Virology Exam 1 Flashcards

Questions and Answers

Which methods are commonly used in viral diagnosis?

Complement fixation

Hemagglutination inhibition

PCR

All of the above (correct)

How is PCR used in viral diagnosis?

PCR detects viral genomes, quantifies viral load, and characterizes viral mutations.

List 7 human coronaviruses.

HCoV-229E, HCoV-OC43, SARS-CoV-1, HCoV-NL63, HCoV-HKU1, MERS-CoV, SARS-CoV-2.

What are some advantages of using PCR in viral diagnosis?

High sensitivity, ability to detect specific nucleic acids, and no need to culture the virus. Signup and view all the answers

ELISA is used primarily for detecting viral genomes.

False Signup and view all the answers

What are common diagnostic strategies for influenza?

Rapid tests, PCR, and rapid influenza tests. Signup and view all the answers

Describe the structure of the coronavirus.

Coronaviruses have a linear (+)ssRNA genome and an envelope with spikes (S) and membrane proteins (M). Signup and view all the answers

What are some risk factors for severe COVID-19 disease?

Elderly age, cardiovascular disease, diabetes, chronic respiratory disease, hypertension, cancer. Signup and view all the answers

List one treatment for COVID-19 and its mechanism of action.

Remdesivir: It is an adenosine nucleotide analogue with broad-spectrum antiviral activity against RNA viruses. Signup and view all the answers

What are the main disadvantages of culture methods in viral detection?

They are slow, expensive, require refrigeration, and need specialized equipment. Signup and view all the answers

What is a common method of detecting SARS-CoV-2?

RT-PCR. Signup and view all the answers

Match the viral diagnostic methods with their main characteristics:

RT-PCR = Amplifies RNA for detection ELISA = Detects antibodies or antigens Culture = Direct detection of viable virus Lateral flow assay = Rapid, no amplification required Signup and view all the answers

What are the major routes of viral transmission?

Respiratory, GI tract (oral-fecal route), Genital tract, Conjunctiva, Blood (parenteral), Vector bite. Signup and view all the answers

Define permissive cells and non-permissive cells.

Permissive cells can support productive infection; non-permissive cells cannot. Signup and view all the answers

Define CPE (cytopathic effects).

Virus-caused effects in host that show changes in cell morphology, cell-cell fusion, aggregations, and cell lysis. Signup and view all the answers

Define productive infection and abortive infection.

Productive infection produces infectious virions; abortive infection does not. Signup and view all the answers

Define latent infection.

Does not produce infectious virions immediately but has potential to later, can still detect genome. Signup and view all the answers

Define acute infection.

An infection that appears within a few days and can go away, can become latent. Signup and view all the answers

Define chronic infection.

Acute infection that clears and becomes stagnant. Signup and view all the answers

What is the main cause of continued measles activity in the developed world?

Unvaccinated US residents contracting it and traveling to/from affected regions. Signup and view all the answers

What is Baltimore's classification system?

Viruses classified into 7 groups based on replication and genome. Signup and view all the answers

Explain how viruses are classified by ICTV.

Classified based on physical and chemical properties into orders, families, subfamilies, genera, and species. Signup and view all the answers

List each part of a virus' structure.

Capsid, nucleocapsid, envelope, and virion. Signup and view all the answers

Describe icosahedral symmetry and helical symmetry.

Icosahedral: capsomers arranged in a geometric pattern; Helical: subunits stacked around a central axis. Signup and view all the answers

What is Transmission EM?

A microscopy technique to visualize viruses by making samples thin and stained with metal/gold. Signup and view all the answers

The two major routes of virus entry are _ and _ .

endocytosis, fusion Signup and view all the answers

What are the 6 steps of virus replication?

<ol> <li>Virus attachment 2. Entry into host cells 3. Uncoating 4. Genome replication 5. Assembly 6. Virion release</li> </ol> Signup and view all the answers

What is positive sense in single-stranded RNA viruses?

Positive sense serves as mRNA. Signup and view all the answers

What is the role of structural proteins?

Viral proteins in virions that contribute to the virus' structure. Signup and view all the answers

What are routinely used methods for virus culture?

Animal inoculation, chick embryo culture, cell culture. Signup and view all the answers

Describe principles of sample collection for diagnosing viral diseases.

Collect specimens ASAP after symptom onset, aseptically, and transport immediately to maintain viral viability. Signup and view all the answers

Study Notes

Viral Transmission Routes

Respiratory: Commonly transmitted by Rhinovirus, Coronavirus, Influenza A & B.
GI Tract (Oral-Fecal): Transmission includes Norovirus, Poliovirus, Hepatitis A & E.
Genital Tract: Viruses such as Papillomaviruses, Ebola, and Zika are transmitted.
Conjunctiva: Enterovirus type 70, Ebola, and Zika can cause conjunctivitis.
Blood (Parenteral): HIV and Hepatitis B are transmitted, often during vertical transmission.
Vector Bite: Diseases such as Yellow fever, Dengue, and West Nile viruses are spread this way.

Cell Types in Viral Infections

Permissive Cells: Cells that can support a productive viral infection.
Non-Permissive Cells: Cells that cannot support a viral infection.

Cytopathic Effects (CPE)

CPE refers to observable effects in host cells due to viral infection.
Observations include changes in cell morphology (size, shape), cell fusion (syncytia), aggregations, and cell lysis.

Types of Viral Infections

Productive Infection: Results in the production of infectious virions.
Abortive Infection: Fails to produce infectious virions.
Latent Infection: Non-infectious at first, but can become reactivated later.
Acute Infection: Brief infection that usually resolves quickly but can lead to latency.
Chronic Infection: Initial clearance followed by a persistent, stagnant infection.

Measles Activity in Developed Regions

Continued outbreaks attributed to unvaccinated individuals traveling to/from affected regions.
Controversy arose from Andrew Wakefield linking the MMR vaccine to autism.

Baltimore Classification System

Classifies viruses into 7 groups based on replication and genome type:
- I: dsDNA
- II: ssDNA
- III: dsRNA
- IV: +ssRNA
- V: -ssRNA
- VI: reverse transcribing ssRNA
- VII: reverse transcribing dsRNA

ICTV Classification System

Viruses are categorized based on physical and chemical properties through:
- Order (-virales), Family (-viridae), Subfamily (-virinae), Genus (-virus), Species.
Employs a nonsystemic, polythetic, and hierarchical classification.

Virus Structure

Composed of capsid, nucleocapsid, envelope, and virion:
- Capsid: Protein shell, shapes include icosahedral, helical, and complex.
- Nucleocapsid: Combination of capsid and nucleic acid.
- Envelope: Lipid bilayer from host; contains glycoprotein spikes for attachment.
- Virion: A complete virus particle.

Symmetry in Virus Structure

Icosahedral Symmetry: Regular geometric pattern of capsomers; requires 12 pentons and hexons varying in number.
Helical Symmetry: Identical subunits stacked in a helical arrangement; characterized by specific parameters like unit/turn and pitch.

Transmission Electron Microscopy (EM)

Utilizes thin samples stained with metals to produce 2D images of viruses' interior, aiding in visualization.

Mechanisms of Virus Entry and Release

Entry Mechanisms: Endocytosis (receptor-mediated) and fusion with the host membrane.
- Examples include Influenza (enveloped) and Adenovirus (naked).
Release Mechanisms: Lysis (often cytolytic) and budding (enveloped viruses).
- Examples include Smallpox (lysis) and Influenza A (budding).

Virus Replication Steps

Steps include attachment, entry, uncoating, genome replication, assembly, and release.
Attachment Factors: Enhance virus entry but are not selective (e.g., heparan sulfate).
Receptors and Co-receptors: Highly selective; essential for viral entry (e.g., CD4, CCR5).

RNA Virus Classification

Positive Sense: Serves directly as mRNA.
Negative Sense: Requires own enzyme to act as mRNA template.
Replication varies for positive and negative sense, with retroviruses using reverse transcription.

DNA Virus Replication

Single-stranded DNA (ssDNA) must convert to double-stranded DNA (dsDNA) for gene expression.
Double-stranded DNA (dsDNA) typically uses host cell nucleus for replication and transcription.

Structural and Nonstructural Proteins

Structural Proteins: Included in virions; consist of capsid, envelope proteins, and some enzymes.
Nonstructural Proteins: Present only in infected cells and often have enzymatic functions.
Retroviruses and negative-sense RNA viruses depend on carrying their own polymerase enzymes for replication.

Viral Culture Techniques

Common methods include animal inoculation, chick embryo usage, and various cell culture types (primary, diploid, continuous).
Plaque Assay: Quantifies infectious virus by counting plaques formed due to cell lysis.

Serological Assays for Viral Diagnosis

Techniques include ELISA, immunofluorescence, and latex agglutination.
ELISA: Utilizes antibodies for detection of antigens or antibodies in samples.
Immunofluorescence: Detects viral antigens in cells using direct or indirect methods.
Latex Agglutination Test: Detects antigen-antibody interaction using latex beads.### Viral Detection Techniques
Primary Antibodies: Two types are used in assays—one stains the host cell and the other stains the virus. Each antibody must be produced in distinct hosts.
Latex Agglutination Test:
- Detects antibodies or soluble antigens in saliva, urine, cerebrospinal fluid (CSF), or blood.
- Involves attaching antibody or antigen to latex beads; agglutination occurs if the corresponding partner is present in the sample.
- The technique is easy to perform and delivers a semi-quantitative result, essentially providing a simple yes or no answer.
- Faster than traditional methods using dyes, substrates, or enzymes.

PCR in Viral Diagnosis

Detection of Viral Genome: PCR identifies specific viral nucleic acids, enabling diagnosis without the risk of live virus propagation.
- Essential for viruses hard to detect by other methods, including HBV, HCV, and SARS-CoV-2.
- Applicable in small sample collections (ocular, amniotic fluid, CSF).
- Useful during antibody testing failures, particularly for HIV and HCV.
Quantification of Viral Load: PCR provides information on the quantity of viral genome, serving as:
- Diagnostic marker (e.g., CMV).
- Prognostic marker (e.g., CD4 count and viral load for HIV).
- Therapeutic marker to monitor treatment efficacy (e.g., HIV, HCV).
Characterization of Viral Genomes: PCR can also sequence viral genomes to identify mutations and track epidemiology.
Advantages of PCR:
- High sensitivity allows detection of minute amounts of viral RNA without needing to culture the virus.
- Provides rapid assessment of patient recovery.
- Detects mutations and emerging strains effectively.

Diagnostic Strategies for Specific Viruses

Influenza: Rapid tests identify nucleic acid without amplification; while PCR is common, rapid influenza tests yield lower accuracy.
HIV: Screening generally uses rapid tests or ELISA, with confirmation via Western blot. OraQuick provides results in 20 minutes.
HPV: Detection is performed using PCR targeting viral DNA.
Measles: Diagnosed using Enzyme Immunoassay (EIA), focusing on specific IgM post-rash onset.

Human Coronaviruses Overview

Seven Known Strains:
- HCoV-229E and HCoV-OC43 (common cold),
- SARS-CoV-1 (2003 outbreak),
- HCoV-NL63, HCoV-HKU1, MERS-CoV, and SARS-CoV-2 (COVID-19).
Structure:
- Coronaviruses feature a linear (+) single-stranded RNA genome and an envelope with spike glycoproteins vital for cell membrane fusion.
Pathogenesis:
- Commonly causes upper respiratory infections, with significant seasonal peaks.
- High prevalence by age six, predominantly transmitted through droplets.
- COVID-19 presents a significant danger post 3-10 days after infection.

SARS-CoV-2 Transmission and Risk Factors

Transmission:
- Person-to-person via respiratory droplets during coughing, sneezing, or conversation.
- Asymptomatic individuals can still spread the virus.
Risk Factors for COVID-19:
- Higher infection and severity rates in older adults and individuals with chronic diseases (e.g., cardiovascular issues, diabetes).

Challenges in COVID-19 Treatment

Severity Factors:
- COVID-19 can damage multiple organ systems (lungs, heart, kidneys, brain, intestines) leading to severe complications.
Immunopathogenesis:
- Viral replication triggers inflammation, increasing vascular permeability, cell damage, and attracting immune cells, resulting in symptoms such as pneumonia and acute respiratory distress syndrome (ARDS).

Drugs in COVID-19 Trials

Hydroxychloroquine & Chloroquine: Anti-parasitics with potential viral effects.
Favipiravir: Broad-spectrum RdRp inhibitor, efficacy questioned.
Remdesivir: Nucleotide analogue targeting RNA viruses; previously developed for Ebola.
Oseltamivir: Antiviral inhibiting neuraminidase.
Thalidomide & Tocilizumab: Immunomodulators affecting cytokine response.
Convalescent Plasma: Infusion of antibodies from recovered patients to mitigate disease severity.

Animal Models for SARS-CoV-2 Research

Mice: Economical for large studies but show no disease response to SARS-CoV-2.
Transgenic Mice: Adapted to express hACE2, enabling severe disease modeling not observed in humans.
Ferrets: Inconsistent reports on clinical illness show variability in disease manifestation.
Syrian Hamsters: Disease symptoms observed with virus clearance after a week.
Non-Human Primates: Virus replicates in lungs but practical limitations exist for use.

Detection Methods for SARS-CoV-2

RT-PCR: High sensitivity due to amplification, though more expensive.
ELISA & Plaque Assays: Common methods; specifics on performance not detailed.
Lateral Flow Assays: Quick, cost-effective, but less sensitive compared to PCR.
Culture: Direct virus detection; highly sensitive but slow, expensive, requiring specialized equipment.

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Test your knowledge on the major routes of viral transmission with this comprehensive set of flashcards. Each route features examples of viruses associated with that transmission method, including respiratory, GI tract, genital tract, conjunctiva, and blood. Perfect for students preparing for virology exams.