Regional evolutionary dynamics of peste des petits ruminants virus in West Africa: influence of livestock trade

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1 P. Dugué Cirad Regional evolutionary dynamics of peste des petits ruminants virus in West Africa: influence of livestock trade Arnaud Bataille Cirad-INRA Unit for Control of Emerging and Exotic Animal Diseases Montpellier, France

2 Peste des Petits Ruminants (PPR) Most widespread and devastating infectious disease of domestic small ruminants (goats, sheep) Camels and some wild ruminants also susceptible High economic impact and food security threat New target for global eradication (FAO/OIE, 2015) Georgia 2016 pictures: H. Salami

3 Peste des Petits Ruminants virus (PPRV) Envelopped, single-stranded negative-sense RNA virus (genus Morbillivirus) ~16kb genome coding for 6 structural and 2 non-structural proteins figure: Liu et al. (2016)

4 Peste des Petits Ruminants virus (PPRV) Four distinct phylogenetic lineages Lineage IV spreading from Asia to Africa, L-II replacing L-I Lineage I Lineage II Lineage III Lineage IV figure: Libeau et al. (2014)

5 PPRV phylodynamics and livestock trade PPR transmission and spread linked to livestock trade Need for better understanding of regional virus transmission dynamics for efficient control and eradication Can virus phylodynamics be correlated to animal trade? figure: Baron et al. (2016)? Small ruminant market trade network in Mauritania and Senegal

6 PPRV endemic transmission in West Africa Sampling of PPRV in Senegal (N=41) and neighbouring countries (N=14) in Mauritania Senegal Mali 3 Dakar 6 Thiès Fatick Louga Kaolack 2 Matam Tambacounda 2 Guinea 2 7 Kolda 2 Kédougou 2 N Positive sample N positive samples

7 PPRV lineage II (PPRV-II) in West Africa Sequencing of 255bp of N gene: 54/55 samples of PPRV-II One sample of lineage I obtained in Mali ( ) Our samples Lineage I Lineage II Lineage III Lineage IV Maximum Likelihood tree (<50% bootstrap support) outgroup (rinderpest)

8 PPRV lineage II (PPRV-II) in West Africa Phylogeny of PPRV-II based on N gene (255bp) Highly informative Complex phylogeny with multiple clusters Mali and Benin with highest diversity Common ancestry Senegal* Guinea* Mauritania* Mali* Sierra Leone Benin (*samples from this study) Burkina F./Mali*/Iv. C. Maximum Likelihood tree (<50% bootstrap support) Ghana/Nigeria/Benin Nigeria-Benin ( ) Ghana-Nigeria ( )

9 Dakar Transmission dynamics of PPRV-II PPRV-II phylogeny (N and H genes) in Senegal and neighbours to identify of transmission clusters Mekhe Thiès Joal Fatick Louga Kaolack Kolda Matam Tambacounda Mali 2014 Mauritanie 2012 Guinée 2013 Kedougou Me Jo Th Ma Da Lo Da Da Fa Da Th Fa Ma Da Me Fa Ta Ka Ka Ka Ta Ma Ko/Ta Ma Ke Ke Ta Clu3 Clu2 Clu4 Clu1 Clu5 Maximum Likelihood tree (<50% bootstrap support) Th Da Ko Me Ko Clu6 Clu7

10 Association with animal trade Figure: Cesaro et al., 2010 Market importance Flow importance Type Transboundary Local Regional hub Intermediary Consumption

11 Association with animal trade Figure: Cesaro et al., 2010 Clu1 Market importance Flow importance Type Transboundary Local Regional hub Intermediary Consumption

12 Association with animal trade Figure: Cesaro et al., 2010 Clu4 Market importance Flow importance Type Transboundary Local Regional hub Intermediary Consumption

13 Association with animal trade Figure: Cesaro et al., 2010 Clu3 Market importance Flow importance Type Transboundary Local Regional hub Intermediary Consumption

14 Association with animal trade Figure: Cesaro et al., 2010 Clu5 Market importance Flow importance Type Transboundary Local Regional hub Intermediary Consumption

15 Association with animal trade Figure: Cesaro et al., 2010 Market importance Type Transboundary Intermediary Clu6 Flow importance Local Consumption Regional hub

16 Association with animal trade Figure: Cesaro et al., 2010 Market importance Type Flow importance Transboundary Local Intermediary Consumption Clu7 Regional hub

17 Association with animal trade Quantitative data on animal movement (from national veterinary services) translated to Social Network Data Linear models: genetic distance ~ geo distance + environmental variables + SNA Animal movement Goat density

18 Conclusions Lineage II predominant, but lineage I circulating in Mali Complex phylogeography of lineage II retrieved with short N gene sequences Phylogenetic analyses of PPRV-II confirm frequent movement of virus within Senegal and across countries Movements follow patterns of livestock trade, including those associated with transhumance Quantitative analysis of genetic and trade data could provide guidance on important targets for control and eradication effort Such analysis could be done in all PPR-infected regions

19 Acknowledgements Habib Salami 1,2,3 : sample collection, sequencing, data analysis Caroline Coste 1,2 : SNA and sequence data analysis Renaud Lancelot 1,2 : SNA data analysis, supervision Olivier Kwiatek 1,2 Geneviève Libeau 1,2 : lab work, supervision Moustapha Lo 3, Ismaïla Seck 4, Mariam Diop 3, Ahmed Bezeid El Mamy 5, Ahmed Salem El Arbi 6, Lancéï Kaba 7, Mamadou Niang 8 : sampling and livestock trade data collection 1 CIRAD, UMR CMAEE, Montpellier, France; 2 INRA, UMR CMAEE, Montpellier, France; 3 ISRA/LNERV, Dakar, Senegal; 4 Direction des Services Vétérinaires, Dakar, Senegal ; 5 CNERV, Nouakchott, Mauritania; 6 Ministère du Développement rural, Services Vétérinaires, Nouakchott, Mauritania, 7 ISSMV de Dalaba, Dalaba, Republic of Guinea; 8 LCV, Bamako, Mali