Viral Infection Patterns, Transmission Dynamics, and Innate Immune Defenses

Comprehensive vocabulary flashcards covering routes of entry, transmission mechanisms, epidemiology metrics, and intrinsic/innate pattern recognition signaling pathways from BIOL4090 Lectures 013 and 014.

Acute Infection

A pattern of viral infection characterized by a rapid burst of replication lasting days to weeks, after which the adaptive immune response clears the virus (e.g., Influenza A virus, SARS-CoV, and adenoviruses).

Persistent Infection – Chronic

A pattern of infection where an initial acute phase is followed by continuous, ongoing viral replication and spread spanning months, years, or a lifetime (e.g., HIV, HBV, and HCV).

Persistent Infection – Latent

A pattern of infection where an acute phase is followed by long periods of viral dormancy with no detectable replication, punctuated by intermittent bursts of reactivation and viral replication (e.g., herpesviruses including HSV, CMV, VZV, EBV, and KSHV).

Abortive Infection

A viral infection in which little to no viral replication occurs beyond the first few infected cells, failing to produce a full productive cycle.

Virus 'Lifestyle' Strategy Graph

A comparative plot of viral load versus time illustrating acute infection (sharp peak resolved in days–weeks), persistent–chronic infection (sustained plateau over months/years), and persistent–latent infection (baseline dormancy interrupted by reactivation peaks).

Reservoir

The natural host organism or host population in which a virus naturally resides, replicates, and maintains itself in nature.

Chain-of-Transmission

A continuous sequence of individual hosts linked together by successive, successful pathogen transmission events.

Cross-Species Transmission (Spillover)

The transmission event in which a pathogen jumps from its natural reservoir host species into a novel recipient host species.

Zoonotic Transmission

The transmission of a pathogen directly or indirectly from an animal host to a human host.

Dead-End Infection

A zoonotic or spillover infection where the pathogen does not establish a sustained chain of transmission beyond the initially infected individual (e.g., avian influenza in humans, or West Nile virus in humans and horses).

Iatrogenic Transmission

The unintended transmission of a virus or other pathogen as a direct consequence of a medical intervention or healthcare procedure (e.g., contaminated blood transfusions, organ transplants, unsterilized surgical tools, or needle injections).

Direct Physical Contact Transmission

Direct transfer of virions through immediate individual-to-individual contact such as touching, kissing, sexual contact, predation, or fighting (e.g., HIV, herpes simplex viruses, and poxviruses).

Droplet Transmission

A form of direct transmission mediated by large respiratory droplets propelled short distances through coughing or sneezing (e.g., Influenza virus, SARS-CoV-2).

Airborne (Aerosol) Transmission

A mode of indirect transmission mediated by small microscopic particles containing infectious virions that remain suspended in the air over distance and time (e.g., Measles virus, varicella/chickenpox, and SARS-CoV-2 under certain conditions).

Fomite Transmission

Indirect transmission of an infectious pathogen through contact with contaminated inanimate surfaces or objects (e.g., Rhinoviruses and noroviruses).

Vehicle-Borne Transmission

Indirect transmission occurring through contaminated media such as food, water, or biological therapeutic products (e.g., Hepatitis A through food/water; Hepatitis B and C through blood products).

Biological Vector

An arthropod vector in which a virus enters, infects cells, and replicates biological virions before being transmitted to a vertebrate host (characterizing arboviruses such as Dengue, Zika, and West Nile virus).

Mechanical Vector

An insect or arthropod that carries a virus passively on its body surfaces without supporting viral infection or replication within itself.

Sylvatic Cycle

An enzootic transmission cycle in which an arbovirus (such as Yellow fever virus) circulates continuously between wild non-human primates and forest-dwelling mosquitoes.

Urban Cycle

An epidemic transmission cycle in which an arbovirus (such as Yellow fever virus) is transmitted directly between human populations and domestic mosquito vectors such as $Aedes$ spp.

Vertical Transmission

Transmission of an infectious agent from mother to offspring, occurring across the placenta (transplacental), during childbirth (intrapartum), or via breast milk ingestion (e.g., HIV, rubella, Zika virus, CMV, and mouse mammary tumor virus).

Incubation Period

The elapsed time between initial exposure to an infectious pathogen and the onset of observable clinical signs or symptoms.

Infectious Period

The time window during an active infection during which an infected individual is capable of shedding and transmitting viable virus to susceptible contacts.

Serial Interval

The epidemiological duration of time between consecutive illness onsets in successive cases within a chain-of-transmission.

Superspreader

An infected individual who transmits a pathogen to an unusually high or above-average number of secondary cases, driven by high viral shedding, host physiology, behavior, or contact frequency.

Superspreading Event

An event or gathering where one or a few infected individuals transmit a pathogen to an exceptionally large number of secondary cases, typically facilitated by crowding, poor ventilation, and prolonged contact.

Herd Immunity

Population-level resistance to the spread of an infectious pathogen achieved when a sufficiently high proportion of individuals possess immunity through prior infection, vaccination, or both, thereby interrupting transmission chains.

Basic Reproduction Number ($R_0$)

An epidemiological metric denoting the average number of secondary infections generated by a single infectious individual introduced into a completely susceptible population during the mean infectious period. A value of $R_0 < 1$ indicates the chain of transmission will terminate.

Isolation

A public health measure that separates individuals who are symptomatic or confirmed positive for an infection from the uninfected population until they are no longer contagious.

Quarantine

A public health intervention that restricts the movement of asymptomatic individuals who have been exposed to a contagious pathogen for the duration of the incubation period to monitor for symptom development.

Intrinsic Defenses

Immediate, continuous, physical and chemical host barriers (such as the skin, mucosal membranes, gastric acid, saliva, tears, antimicrobial peptides, and mucociliary clearance) that constitutively prevent viral entry.

Innate Immunity

A non-adaptive, inherited arm of the immune system present at birth that deploys germline-encoded sensors, signaling pathways, and effectors within minutes to hours to rapidly restrict pathogen replication without immunologic memory.

Pathogen-Associated Molecular Patterns (PAMPs)

Conserved, characteristic molecular motifs shared across broad classes of related microorganisms that are foreign to eukaryotic hosts and generally not strain-specific.

Pattern Recognition Receptors (PRRs)

Host cellular sensor proteins located on the plasma membrane, endosomal membranes, cytosol, or nucleus that have evolved to recognize and bind specific PAMPs or DAMPs.

Damage-Associated Molecular Patterns (DAMPs)

Endogenous intracellular host molecules released into extracellular or inappropriate compartments following cellular stress, injury, necrosis, or lysis that trigger sterile PRR activation.

Lipopolysaccharide (LPS)

A major glycolipid component of the outer membrane of Gram-negative bacteria that acts as a classical bacterial PAMP recognized by cell-surface TLR4.

Peptidoglycan

A thick, cross-linked glycan polymer found abundantly in the bacterial cell wall (especially prominent in Gram-positive species) that acts as a bacterial PAMP.

Flagellin

The major proteinaceous subunit of bacterial flagella that functions as a recognized bacterial PAMP.

Lipoteichoic Acid (LTA)

A surface-associated anionic polymer anchored to the cell wall and membrane of Gram-positive bacteria that serves as a recognized PAMP.

Unmethylated CpG DNA

DNA motifs featuring high frequencies of unmethylated cytosine-phosphate-guanine dinucleotides typical of bacterial and viral genomes that function as an endosomal PAMP.

Viral PAMPs

Distinctive molecular features of viruses recognized by host PRRs, including single-stranded RNA (ssRNA), double-stranded RNA (dsRNA), large symmetrical capsid lattices, and nucleic acids in abnormal cellular locations (such as cytosolic DNA).

Cytokines

Soluble protein messengers secreted by host cells following PAMP detection that bind specific high-affinity receptors on neighboring cells to initiate intercellular defense signaling.

Interferons (IFNs)

A specialized family of antiviral cytokines produced in response to viral nucleic acid sensing that stimulate the transcriptional induction of hundreds of interferon-stimulated genes (ISGs).

Interferon-Stimulated Genes (ISGs)

A suite of hundreds of host genes transcriptionally activated in target cells downstream of interferon receptor engagement that encode diverse antiviral effector proteins.

Interleukins (IL)

A group of secreted cytokines that function primarily to mediate communication, activation, and differentiation among various leukocyte populations.

Chemokines

Chemotactic cytokines that establish chemical concentration gradients to recruit circulating leukocytes and macrophages to anatomical sites of infection or tissue damage.

Cytokine Storm

A dangerous systemic hyperinflammatory state caused by massive, unchecked overproduction and release of pro-inflammatory cytokines, frequently causing acute tissue and organ pathology.

Toll-Like Receptors (TLRs)

A prominent family of membrane-associated PRRs situated either on the cell surface or within endosomal membranes that dimerize upon ligand binding to initiate downstream kinase cascades.

TLR3

An endosomal membrane PRR that specifically recognizes double-stranded RNA (dsRNA) generated during viral replication cycles.

TLR4

A plasma-membrane PRR that binds bacterial lipopolysaccharide (LPS) as well as certain viral surface glycoproteins to initiate MyD88- or TRIF-dependent signaling.

TLR7 and TLR8

Endosomal Toll-like receptors that recognize viral single-stranded RNA (ssRNA) motifs within internalized virions.

TLR9

An endosomal Toll-like receptor that detects unmethylated CpG dinucleotide motifs in microbial and viral DNA.

RIG-I-Like Receptors (RLRs)

A family of cytosolic RNA sensors containing RNA helicase and CARD domains (including RIG-I and MDA5) that detect cytoplasmic viral RNA and signal via the adaptor protein MAVS.

RIG-I

A cytosolic RNA sensor that recognizes short viral double-stranded or 5'-triphosphate/uncapped single-stranded RNAs; ligand binding induces a conformational change that unmasks its CARD domains to bind MAVS.

MDA5

A cytosolic RLR sensor that binds long double-stranded RNA (dsRNA) intermediates to expose tandem CARD domains for downstream signaling.

MAVS (Mitochondrial Antiviral-Signaling Protein)

An outer mitochondrial membrane-anchored adaptor protein whose CARD domain interacts with the activated CARD domains of RIG-I or MDA5, organizing the activation of TBK1 and IKK kinases.

cGAS (Cyclic GMP-AMP Synthase)

A cytosolic DNA PRR and nucleotidyltransferase enzyme that binds double-stranded DNA in the cytoplasm and catalyzes the synthesis of $2'3'\text{-cGAMP}$ from ATP and GTP.

STING (Stimulator of Interferon Genes)

An endoplasmic reticulum-associated dimeric adaptor protein that binds the cyclic dinucleotide $2'3'\text{-cGAMP}$, subsequently recruiting and activating TBK1 to phosphorylate IRF3.

$$2'3'\text{-cGAMP}$$

An endogenous cyclic dinucleotide secondary messenger synthesized by activated cGAS that acts as the direct activating ligand for STING.

IRF3 (Interferon Regulatory Factor 3)

A cytoplasmic transcription factor that becomes phosphorylated and dimerized downstream of TBK1/IKK complexes, subsequently translocating into the nucleus to induce transcription of Type I interferon genes.