VSC329 Reading Week 2: Seargent: Animal Epidemiology: Disease Patterns PART 1

Introduction

• Epidemiology studies disease patterns in animal populations, not random occurrences
• Epidemiologists analyze these patterns to understand disease causes for prevention and control
• Understanding patterns requires knowledge of individual animal disease behavior and disease agent movement
• Basic disease principles influence population-level patterns

Unit of Study

• Disease patterns are examined in individual animals or aggregated animal groups
• Aggregations are assumed to be randomly mixing for disease transmission, e.g., farms, herds
• Medical epidemiology studies individuals, while others study aggregations
• The unit of study is the primary biological unit in epidemiological investigations
• Foot-and-mouth outbreaks are more common in young cattle, with the individual animal as the unit of study
• Unit of study can be an aggregation such as a farm or village

Characteristics of the Unit of Study

• When describing disease patterns, relevant characteristics of the study unit are vital
• Species, sex, and age matter for individual animals, not for farms or ponds
• Hierarchical order: Animals in management units (pen, cage), then farms, then villages
• Characteristics relevant at a higher level apply equally to lower levels

Population Matters

• Epidemiologists focus on disease patterns in populations
• Understanding and differentiating involved populations is important
• Population at risk: individuals susceptible to a disease with exposure likelihood
• This includes non-diseased individuals, which provides the denominator for prevalence and incidence calculations
• The population at risk excludes those with innate or acquired immunity
• For pregnancy toxaemia outbreaks in sheep, the population at risk includes pregnant female sheep
• If the study unit is a pen or farm, the at-risk population is the farms or management units susceptible to the disease
• The at-risk population may be all animals on a farm or a specific subset such as age or management group
• Classical swine fever in Australia considers the at-risk population to be the entire pig population

Natural History of Disease in Individuals and Populations

• The natural history of a disease consists of its progress in an individual animal over time without intervention
• It begins with exposure to the disease agent and ends in recovery or death
• Epidemiologists use population-based methods to identify factors that affect the natural history, aiming to find prevention and control methods
• The starting point in infectious diseases is a host animal that can be infected and is susceptible
• Exposure involves interaction between the infectious agent and the host
• Infection occurs when the agent is present and replicates
• The incubation period is the time before clinical signs develop
• Animals with the disease can recover, become carriers, or die
• Infected animals may or may not develop clinical signs of disease
• Diseases can cause persistent infection or carrier states, where animals show little to no signs but shed the agent
• Recovered animals may gain immunity, which can be lifelong or temporary
• The spectrum of disease refers to these different stages collectively

Incubation Period

• The incubation period is the time between exposure to infection and the manifestation of clinical signs

Infectivity, Pathogenicity, and Virulence

• These terms relate to disease severity in populations
• Infectivity: proportion of susceptible individuals exposed to an agent who becomes infected
• Pathogenicity: percentage of infected individuals who develop clinical disease
• Virulence percentage of individuals with clinical disease who become seriously ill or die

Herd Immunity

• Progress of a disease is affected by herd immunity
• Herd immunity is the immunologically derived resistance of a group based on a large proportion's resistance
• Herd immunity can arise from innate immunity, natural infection, or vaccination
• Transmission slows within the population depending on the level of herd immunity
• High herd immunity may prevent establishment or eliminate infection
• Only a critical proportion of immune animals is needed
• If a minimum proportion of animals can be kept immune to infection, a disease can be eliminated from the population

Transmission and Spread

• To understand disease patterns, understanding the movement of disease agents through a population is key
• Need to know how agents can persist in a population
  • Transmission and Spread
• The chain of infection describes mechanisms by which an infectious agent moves from an infected agent to a susceptible host
• Disease agents need to escape from infected hosts and find new susceptible hosts to move around in a population
  • Transmission
• Refers to the movement of infection from an infected animal or susceptible animal
  • Spread
• Refers to the movement of infection from an infected population or sub-population to a susceptible population or sub-population

Methods of Transmission and Spread

• Interest in how a particular disease agent moves around will focus on different mechanisms depending on the unit of interest of the epidemiological investigation
• Transmission from animal to animal is the most fundamental level of interest
• Within a particular farm there may be interest in methods of spread from one management group to another
• Finally, quarantine authorities are interested in mechanisms of spread from country to country
  • Methods of transmission can be broadly classified as direct transmission or indirect transmission

Maintenance of Infection

• Infectious agents must survive in host animals, external environment, vectors, or reservoirs to remain active
• Host defense mechanisms may terminate infection, or the host may die, but in some cases infection persists and the host appears normal - carrier
• A carrier is an animal capable of transmitting infection, but shows no clinical signs
• Carriers can be incubatory, convalescent, or chronic and are very important in maintaining infectious diseases in populations.

Disease Reservoirs

• Infectious agents like foot-and-mouth disease virus can infect multiple host species
• Persistence in an area is facilitated by host species with varying disease susceptibility
• A host species is a reservoir when the disease agent normally lives and persists in it, spilling over to other hosts
• Hendra and Nipah viruses commonly occur in fruit bats, causing little disease in them but severe disease in other species
• Fruit bats act as a reservoir host for these viruses
• Generally, a disease reservoir is an animal, plant, environment, or combination in which an infectious agent lives and multiplies

Ecology of Disease

• Investigating natural disease requires understanding relationships among hosts, agents, and natural environments
• This determines the observed pattern of disease in time and space
• Climate significantly impacts the distribution of animals, disease agents, and vectors
• Ecology of disease extends the basic concept to include pathogens, which is the relationship among animals, pathogens, and their environment in a natural situation

Agent, host, and environment factors

• Humans intervening in natural ecological relationships affect organisms/disease, such as intensively farming livestock or encroaching on natural wildlife habitat
• This relationship is the epidemiological triad, where a particular set of conditions relating to the agent, host, and environment cause disease

Patterns of Disease by Animal or Other Unit of Study

• Epidemiologists document patterns of disease and analyze them for better cause understanding
• Disease patterns occur in time (temporal) and space (spatial), extend to characteristics of the unit of study
• Some species, sex, or age can be more affected by sharing a similar environment
• Understanding reasons for disease differences can lead to prevention and control strategies

Patterns of Disease by Time

• Analyzing disease occurrence over time can suggest causes and control measures
• Disease cases in a population tend to follow one of four patterns:
• Sporadic: Cases occur randomly
• Endemic: Cases occur regularly at a constant level
• Epidemic: Cases occur in time clusters
• Pandemic: An epidemic takes international proportions

Epidemic Curves

• The pattern of disease events over time is summarized here
• Provides a visual display of the magnitude of the event.
• It graphically represents the onset of cases, using a histogram, bar graph, or frequency polygon
• Frequency of new cases/outbreaks is plotted on the y-axis over a time scale on the x-axis

Different Types of Epidemic Curve

• Epidemic curves exist for sporadic, endemic, and epidemic diseases
  • Sporadic: Most time periods have no cases, occasional occurrences
  • Endemic: Varies between time periods, but fairly level
  • Epidemic Sharp initial increase, followed by slow decline

The Shape of the Curve

• An epidemic occurs when the frequency of cases exceeds the normal
• The slope of the ascending branch can reveal exposure, transmission
• The plateau and descending branch relate to susceptible-animal availability

Population Dynamics

• The plateau & slope depend on susceptible animals in the population
• Contact rate among animals impacts rate of spread
• Individuals described as:
  • susceptible
  • resistant
  • immune
  • incubating
  • diseased
  • dead
  • convalescent
  • recovered

Main and Secondary Peaks and Index Case

• A secondary peak arises from susceptible animals or movement between epidemic population
• The main peak may be preceded by a smaller one - index case
• Closed populations are easy to appreciate, but often become more complex
• Interventions like quarantine/treatment can change the curve shape

Why Do Epidemics Occur?

• Can occur by:
• Introducing an agent into a susceptible population
• Introducing a population into an infected area
• An increase in virulence
• Mode of transmission change
• Host susceptibility change
• Increased host exposure

Longer Term Patterns in Temporal Distribution of Disease

• Patterns or trends may be visible with longer data collection, such as :
  • Cyclic fluctuations
  • Seasonal variations
  • Secular trends
• Cyclical Trends: Patterns increase or decrease over months or years
• Seasonal Variations: Disease Occurrence changes seasonally
• Secular Trends: Long term changes occur

Identifying Temporal Patterns

• Time variations may not always be obvious from the curve
• Moving averages help identify cyclical/seasonal fluctuations
• Statistical methods can formally detect pattern types

Other representations of temporal patterns

• The estimated dissemination ratio (EDR) is a calculated measure that provides useful information on the rate of spread in an outbreak
• Calculated by # of cases found in defined period (7 days) / by the # of cases found in the previous 7 day period
• An eDR greater than 1, the epidemic is expending or declining if under 1

Mathematical Models

• Applied to describe the occurrence of disease + understanding risk factors + impact of control measures
• An example is the SIR (susceptible -infected-recovered) model & inclusion with the addiction of an exposed category in a SEIR (susceptible-exposed-infected-recovered) model/an approach assuming that infected animals that recover= susceptible again (SIS; susceptible infected susceptible modes)
• Models can be predictive or understanding

Patterns of Disease by Place

• The visual display of clustering of disease cases in time can provide a visual display of clustering in space
• Spatial Clustering of these disease cases can provide insights into possible exposure.
• Can be clustered with point exposure to soil deficiencies/ toxins
  • Spatially Limited to one paddock
• Spatial Patterns - Associated w/ animal movement
• Variations/Patterns that can be evaluated at varying scales
  • Local (paddock, pond or farm)
  • District
  • State
  • Regional levels
• Simple Maps Hand drawn, crude representations may be made
• Developments - Mapping software, and GPS

Plot both cases and non-cases

• Plot non-cases/diseases
• Mapping Prevalence/incidence is more important than disease
• Show the layout of a feedlot experiencing more mortalities
• Show diagrams of affected pens light shading
• Affected pens- cumulative percentages of mortality
• Look at spatial pattern in this outbreak