Book notes: Epidemics, Models and Data using R (Ottar N. Bjørnstad, 2018)

This post records the notes when I read Epidemics, Models and Data using R byOttar N. Bjørnstad.

The text in this book is designed to be more of a “practicum in infectious disease dynamics.”

Introduction

In-Host Persistence

• “in-host persistence” refers to the ability of a pathogen to persist in a host for a long time, e.g., retroviruses as HIV, latent viruses as herpes viruses, symbionts that are beneficial to the host (viz. commmensals and mutualists) etc.
• Acute infections are those that are cleared by the immune system, e.g., influenza, measles, and chickenpox.
• From an epidemiological point of view, it is important to make the functional—as opposed to taxonomical—classification of pathogens because it allows us to under- stand the differences in age-specific attack rates and contrasting disease dynamics.

Patterns of Endemicity

• Local persistence fails when a local chain-of-transmission breaks. This can happen for two very different reasons:
  1. The transmission bottleneck is when a pathogen is insufficiently transmissible to sustain a chain of transmission (Note that this is different from the transmission bottleneck describing virions passed between individuals);
  2. at the opposite end of the spectrum is the susceptible bottleneck for acute pathogens that are so transmissible that they burn through susceptibles much faster than they are replenished.
• The locally persistent infections can be classified as:
  1. Stable endemics that show little variation in incidence through time. (e.g. HIV)
  2. Seasonal endemics that show low’ish-level predictable seasonal variation around some mean. (e.g. Cholera)
  3. recurrent epi- demics that may be regular or irregular are characterized by violent epidemic fluc- tuations over time. (e.g. measles)

SIR