AIDS Incubation Period Factors

Lecture 3: Epidemiology of Infectious Diseases

• The lecture was given by Marina Treskova, PhD, Head of Research Group, Eco-Epidemiology, Heidelberg Institute of Global Health & Interdisciplinary Centre for Scientific Computing, Heidelberg University.

Outline

• Infectious Diseases and Public Health
• Foundations of infectious diseases
• Endemic, epidemic, and pandemics
• Modeling epidemics

Infectious Diseases

• Caused by micro-organisms (viruses, bacteria, parasites, fungi, prions)
• Transmitted by humans, insects, animals, or the environment
• Follow patterns of symptoms, timing, and natural history
• Change over time due to evolving agents and changing environments (land use, climate change)

Infectious Disease Epidemiology: Specifics

• Addresses biology and patterns of specific infectious diseases
• Studies transmission patterns and distribution of risks
• Explores understanding of interactions, drivers, and processes
• Small-scale investigations (e.g., outbreaks) using "shoe-leather" epidemiology
• Studies population-level disease dynamics using mathematical models for surveillance and control strategies

Infectious Diseases: Terminology

• Endemic: Habitual presence of a disease within a geographic area
• Epidemic: Occurrence in a community or region of a group of illnesses exceeding normal expectancy
• Pandemic: A worldwide epidemic
• Zoonosis: Infection transmissible under natural conditions between vertebrate animals and humans
• Enzootic: Endemic among animal populations
• Epizootic: Epidemic among animal populations
• Spillover: Cross-species transmission of pathogen, where the recipient host is a dead-end host

Infectious Diseases: Terminology (Continued)

• Infectious Disease Agent: Microorganisms constantly adapt to changing conditions (antibiotics)
• Host: Human and animal populations constantly grow and move into new environments; influenced by factors including sex, race, age, occupation, nutrition, heredity, marital status, socioeconomic status, religious and social customs, immunization history, and previous history of disease
• Environment: Changes occur (locally and globally) naturally and through human intervention; such as temperature, pollution, water.

Infectious Disease: From Exposure to Disease

• Exposure: Person in a situation where effective transmission can occur
• Colonization: Presence of micro-organisms in or on a host with growth and multiplication, but without overt clinical expression
• Infection: Replication of the infectious disease agent in the human/animal body
• Asymptomatic: No symptoms are visible
• Symptomatic: Clinical symptoms are shown
• Recovery or Death

Infectious Disease Transmission: Reservoirs, Vector, and Vehicle

• Reservoir: Person, animal, plant, or environmental medium (soil, water) in which micro-organisms live and multiply, and may reproduce to infect the susceptible host
• Human reservoirs: Acute clinical cases, carriers (incubatory carriers, inapparent infections, convalescent carriers)
• Chronic carriers: People who harbor infections for a year or longer
• Animal reservoirs: Acute clinical cases and carriers
• Environmental reservoirs: Plants, soil, and water
• Vehicle: Inanimate object that transmits disease (e.g., glass of water, dirty rag)
• Vector: Living organism that transmits disease (e.g., Mosquitoes, flies, ticks)

Transmission: Portals of Exits and Entry

• Transmission depends on the source of the infectious agent and the portal of entry in the recipient host
• Respiratory: Respiratory diseases, droplet and airborne transmission
• Genitourinary: Sexually transmitted diseases
• Alimentary: Enteric diseases, fecal-oral transmission (food- and waterborne diseases)
• Skin: Superficial lesions and percutaneous transmission
• Transplacental: Portal of exit from mother to fetus

Mode of Transmission

• Two basic modes: Direct (contact with reservoir, droplet transmission) and indirect (animate/inanimate mechanisms, vectors, environmental vehicles including objects, food, water, milk, or biological products or surgical instruments)

Susceptible Host

• Susceptibility is affected by genetic factors and general resistance factors (body functions)
• Specific, acquired immunity is relevant (natural and artificial/vaccination)

Epidemic Development

• Epidemic peaks and sustained disease transmission, equilibrium, or recurrent epidemics, stages of the epidemic curve.

Natural History

• Incubation period: Time from infection to symptoms onset
• Latent period: Time from infection to infectiousness onset
• Infectious period: Time when the infected person is infectious
• Not directly observable but inferred from exposure history
• Observation-based infectiousness

Incubation Period

• Varies substantially among individuals due to route and dose of transmission, host genetics (age, immunity), interventions (pharmacologic prophylaxis and treatment).

Mode of Transmission

• Two basic modes are direct (contact with reservoir and droplet transmission) and indirect (animate or inanimate mechanisms.

Measures for Transmissibility

• Infection attack rate: Proportion of a population (subgroup) infected over the course of an epidemic
• Secondary attack rate: Proportion of individuals infected in a semi-closed setting by an index case
• Basic reproductive number (Ro): The average number of secondary cases generated by an index case in a fully susceptible population.

Disease Transmission

• Index case: First case identified
• Primary case: Case bringing infection to a population
• Secondary case: Infected by a primary case
• Tertiary case: Infected by a secondary case

Secondary Attack Rate (SAR)

• Measures infectiousness of a disease
• Represents the proportion of susceptible individuals infected after exposure to a primary case (e.g., household, workplace)

SAR: Interpretation and Application

• Higher SAR = Disease spreads easily in close-contact settings
• Lower SAR = Disease is less contagious or that interventions are effective

Basic Reproductive Number (Ro)

• Average number of secondary cases generated by an index case in a fully susceptible population
• R₀<1: Outbreak dies out
• R₀=1: Disease persists at a stable level
• R₀>1: Disease spreads exponentially, leading to an epidemic

Ro Interpretation

• Ro < 1: Each infected person causes less than one new infection, outbreak dies out
• Ro = 1: Each infected person causes one new infection, disease persists at a stable level
• Ro > 1: Each infected person causes more than one new infection, disease spreads exponentially, leading to an epidemic.

Basic Reproductive Number

• Average number of secondary cases generated by index cases in a fully susceptible population.

Ro Estimation

• Depends on specific disease transmission dynamics
• Formula: Ro = β / γ (β = transmission rate, γ = recovery rate)

SAR and RO

• SAR is a measure of transmission within specific close-contact settings
• RO measures population-wide transmissibility
• RO and SAR may differ due to diverse circumstances (no effective protection)

Timescale of Disease Transmission

• Generation time: Time between infection of one individual and the infection of another
• Serial interval: Time between symptom onset in primary cases and symptom onset in secondary cases

Latent Period

• Time between infection and becoming infectious
• Can be longer or shorter than the incubation period
• Isolation upon symptom onset is more effective for preventing transmission

Epidemic Growth Rate

• Depends on Ro and generation time (Tg)
• Ro = 1 + rTg
• Shorter generation time means faster epidemic growth

Examples

• Scenarios illustrating how Ro and generation time affect epidemic growth rate

Basic Reproductive Number

• Average number of secondary infections caused by one infected individual in a fully susceptible population
• Ro < 1, means that the epidemic will die out without exponential growth.
• Ro > 1, means that the pathogen can lead to an exponentially growing epidemic.

Exercises

• Exercises are provided for calculating SAR and RO, and applying concepts to various scenarios.

Infectious Disease Modeling

• Systematically translates assumptions and data regarding disease transmission into a quantitative description of epidemic evolution
• Aids in generating and testing epidemiological hypotheses; estimating transmission, the effectiveness of interventions, cost and effectiveness of strategies.

The Simplest Epidemic Model (SIR Model)

• Closed population divided into susceptible, infected, and recovered compartments
• Individuals are identical in susceptibility, infectiousness, and mixing behavior
• Hallmarks of an epidemic include exponential growth during the early phase, a unimodal epidemic curve, and peaks when Ro < 1.

SIR Epidemic Dynamics

• Visual Representation of the stages of the infectious disease spread, showing the various stages.

Vaccination

• Herd immunity is when a large proportion of a population is vaccinated therefore individuals are protected even if they are not vaccinated.
• Vaccination reduces risk of infection to an individual and also protects their contacts

Critical Vaccination Coverage

• Minimal proportion needed to be vaccinated to prevent epidemic
• Calculated as c* = 1-1/Ro (1-p = 1/Ro )

Herd Immunity and Vaccination Coverage

• Impacts of vaccination coverage on infection spread

Building More Complexities into the Model

• Considering stochasticity (random effects), detailed natural history, age structure of the population, and other time-dependent factors (e.g., seasonality or various populations connected by travel patterns)

Additional Topics

• Various more detailed models such as SEIR (with an explicit latent period) models and age structure models.