This document provides an introduction to the course PPATH 503: Epidemiology and Forecasting of plant disease. It defines key epidemiological concepts such as epidemic, epidemiology, monocyclic and polycyclic pathogens. It discusses how host, pathogen and environmental factors influence disease development. It also examines the history of epidemiology from ancient times to modern developments. Disease progress curves and mathematical modeling of epidemics are introduced.

1. WELCOME
PPATH 503: Epidemiology and
Forecasting of plant disease
K. M. GOLAM DASTOGEER
LECTURER
DEPARTMENT OF PLANT PATHOLOGY
BANGLADESH AGRICULTURAL UNIVERSITY

2. Epidemic
Gr. Epi=upon, among and Demons=people
Epidemic What is among people
"Change in disease intensity in a host population over time and space."
Change: often increase -- a dynamic process
Disease: dealing with diseases, not just the pathogen (or plant/crop)
Host: Organism infected (or potentially infected) by another organism
Population: a population phenomenon
Time and space: two physical dimensions of interest.

3. 3
Epiphytotic Unger (1833), Whetzel (1920's)
However, equally valid meaning from Greek:
"what is in (or among) a population" ("demio")
"Epidemic" used for plants for a long time…..
•1728: Duhamel 1691,1842: book titles
•1858: Kuhn 1901: Ward
Thus, no valid reason to use "epiphytotic“
Therefore the issue has been resolved!!!
NOTE:
If one used epiphytotic
(instead of
epidemic), then one
should use
epiphytotiology instead
of epidemiology!
-(Epiphytology is the
study of epiphytes).

4. Epidemiology
• Study of epidemics.
• Science of disease in populations. Vanderplank (1963)
• Ecology of disease.
• Study of the spread of diseases, in space and time, with the objective to trace
factors that are responsible for, or contribute to, epidemic occurrence.
• The science of populations of pathogens in populations of host plants, and the
diseases resulting therefrom under the influence of the environment and human
interferences.
4

5. History (ancient to modern times)
Disease
5
Hippocrates (~400 BC): First use of "epidemic", widespread disease (human diseases
Theophrastus (~340 BC): Plant diseases in fields, Environmental influences
Pliny (~50 AD): Plant diseases; soil; climate
Duhamel de Monceau (1728 AD): Disease progress curves, Comparison of plant and
animal epidemics
Late 19th Century and forward…
Kuhn (1858) - 1st textbook of plant pathology
Ward (1901): book "Diseases in Plants" emphasized ecology (populations) of disease
Jones (1913) - role of the environment
Gaumann (1946): "Principles of Plant Infection” -Disease spread, -Conditions leadin
to an epidemic, -'Infection Chain' (= disease cycle), -compare with medicine (diseases
of humans)

6. 6
Large (1952, and others)
-Disease progress curves
-Crop losses
-Disease assessment (measurement)
Horsfall & Dimond (1960)- "Plant Pathology, Volume
3"
-Populations
-Inoculum density:disease relations
-Spore dispersal
-Analysis (mathematics)
-Forecasting, prediction
-Traditional definition ---> Modern definition
Gregory (1963, 1973)
"The Microbiology of the Atmosphere"
-spore dispersal, disease spread
Aerobiology
Vanderplank (1963) (used to be van der
Plank)
"Plant Diseases: Epidemics and Control"
-Populations
-Rates (dynamic processes)
-Analysis, mathematics
-Models, theory
-Link epidemiology and control
-Established the science of plant disease
epidemiology
Other pioneers:
Zadoks (1960-1995), The Netherlands
Kranz (1968-1995), Germany
Waggoner (1960-mid --1980s), USA
S. Nagaranjan 1983-India
Note: many developments in other fields…
Ecology, medical epidemiology,
Biomathematics, etc.

7. Elements of an Epidemic
1.Host
2. Pathogen
3. Environment
Interactions of the 3 main components
are described by the disease triangle.
The Disease Triangle
Disease development is also affected by
4. Time
5. Humans
Disease Tetrahedron
Interactions of the 5
components are
described by the disease
pyramid.

8. Elements of an Epidemic (cont’)
i. Genetic resistance or susceptibility of Host
–Vertical Resistance
–Horizontal Resistance
ii. Degree of genetic uniformity of host in a particular field
–Monoculture, especially Clones
–Natural, Intermingled Populations
iii. Type of crops
- Annual crops & foliar or fruit diseases develop much
more rapidly (in weeks)
- Perennial woody diseases take longer time to develop
(in years)
iv. Age of host plants
- Some plants are susceptible only during growth period
& become resistant during mature period
8
How the Plant Affects Development of Epidemics

9. How Pathogens Affect Development of Epidemics
i. Levels of virulence
–Faster Production of Larger # Inoculum
ii. Quantity of inoculum near hosts
iii. Type of reproduction of the pathogen
–Monocyclic
–Polycyclic
•Responsible for most Sudden, Catastrophic Epidemics
–Polyetic
iv. Ecology of the pathogen
–Reproduce on Surface of Aerial Parts of Plant
–Reproduce inside Plant
–Reproduce on Infected Plant Parts in Soil
v. Mode of spread of the pathogen
–Breezes or Strong Winds
•Most Sudden & Widespread Epidemics
–Inoculum Carried by Airborne Vectors
–Wind-Blown Rain
–Carried on Seed, Tubers, Bulbs
–Beetles
–Pathogens Spreading through Soil
•Usually Local, Slow-Spreading Diseases of Considerable Severity
Elements of an Epidemic (cont’)

10. Elements of an Epidemic (cont’)
3. Environmental factors
i. Moisture
- Rain, dew, high humidity
- Dominant factor in diseases caused by
oomycetes, fungi, bacteria & nematodes
ii. Temperature
- Affects disease cycles of pathogens
Disease development is also
affected by
4. Time
Time factors
 Season of the year
 Duration & frequency of favorable temp. &
rains
 Appearance of vectors, etc.
5. Humans
 Site Selection & Preparation
 Selection of Propagative Material
 Introduction of Exotic Pathogens
 Cultural Practices
 Disease control measures
I ntroduction of new pathogens or disease
How Humans Affect Development
of Epidemics

11. Monocyclic pathogen
A monocyclic pathogen completes just
one disease cycle per season. In
monocyclic pathogens the primary
inoculum is the only inoculum
available for the entire season, and
there is no secondary inoculum and
no secondary infection.
Can you think of
some examples
of monocyclic
 Soilborne pathogens are usually
monocyclic due to physical constraints--
inoculum is not dispersed within the
growing season.
11

12. Monocyclic Disease
12
• Examples: smuts, rusts, which require two
alternate hosts, many soil-borne diseases,
root rots and vascular wilts
• In general, there are three types of plant
diseases that tend to produce only one
infection cycle per host cycle (1)
postharvest diseases, (2) diseases caused
by soil-borne plant pathogens, and (3)
rusts without a urediniospore stage.

13. 13
Some rust and smut fungi are
monocyclic because their life cycles
take a full season to complete.
Oat smut
Cedar-apple rust

14. Polycyclic pathogens/Disease
14
Pathogens that produce more than one
(2 to 30) infection cycle per crop cycle
Disseminate primarily by air or airborne
vectors (insects)
Responsible for epidemics on most
crops
downy mildews, late blight of potato,
powdery mildews, leaf spots and
blights, grain rusts, and insectborne
viruses.
In polycyclic fungal pathogens, the primary
inoculum often consists of the sexual spore or
sclerotia.
once primary infection takes place, large
numbers of asexual spores (secondary
inoculum) are produced at each infection site
and these spores can themselves cause new
(secondary) infections that produce more
asexual spores for more infections.

15. 15

16. Polyetic(multiyear) pathogens
 polyetic(multiyear) pathogens: In some
diseases of trees,fungal vascular
wilts,phytoplasmal declines, and viral
infections, pathogen may not complete a
disease cycle, it may not produce inoculum
that can be disseminated and initiate new
infections, until at least the following year
and some may take longer.
 Such diseases are basically monocyclic, but
if they take more than a year to complete
the cycle, they are called polyetic
• Several rusts of trees and the
mistletoes,they attak several years to go
through all the stage sof their life cycle
and to initiate new infections. Dutch elm
disease, cedar apple rust, white pine
blister rust, and citrus tristeza
16

17. 17
Disease progress curve for a typical monocyclic pathogen

18. Disease progress curve for polyclicic epidemic
18

19. Why use disease progress curves?
19
‐ Compare control measures
‐ Compare effect of environment on disease development
‐ Predict future disease development
‐ Disease forecasting for improved control

20. 20
•All Measurable Components Considered
–Virulence of Initial Inoculum
–Effects of Environment
–Crop’s Disease Resistance
–Crop’s Growth Stage
–Length of Time Plant & Pathogen Interact
–Effectiveness of various Disease Management Strategies
–Weather Stations or Sensors over Crop Canopies
•Mathematical Equations Developed to Describe the Epidemic
•Models often Limited to specific Climates & Regions
•Some Models Better than Others
•Refined over Time when Additional Data can Be Included
Modeling Epidemics

21. Why modeling?
21
Summarize the behavior of a disease in a population
Provide quantitative estimates of the relationships of interest
Identify the critical factors driving epidemics
A model to simplify reality that describes and predicts disease behavior
used to predict the effect of disease control strategies or their timing

22. 22
To reduce disease incidence, x, at any
point in the epidemic:
1. Reduce initial inoculum, x0
2. Reduce rate of infection, r
3. Reduce duration of epidemic, t

23. 23
Diseases caused by monocyclic pathogens are analogous to investment
with simple interest; diseases caused by polycyclic pathogens are analogous
to investment with compound interest.
Disease increase in plant populations is sometimes compared to the increase
of invested capital over time.

24. • With simple interest, capital grows at a constant rate
(the interest bearing capital remains unchanged).
• With compound interest, invested capital grows at an
increasing rate over time as the earned interest is
reinvested.
24

25. • To reduce disease incidence, x, at any point in the epidemic:
• 1. Reduce initial inoculum, Xo
• 2. Reduce rate of infection, R
• 3. Reduce duration of epidemic, t 25

26. 26

27. 27

28. 28
Measuring Disease in a Population
Disease incidence
Actual number or proportion of plants diseased
Number diseased out of total number of plants
observed
Disease severity
•Area of plant tissue affected by disease
•For many diseases, severity is the area of plant surface covered by lesions
•Measured using assessment scales or by determining the area under a disease
progress curve (AUDPC)
3. Yield loss
•The proportion of yield that the grower will not be able to harvest due to disease
•Results in economic loss

29. 29
1. Molecular tools
 Polymerase Chain Reaction (PCR), Enzyme
Linked Immunosorbant Assay (ELISA), DNA
Fingerprinting, etc.
 For rapid & accurate detection & identification of
pathogens
2. Data management
 Geographic Information System (GIS), Global
Positioning System (GPS), Remote Sensing, etc.
 To assist in disease control strategies
3. Disease modeling & forecasting
 To predict the probability of outbreaks
New Tools in Epidemiology

30. Disease-gradient or dispersal curve
• The amount of disease is greater near the source
of inoculum
30
•The amount of
disease decreases
with increasing
distance from the
source

31. Managing Epidemics
• Monocyclic Model X = XoRt
• Polycyclic Model: X = Xoert
• Two ways to reduce X (disease):
• Reduce the initial inoculum X0
– delay onset and reduce the duration of the epidemic
• Reduce the rate of disease development (R or r)
31

32. Effect of X0 on Epidemic Development
X0 depends upon:
• inoculum from previous crops within a field
• inoculum from crops in adjacent fields
32
X0 is affected by:
• destroying infested plant debris
• removing diseased plants
• chemical seed treatments
• protective fungicides
• race specific disease resistance‐
• biological control agents targeted at initial inoculum

33. 33

34. Effect of r on Epidemic Development
r depends upon:
• reproductive potential of the
pathogen
• virulence of the pathogen
• susceptibility of the host
• conduciveness of environment
r is affected by:
• non-specific disease resistance
• systemic fungicides
• cultural practices that alter
environment
• removal of diseased plants
34

35. 35

36. Disease Control
Effect of Reducing Primary Inoculum
36

37. Mathematical modeling in plant disease epidemiology
• Monomolecular:
– appropriate for modeling
monocyclic epidemics
– also called negative
exponential model
• Exponential
– also known as the logarithmic,
geometric or Malthusian model.
• Logistic
– more appropriate for most
polycyclic diseases
– most widely used for describing
epidemic
• Gompertz
– appropriate for polycyclic diseases as an
alternative to logistic models. Gompertz
model has
– an absolute rate curve that reaches a
maximum more quickly and declines more
gradually than the logistic
– models
37
1. Disease progress curves

38. 38

39. 2. Linked differential equations
(LDE)
3. Area under disease progress
curve (AUDPC)
• generally used to make
comparison between
treatments
• to evaluate the resistance of
plant species
• Computer simulation
– EPIDEM
– MYCOS
– EPIMAY
– EPIVEN
– EPIMUL
– EPIDEMIC
– PLASMO
39

40. 40

41. Applications of Geographic Information Systems and Geostatistics
in Plant Disease Epidemiology and Management
• These satellites broadcast signals
containing time and position
information. GPS receivers on the
ground collect the satellite signals
and determine position in a
spherical coordinate system such
as latitude and longitude or a
planar coordinate system
41
Global positioning systems (GPS)
• GPS receivers determine location
and are among the most important
tools for spatially referencing
agriculture data.
• GPS depends on a system of
navigation satellites operated by
the U.S. Department of Defense
(the NAVSTAR system).

42. GIS
• GIS relates the data collected by
GPS to other sources of geo-
referenced information.
• GIS has the ability to integrate
layers of spatial information and
to uncover possible relationships
• The process of transforming one
layer of spatial information to
match a second layer is called
registration . 42
• A GIS is a computer system
capable of assembling, storing,
manipulating, and displaying
data referenced by geographic
coordinates.
• GIS can now be installed on
any recent model desktop
computer

43. There are two main forms of GIS data:
vector and raster.
• In vector data sets, map
features such as points,
lines, and polygons are
organized and manipulated
in a database.
• In raster data sets, the
data are organized as a
matrix of numerical
values and referenced
spatially by row and
column position
43

44. Geostatistics
• a statistical model
appropriate for estimates
across continuous areas
• Create surface maps
based on point samples
or observations.
• A surface map is a map
with an area shaded in a
color or gray scale keyed
to a variable.
44

45. 45

46. Benefits
• provides a tool for the refined analysis of traditional
and contemporary biological/ecological information
on plant diseases.
• It will aid practitioners in the design of disease
management in IPM programs, particularly on a
regional scale.
• It will also provide a way of analyzing and
communicating results of regional programs on a
continuing basis. 46

47. 47
Books Recommended

48. Two more books
• Plant disease Epidemiology–S. Nagaranjan-
India
• A text book of plant pathology- H.
Ashrafuzzaman-Bangladesh
48

49. 49