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International Society for Infectious Diseases

Date: January 2018
Source: ScienceDirect, Virus Research journal [edited]
<https://www.sciencedirect. com/science/article/pii/ S0168170217306743>

[ref: Muller E, Ravel S, Agret C, et al. Next generation sequencing
elucidates cacao badnavirus diversity and reveals the existence of
more than ten viral species. Virus Res. 2018 Jan 15;244:235-251. doi:
10.1016/j.virusres.2017.11. 019]
------------------------------ ------------------------------ ----------
_Cacao swollen shoot virus_ (CSSV) populations in West Africa are
highly variable and genetically structured into several different
groups. To unravel the extent of isolate diversity and address the
problems of low titer and mixed viral sequences in samples, we used
Next Generation Sequencing technology.

We were able to reconstruct de novo 20 new complete genomes from cacao
samples in the Cocoa Research Institute of Ghana (CRIG) Museum and
from field samples collected in Côte d'Ivoire or Ghana. Based on
thresholds of nucleotide divergence denoting species demarcation, we
conclude there exist 7 new species associated with the cacao swollen
shoot disease [CSSD]. These new species along with the 3 already
described [see also ProMED-mail post 20171025.5404488] leads to 10, the total
number of the complex of viral species associated with the disease.

CSSD has always been described as a disease endemic to West Africa. An
attenuated form of CSSD in Malaysia, Indonesia, and Sri Lanka has been
mentioned [but] to date, beyond West Africa, swellings were only
reported in Sri Lanka. A sample from Sri Lanka exhibiting similar leaf
symptomology to West African CSSD-affected plants was also included in
the study and the corresponding sequence represents the genome of a
new virus named cacao bacilliform Sri Lanka virus (CBSLV).

Communicated by:
Plantwise Knowledgebank

[Swollen shoot disease of cocoa (CSSD) caused by species of genus
_Badnavirus_ can lead to severe crop losses. The viruses are thought
to have been transferred to cocoa from West African forest trees.
Symptoms vary with different viral strains, from severe effects on
shoots and roots resulting in serious dieback or even death of the
tree, to no symptoms at all. The viruses are spread by several species
of mealybugs (_Pseudococcidae_) and may also be transmitted by
grafting and mechanical inoculation. Seed transmission is also

Disease management relies on phytosanitation and clean planting
material. Most affected countries require the removal of all infected
trees and their neighbours. Mealybugs are difficult to control, and
native forests serve as pathogen reservoirs. Keeping replanted trees
from becoming reinfected would be challenging under local conditions,
thus ongoing breeding programmes for virus- or vector-resistant crop
varieties are crucial. Cross protection against severe viral strains
by mild strains is also being trialled (see link below).

A westward spread of CSSD in Ghana led to a serious outbreak with more
severe symptoms in 2008 (ProMED-mail post 20081030.3416) and the possibility of the
involvement of a new viral strain was considered. Ghana, Togo,
Nigeria, and Côte d'Ivoire have signed an agreement to tackle the
disease and subsequently molecular work has increased. The 3
badnaviruses currently recognised as cause of the disease are _Cacao
swollen shoot virus_, _Cacao swollen shoot CD virus_, and _Cacao
swollen shoot Togo A virus_. An additional proposed species, Cacao red
vein virus (CRVV) was isolated from field samples (ProMED-mail post 20171025.5404488 and link below) and is
suspected to be the causal agent of the rapid decline phenotype of

Whether the additional virus sequences constructed by _in silico_
analysis in the report above are associated with intact virus
particles and thus represent actual infectious viruses involved in
CSSD _in vivo_ will need to be verified by pathogenicity and
epidemiology studies.

Africa, overview:
< webimage/countrys/africa/maps/ africa.jpg>
West Africa:
< maps/west-africa-political- map.jpg> and
< p/40192>
Sri Lanka:
< maps/middle_east_and_asia/sri_ lanka_pol01.jpg>
< p/144>
Asia, overview:
< webimage/countrys/as.htm>

CSSV symptoms:
< thamesvalleycocoa/CSSV_Andy_ Wetten_s.jpg>,
<http://www. content/uploads/CSSV.jpg>,
< wikipedia/commons/e/ef/Cocoa_ Swollen_Shoot_Stem_symptom.jpg >,
< plantvillage/images/pics/000/ 001/801/large/IMG_6339.jpeg? 1382470857>,
< 20081127_SwollenShoots_ HighRes.jpg>, and
< cocoa/cocoa_prob.htm#virus>
Mealy bugs:
< content/image/wv/wv_2009-06- 03_bugs.jpg>

Cocoa swollen shoot disease information:
< KnowledgeBank/Datasheet.aspx? dsid=12380>,
< science/article/pii/ S0261219414002142>,
<http://www.worldagroforestry. org/sites/default/files/ Brochure-Cocoa-Swollen-Shoot- Virus-Disease.pdf>,
<http://www. frontiers-in-the-fight- against-deadly-cocoa-disease/> ,
< chapter/10.1007%2F978-3-319- 24789-2_10>
CSSV mild strain cross protection:
<http://apsjournals.apsnet. org/doi/abs/10.1094/PDIS-09- 15-0974-RE>
CSSV description:
< showdpv.php?dpvno=10> and
< swollen-shoot-virus-2002940-W>
CRVV characterisation:
<https://virologyj. 1186/s12985-017-0866-6>
Genus _Badnavirus_ taxonomy and species list via:
< taxonomy/>
Pests of cocoa including CSSV vectors:
< thamesvalleycocoa/Colin% 20Campbell.pdf>
Information on mealy bugs:
< Mealybugs.htm> (with pictures)
- Mod.DHA]

[See Also:
Swollen shoot, cocoa - West Africa: new virus 20171025.5404488
Swollen shoot, cocoa - Ghana: replanting 20170505.5014688
Black pod & swollen shoot, cocoa - Cote d'Ivoire: (BS) 20100709.2296
Coffee & cocoa diseases - Central Africa: update 20100421.1289
Swollen shoot, cocoa - Cote d'Ivoire (02) 20091130.4094
Swollen shoot, cocoa - Ghana: update 20090904.3115
Swollen shoot, cocoa - Cote d'Ivoire: spread 20090327..1196
Swollen shoot, cocoa - Ghana 20081030.3416
Swollen shoot, cocoa - Ivory Coast: control 20080302.0860
Cocoa swollen shoot virus - Ghana (02): westward spread 20071026.3475
Cocoa swollen shoot virus - Ghana: control attempts 20070813.2636]
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