (II)

• synthesis of other strand

  • dsDNA intermediate

• transcription onto mRNA

RNA viruses synthesis of viral proteins

dsRNA (III) and -ssRNA (V)

• need own RNA dependent RNA polymerase to transcribe -RNA strand to create +RNA strand (mRNA)

+ssRNA (IV)

• +RNA used directly as mRNA

Class VI retroviruses (+ssRNA with dsDNA intermediate)

• reverse transcription to make dsDNA intermediate

• dsDNA intermediate transcribed to make mRNA

Replication of +ssRNA virus (IV)

genome used directly as mRNA to make viral proteins

RNA dependent RNA polymerase (RNA replicase) made

• -ve strand synthesised

• more copies of +ve strand synthesised

Asymmetric strand synthesis

• more +ve than -ve (only need some -ve as template)

Replication of -ssRNA virus (V)

RNA replicase enzymes brought into cell as part of virion

-ve strand RNA released into cytoplasm, replicase makes +RNA for translation of viral proteins

using +RNA, -ve strand genomic RNA produced

Virus assembly and release

Assembly

• relatively spontaneous for simple viruses

• stages for complex viruses

Release

• enveloped

  • gradually bud from cell

• naked

  • accumulate in cell until cell lyses

    • known as one step growth curve

    • may also be secreted gradually through exosomes

Examples of Class IV and V viruses

IV (+ssRNA)

• flaviviruses (dengue)

• togaviruses (rubella)

• COVID

V (-ssRNA)

• RSV

• orthomyxoviruses (influenza)

• paramyxoviruses (measles, mumps)

• filoviruses (ebola)

Targets for antiviral agents

viral specific enzymes or nucleic acid

• viral protease (necessary for viruses to cut up viral polyproteins)

• RNA dependent RNA polymerase (RNA replicases)

viral DNA synthesis - acyclovir

• affects host polymerase function

• incorporation into DNA results in termination of viral replication

• not toxic to host cells as activated by viral enzymes only produced in infected cells

Viral disease syndromes and what causes them

Cell damage due to viral replication

• cell rupture during virus release

  • necrosis

• cell death to control infection (apoptosis)

• infected cells lose function

• infectious cell transformed by virus, virus activates oncogenes by inserting into cell genome

  • causes tumours

Damage due to host response to infection

• immunopathology - antibodies and immune cells destroy infected cells

  • tissue damage

• fever invoked to stimulate immune response, inhibit virus replication

• inflammation caused by immune cells infiltrating infection site

• excessive cytokine production

  • can cause tissue damage and inflammation

Host factors affecting viral pathogenesis

Age

• some viral infections more severe at different ages

• immune system maturity/waning

• hormonal influences

Genetics

• e.g., cell receptor CCR5 doesn’t protrude through membrane, reducing susceptibility to HIV as it needs this coreceptor to CD4

Metabolic state (body condition)

• generalised malnutrition or vitamin A deficiency increase susceptibility and severity

• pregnancy (change in hormonal balance) alters susceptibility to some viruses 

Altered immune responses

• impaired immune system due to:

  • genetics

  • consequence of infection (HIV)

  • Iatrogenically/therapeutically acquired (after transplant)

• enhanced immune system

  • auto-immunity

Routes of viral entry

Skin

• mechanical trauma (microtears)

• injection

• infected mosquito bite

• bite of infected animal

Genitourinary tract

• tears or abrasions allow viral entry

• sexually transmitted (HIV, Herpes Simplex)

• host defence

  • cervical mucus

  • pH of vaginal secretions

  • chemical composition of urine

Respiratory tract

• droplet infection in aerosols

• generally enveloped viruses

GI tract

• invasion of tissues underlying mucosal layer

• virus survivability depends on:

  • acid stability

  • resistance to bile salts

  • resistance to inactivation by proteolytic enzymes

• generally naked viruses

Conjunctiva - eyes

localisation vs systemic spread

localised infections

• virus multiply in epithelial cells at site of entry

• produce spreading infection then shed directly to exterior

  • infection back out apical side of cells since cells are polarised

  • none through basal layer

systemic spread

• polarised infection of epithelial cells and spread

• targeting of viral budding to apical or basal surfaced of polarised cells may define subsequent spread

Modes of viral transmission

Person-person transmission:

Respiratory/salivary

• influenza, measles, rhinoviruses

Fecal-oral

• enteroviruses, rotaviruses

Contact (sexual)

• Herpes simplex 2, genital warts, HIV

No person-person transmission:

Vector (biting arthropod)

• sandfly fever, dengue

Vertebrate reservoir

• rabies, cowpox

vector-vertebrate

• arbovirus

How to measure transmissibility/contagiousness of viruses?

Basic reproduction number (R0) = Attack rate (#ppl infected) * contacts

Acute vs chronic vs recurring infections

Acute

• rapid onset of symptoms

• usually complete recovery or death

• influenza, cold

Chronic/persistent

• long, slow infections (HIV, HCV)

• may have insidious onset (no symptoms)

• symptoms may be present most of time, sometimes for life

Recurrent/latent

• infection occurs

• virus replication dies down, minimal until triggered by stimuli

• reoccurrence of symptoms from virus which has been latently present (herpes simplex)

Non-persistent vs persistent microbes

Non-persistent

• retained briefly, transmitted quickly

• don’t multiply within vector’s body

• in small community will infect everyone acutely then die out

• in large community infects susceptibles, spreads causing repeated outbreaks as fresh susceptibles appear

  • continuous circulation

Persistent

• longer acquisition, can persist longer

• replicates within vector’s body

• microbe infects susceptibles

• microbe remains latent

• microbe reactivates, infects next generation of susceptibles - in large or small community

Plant virus structure

icosahedral or helical symmetry

most are naked

most have small +ssRNA genomes for better systemic spread btwn cells

some have circular DNA genomes

Multipartite plant viruses

Segmented genomes, each segment encased in individual nucleocapsid as opposed to segments within a single particle

need to infect plant with all segments for productive infection

way to regulate gene expression

• control ratios of particles, can control the amounts of proteins each particle makes (e.g., make less of particle A which has gene for polymerase so less polymerase)

plant virus transmission

plants have rigid cell wall - no endocytosis or fusion

enter through vectors or infected seeds

How do plant viruses spread systemically and from cell to cell?

systemic infection via phloem

cell-cell

• plasmodesmata connect cells, too small for viruses

• movement protein

  • lining with protein tubule to wedge open (CPMV)

  • making viral proteins to wedge open plasmodesmata and allow virion to pass through (PVX)

Coevolution of virus, fungi and plant

Virus, fungi and plant live in hot spring

virus causes fungi to produce heat shock protein which protects plant