Epidemics and Management Decisions Kari Arnold, A.J. Campbell, Neil McRoberts.

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Epidemics and Management Decisions

Kari Arnold, A.J. Campbell, Neil McRoberts

Concerns in Leafroll Management• Is leafroll spreading in California?

– Yes, Golino et. al. 2008, Oakville study (GLRaV-3)• How is it spreading?

– Patterns, rate, epidemiology– Mealybugs, scale insects

• Late 1980’s, initial discovery, now more real than ever• Can we control the vector? • Where are they coming from?• If I remove and replace a block, how quickly will it become re-infected?

• Certified stock– Why invest in certified wood if my block will just become re-

infested?• Region Based Management

– What if I decide to control leafroll, but my neighbors don’t?

Biology Impacts Epidemiological Characteristics of a Disease

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• Vectors– Acquisition/transmission/

persistence– Life cycles – Mode of travel

(crawling/flying/nematodes)

• Spores– Wind spread/rain splash– Life cycles

• Humans– Machinery/clothing– Grafting

• Weather Patterns– Wind/Rain/Drought– Temperature

• Point of entry on host– Seed borne– Soil borne– Susceptible tissue

• Monocyclic/Polycyclic– Primary inoculum sources– Secondary inoculum sources

The Importance of Mapping

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“An epidemic is the progress of disease in TIME and SPACE”

Kranz, J. 1990. Epidemics, their mathematical analysis and modeling: An introduction. In: Epidemics of Plant Diseases: Mathematical Analysis and Modeling, 2nd Edn. Springer, Berlin.

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5 years of census data*

The Importance of Mapping

5 2 0 0 0 0 5 2 2 2 2 1 2 2 2 5 3 2 3 2 3 3 3 3 2 3 3 1 1 2 2 3 3 5 5 5 0 0 0 0 0 1 3 1 4 1 3 0 5 0 0 2 0 5 1 0 1 1 1 1 1 1 1 1 1 2 2 2 0 0 0 2 4 5 4 4 3 0 5 5 5 3 4 5 5 0 3 2 2 2 0 5 0 5 0 4 0 42 2 0 0 0 0 0 3 2 1 2 2 2 2 2 5 3 2 3 1 2 3 3 2 3 2 2 2 1 2 5 3 3 5 5 5 3 0 0 0 0 0 2 1 1 2 3 5 0 0 0 2 0 5 1 5 3 1 1 1 1 1 1 1 1 2 3 1 0 0 0 3 5 4 5 5 3 5 5 5 0 3 5 5 5 0 3 2 2 2 0 3 0 5 0 3 0 05 0 5 2 0 0 0 5 2 1 2 1 2 2 2 2 5 3 2 3 3 3 3 5 2 2 2 2 1 3 5 2 2 5 5 5 3 0 5 0 0 0 1 1 5 1 3 0 0 5 5 1 0 4 3 5 1 1 1 1 1 1 1 1 1 1 2 1 0 0 0 5 0 3 4 5 4 5 5 0 5 2 0 0 5 0 5 1 2 2 2 5 2 0 2 4 0 02 0 0 0 0 0 0 5 2 1 2 1 2 2 2 2 3 2 2 1 2 2 3 5 4 5 2 2 1 2 4 3 3 3 3 0 4 5 5 5 0 0 2 1 0 0 5 0 0 0 0 0 3 4 3 5 1 1 1 1 1 1 1 2 1 2 2 2 0 0 0 2 0 2 5 0 5 0 5 0 5 3 5 0 0 5 5 1 2 2 2 5 3 0 0 0 0 02 0 0 0 0 0 5 5 2 1 1 2 2 2 5 4 4 1 3 1 3 3 3 5 5 5 3 2 2 2 4 5 4 5 2 0 5 5 5 5 5 0 3 1 5 0 0 5 0 0 4 0 3 4 3 3 1 1 1 1 1 1 1 1 1 1 3 3 0 0 3 1 2 1 5 4 0 0 5 0 4 4 5 5 0 1 5 3 2 2 2 5 2 0 2 1 0 00 2 0 5 0 0 5 5 2 1 1 2 2 2 4 5 4 1 3 1 3 4 2 5 5 5 5 2 2 3 5 5 4 3 3 5 5 5 0 4 0 5 2 2 3 2 3 0 0 0 0 0 4 4 3 3 1 1 1 1 1 1 1 2 1 1 5 4 0 0 3 2 2 2 5 2 5 2 0 0 5 5 5 5 5 5 5 2 2 4 2 5 5 0 0 5 2 01 2 0 0 0 0 0 5 1 1 1 2 2 2 2 2 2 2 2 1 2 4 3 5 4 5 3 1 2 2 5 5 4 2 4 0 5 5 5 4 5 5 1 2 4 5 0 0 0 0 0 5 3 3 3 1 1 1 1 1 1 1 1 2 1 1 0 0 0 0 0 2 2 1 5 3 5 2 5 0 0 5 5 0 0 5 2 2 5 0 2 5 2 0 2 0 0 00 2 0 3 0 0 0 4 2 1 2 2 2 4 2 2 3 2 2 2 1 5 5 3 5 5 2 2 3 3 4 5 5 2 5 5 3 5 5 4 0 5 2 2 5 0 0 0 5 0 0 5 2 1 3 1 3 1 1 1 1 1 1 1 1 1 0 0 4 0 4 3 3 2 5 2 4 2 5 0 0 0 5 0 0 5 5 3 4 0 2 5 2 0 2 0 0 10 2 0 2 0 0 0 2 1 1 2 3 2 3 2 5 3 2 3 3 2 5 5 2 5 5 5 2 2 3 4 5 5 4 5 3 5 4 5 3 0 0 2 2 0 0 0 5 0 1 0 5 3 1 3 0 1 1 1 1 1 1 1 1 2 1 3 0 0 0 0 5 4 2 0 4 5 5 0 5 5 0 0 0 0 5 5 2 5 0 2 0 2 2 1 0 0 20 0 0 3 0 0 5 2 2 1 2 2 4 4 2 5 4 2 4 2 3 5 3 3 5 5 4 2 2 2 3 5 5 5 3 1 5 5 0 2 0 0 0 5 5 0 0 0 4 0 0 5 3 1 3 0 1 3 1 1 1 1 1 1 1 1 4 0 0 0 0 5 4 4 5 4 5 5 0 2 5 5 5 0 0 5 5 1 5 0 2 2 5 0 1 0 0 00 2 0 4 0 0 5 2 2 2 2 3 4 2 4 5 5 4 3 4 2 4 2 2 5 5 5 2 1 2 4 5 5 5 3 2 5 3 5 2 0 0 5 0 3 5 0 5 3 0 0 5 1 1 2 3 1 1 1 1 1 1 1 1 1 1 3 0 0 0 0 5 5 4 5 3 5 5 0 5 0 5 0 5 0 0 0 1 5 0 2 0 0 0 1 0 2 00 2 0 5 0 5 0 2 2 2 2 4 3 2 5 2 2 4 3 4 2 3 1 2 5 5 5 2 1 2 4 5 4 3 5 3 5 2 5 4 5 5 5 5 5 0 0 2 4 0 0 5 3 1 1 2 1 2 1 1 1 1 1 1 2 1 3 0 0 0 0 5 3 4 5 5 5 5 0 3 0 5 0 0 0 5 0 2 0 0 2 2 0 4 1 0 5 00 0 0 5 0 5 0 5 2 2 2 4 2 5 5 2 3 5 5 5 4 2 1 2 4 5 5 2 2 2 5 5 5 0 0 4 5 3 5 5 0 5 0 5 0 0 0 2 2 0 0 5 3 1 2 2 1 2 1 1 1 1 1 1 2 2 3 0 0 0 0 5 3 2 4 0 5 0 5 5 5 5 5 5 0 5 0 2 0 0 2 2 0 4 1 5 0 50 0 0 0 0 0 0 5 3 2 2 2 4 2 5 2 3 5 3 4 4 4 1 2 3 4 5 2 2 4 5 5 5 5 5 5 5 4 5 5 0 0 4 5 0 0 0 3 2 0 0 5 2 1 2 3 1 1 1 1 1 1 1 1 3 2 3 0 0 0 0 0 4 3 5 0 0 0 5 0 5 5 4 5 0 5 0 2 0 5 2 2 0 5 2 3 3 50 1 0 0 0 0 0 5 3 2 2 2 4 2 2 4 5 3 3 4 4 2 1 1 2 3 5 3 4 5 5 5 5 5 5 5 5 5 5 5 0 5 3 0 0 0 0 0 2 0 0 5 3 1 2 2 1 3 1 1 1 1 1 1 2 2 3 3 0 0 0 5 3 4 5 5 5 5 5 0 0 0 3 5 5 0 1 2 0 4 2 2 0 3 2 2 2 00 1 0 0 0 0 0 5 3 2 2 2 4 2 2 2 5 4 4 2 3 3 1 1 2 2 5 5 4 5 5 5 5 4 5 5 5 5 5 0 0 5 4 0 5 0 0 5 2 0 0 0 5 1 1 2 1 1 1 1 1 1 2 2 1 2 3 2 3 0 4 2 2 5 5 2 5 5 0 0 0 0 5 0 0 5 0 2 5 4 2 2 0 2 4 1 2 50 2 0 0 0 5 5 2 3 2 2 1 2 5 2 2 5 4 4 3 3 5 1 1 1 2 5 5 2 5 5 0 5 4 5 5 5 5 0 0 0 5 5 5 0 0 0 5 1 1 4 5 5 1 1 1 1 1 1 1 1 1 2 2 3 2 4 3 4 0 3 0 3 5 3 4 4 5 0 5 0 5 1 0 0 4 5 4 0 4 2 2 2 2 2 1 2 00 0 0 0 0 5 5 2 3 2 1 2 2 0 2 2 5 5 4 4 2 5 1 1 1 3 5 5 5 3 5 5 5 3 5 5 5 5 5 0 0 5 0 0 0 0 0 0 3 2 4 5 5 1 1 2 1 1 1 1 1 2 2 3 3 1 3 4 0 0 4 0 0 4 2 3 5 0 5 0 0 5 2 0 0 5 4 5 0 2 2 2 2 2 2 1 2 0

TIME and SPACE

Epidemiology

TIME

% I

NCI

DEN

CE

5 2 0 0 0 0 5 2 2 2 2 1 2 2 2 5 3 2 3 2 3 3 3 3 2 3 3 1 1 2 2 3 3 5 5 5 0 0 0 0 0 1 3 1 4 1 3 0 5 0 0 2 0 5 1 0 1 1 1 1 1 1 1 1 1 2 2 2 0 0 0 2 4 5 4 4 3 0 5 5 5 3 4 5 5 0 3 2 2 2 0 5 0 5 0 4 0 42 2 0 0 0 0 0 3 2 1 2 2 2 2 2 5 3 2 3 1 2 3 3 2 3 2 2 2 1 2 5 3 3 5 5 5 3 0 0 0 0 0 2 1 1 2 3 5 0 0 0 2 0 5 1 5 3 1 1 1 1 1 1 1 1 2 3 1 0 0 0 3 5 4 5 5 3 5 5 5 0 3 5 5 5 0 3 2 2 2 0 3 0 5 0 3 0 05 0 5 2 0 0 0 5 2 1 2 1 2 2 2 2 5 3 2 3 3 3 3 5 2 2 2 2 1 3 5 2 2 5 5 5 3 0 5 0 0 0 1 1 5 1 3 0 0 5 5 1 0 4 3 5 1 1 1 1 1 1 1 1 1 1 2 1 0 0 0 5 0 3 4 5 4 5 5 0 5 2 0 0 5 0 5 1 2 2 2 5 2 0 2 4 0 02 0 0 0 0 0 0 5 2 1 2 1 2 2 2 2 3 2 2 1 2 2 3 5 4 5 2 2 1 2 4 3 3 3 3 0 4 5 5 5 0 0 2 1 0 0 5 0 0 0 0 0 3 4 3 5 1 1 1 1 1 1 1 2 1 2 2 2 0 0 0 2 0 2 5 0 5 0 5 0 5 3 5 0 0 5 5 1 2 2 2 5 3 0 0 0 0 02 0 0 0 0 0 5 5 2 1 1 2 2 2 5 4 4 1 3 1 3 3 3 5 5 5 3 2 2 2 4 5 4 5 2 0 5 5 5 5 5 0 3 1 5 0 0 5 0 0 4 0 3 4 3 3 1 1 1 1 1 1 1 1 1 1 3 3 0 0 3 1 2 1 5 4 0 0 5 0 4 4 5 5 0 1 5 3 2 2 2 5 2 0 2 1 0 00 2 0 5 0 0 5 5 2 1 1 2 2 2 4 5 4 1 3 1 3 4 2 5 5 5 5 2 2 3 5 5 4 3 3 5 5 5 0 4 0 5 2 2 3 2 3 0 0 0 0 0 4 4 3 3 1 1 1 1 1 1 1 2 1 1 5 4 0 0 3 2 2 2 5 2 5 2 0 0 5 5 5 5 5 5 5 2 2 4 2 5 5 0 0 5 2 01 2 0 0 0 0 0 5 1 1 1 2 2 2 2 2 2 2 2 1 2 4 3 5 4 5 3 1 2 2 5 5 4 2 4 0 5 5 5 4 5 5 1 2 4 5 0 0 0 0 0 5 3 3 3 1 1 1 1 1 1 1 1 2 1 1 0 0 0 0 0 2 2 1 5 3 5 2 5 0 0 5 5 0 0 5 2 2 5 0 2 5 2 0 2 0 0 00 2 0 3 0 0 0 4 2 1 2 2 2 4 2 2 3 2 2 2 1 5 5 3 5 5 2 2 3 3 4 5 5 2 5 5 3 5 5 4 0 5 2 2 5 0 0 0 5 0 0 5 2 1 3 1 3 1 1 1 1 1 1 1 1 1 0 0 4 0 4 3 3 2 5 2 4 2 5 0 0 0 5 0 0 5 5 3 4 0 2 5 2 0 2 0 0 10 2 0 2 0 0 0 2 1 1 2 3 2 3 2 5 3 2 3 3 2 5 5 2 5 5 5 2 2 3 4 5 5 4 5 3 5 4 5 3 0 0 2 2 0 0 0 5 0 1 0 5 3 1 3 0 1 1 1 1 1 1 1 1 2 1 3 0 0 0 0 5 4 2 0 4 5 5 0 5 5 0 0 0 0 5 5 2 5 0 2 0 2 2 1 0 0 20 0 0 3 0 0 5 2 2 1 2 2 4 4 2 5 4 2 4 2 3 5 3 3 5 5 4 2 2 2 3 5 5 5 3 1 5 5 0 2 0 0 0 5 5 0 0 0 4 0 0 5 3 1 3 0 1 3 1 1 1 1 1 1 1 1 4 0 0 0 0 5 4 4 5 4 5 5 0 2 5 5 5 0 0 5 5 1 5 0 2 2 5 0 1 0 0 00 2 0 4 0 0 5 2 2 2 2 3 4 2 4 5 5 4 3 4 2 4 2 2 5 5 5 2 1 2 4 5 5 5 3 2 5 3 5 2 0 0 5 0 3 5 0 5 3 0 0 5 1 1 2 3 1 1 1 1 1 1 1 1 1 1 3 0 0 0 0 5 5 4 5 3 5 5 0 5 0 5 0 5 0 0 0 1 5 0 2 0 0 0 1 0 2 00 2 0 5 0 5 0 2 2 2 2 4 3 2 5 2 2 4 3 4 2 3 1 2 5 5 5 2 1 2 4 5 4 3 5 3 5 2 5 4 5 5 5 5 5 0 0 2 4 0 0 5 3 1 1 2 1 2 1 1 1 1 1 1 2 1 3 0 0 0 0 5 3 4 5 5 5 5 0 3 0 5 0 0 0 5 0 2 0 0 2 2 0 4 1 0 5 00 0 0 5 0 5 0 5 2 2 2 4 2 5 5 2 3 5 5 5 4 2 1 2 4 5 5 2 2 2 5 5 5 0 0 4 5 3 5 5 0 5 0 5 0 0 0 2 2 0 0 5 3 1 2 2 1 2 1 1 1 1 1 1 2 2 3 0 0 0 0 5 3 2 4 0 5 0 5 5 5 5 5 5 0 5 0 2 0 0 2 2 0 4 1 5 0 50 0 0 0 0 0 0 5 3 2 2 2 4 2 5 2 3 5 3 4 4 4 1 2 3 4 5 2 2 4 5 5 5 5 5 5 5 4 5 5 0 0 4 5 0 0 0 3 2 0 0 5 2 1 2 3 1 1 1 1 1 1 1 1 3 2 3 0 0 0 0 0 4 3 5 0 0 0 5 0 5 5 4 5 0 5 0 2 0 5 2 2 0 5 2 3 3 50 1 0 0 0 0 0 5 3 2 2 2 4 2 2 4 5 3 3 4 4 2 1 1 2 3 5 3 4 5 5 5 5 5 5 5 5 5 5 5 0 5 3 0 0 0 0 0 2 0 0 5 3 1 2 2 1 3 1 1 1 1 1 1 2 2 3 3 0 0 0 5 3 4 5 5 5 5 5 0 0 0 3 5 5 0 1 2 0 4 2 2 0 3 2 2 2 00 1 0 0 0 0 0 5 3 2 2 2 4 2 2 2 5 4 4 2 3 3 1 1 2 2 5 5 4 5 5 5 5 4 5 5 5 5 5 0 0 5 4 0 5 0 0 5 2 0 0 0 5 1 1 2 1 1 1 1 1 1 2 2 1 2 3 2 3 0 4 2 2 5 5 2 5 5 0 0 0 0 5 0 0 5 0 2 5 4 2 2 0 2 4 1 2 50 2 0 0 0 5 5 2 3 2 2 1 2 5 2 2 5 4 4 3 3 5 1 1 1 2 5 5 2 5 5 0 5 4 5 5 5 5 0 0 0 5 5 5 0 0 0 5 1 1 4 5 5 1 1 1 1 1 1 1 1 1 2 2 3 2 4 3 4 0 3 0 3 5 3 4 4 5 0 5 0 5 1 0 0 4 5 4 0 4 2 2 2 2 2 1 2 00 0 0 0 0 5 5 2 3 2 1 2 2 0 2 2 5 5 4 4 2 5 1 1 1 3 5 5 5 3 5 5 5 3 5 5 5 5 5 0 0 5 0 0 0 0 0 0 3 2 4 5 5 1 1 2 1 1 1 1 1 2 2 3 3 1 3 4 0 0 4 0 0 4 2 3 5 0 5 0 0 5 2 0 0 5 4 5 0 2 2 2 2 2 2 1 2 0

Random Introduction of Infection Events (Wind, machinery etc) neighboring blocks matter*

0%-5% 1

1

Aggregation Stage, spread is predominantly within the block, with small levels of random infection events

25%-50%+ 2 22 2 2

3 2 31 2 32 2

22 2 2

3 2 22 3 3 3

2 31 2 2 2

Random Infections and Aggregated Infections less successful*, great source of inoculum

70%+2 2 3 32 2 2 5 2 5 53 2 2 3 5 2 5 3 52 1 2 1 2 2 2 2

2 1 2 3 1 1 35 1 2 2 1 3 3 25 5 1 1 2 3 2 23 2 3 3 2 1 2 35 2 5 2 2 1 2 25 5 5 5 2 3 2 1 2 35 5 5 3 1 2 3 1 2 2

Quality and disease supply chains in the wine industry

FPSNurseriesor othersources

Production Consumers

$

Supply of quality

Disease

Disease increases production costs, reduces efficiencyof supply of quality per unit effort along the chain

Disease supply chain interactions in maintaining vine block health

I

R

H

r

C

β

FPSNurseriesor othersources

Production Consumers

r c

Some things areonly controlled inproduction

β

Some things areonly controlled byinteractions

Interaction model of block health

I

R

H

r

C

β

RRHcIdt

dR

IHrHRdt

dH

IRcIrHdt

dI

)1(

)1(

Production Chain

Baseline prediction using leafroll group guesstimates of parameter values

From low initial infection,system stabilizes with:

66% Infected blocks28% Healthy blocks (no LR)6% blocks in rotation

What is the effect of keeping blocks out of production for longer?

Fallow cleared blocks for oneseason:


3-3.5% reduction in Infected blocks1.5% reduction in Healthy blocks5% increase in blocks in rotation

Net gain (?) because blocks coming out of rotation are more likely to be healthy

Decrease inter-block spread?


10% reduction in Infected blocks10% increase in Healthy blocks<1% decrease in blocks in rotation

Big gain in healthy blocks (10% compared with baseline). Is it feasible?

Production

Where is it coming from?The predominant reason for reinfection and spread is…

…NEARBY INFECTED BLOCKS.

My neighbor’s leafroll is my leafroll….

My leafroll is my neighbor’s leafroll….

My leafroll is my leafroll….

What if I do, but Others Don’t?

Is there a tipping point for area wide disease management in terms of GLRaV-3?

Analysis of subjectivities about leafroll disease management among California grape growers and winemakers

Analysis/Results• Initial PCA via MVSP (37 individuals)• Approx. 16% similarity– Approx. 84% different– 37 people, 37 distinctly different opinions (Grp.1)

-4 -2 0 2 4

-4-2

02

4

Axis 1 [%Variance=14.1]

Axi

s 2

[%V

aria

nce

=9.1

]

-4 -2 0 2 4

-4-2

02

4

A

-4 -2 0 2 4

-4-2

02

4

Axis 3 [%Variance=8.5]

Ax

is 2

[%

Va

ria

nc

e=

9.1

]

-4 -2 0 2 4

-4-2

02

4

B

Certified Wood

EUREKA!EVERYONE FEELS

STRONGLY ABOUT THE CERTIFICATION

PROCESS AND VIRUS TESTING…YEAH!

Bridging the GapInitial group, production side

Second group, predominantly nursery growers

-20 -10 0 10 20

-20

-10

010

20

Axis 1

Axi

s 2

-20 -10 0 10 20

-20

-10

010

20

A

-20 -10 0 10 20

-20

-10

010

20

Axis 3

Axi

s 2

-20 -10 0 10 20

-20

-10

010

20

B

Bridging the Gap

Nurseries feel strongly about these issuesAND concerns differ based on your business goals

-20 -10 0 10 20

-20

-10

010

20

Axis 1

Axi

s 2

-20 -10 0 10 20

-20

-10

010

20

A

-20 -10 0 10 20

-20

-10

010

20

Axis 3

Axi

s 2

-20 -10 0 10 20

-20

-10

010

20

B

These 6 statements enforced the importance of virus testing and the certification program in

terms of leafroll management

Bridging the Gap

Try to see the world from the other person’s perspective.

Build good relationships within the supply chain, and nurture those relationships. Work with each other.

Honesty is a good thing.

Remember* you may not realize what you have, until it’s gone….

Leafroll Symptoms (depending on grape variety and leafroll type)

Red fall color in red varietiesGreen vein banding

Rolling under of leaves in some varieties

Reduced vigorReduced yieldIrregular/delayed ripening of fruitReduced sugar content in fruit

Don’t be fooled…Potassium deficiency?Girdling?J rooting?Pierce’s disease?Other viruses?…

Leafroll…

How can I be sure?

Diagnostic Tests Sampling Structures

COMPOSITE SAMPLE vs. INDIVIDUAL SAMPLEEx. 5 vines per sample *1 vine per sample Benefit:More field coverage

Set back:Not a good estimate of disease incidence in field

Benefit:Better estimate of disease incidence in field

Set back:Less field coverage

Ask yourself:What do I want to know about my block?

What do I intend to sample?

0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 00 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 00 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 00 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 00 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 00 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 00 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 00 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 00 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 00 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 00 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 00 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 00 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 00 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 00 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 00 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 00 0 0 0 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 00 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 00 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 00 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 01 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 00 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 00 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 00 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 00 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 10 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 00 0 0 1 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 00 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

COMPOSITE SAMPLE vs. INDIVIDUAL SAMPLEEx. 5 vines per sample *1 vine per sample Benefit:More field coverage

Set back:Not a good estimate of disease incidence in field

Benefit:Better estimate of disease incidence in field

Set back:Less field coverage

Sampling StructuresWhat do I want to know about my block?

What do I intend to sample?

Symptom Based vs. “Blind” Sampling• Verification of visual

symptoms in red varieties in the “fall”

• If assessing incidence (%) without mapping entire block, make sampling plan prior to entering block to avoid positive bias*

• Many white varieties• Sauvignon blanc?

• Need an estimate of incidence or knowledge of infested areas prior to symptom expression

Sampling in the Real World• Large Cabernet Block• Blind Sample*

needed an estimate of disease incidence in January

• Wanted to know disease incidence and locations of leafroll-3 and red blotch to help in deciding on block removal

How do we sample for something we know so little about?

Red Blotch

Enter Neil and A.J. – assess what we do know

• Data collection, going to the field: what are we looking for?

• Vineyard maps: what is the current situation?

• Epidemiological analysis: what does it all mean?

• Recommendations: what can we advise based on the data?

Learning symptoms and making maps

• Analyze data covering multiple years to obtain a clearer picture of virus “spread”

• Characterize Red Blotch patterns statistically to allow sample size/reliability calculations

What do we want to know?

Rate of Increase

*based on initial data; a more accurate picture may emerge with more information

Potential development of Red Blotch epidemics over time based on parameters gathered from Cab. Sauv. blocks at Oakville station

Potential Disease Progress Curves

Data collected in 3 blocks over 3 year period

Characterizing patchiness – the key to sampling efficiency

• Develop best management plans for different types/sizes of vineyard operations to facilitate use of sampling

How Many Samples Do I Take?

Mean disease incidenceDisease patchiness index

Group size (composite size)Desired confidenceinterval

nNumber of samples

It depends on your goals

Sampling at the Vine LevelCanes

Petioles

*At least 2 samples, 1 from each cordon (more is better)

Talk to your diagnostics lab….

Visual sampling can be accurate and people can quickly become proficient

Disease Ratings PCR result0 neg0 neg0 neg1 neg1 neg1 neg2 neg2 neg2 pos3 pos3 pos3 pos4 pos4 pos4 pos5 pos5 pos5 neg

Visual ratings against PCR resultsin 12 Zinfandel vines

Visual rating PCR- PCR+<=2 8 1>2 1 8

0.9 0.10.1 0.9

True Negative Proportion

False Positive Proportion = 1-TNP

True Positive Proportion

False Negative Proportion = 1-TPP

LR+= 8LR-= 0.125

For decision-making under uncertainty, the likelihoodratios are important

¿Want more details?

http://qbelab.plantpathology.ucdavis.edu/working-papers/

Acknowledgements• American Viticulture Foundation• Dominus Estates• Study participants and Workgroup members• FPS, Deborah Golino, Michael Anderson, Neil

McRoberts, Bob Gilbertson, QBE lab colleagues• Mark Lubell and the Environmental Pol. Lab• Monica Cooper with UCCE• Current and past Plant Path grads• Grapevines, mealybugs, and leafroll • VIRUSES!!

http://qbelab.plantpathology.ucdavis.eduQuestions/Concerns/Comments?

http://qbelab.plantpathology.ucdavis.edu/

http://qbelab.plantpathology.ucdavis.edu/

Epidemics and Management Decisions Kari Arnold, A.J. Campbell, Neil McRoberts.

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Transcript of Epidemics and Management Decisions Kari Arnold, A.J. Campbell, Neil McRoberts.