Taming the Cassava Virus Monster: A Research for Development Case Study

Taming the Cassava Virus Monster:

A Research for Development Case Study

James Legg: Review Seminar – IITA-Ibadan, March 22, 2011

CLARFIYING DEFINITIONS

1. A creature of abnormal form or

structure

2. One who deviates from normal or

acceptable behaviour or character

3. A threatening force

4. One that is highly successful

Merriam-Webster Definition

How do you tame it?

1. Stab it through the heart with a knife

Outcome. DEATH (unless it’s a vampire, in which

case you need a wooden stake)

2. Put some fresh cassava leaves in its supper

Outcome. DEATH

3. Infect it with a nasty chronic disease

(preferably a virus) Outcome. WEAKNESS

4. Be extra nice to it (and hope it reciprocates

the favour)

Outcome. UNAFFECTED

Chase it away

Effect of Taming Strategies on Outcomes

for Monsters and Humans

Taming Strategy Also Called Who Wins?

1 (Murder) Eradication Humans

2 (Infection) Mitigation Mainly humans

3 (Friendship) Co-existence Mainly monsters

4 (Chasing) Chasing Monsters Humans

…….but they can look pretty scary…

And together ‘attack’ humans indirectly through

removing ca. 1/3 of all production of one of their

food staples in Africa: Cassava

0

0.5

1

1.5

2

2.5

3

3.5

4

4.5

Hea

lthy

EACM

V-U

g

EACM

V-U

g+ACM

V

Kg/p

lant

Primarily Strategy 2

Mitigation

Human Defense Strategy Against this Attack ?

Adequate ?

CBSD incidence

2010(GLCI)

Map: Hein Bouwmeester

CBSDincidence

change2009-10

Map: Hein Bouwmeester

How Good has our Taming

been so far?

Cassava Mosaic Geminiviruses (CMGs)

Conventional HPR – virtual immunity

Cassava Brown Streak Viruses (CBSVs)

Limited effort

Promotion of ‘tolerant’ varieties

Cassava Whiteflies

Largely ignored. Virus management perceived

to be more straightforward

Problems in Taming CBSVs

Knowledge. Almost none prior to 2008

Symptoms. Cryptic. Field diagnosis hard

Awareness. Little before late 2000s

One-dimensional. Existing mitigation work

Status of CBSD Knowledge

Element Pre-2008 Post-2008 IITA

1. Partial sequencing S

2. Whole genome sequencing X

3. Confirmation of aetiology X

4. Symptom relationship characterization L

5. Crop loss assessment L

6. Determination of vector X

7. Characterization of transmission L

8. Field-based epidemiology L

9. Regional epidemiology L

10. Development of diagnostics S

11. Molecular markers L

12. Conventional HP tolerance L

13. Transgenic resistance X

Framework for CBSV

Research at IITA

Foundation of support through CORE

GLCI Project (IITA-Ibadan, IITA-Tanzania)

Biotechnology Project (IITA-Kenya)

Malawi CBSV Project (IITA: Tanzania, Ibadan

and Malawi)

167 (

f3/r

3)4

20

8(f

3/r

3)4

217(F

3R

3)2

292 (

F3R

3)1

168(f

3/r

3)4

229(f

3/r

3)4

170(f

3/r

3)4

231(f

3/r

3)4

178(f3/r3)4

21 (f3

R3)1

280

(f3R

3)1

177(

f3/r3)

4

173(

f3/r3)

4

186(

f3/r3

)4

207(

f3/r3

)4

293(f3/r3

)4

318(f3/r3

)4

326(f3/r3

)4

324 (F3R3)1

335(F3/R3)3

275(F3R3)2

243(10-11)2

173(10/11)3

335(10/11)3

209(10/11)3

273 (10/11)3

332(f3/r3)4

181(f3/r3)4273(F3R3)2271(F3R3)2173(F3/R3)3241(F3R3)1138(F3/R3)3243(F3/R3)3261(F3R3)2

250 (F3R3)1

247(F3/R3)3

248(F3R3)2

259(F3R3)2

EU916831 CBSV (BSA2) CP

EU916829 C

BSV (LWR2) C

P

EU916828 C

BSV (H

MA9) C

P

EU916827 C

BSV (N

TG10) C

P

EU

916832 CBSV (B

SA4) C

P

EU

916830 CBSV (IG

A8) C

P

295(f3

/r3)4

296(f3

/r3)4

298(f3

/r3)4

285(F

3/R

3)3

80(F

3R

3)2

EU

916825 C

BS

V (M

LB

3) C

P

FJ039520 C

BS

V-M

LB

Tz

EU

916826 C

BS

V (M

LB

9) C

P

209 (F

3R

3)1

32

8(F

3/R

3)3

33

7(f3

/r3)4

321(F

3/R

3)3

81 (F

3/R

3)3

14 (F

3R

3)1

23(1

0-1

1)2

274(1

0-1

1)2

281 (1

0-1

1)2

138(1

0-1

1)2

43 (F

3R

3)1

137(F

3/R

3)3

269 (F3R

3)1

82 (F3R

3)1

249 (F3R3)1

80 (1

0/11

)3

294(

f3/r3

)4

255(F3R3)2

289(f3/r3

)4

AY008441 CBSV (t

ype B) C

P

314(f3/r3

)4

FN423418 CBSV-Naliendele-2 (Tz

FN423416 CBSV-CP (Naliendele-1 Tz

FN423416 CBSV-Naliendele-1 ( Tz-N

FN423418 CBSV-CP (Naliendele-2-Tz

355(10/11)3357 (10/11)3359(10-11)2354 (10/11)3

355(F3R3)2

354(F3R3)2

357(F3R3)2

AY007597 CBSV CP

AY008440 CBSV (type C) CP

FN423417 CBSV-CP (Nam-Moz)

FN423417 CBSV Nam-Moz

AY008442 CBSV (type A) CP

AF311053 CBSV

FJ821794 CBSV (KBH2) CP

FJ821795 CBSV (KBH1) CP

AF311052 CBSV

356 (10-11)2

358(10-11)2

276(10-11)2

278(10-11)2

353(10/11)3

352(10-11)2

353(F

3R

3)2

279(1

0-1

1)2

280(1

0-1

1)2

FJ795780 S

PF

MV

-ug

0.1

CBSV

Karonga & Rhumpi

UCBSV

All areas

Diversity of CBSVs in Malawi(Slide from Lava Kumar)

70 isolates were analyzed from six districts

Based on 3’ coat protein gene sequence

Neighbor-Joining method; 1000 bootstraps

Reference sequences from GenBank are with accession numbers

CBSV Diagnostics

at IITA-Tanzania

CBSV Diagnostics Validation

CBSV 10/11

CBSV Real CBSV UG

F/R

CBSUV Real

CBSV + + - -

UCBSV-1 - - + +

UCBSV-2 + - + +

CBSV+UCBSV-1/2 + + + +

Tanzania CBSVs detected by primers combination

CBSV 10/11 with CBSV UG F/R detect > 99% real-time +ves

Working with IITA-Ibadan/NRI to add F3/R3, new primers

Putting PCR into practise

PCR underway: ISABU,

Bujumbura, Burundi

PCR results: ISAR,

Ruhengeri, Rwanda

Can it spread through plant parts ?

Can it spread via other plants ?

Is there a vector ?

If so, how good is it?

How important is plant vs. vector spread ?

What are the effects of environment ? (crop

intensity, crop management, variety, temperature)

Are all these things the same or different for

different viruses ?

New Understanding of EpidemiologyEpidemiology Questions

What are the conditions for doing

epidemiology experiments ?

Guaranteed CBSV-free planting material

TC introductions through NRI partnership

Establishment of isolated nuclear multiplication sites

Usambara Mountains – eastern Tanzania

Sensitive, reliable and robust diagnostics

Developed with IITA-Ibadan, NRI and FERA

Routine RT-PCR and real-time RT-PCR in Tanzania

Extensive experimental programme

Field and screenhouse experimental sites set up

Whitefly Control – CBSV Epidemiology

TC Epidemiology Trial – Kibaha,

Tanzania

TC Epidemiology Trial – Kibaha,

TanzaniaSecond Planting, cv. Kiroba – 4 sites

CBSD Epidemic Simulation - Kibaha

Materials: CBSD-infected spreader, CBSD-free test plants,

whiteflies introduced

Treatments: Drought and fertilization

Replicates: 1 (next to spreader) to 4 (far from spreader)

CBSD Epidemic Simulation Results

Inoculum Pressure Assessment StudyTertiary Multiplication Sites

Question? How does the location of a tertiary site

affect CBSD infection

Plan: Assess inoculum pressure for 20 tertiary

sites in Lake Zone, Tz

Measured: CBSD in multiplication sites as well as

surrounding farmers’ fields

Factors Compared: District, Source of planting

material, Inoculum pressure, Virus species

Virus Diagnostics: Used to confirm virus

presence and identity

CBSD incidence in multiplication sites vs.

surrounding farmers’ fields

Effect of distance from surrounding farmers’ fields

on CBSD incidence in multiplication sites

CBSVs in Inoculum

Pressure Study

(IITA-Tanzania)

21 CBSV 10-11

138 CBSV 10-11

120 CBSV 10-11

57 CBSV 10-11

108 CBSV 10-11

121 CBSV 10-11

116 CBSV 10-11

101 CBSV 10-11

94 CBSV 10-11

92 CBSV 10-11

141 CBSV 10-11

12 CBSV 10-11

135 CBSV 10-11

26 CBSV 10-11

80 CBSV 10-11

102 CBSV 10-11

18 CBSV 10-11

106 CBSV 10-11

131 CBSV 10-11

145 CBSV 10-11

137 CBSV 10-11

AY008440 short

AY008442 short

AY008441 short

AF311052 short

AF311053 short

141 CBSV UG

142 CBSV UG

123 CBSV UG

CBSV MLB9 short

129 CBSV UG

96 CBSV UG

54 CBSV UG

62 CBSV UG

DQ837303 short

DQ837302 short

DQ837304 short

22 CBSV UG

72 CBSV UG

98 CBSV UG

121 CBSV UG

105 CBSV UG

122 CBSV UG

35 CBSV UG

25 CBSV UG

25 CBSV 10-11

35 CBSV 10-11

98 CBSV 10-11

72 CBSV 10-11

52 CBSV 10-11

93 CBSV 10-11

CVYV short

25

65

65

37

45

90

37

18

14

48

50

19

49

10

57

72

43

75

36

98

65

32

62

30

50

43

0.02

CBSV

UCBSV

Farmers’ Fields:

Both UCBSV and CBSV

Tertiary Sites:

Mainly CBSV

Inoculum Pressure Assessment StudyOutcomes

Key Factors in CBSD infection?

Source of planting material: No

District location: No

Virus species prevalent: No

Proximity to neighbouring fields: YES

QMP outcomes: 8 out of 22 fields failed. All

isolated fields passed

Control implications: Isolation critical.

Training required

Vector TransmissionIITA partnering with NRI, UK (Maruthi)

CBSV/UCBSV: Summary of NRI/IITA PhD

results

Irrefutable confirmation of B. tabaci as vector

Min. acquisition period – 5 mins

Min. Inoculation period – 30 mins

Max. retention time – 1 hour

Results suggest semi-persistent transmission

Regional EpidemiologyTanzania Lake Zone Surveys 2000-2009

(Jeremiah and Ndyetabula)

Wf Pk 1 Wf Pk 2 Wf Pk 3 CBSD>10 CMD >50

Bukoba 2000 2004 2007 2008 2000

Muleba 2000 2004 2007 2007 2001

Biharamulo 2000 2004 2007 2007 2001

Karagwe 2002 2004 2009 2008 2005

Ngara 2002 2007 2009 2008 2005

Ukerewe 2000 2002 2009 2007 2001

Geita 2002 2009 2008 2001

Sengerema 2004 2009 2008 2005

Mwanza 2004 2009 2009 2003

Magu 2004 0 2009 2005

Kwimba 0 0 0 2007

Misungwi 2004 0 0 2007

Kibondo 2004 2007 0 2003

Kasulu 2004 2007 2008 2003

Kigoma 2004 2007 2009 0 2007

Bukombe 2004 2007 2009 2008 2005

Kahama 0 0 0 2009 0

Bunda 2004 2007 2007 2007

Musoma 2004 2007 2009 2007 2005

Tarime 2004 2007 2009 2007 2005

Serengeti 2007 2009 2008 2005

Whitefly Population Peaks vs.

Disease Outbreaks

0

2

4

6

8

10

12

W h it e ly a b u n d a n c e p e a k s

A v e r a g e D if f e r e n c e in Y e a r s

Proposed Model for Epidemiology

of CMD and CBSD Pandemics

Monster Taming StrategiesThe Case of CBSD

Taming Strategy Also Called Who Wins?

1 (Murder) Eradication Humans

2 (Infection) Mitigation Mainly humans

3 (Friendship) Co-existence Mainly monsters

4 (Chasing) Chasing Monsters Humans

Monster Taming StrategiesThe Case of CBSD

Taming Strategy Also Called Who Wins?

1 (Murder) Eradication Humans

2 (Infection) Mitigation Mainly humans

3 (Friendship) Co-existence Mainly monsters

4 (Chasing) Chasing Monsters Humans

Resistance breeding for CBSV

Tolerance and resistance. Continue

existing search

Wild relatives. Identify new sources of

resistance

Biotech approaches. Molecular markers

and GM

Resistance breeding for whiteflies

Existing germplasm

Strengthen Mitigation

Application to Introduce Eretmocerus

hayati for the control of Bemisia whiteflies in

Tanzania

Presented at the 16th Biological Control Agents sub-Committee

(BCAS) Meeting

SRI, Kibaha – February 25, 2011

Strategic Laboratory Network

Virus testing and indexing. Standard

protocols

NARS facilities. Regional support from IITA

Virus-free propagation material. In TC

Virus-free Strategic Propagation Sites

‘Holding site’, ‘Clean seed site’

Regional sites for decentralized

propagation

Virus-free Cassava Seed Systems

Community PhytosanitationCollective Action to Eradicate Viruses

Primary

Recipient

Community

Secondary

Recipient

Community

> 200m