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Food safety
Better Training for Safer FoodInitiative
Sofia, Bulgaria 6th -8th June 2018
Molecular epidemiology and regional transmission dynamics of
PPR
Arnaud Bataille
Peste des Petits Ruminants (PPR) BTSFThis presentation is delivered under contract with theConsumers, Health, Agriculture and Food Executive Agency(http://ec.europa.eu/chafea). The content of this presentation isthe sole responsibility of Opera S.u.r.l., the IstitutoZooprofilattico Sperimentale Lombardia e Emilia Romagna andthe State Food and Veterinary Service of Latvia and it can in noway be taken to reflect the views of the Consumers, Health,Agriculture and Food Executive Agency or any other body of theEuropean Union. The Consumers, Health, Agriculture and FoodExecutive Agency or any other body of the European Union willnot be responsible under any circumstances for the contents ofcommunication items prepared by the contractors.
Food safety
Molecular epidemiology and regional transmission
dynamics of PPR
Arnaud Bataille
CIRAD, UMR ASTRE, Montpellier, France
OIE/FAO/EU Reference Laboratory for PPR
arnaud.bataille@cirad.fr1
Food safety
Molecular epidemiology
2
▪ PPRV characterised by a high
plasticity of its genome (RNA virus)
▪ Potential to undergo mutations and
evolve quickly
▪ Evolution of the genome results in
different genotypes
▪ Genetic distance can be translated
in relatedness
▪ Provide information on ecology and
virus transmission dynamics
Food safety
Molecular epidemiology
3
▪ Provide information
on ecology and virus
transmission dynamics
At multiple scales
(within-host, inter-host,
metapopulation,…)
Food safety
Phylogenetic studies
4
▪ Translation of genetic distance in a
phylogenetic tree
▪ Visualisation of relatedness
between viral strains
▪ With quantification of statistical
support
Food safety
Phylogenetic studies
5
▪ Translation of genetic distance in a
phylogenetic tree
▪ Visualisation of relatedness
between viral strains
▪ With quantification of statistical
support
▪ Short N gene sequence (255bp) are
informative
▪ Hundreds of N gene sequences
available on GenBankNP3/NP4
Food safety
Phylogenetic studies
6
Information from NP3/NP4 studies:
▪ Identification, spread of genetic lineage
▪ Identification of most closely related
strains with the lineage
▪ Potential origin of emergence
Food safety
Example: outbreak in Georgia
7
▪ Outbreak of PPR in early 2016
▪ Tushuri sheep in 3 farms near Tbilisi
▪ 451 out of 3,740 animals with symptoms
(11%)
▪ 204 animals (49%) died
Where did it come from?
Food safety
Example: outbreak in Georgia
8
Where did it come from?
First hypothesis: neighbouring countries
PPR in Turkey, Iran, Iraq
No information from Armenia or Azerbaijan
Legal or illegal transboundary movements of
animals?
Food safety
Example: outbreak in Georgia
9
Phylogenetic study on NP3/NP4 sequences
obtained with 3 samples from Georgia
PPR from Georgia belongs to lineage IV as
expected
But not related to Turkey, Iran, Iraq
Outbreak not due to spread of disease from
Turkey, Iran, Iraq
JQ519922 (Turkey 2010)
JQ388660 (Turkey 2010)
KF478928 (Turkey 2009)
AJ563705 (Turkey 2000)
JX898862 (Iran 2011)
JX898847 (Iran 2010)
JF969755 (Kurdistan 2011)
KF478926 (Turkey 2013)
KF478931 (Turkey 2011)
JQ519949 (Turkey 2011)
KU987610 (Turkey 2015)
KU325493 (Turkey 2015)
KF478927(Turkey 2012)
DQ840198 (Tajikistan 2004)
KJ508833 (Bangladesh 2013)
JF939201 (China 2007)
DQ840181 (Israel 1995)
DQ840184 (Turkey 1996)
DQ840179 (India 1994)
DQ840197 (Saudi Arabia 1998)
KC207867 (Pakistan 2012)
DQ840185 (Iran 1998)
HQ131927 (Morocco 2008)
KP793696 (Algeria 2012)
KJ867541 (Ethiopia 2010)
KX189065 (Egypt 2015)
KX189064 (Egypt 2015)
JX398127 (Eritrea 2011)
KT006588 (Egypt 2014)
JN202923 (Egypt 2010)
HQ131931 (Sudan 2008)
JN202924 (Egypt 2010)
PPRV/Georgia/G1/2016
PPRV/Georgia/G2/2016
PPRV/Georgia/G4/2016
JX312807 (Egypt 2012)
Lineage IV
Lineage II
Lineage I
Lineage III
Turkish PPR
strains
Food safety
Example: outbreak in Georgia
10
Phylogenetic study on NP3/NP4 sequences
obtained with 3 samples from Georgia
Closely related to strains from Egypt, Eritrea,
Sudan
Georgia exports sheep by plane to NE Africa
(Egypt) and Middle East (airport in Tbilisi)
Hypothesis: Infected animal came back with
plane
Food safety
Phylogenetic studies
11
▪ Longer nucleotide sequence
provide more information
▪ Genome of 16kb
▪ Can be used for more
complex analyses
Food safety
Full genome sequencing
12
▪ Classical sanger sequencing
▪ By portions of ~800bp
▪ Long and costly
▪ Some sequencing errors
Food safety
Full genome sequencing
13
▪ Next generation sequencing
▪ High through-put, large
amount of data generated
▪ Many PPRV genomes
sequenced in one run
▪ Deep sequencing: information
on mutant populations
Over 50 PPRV genomes
sequenced at CIRAD
Illumina sequencing
Food safety
Time-dependent phylogenetic studies
14
▪ Using historical and recent
samples, with dates
associated to sequences
▪ Evaluation of mutation rate
0.0014 sub/site/year
(human DNA: 10-8 sub/site/year)
▪ Date of emergence of PPRV/
lineage
PPRV: 1904 (1730-1960)
Lineage IV: 1967 (1957-1998)
But not enough historical samples
Food safety
15
Transmission dynamics in endemic regions
▪ PPR transmission and spread linked to livestock trade
▪ Need for better understanding of regional virus transmission dynamics for
efficient control and eradication
▪ Need phylogenetic data to link transboundary transmission with trade
?
Small ruminant market trade network in Mauritania and Senegal
figure: Baron et al. (2016)
Food safety
16
PPRV transmission dynamics in endemic regions
Study in West Africa
Sampling in Senegal (N=41) and neighbouring countries (N=14) in 2010-2014
Food safety
17
PPRV transmission dynamics in endemic regions
Study in West Africa
Sequencing of 255bp of N gene: 54/55 samples of PPRV-II
Food safety
Phylogenetic studies
18
Information from NP3/NP4 studies:
▪ Identification, spread of genetic lineage
▪ Identification of most closely related
strains with the lineage
▪ Potential origin of emergence
Food safety
19
PPRV transmission dynamics in endemic regions
Study in West Africa
Sequencing of N and H gene (N=41, ~ 5000bp) or complete genome (N=14) for
new PPRV-II samples and historical samples
Food safety
20
PPRV transmission dynamics in endemic regions
Study in West Africa
PPRV-II phylogeny (N and H genes) in Senegal and neighbours to identify of
transmission clusters
Food safety
21
PPRV transmission dynamics in endemic regions
Study in West Africa: Association with animal trade
Food safety
22
PPRV transmission dynamics in endemic regions
Study in West Africa: Association with animal trade
Food safety
23
PPRV transmission dynamics in endemic regions
Study in West Africa: Association with animal trade
Food safety
24
PPRV transmission dynamics in endemic regions
Study in West Africa: Association with animal trade
Food safety
25
PPRV transmission dynamics in endemic regions
Study in West Africa: Association with animal trade
Food safety
26
PPRV transmission dynamics in endemic regions
Study in West Africa: Association with animal trade
Food safety
27
PPRV transmission dynamics in endemic regions
Study in West Africa: Association with animal trade
Food safety
28
PPRV transmission dynamics in endemic regions
Study in West Africa: Association with animal trade
Identical sequences = Direct links between two markets separate by long distance
Food safety
29
PPRV transmission dynamics in endemic regions
Study in West Africa: Association with animal trade
Data on animal movement between markets (from veterinary services)
Data on roads, animal density, environmental variables
Which factors explain the distribution of virus (as given by genetic data)?
Food safety
30
PPRV transmission dynamics in endemic regions
Study in West Africa: Association with animal trade
Data on animal movement between markets (from veterinary services)
Data on roads, animal density, environmental variables
Which factors explain the distribution of virus (as given by genetic data)?
Modelling shows:
▪ Market community (connected by animal trade) correlates with genetic groups
▪ The more two markets are connected by animal trade, the more closely related
are virus strains sequenced
Strong support for importance of animal trade in virus tranmission dynamics
Food safety
31
PPRV transmission dynamics: conclusion
To understand PPRV transmission and better control disease spread, we
need:
▪ Partial sequence of PPRV strains to follow PPRV distribution and identify origin
of emergence
▪ Genome of historical samples to understand the evolutionary history of PPRV
▪ Genetic data to understand PPRV transboundary transmission dynamics
▪ Complete data on animal trade within country and across borders crucial to
better evaluate risk of spread
▪ Genetic data combined with animal movement data provide better information
than the two type of data separated
Food safety
Better Training for Safer Food
BTSF
OPERA
Viale Parioli 96, 00197 Roma - Italy
Tel +39 06 96042652- / +39 06 8080111
Fax +39 06 89280678
info@opera-italy.it; www.btsftraining.com; www.opera-italy.it
This presentation is delivered under contract with the Consumers, Health, Agriculture and Food Executive Agency (http://ec.europa.eu/chafea). Thecontent of this presentation is the sole responsibility of Opera S.u.r.l., the Istituto Zooprofilattico Sperimentale Lombardia e Emilia Romagna and theState Food and Veterinary Service of Latvia and it can in no way be taken to reflect the views of the Consumers, Health, Agriculture and FoodExecutive Agency or any other body of the European Union. The Consumers, Health, Agriculture and Food Executive Agency or any other body of theEuropean Union will not be responsible under any circumstances for the contents of communication items prepared by the contractors.
• European CommissionConsumers, Health and Food Executive Agency
DRB A3/042L-2920 Luxembourg
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