Comparative evolutionary analyses of peste des petits ruminants virus genetic lineages.

Peste des petits ruminants virus (PPRV) causes a highly infectious disease affecting mainly goats and sheep in large parts of Africa, Asia, and the Middle East and has an important impact on the global economy and food security. Full genome sequencing of PPRV strains has proved to be critical to increasing our understanding of PPR epidemiology and to inform the ongoing global efforts for its eradication. However, the number of full PPRV genomes published is still limited and with a heavy bias towards recent samples and genetic Lineage IV (LIV), which is only one of the four existing PPRV lineages. Here, we generated genome sequences for twenty-five recent (2010-6) and seven historical (1972-99) PPRV samples, focusing mainly on Lineage II (LII) in West Africa. This provided the first opportunity to compare the evolutionary pressures and history between the globally dominant PPRV genetic LIV and LII, which is endemic in West Africa. Phylogenomic analysis showed that the relationship between PPRV LII strains was complex and supported the extensive transboundary circulation of the virus within West Africa. In contrast, LIV sequences were clearly separated per region, with strains from West and Central Africa branched as a sister clade to all other LIV sequences, suggesting that this lineage also has an African origin. Estimates of the time to the most recent common ancestor place the divergence of modern LII and LIV strains in the 1960s-80s, suggesting that this period was particularly important for the diversification and spread of PPRV globally. Phylogenetic relationships among historical samples from LI, LII, and LIII and with more recent samples point towards a high genetic diversity for all these lineages in Africa until the 1970s-80s and possible bottleneck events shaping PPRV's evolution during this period. Molecular evolution analyses show that strains belonging to LII and LIV have evolved under different selection pressures. Differences in codon usage and adaptative selection pressures were observed in all viral genes between the two lineages. Our results confirm that comparative genomic analyses can provide new insights into PPRV's evolutionary history and molecular epidemiology. However, PPRV genome sequencing efforts must be ramped up to increase the resolution of such studies for their use in the development of efficient PPR control and surveillance strategies.

Exposure to multiple pathogens - serological evidence for Rift Valley fever virus, Coxiella burnetii, Bluetongue virus and Brucella spp. in cattle, sheep and goat in Mali.

An important problem for livestock production in Mali is occurrence of several infectious diseases. A particular challenge for control of pathogens that affect different species, especially in a system with mixed herds with cattle, sheep and goats. Therefore, this study aimed to investigate co-exposure with Rift Valley fever virus (RVFV), Coxiella burnetii, Bluetongue virus (BTV) and Brucella spp. in different livestock species in mixed herds. With the exception of BTV these pathogens are also zoonotic. A retrospective assessment was carried out on a biobank of sera of cattle and small ruminants collected from Sikasso and Mopti regions. Nine hundred and twelve samples from cattle (n = 304), sheep (n = 318) and goat (n = 290) were screened. Serology tests were conducted using commercial kits as per the protocol of the manufacturers. Sero-prevalence for RVFV was 12.8% (Confidence Interval 95%: 9.3-17.1%); 4.7% (2.7-7.7%) and 3.1% (1.4-5.8%) in cattle, sheep and goat respectively. For Coxiella burnetii, the sero-prevalence was 55.3% (49.5-60.9%), 22.6% (18.2-27.6%), and 16.9% (12.8-21.7%); in cattle, sheep and goat respectively; and for BTV sero-prevalence was 88.8% (84.72-92.13%), 51.6% (45.9-57.2%), 56.2% (50.3-62.0%) in cattle, sheep in goat respectively. Brucella sp. had the lowest sero-prevalence and was only detected in cattle and sheep. Regional differences were observed with sero-prevalence of Coxiella burnetii in sheep and goat with BTV in goat being significantly higher in Sikasso than in Mopti (p<0.001). Evidence of exposure to two pathogens in the same animal was most common for the combination Coxiella burnetii and BTV in cattle (51.6%), followed by sheep (17.0%) and goat (15.5%). Considering the scarcity of disease occurrence and epidemiological data in most sub-saharan countries including Mali, this multi-pathogen survey provides important evidence that cattle, sheep and goat are exposed to pathogens that may negatively impact productivity and pose a risk for public health. The results from this study highlight the urgent need for a better understanding of pathogen diversity and their impact on human and animal health in order to minimize resulting risks. Given that some of the pathogens investigated here are zoonotic, establishment of One-Health surveillance system to monitor disease in animals and people is warranted. Therefore, intersectoral collaboration is recommended.

Persistence of the historical lineage I of West Africa against the ongoing spread of the Asian lineage of peste des petits ruminants virus.

Peste des petits ruminants (PPR) is a highly contagious disease of small ruminants. The causal agent, PPR virus (PPRV), is classified into four genetically distinct lineages. Lineage IV, originally from Asia, has shown a unique capacity to spread across Asia, the Middle East and Africa. Recent studies have reported its presence in two West African countries: Nigeria and Niger. Animals are frequently exchanged between Mali and Niger, which could allow the virus to enter and progress in Mali and to other West African countries. Here, PPRV samples were collected from sick goats between 2014 and 2017 in both Mali and in Senegal, on the border with Mali. Partial PPRV nucleoprotein gene was sequenced to identify the genetic lineage of the strains. Our results showed that lineage IV was present in south-eastern Mali in 2017. This is currently the furthest West the lineage has been detected in West Africa. Surprisingly, we identified the persistence at least until 2014 of the supposedly extinct lineage I in two regions of Mali, Segou and Sikasso. Most PPRV sequences obtained in this study belonged to lineage II, which is dominant in West Africa. Phylogenetic analyses showed a close relationship between sequences obtained at the border between Senegal and Mali, supporting the hypothesis of an important movement of the virus between the two countries. Understanding the movement of animals between these countries, where the livestock trade is not fully controlled, is very important in the design of efficient control strategies to combat this devastating disease.

Combining viral genetic and animal mobility network data to unravel peste des petits ruminants transmission dynamics in West Africa.

Peste des petits ruminants (PPR) is a deadly viral disease that mainly affects small domestic ruminants. This disease threaten global food security and rural economy but its control is complicated notably because of extensive, poorly monitored animal movements in infected regions. Here we combined the largest PPR virus genetic and animal mobility network data ever collected in a single region to improve our understanding of PPR endemic transmission dynamics in West African countries. Phylogenetic analyses identified the presence of multiple PPRV genetic clades that may be considered as part of different transmission networks evolving in parallel in West Africa. A strong correlation was found between virus genetic distance and network-related distances. Viruses sampled within the same mobility communities are significantly more likely to belong to the same genetic clade. These results provide evidence for the importance of animal mobility in PPR transmission in the region. Some nodes of the network were associated with PPRV sequences belonging to different clades, representing potential "hotspots" for PPR circulation. Our results suggest that combining genetic and mobility network data could help identifying sites that are key for virus entrance and spread in specific areas. Such information could enhance our capacity to develop locally adapted control and surveillance strategies, using among other risk factors, information on animal mobility.

Integrated Approach to Facilitate Stakeholder Participation in the Control of Endemic Diseases of Livestock: The Case of Peste Des Petits Ruminants in Mali.

In Mali, small ruminants (SRs) are an important means for enhanced livelihood through income generation, especially for women and youth. Unfortunately, opportunities for livestock farmers to tap into these resources for economic growth are hindered by high burden of endemic diseases such as peste des petits ruminants (PPR). A key component for the control of PPR is vaccination of SRs. However, low participation of farmers to vaccination was identified by stakeholders of the livestock value chains as a key constraint to successful vaccination programs. This study was implemented in the framework of a project which aimed at improving the domestic ruminant livestock value chains in Mali by upscaling proven interventions in animal health, feeds and feeding and livestock marketing. The objectives of the study were to review the context of livestock vaccination in Mali and evaluate the impact of innovation platforms (IP) as a means for engaging stakeholders in the vaccination process. Desk review, key informant interviews (KII) and net-mapping were used to understand the context of livestock vaccination, while vaccination coverage and sero-monitoring together with group interviews were used to measure the impact of the intervention. IPs were created in 24 communes in three regions: 15 IPs in Sikasso, 4 IPs in Mopti and 5 IPs in Timbuktu. They developed work plans and implemented activities focusing on improving interaction among key vaccine chain delivery stakeholders such as farmers, private veterinarians, vaccine manufacturers, local leaders and public veterinary services; involving them in the planning, implementation and evaluation of vaccination programs and fostering knowledge sharing, communication and capacity building. After 2 years of implementation of IPs, vaccination coverage for SRs increased significantly in target communes. During the first year, seroprevalence rate for PPR increased from 57% (CI95: 54-60%) at baseline to 70% (CI95: 67-73%) post-vaccination in Sikasso region, while in Mopti region, seroprevalence increased from 51% (CI95: 47-55%) at baseline to 57% (CI85: 53-61%) post-vaccination. Stakeholder engagement in the vaccination process through facilitated IPs was successful in fostering participation of farmers to vaccination. However, a sustainable vaccination strategy for Mali would benefit from consolidating the IP model, supported by Government investment to strengthen and adjust the underlying public-private-partnership.

Seroprevalence of contagious bovine pleuropneumonia (CBPP) in Mali.

A serological survey to determine the prevalence of contagious bovine pleuropneumonia (CBPP) in Mali was carried out by using the competitive enzyme linked-immunosorbent test (c-ELISA) on 8007 serum samples systematically collected from 199 cattle herds collected throughout the whole country. Results showed a national prevalence of 18.11 % at the individual level and 85.93 % at the herd level. Significant variations in the individual prevalence were observed between regions of the country and ranged from 4.63 % in Tombouctou to 54.88 % in Kidal. At the herd level, although there were variations between regions, a high prevalence was constantly observed ranging from 60 to 100 %, hence confirming the endemic nature of the disease across the country. The CBPP risk varied also between regions and was very low in Tombouctou (odds ratio (OR) = 0.4) but very high in Kidal (OR = 9.8). Similarly, the risk seemed higher in the animals of the over 3-year age group (OR = 1.6) compared to the other age groups. It was also observed that there was a slightly higher risk (OR = 1.3) in the females than in the males. This study confirms the presence of CBPP across the country and should help to elaborate strategies for the effective control of the disease.

Performance evaluation of two serological tests for contagious bovine pleuropneumonia (CBPP) detection in an enzootic area using a Bayesian framework.

A Bayesian approach, allowing for conditional dependence between two tests was used to estimate without gold standard the sensitivities of complement fixation test (CFT) and competitive enzyme-linked immunosorbent assay test (cELISA) and the serological prevalence of CBPP in a cattle population of the Central Delta of the Niger River in Mali, where CBPP is enzootic and the true prevalence and animals serological state were unknown. A significant difference (P = 0.99) was observed between the sensitivities of the two tests, estimated at 73.7% (95% probability interval [PI], 63.4-82.7) for cELISA and 42.3% (95% PI, 33.3-53.7) for CFT. Individual-level serological prevalence in the study population was estimated at 14.1% (95% PI, 10.8-16.9). Our results indicate that in enzootic areas, cELISA performs better in terms of sensitivity than CFT. However, negative conditional sensitivity dependence between the two tests was detected, implying that to achieve maximum sensitivity, the two tests should be applied in parallel.