Virology Flashcards
Are viruses alive?
No, but are obligate intracellular parasites that infect all forms of life
Potato viruses
Mop-top - yellow spots on centres of leaves Leaf role virus - total yellow leaves Virus X - small and shriveled plant
Nuclear polyhedrosis virus
- foot and moth disease virus
- 6.24 million animals slaughtered in 2001
- cost £20 billion, £333 for every man, woman and child
Total deaths world-wide
- 51.9 million per annum
- 67% other causes
- 33% infectious diseases
10 biggest killers
- Malaria (2.1 m)
- Hepatitis B (1.1 m)
- HIV/AIDS (>1m)
- Measles (>1m)
- Neonatal tetanus (0.5m)
- Whooping cough (0.35m)
- Acute respiratory infections (4.4m)
- Diarrhoeal diseases (3m)
- TB (3.1m)
Infections as killers, developed vs developing countries
- developed: 1%
- developing: 46%
Cancers as killers, developed vs developing countries
- developed: 21%
- developing: 9%
Perinatal and maternal killers, developed vs developing countries
- developed: 1%
- developing: 9%
Circulatory killers, developed vs developing countries
- developed: 46%
- developing: 23%
Respiratory killers, developed vs developing countries
- developed: 8%
- developing 5%
Accidents and other killers, developed vs developing countries
- developed: 23%
- developing: 8%
Virus life cycle
- recognition
- attachment
- penetration
- uncoating
- transcription
- protein synthesis
- replication
- assembly
- lysis and release
Virus growth curve
Latent Period - before first rapid increase Eclipse Period - before second rapid increase Intracellular Virus - first rapid increase Extracellular Virus - second rapid increase
Simple forms of virions
- Naked icosahedral capsid (nucleic acid surrounded by a hexagonal arrangement of protein capsomers)
- Enveloped icosahdral
- Naked helical nucleocapsid (two parallel chains of protein capsomers with nucleic acid between)
- enveloped helical nuclepcapsid
Properties of genome
- type of nucleic acid (DNA or RNA)
- strandedness (single or double stranded)
- linear or circular
- sense: [positive, naked RNA infectious negative, naked RNA non-infectious and needs an enzyme to copy RNA)
- number of segments
- nucleotide sequence
Types of virus DNA molecules
- linear single stranded
- circular single stranded
- linear duplex
- duplex with closed ends
- closed circular duplexes (with and without supercoils)
Types of virus RNA molecules
- linear, single stranded infectious, “positive” strand
- linear, single strand non-infectious “negative” strand
- segmented positive strands
- segmented negative strands
- double strand segmented
- diploid single strands
Sites of virus entry and release
- conjuctiva (eyes)
- respiratory tract
- alimentary tract
- urinogenital tract
- anus
- arthropod
- capillaru
- scratch, injury
- skin
Brain diseases
- HSV
- rabies
- picornaviruses
- HIV
- measles
- mumps
- toga
- bunya
- flavi
- encephalitis
Mouth diseases
- HSV
- coxachie virus
Skin and mucous membrane diseases
- HSV
- VZY
- measles
- rubella
- papilloma
- B19 parvovirus
Liver diseases
- Hepatitis !, B, C, D, E, F
- yellow fever
- CMV
- EBV
Heart diseases
- coxachie virus
Eye diseases
- HSV
- adenovirus
- measles
Nose diseases (common cold)
- rhinovirus
- infleunza
- coronavirus
- RSV
- adenovirus
- parainfluenza
Nose diseases (pharangitis)
- adenovirus
- HSVV
- EBV
- coxachie virus
Nose diseases (lower respiratory)
- influenza
- parainfluenza
- RSV
- adenovirus
Enteric diseases
- rotavirus
- norwalk
- adenovirus
- picornaviruses
Urogenital
- HIV
- HSV
- papilloma
Lymphoid
- EBV
- CMV
General patterns of infection
Acute infection - left peak Persistent infection - constant peak Latent, reactivating infection - larger peaks on each side and smaller in centre Slow virus infection - large peaks on each side and small bumps in middle
Do different diseases have the same incubation periods?
no
Herpes simplex virus features
- envelope glycoproteins
- tegument
- DNA
- lipid envelope
- capsid
Chickenpox
Varicella zoster virus (VZY)
Determinants of viral disease
- target tissue (portal of entry, access of virus to target tissue, tissue tropism of virus, permissiveness of cells for replication)
- viral pathogen (strain)
- immune status (competence of the immune system, prior immunity to the virus)
- cytophathic ability of the birus
- immunopathology
- virus inoculum
- general health of the individual
- genetic make-up of the individual
Mechanisms of virus transmission
- respiratory or salivary spread
- formites (e.g. tissues, clothes)
- sexual contact
- zoonoses (animals, insects [arboviruses])
- blood transfusions, organ transplant, needle sharing
Geographical season
- presence of cofactors or vectors in environment
0 habitat and season for arthropod vectors (mosquitos) - school/university session (close proximity)
- climatic conditions
Respiratory or saliva spread
- flu
- EBV
- mumps
Faecal-oral spread
rotaviruses
Venereal spread
- HSV
- HIV
- warts
Vector
sandfly fever
Vertebrate resevoir
rabies
Vector-vertebrate
yellow fever
Contaminated needs, instruments and blood products etc.
- HIV
- Hep B
- Hep C
Control of viruses
- public health care
- vaccination
- chemotherapy
No vaccines to…
- HIV
- RSV
- rotavirus
Difficulties associated with the design and use of anti-viral drugs
- few biochemical pathways unique to viruses
- therapeutic index often very low
- selection of drug resistant mutants
- many viruses which cause similar diseases have very different modes of replication and may not be sensitive to some drugs
- by the time symptoms appear often chemotherapy is too late to make much difference to clinical course of disease
- expense
Symptoms of influenza
Central - headache Systemic - fever (usually high) Muscular - (extreme) tiredness Joints - aches Nasopharynx - runny or stuffy nose - sore throat - aches Respiratory - coughing Gastric - vomiting
Main source of transmission
- sneeze
- if you breath this in and the dose of virus is not high enough, the innate immune response will deal with it
1918 flu pandemic
- 50 million people died
- more people killed in this than in the first world war
- immune system overreacting, creating a cytokine storm
- if this were to happen now, it wouldn’t have such an effect due to advances in medicine
Influenza virus
- membrane around virus
- Studs - 2 proteins
- hemagglutinin (HA) (recognises receptor, virus gets in)
- neuraminidase (NA) (enzyme, gets virus out)
- these are the things the mmune system reacts to and produces antibodies for (as well as t-cells)
Naming a virus
- virus type
- geographic origin
- strain number
- year of isolation
- virus subtype
Human influenza viruses
A - H1N1 (1918-1957) - H2N2 (1957-1967 - H3N2 (1968 - ) - H1N1 (1977) B - none defined (1940 - ) C - none defined (1949 - )
Virus genome
- can only replicate in living cells
- virus has segmented genome
- 8 segments each codes for a particular gene
Influenza replication
- virus binds and enters cell
- enters the endosome
- endosome acidified
- virus uncoated
- delivers genome to a site where it can produce new copies of viral proteins and RNA
- segments of genome into nucleus
- RNA replication
- copying to mRNA
- translation
- assemble these components into new viral particles
- viral proteins sent to golgii
- appear on cell surface
- come together
- export genomes produced to cytoplasm
- cell membrane buds off
- exit the host cell
- another virus can infect a new host cell
Antigenic drift
- existing antigens are subtly altered
- causes slight flu mutations year on year, from which humans have partial, but not complete, immunity
Antigenic shift
two or more strains combine to produce a new strain
HA trimer
- a target
- inserted into membrane of host cell
- receptor cite binds to sialic acid
- conformational change
Neutralisation sites on influenza virus HA
- sialic acid (binding site)
- fusion peptide
- sticks into cell membrane
- acidification
Why do amino acids surround Influenza HA
- to keep access open to the cell
- gives them an advantage when they do change
Different species harbour different strains of the flu virus
- flu viruses mutate over time causing small changes to proteins on their surface called antigens
- if the immune system has met a particular strain of the virus before, it is likely to have some immunity; but if the antigens are new to the immune system, it will be weakened
- viruses which infect birds and pigs don’t usually infect humans
- but birds can infect pigs and humans can infect pigs
- the pig is the melting point for the production of these arranged viruses
Genetic reassortment
- pigs = swine
- swine serve as “mixing vessels” for the genes of avian, porcine and human forms of the influenza virus
- in the host pig, the avian and mammalian viruses can share (reassort) their genes and so create new strains of flu
- swine have probably played an important role in the history of human influenza epidemics
- segmented genomes
- pig infected with both strains (reassorted)
- if this codes for a surface protein then our immune system has never seen this virus before
- no protection
- shift
PB
polymerase for replication of viral genome
Asian flu
- cell infected with human (H1N1) and avian strains of influenza
- reassortment of vRNAs
- mixture of viruses, including H2N2 virus
- PB1, HA and NA genes from avian strain, kept 5 genes from circulating human strain (H3N8, H1N1, H2N2 and H3N2)
Vaccination discovery
- 1770s
- Edward Jenner heard a milkmaid boast that she would never have smallpox because she had already had cowpox
- 1796 Jenner took pus from hand of milkmaid with cowpox, inoculated an 8 year old boy with it and six weeks later did the same with smallpox
- boy did not catch smallpox
Vaccine
- a biological preparation that improves immunity to a particular disease
- typically contains a small amount of an agent that resembles a microorganism
- the agent stimulates the immune system to recognise as foreign, destroy it and remember it so the immune system can more easily recognise and destroy these microorganisms that it later encounters
Side effects of vaccines
- it has been disproven that any deaths have bee related to the flu vaccine
- actual side effeccts include swelling, redness, pain on injection site, fever, headache, muscle ache
- will clear up in 48 hours
Neuraminidase
- cleaves sialic acid
- virus can escape cell surface, releasing virus from the cell
- relenza binds in this active site
Tamiflu
- contains oseltamivir, an antiviral drug that slows the spread of influenza virus between cells in the body by stopping the virus from chemically cutting ties with its host cell
- median time to symptom alleviation is reduced by 0.5-1 day
- taken orally in capsules or as a suspension
- it has been used to treat and prevent influenza A and B in over 50m people since 1999
Zanamivir
- neuraminidase inhibitor used in treatment of prophylaxis of influenza
- binds to active site of neurominidase, rendering influenza virus unable to escape its host cell and infect others
- reduces time to symptom resolution by 1.5 days if therapy started within 48 hours of symptoms
- better than tamiflu
- spray, protects airways
H1N1 vs H5N1
- H1N1 easily spread, rarely fatal
- H5N1 spreads slowly, often fatal
- they differ in the extent at which they penetrate the lungs
- sneezing can cause easy spread
- coughing spreads less but can be fatal due to inflammation in lungs
HIV/AIDS
- acquired immunodeficiency syndrome
- recognised in 1981
- major worldwide epidemic
- caused by HIV virus
- leads to destruction of cells of immune system e.g. CD4+T cells
- destroys the body’s ability to fight infections and certain cancers
- an individual with a CD4+T cell count less than 200/cells per cubic mm of blood
AIDS pandemic
- killed 2.1 million people, including 330,000 children in 2007
- sub-saharan africa is the worst effected region (in 2007 it accounted for 68% of global total)
Initial spread of AIDS
- initially amongst homosexual community
- blood transfusions no longer a problem
- major causes: homosexual and intravenous drugs
- rest of world mainly heterosexual and blood transfusions
What type of virus is HIV?
- a lentivirus (retrovirus) causes slow chronic diseases
- HIV-1 particle composed of 2 copies of +ve single stranded RNA (codes for virus’ 9 genes enclosed by capsid of viral protein p24)
- RNA bound to nucleocapsid containing virion proteins
- matrix surrounds capsid (2 layers of phospholipids (taken from host cell membrane when virus particle buds out)
What are the virion proteins RNA binds to in HIV?
- reverse transcriptase
- protease
- integrase
Viral envelope of HIV
- contains trimeric proteins ecoded by Env gene
- bud composed of glycoprotein (gp) 120, and the stem consists of gp41
- this glycoprotein complex enables the virus to attach to and fuse with target cells to initiate the infectious cycle
HIV lifecycle
- Binding (adsorption)
- HIV binds to receptors (glycoproteins gp120) on surface (trimeric envelope) of a CD4 cell
- can be stopped by CCr5 antagonist or post-attachment inhibitors - Fusion
- HIV envelope and CD4 cell membrane fuse, which allows HIV capsid to enter the CD4 cell
- mediated by gp41
- can be stopped by fusion inhibitors - Reverse Transcription (uncoating)
- cytoplasm of CD4 cell
- HIV releases and uses RT and various viral proteins to convert its genetic material (HIV RNA) into HIV DNA
- the conversion allows HIV to enter CD4 cell nucleus and combine with cell DNA
- can be stopped by non-nucleoside RT inhibitors or nucleoside RT inhibitors
- extremely error-prone,, can cause drug resistance or allow virus to evade body’s immune system - Integration
- inside CD4 cell nucleus
- HIV releases integrase and uses it to insert its viral DNA into the DNA of the DNA of CD4 cells
- can be stopped by integrase inhibitors - Replication
- HIV begins to use the machinery of the CD4 cell to make long chains of HIV proteins
- the protein chains are the building blocks for more HIV - Assembly
- new HIV proteins and HIV RNA move to the surface of the cell an assemble into immature HIV - Budding
- immature HIV pushes itself out of the host CD4 cell
- the new HIV releases protease which acts to break up the long protein chains that form the immature virus
- the smaller HIV proteins combine to form mature HIV
- stopped by protease inhibitors
Immature HIV
non-infectious
Following HIV infection
- immune system begins to fail
- leads to life-threatening opportunistic infections and progression towards AIDS
- eventually most HIV-infected individuals develope AIDS
Which vital cells in the immune system does HIV infect?
T-cells, monocytes and macrophages
HIV replication in helper T-cells (CD4+)
- highly productive and cytopathic
- when CD4+T-cell numbers decline below critical levels, the body becomes more susceptible to opportunistic infections and malignancies
How is level of HIV determined?
patient’s CD4+T-cell count and level of HIV in blood
Without treatment of HIV
- 9 out of 10 persons will progress to AIDS within 10-15 years
- many progress much sooner
Early incubation period
This period is asymptomatic and usually lasts between two and four weeks.
Acute infection
This lasts an average of 28 days and can include symptoms such as fever, lymphade-nopathy, pharyngitis, rash, myalgia,
malaise, and esophageal sores.
Latency stage
This shows few or no symptoms and can last anywhere from two weeks to up to twenty years and beyond.
AIDS
Symptoms of opportunistic infections associated with a
progressive decrease of the CD4+ T cell count and an increase in viral load. Without antiretroviral therapy, death normally occurs within a year after the onset of AIDS.
Roles of T4 cell
- stimulates B cells
- proliferation into memory clone
- activation of cytotoxic T cells (T8 cells)
- late suppression of B and T8 cells
The boosted PI concept
- ritonavir is used for its antiviral activity (due to its major side effects at full dose) but for its pharmacokinetc efffects
- it strongly inhibits CYP450, and inhibits the metabolism of other Pis
- used at low dose allows for reduction in the dose (less pills and/or frequency) of other PIs
- thus serum levels much higher than unboosted regimens
- all PIs, except nelfinavir, can be administrated in a ritonavir-boosted regimen
Lopinavir/ritanovir (kaletra)
only co-formulated capsule
Ebola outbreak 2015
- west africa
- recent rapid fall in cases has stalled in sierra leone and guinea
Hidden disease spread
high proportion of new ebola cases in people who are not on the ‘contact lists’ of previously infected patients means that new cases are still going undetected
Ebola virus
- formerly zaire virus
- zoonotic virus - bats the most likely reservoir, although species is unknown
- spillover event from infected wild animals (e.g. fruit bat, monkey) to humans followed by human-human transmission
Ebola virus transmission
- virus present in high quantity in blood, body fluids and excreta of symptomatic EVD-infected patients
- human-to-human transmission
- contact with blood, fluids or meat of an infected animal (limited evidence that dogs become infected, no reports of dogs or cats becoming sick or transmitting)
Opportunities for human-to-human transmission
- Direct contact (through broken skin or unprotected mucous membranes) with an EVD-infected patient’s blood or body fluids
- Sharps injury (with EVD-contaminated needle or other sharp)
- Direct contact with the corpse of a person who died of EVD
Indirect contact with an EVD-infected patient’s blood or body fluids via a contaminated object (soiled linens or used utensils)
Ebola detective 1976
- Peter Piot
- received a sample sent in hand luggage from belgian doctor bases in Congolese forest
- sample consisted f blood from a missionary ill with unknown disease
- worm like structure discovered
- hemorrhagic fever virus discovered in 1967
Ebola ribonucleocapsid proteins
- nucleoprotein (NP) Gene 1
- viral protein 53 (VP35) Gene 2
- viral protein 30 (VP30) Gene 5
- Polymerase L - gene 7
Ebola matrix proteins
- viral protein 40 (VP40) Gene 3
- viral protein 24 (VP24) Gene 6
Ebola membrane protein
Glycoproteins (GP) Gene 4
Ebola secreted protein
Secretory glycoprotein (sGP) Gene 4
Virus entry and replication in host cells
- Viral surface spikes recognize and bind surface receptors of host
- Virus enters cell via endocytosis
- Release of nucleocapsid into cytoplasm
- Transcription (viral RNA -> polyadenylated, monocitronic mRNA)
- Translation and buildup of viral proteins, primarily NP
- Budding and release of viruses
- Host Cell – dies (intracytoplasmic vesiculation, mitochondrial swelling, organelle breakdown)
Ebola virus diagnosis
Real time PCR (RT-PCR)
- used to diagnose acute infection
- more sensitive than antigen detection ELISA
- identification of specific viral genetic fragments
- performed in select CLIA-certified laboratories
RT-PCR sample collection
- volume: minimum of 4ml whole blood
- plastic collection tubes
- whole blood preserved with EDTA
Ebola: nonspecific early symptoms progress to…
- hypovolemic shock and multi-organ failure
- heamorrhagic disease
- death
Ebola: how long does it take to improve non-fatal cases after symptoms onset?
6-11 days
Ebola: Fatalily
- associated with more severe early symptoms
- rates of 70% have been historically reported in rural africa
- intensive care may increase survival rate
Destruction of immune system
- infects mononuclear phagocytes with fibroblastic reticular system (associated with lymph nodes)
- failure of early T-cell activation
- disrupts antigen trafficking and cytokine production
- extensive apoptosis of blood leukocytes
- lymphopenia (reduction in lymphocyte#) and severe damage to lyphoid tissue - macrophages and circulating monocytes help transmit virus to other tissues
- VP35 protein - type IFN antagonist
- combats the hst interferon response (possibly enhancing the replicative ability of the virus)
Intensive care effect on ebola
- under the worst conditions, 90% mortality rate
- intensive care maybe 20% or less
EVD therapeutic medications
Zmapp
- three chimeric human-moise monoclonal antibodies
Tekmira
- lipid nanoparticle small interfering RNA
Favipiravir
- oral RNA-dependent RNA polymerase inhibitor
