Microbiology - Viral Disease Flashcards
Ways viruses can be classified
Historical classification by host (human,plant, animal)
According to disease or target organ
According to vectors
Molecular biology new permits classification by genetic sequence and biophysical structure
Virus classification (taxonomy)
Virus order Virus family Subfamily Type species Morphology Genetic material (DNA or RNA) Envelope
Baltimore classification of viruses
Based on method of viral synthesis
Groups viruses into families according to their type of genome
Groups I to VII
Differentiating between bacterial and viral causes of infection
Pathognomonic symptoms
Secondary bacterial infection symptoms persist longer than the expected 10 days virus tends to last and fever is usually higher
Diagnostic tests
Purpose of diagnosing viral infection
Medical (therapeutic) patient management
Epidemiological (public health)
Intrahospital infection prevention and control
Academic
Molecular techniques used in virology
Nucleic-acid based technologies e.g. PCR
Next Generation Sequencing (NGS)
Monoclonal antibodies
Enzyme inmune assays
Point of Care Test
Test for key respiratory virus done by the bed side
Tests for influenza A/B and RSV
PCR based
Methods of detecting virus infections
Detection of viral antigens Detection of nucleic acids (PCR) Electron microscopy Virus culture Histopathology staining Serology testing
Serology testing
Presence of virus-spp antibodies (IgM and IgG)
What is detection of viral pathogens highly dependable on
Obtaining an adequate specimen from the appropriate site
Proper timing of specimen collection relative to onset of symptoms
Timely processing of the sample
When does viral shedding begin for most infections
Shortly after symptoms occur, peaks rapidly after onset and declines steadily as infection resolves (excluding chronic viral infections e.g. HIV)
Needlestick injury
An incident in which the blood of a patient comes into contact w/ the blood of a Health Care Worker
Types of exposure in health care setting associated w/ significant risk from blood or higher risk body fluids
Percutaneous injury
Exposure of broken skin - intact skin is a safe protective barrier against BBV transmission
Exposure of mucous membranes incl eyes and mouth
BBV
Blood borne viruses e.g. Hepatits B/C and HIV
Viruses which can be present in blood or other body fluids and which have high potential for transmission to another person by direct contact w/ their blood or susceptible fluids
BBV’s organised by how infectious they are
Hep B
Hep C
HIV
Transmission rates for susceptible fluids in BBV’s
HBV - 30%
HCV - 3%
HIV - 0.3%
Recipient
Individual who has been exposed to the possibility of acquiring a BBV as a result of an incident w/ the potential to transmit a BBV
Source
Individual who was the source of the blood or body fluid, which made contact w/ the recipient
Usually a patient but may be a HCW as in a bleed back incident
Post Exposure Prophylaxis (PEP)
Treatment which may be advised and supplied to the recipient and supplied to the recipient following a risk assessment from a known or high-risk HIV or HBV exposure incident
Main infectious material
Blood
Potential infectious material
Amniotic fluid Vaginal secretion Semen Human breast milk Cerebrospinal fluid Peritoneal fluid Pleural fluid Saliva in association w/ dentristy (likely to be contaminated w/ blood even when not visibly so)
Non-infectious bodily fluids
Urine
Vomit
Saliva
Faeces
What to do if you pierce/ puncture your skin w/ a used needle
Encourage the wound to bleed
Wash the wound using water and plenty of soap
Don’t scrub the wound while you’re washing it or suck it
Dry the wound and cover it w/ a waterproof plaster or dressing
Measles
Acute viral illness caused by a Morbillivirus
Important global cause of child mortality
What are measles deaths largely due to
Increased susceptibility to secondary bacterial and viral infection due to a prolonged state of immunosuppression
Presentation of measles
Prodromal stage
Characteristic rash
Koplik spots may appear on mucous membranes of mouth 1-2 days before rash appears and may stay for further 1-2 days
Prodromal stage of measles
Onset of fever Malaise Coryza Conjunctivitis Cough
Characteristic rash of measles
Erythematous and maculopapular
Starts at head and spreads to trunk and limbs over 3-4 days
Koplik spots
Small red spots w/ blueish-white centres
Infection of measles
Spread by airborne or droplet transmission
Individuals are infectious from beginningof prodromal period to 4 days after rash appears
Incubation period of measles
10 days (ranges between 7-18 days) w/ a further 2-4 days before rash appear
Which features are strongly suggestive of measles
Rash for at least 3 days
Fever for at least 1 day, and
At least one of the following - cough, coryza or conjunctivitis
Most common complications of measles
Otitis media Pneumonia Diarrhoea Convulsions Encephalitis Subacute sclerosing pan-encephalitis (SSPES)
Different forms of measles encephalitis
Post-infectious encephalitis ~ one week after onset of rash
Measles inclusion body encephalitis
SSPE
Measles inclusion body encephalitis
Occurs in immunocompromised patients
Characterised by deterioration of consciousness, seizures and progressive neurological damage
SSPE
Rare, fatal, late complication of measles
Influenza
Acute viral infection of the respiratory tract w/ freq antigenic changes
Highly infectious
Can cause explosive outbreaks of febrile respiratory illness and death in those w/ chronic disease
Types of influenza
A, B, C
A & B are responsible for most clinical illness
Incubation period of influenza
1-3 days
Virology of influenza
Segmented -ve strand RNA genome
A and B carry 8 diff RNA segments that code for 11 diff proteins
Subtypes only occur for A viruses
Pathogenesis of influenzas
Initial site of infection is mucosa in respiratory tract
Human influenza viruses prefer the a2,6-linked sialic acid receptors present in URT & LRT
Infection results in degeneration of respiratory epithelial cells wil loss of ciliated tufts, desquamation oedema, hyperaemia and mononuclear cell infiltrates in lamina propria
Risk of complications from influenza
Infection of LRT
Admission to Hosp
Death
At risk group for influenza incl patients w/
Chronic respiratory system diseases Cardiovascular system diseases Endocrine system diseases Hepatic system diseases Renal system diseases Neurological/ neuromuscular conditions
Additional risk factors for influenza
Any condn compromising respiratory functions eg. BMI>40, age >65
Immunosuppression
Antenatal women
Treatment for influenza
Neuraminidase inhibitors:
Oseltamivir - 75 mg BDS for 5 days (10 days if immunocompromised)
Zanamivir - inhalation of powder, 10mg BDS for 5 days
Influenza vaccines
Live attenuated vaccine quadrivalent - children’s
Inactivated influenzas vaccine (quadrivalent: H1N1,H3N2, influenza B two subtypes)
Trivalent adjuvanted inactivated vaccine (age over 65)
Human immunodeficiency virus
HIV-1 and HIV-2 are enveloped viruses
RNA viruses
Reverse transcribe their genome to form double - stranded DNA which integrates into host genomic DNA
Genetic groups of HIV-1
M,N,O,P
HIV life cycle
HIV approaches human CD4 T-lymphocyte Binding Fusion Reverse transcription Integration Transcription Assembly Budding Immature virus breaks free of infected cell Maturation
HIV - Binding
HIV binds w/ glycoproteins to CD4 receptor and another co-receptor protein
HIV - Fusion
Virus fuses w/ host cell and releases RNA
HIV - reverse transcription
Reverse transcriptase converts single stranded RNA into double stranded HIV DNA
HIV - integration
HIV DNA enters host nucleus and is integrated into hosts DNA using integrase, creating a provirus
HIV - transcription
Provirus becomes active and creates copies of HIV genomic material using RNA polymerase
HIV - assembly
Protease cuts long chain and assembles virus particle containing HIV RNA
HIV-budding
Newly assembled virus buds and takes a part of cells outer envelope
HIV - maturation
Protease completes cutting and HIV can go and infect other cells
HIV transmission
When certain fluids come into contact w/ mucous membranes, damaged issue or is injected into the body
Fluids that can transmit HIV
Blood
Semen
Vaginal secretions
Breast milk
Clinical manifestations of HIV
Fever Pharyngitis Headache Myalgia Arthralgia Malaise Non-pruritic, maculopapular rash on face and trunk Generalised lymphadenopathy
HIV lab tests
CD4 count - measures state of a person’s immune function
HIV virological tests
Serological diagnosis - HIV- 1 virus load
Defects amount of virus present - higher viral load increases risk of disease progression and HIV transmission
Monitors effectiveness of ART
Used during acute infections to detect virus
Measured by HIV-1 RNA PCR
5 C’s
Informed consent Confidentiality Counselling pre- and post-testing Correct test results Connection (linkage to care, treatment and other HIV services)
Management of HIV infection
No cure but effective anti retroviral drugs can control virus and prevent transmission
Anti-retroviral treatment
ARV’s divided into 56 classes, each of which blocks HIV in a diff way
Always 3 or more diff ARV medications for therapy
Examples of ARV medications
Nucleoside reverse transcriptase inhibitors (NRTI’s)
Non-nucleside reverse transcriptase inhibitors (NNRTI’s)
Protease inhibitors (PI’s)
Integrase inhibitors (INSTI’s)
Fusion inhibitors
Chemokine receptors antagonist (CCRS antagonists)
When is AIDS diagnosed
When CD4 count is less than 200
Systemic and organ-spp manifestations of AIDS
Opportunistic infections
Oncological complications
Cardiovascular complication
CNS complications
RSV
Respiratory Syncytial virus
Major cause of LRT infection in young children and adults
Predisposing factors for RSV
Prematurity Low birth weight Congenital cardiopulmonary disease Male sex Attending day care Overcrowding Maternal smoking (tobacco exposure)
Virology of RSV
Pneumovirus
Two genetically distinct subgroups: RSV/A and RSV/B
RSV transmission
Small inoculum is necessary to infect
Trasnmitted via respiratory secretions
Respiratory secretions that transmit RSV
Direct contact
Via fomites
By large droplets
Entry of RSV
Occurs through contact w/ nasal mucosa or eyes
Incubation period of RSV
Varies from 2-8 days
Bronchiolitis pathophysiology
Mucus buildup inside bronchial tube Inflamed tissue Collapsed alveoli Alveoli over-inflated w/ trapped air Smooth muscle tightening around bronchial tubes Necrosis and loss of epithelium
What does the antibody response in infants hospitalised following infecting w/ RSV consist of
Virus - spp IgM (persists for 10 weeks)
Virus - spp IgG and IgA (produced during 2nd week, peak by 3-4 weeks)
Clinical symptoms of bronchiolitis
Expiratory wheezing Cough and coryza Air trapping Nasal flaring Subcostal retractions Cyanosis Fever only in 50% of infants requiring admission
Clinical manifestations of RSV in infants
Bronchiolitis Pneumonia Croup Exacerbation of asthma URT infection Otitis media
Clinical manifestations of RSV in older children and adults
URT infection Croup Laryngitis Bronchitis Exacerbation of asthma Pneumonia (in elderly) Exacerbation of chronic obstructive pulmonary disease
Diagnosis of RSV
Clinical (age, season, clinical manifestations)
Lab diagnosis
Nucleic acid detection (Rt-PCR)
Antibody (acute and convalescent sera in adults)
Lab diagnosis for RSV
Nasopharyngeal aspirate
Nasal swabs
Endotracheal aspirate/ BAAL from those intubated
Passive immunoprophylaxis for RSV
Humanised monoclonal antibody spp for antigenic epitope A and the F protein of RSV
Who is passive immunoprophylaxis recommended to
Bronchopulmonary dysplasia
Congenital Heart Disease
Severe combined Heart Disease
+ve polarity of viruses
Genomic RNA can serve directly as mRNA
-ve polarity of viruses
Genomic sequence is complementary to the mRNA
Group I - Baltimore classification
Double stranded DNA
mRNA is transcribed directly from the DNA template
Example - Herpes simplex
Group II - Baltimore classification
Single stranded DNA
DNA is converted to double stranded form before RNA is transcribed
Examples - parvovirus
Group III - Baltimore classification
Double stranded RNA
mRNA is transcribed from the RNA genome
Examples - rotavirus
Group IV - Baltimore classification
Single stranded RNA (+)
Genome functions as RNA
Examples - common cold (picornavirus)
Group V - Baltimore classification
Single stranded RNA (-)
mRNA is transcribed from the RNA genome
Group VI - Baltimore classification
Single stranded RNA viruses w/ reverse transcriptase
Reverse transcriptase makes DNA and is then incorporated into host genome to transcribe RNA
Example - HIV
Group VII - Baltimore classification
Double stranded DNA viruses w/ reverse transcriptase
Viral DNA replicated through RNA intermediate, RNA serves directly as mRNA or as a template for RNA
Example - Hep B
Where is the genetic material found in viruses
Contained within an coat or capsid, made up of a number of individual protein molecules known as capsomeres
Nucleocapsid
Combined structure of capsid surrounding the nucleic acid
Usually comprises virion
Virion
Entire virus particle
Nucleocapsid surrounded by outer envelope/ membrane
Generally consists of a lipid bilayer originating from the host cell membrane, into which viral proteins and glycoproteins are inserted
Host specificity
Pathogen usually only infects a restricted range of host species
What does the process of attachment of a virus to a host cell depend on
General intermolecular forces, then on more specific interactions between the molecules on the surface of the virus (nucleocapsid in unenveloped viruses and virus membrane in enveloped viruses) and the molecules of the host cell membrane
What happens when a virus has attached to a host cell membranes
The virus particle is carried into the cytoplasm across the plasma membrane
Uncoating
Occurs after virus has entered plasma membrane
Enzymes from the virus or host degrade the capsid releasing the genomic material into the host cell cytoplasm
Eclipse
Stage where virus is no longer infective
How is viral mRNA translated
Using host ribosomes to synthesise viral proteins
The viral mRNA can displace host mRNA from ribosomes so that viral products are synthesised preferentially.
Which viruses don’t have an envelope
Those released during lysis of the infected cell
