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PPATH 503: Epidemiology and Forecasting of plant disease

K. M. GOLAM DASTOGEERLECTURERDEPARTMENT OF PLANT PATHOLOGYBANGLADESH AGRICULTURAL UNIVERSITY

EpidemicGr. Epi=upon, among and Demons=peopleEpidemic 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.

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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 ofepidemic), then one

should useepiphytotiology instead

of epidemiology!-(Epiphytology is the study of epiphytes).

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.

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History (ancient to modern times)Disease

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Hippocrates (~400 BC): First use of "epidemic", widespread disease (human diseases)Theophrastus (~340 BC): Plant diseases in fields, Environmental influencesPliny (~50 AD): Plant diseases; soil; climateDuhamel de Monceau (1728 AD): Disease progress curves, Comparison of plant and animal epidemics

Late 19th Century and forward…Kuhn (1858) - 1st textbook of plant pathologyWard (1901): book "Diseases in Plants" emphasized ecology (populations) of diseaseJones (1913) - role of the environmentGaumann (1946): "Principles of Plant Infection” -Disease spread, -Conditions leading to an epidemic, -'Infection Chain' (= disease cycle), -compare with medicine (diseases of humans)

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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 NetherlandsKranz (1968-1995), GermanyWaggoner (1960-mid --1980s), USAS. Nagaranjan 1983-IndiaNote: many developments in other fields…Ecology, medical epidemiology,Biomathematics, etc.

Elements of an Epidemic

1.Host2. Pathogen3. Environment

Interactions of the 3 main componentsare described by the disease triangle.

The Disease Triangle

Disease development is also affected by4. Time

5. Humans

Disease Tetrahedron

Interactions of the 5 components are

described by the disease pyramid.

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 period8

How the Plant Affects Development of Epidemics

How Pathogens Affect Development of Epidemics i. Levels of virulence

–Faster Production of Larger # Inoculumii. Quantity of inoculum near hostsiii. 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’)

Elements of an Epidemic (cont’)

3. Environmental factorsi. Moisture

- Rain, dew, high humidity- Dominant factor in diseases caused byoomycetes, fungi, bacteria & nematodes

ii. Temperature - Affects disease cycles of pathogens

Disease development is also affected by4. 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 measuresI ntroduction of new pathogens or disease

How Humans Affect Development of

Epidemics

Monocyclic pathogenA 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 pathogens?

Soilborne pathogens are usually

monocyclic due to physical constraints--inoculum is not dispersed within the

growing season.

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Monocyclic Disease

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• 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.

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Some rust and smut fungi aremonocyclic because their life cyclestake a full season to complete.

Oat smut

Cedar-apple rust

Polycyclic pathogens/Disease

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Pathogens that produce more than one (2 to 30) infection cycle per crop cycleDisseminate 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.

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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 (multiyear).

• 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

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Disease progress curve for a typical monocyclic pathogen

Disease progress curve for polyclicic epidemic

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Why use disease progress curves?

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‐ Compare control measures

‐ Compare effect of environment on disease development

‐ Predict future disease development

‐ Disease forecasting for improved control

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•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

Why modeling?

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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

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To reduce disease incidence, x, at any point in the epidemic:1. Reduce initial inoculum, x02. Reduce rate of infection, r3. Reduce duration of epidemic, t

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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.

• 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.

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• 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

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Measuring Disease in a Population

Disease incidenceActual number or proportion of plants diseasedNumber diseased out of total number of plantsobserved

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

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1. Molecular tools Polymerase Chain Reaction (PCR), EnzymeLinked Immunosorbant Assay (ELISA), DNAFingerprinting, etc. For rapid & accurate detection & identification ofpathogens

2. Data management Geographic Information System (GIS), GlobalPositioning 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

Disease-gradient or dispersal curve

• The amount of disease is greater near the source of inoculum

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•The amount of disease decreases with increasing distance from the source

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)

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Effect of X0 on Epidemic Development

X0 depends upon:• inoculum from previous crops within a field• inoculum from crops in adjacent fields

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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

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Effect of r on Epidemic Developmentr 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

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Disease ControlEffect of Reducing Primary Inoculum

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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

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1. Disease progress curves

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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

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Applications of Geographic Information Systems and Geostatisticsin 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

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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).

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 .

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• 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

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

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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.

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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.

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Books Recommended

Two more books• Plant disease Epidemiology–S. Nagaranjan-

India• A text book of plant pathology- H.

Ashrafuzzaman-Bangladesh

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