Microbiology Flashcards
(297 cards)
1
Q
What is the purpose of gram staining?
A
It differentiates between 2 types of bacterial cell wall
2
Q
What are gram positive bacteria?
A
They have a thick peptidoglycan wall so retain the dye so it turns PURPLE
3
Q
What are gram negative bacteria?
A
They have a thinner peptidoglycan wall so dye is lost, leaving the bacteria stained by the counter stain - RED
4
Q
What is the cell wall structure of gram + bacteria?
A
Thick layer of peptidoglycan on top of a cytoplasmic membrane
5
Q
What is the cell wall structure of gram - bacteria?
A
Have a layer of peptidoglycan sandwiched between 2 membranes with channel proteins embedded Outer membrane is mainly composed of lipopolysaccharides (type of PAMP) - only in g-b
6
Q
What happens after gram staining to identify the bacteria?
A
Culture and microscopy > biochem and serological tests > DNA techniques > sensitivity to Abio determined > so clinicians know what Abio to give
7
Q
What is the main difference between gram +/- bacteria?
A
GNB has 2 membranes (inner and outer) and GPB has 1 membrane
GNB have lipopolysaccharides (which is a PAMP) and is very important
8
Q
List some pathogenic GNB
A
Escherichia Coli - EP=diarrhoea, EH=toxin produced, dysentery, kidney failure Salmonella - typhimurium=food poisoning, typhi=typhoid Shigella - dysentery Vibrio Cholerae - cholera Neisseria - meningitidis=meningitis, gonorrhoeae=gonorrhea
9
Q
List some pathogenic GPB
A
Staphylococcus aureus - skin disease, endocarditis, bacteraemia, joint diseases, pneumonia Streptococcus pneumoniae - pneumonia, meningitis, otitis media Strepto pyogenes - tonsillitis, necrotising fasciitis, bacteraemia, scarlet fever
10
Q
List 2 mycobacterium
A
Mycobacterium tuberculosis - TB Mycobacterium leprae - leprosy
11
Q
How do you distinguish between bacteria types?
A
Gram staining
12
Q
What are the requirements to be a pathogen?
They need to be able to:
A
Colonise - pili/fimbriae formed allow them to cling onto surfaces
Persist - ability to avoid host defences
Replicate - acquire nutrients needed for replication (specifically iron which is scarce in host)
Disseminate within cells, tissues, between organs and hosts
Cause disease - produce toxins that kill host cells
13
Q
What’s the difference between pili and fimbriae?
A
Pili - longer, thicker, tubular structures made up of pilin, found ONLY in in GNB, 3-5 per cell, involved in cell-2-cell attachment during bacterial conjugation so sex pili Fimbriae - shorter, thinner than pili, found in both GNB/GPB, around 300-400 per cell, involved in cell to surface attachment of bacteria
14
Q
What is another way of classifying bacteria (not gram staining)?
A
Extracellular - Staph, Strep, Yersinia, Neisseria
OR
Intracellular - Listeria, Shigella, Salmonella, Mycobacteria, Chlamydia, Coxiella
15
Q
How do the intracellular bacteria gain entry into the cell without being lysed?
A
Enter cell via invagination and remain in endosome
16
Q
What are the 3 methods to survive in a host cell?
A
Prevent fusion with lysosomes (Salmonella, Mycobacteria and Chlamydia by changing the endosome)
Escape (Listeria and Shigella break down endosome and escape into cytoplasm)
Survive in phagolysosome (Coxiella can survive in harsh env)
17
Q
What is the motility and how does Salmonella invade the host?
A
Polymerises actin into filaments, which ruffles the plasma membrane and bacteria get stuck in ruffle. As process dies down and returns to normal, the trapped bacteria becomes internalised
18
Q
What are the 3 shapes of bacteria?
A
Cocci, spirilli, bacilli
19
Q
What are the 2 related multi-protein machines that are required for motility and invasion?
A
Flagella and the Type III secretion system
20
Q
What is the type III secretion system?
A
Only exists in GNB - In salmonella, the type III secretion system delivers virulence proteins across the membrane into host cell, which induce actin polymerisation, membrane ruffling and bacterial internalisation
Evolutionary linked to flagellum, acts as a translocon which inserts into host membrane, allowing effector proteins to be transferred from bacteria to host cell
21
Q
What is another example of manipulation of actin by Listeria and Shigella?
A
Bacteria breaks out of vacuole and assembles/polymerises actin at one pole of bacterial cell, which generates force, propelling the bacterium through the cytoplasm, leading to spread of bacterium from one cell to another
Streams of actin known as Comet tails
22
Q
How are genes transmitted in bacteria to evolve such complex structures?
A
Bacterias have around 500-4500 proteins in genome, of which the majority are housekeeping functions - core genome (40%) and 60% non-core genes which are different in each bacteria
Genes are either transmitted via horizontal or vertical transmission, with vertical being through binary fission
23
Q
What are the 3 main mechanisms of horizontal gene transmission?
A
Transduction, Conjugation and Transformation
24
Q
What is transformation?
A
Uptake of naked DNA, sucking it up from outside, which is recognised from lysed bacteria
Transport mechanism allows uptake of DNA and incorporation into bacterial chromosome
Nisseria and Strep can do this
25
What is transduction?
Phages invade bacteria and replicate its DNA in the bacterium and cuts the DNA into small pieces. Some of the DNA may be packaged into phage heads and new phage particlesare released, which then injects the DNA into the next bacterium, which may be incorporated into chromosome. Many GN/PB do this.
26
What is conjugation?
A physical bridge between bacteria forms, allowing transfer of plasmid between bacteria
27
What is a pathogenicity island?
Horizontally acquired DNA that contributed to virulence - main drivers of evolution of bacterial properties and origin is usually unknown
28
What is responsible for the sophisticated processes the bacteria posess?
Huge variety of DNA accessible through horizontal transmission, so occupy a huge biodiversity component. Their high reproductive rate and ability to mix DNA means that there is a huge selection pressure.
29
What are the sources and routes of bacterial infection?
Extrinsic, intrinsic, mythical (mythical explanations such as catching a cold from being outside in the cold)
30
Which are the sterile and non-sterile sites?
Sterile: Liver, stomach, brain, trachea, lungs, heart, spleen, kidney, bladder, gall bladder, pancreas
Non-sterile: Nasal cavity, sinuses, mouth, URT, large intenstine, small intestine, lower genital tract (vagina), skin, appendix, stomach
NB: smal intestine only has GNB
31
What are the portals of entry for bacteria?
Expected and unexpected
32
What pathogens enter via the URT?
Usually extrinsically acquired from resp tract droplets/airborne or hand transmission as intermediate
Viruses: influenza, measels, varicella,other herpes viruses
Bacteria: Strep. pneumoniae/pyogenes, nisseria meningitidis, staph aureus
33
What are the consequences of bacterial infections acquired through URT?
URTI: pharyngitis, tonsilitis, sinusitis
LRTI: bronchitis, pneumonia, pneumonitis
Spread to adjacent tissues: brain abcess, meningitis, empyema (pus in pleural space), pericarditis
Spread to bloodstream: bacteraemia
34
What pathogens enter via the Urogenital tract?
Intrinsic (from large intestine): E. coli, Klebsiella, Candida
Extrinsic: Nosocomial - urinary catheters, STI: Nisseria gonorrhoeae, chlamydia trachomatis, syphilis, HIV
35
Which pathogens enter via broken skin?
Staph aureus, strep pyogenes (group A strep), may get MRSA or pseudomonas
36
How is the skin broken to allow pathogens to enter?
Surgery, varicella, eczema, pressure sores, injecting drug use, human/animal bites
37
What are the consequences of infection via broken skin?
If infection spreads across skin layer - cellulitis (red inflammation of skin), Abscess - pus filled pocket, necrotising infection - cell death underneath superficial layer, myositis - infection spread deeper into muscle causing inflammation, gangrene/necrotic infection - anly layer of skin, bacteraemia
Staph aureus main cause of this
38
Which pathogens enter via the GI tract?
Virsuses: Hep A/E, norovirus
Bacteria: E. coli, shigella (dysentry), salmonella enterica/typhi, listeria
Toxins: enterotoxins
39
What are the consequences of infections of GI tract?
DIARRHOEA, bacteraemia/systemic infections, typhoid, listeriosis, salmonellosis, septic arthirits, aortitis
Listeria isn't major cause of D&V but if it gets into bloodstream, can cause serious disease in neonates/elderly/immunocompromised
40
What is the pathogenicity of a bacteria?
The ability of organism to cause disease
Commensals - don't cause disease, true pathogens - cause disease in normal/healthy people, opportunistic pathogens - only cause disease when given the chance (staph epidermidis which colonises metal in hip and causes infection)
41
What affects the pathogenicity?
Infectivity and virulence
42
What is infectivity?
The ability to enter host system and establish themselves, initiating infection - factors involved: transmission to host, ability to colonise host/find niche/replicate, immune evasion
43
What is virulence?
Features that enhance disease causation, enhancing bugs ability to make you unwell - toxins, enzymes, complete immune evasion
44
What is the infectious dose of a bacteria?
The no of bacteria required to initiate an infection, affected by: route of transmission (stomach acid=higher dose required), ability to colonise host, tropism/motility, replication speed, immune evasion
If pathogen can kill/subvert phagocytes then infectious does is lower
45
What is the virulence for strep pneumoniae?
Toxin production - pneumolysin
Degradation of host molecules
Interference with host function - superantigens made to infterfere with normal T cell function
Immune evasion - leukocydins made causing neutrophil death and abscess formation
46
What infections are caused by droplet transmission (mouth)?
Tonsilitis - strep pyogenes
Meningococcal septicaemia - nisseria meningitidis colonises nasopharynx theninvades epithelial \> endothelial cells
47
What infections are caused by entry through U to LRT?
Pneumonia
Nasal sinuses and into brain - Strep pneumoniae, strep milleri, haemophilus influenzae
48
What is vibrio cholerae's pathogenicity?
Huge infective dose, uses flagella to penetrate mucus, makes 2 component toxins A+B which bind to GM gangliosides on gut. This triggers cAMP production, chloride efflux occurs, so Na+ and water flood out leading to watery stool
49
Why is pus produced in skin infections (staph aureus)?
Leukocydins are produced which destroy neutrophils, so pus is dead neutrophils
50
What are the important GNB and GPB that you should know?
GNB: Neisseria meningitidis/gonorrhoeae, haemophilus influenzae, E. coli, salmonella species, virbrio cholerae, shigella
GPB: Staph aureus (major skin pathogen), Strep pyogenes(A)/agallactiae(B)/viridans strep/pneumoniae, clostridium difficile/tetan/botulinum/pergringens, listeria spp.
51
Which bacteria are opportunistic?
GNB: P. aeruginosa - urinary catheters dweller, acinetobacter baumanii - battlefields
GPB: Staph epidermidis - prosthetic joint dweller, Enterococcus faecalis - abnormal heart valves
52
What are the main routes of infection?
URT, Faeco-oral, urogenital tract, skin, intravenous
53
What are the sources of bacteria?
URT, lower GI tract, Sexual/urogenital tract, skin (extrinsic and intrinsic)
Nosocomial (all above)
Food and water
Animals
54
What does bacteriostatic mean?
Inhibits growth of bacteria
55
What is the resistance of an organism?
The ability of an organism to replicate in presence of an antibiotic at a particular concentration
56
What is the breakpoint of an AB?
An estimate of reasonable concentration that might be achieved clinically - any organism that grows at concentration of breakpoint or higher is resistant
57
What is an antibiotic?
Antimicrobial agent produced by MO that kills/inhibits other MO's
58
What is the minimal inhibitory concentration?
Lowest concentration of Antibiotic required to inhibit growth
59
What are some misconceptions at the beginning of the AB era?
Resistance against more than one class of AB couldn't occur, no horizontal gene transmission, resistant organisms would be less fit (virulent)
60
When does resistance to AB emerge?
Usually soon after introduction of AB to clinical use in hospitals, EXCEPT vancomycin (toxic so not used much at time of discovery)/erythromycin
61
What is the problem with AB resistance?
Leads to increased time for effective therapy, additional approaches required, use of expensive therapy, use of more toxic drugs, use of less effective "second choice" AB
62
Which are the major resistant bacterial pathogens?
GNB: P. aeruginosa, E. coli (ESBL), Klebsiella spp. (NDM-1), Salmonella spp. (MDR)
GPB: Staph aureus (MRSA, VISA), strep pneumoniae, clostridium difficile, enterococcus spp. (VRE), mycobacterium tuberculosis (MDRTB, XDRTB)
63
What is the main mechanism of action of AB?
Tend to inhibit processes unique to bacteria - SELECTIVE TOXICITY
64
What are the main AB?
Beta-Lactams, Quinolones, Sulphonamides, aminoglycosides, macrolides
65
What is the mechanism for beta-lactams?
Interfere with cell wall synthesis of peptidoglycan component of cell wall - penicillin, methicillin
Binds to penicillin binding proteins (PBP) which catalyse a no of steps in peptidoglycan synthesis
Beta-lactam ring has similar structure to precursor of peptidoglycan - NB: MRSA has different PBP - 2a so it doesn't bind with high affinity to beta-lactams
66
What is the mechanism for tetracycline?
It's bacteriostatic, and has a broad spectrum - inhibits protein synthesis
Binds to the 16S component of the 30S ribosomal subunit, preventing charged aminoacyl tRNAs from binding to the mRNA/ribosome complex, preventing the elongation of the peptide
67
What is the mechanism for chloramphenicol?
Bacteriostatic, broad spectrum - inhibits protein synthesis
Binds to 50S subunitand blocks peptidyl transfer step, often used topically due to toxicity
68
What is the mechanism for quinolones?
Bactericidal, synthetic, broad spectrum
Target DNA gyrase (in GNB), topoisomerase (in GPB) - both are responsible for unravelling DNA
69
What are the mechanims for sulphonamides?
They're bacteriostatic, used to treat UTI, Reproductive tract infection and bacteraemia
Interferes with folate pathway
70
What is the mechanism for aminoglycosides?
Bactericidal, target protein synthesis - 30S ribosomal subunit, RNA proofreading and cause damage to cell membrane
Toxicity has limited use, but resistance to other AB has led to increasing use
Eg: Gentamicin, streptomycin
71
What is the mechanism for macrolides?
GPB infections, targets 50s ribosomal subunit preventing aminacyl transfer, causes truncation of polypeptides
Erythromycin
72
What are the 4 main mechanisms of AB resistance?
Altered target site, inactivation of AB, altered metabolism, decreased drug accumulation
73
How can the bacteria alter their target site to be resistant to AB?
Arise from acquisition of alternative gene/gene that encodes a target-modifying enzyme
Eg: MRSA encodes an alternative PBP with low affinity to beta-lactams, Step pneumoniae resistance to erythromycin is due to acquisition of gene which encodes enzyme that methylates AB target site in 50s ribosomal subunit
74
How is the AB inactivated?
Acquired gene for enzyme which breaks down AB via enzymatic degradation/alteration, AB becomes ineffective
Eg: beta-lactamase (bla), chloramphenicol acetyl-transferase (cat)
ESBL/NDM-1 are examples of broad-spectrum beta-lactamases
75
How can bacteria alter their metabolism to be resistant to AB?
Re-engineer metabolic pathways so that it bypasses step which is interfered with by AB
Increased production of enzyme substrate can outcompete AB inhibitor or can switch to alternative pathways, reducing need for PABA (example)
76
How is drug accumulation decreased?
Reduced penetration of AB into bacterial cell and/or increased efflux of AB out of cell - drug doesn't reach concentration required to be effective
77
Summary of AB examples:
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78
What are the sources of AB resistance genes?
Plasmids - selection for one maintains resitance to all
Transposons - integrate into chromosomal DNA, allows transfer of genes from plasmid to chromosome and vice versa
Naked DNA - from dead bacteria released into environment
Horizontal gene transfer allows rapid spread of AB resistance
79
What are other reasons for treatment failure?
Inappropriate choice of organism, poor penetration of AB into target site, inappropriate dose, inappropriate administration, presence of AB resistance within commensal flora
Biofilm (bacteria lower metabolism and covered in hard protein case so difficult for immune system to reach), intracellular location, slow growth, spores, persisters
80
How is resistance measured?
On agar and grown for 24hrs, then placed on other agar which has AB discs, overall takes 48hrs which is too long to wiait for an infection
81
Examples of nosocomial infections with their AB resistance
Strong selective pressures in hospitals due to regular AB use lead to more AB resistant bacteria
MRSA, Vancomycin-insensitive Staph aureus, clostridium difficile, vancomycin resistant enterococci, e. coli, p. aeruginosa, acineterbacter baumannii, stenotrophomonas maltophilia
82
What are the risk factors for hospital acquired infections?
High no of ill people, crowded wards, presence of pathogens, broken skin, indwelling devices, AB therapy may suppress normal flora, transmission by staff - contact with many patients
83
Why does AB therapy have negative effects on commensal flora?
Broad spectrum can affect gut flora, leading to decreased competition for nutrients, so pathogen can proliferate and cause disease
84
How can we prevent emergence of drug resistant bacteria and nosocomial infections?
Tighter prescription controls, reduce use of broad spectrum AB, quicker ID of infections caused by resistant strains, combination therapy, knowledge of local strains/resistance patterns
85
How can we overcome resistance?
Modification of existing medication to prevent cleavage (beta-lactams) or enhance efficacy (methicillin)
Combine AB and inhibitor of beta-lactams \> augmentin
86
Beta lactam AB work by targeting...?
Cell wall biogenesis
87
Hospitals are associated with AB-resistant pathogens because of...?
Lots of vulnerable patients, high AB usage, high prevalence of broken skin
88
What are the 2 phylae in the fungus kingdom?
Basidiomycota, ascomycota
89
How many fungal infections exists in humans?
150 - most ascomycetes (90%) and basidiomycetes consists of mushrooms - Cryptococcus neoformans and Cryptococcus gatii are the main burden of dsease, causing Cryptococcal meningitis (can be inhaled into lungs but alveolar macrophages tend to mop them up well) by getting into the brain
90
How do fungi digest their food?
Extracellularly - produce hydrolytic enzymes which are pumped into environment, and rot the material around them, so fungus is suspended in its food source - **saprophytes**
91
How are spores dispersed?
Fungi produced large numbers of spores, which are dispersed over large distances , so humans are constantly exposed to fungal spores
92
What are the 3 types of illness caused by fungi?
Allergies, Mycotoxicoses, mycoses
93
How can the level of tisue affected by fungi be classified?
Superficial, subcutaneous, systemic
94
Which fungal allergies exist?
Inhalation of fungal spores cause allergic diseases: Rhinitis, Dermatitis, asthma, Allergic Broncho-pulmonary aspergillosis
Responses vary by individual and fungal species
95
What is mycotoxicoses?
Toxic reaction caused by ingestion/inhalation of a mycotoxin
Mycotoxins are secondary metabolites of moulds that exert toxic effects on animals and humans
96
What are the symptoms and treatment for mycotoxicoses?
Symptoms: breathing problems, dizziness, severe vomiting, diarrhoea, dehydration, hepatic and renal failure (6 days later)
Treatment: gastric avage, liver transplant
97
What is aflatoxin?
Toxin produced by Aspergillus flavus (astomycetes) and is the most carcinogenic natural compound known
Contaminates grain
Symptoms: liver damage from hep B and particukar risk of cancer
South-East Asia has higher levels of liver cancer, possibly due to greater exposure to aflatoxin
98
What is mycoses?
Disease caused by fungi which is classified by level of tissue affected: superficial, cutaneous, subcutaneous, systemic
99
What does superficial mycoses affect?
Skin/hair, with no living tissue invaded so no host response
Black piedra (Piedraia hortae), White piedra (Trichosporon beigelii), dandruff (Malassezia globosa), Tinea nigra (Phaeoannellomyces werneckii)
100
What does cutaneous mycoses affect?
Produce keratinases which hydrolyse keratin
Inflammation caused by the host response to metabolic by-products - *Trychopyton* and *Microsporum*
Also called dermatophytoces/dermatomycoses
101
What was cutaenous mycoses thought to be caused by, and hence describe 3 conditions?
Worms so called Tinea (ringworms)
Tinea: capitis (head/neck - common paediatric condition), pedis (athlete's foot), corporis (body), cruris (groin - jock itch), unguium (finger/toenails)
102
What is tinea capitis?
Superficial infection of skin/scalp/eyebrows/eyelashes, attacks hair shafts/follicles
Affects children self esteem as disfiguration occurs if not treated fast
103
What fungus causes athlete's foot?
Tinea pedis is caused by Trichophyton rubrum
104
What is cutaneous mycoses treated with?
Antifungal creams - miconazole, clotrimazole - or orally - griseofulvin
105
What is subcutaneous mycoses?
Chronic, localised infections of the skin and subcutaneous tissue following traumatic implantations of aetilogic agent
Sporotrichosis, chromoblastomycosis, mycetoma
106
What is mycetoma?
Chronic infection of the skin, subcutaneous tissue and bone, characterised by discharging sinuses filled with organisms
107
What are systemic mycoses?
When superficial mycoses starts digging into the skin and eventually becomes systemic
108
What are some examples of deep/systemic mycoses?
1ry - Coccidioides immitis, Histoplasma capsulatum, Blastomyces dermatiditis, Paracocidioides brasiliensis
Oppotunistic - Cryptococcus neoformans, candida, aspergillus, penicillium marneffei, the zygomycetes, trichosporon beigelii, fusarium
109
Where are fungal infections a big problem?
Transplant setting - aspergillosis - high mortality for systematic mycoses, they're on the rise with a very high mortality rate
110
What about Candida infections?
Superficial mycoses - opportunistic commensal (in GI and GU tracts), so when immunocompromised, it can colonise and invade host tissue
111
List some superficial Candida infections
Mouth, throat, skin, nails, scalp, vagina, fingers, bronchi, lungs, GI tract - usually due to impaired epithelial barrier function, most common in newborn/elderly
112
List some mucosal Candida infections
Occurs in newborn and elderly - mucocutaneous candidasis occurs in 3 forms in ppl with HIV:
Oropharyngeal, oesophageal, vulvovaginal
Once systemic, high mortality rates are seen
113
Systemic Candida infections risk factors:
Not seen in normal healthy ppl, with main risk factors being:
Chemotherapy, Gut-related surgery, Catheters
114
What has invasive aspergillosis emerged as?
The major clinical problem of common mycology - in lung, brain, kidney, heart
Responsible for 60,000 death/year worldwide
115
How do you diagnose fungal infections?
Few signs and symptoms are specific to systemic fungal infections so:
Acquire a sample (skin, sputum, blood, spinal fluid, tissue biopsy, bronchoalveolar lavage, vaginal swab), microscopy (well established fungal infection to be able to see it), culture (can be cultured, to allow susceptibility testing), non-culture methods (Ab/Ag based assays detect fungal polysaccharides: mannan, glucan, endolase, proteinase)
116
What are targets for antifungal therapy?
Cell membrane - ergosterol used instead of cholesterol
DNA synthesis
Cell wall
Fungi are quite similar to humans so anything toxic to them will be slightly toxic to humans, so need to be used with care
117
Which antifungals attack the cell membrane?
Polyene AB - amphotericin B, lipid formulations, nystatin
Azole antifungals - ketoconazole, **_itraconazole, fluconazole_**, voriconazole, miconazole, clotrimazole
118
What is the aim of cell membrane active antifungals?
Attack cell membrane to inhibit synthesis of ergosterol (main sterol in fungal membrane) - azoles are main drug group
119
Which antifungals inhibit synthesis of DNA/RNA?
Pyrimidine analogues, commonly used for this and Flucytosine is commonly used for Cryptococcus
120
Which antifungals attack the cell wall?
Echinocandins - good antifungal if inhibits cell wall
121
Why is the cell wall a target in antifungal therapy?
Most overt distinction between mammalian and fungal cells and its uniqueness makes it a premier target for antifungal therapy
The major components in the cell wall are glucans and chitin - caspofungin works by non-specific inhibition of beta-1,3 glucan synthase
122
Name the basidiomycete fungal pathogen that causes meningitis?
Cryptococcus neoformans
123
Name an Ascomycete fungal pathogen that causes nosocomial fungal infections
Aspergillus
124
Name a highly carcinogenic mycotoxin and what fungus produces it?
Aflatoxin by Aspergillus flavus
125
What mycotoxin will you find produced by liberty caps during the British autumn?
Psilocybin produced by Psilocybe
126
How do you prove that a virus causes disease? - Koch's postulates
MO must be found in large numbers in diseased animals but not healthy ones
Organism must be isolated from diseased animal and grown outside body in pure culture
When isolated MO is injected into healthy animals it must produce same disease
Suspected MO must first be recovered from experimental hosts, isolated, compared to first MO and found to be identical
127
What is the definition of a virus?
Viruses are infectious OBLIGATE intracellular PARASITES
Cannot complete life cycle without being inside host cell - genome is DNA/RNA
128
What is the average size of a virus?
100nm
129
What are the 2 types of virus morphology?
Non-enveloped and enveloped
130
What is a non-enveloped virus?
Has a protein capsid (but no lipid), often symmetrcal
Adenovirus, picornavirus, calicivirus
131
What is an enveloped virus?
Have proteins around their genome, have a lipid envelope around which is dervied from host membrane
Are pieiomorphic - have various shapes e.g. measels virus
OR typical shapes like ebola virus
Herpes is a capsid and envelope type
132
How are viruses named?
After disease caused: poliovirus, rabies
After person who discovered it: Epstein Barr virus
After place it was discovered: Coxsackievirus
Part of body affected by virus: Rhinovirus, Hepatitis
The way it is spread: Dengue, Influenza
133
What is the baltimore classification? (written)
**_Classified by type of genome that the viruses have_**, made from DNA (some may have 2x stranded DNA or single stranded)/RNA (positive/sense, negative/anti-sense or double stranded RNA)
Some following a different manufacture cycle for DNA/RNA
134
What is the only way to classify viruses?
Based on their genome - if DNA, it can be transcribed to RNA then protein; if RNA+ then can be directly translated into proteins; if RNA- then it can't be directly translated, so transcribed into +RNA. This means viruses with **RNA- carry proteins/enzyme/machinery around** otherwise they are inert
135
What are the consequences associated with RNA viral genome type?
They use their own polymerase to replicate, whcih are pretty **error prone**, and lack proofreading capability -\> HIGH MUTATION RATE, so fast evolution
RNA viral genomes limited in size due to instability of RNA, largst being 30kb (Coronavirus) - often use complex coding strategies to encode more proteins that expected from the small grenome - use all 3 reading frames
136
What are the consequences of a DNA viral genome type?
Can be big, but DNA more stable - so space for accessory genes available
Some viruses have their genome in a long strand, others in little pieces (segmented genome) - influenza has 8 RNA segments
137
What are accessory genes in viruses?
Things that virus doesn't inherently need to survive but gives some adv (suppresses immune system)
They are lost in culture as there is no IS, so is a way of producing attenuated vaccines
138
What are the good and bad points about a segmented genome?
Good: can pick up new genes and evolve
Bad: RNA needs to be gathered together when virus tries to leave the cell to another cell
139
What is the generic replication cycle of a virus?
Virus on outside, inert with coat (viral attachment protein) which binds to receptor on host cell membrane, injecting DNA/RNA into cytoplasm
Other viruses enter the cell via endosomes and once it is in the cell it is made into mRNA, uses the host ribosomes and translates the mRNA into proteins - at same time virus replicates its own genome using host/own polymerase and copies of genome and viral protein assembles to form new virus particles which leave the cell
140
What is the replication cycle of HIV-1?
Virus on outside - GP120 on virus interacts with CD4 on host cell membrane, then interacts with co-receptor, bringing virus closer to cell membrane. Virus and cell membrane fuse and viral content is inserted into cell, where viral genome copied by reverse transcriptase to viral DNA - **DNA moves to nucleus** and is integrated into host genome, transcribed to mRNA \> proteins. All come together at cell membrane, produce new virus particle, which leaves the cell
141
What is the replication cycle of influenza?
Spike proteins attached to surface of cell, virus engulfed and taken into endosome, where it fuses and releases genome to enter the nucleus, where it replicates and directs synthesis of proteins, coming together to form new virus particles
142
How does the ebola virus replicate?
Starts off as a worm like virus outside the cell, where it attaches to the membrane and is engulfed by macropinocytosis. In the early endosome it undergoes various cleavages which allow interaction with different receptors, with genome released and copied into new genomes and into mRNA which produces proteins. Proteins and genomes assemble and bud out to form new virus particles
143
How can we investigate viruses in the lab?
They need to be grown inside host cells, so cells need to be grown before infection with virus. Infecting healthy cells with virus causes **cell shape change and cell death** called the CYTOPATHIC EFFECT, with death of cell probably due to apoptosis.
Virus uses the host's cell machinery so aggressively that it destroys the host cell's capability
144
What is the cytopathic effect?
Death of cell as a result of being infected by a virus - could be due to virus taking over genetic machinery so cell is no longer able to produce the proteins necessary for survival
145
How do you find out how much virus is present in a patient?
Use a plaque assay where viruses form plaques on cell monolayers due to cell death, where each plaque is the result of one single virus put into the cell monolayer - counting the plaques gives the name of how many viruses in one sample
146
What are plaques?
Result of an individual virus infecting one cell and then infecting other cells
147
How is a plaque assay carried out?
Take a sample from the patient that contains the virus, make serial 10 fold dilutions. Take known vol of dilutions and put into susceptible cells. Plaques present on susceptible cells showing how many viruses are in dilution
148
What is syncytia and when does it form?
Sine viruses don't make plaques but syncytia, which is the fusion of many cells which effectively forms a huge cell with many nuclei.
Eg: HIV has the ability to fue with the cell membrane, and when a person has been infected by HIV, it begins expressing HIV glycoproteins on its surface which can fuse with another cell.
This can be seen in the lab
149
Why can we visualise viruses (immunostaining)?
Due to the different things produced in the cell - sample can be innoculated (RSV) onto cell and wait for unique to virus proteins begin to be produced and then use an Ab to detect the protein
150
What are the single step growth kinetics of a virus?
Experiment: virus put onto cells and samples taken at various times and titrated out - at start of infection, known amount of virus present. Sample early on = NO virus as it is inside the cell (ECLIPSE phase). After a while virus begins making new copies and exting the cell, so become detectable - logarithmic increase occurs afterwards and then tails off as cells start dying
151
How do we diagnose viruses? Viral genome, viral antigen, viral particles, virus cytopathic effect in cultured cells, antibodiesto virus
VG: **PCR** (primers specific to part of viral genome, with one that shows up +ve IDing the virus
VA: Indirect fluorescence antibody, ELISA
VP: electron microscopy, haemoagglutination assay
VCEICC: virus isolation
Ab to virus: serology
152
How is the virus propagated?
Virus can be passaged in lab by providing permissive cells, where they can accumulate mutations to adappt to new host, leading to attenuation = basis of generation of vaccines in past
Some viruses (hep C and norovirus) have no permissive cell lines so are more difficult to work with
153
How can we manipulate viruses?
Virus genomes are so small that they can be synthesised, allowing reverse genetics - production of new viruses
154
What is a tropism for viruses?
The predilection of viruses to infect certain tissues and not others
155
What is viral tropism based on?
Susceptibility (receptor interactions), permissivity (ability to use host cell to complete replication), accessibility (ability of virus to rech tissue)
156
Give an example of viral tropism using HIV
HIV tropism determined by receptor use - 1ry receptor is CD4 so HIV infects Tcells, GP120 (HIV) interacts with CD4 (T cell), then attaches to co-receptor CCR5/CXCR4
BUT: some people have a mutation in CCR5 so are resistant to HIV, some who are exposed and unaffected produce large amounts of chemokine which blocks the use of co-receptors
Can get tropism switch during HIV replication, where viruses evolve to bind to other receptors (from CCR5 to CXCR4)
157
Which receptors are present on measles virus?
H receptor (haemagglutinin) whicih binds to SLAM (CD155) and Nectin 4 - vaccine strain uses CD55
158
What are SLAM and Nectin 4 used by the measles virus?
SLAM is used when first infecting (through the resp tract) by binding to SLAM on dendritic cells and riding to the lymph nodes, where it infects many cells expressing SLAM, causing immunosuppression.
When measles is ready to leave the host, it uses Nectin 4, carried to the lungs where it binds to Nectin 4 to cross from blood to air space through airway epithelial cells where the virus replicates then bursts out into airspace to spread via resp route
159
What is influenza's tropism determined by?
Accessibility - influenza is enveloped by haemagglutinin which helps it latch onto surface of cells as HA binds to sialic acid (ubiquitous), so technically influenza can enter any cell of your body, but affects resp route due to accessibility
Once attached to sialic acid, it can enter cell via endosome, with low endosomal pH allowing a massive conformational change which the virus neeeds to fuse with endosome membrane and uncoat - can only happen if _protein of virus has been snipped in 2 at point_ (cut determines tropism as only fluid in lungs which has the right proteases to activate the virus)
160
What extends influenza's tropism?
Tropism= determined by availability of host proteases
Extended by mutation at HA cleavage site - some chickens have mutation of region where protease cleaves, so can be cleaved by many proteases found in areas of body, so allows virus replication in every organ of body
161
What does the outcoome of a virus infection depend on?
Balance between virus virulence and host response
162
What does: iatrogenic, nosocomial, vertical, horizontal and germ line mean?
I: due to medical care, N: acquired in hospital, V: from parent to offspring, H: other forms of gene transmission, GL: part of host genome
163
What causes viral rashes?
If systemic infection, blood can enter skin and cause rash, or if virus leaves blood and enters skin, cells are destroyed by virus replication
164
What is the viral dissemination from point of entry?
Local infection, primary viraemia, amplification, secondary viraeima, target organ
165
Using Varicella Zoster virus, what are the symptoms after secondary viraemia?
Virus enters via resp route, where it can infect many cells including peripheral blood mononuclear cells and skin cells
From skin site it can infect sensory neurones where it remains latent, and is reactivated when cellular immunity is impaired, causing painful rash at nerve endings - SHINGLES
Only get symptoms after 2ry viraemia - 14 days incubation period
166
Wht are the 4 patterns of viral infection? (APLO)
Acute - followed by viral clearance, persistent - latent, slow transforming, long incubations, oncogenesis - affect way in which cells control themselves
167
What are the 2 different types of outcome of acute infections?
Clearance - cold and influenza, adaptive immune response provides immunity
Death - smallpox and dengue
W/accidental pathogenesis: Polio - infects motor neurones and can cause paralysis, Rubella - strong tropism for dividing neuronal tissue leading to deafness, eye abnormalities (cataracts) and congenital heart disease
168
What are 2 types of persistent viral infections?
Chronic: low level replication in tissues which regenerate - papilloma viruses in warts
Latent: viral genomes maintained but no virus seen until episodes of reactivation at times which you are immunocompromised - herpes viruses
169
What are some strategies of viral persistence?
Lot of accessory genes, which allow viruses to evade immune responses:
Evade immune surveillance - MHC downregulation, CTL escape by mutation - Hep C, infecting tissues with reduced immune surveillance - CNS
170
Why is latency possible?
Neurones don't divide, so live until you die
If it gets infected it may contain many copies of viral genome and every now and the it will get reactivated
171
How does latency work, using herpes?
Virus enters through skin (epithelial cells) and enters the nerve (retrograde transport), stays there (sensory neurone) in latent state
When reactivation occurs, new copies are made and it travels back up the nerve (anterograde transport) and replicates through the skin
172
How can viruses cause cancers?
May encode an oncogene, interfere with host cycle to enhance own replication - by making cell cancerous, virus can replicate more and keep moving onto new cells
173
What viruses cause cancers?
Papilloviruses encode inhibitors of tumour suppressor p53, E6 and E7 genes, forcing cells into S phase
Kaposi Sarcoma-associated herpes virus and merkel cell polyoma
HTLV-1 causes adult leukaemia
Hep B/C
Epstein-Barr Virus
174
What type of cancer does Hep B/C cause?
Hepatocellular carcinoma - 350 million carriers, 600,000 annual death
Hep B is a hepadnavirus (DNA genome) but uses reverse transcriptase during stage in life cycle
Transmitted via blood and semen, but vaccine present
Hep C is blood borne - 4% will go on to get HCC
175
What type of cancer does EBV cause?
95% of ppl infected with EBV, some will go on to develop cancer:
Burkitt's lymphoma, Hodgkins lymphoma, nasopharyngeal carcinoma
176
What does the outcome of infection depend on?
Viral sequence, Virus load, Host immune repsonse/status, Host co-morbidity, Co-infections, Other medications, Host genetics, Host age/gender
177
How does viral sequence affect outcome of infection?
2 strains of polio may vary in virulence, one may turn it into a live attenuated bacteria, and the other may make it invade the motor neurone and cause paralysis
178
How does viral load affect the outcome of infection?
First child in family to contract chicken pox has a milder illness - may be due to 2nd child being in closer contact to infected individual and hence gets infected by higher dose
179
How do co-infections affect the outcome of infection?
HHV8 causes Kaposi Sarcoma in HIV infected individuals
Hepatitis Delta Virus only infects people with HBV infection, suppressing HBV replication and causes severe liver disease with rapid progression to cirrhosis and hepatic decompensation
180
How does genetic resistance and susceptibility affect the outcome of an infection?
CCR5 delta 32 mutation protects against HIV-1 infection
Killer-cell immunoglobulin-like receptor can determine the outcome of a hepC virus infection
Interfron-induced transmembrane protein 3 was associated with a severe outcome in 2009 H1N1 pandemic
181
Which predisposing co-morbidities and conditions affect outcome of infection?
Asthmatics and resp viruses, obesity, immunosuppression, immunodeficiency, elderly, diabetes mellitus, pregnancy
182
What virus is often associated with nosocomial infection?
Norovirus
183
Tropism and pathogenesis of which of these viruses is NOT determined by receptor use?
HIV, influenza, measles, Kaposis sarcoma herpes virus
Influenza
184
Which of the following is NOT spread by iatrogenic route?
HIV, Hep B/C/A
Hep A
185
Which of the following is NOT associated with cancer?
Polio, Hep C, Papillomavirus, Hep B
Poliovirus
186
Why is rubella harmful in early stage pregnancy?
Infects dividing fetal neuronal tissue leading to deafness
187
What are the 2 host defence types against infectious agents?
Innate and acquired immunity
188
What are the 2 types of acquired immunity?
Humoral (mediated by Ab produced by B cells) and Cell mediated (mediated by T and NK cells mainly, with other cell types playing a role and Abs being used)
Protection is a combination of both
189
What is the role of Abs in immunity to bacterial infections?
Toxin neutralisation (tetanus, diptheria, botulinism, anthrax), focus for complement binding and opsoni promoting phagocytosis - Ab mediated bactericidal activity
190
What is the role of cell mediated immunity in immunity to bacterial infections?
Important for eliminating intracellular bacteria (TB, typhoid, legionella)
Interaction of reactive T cells and macrophages is key to clearance of infection
191
What are the properties of a good vaccine?
Substantial benefit at a low cost and low risk
Stimulates effective immune response, safe and doesn#t cause adverse reactions, inexpensive to manufacture and distribute, stable, easy to administer, simple for manufacturer and regulatory authorities to control
192
What are the two types of vaccination strategies?
Direct protection and herd immunity
193
How does direct protection work?
There is no invasion, so individual doesn't get disease
Eg: tetanus
194
How does herd immunity work?
There is indirect protection at the release stage of the bacteria, so there is no acquisition and no invasion - no spread of disease
195
What are the equations for herd immunity and endemic state?
Endemic state has an inverse relationship between basic production number and proportion of popn susceptible to disease -\> R0=1/S
Herd immunity: if q is high enough, the disease will die out: q\>= 1-1/R0
**_R0_** is basic reproduction no. (no. of individuals infected person wiill infect if popn has no immunity to disease), **_S**_ is proportion of popn susceptible to disease, _**q_** is the herd immunity level
196
How is vaccine safety tested for?
Clinical trials - phase 1, 2, 3
197
What is vaccine efficacy?
The reduction in the incidence of disease among people who have received a vaccine compared to the incidence in unvaccinated people.
Determined in phase III trials (blinded/placebo controlled)
VE= 1 - attack rate in vaccinated/attack rate in unvaccinated (expressed as %)
198
What is herd immunity?
Form of immunity that occurs when the vaccination of a significant portion of the population provides a measure of protection for individuals who have not yet developed immunity.
Determined post-vaccine introduction:
Herd effect = 1 - attack rate unvaccinated post intro/attack rate unvaccinated pre intro
199
What is present in vaccine formulations?
Antigen - to stimulate immune respone to target disease
Adjuvant - to enhance and modulate immune response
Excipients - buffer, salts, saccharides, proteins to maintain pH, osmolarity and stability of vaccine/preservative
200
What are the type of vaccine antigens present in vaccines?
**Live attenuated organisms, killed whole organisms,** _purified component vaccines, conjugates, DNA vaccines_
_Individual/small number of well defined Ag_
**Complex, multpile Ag, ill defined**
201
What is the UK child immunisation programme?
DTaP-Hib-IPV and pneumococcal conjugate at 2 months, MenC conjugate and DTaP-Hib-IPV at 3 months, pneumococcal/MenC conjugate and DTaP-Hib-IPV at 4 months, pneumococcal conjugate/Hib+MenC booster/MMR at 1 year
From three years four months onward:- • Pre-primary school: DTaP-IPV booster, MMR booster • Girls 12-13 years old: HPV • During secondary education: DT-IPV
202
In the paediatric combination vaccine DTaP-Hib-IPV, what does the DT part consist of?
Tetanus and diptheria toxoids (chemical inactivation of bacterial exotoxin), simple to produce, relatively pure, safe, high protective efficiency (very immunogenic, appropriate immune response)
203
In the paediatric combination vaccine DTaP-Hib-IPV, what does the aP part consist of?
Whooping cough caused by Bordetella pertussis, infects ciliated epithelium, releasing toxin, causing a convulsive cough
Used to have a whole cell pertussis vaccine, which had 90% efficacy rates but had adverse reactions such as anaphylaxis, prolonged crying, febrile seizures, so acellular vaccine driven to production
Acellular: multicomponent - attachment parts to ciliated epithelium, adherence and complement resistance and toxins - safe and efficacious (75-90%)
204
Why was the acellular vaccine failing?
When this vaccine began, an increase in whooping cough occurred, so pregnant women were offered the vaccine, to try and immunise children, where it is most common
Immune response is different with new vaccine than old vaccine, so not complete protection
205
In the paediatric combination vaccine DTaP-Hib-IPV, what does the Hib part consist of?
Haemophilus influenzae type b which causes meningitis and septicaemia in young, with bacterial surface covered by polyribosyl-ribitol phosphate capsule - conjugate vaccine
206
Why are polysaccharides poorly immunogenic?
Ag is large and linear, not easily degraded and highly repetitive/determinant
So the immune response whcih is predominantly IgM, has a poor memory effet and low avidity antibody
207
What are conjugate vaccines?
_Carb chemically linked to immunogenic protein_ - expensive (sophisticated tech), highly purified components (safe, simple for licensure and control, purified saccharide and carrier proteins - tetanus/diptheria toxoid ro CRM197), **very effective when humoral immunity required - long lived boostable immunity, offers herd immunity**
208
How are conjugate vaccines prepared?
3 ways: 1) Random activation of high molecular weight/partly size reduced polysaccharide, forming a complex
2) Degradation of polysaccharide to form active functional groups at both terminals, forming smaller complex
3) Degradation of polysaccharide to form active functional group at only one termina, forming a star shaped vaccine
209
How do conjugate vaccines work?
Vaccine is processed as a normal Ag as it is a protein, so T cells are primed by interaction with Ag, presenting it to B cells, whcih are activated and turn into plasma cells and memory B cells
210
In the paediatric combination vaccine DTaP-Hib-IPV, what is present in the vaccine?
Pediacel and Infanrix (manufacturers), Ag: Tetanus/diptheria toxoid, Pertussis components (pertussis toxoid, filamentuous haemagglutinin, pertactin, fimbriae types 2/3), Hib PRP-conjugate, inactivated polio virus type 1/2/3
Adjuvant aluminum phosphate
211
What are some licensed conjugate vaccines?
Hib vaccine (PRP conjugated to CRM197 or tetanus toxoid, MenC+Hib booster manufactured by Menitorix)
Pneumococcal conjugates (7, 10 and 13 valent formulations)
MenC conjugates (apha 2-9 inked polysialic acid conjugated to CRM197 or tetanus toxoid)
Other: Meningococcal A,C,W,Y conjugates
212
What are the three causes of meningitis that can be vaccinated against?
Hib, meningococcus and pneumococcal disease
213
What other infections can pneumococcal disease cause?
Meningtisis, septicaemia, mucosal infections (otitis media, pneumonia)
214
What vaccines are used against pneumococcal disease?
Pneumovax II - 23 valent, unconjugated, polysaccharide vaccine
Prevenar 7/13 and synflorix conjugate vacccines
More then 90 serotypes determined by capsular polysaccharide
215
What are the meningococcal outer membrane vesicle vaccines?
Released spontaneously by meningococci in vivo and in culture, which contain all the protein Ag usually associated with outer membrane - vaccine produced by detergent extraction to reduce endotoxin content, with hyper producing mutants have been isolated
216
Why can't meningococcal B be vaccinated against?
It is too similar to the human self markers, so it is feared that by causing an immune response, there would be a response against all self cells - so protein vaccines are made instead - however only protect against strain that their made from so used during outbreaks
217
What is the reverse vaccinology approach?
Start with genome sequence of bacteria and see which genes would go onto surface cell markings, injected it into mice to see which was best and then into humans - such as factor H binding protein, neisseria adhesin, heparin binding protein whcih are added to the vaccine for MenB
218
What is the BCG vaccine made from?
Attenuated strain of Mycobacterium bovis - not sure if works completely but does prevent severe childhood TB and leprosy
219
What is in the typhoid vaccine?
Either live attenuated vaccine based on strain Ty21a or polysaccharide Vi (only for over 2 yolds)
220
What is the cholera vaccine?
Kiled whole cell: parenteral vaccine (poor efficacy, short lived strain specific) or whole cell oral vaccine (good efficacy, oral delivery, safe) or Dukoral (killed whole cell and CtxB oral vaccine, drink formulation and may protect aganst ETEC)
221
What are adjuvants, their delivery systems and immune potentiators?
Key element of effective vaccines - potentiate immune response (toxins and lipids, nucleic acids, peptidoglycan, carbs, peptides, cytokines and hormones)
Delivery systems - depot of Ag slowly released (mineral salts, surface active agents, synthetic microparticles, oil-water emulsions, liposomes
222
What do adjuvants react with?
Pattern recognition receptors, each creating a different immune response
223
What is the risk benefit analysis for vaccinating the immunocompromised?
Need to protect vulnerable patient, from public health perspective (herd immunity), protecting patient by immunising those close contacts, live vaccines need consideration, decision on whether to vaccinate depends on nature of immunodeficiency and the vaccine
224
What is prophylaxis?
Preventing disease before the aetiologic agent is acquired by vaccination or giving drug before infection
225
What is therapy?
Treating the disease after host has been infected
226
What can presence of Ab in serum be used for?
Diagnosis as shows there was infection at some point
227
What do vaccines replace?
First infection to generate Ab production without having pathological effects
228
What are 2 successful virus vaccinations?
Polio and smallpox (possible because no animal reservoir and you can see who has smallpox and can work out who they've come into contact with)
229
Vaccines vs Antiviral drugs
Prophylactic vs Therapeutic
Live/Inactive vs Random screen/Rational design
Herd immunity/defined target group vs defined target group
safety\>efficacy (vaccines)
Gov and WHO vs individuals
230
How are vaccines eradicated?
When there is no: animal reservoir, latent/persistent infection, smallpox easily recognised disease, vaccine effective against all strains of virus, vaccine properties - potency, low cost, abundance, heat stability, easy administration; WHO determination, $250 million
231
What are the different types of viral vaccines?
Live attenuated (Smallpox, natural virus with geome inside capsid with virulence reduced, so only mild infection caused and kick starts IR), Inactivated (Parental virus and treat with chemicals and heat to destroy genome so no longer infectious - presents fragments to IS and reacts as if infected), Sub unit (similar to inactivated, but chopped up into pieces by proteases, can't cause disease but response is caused) or cloning (from virulent and either put DNA into virus like particles, inject directly into person or make new virus which doesn't cause illness but has virulent material from originl virus)
232
Which live attenuated human virus vaccines?
Adenovirus, influenza, measles, mumps, polio, rotavirus, rubella, smallpox, varicella, yellow fever
233
Which human vaccines are inactivated virus, purified/cloned subunits?
IV: Hep A, Jap encephalitis, Polio, Rabies, Tick bone encephalitis
PS: Influenza
CS: Hep B, human papillomavirus
234
How is a live virus vaccine attenuated?
Pathogen isolated from patient and grown on culture of human cells \> culture virus used to infect monkey cells \> virus acquires many mutations that allow it to grow well in monkey cells \> but no longer grows well in human cells and may be candidate for a vaccine - passaging can also be passed through temp rather than species
235
What is the theory of attenuation?
Virus passed through wrong cell/species and makes virus evolve so no longer virulent to humans
236
Pros and cons of live vs inactivated vaccines
LIVE: Rapid broad (all arms of IR), long lived immunity, dose sparing, cellular immunity BUT requires attenuation, may revert
INACTIVATED: Safe, can be made from wild type virus BUT frequent boosting required, high doses needed
237
Which viruses have inactivated and attenuated versions?
Influenza: inactivated consists only of spike proteins, given to people at risk and heathcare workers, FLU NOT given. Children strategy: mist and can only replicate in nose. Needs to be updated regularly as influenza evolves fast
Poliovirus: Salk inactivated vaccine and Sabin live attenuated, 1 in 7 million vaccinations associated with poliomyelitis, persisting in immunosuppressed individuals - so Salk inactivated vaccine will be needed for end game
238
How are recombinant attenuated vaccines made?
Pathogenic virus genome consists of receptor binding gene, virulence gene and capsid protein genes - either mutate virulence gene or delete it - can get a virus which is immunogenic, not virulent
239
Example of rotarvirus vaccine given in UK
Rotarix is live attenuated rotavirus reassortant vaccine, which massively reduces deaths due to rotavirus infection leading to D&V
Early use of vaccine showed that it caused intusseption in older babies so give to babies less than 15w
240
Which subunit vaccines exist?
Hep B virus - Surface Ag cloned and expressed in yeast
HPV - virus like particles from recombinant coat proteins - Gardasil and Cervarix
241
Example of Shingles vaccine:
Shingles causes painful rash resulting from reactivation of varicella zoster virus infection - more common and serious in elderly as immune system wanes - even after rash, pain could remain as post herpetic neuralgia - similar but distinct to chicken pox vaccine
Given to those aged 70/79 on that year
242
How do viruses work as vectors of pathogens?
Clone of individual genes from pathogenic virus and insert into vaccinia virus genome - eg: HIV using canary pox vector, and boost with subunit gp120 of clade E - 38% efficacy
243
What other examples of viruses as vectors exist?
For ebola - chimpanzee adenovirus vctored ebola G protein
Vesicular Stomatitis virus vectored vaccine expresses Ebola G protein
244
How does antiviral treatment work?
Either by boosting patients own IR - interferons or use drugs with specific antiviral activity
OR treatment to alleviate symptoms but doesn't treat virus
245
What are interferons?
Natural chemicals which our bodies make in response to viruses - switch on natural antiviral response BUT switches on everything including inflammation and fever, so makes patient feel worse
246
How do you target viruses?
Don't have distinctive features, as they don't have unique features - so antiviral enzymes used to target VIRAL ENZYMES, often acting as substrate analogues
247
What are the best antivirals?
Nucleoside analogues - as all viruses have to replicate their genome - so have to incorporate into growing RNA chain - look like normal bases with a bit missing
248
What is an example of a nucleoside analogue?
Acyclovir - analogue of guanosine and acts as a chain terminator, as it lacks the 3' hydroxyl group, so nothing else can bind to it
249
Why is acyclovir a good antiviral?
Targets Herpes Simplex virus. Specific to virus infected cells - administer as an unphosphorylated compound and can only be phosphorylated by a virus infected cell, so if not infected then drug does nothing - **thymidine kinase** is the enzyme which can phosphorylated
Also has a higher affinity to viral DNA than human DNA
250
What does neuraminidase do?
As the virus leaves an infected cell, it destroys the cell surface receptors, so that it won't reinfect that cell
Present on influenza virus
251
How can we use neuraminidase as an antiviral?
Analyse the enzyme and then create inhibitors such as Sialic acid, relenza and tamiflu
252
What can we inhibit on HIV?
Entry to cell inhibitors (Maraviroc - blocks gp120/CXCR4 interaction, enfuviritide - binds HIV gp41 preventing membrane fusion, pore formation and entry), proteinase inhibitors (atazanavir, taken with ritonavir, binds enzyme active site, inhibits activity), non (efavirenzd, viramune - allosteric inhibitors)/nucleoside (zidovudine, stavudine - chain terminators) reverse transcriptase inhibitors, integrase inhibitors (raltegravir - blocks virus/host DNA transfer)
253
What is the hep C treatment?
HCV is a hepatotrophic flavivirus, with 4% of infected will get HCC - interferon treatment with ribavirin whcih was only effective in 50% patients infected with unpleasent side effects
Antiviral drugs - NS3-4A proteases were targeted (telaprivir and boceprivir), and are used combined with Interferon and RBVN, as monotherapy leads to rapid resistance
New targets - NS5B(viral polymerase that replicates RNA genome)/ A(phosphoprotein required by virus for replication - Daclastivir). Crystallography has solved structures and allowed for directly acting antiviral design
254
What does the new hep C therapy combine?
Protease inhibitor - asunaprevir, NS5A inhibitor - daclastivir, w/wout IFN and RBVN
There was sustained virological response - patients feel better and viral load has decreased
255
How is ebola treated?
Zmapp - passive immunotherapy, monoclonal antibodies raised and produced inplants OR serum therapy (blood from survivors)
Favipiravir - nucleoside analogue
256
Which viruses are currently vaccinated against in children in UK?
Rotavirus, poliovirus, MMR, influenza
257
Which of the following antiviral drugs and virus pairs are wrongly paired?
## Footnote
1. Herpes simplex virus and acyclovir (zovirax)
2. HIV and Zidovudine (NRTI)
3. Influenza and oseltamivir (Tamiflu)
4. Hepatitis C and amantadine
Hep C and amantadine - should be asunaprevir, daclastivir, IFN/RBVN
258
To treat HIV a combination of different drugs known as HAART highly active antiviral therapy is used because:
The reverse transcriptase of the virus is so error prone that virus resistance to a single drug emerges rapidly
259
Why do viruses evolve fast?
Replicate fast, in large numbers and have a high mutation rate
260
What is a quasispecies?
When a virus in a single infected person has slightly different genomes, because they evolve inside the host
261
How can mutations change the virus?
They can improve vira replication, and some emerge to be more dominant than others - sometimes a bottleneck will form at transmission/replication under limiting conditions
262
How can we see the impact of evolution of viruses?
If a resistant virus is put into someone who doesn't have that drug, then it may revert to its wild type
Also, look at a phylogenetic tree
263
How can we prevent HIV drug resistance (example)?
Drugs which target different part of HIV life cycle - if given monotherapy, then one single nucleotide can change and may make it resistant
Must give a combination of antiviral drugs, as error rate 1 in 10,000 and each HIV is around 10,000 nucleotides long, each HIV genome is slightly different, so monotherapy is very likley to cause resistance
264
What other things exert selection pressure on viruses?
Ab - if person is infected with virus for which patient has Abs then person is immune - but if person infected has a subneutralising amount of Ab virus will replicate in body and only fittest survive (the ones which change the spike proteins)
265
What is antigenic drift and what is it caused by?
Ag gradually change over period of time due to pressure exerted by Ab
NB: rhinovirus don't show antigenic drift, but so many are present that it is likely you will catch many during your lifetime
266
How do new viruses emerge?
Zoonosis, Genetic Variation, Increased exposure - travel/world popn, increased exposure - spread of vector, new discoveries
267
Which new viruses have been discovered/detected?
Hep C, human papillomaviruses 16/18, HHV8 causes kaposi's sarcoma, merkel's cells polyomavirus causes merkel cell carcinoma
268
Which global influences on emerging infections exist?
Env. modifications/demographics, world popn, climate change, travel, farming practices/monocultures, immunosuppressed humans, war, medical progress
269
What are arboviruses?
Class of viruses transmitted to humans by arthropods, such as mosquitoes and ticks
270
What are some examples of arboviruses?
Yellow fever, dengue, west nile, chikingunya
271
What kind of viruses are arboviruses?
Flaviviruses (single strand +RNA), which use mosuitoes as host
Sometimes, humans and horses are dead end hosts so it doesn't spread any further
272
Why are arboviruses a concern?
Global warming leads to increase of global distribution of mosquitoes
273
What is the west nile virus?
Vector: Culex tarsalis, belongs to Japanese encephalitis group of flaviviruses and cause disease by going to the brain
Carried in mosquitoes that bite birds, which are bitten by mosquitoes which bite birds again and occasionally humans
1999- boom in mosquitoes, which meant people came in with encephalitis, then RT-PCR showed that it was from Isreal
274
What is Dengue haemorrhagic fever?
4 stereotypes of Dengue virus - 3billion live at risk
First time infected is not serious, but second time is a different stereotype, so Ab from first time make you more sick - Ab dependent enhancement of infection
Ab can either neutralise infection or enhance it
275
What are the risk factors for Dengue haemorrhagic fever?
Pre-existing anti-dengue Ab, virus strain, age, higher risk in secondary infections/areas where 2 or more stereotypes are circulating at similarly high levels (hyperendemic transmission)
276
How do dengue Ab either enhance/neutralise infection?
Binding to wrong anti-dengue Ab, viruses are given another way of entering the cells - but usually to enter cell it binds to specific receptor
If homologous Ab then viral Ag matched perfectly and held tightly to stop it entering the cell. If not, then Ag is held loosely and isn't blocked - Ab bind to Fc receptors on immune cells, carrying virus into immune cells, so cytokine storm, leading to dengue haemorrhagic fever
277
Examples of other zoonosis:
Disease transmitted from animals to humans - HIV-1 from chimpanzees, HIV-2 from sooty mangabeys, ebola from bats
Some have the potential to start pandemic but don't transit efficienty= SARS, Ebola, Hendra, Nipah
278
What is SARS?
Severe acute respiratory syndrome, virus contained within a year, transmitted via resp droplets - nebulizers in hospitals brought up viruses from deep within the lungs.
Elderly people showed high mortality - patients become contagious when quite late stage/symptomatic so can be isolated
Comes from bats, civets, racoons
279
What is Ebola?
Began in guinea, transferred to Sierra Leone, transferred from bats to child
Ebola can transfer from sweating and bodily fluids, so full body protection was needed - funerals/body preparation can lead to even more transmission from dead host to other people
280
What are coronaviruses?
3 groups: group 1/2 contain mammalian viruses and 3 only avian viruses. Human CV are in both group 1 and 2 and are responsible for 30% of mild URTI
Human coronaviruses NL63 and HKU1 have been associated with more severe hospitalised cases
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What is the virus type of SARS?
Coronavirus - positive sense RNA, enveloped in spike protein (highly plastic and can adapt to bind to different receptors, with ACE-2 receptor in humans
Lots of coronaviruses in bats which can emerge and become pandemic
282
What is MERS?
Middle eastern respiratory syndrome, coronavirus, originates from bats and is endemic in camels
Closely related to HKU4/5, causes acute resp distress syndrome in older people, uses DPP4 receptor in lungs
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How are outbreaks identified?
Formal reports - infections on notable disease list will be reported to public health by doctor who diagnosed
Informal reports - community tells local health about a large group of food related illness (dinner party)
Labs do special testing/stereotyping on pathogen to determine what it is
All coordinated by public health
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What happens when 2 viruses combine?
Can give rise to a new virus - 2009 swine flupandemic has antigenic subtype of H1N1, which is similar to virus ciculating in humans - happens because of antigenic drift
Virus H1N1 circulates in humans and changes a bit at a time, as humans live long enough to be reinfected but in pigs don't live as long so there is no antigenic drift, so flu in 1918 stayed in pigs so are completely different to those in pigs
285
What is H7N9?
High proportion in elderly men, linked with infected poultry in wet markets, but virus shows human adaptive changes so could be another pandemic
286
In which patients are drug resistant viruses less likely to emerge?
In patients taking a combination of antiviral drugs
287
Which of the following statements is not true?
1. Arboviruses are viruses spread by biting mosquitoes and midges
2. Example of arboviruses are yellow fever virus, Dengue, West Nile and Ebola
3. Arbovirus spread can be controlled by releasing mosquitoes infected with a bacteria known as Woolbachia
4. Birds are important hosts in the spread of arboviruses such as West Nile virus.
2
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Examples of zoonoses that have lead to pandemic include:
1. SARS
2. H5N1 bird flu
3. HIV
4. MERS
HIV
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Which of the following statements is true?
1. SARS and MERS are the only coronaviruses known to infect humans.
2. More people have died following infection with MERS coronavirus than with H7N9 avian influenza.
3. There is a vaccine that can protect against human coronaviruses but it does to work against SARS
4. Bats are an important reservoir of coronaviruses that can cross into humans.
4
290
Define an outbreak
The occurrence of more cases of disease than normally expected within a specific place or group of people over a given period of time.
291
Give 3 characteristics of bacterium causing 2011 E. Coli outbreak
Gram negative, 2 cell membranes, have lipopolysaccharides on outer membrane
292
List 3 symptoms of haemolytic uraemia syndrome
Bloody diarrhea, Vomiting, Abdominal pain, Pale skin tone, Fatigue and irritability, Fever, usually not high and may not be present at all, Blood in the urine, Small, unexplained bruises or bleeding from the nose and mouth, Decreased urination or blood in the urine, Swelling of the face, hands, feet or entire body, Confusion
293
Name 2 gram positive and 2 gram negative bacteria
GPB: Staphylococcus aureus, Streptococcus pyogenes, strep pneumoniae
GNB: Salmonella typhi, Escherichia Coli, Klebisella
294
Give 3 examples of transferred genes during transduction/translation/conjugation
Toxins, resistance, enzyme
295
What is HAART?
Highly active anti-retroviral therapy - combination of 3 or more drugs to tackle a virus
296
Name 2 antiflu drugs
Tamiflu, Relenza and rapivab
297
List 2 classes of bactericidal Ab and what they target
Quinolones - DNA gyrase (GNB), topoisomerase (GPB) = unravelling DNA
Aminoglycosides - affect protein synthesis by RNA proofreading
