General Virology - Virus Structure, Genome, Replication, and Diagnostics

Vocabulary-style flashcards covering key virology terms and concepts from the notes.

Virus

An obligate intracellular parasite; smallest infectious particles, 18–600 nm in diameter; all viruses require a host cell to replicate.

Virion

The extracellular infectious form of a virus, outside the host cell.

Capsid

Protein coat that encloses the viral genome, made of capsomeres; can be helical or icosahedral in symmetry.

Capsomere

Individual protein subunits that assemble to form the capsid.

Envelope

Lipid bilayer surrounding the capsid, containing viral glycoproteins; usually derived from the host cell membrane during budding.

Enveloped virus

Virus that has a lipid envelope surrounding the capsid.

Nonenveloped (naked) virus

Virus lacking a lipid envelope; more resistant to environmental conditions.

DNA virus

Virus with a DNA genome; replication and transcription mechanisms vary by family.

RNA virus

Virus with an RNA genome; replication strategies differ from DNA viruses.

Double-stranded DNA (dsDNA)

DNA genome consisting of two complementary strands; most DNA viruses replicate in the nucleus.

Single-stranded DNA (ssDNA)

DNA genome consisting of a single strand; host polymerases convert to dsDNA for transcription.

Linear genome

Genome with linear DNA or RNA molecules, as opposed to circular genomes.

Circular genome

Genome that forms a closed loop; many DNA viruses (e.g., Papillomaviridae, Polyomaviridae) are circular.

Papillomaviridae

Family of circular dsDNA viruses; includes human papillomavirus (HPV); associated with warts and some cancers.

Polyomaviridae

Family of small circular dsDNA viruses; examples include JC and BK viruses.

Hepadnaviridae

Family of partially double-stranded DNA viruses; includes hepatitis B virus (HBV); replication involves reverse transcription.

Double-stranded RNA (dsRNA)

RNA genome consisting of two complementary strands.

Single-stranded RNA (ssRNA)

RNA genome consisting of a single strand.

Positive-sense RNA (+ssRNA)

RNA genome that can function directly as mRNA and be translated by host ribosomes.

Negative-sense RNA (-ssRNA)

RNA genome that must be transcribed to a positive-sense mRNA before translation; carries or relies on its own RNA-dependent RNA polymerase.

Segmented genome

Genome divided into multiple RNA segments; facilitates reassortment among strains.

Bunyavirus

Negative-sense, segmented RNA virus with 3 genome segments.

Orthomyxovirus

Negative-sense, segmented RNA virus with 8 genome segments (e.g., influenza).

Arenavirus

Negative-sense, segmented RNA virus with 2 segments.

Reovirus

Double-stranded RNA virus with 10–12 genome segments.

Icosahedral

Capsid symmetry with 20 triangular faces; common among many DNA and RNA viruses.

Helical

Capsid symmetry where the protein subunits form a helical structure around the genome; often enveloped.

Poxviridae/Poxvirus

DNA viruses that replicate in the cytoplasm; an exception to the rule that DNA viruses replicate in the nucleus.

Capsid (note)

Protein shell protecting the genome; can be icosahedral or helical.

Envelope (note)

Lipid outer layer derived from host membrane; contains viral glycoproteins.

Attachment

Initial binding of a virus to specific host cell receptors.

Penetration

Entry of the virus into the host cell, via endocytosis or membrane fusion.

Uncoating

Removal of the capsid to release the viral genome inside the host cell.

Replication

Synthesis of viral genomes and transcripts; location and mechanism depend on genome type.

Assembly

Packaging of new viral genomes into virions.

Release

Exit of new virions from the host cell; can occur by lysis, budding, or exocytosis.

Fusion

Entry mechanism for enveloped viruses where viral and cellular membranes fuse.

Nuclear replication (DNA viruses)

DNA viruses generally replicate in the host cell nucleus; exceptions include Poxviridae.

Cytoplasmic replication (RNA viruses)

Most RNA viruses replicate in the cytoplasm; exceptions include Retroviridae and Influenza (nucleus for influenza).

Reverse transcriptase

RNA-dependent DNA polymerase used by retroviruses and Hepadnaviridae to convert RNA into DNA.

RNA-dependent DNA polymerase

Enzyme used to convert RNA to DNA during reverse transcription (e.g., in HBV replication).

Retroviridae

RNA viruses that use reverse transcription to integrate into the host genome (e.g., HIV).

Receptors used by viruses (example list)

Cell surface molecules widely used as viral receptors: ACE2 (SARS-CoV-2), CD4/CXCR4/CCR5 (HIV), CD21 (EBV), P antigen on erythrocytes (Parvovirus B19), ICAM-1 (Rhinovirus), Integrins (CMV), Nicotinic acetylcholine receptor (Rabies).

ACE2

Angiotensin-converting enzyme 2 receptor used by SARS-CoV-2 for entry.

CD4

Primary receptor for HIV entry; co-receptors include CXCR4 and CCR5.

CXCR4

Chemokine receptor acting as a co-receptor for HIV entry.

CCR5

Chemokine receptor acting as a co-receptor for HIV entry.

CD21

Receptor on B cells used by Epstein-Barr Virus (EBV) for infection.

P antigen

Receptor on erythroid cells used by Parvovirus B19.

ICAM-1 (CD54)

Intercellular adhesion molecule 1; receptor for Rhinovirus.

Nicotinic acetylcholine receptor

Neuron receptor used by Rabies virus for entry.

Innate immune response

Non-specific host defenses including NK cells, complement, and interferons.

Adaptive immune response

Specific defenses involving immunoglobulins (antibodies) and T cells.

NK cells

Natural killer cells; important innate immune effectors against virally infected cells.

Interferon

Cytokines that establish an antiviral state in cells and modulate the immune response.

Complement system

Group of plasma proteins that enhances immunity by opsonization, inflammation, and lysis.

Immunoglobulins (antibodies)

Proteins produced by B cells that bind to viral antigens and neutralize pathogens.

T cells

Adaptive immune cells (CD4+ helper and CD8+ cytotoxic) that coordinate and execute antiviral responses.

Cytolysis

Destruction of host cells due to viral replication and/or immune responses.

Immunopathology

Host immune responses that contribute to disease severity during viral infections.

Virulence factors

Genes or products that enhance viral pathogenicity or transmission.

Bacteriophage

Virus that infects bacteria; often injects genetic material and may lyse the bacterial cell.

Genetic diversification

Mechanisms by which viruses change genetically: recombination, reassortment, complementation, phenotypic mixing, and antigenic drift/shift.

Recombination

Exchange of genetic material between related viral genomes in coinfected cells.

Reassortment

Exchange of genome segments between segmented viruses during coinfection; can cause antigenic shift.

Complementation

Two mutants in the same cell complement each other's deficiencies to restore function.

Phenotypic mixing

Co-infection where one virus acquires surface proteins from another, altering observed phenotype.

Transcapsidation/Phenotyping masking

Capsid of one virus encloses another genome, masking true genotype.

Antigenic drift

Gradual accumulation of point mutations in viral antigens, leading to gradual immune escape.

Antigenic shift

Abrupt change in viral antigens due to reassortment of segmented genomes; can cause pandemics.

Hemagglutination inhibition test

Serologic assay to detect antibodies that block viral agglutination of red blood cells; indicates past infection or immunity.

ELISA

Enzyme-linked immunosorbent assay; detects soluble antigens or antibodies in a sample.

Direct immunofluorescence

Diagnostic technique using fluorescent-labeled antibodies to detect viral antigens in specimens.

PCR (polymerase chain reaction)

Technique to amplify and detect specific viral genome sequences; highly sensitive.

Virus isolation

Culturing viruses in suitable cells or systems as a prerequisite for resistance testing or diagnosis.

Oncogenesis (viruses)

Viral infection linked to cancer development; examples include EBV (Burkitt lymphoma/Nasopharyngeal carcinoma), HBV (hepatocellular carcinoma), and high-risk HPV (16, 18).