Bacteria and Viruses: Focus on HIV & COVID-19

Comprehensive vocabulary flashcards covering bacterial and viral structures, antibiotic mechanisms and resistance, HIV replication and phases of AIDS, HAART, SARS-CoV-2 infection pathways, vaccine development stages, and antiviral treatments.

Pathogens

Disease-causing agents that encompass living organisms (such as bacteria, fungi, and parasites) as well as nonliving infectious particles (such as viruses and prions).

Bacteria

Single-celled prokaryotic microorganisms lacking a membrane-bound nucleus and membranous organelles, possessing a single strand of DNA and ribosomes, and capable of doubling in number every $20\,\text{minutes}$.

Prions

Nonliving, infectious misfolded proteins that cause normal cellular proteins to misfold into disease-associated forms, leading to transmissible spongiform encephalopathies such as Mad Cow disease and Creutzfeldt-Jakob disease.

$\text{PrP}^C$ and $\text{PrP}^{Sc}$

$\text{PrP}^C$ is the normal alpha-helical cellular form of the prion protein, whereas $\text{PrP}^{Sc}$ is the misfolded, aggregated beta-sheet form associated with fatal neurodegenerative prion disease.

Creutzfeldt-Jakob Disease

A rapidly progressive, fatal human neurodegenerative disease caused by prions, characterized by rapid brain shrinkage, deterioration, and spongiform pathology in brain tissue.

Antibiotics

Drugs formulated to stop the growth or spread of pathogenic bacteria, which can also inadvertently destroy beneficial bacteria.

Bacterial Resistance via Natural Selection

The evolutionary process in which an antibiotic acts as a selective agent on pre-existing genetic diversity, killing susceptible bacteria while allowing rare, pre-existing resistant mutants to survive and multiply, shifting gene frequencies in the bacterial population.

Viruses

Extremely small, nonliving infectious agents containing a protein coat (capsid) enclosing either RNA or DNA (not both) that lack metabolic activity and can only replicate inside a living host cell.

Human Immunodeficiency Virus (HIV)

A retrovirus (RNA virus) that causes progressive destruction of the human immune system by infecting helper T ($\text{CD4}$) cells via binding to $\text{CD4}$ and chemokine co-receptors such as $\text{CCR5}$.

Acquired Immunodeficiency Syndrome (AIDS)

A pandemic condition resulting from advanced HIV infection, diagnosed when helper T cell counts fall below $200\,\text{cells/mm}^3$ or when specific opportunistic infections and cancers appear.

Reverse Transcriptase

A viral enzyme in retroviruses like HIV that transcribes single-stranded viral RNA into double-stranded DNA; its high replication error rate produces frequent mutations, driving drug resistance and vaccine evasion.

Helper T Cells ($\text{CD4}$ Cells)

Immune cells that multiply upon pathogen detection to secrete cytokines and activate B cells to produce antibodies; they are the primary host cell targets destroyed by HIV.

HIV Infection: Phase I

The acute initial stage of HIV infection lasting weeks to years, characterized by rapid viral replication, an ineffective antibody response, and transient flu-like symptoms (swollen lymph nodes, chills, fever, fatigue, body aches).

HIV Infection: Phase II

The chronic stage of HIV infection occurring within $6\,\text{months}$ and lasting up to $10\,\text{years}$, characterized by a steady decline in helper T cells; $95\%$ of untreated individuals progress to clinical AIDS.

HIV Infection: Phase III (Clinical AIDS)

The terminal stage of HIV infection where helper T cell levels drop below $200\,\text{cells/mm}^3$, resulting in severe opportunistic diseases including pneumonia, tuberculosis, meningitis, Kaposi's sarcoma, and Non-Hodgkin lymphoma.

Kaposi's Sarcoma

An opportunistic cancer causing characteristic red or purple skin lesions that frequently manifests during Phase III (Clinical AIDS).

Highly Active Antiretroviral Therapy (HAART / cART)

A multi-drug combination treatment initiated early in HIV infection that targets multiple stages of viral replication (entry, reverse transcription, integration, assembly) to delay or prevent progression to clinical AIDS.

Entry Inhibitors

A class of antiretroviral drugs that obstruct HIV from attaching to host $\text{CD4}$ receptors and co-receptors ($\text{CCR5}$ or $\text{CXCR4}$), thereby blocking fusion with the host cell membrane.

Integrase Inhibitors

A class of antiretroviral medications that block the viral integrase enzyme, preventing the integration of viral DNA into the host cell's nuclear genome.

Protease Inhibitors

A class of antiretroviral drugs that inhibit the viral protease enzyme responsible for cleaving viral polyproteins, thereby halting the assembly and maturation of infectious viral particles.

Pre-exposure Prophylaxis (PrEP)

An HIV prevention regimen taken by HIV-negative individuals that achieves $99\%$ effectiveness when taken $7\,\text{days/week}$ to block viral reverse transcription or integration before infection takes hold.

Truvada and Descovy

Daily oral PrEP medications containing a fixed combination of two distinct reverse transcriptase inhibitors: Emtricitabine and Tenofovir diphosphate.

Apretude

An extended-release injectable PrEP medication containing cabotegravir, an integrase inhibitor administered monthly to prevent HIV infection.

Berlin Patient

A historically significant HIV-positive individual who attained long-term viral remission after receiving a bone marrow transplant from a donor carrying a homozygous mutation in the $\text{CCR5}$ receptor gene.

Coronavirus

A family of enveloped, positive-sense single-stranded RNA viruses named for their crown-like surface protein spikes, divided into alpha, beta, gamma, and delta subgroups.

SARS-CoV-2

A novel beta coronavirus originating in bats and first identified in Wuhan, China in 2019 that binds to human respiratory and vascular receptors to cause COVID-19.

Angiotensin-Converting Enzyme 2 (ACE2)

A host cell surface receptor that normally regulates blood pressure, which the SARS-CoV-2 surface spike protein binds to facilitate viral entry into lung, heart, kidney, intestine, and endothelial cells.

TMPRSS2

A host cell surface transmembrane serine protease that cleaves the SARS-CoV-2 spike protein at the cell membrane, activating viral-host membrane fusion and RNA entry.

Viral Replicase

An RNA-dependent RNA polymerase complex encoded by SARS-CoV-2 that directs the replication of viral genomic RNA and the transcription of subgenomic mRNAs inside host cytoplasmic complexes.

Exploratory Stage (Vaccine Development)

The initial phase of vaccine development involving basic laboratory research to discover natural or synthetic antigens capable of preventing disease, typically taking $2\text{ to }4\,\text{years}$.

Pre-clinical Stage (Vaccine Development)

The second phase of vaccine development lasting $1\text{ to }2\,\text{years}$, during which candidate vaccines are formulated, optimized for dosage, and evaluated for safety and immune responses in cell cultures and animal models.

Phase 1 Clinical Trial

The first stage of human vaccine testing involving up to $100$ healthy volunteers, lasting several months, focused primarily on evaluating safety and identifying adverse side effects.

Phase 2 Clinical Trial

The clinical trial phase lasting several months to $2\,\text{years}$ in a larger group of participants to continue safety monitoring, evaluate side effects, and gather preliminary data on effectiveness.

Phase 3 Clinical Trial

The extensive human testing phase involving hundreds to thousands of participants over $1\text{ to }4\,\text{years}$ to prove efficacy and safety before submitting an approval application to the FDA.

Phase 4 Clinical Trial

The ongoing post-licensure research and monitoring stage conducted after FDA marketing approval to evaluate long-term outcomes and compare the vaccine against competing therapies.

Paxlovid

An oral antiviral therapy combining nirmatrelvir and ritonavir, best administered within $5\text{ to }7\,\text{days}$ of symptom onset to inhibit viral replication in COVID-19 patients.

Veklury (Remdesivir)

An intravenous antiviral drug administered once daily for $3\,\text{days}$ to treat COVID-19 patients who are at elevated risk for developing severe disease.

Lagevrio (Molnupiravir)

An oral antiviral medication authorized exclusively for adult COVID-19 patients when initiated within $5\text{ to }7\,\text{days}$ of symptom onset.