Chapter 13: Viruses, HIV, Influenza, Common Cold, and COVID-19

Comprehensive vocabulary flashcards covering Chapter 13 Parts 1 and 2: viral morphology, bacteriophages, animal virus replication, Varicella-Zoster, HIV pathogenesis and treatments, Influenza, the Common Cold, and COVID-19.

Virus

An obligate intracellular parasite consisting of a nucleic acid genome enclosed within a protein coat (capsid), incapable of reproducing or carrying out metabolic processes outside of a host cell.

Viral Living Status

Viruses are not classified as living organisms because they lack cellular organization, independent metabolic machinery, internal energy ($ATP$) generation, and autonomous reproduction.

Viral Host Range

The spectrum of host species and specific cell types that viruses are capable of infecting, which collectively spans all domains of cellular life (bacteria, archaea, animals, plants, and fungi).

Viral Size Range and Scale

Viruses range from approximately $10\,nm$ to about $800\,nm$ in size, making them roughly $100$ to $1{,}000$ times smaller than the host cells they infect.

$$10\text{ Nanometer Metric Conversions}$$

The diameter of the smallest known viruses, $10\,nm$, is equivalent to $0.01\,\mu m$ (micrometers) and $0.00001\,mm$ (millimeters).

Capsid

The protective outer protein shell that encloses the viral nucleic acid genome and facilitates delivery of genetic material into host cells.

Viral Nucleic Acid Diversity

Viral genetic material can consist of either $DNA$ or $RNA$, which may be single-stranded ($ss$) or double-stranded ($ds$), linear, circular, or segmented.

Non-Enveloped (Naked) Virus

A virus composed exclusively of a nucleic acid core enclosed by a protein capsid without an outer lipid bilayer membrane, typically released via host cell lysis.

Enveloped Virus

A virus surrounded by an outer phospholipid bilayer membrane containing viral spikes, stolen from host cellular membranes during budding.

Viral Spikes (Peplomers)

Carbohydrate-protein complexes projecting from the outer surface of a virion that bind specifically to complementary receptor molecules on the host cell membrane.

Host Cell Attachment Necessity

Specific attachment is required because viruses possess no independent motility and must bind to host receptors to initiate the penetration and entry process.

Bacteriophage (Phage)

A specialized category of virus that exclusively targets, infects, and replicates within bacterial cells.

Bacteriophage Head (Capsid)

The icosahedral protein structure of a complex phage that packages, encloses, and protects the double-stranded viral genomic $DNA$.

Bacteriophage Tail and Tail Fibers

Phage tail fibers specifically recognize and anchor the phage to receptors on the bacterial surface, while the tail sheath contracts to inject viral $DNA$ across the bacterial envelope.

Human Immunity to Bacteriophages

Bacteriophages cannot infect human or eukaryotic cells because animal cell membranes lack the specific bacterial surface receptors required for phage attachment.

Gut Bacteriophage Abundance

The human gastrointestinal tract harbors approximately $10^{15}$ bacteriophages, forming a predatory viral community that regulates bacterial microbiome populations.

Coronavirus Genome

A positive-sense single-stranded $RNA$ ($+ssRNA$) genome, which functions directly as messenger $RNA$ upon entry into host cell cytoplasm.

Coronavirus Etymology

Named from the Latin word corona ("crown") because the large, club-shaped glycoprotein spikes projecting from its envelope resemble a royal crown or the solar corona.

Lytic Phage

A virulent bacteriophage whose infection cycle culminates in the enzymatic rupture (lysis) and death of the bacterial host cell to liberate newly formed virions.

T4 Bacteriophage

The classical model lytic bacteriophage possessing a complex head-tail morphology used to investigate the five-step viral lytic cycle.

T4 Phage Target and Replication Duration

Specifically targets the bacterium Escherichia coli (E. coli), completing its entire reproductive cycle from attachment to host cell lysis in approximately $20$ to $30\text{ minutes}$.

Attachment (T4 Phage Step 1)

The initial stage where T4 phage tail fibers collide with and bind specifically to lipopolysaccharide and protein receptors on the E. coli outer membrane.

DNA Entry (T4 Phage Step 2)

The T4 tail sheath contracts like a syringe needle, driving the central tube through the bacterial cell wall and membrane to inject viral $DNA$, leaving the empty protein capsid outside.

Synthesis (T4 Phage Step 3)

Host bacterial $DNA$ is degraded while host transcription and translation machinery are hijacked to produce viral proteins and replicate the phage $DNA$ genome.

Assembly (T4 Phage Step 4)

The spontaneous self-assembly of viral components into mature phages, packaging replicated $DNA$ into newly built capsid heads and attaching tails and tail fibers.

Release (T4 Phage Step 5)

Phage-encoded lysozyme breaks down the bacterial peptidoglycan cell wall from within, causing the host cell to burst osmotically and liberate infectious progeny virions.

T4 Phage Burst Size and Host Searching

Lysis produces a burst size of approximately $100$ to $200$ progeny phages per bacterial cell, which locate subsequent host bacteria exclusively through passive brownian motion and fluid diffusion.

Animal Virus Entry and Uncoating

Unlike phages that inject only naked $DNA$, animal viruses enter host cells intact via endocytosis or membrane fusion, requiring an enzymatic uncoating step to separate the nucleic acid from its capsid.

Viral Budding

The exit mechanism used by enveloped animal viruses where assembled nucleocapsids push through the host plasma membrane, acquiring their lipid envelope without immediately lysing the cell.

Host Membrane Theft

The phenomenon during viral budding wherein an exiting enveloped virus steals host plasma membrane phospholipids, cholesterol, and proteins to form its outer bilayer envelope.

Animal Virus Lysis

The exit mechanism used predominantly by non-enveloped (naked) animal viruses, resulting in the rupture and death of the host animal cell to release mature progeny virions.

Acute Viral Infection

An infection pattern characterized by rapid onset of symptoms, intense viral replication, and swift resolution or elimination by the host immune defenses (e.g., Influenza or Common Cold).

Persistent Viral Infection

An infection where the viral genome remains inside host tissues for months, years, or lifetime, continuously or intermittently producing virions (divided into chronic and latent).

Chronic Viral Infection

A persistent infection characterized by the continuous release and shedding of infectious viral particles at low to moderate levels over an extended duration (e.g., Hepatitis B).

Latent Viral Infection

A persistent infection characterized by dormant periods where viral replication ceases completely and no symptoms are observed, punctuated by episodes of reactivation (e.g., Varicella-Zoster Virus).

Varicella-Zoster Virus (VZV)

The herpesvirus that causes chickenpox as an acute primary infection and shingles (herpes zoster) upon reactivation from long-term latency.

VZV Latency and Dermatomal Shingles

Following chickenpox, VZV retreats into sensory nerve ganglia; upon reactivating years later, it travels down sensory axons to cause painful shingles lesions restricted to a single dermatome.

Shingrix and Pox Parties

Shingrix is the recommended recombinant subunit vaccine administered to prevent shingles; 'pox parties' were unsafe historic gatherings where children were intentionally exposed to chickenpox.

Human Immunodeficiency Virus (HIV)

An enveloped retrovirus carrying two copies of single-stranded $RNA$ that infects and progressively depletes vital CD4+ T helper lymphocytes in the human immune system.

CD4+ T Helper Cells

White blood cells vital for coordinating adaptive cellular and humoral immune responses, serving as the primary host targets destroyed during an HIV infection.

HIV Zoonotic Origin and History

Originated from Simian Immunodeficiency Virus (SIV) in chimpanzees, crossing into humans around the early $1900\text{s}$ (circa $1920$) in Central Africa through blood contact during bushmeat hunting.

Mechanism of AIDS Mortality

HIV causes death indirectly by destroying CD4+ T cells, resulting in profound immunosuppression that leaves the body defenseless against lethal opportunistic pathogens and secondary cancers.

Pandemic

An outbreak of an infectious disease that has spread across multiple international boundaries, continents, or worldwide, affecting a large proportion of the population.

Global HIV Prevalence ($2019$)

Approximately $38\text{ million}$ individuals globally were living with HIV in $2019$, with eastern and southern Sub-Saharan Africa accounting for the largest proportion of infections.

United States HIV Statistics

About $1.2\text{ million}$ people in the United States live with HIV (under $0.5\%$ of the US population), with annual AIDS-related deaths currently standing around $13{,}000$ to $15{,}000$.

gp120 Envelope Glycoprotein

The surface spike glycoprotein on the HIV envelope that specifically recognizes and binds to host CD4 surface receptors and chemokine co-receptors.

HIV Host Receptors (CD4 and CCR5/CXCR4)

The CD4 receptor and chemokine co-receptors (CCR5 or CXCR4) on human immune cells required for gp120 binding, conformational change, and viral envelope fusion.

Reverse Transcriptase (HIV)

An essential HIV enzyme that synthesizes a complementary double-stranded $DNA$ molecule from the viral single-stranded $RNA$ genome inside the host cell cytoplasm.

Integrase (HIV)

An essential HIV enzyme that transports and permanently splices viral double-stranded $DNA$ into the host cell's nuclear chromosomal $DNA$.

Protease (HIV)

An essential HIV enzyme that cleaves long, nonfunctional viral precursor polyproteins into smaller, functional structural proteins and enzymes during virion maturation.

Provirus

A viral genome that has permanently integrated into the host cell's nuclear chromosomes, remaining a permanent genetic feature for the life of that cell (e.g., HIV).

Human Endogenous Retroviruses (HERVs)

Remnants of ancient retroviral infections that integrated into human ancestral germline cells millions of years ago, comprising approximately $8\%$ of the modern human genome.

Acute HIV Infection (Stage 1)

The initial $2$ to $4\text{ weeks}$ following HIV exposure marked by extremely high viral replication, flu-like symptoms, and a transient sharp drop in CD4+ T cell counts.

Clinical Latency / Chronic HIV (Stage 2)

An asymptomatic or mildly symptomatic stage lasting up to a decade or more in untreated patients, during which HIV replicates at low levels while CD4+ T cell counts gradually decline.

AIDS (Stage 3 HIV)

The final stage of untreated HIV infection, diagnosed when the CD4+ T cell count falls below $200\text{ cells}/\mu L$ of blood or when an AIDS-defining opportunistic infection develops.

Opportunistic Infections in AIDS

Severe infections caused by pathogens that rarely produce disease in healthy individuals but exploit the depleted immune defenses of patients with advanced AIDS.

AIDS-Associated Bacterial Pneumonia

The leading cause of mortality in AIDS patients, frequently triggered by respiratory pathogens such as Streptococcus pneumoniae or atypical organisms like Pneumocystis jirovecii.

HIV Environmental Fragility

HIV is incapable of surviving long outside a living host because its delicate host-derived lipid envelope rapidly dries out and breaks down upon exposure to air and disinfectants.

HIV Transmission Routes

Transmitted exclusively through direct contact with infected blood, semen, pre-seminal fluid, vaginal fluids, rectal fluids, and breast milk; it cannot spread through casual contact, saliva, or insects.

Contaminated Blood Transfusion Risk

The exposure route with the highest single-act probability of transmitting HIV (exceeding $90\%$) due to the direct intravenous introduction of large volumes of live virus.

HAART (Highly Active Antiretroviral Therapy)

A customized combination regimen of three or more antiretroviral medications targeting distinct viral enzymes to suppress HIV replication below detectable levels.

PrEP (Pre-Exposure Prophylaxis)

A daily preventative oral medication taken by HIV-negative individuals at high risk of exposure to reduce the risk of acquiring HIV from sex by approximately $99\%$.

Truvada

The leading daily oral PrEP drug, formulated with two reverse transcriptase inhibitors (emtricitabine and tenofovir) that prevent HIV from establishing a permanent proviral infection.

PEP (Post-Exposure Prophylaxis)

An emergency antiretroviral regimen that must be initiated within $72\text{ hours}$ of a potential HIV exposure and taken consistently for $28\text{ days}$ to prevent infection.

Influenza Virus

An enveloped, negative-sense segmented $RNA$ virus that primarily infects epithelial cells of the respiratory tract in humans, birds, and swine.

Influenza Animal Reservoirs

Aquatic wild birds (the primary natural reservoir), domestic poultry, and swine (pigs), which harbor diverse flu strains capable of genetic reassortment.

Hemagglutinin (HA / H Spike)

An influenza surface glycoprotein spike responsible for binding to sialic acid receptors on respiratory epithelial cells to mediate viral attachment and entry ($18$ known subtypes).

Neuraminidase (NA / N Spike)

An influenza surface enzyme that cleaves sialic acid residues on host cell surfaces, enabling newly assembled progeny virions to detach and disperse ($11$ known subtypes).

Influenza Subtype Diversity ($18\text{ H, } 11\text{ N}$)

The structural classification system for Influenza A viruses based on combinations of its $18$ different hemagglutinin and $11$ different neuraminidase surface glycoprotein spikes.

$2017\text{--}2018$ American Flu Season

An exceptionally deadly influenza season in the United States that killed an estimated $61{,}000$ Americans, driven predominantly by a virulent H3N2 subtype strain.

Cytokine Storm

A life-threatening hyper-inflammatory response wherein an overactivated immune system floods lung tissues with cytokines, causing fluid accumulation and asphyxiation in healthy patients.

$1918\text{--}1920$ Influenza Pandemic

A catastrophic global pandemic caused by an aggressive H1N1 influenza strain that killed an estimated $50\text{ million}$ people worldwide, largely through cytokine storms and secondary pneumonia.

Tamiflu (Oseltamivir)

The standard oral antiviral drug prescribed for influenza that acts as a neuraminidase inhibitor, preventing progeny virions from detaching from infected host cells.

Seasonal Flu Vaccine Composition

An annual immunization containing inactivated (killed) whole virions or purified surface protein subunits ('empty shell' antigens) that stimulate protective antibody production without causing illness.

Cold vs. Flu Clinical Distinction

Influenza causes sudden high fever, chills, severe muscle aches, and profound fatigue, whereas the common cold typically features gradual nasal congestion, sore throat, and rarely a high fever.

Rhinovirus

A non-enveloped single-stranded $RNA$ virus that serves as the most frequent causative agent of the common cold, accounting for over $50\%$ of all cases.

ICAM-1 (Intercellular Adhesion Molecule-1)

The specific cell surface adhesion receptor on human upper respiratory epithelial cells that Rhinovirus binds to in order to initiate infection.

Evolutionary Advantage of Cold Symptoms

Inducing sneezing, coughing, and a runny nose forces the host to expel aerosolized droplets and contaminate hands and fomites, maximizing viral transmission to new hosts.

Pertussis (Bordetella pertussis - Cold Mimic)

A bacterial respiratory pathogen that initially produces a catarrhal stage identical to a common cold (runny nose, mild cough) before progressing to severe paroxysmal coughing fits.

COVID-19 Top Three Reported Symptoms

According to a CDC analysis of $373{,}883$ confirmed COVID-19 patients, the top three most commonly reported symptoms are fever, cough, and shortness of breath (dyspnea).