Health Inequities and Pandemic Risks in the COVID-19 Era

Horizontal Gene Transfer (HGT)

Movement of genetic material between non-parent organisms.

Adaptive Differences

Variations that enhance survival in specific environments.

Neutral Theory of Molecular Evolution

Most nucleotide substitutions are neutral, not adaptive.

Nucleotide Substitutions

Changes in DNA sequence that may not affect fitness.

Genetic Drift

Random changes in allele frequencies in populations.

Genome Content

Presence or absence of specific genes in genomes.

Gene Clusters

Groups of related genes that can be gained or lost.

Microbial Adaptation

Rapid changes in bacteria to survive environmental shifts.

Antibiotic Resistance

Ability of bacteria to survive exposure to antibiotics.

Metabolic Capabilities

Bacteria's ability to utilize different energy sources.

Thermal Niches

Specific temperature ranges where organisms thrive.

Synechococcus

Cyanobacterium found in hot spring microbial mats.

Upstream Populations

Bacterial populations in hotter areas of hot springs.

Downstream Populations

Bacterial populations in cooler areas of hot springs.

Stress-Response Genes

Genes that help organisms cope with environmental stress.

Enzymes Adapted to Temperature

Proteins that function optimally at specific temperatures.

Sequence Divergence

Difference in DNA sequences between species over time.

Outgroup Analysis

Using a closely related species to infer evolutionary relationships.

Ingroup

Group of species being studied for evolutionary traits.

Phylogeny

Evolutionary history and relationships among species.

Functional Genes

Genes that provide specific traits or capabilities.

Environmental Changes

Shifts in conditions affecting organism survival.

Mechanisms of Gene Transfer

Processes through which genes are exchanged between organisms.

Neutral Theory

Evolutionary changes driven by neutral mutations and drift.

Molecular Clock

Constant rate of neutral substitutions over time.

Rate of Molecular Evolution (r)

Equals neutral mutation rate μ under neutral theory.

Neutral Mutation Rate (μ)

Rate of neutral mutations per gene per generation.

Diploid Population Size (N)

Total number of alleles in a population.

Fixation Probability

Chance a mutation becomes established in a population.

Substitution Rate Formula

Rate (r) = (2Nμ) × (1/2N) = μ.

Cichlids of Lake Victoria

Diverged rapidly within ~15,000 years.

Monophyletic Group

Group sharing a common ancestor, not with others.

Convergent Evolution

Similar traits evolve independently in different lineages.

Purifying Selection

Elimination of deleterious mutations from a population.

Adaptive Mutations

Rare mutations fixed by positive selection.

Sequence Divergence

Genetic differences accumulated over time.

Outgroup Analysis

Using a related species to infer evolutionary relationships.

HIV-1 Zoonotic Transfer

HIV-1 entered humans from chimpanzees in early 1900s.

Active Sites

Functionally important regions conserved under purifying selection.

Orthologous Sequences

Genes in different species derived from a common ancestor.

Fossil Calibration Data

Used to establish timelines for molecular evolution.

Genetic Divergence Plot

Graph showing % substitutions against divergence time.

Evolutionary Rate Differences

Varies across proteins; some evolve faster than others.

Variable Regions

Parts of proteins subject to neutral drift.

Evidence for Constant Rate

Straight line in divergence vs. time plot.

Convergent Evolution

Independent evolution of similar traits in different species.

DNA Sequence Convergence

Rare occurrence of similar DNA sequences evolving independently.

Neutral Theory

Molecular evolution primarily driven by neutral drift.

Mutation Categories

Deleterious, Neutral, Adaptive mutations in evolution.

Rate of Evolution

Constant rate equal to neutral mutation rate.

Molecular Clock

Method to date evolutionary events using mutation rates.

Outgroup Analysis

Infers divergence using related species without fossils.

Lake Victoria Cichlids

Monophyletic group that diversified in Lake Victoria.

HIV Origin

Molecular clock used to date zoonotic transmission.

Variation in Rates

Predicts conserved vs. variable regions for function.

Functional Inference

Determining function based on evolutionary conservation.

Human Virus Definition

Criteria for classifying a virus as human-associated.

Long-Term Evolution

Virus adaptation through prolonged circulation in humans.

Sustained Transmission

Virus spreads sustainably among humans (Rt > 1).

Evolution of Adaptations

Genetic changes enhancing infection and transmission in humans.

Exclusive Human Reservoir

Virus exists only in humans, no animal reservoirs.

SARS-CoV-1

Virus with sustained human transmission during 2002-03 outbreak.

SARS-CoV-2

Transitioned to a pandemic virus with human adaptations.

Ebola Virus

Adapted for human transmission during West Africa epidemic.

Measles Virus

Long-term human virus with specific adaptations.

Polio Virus

Exclusive to humans, significant for eradication efforts.

Smallpox Virus

Eradicated virus with no animal reservoirs.

Transmission Dynamics

Patterns of virus spread among human populations.

Human Virus

Virus that primarily infects humans.

Eradication

Complete elimination of a virus from a population.

SARS-CoV-1

Virus responsible for the 2003 SARS outbreak.

Ebola

Virus causing severe hemorrhagic fever outbreaks.

Transmission Chain

Sequence of virus spread among hosts.

Human Adaptation

Virus changes enabling it to infect humans.

Public Health Threat

Potential risk posed by infectious diseases.

Virus Evolution

Changes in virus genetics over time.

Emergence

Initial appearance of a virus in a population.

Criterion

Standard used to classify human viruses.

Measles

Virus with a long history of human infection.

Smallpox

Human virus targeted for eradication.

Global Virome Project (GVP)

Initiative to catalog unknown viral species.

PREDICT

Surveillance program for high-risk virus spillovers.

Virosphere

Global ecosystem of viruses in various hosts.

High-Throughput Sequencing

Rapid DNA sequencing technology for virus discovery.

Biosafety Level (BSL)

Classification of laboratory safety protocols.

Field Sampling

Collecting samples from natural environments.

Cost-Effectiveness

Economic efficiency of a public health strategy.

Spillover

Transmission of viruses from animals to humans.

Hotspot

Area with high risk of virus transmission.

Actionability

Ability to implement public health responses.

Early Detection

Identifying viruses before they spread widely.

Virus Cataloging

Systematic documentation of viral species.

Global Virome Project (GVP)

A global catalog of viruses for research.

PREDICT Approach

Surveillance method for early epidemic prevention.

Horizontal Genetic Transfer (HGT)

Gene acquisition from other organisms, not parents.

Adaptive Evolution

Evolutionary changes enhancing survival and reproduction.

Point Mutations

Single nucleotide changes affecting protein function.

Gene Duplications

Copying genes to increase expression potential.

Adaptive Divergence

Evolution of duplicated genes into specialized functions.

Conservatism in Evolution

Morphological stability despite molecular changes over time.