Virus diseases in Carrots:

The UK experience

Adrian Fox

Fera Science Ltd

What is Fera Science Ltd?

Carrot virus research in Europe (up to 2012)

Scotland: Carrot Motley Dwarf complex

Hogweed virus 6 (and others…)

Netherlands: Carrot Motley Dwarf complex

HV6 (Carrot yellow leaf virus)

Parsnip yellow fleck

Germany: Carrot Yellow leaf virus

Carrot thin leaf virus

England: Parsnip Yellow fleck virus

Carrot Red leaf virus

Carrot red leaf associated viral RNA

Current state of Knowledge

Carrot necrotic dieback virus

(Formerly Parsnip yellow fleck

virus – Anthriscus strain)

• Important early season disease

• Sporadic outbreaks

• Associated with seedling death

• Stunted, misshapen roots in

mature plant infections

• Needs Anthriscus yellows virus

(AYV) for transmission

• Carrot is not a host AYV therefore

NO onward transmission in carrot

crops

Source: AAB DPV394

Current state of Knowledge

Carrot Motley Dwarf disease

• Three pathogen complex Carrot

red leaf virus (CtRLV), Carrot

mottle virus, Carrot red leaf

associated viral RNA

• Needs CtRLV for aphid

transmission

• CAN be spread from carrot to

carrot

• Causes reddening of leaves and

mottle

• Thought to cause splits in roots

called ‘kippering’

Rooting out the cause of internal browning

Viral browning of carrots (HDC FV382a)

0

10

20

30

40

50

60

70

80

90

100

PYFV CRLV CRLaV CMoV CYLV Negative

sa

mp

les p

osit

ive

Virus

affected

unaffected

Stocks of carrots rejected due to the

presence of internal necrosis linked

to viruses.

Conventional PCR of

affected &

unaffected carrots

showed no

association with

expected viruses

MiSeq sequencing identified

Carrot yellow leaf virus in

necrotic samples. Sequencing

also detected a Closterovirus

(CtCV-1) and a Torradovirus

(CaTV-1) plus several other

viruses which were new to

science.

Real-time PCR

demonstrated a

strong association

between CYLV and

necrosis,

suggesting that

removal of this

virus would reduce

necrosis by 96%

Adams et al. (2014) Carrot yellow leaf virus Is Associated with Carrot Internal Necrosis. PLoS ONE 9(11):

e109125. doi:10.1371/journal.pone.0109125

AHDB FV382b and Defra projects : understanding the novel viruses

Field sampling 2014

197 208 219 230 241 252 263 274 285 297 308

198 209 220 231 242 253 264 275 286 298 309

199 210 221 232 243 254 265 276 287 299 310

200 211 222 233 244 255 266 277 288 300 311

201 212 223 234 245 256 267 278 289 301 312

202 213 224 235 246 257 268 279 290 302 313

203 214 225 236 247 258 269 280 291 303 314

204 215 226 237 248 259 270 281 292 304 315

205 216 227 238 249 260 271 282 293 305 316

206 217 228 239 250 261 272 283 294 306 317

207 218 229 240 251 262 273 284 295 307 318

CYLV 23%

CTV 25%

DUAL 9%

Total Virus 39%

Field Margin and Road

Hedgero

w

N

Relative virus incidence Carrots 2015 (Two regions)

0

50

100

150

200

250

Stamford Bridge Stamford Bridge Late Sutton of the Forest Elvedon Estate Highman 'Healthy' Highman 'Infected'

CMD CYLV CaTV CtCV1

Yorkshire (North) Norfolk (East)

Virus %

Sources of virus?

• Cow Parsley (Anthriscus sylvestris)

• Hogweed (Heracleum sphondylium)

• Ground Elder (Aegopodium podagaria)

• Hemlock (Conium maculatum)

• Rough Chervil (Chaerophyllum temulum)

• Alexanders (Smyrnium olusatrum)

Warwick Crop Centre weed samples

• 1555 samples

• UK Wide sampling

• Collected over 3 years

(2010-2012)

• 10 species

• 20-30 sample locations per

year

• Previously tested for

CtRLV, PYFV, AYV

• RNA extracts retained at

Warwick (-80oC)

• PYFV and CtRLV findings

sequenced to look at

population genetics

Carrot red leaf virus from Defra IF0188

Many wild hosts,

few carrot

Cow Parsley only

Carrot/Wild Carrot

Relative proportion of viruses in weeds

0

10

20

30

40

50

60

70

CtRLV PYFV AYV CYLV CtCV-1 CaTV

2011 2012

% P

roport

ion o

f posi

tive v

irus

case

s

2011 = 472 virus cases

2012 = 174 virus cases

Viruses detected by host speciesPerc

enta

ge infe

cti

on (

%)

0

10

20

30

40

50

60

Alexanders Cow Parsley Ground Elder Hemlock Hogweed Rough Chervil

CRLV PYFV AYV CYLV CtCV-1 CaTV

Aphid Transmision of CaTV-1 and CtRLV

Aphid vectors of carrot viruses

Virus Vectors? Transmission

mode?

CMD: Carrot red leaf virus (CtRLV),

Carrot mottle virus (CMoV) and carrot

red leaf associated viral RNA

(CtRLVaRNA)

C. Aegopodii

M. persicae

Circulative,

persistent

Parsnip yellow fleck virus (PYFV)

requires helper - Anthriscus yellows

virus (AYV)

C. aegopodii

C. pastinacae

non-circulative,

semi-persistent

Carrot yellow leaf virus (CYLV) C. aegopodii

C. pastinacae

C. theobaldi

M. persicae

non-circulative,

semi-persistent

Carrot torrado virus (CaTV) M. persicae

C. aegopodii

?

Carrot closterovirus-1 (CtCV-1) ? ?

Sources of carrot viruses….

Aphids/Eggs on

winter host

Aphids

Migrate

Transmit to

Carrot

Pick up

Virus� ��

CtRLV

(CMoV)

(CtRLVaRNA)

From Cow

parsley

CaTV-1?From Carrots

AYV PYFV

Knowledge gaps

• Relative influence of peach-potato aphid in carrot crops

• Aphicide resistance status for willow-carrot aphid

• How much does this species contribute in the field in the UK?

• should we worry about this….?

� Can we spray the right chemical at the right time?

• Epidemiology of CYLV and CtCV-1

• Is crop to crop transmission the major concern (e.g. CMD)?

• Is weed to crop transmission the major concern (e.g. PYFV)?

• When is the virus coming in?

• How long is it being spread within crop throughout the season?

� Can we tailor crop management practices to minimise virus

risk?

So what does this all tell us?

0

50

100

150

200

250

Stamford

Bridge

Stamford

Bridge

Late

Sutton of

the Forest

Elvedon

Estate

Highman

'Healthy'

Highman

'Infected'

CMD CYLV CaTV CtCV1

• PYFV possibly underreported

due to sampling time

• Highest incidence viruses may

come from carrot as a source

• Is the source overwintered

carrots or volunteers?

• Virus control appears to be

breaking down.

• Length of season?

• Vector resistance?

• Limited range of control

measures?

Virus

%

?

The principles of plant virus management :

• Plant ‘clean’ seed

• Grow in absence of vectors

• Grow in absence of virus reservoirs

• Isolate from similar crops

• Use resistant (or tolerant?) varieties

Acknowledgements

• Dr Derek (Dez) Barbara (1948-2012)

• Zurine Rozado’s Carrot torrado virus PhD work conducted under UK

Government-Defra Plant Health Capability funding

• Initial carrot necrosis work and Carrot yellow leaf virus work funded by

AHDB-Horticulture (FV382a & b)

• Fera Staff in Virology, the MTU and Applied Entomology

• Staff of Warwick Crop Centre