Virology, prions and molecular techniques

Prions disease

• progressive neurodegenerative diseases induced by formation of prion proteins

• they have a long incubation period usually of many years — median age of death ~68 years

• once symptoms commence they are invariably fatal

types of prion diseases

• Kuru — 1975, PNG

• Creutzfeldt-Jakob disease (CJD)

• New variant CJD (BSE)

• Gerstmann-Strussler-Scheinker syndrome

• Fatal familial insomnia

what are prions

• protein molecules composed of sialoglycoproteins called PrP27-30 (27-30 KD)

• all mammals have normal prion protein genes

• they prevent neuronal dysfunction and resist oxidative stress — 145 aa

• Abnormal PrP^Sc Prion protein converts normal PrP^c protein - leads to misfolding

• Once symptoms commence → fatal, ‘infectious’ via converting normal proteins to prions on contact

function of prion protein

• highly conserved in mammals

• Mis-folding → sever neurodegenerative disease

• transport of copper into cells and protects brain cells from stress

• thought to regulate sleep patterns and memory

• Aids communication between neurones

Diagnosis — symptoms of prion disease

• initial neurological symptoms — rapidly progressive dementia and memory loss, loss of physical coordination such as stammering and jerky movements, irritability and mood changes

• ambulatory stage — unsteadiness of stance/gait, slurring of speech, tremors, lack of coordination of limbs that progresses upwards

• sedentary stage — cannot walk, severe tremors, ataxia, inappropriate emotions, cognitive decline and depression

• Terminal stage — intensifying symptoms from above, incontinence, dysphagia, coma and loss of control of breathing

neuropathology of prion diseases

• infect and proliferate in neurons leading to neuronal apoptosis

• proliferation of glial cells and general abscence of an inflammatory response

• accumulation of plaques of misfolded prion proteins

• tissue degeneration leads to small vacuoles or microscopic holes and the characteristic spongy appearance

• location and appearance of the infected tissue distinctive for each disease

routes of infection

• prion infected material is very infectious

• ingestion of infected material commonest (BSE and Kuru)

• cases can also arise due to spontaneous mutation and inherited genetic predisposition

Creutzfeldt-Jakob disease

• Classic form of the disease has three etiologies

  • sporadic (~85%)

  • hereditary (familial or inherited CJD, ~10%)

  • Iatrogenic CJD — infection via medical procedures (from pituitary growth hormone, ~5%)

• Variant CJD (BSE) — new form that emerged in 1990s linked to consumption of meat products infected by Bovine spongiform encephalopathy

  • 90% die within a year of diagnosis

  • incubation up to 50 years (kuru)

  • general rate is ~1:1,000,000

sporadic CJD

• normal brain protein undergoes an abnormal change to prion protein

• occurs spontaneously in populations at a rate of 1:1000000 — occurs in every country at similar incidence

• Illness — duration varies

  • generally less than a year (6 weeks - 3 years)

  • sporadic symptoms — insidious onset followed by rapid decline

  • most patients suffer from severe dementia

inherited/familial CJD

• inherited gene carries mutation that causes formation of prions — family history of CJD

• Occurs in about 1: 5 000 000

• autosomal dominant inheritance, high penetrance (50 chance inheritance if parent affected)

• mutation at codon 178 of Prion protein and valine at position 129

• mutation changes the conformation of normal PrP^c protein to PrP^sc

• age of onset depends on mutation (~30-80)

Gerstmann-Straussler-Scheinker disease (GSS)

• Very rare familial prion disease, onset between 20-60 years

• specific mutation at codon 102 — proline — leucine in prion protein gene

fatal familial insomnia

• rare inherited condition. Mutation at codon 178 and valine at position 129

• Increasing insomnia, panic attacks, paranoia, hallucinations — complete inability to sleep, rapid weight loss, dementia, coma

Iatrogenic CJD

• Caused by contamination of patients by infective human tissue or fluid as a result of a medical procedure

• if via brain surgery then symptoms akin to sporadic CJD

• more commonly due to treatment of patients with contaminated human growth hormone from pituitary given to children with short stature — symptoms like Kuru (high ataxia, less dementia)

• Incubation period of ~15 years

• no evidence of blood borne transmission

Kuru

• caused by consumption of human flesh in the Fore people of PNG

• AKA laughing sickness

• funerary cannibalism — consumption of deceased family members to help free spirit of the dead

• females and children mainly affected → they consume the brains

• incubation period of 5-50 years

• discovery of naturally occuring resistance genotype of the prion protein in PNG protein

variant CJD (BSE)

• caused by consumption of meat contaminated with the cattle prion bovine spongiform encephalopathy

• illness similar to kuru with a longer duration of illness

• euphemistically term “mad cow disease” → lead to bans on imports of UK beef

Prion disease gene variants

• numerous sites of mutations but most significant is the position 129 codon — either Valine (V) or Methionine (M) residue

• This variant differ between different types of CJD and normal populations

diagnosis of prions

• many cases diagnosed clinically and confirmed at postmortem, aim to improve antemortem

• detection of surragate biomarkers in csf 14-3-3 protein family, Tau, phospho-tau and amyloid-beta — not 100%

• Immunoassay for detection of prion proteins - various body fluid

• immunohistochemical PrP^Sc test — brain biopsy required

• electroencephalogram

• MRI

predictive prion biomarkers

• D178M, V180I, E200K, R208H

• mutations that lead to CJD

biomarkers prion prognostic

• M232R (slow), V1801 (slow), others fast

treatment of prion diseases

• no effective treatment for any human prion diseases, they are invariably fatal once symptoms appear

• flupirtine maleate is a non-opoid analgesic that has cytoprotective activity in vitro in neurons treated with prion protein

• chlorpromazine and quinacrine inhibit conversion of PrPc to PrPsc

• possible use of antibodies against prions to target the PrP^Sc variant

influenza

• RNA viruses that belong to Orthomyxoviridae

• three different genera infect humans — influenza A, B, C

influenza A

high mutation rate humans, animals and birds — causes pandemics

• Undergoes antigenic variations with the haemagglutinin (H) and neuraminidase (N) proteins. 18 H, 11N

• antigenic shifts in H → results in pandemics

• antigenic drifts in H and N → results in epidemic, can get re-assortment between avian and human virus

• usually mild febrile illness

• dealth from new variant or complications ie viral/bacterial pneumonia

influenza A epidemiology

• pandemics — new haemagglutinin subtypes emerges as a result of antigenic shift and genetic reassortment

• population has no immunity against the new strain

• epidemics — arise through more minor anitgenic drifts as a result of mutation

influenza B

almost exclusive to humans, slower rate of mutation

• only infects humans and seals

• lack of pandemics due to limited host range

• two currently circulating lineages

• evolve slower than A viruses but faster than C virus

• less seasonal than A virus, significant cause of mortality and morbidity

influenza C

infects humans, dogs and pigs, less common and less severe

• less frequent than A or B

• usually found in dogs, pigs an humans

• generally a milder disease, commoner in children. Does cause occasional epidemics

• lacks seasonality. Evolves via antigenic drift only

• vaccine does not normally protect against the influenza C virus

diagnosis of influenza

• will it the result change the clinical care of the patient

• are symptoms severe or are they high risk patients

• will it influence the management of other patients/contacts

• samples — throat, nasal and nasopharyngeal swabs, nasal washings lavages and sputum (take appropriate sample for symptoms)

methods for influenza testing

• Isolation and culture of virus — cell culture, inoculation of chicken eggs, shell viral culture (svc)

• serological methods — direct fluorescent antibody test, haemagluttination inhibition assay, virus neutralization assay, ELIZA, complement fixation

• NAAT

• Sequencing

• rapid antigen capture/detection tests

influenza cell culture

• used to be gold standard

• slow time to result

• useful for epidemiology

• vital for vaccine development

influenza cell culture and detection

• introduced 1940s

• takes 5-10 days — used on established cell lines and used in parallel with NAAT assays

egg culture and detection

7-10 days and visualize cytopathic effects and confirmation by immunofluorescence microscopy

shell viral culture

1-3 days, propagate virus in mammalian cells in small shell vials followed by staining with fluorescent antibodies

direct fluorescent antibody test (DFA)

• high specificity

• poor sensitivity

haemagglutination assay

• use either haemaglutination and haemaglutination inhibition

ELISA assay for influenza

• either against antibodies or antigens

• lower sensitivity than NAATs

• ENIA test — uses antibodies against nucleoprotein from influenza A — differentiates 29 different strains and subtypes

complement fixation test

• uses serum with antibody against antigen and sheep red blood cells

• cheap

• can be automated (seramat)

immunoassays — rapid antigen direct tests (RADTs)

Sensitivity effected by timing of viral shedding (24-60 hours)

• live attenuated vaccine can lead to false +ve

• rapid — 15-30 minutes

• does not differentiate serotypes

• POC testing

NAAT — RNA detection

• samples used — throat, nasal and nasopharyngeal swabs, lavages and sputums

• generally preferred method, best sensitivity and specificity

• can differentiate subtypes and pandemic strains

• can multiplex many resp viruses — pathwest do 22 resp viruses

• takes 2-8 hours (plus RNA extraction time)

• noval viruses not detected

sequencing

• used for epidemiology studies and tracking outbreaks

• two techs — sanger sequencing and next generation sequencing

• SARS virus first time novel virus fully sequenced before it had been isolated

influenza treatment

• can reduce the duration and severity

• recommended for hospitalized, severe, complicated or those with progressive disease

• treatment for 5 days

• two types of drugs

  • neuraminidase inhibitor (oseltamivir (Tamiflu) and zanamivir (Relenza))

  • M2 protein inhibitor (adamantane)

viral haemorrhagic fever (VHF)

• range of enveloped RNA viruses from several families

• Arenaviruses

• Filoviruses (SSA)

• Bunyaviruses

• Flaviviruses

general characteristics of VHF

• specific clinical symptoms vary by pathogen but generally

  • initial symptoms — fever, fatigue, dizziness, myalgia, loss of strength, exhaustion, nausea

  • patients suffer from bleeding disorders (petechia, echymoses), conjunctivitis, oedema, hypotension

  • in sever cases bleeding can occur in internal organs and from orifices like the mouth, nose and eye

  • other symptoms can include rash, haemorrhagic diathesis, and shock

• humans are often not the natural hosts

• some are vector borne and some are by contact with infected patients or animals

arenaviruses

• lassa haemorrhagic fever

• acute haemorrhagic illness of 2-21 days duration, incubation 6-21 days

• 80% infected people remain asymptomatic

• endemic to west Africa

• transmitted by contamination of food with rodent urine or faeces or human to human.

• Hospital acquired outbreaks

lassa fever diagnosis

• clinically challenging due to array of symptoms

• normally to ELISA to detect IgM and IgG antibodies

• QRT-PCR useful for early diagnosis

Marburg virus

• filoviruses

• BSL4 pathogen, NIH category A pathgen, CDC category A bioterrorism agent

• first detected in simultaneous outbreaks in Marburg, Frankfurt and Belgrade in 1967

• incubation period 3-7 days, death 3-7 days later

• transmission and natural animal host are poorly defined, bats implicated as reservoir

• transmission occurs readily between humans by direct contact or exporsue to body fluids

Ebola virus

• filoviruses

• BSL4 pathogen, NIH category A pathogen, CDC category A bioterrorism agent

• first identified simulateously in Sudan and Zaire in 1976

• subtypes Zaire and Sudan 80-90% mortality rate, Reston only primate

• Incubation period 2-21 days, death 3-7 days later

• transmission from butchering or eating infected animals → once infected, transmission occurs readily between humans by direct contact or exposure to body fluids

Marburg and Ebola diagnosis

• RT-PCR assays, real time assays on nested PCRs

• ELISA to detect IgM and IgG antibodies — repreated to look for serconversion

• ELISA to detect antigen

• virus culture and isolation in Vero cells

• intitial diagnosis at start of outbreak is critical diagnosis normally by ore than one method

Marburg and Ebola Treatment

• initial treatment is of supportive nature

• no specific treatment available

  • fluid replacement, maintain blood pressure, replace lost blood via transfusion

  • patients normally in quarantined intensive care facility

  • Ribavirin — useful in some haemorrhagic fever viruses but not Marburg or Ebola

• vaccine fast tracked, 36 trials completed and now being used in the 2018-19 outbreak

working with BSL 4 pathogens

In endemic region

• Full protective clothing

• prevent contact with fluid or aerosol or tissue

• safe disporal of needles and all contaminated supplies

• burial of bodies performed with care

In Australia/UK/USA

• only handle in BSL4 lab or secure isolation unit

Hantavirus

• bunyavirus

• normal host is the rodent

• transmitted by contamination of food with rodent urine or faeces and occasionally human to human transmission

• 2 severe syndromes — Hantavirus pulmonary syndrome, hanatavirus haemorrhagic fever with renal syndrome

hantavirus pulmonary syndrome

rapid onset of pulmonary oedema, ~35% death rate — Americas

hantavirus haemorrhagic fever with renal syndrome

1-8 week incubation, ~40% death rate — Eurasia

diagnosis of hantavirus

• serological tests — ELISA for IgM acute phase, IgG for later monitoring. Also western immunoBlot assay

• NAAT — RT-PCR tests

coronaviruses

• large group of single-stranded, positive-sense RNA viruses (~200) that infect mammals and birds

• in human (and birds) coronaviruses primarily cause respiratory tract infection

• four species endemic in human population and causes of “common-cold” (HKU1, OC43, 229E, NL63)

virology of SARS-CoV-2

• Nucleocapsid

• Spike glycoprotein (S)

• Membrane protein (M)

• Envelope (E)

• RNA

• Hemagglutinin esterase-dimer

clincal features of COVID-19

• Incubation period 4-5 days (2-12)

• common symptoms of mild disease

  • cough, myalgia, headache

  • sore throat, smell or taste abnormalities, diarrhoea

  • coryza, nasal congestion, sneezing (especially Delta and Omicron)

• severe disease

  • usually begines 5-8 days after initial symptom onset

  • respiratory failure causing shortness of breath

  • cardiovascular, thromboembolic, neurological, inflammatory complications

risk factors for severe disease COVID-19

• increasing age

• cardiovascular disease

• chronic respiratory disease

• chronic kidney disease

• cancer, organ transplantation

• immunosuppression

• diabetes

• obesity

• smoking

• physical inactivity

• male sex

• pregnancy

• unvaccinated status

commonly used treatments in Australia

• Paxlovid (nirmatrelvir/ritonavir) — oral antiviral for 5 days for mild disease in patients with risk factors for disease progression

• Molnupiravir (fewer contraindications than paxlovid)

• Remdesivir — intravenous antiviral for 5-10 days for use in severe disease, also short course in pregnancy

transmission of COVID-19

• infected individuals are infectious from ~2 days prior to symptom onset and until 7-10 days after

• most infectious around symptom onset → possibly later fro omicron

• direct person-person transmission via close-range contact via respoiratory particles is primary route of transmission

• indirect contact via contaminated surfaces also possible — not thought to be major route of transmission

• longer-distance ‘airborne transmission’ via respiratory aerosols well documented — mainly poorly-ventilated spaces

Pfizer Comirnaty

• mRNA encoding spike protein

• associated with very low risk of myocarditis, mainly younger males

• original vaccine had ancestral SARS-CoV-2 strain

• later generations available incorporating Omicron BA.4/5, XBB, JN.1

Moderna Spikevax

• mRNA encoding spike protein

• associated with very low risk of myocarditis

• strain updates like Pfizer

AstraZeneca Vaxzevria

• Non-replicating adenovirus vector encoding spike protein

• associated with very low risk of thrombosis syndrome and Guillain-Barre syndrome

• no longer available in Australia

Novavax Nuvaxovid

• adjuvanted recombinant spike protein

• less safety data than others

• possible associated with myocarditis

• no longer available in Australia

COVID-19 vaccines in general

• mild local and systemic reactions (pain, fever, fatigue) are common with all vaccines

• all vaccines were shown to have good efficacy against symptomatic disease and severe disease after two doses in their initial trials

• waning immunity in the months after vaccination → recommendation by new strains

• annual boosters currently recommended for >65y (>18 if immunocompromised)

SARS-CoV-2 diagnostic tests

• NAT/PCR

• RAT (antigen detection)

• Culture — lower sens than NAT, high specificity, slow - limited clincal utility

• Whole genome sequencing — assign a lineage, mostly direct from specimen

NCT/PCR for COVID

• gold standard (highest sensitivity and specificity)

• performed on respiratory tract specimens, mainly nose and throat swabs

• requires expensive equipment

• point of care tests (POCT) available but low throughput

• high throughput testing equipment very expensive

• marginal cost/test is minimal

RAT (antigen detection)

• also performed on nose and throat swabs

• no extra equipment needed

• rapid, simple and suitable for POCT

• lower sensitivity and specificity than NAT

• per CDC, should be used within 5 days of symptom onset

• cost scales with numbers of tests

antibody detection of COVID

• retrospective diagnosis, limited utility

• antibody response usually detectable 1-3 weeks after infection

• spike antibodies develop soon after nucleocapsid antibodies and persist for longer

• neutralising antibodies mainly target spike protein

• spike antibodies also develop after vaccination

Hepatitis virus

• can be caused by five hepatitis viruses — HAV, HBV, HCV, HDV and HEV

• HBV, HCV, HDV — transmitted parenterally

• HAV, HEV — transmitted enterically

• HBV AND HCV → chronic infection → cirrhosis and hepatocellular carcinoma (HCC)

• HDV is satellite virus of HBV → can only replicate in presence of HBVa

• HDV + HBV can infect infect cell simultaneously, HDV can infect HBV-infected cell

Hepatitis B Virus

• partially double stranded circular DNA — about 3.2 kb

• parenteral transmission — organ transplantation, blood transfusion, needlestick injury, needle sharing, tattooing

• sexual, vertical, intra-familial

• in aus — injecting drug users, MSM, inmates, immigrants from endemic regions, Aboriginal and Torres Strait Islander peoples

• 45-180 day incubation

• can cause acute and chronic disease — flu like symptoms, jaundice, pruritis

• approximately 10% of infections are not cleared and the virus continue to replicate → chronic carriers

HBV DNA

• HBV DNA levels become detectable about 30 days after infection → peak at about 6 weeks

• trace HBV DNA levels can persist for many years after clearance of HBsAg and appearance of anti-HBS

• not used for diagnosis of acute or chronic infection; most often monitoring disease and response to therapy

• 4 overlapping open reading frames (S, C, P, and X) that encode HBV surface proteins (HBsAg), structural core protein (HBcAg), polymerase, and non-structural precore proteins (secreted e-antigen (HBeAg) and the X protein)

clinical and virological course of acute infection with HBV

• Hepatitis B surface antigen (HBsAg) detectable in blood soon after infection

• clearance of HBsAg from blood, and appearance of anti-HBs, indicates recovery

• Persisence of HBsAg (>6 months after infection), lack of anti-HBs, indicates chronic infection — carrier state

• HBsAg — if +, indicate infection (>6 months = chronic infection)

• anti-HBs (ab) — recovery and/or immunity to HBV

• HBeAg — active viral replication

• Anti-Hbe (Ab) — recovery

• Anti-HBc (Ab) — if positive, indicates HBV exposure

chronic hepatitis B management

• based on the levels of serum HBV DNA, ALT, and severity of liver disease

• Nucleoside or nucleotide analogues (NUCs) — i.e Lamivudine — inhibits HBV DNA synthesis → suppression of viral replication and reduction of hepatic necrosis and HBeAg seroconversion

• antiretroviral treatment can select for drug resistant virus — approximately 70% of patients after 5 years on lamivudine have resistant HBV

Hepatitis D virus

• Circular, ssRNA (-) genome of 1,68 kb

• unique virus dependent on HBV - enveloped (HBsAg)

• considered a satellite virus of HBV but does not share sequences similarity; can replicate independently of HBV

hepatitis D infection

• causes a range of clinical outcomes from asymptomatic infection to fulminant hepatitis

Coninfection

• both HBV and HDV are acquired simultaneously

• severe acute disease/low risk of chronic infection

Superinfection

• chronicc HBV carriers are infected with HDV

• usually develop chronic HDV infection/high risk of severe chronic hepatitis

• may present as an acute hepatitis

• infection can be prevented by hepatitis B immunisation

Dengue virus

• acute viral disease that resolves within 4-6 weeks

• (+) ssRNA enveloped virus, genus flavivirus, Family Flaviviridae

• four distinct serotypes: DENV1-4, about 30% divergent — all 4 serotypes can cauuse severe and fatal disease

• RNA genome — high mutation rate, exists as quasispecies and as clades or genotypes

• ~390 million infections each year worldwide

dengue fever and sever dengue

• can be flu-like illness (dengue fever) or more sever illness like haemorrhagic manifestations and vascular leakage resulting in hypovolemic shock (aka severe dengue, previously dengue haemorrhagid fever/dengue shock syndrome)

• time of onset of severe illness coincides with end of viraemic period — suggests immunopathogenic basis

• severe disease frequently occurs in the setting of secondary infection and with heterologous serotype

• immunity to one serotype is thought to be life long, but only transient cross-protection against other serotypes of the virus

dengue serology

• time course of acute infection and immune response during symptomatic dengue virus infection

• peak viraemia → high fever and initiation of IgM and IgG production → promote clearance of virus infection

• during 2ndary heterologous DENV infection → period of viraemia is shorter, likely owing to cross-reactive immunity, including pre-existing antibodies

• cross reactive memory T cells promote an earlier and potentially stronger T cell responses than that during primary infection → risk of severe dengue is higher in patients who experience secondary heterologous DENV infection

acute dengue diagnosis and case classification

• definitive diagnosis of dengue rests on the detection of the infective virus, virus-encoded antigens, virus genomic RNA, or virus-induced antibodies

• acute phase (initial 1-7 days after symptom onset) — PCR, NS1, serology and tissue tests

• convalescent phase (>7 days post symptom onset) — serology and tissue tests

• specimens can include serum, plasma, whole blood, cerebrospinal fluid

• neutralisation assays allow assessments of cross-recognition of viral antigen by immune sera

human immunodeficiency virus (HIV)

• acquired immune deficiency syndrome (AIDS) is then end stage disease caused by infection with human immunodeficiency virus (HIV)

• Enveloped, ss (+) RNA virus with a DNA intermediate, which replicates using viral RNA-dependent DNA polymerase: reverse transcriptase (RT)

• chronic, life-long infection — blood viral RNA remains detecable in most patients, in the absence of ART

HIV-1 diversity

• high mutation rates (low fidelity of RT/ host cell factors — APOBEC proteins)

• retroviral recombination (via template switching)

• high viral turnover, host immune system selection etc

• Group M (main) HIV-1 is the dominant worldwide

• clade B in australia, clade-C is dominant form

• circulating recombinant forms (CRF) and unique recombinant forms (URF) are emerging variants of HIV-1: recombined clades

laboratory tests used in diagnosis of HIV infection

• detection of antigen by:

  • Immunoassay to detect HIV p24 protein

  • PCR or other genome detection method — viral RNA or proviral DNA

• detection of antibody by immunoassay by IA

  • screening tests which tests for anti-HIV Ab, usually ELISA

  • confirmatory tests which test from antibody to specific HIV proteins: very specific, used to confirm result screening test — west blot

• combination tests for simultaneous detection of antigen and antibody

• rapid tests for anti-HIV ab and p24 Ag — POC and home use, must be confirmed by more specific tests

HIV diagnosis

• australian lab use fourth generation HIV tests (antigen/antibody combination test), which becomes positive 2-6 weeks after exposure

• the point-of-care test (POCT) is licensed in Australia

• average window period for NAT Ag tests is <1-2 weeks

• confirmation by western blot: CDC criteria require 2 bands of the following: p24, gp41, or gp120/160

western blot diagnosis disadvantages

• possible misclassification of HIV-2 infections as HIV-1

• longer time to confirm HIV infection

• practical limitations

diagnostic testing in infants

• virologic testing of HIV-exposed infant: 14-21 days of age, 1-2 months and 4-6 months

• in infants <18 months, use virologic assays that directly detect HIV: HIV DNA or RNA PCR - persistent maternal antibodies can give false positive results

• virologic testing at birth should be considered for infects at high risk of infection

• HIV antibody test — 12-18 months to document seroconversion in HIV-uninfected infants/diagnostic test for children >18 months

AIDS

presence of HIV infection and either a CD4+ T cell counts of <200 cells per ul or and AIDS defining complication

AIDS-Defining conditions

• candidiasis of bronchi, trachae, oesophagus, or lungs

• cytomegalovirus diseases (particularly retinits); CMV

• Kaposi’s sarcoma (KS) (HHV-8)

• Tuberculosis

• Pneumocystis jirovecii pneumonia

• Toxoplasmosis of brain

correlates of protective immunity against HIV-1

• have not been well defined

possible requirements for protective immunity against HIV-1 infection

• Cytotoxic lymphocyte activity (CD4+ and CD8+ T cells)

• innate immune responses (plasmacytoid dendritic cells)

• NK cell activity

• antibody dependent cellular cytotoxicity

• neutralising antibodies

pathogens interact with the host by

• physically damaging cells and tissues

• by binding to specific receptors inducing change

• secreting pathogen molecules that modulate host functions (interactome) — extracellular, intracellular

• releasing toxins

• releasing immunogenic molecules

• produing ‘mimic’ molecules to modulate host

• unknown mechnisms

infections and chronic disease

• changes may be relatively rapid, often easy to associate with the infection i.e anaemia, hemolyticuremea, Guillain-Barre syndrome

• changes may take months, years or even decades, more difficult to associate pathogen to disease

  • diseasen may be mild/asymptomatic

  • often linked by using large association type studies

  • may differ between populations

  • may remain contentious

  • i.e many neurological disorders, cancers and ulcers

modern view of pathogen host interactions

microbes interact with host in many different ways inducing a whole range of effects that range from beneficial to pathogenic, short lived or life long, rapid to insidious and chronic

cervical cancer and human papillomavirus

• HPV is very common, there are >100 types of HPV

• 13 types are cancer causing though HPV type 16 and 18 cause 70% of cancers

• approximately 250,000 deaths per year eps in developing countries

• generally sexually acquired

• also linked to anal, vulval, vaginal, and penile cancers

• HPV vaccination program for girls and boys 12-13 years, only effective if given before infection

liver cancer and hepatitis

• chronic hepatitis is commonest cause of liver cancer

• Hepatitis B → about 80% of liver cancedrs

• Hep C main cause of liver cancer in the USA

• risk of liver cancer 100x greater with hepatitis

• predicted that >50% of liver cancers could be prevented by HepB vaccine

• also leads to cirrhosis and other damage to liver

colorectal cancer and Bacteroides fragilis

• Bacteroides fragilis colonises most humans though in most only makes up 1-2% of bacteria

• some classes of B.fragilis (enterotoxigenic) can produce a toxin (BFT) associated with acute diarrhoea, IBD and colorectal cancer

• toxin shown to induce carcinogensis in animal models

• association with colorectal cancer in humans

stoman ulcers and H.pylori

• ~50% of the worlds population have Helicobacer pylori infection in stomach

• >80% remain asymptomatic

• association to gastric ulcers was contentious issue until proven by BJ Marshall and Robin Warren in 1982 — novel prize 2005

• 10-20% lifetime risk of developing peptic ulcers, 1-2% risk of stomach cancer; also associated with colorectal cancer

• effects cause by ammonia, proteases and vacuolating cytotoxin damage the stomach

• indicated association between H.pylori infection and gastric adenomcarcinoma

• decline in H.pylori infection in western countries → increase in esophageal cancer → suggestion H.pylori may be protective for esophageal adenocarcinoma

amyloidosis

• disorder of protein metabolism leading to abnormal deposition of normally soluble plasma proteins as proteinaceous material (amyloid) — beta pleated sheet

• can be microscopic amounts to massive deposits in organs

• heterogenous group of diseases

amyloidosis AA

• commonest form of the disease worldwide

• caused by deposition of protein fibrils from serum amyloid A protein (acute phase reactant protein)

• protein is produced by the liver in response to chronic inflammatory process

• mainly initiated by chronic infection (developing countries)

• rheumatic arthritis can also lead to this type

• deposited mainly in liver, kidney, and spleen

• dianosed by demonstrating amyloid depositis in tissue

autoimmunity and infection

• infection is one of several environmental factors that can induce autoimmunity

• >80 autoimmune diseases

• breakdown of ‘self tolerance’ during an infection

• B cells selected to fight infection can lead to B cells generating autoantibodies i.e Rheimatoid arthritis, Guillain-Barre syndrome

mechanisms by which infection induce autoimmunity

• molecular mimicry

• epitope spreading

• bystander activation

• cryptic antigens

molecular mimicry

pathogen antigen is similar to a host antigen so antibodies produced against the pathogen attack the host

epitope spreading

direct lysis of self-tissue by the persisting pathogen, causes damage to self-tissue. Antigens released from damaged tissue are taken up by APCs, and this initiates an immune response directed towards self-antigens