Virology Flashcards
Infectious, obligate intracellular parasite
Virus
viral particle
virion
Can a virus have both DNA and RNA?
no (one or the other)
What are virions composed of?
-RNA or DNA
-protein coat
-Envelope
virus size?
Very small
-Pass 0.2 µm filters
If the cell is lysed to spread the virus, it will not have what?
an envelope
True or false:
Viruses lack the complex energy-generating and biosynthetic systems necessary for
independent existence.
True
what are the simplest biologically active agents?
-viroids
-prions
-Single small molecule of non-coding RNA
-Plant pathogens
Viroids
Single protein molecules capable of infection
Prions
HIV —> enzyme —-> ________ transcriptase (RNA to DNA)
reverse
HIV infects what type of cells?
CD4
Infectious progeny virus particles, called _________ , are formed by de novo self-assembly from newly synthesized components.
Virions
What is the vehicle for transmission of the viral genome to the next host cell or organism, where its disassembly initiates the next infectious cycle.
-A progeny virion assembled during the infectious cycle
How can viruses be visualized?
-electron microscope
-x-ray
What is the size of viruses?
10^2 nanometers
Steps of viral infectious cycle?
-Attachment
-Penetration
-Uncoating (envelope)
-Replication: RNA –> mRNA –> more RNA
–> DNA —> mRNA
-Maturation (Assembly)
-Release (Death of cell = apoptosis)
What does ICTV stand for?
International Committee on Taxonomy of Viruses
Organization tasked with viral nomenclature
International Committee on Taxonomy of Viruses (ICTV)
virus taxonomy:
virus order –>
-virales
virus taxonomy:
subfamily —>
-virinae
virus taxonomy:
genus —->
-virus
viruses are not classified beyond _________.
species
-subspecies-level assignments or “types” are not recognized by the ICTV
What are the two systems used for viral taxonomy?
-International Committee on Taxonomy of Viruses (ICTV)
-Baltimore classification
What is Baltimore classification based on?
7 groups based on nucleic acid (DNA, RNA), strandedness (single, double), sense (+,-), method of replication.
BC for Adeno, Herpes?
dsDNA -1
BC for Parvo?
ssDNA - 2
BC for Reo?
dsRNA - 3
BC for Picorna?
(+) ssRNA - 4
BC for Orthomyxo?
(-) ssRNA - 5
BC for Retro?
ssRNA-RT - 6
BC for Hepadna?
dsDNA-RT - 7
***H2A2P2P2y (HAPPy) —>
DNA viruses
Hepadnaviridae
Herpesviridae
Adenoviridae
Anelloviridae
Parvoviridae
Papillomaviridae
Polyomaviridae
Poxviridae
-Usually asymptomatic but can be acute or chronic; self-limiting or fatal
-Liver damage; may require transplant
-Fatal = co-infection with hepatitis D
Hepadnavirus (Hep B)
*DNA virus
What are the serology markers associated with HBV that can be tested?
-Contains surface antigens (HBsAG)
-Core antigen (HBcAg)
-Another core: (HBeAg)
-Also test for HbsAb, HbeAb
What are the two HBV serology markers that come from the envelope?
HBsAG and HBeAG
What HBV serology markers indicate an infected state?
HBsAG
-also HBeAG
What happens during the “window period” for HBV?
-conversion of surface antigen markers to surface antibody markers
-isolated Anti-HBc following acute infection (see chart on slide 14)*
Anti-HBs is associated with…
-resolved HBV infection (will still have total anti-HBc) or,
-HBV vaccination
Serologic Profiles - HBV:
Early acute hepatitis B…
HBsAg
(maybe HBeAg)
Serologic Profiles - HBV:
Acute or chronic HBV…
-HBsAG
-HBeAg
-HBcAb
Serologic Profiles - HBV:
Chronic HBV carrier…
-HBsAg
-HBeAg
-HBcAb
Serologic Profiles - HBV:
Recovery with immunity…
-HBsAb
-HBeAb
-HBcAb
Serologic Profiles - HBV:
Distant infection or vaccine…
-HBsAb
What is the first HBV marker after exposure?
HBsAg
*always indicates current infection
True or false?
Multiple blood infections can cause both HBsAg and HBeAb.
True, but normally not possible
HAV, HCV, and HEV are DNA or RNA viruses?
are they related to each other?
-RNA
No, unrelated
-Often children (daycare settings)
-Occasional epidemics
-Person-to-person
-Acute onset; may take months to recover
-Shed in large numbers in feces
-Low mortality/ no liver damage
-Vaccine available
-Routine vaccination recommended for children
HAV
What are the most frequent food sources of HAV?
-Water, shellfish, and salads are the most frequent sources
-Contamination of foods by infected workers in food processing plants and restaurants is common.
How is HCV transmitted?
blood and body fluids
What was the old name for HCV?***
nonA, nonB
What virus was predicted and sequenced before being viewed with EM?
HCV
True or false:
There is a vaccine available for HCV.
False
New drugs available for HCV, per WHO antiviral drugs can cure ____% of persons-reducing risks of cirrhosis and cancer
95
Long term effects of Hepatitis C:
~___% spontaneously clear their infection within 6 months without treatment
~___% develop chronic HCV
30, 70
Of the 70% of people who develop chronic HCV,
-____% cirrhosis within 20 years
-_____% increased risk of liver cancer (yearly)
-____% increased risk of hepatic decompensation (yearly)
-15-30
-1-5
-3-6
What are the different Herpes virus types?
HSV-1, HSV-2, VZV, EBV, CMV
____ % of American adults have been infected with HSV-1; ____ % have HSV-2 infections
Most are asymptomatic
Oral, genital, neonatal, encephalitis, ocular.
80
20
-Latent viral genomes in peripheral nervous system
-Infect epithelial cells
-Multi-nucleated giant cells at the base of lesion
HSV
How are HSV viruses released?
Lyse, releasing clear fluid containing viruses
What are the antivirals for HSV?
acyclovir, valacyclovir, and foscarnet (cases where acyclovir resistance suspected)
-Most people have been exposed.
-Vast majority asymptomatic, but can recur in compromised patients
-May be life-threatening to immunocompromised, transplant patients, and fetuses.
CMV
CMV:
1 in ____ have been infected by age five ___ % of adults by age 40 have been infected with CMV
3, 50%
How long does CMV stay in the body?
stays in the body for life and can reactivate
What is a distinguishing feature of CMV?
It can be found in almost any part of the body. Most viruses have more specific targets.
Examples: can detect in blood, eye (CMV retinitis), pneumonia, gastrointestinal tract, brain
What type of virus is Epstein-Barr Virus (EBV)?
Herpesviridae
-dsDNA
How is EBV spread?
Spread via saliva
Infects oropharyngeal epithelial cells and then enters B-cells
~1 in 10^6 B cells harbors EBV
EBV:
Latent infection of primary B-cells: Virus infects non-dividing B cells with very high efficiency, then triggers these cells to proliferate and sustains their proliferation, resulting in cellular ____________.
immortalization
Most EBV-associated disease is due to __________ infected cells.
latently
True or false:
Once infected with Epstein-Barr virus, a lifelong carrier state develops whereby a low grade infection is kept in check by the immune defenses.
True
EBV:
Low grade virus replication and shedding can be demonstrated in the epithelial cells of the _________ of all seropositive individuals.
pharynx
EBV is able to immortalize ____-lymphocytes in vitro and in vivo.
B
What are the diseases associated with Epstein-Barr Virus (EBV)?
-Infectious Mononucleosis
-Burkitt’s lymphoma
-Nasopharyngeal carcinoma
-Lymphoproliferative disease and lymphoma in the
immunosuppressed
-Oral leukoplakia in AIDS patients
-Chronic interstitial pneumonitis in AIDS patients
EBV (Epstein Barr Virus):
-Most adults Ab pos.
-Symptoms last a few weeks; malaise may be prolonged; young adults
Infectious mononucleosis
EBV (Epstein Barr Virus):
Rare highly aggressive non-Hodgkins lymphoma
Usually fata if not treated rapidly
Burkitt’s lymphoma/B-cell lymphoma
What is the test for Mono?
heterophile antibodies (Monospot test)
Test that uses horse red blood cells
-agglutination = positive test
-some tests replace RBCs with latex beads
Monospot test (EBV testing)
Chickenpox =
varicella
Shingles =
Zoster
VZV: varicella zoster virus
____% of adults have Abs.
90
Papillomas =
warts
> 70 types of these small, DNA viruses exist
Associated with plantar warts
-Others associated with condylomata acuminata
-Still others are associated with cervical cancer
Human papillomavirus (HPV)
At what age should women begin cervical cancer testing (screening)?
21
Women aged ___ to ____, should have a Pap test every 3 years. HPV testing should not be used for screening in this age group unless it is needed as after an abnormal Pap test result.
21-29
Beginning at age ___ , women should be screened with a Pap test combined with an HPV test every 5 years as long as the test results are normal. This is called co-testing and should continue until age ___.
30, 65
HPV and cervical cancer:
HPV has early genes: _____________: involved in viral replication and transcription.
Late proteins are ___, ____ used for protein coat
E6, E7, E1, E2
L1, L2
-Instead the circular HPV genome inserts itself into host chromosome.
-E1 & E2 may be disrupted, but E6 and E7 can be expressed.
HPV and cervical cancer:
E_ and E_ gene products inactivate host anti-oncogenes (p53, pRB)
6, 7
What are the three types of illnesses that are causes Adenoviruses?
-Respiratory illness
-Conjunctivitis
-Gastroenteritis
Adenoviruses cause more severe disease in immunocompromised including ________.
viremia (virus in blood)
-Outbreaks occur in long term health care facilities
Polyomaviridae has what type of DNA?
Circular DNA
-Replication fork and RNA primers
Polyomavirdae:
-Causes progressive multifocal leukoencephalopathy (PML)
-Inflammation of the white matter (leuko-) of the brain (-encephalo-) at multiple locations (multifocal)
JC Virus
-Fetal loss
-Erythema infectiosum
“Slapped cheek syndrome”
-Aplastic crisis
(Lysis of erythrocytic precursors)
Parvoviridae: Parvovirus B19
The 3 Poxviridae viruses?
-Smallpox
-Monkeypox
-Molluscum Contagiosum Virus (MCV)
*dsDNA genome
-Global pandemic
-Targets are CD4+ T cells and other WBCs
Retrovirus (HIV)
What is a key feature of HIV?
reverse transcriptase
HIV structure?
-3 layer structure
-Center: 2 identical copies of ssRNA
(Reverse transcriptase)
-Capsid
-Envelope (gp)
Retroviruses:
(+) Strand RNA with ____ Intermediate
DNA
Retroviruses:
dsDNA intermediate is produced from genomic RNA by a viral RNA-dependent DNA polymerase called ________________.
DNA then serves as the template for viral mRNA and genomic RNA synthesis.
reverse transcriptase (RT)
Transmitted by mosquitoes, ticks, or arthropods.
Arbovirus
common members of Arbovirus?
-Flavivirus
-Togavirus
-Bunyavirus
Yellow fever
West Nile virus
Zika virus
Dengue fever
Japanese encephalitis
Flavivirus
Ross River virus
Eastern equine virus
Western equine virus
Togavirus
California encephalitis
La Crosse virus
Jamestown Canyon virus
Bunyavirus
The prototype norovirus is virus.
Norwalk
-These are small, non-cultivatable viruses that cause diarrhea in children and adults
-Transmission is via ingestion of virus in food, vomitus, or water (resists disinfection).
Norovirus
How is Norovirus diagnosed?
by symptoms or RT-PCR
Most common cause of acute gastroenteritis in the United States.
Most common cause of foodborne-disease outbreaks in the United States
Norovirus (Norwalk)
-Each year, it causes about 21 million illnesses and contributes to about 70,000 hospitalizations and 800 deaths.
Common locations for Norovirus outbreaks?
-Cruise ships
-Daycares and schools
-Hospitals and long-term care facilities
-Restaurants
-Most common cause of gastroenteritis in infants/children
-Fecal/oral transmission
Common in daycares
-Self-limiting immunocompetent individuals, but can cause fatal dehydration
Rotavirus
What are the best methods for detection of Rotavirus?
Antigen detection or PCR
What is the treatment for Rotavirus?
supportive therapy
Vaccination is available for Rotavirus.
Prior to vaccination ~___% of US children would have disease by 5 years.
80
-Rare but deadly respiratory disease
-transmitted by infected rodents through urine, droppings, or saliva.
-Sin nombre (SNV)
Hantavirus pulmonary syndrome (HPS)
How do humans contract Hantavirus pulmonary syndrome (HPS)?
breathing in aerosolized virus
What are the symptoms of Arboviruses?
-Frequently asymptomatic
-Neuroinvasive and non-neuroinvasive forms of disease
What are the symptoms of neuroinvasive arboviruses?
headache, stiff neck, muscle pain, confusion or disorientation, weakness and seizures.
What are the symptoms of non-neuroinvasive Arboviruses?
fever, headache, muscle aches, joint pain, upset stomach, nausea,vomiting, diarrhea, and rash
How are Arboviruses diagnosed?
-Serology – IgM or paired samples for IgG for serum or IgM in CSF
-PCR – viral detection (frequently performed by public health labs or CDC,
May have limited sensitivity because nucleic acid is only present during the initial infection timeframe
-Picronaviridae
-Common cold
-Usually upper respiratory infection
Lower respiratory less common
Rhinovirus
-Incubation period 12-72 hours
-Very contagious
Person-to person and aerosol
-Can occur year-round but highest incidence is October to March
-Usually supportive therapy (treat symptoms and rest)
Rhinovirus
Rhinovirus cannot be distinguished from _____________ with PCR*
Enterovirus
What are other infections of Non-Polio enterovirus?
-Conjunctivitis
-Foot and mouth disease
-Meninigitis and encephalitis
-Myocarditis and pericarditis
-Acute flaccid parlysis
-Inflammatory muscle disease
*most common in infants, children, and immunocompromised
What are the sources of Non-Polio Enterovirus?
-feces (stool)
-eye, nose, and mouth secretions (such as saliva,
-nasal mucus, or sputum)
-blister fluid
How is non-polio enterovirus transmitted?
-Close person-to-person contact
-Contact with contaminated surfaces
-Fecal-oral route
Cold-like illness, bronchiolitis, or pneumonia in severe cases
Paramyxovirus: Respiratory Syncytial Virus (RSV)
What are the high risk groups for severe disease from RSV?
-premature infants and very young infants, especially those 6 months and younger
-children younger than 2 years old with chronic lung or heart disease
-Immunocompromised or congenital diseases that affect ability to clear mucus secretions
-Common in young children (also elderly)
-Nosocomial problem in nurseries
-Yearly outbreaks in late fall and winter
Paramyxovirus: Respiratory Syncytial Virus (RSV)
How is RSV transmitted and How long are people contagious?
-Transmitted through droplets
-People are contagious for 3 to 8 days.
-In infants and immunocompromised-contagious for as long as 4 weeks.
RSV can survive for________ on hard surfaces.
many hours
How is RSV treated?
-Primarily treat symptoms
-Ribavirin (very expensive) may be used in critical cases.
In high risk groups for RSV, what can be used to prevent infection?
palivizumab (very expensive)
How many types of Human parainfluenza viruses are there?
Four types – 1, 2, 3, 4
Human parainfluenza viral infections are most common in…
infants, children, and immunocompromised
Human parainfluenza viruses:
US-infections associated with ______ are seen more commonly in odd-numbered years and HPIV-__ and HPIV-___ are seen annually (per CDC).
HPIV-1,
2,3
Paramyxovirus:
HPIV ______ – upper and lower respiratory infections, Croup
1 & 2
Paramyxovirus:
HIPV ___ – bronchiolitis, bronchitis, and pneumonia.
3
Paramyxovirus:
HIPV ____ – less common—mild to severe respiratory infection.
4
How is parainfluenza transmitted?
Direct contact with infectious droplets or by airborne spread when an infected person breathes, coughs, or sneezes.
How long does parainfluenza remain infectious in droplet form?
for over an hour and on surfaces for a few hours depending on environmental conditions.
When are people most infectious with parainfluenza?
What is the treatment?
-Infected people are most contagious during early stages
-No vaccine and supportive treatment (treat symptoms)
–Relatively new discovered in 2001
-Causes upper and lower respiratory infection in people of all ages
Human metapneumovirus
Human metapneumovirus
estimated incubation?
-Estimated Incubation 3-6 days
-Late winter and early spring
most activity
How is Human metapneumovirus spread?
What is the treatment?
-Person-to-person spread through secretions
-Supportive therapy
How can Coronaviruses be detected?
Can be detected by multiplex PCR panels (e.g. BioFire FilmArray)
Common human coronaviruses include what types?
229E, NL63, OC43, and HKU1
What are the effects of common human coronaviruses?
-mild to moderate upper-respiratory tract illnesses, similar to the common cold
-Can cause lower respiratory disease in immunocompromised or people with heart issues
How are coronaviruses transmitted?
-Usually person-to-person transmission
-Infections occur most frequently in the fall and winter.
What are 3 severe coronaviruses (betacoronaviruses)?
-SARS CoV-1
-MERS
-SARS CoV-2
-Causes SARs (causes severe acute respiratory syndrome)
-First infections appeared in China
-Outbreak in 2003, no cases since 2004
-8,098 sick, 774 died per CDC
-Spread close person-to-person contact
-Select agent
Coronaviruses:
SARS CoV-1
Coronaviruses:
-Middle East Respiratory Syndrome
-Transmitted from camels to humans in the Arabian peninsula, occasional human-to-human spread
MERS
Coronaviruses:
Range in symptoms: Asymptomatic, lower respiratory infection, respiratory distress and death Still ongoing.
MERS
Coronaviruses:
-Causes COVID-19
-Declared pandemic in 2020
-Wide range of symptoms from asymptomatic to severe respiratory disease and death
-Very high transmission rate
SARS CoV-2
What is the incubation period for SARS CoV-2 ?
(the time from exposure to development of symptoms) ranges from 2–14 days.
As of 4/22/21, SARS CoV-2 worldwide cases?
Deaths?
Death rate?
-141, 000,000 cases worldwide
-3.01 million deaths
~2.9% death rate
How are coronaviruses diagnosed?
-Has been isolated from respiratory, blood, urine, and stool specimens
-Current diagnostic tests are for respiratory specimens:
Investigational treatments (varying reports on success) for SARS CoV-2?
-Remdesivir (Originally created/used for Ebola,
IV antiviral – inhibits viral transcription)
-Hydroxychloroquine and Chloroquine
(Usually treatment for Malaria)
-Convalescent plasma
(Plasma transfusion with plasma from recovered patient)
-Methylprednisone
-Monoclonal antibodies (FDA EUA recently for using as sole treatment)
What are the benefits of mRNA vaccines?
-non-infectious
-non-integrating
-can be given repeatedly
-rapid, inexpensive, and scalable production
Orthomyxovirus:
Influenza virus __ and ___ cause seasonal epidemics
A, B
Orthomyxovirus:
Influenza ___ had caused pandemics = e.g. 20 million World War I
A
Orthomyxovirus:
How does influenza B symptoms compare to A?
milder
Orthomyxoviruses kills _________/year in U.S.
20,000 – 40,000
What is the incubation period for Orthomyxovirus?
1-4 days
How long is Orthomyxoviruses contagious?
contagious one day before symptoms to 7 days after symptoms appear
How are Orthomyxoviruses transmitted?
Person to person and droplets
What are the treatment options for Orthomyxoviruses?
-Four FDA cleared drugs
Oseltamivir (Tamiflu), zanamivir (Relenza), and peramivir (Rapivab), and the newest one-baloxavir marboxil (Xofluza)
-Amantadine and rimantadine – not currently recommended because of resistance in the current circulating strains
H and N are viral __________ proteins.
envelope
H =
hemagglutinin - viral attachment to sialic acid cell receptors
N =
neuraminidase - assist in release from infected cell and spread through mucus to adjacent cells
Antigenic _______– small changes; happen continuously
antigenic _______– major changes (new “H” and “N”); happen suddenly
drift
shift
Specimens for Orthomyxoviruses?
-Specimen quality and preservation
-Viral transport media
-Source depends on virus suspected
What is the transport for Orthomyxoviruses?
-Transport to lab on ice
Set up ASAP for culture
-Store at 4oC for <5 days
-PCR store per package insert
-Most can be frozen but must be at -70 C
Viral transport Media:
Designed for viruses, chlamydia, mycoplasmas and ureaplasmas.
VTM or UTM
Viral transport Media:
UTM includes?
-Hank’s Balanced Salts
-Proteins and nutrients
-Sucrose (cryoprotectant)
-pH buffered with HEPES
-Phenol red indicator
-Vancomycin, amphotericin B and colistin (not antibiotics that inhibit DNA synthesis)
-Dependent on the brand or type on which antibiotics and antifungals are uses.
Tube culture:
-Used to detection many viruses
-Patient specimen is added to a tube of growing cells
-Monitored daily for ___ days and weekly thereafter for 2-6 weeks depending on specimen.
7
Morphological changes in cells caused by viral infection.
Cytopathic Effects (CPE)
Cytopathic Effects (CPE):
Cultures held for ___ weeks
Up to ___ weeks for tissues.
2, 6
__________ antibody staining may be used to confirm viruses found by culture:
Respiratory viruses
HSV
Enterovirus
CMV
Fluorescent
Hemadsorption for Influenza….
-An influenza-infected cell contains virally encoded glycoprotein hemagglutinins in cytoplasmic membrane.
-Add RBCs to culture medium
-A modification of the conventional cell culture technique for rapid detection of viruses in vitro.
-Inoculation of the clinical specimen on to cell monolayer grown on a cover slip in a shell vial culture tube, followed by low speed centrifugation and incubation.
Shell Vial Culture
Shell Vial Culture:
Low speed centrifugation enhances viral…
infectivity to the susceptible cells.
-It is thought that the minor trauma to the cell surface produced as a result of low speed centrifugation mechanical force enhances the viral entry in to the cells, which in turn reduces the total time taken for the virus to produce infection of cells
Shell Vial Culture:
Detection?
FITC-conjugated virus-specific antibody stains
What are the limitations for Direct Fluorescent Antibody (DFA) Staining?
-Must have heavy active infection
- Will not detect all dual infections
Direct Fluorescent Antibody (DFA) Staining:
RSV is what color?
yellow
Direct Fluorescent Antibody (DFA) Staining:
Flu A (FITC) color?
green? (pos)
Direct Fluorescent Antibody (DFA) Staining:
What color is Flu B (Rhodamine)?
red? (pos)
Direct Fluorescent Antibody (DFA) Staining:
Parainfluenza 1-3 (FITC) Adenovirus (Rhodamine) color?
no color (neg)
Classic Virology or Molecular Virology?
-Not routinely used except for tissues and some fluids
-Potential agent is unknown
-Discovery of novel viruses
Inexpensive
-Detects active virus/can be used to monitor treatment
-Viral susceptibility testing
Classic Virology
Classic Virology or Molecular Virology?
-Most common diagnostic method
-Viruses that do not grow in culture
e.g. EBV, HBV, HCV
-More sensitive
-Faster detection and reporting
-More accurate quantification of virus present (Necessary for HIV monitoring
-Minimizes risk to workers for specimens containing highly pathogenic viruses
Ebola, Small POX, SARS (SARS-CoV-1), MERS, COVID-19 (SARS-CoV-2)
Molecular Virology
Two examples of Direct Detection?
-EIA
(Useful for rotavirus)
-Immunostaining
(DFA (Direct Fluorescent Antiody) stain specimens directly Issues with sensitivity)
What are viral serologic assays used for?
-Diagnosis of infections with non-culturable organisms (hepatitis, West Nile Virus and other arboviruses)
-Determination of immune status (Rubella, measles, HBV, HIV)
-Epidemiologic or prevalence studies
Therapy for HSV, VZV?
Acyclovir
Therapy for CMV?
Gancyclovir, Cidofovir
Therapy for HIV?
combination treatment, Zidovudine + protease inhibitor
Therapy for RSV?
Ribaviron
Therapy for Influenza?
Amantadine, zanamivir (Relenza), peramivir (Rapivab), Osteltamivir, Baloxavir (new drug)
HPV cancer viruses
16 and 18
