DISCUSSIONS
In most developing countries, including Nigeria, sheep and goat farming, most especially goat farming is very important and constitutes a vital livelihood for the poorest people. These animals are of paramount important to the economy and the food security of the peasant populations. Among the countries of West Africa, Nigeria has over the years played a preponderant role in the production of small ruminants and constitutes a pool of exchanges with frontier countries, in particular for the import of live small ruminants coming from Niger, Chad and Cameroon. The country, whose small ruminant industry is estimated at 100 million euros, represents a major exchange point for animal products in West Africa. These trade and movement of animals is accompanied by the spread of animal diseases, including peste des petits ruminants, of particular economic importance for trade internationally. The disease, extremely contagious and deadly for livestock, is largely spread across the country and threatens sheep and goat populations.
Two studies, both published in 2016, presented results from the analysis phylogeny of the PPRV partial N gene from samples collected in Nigeria (Mantip, et al., 2016; Woma, et al., 2016) based on sampling similar to that of this study, showed the presence of lineage II and lineage IV between 2010 and 2011 in Nigeria. Two sub-lineages of the lineage IV strain were found: a first sub-lineage composed of strains from the states of Plateau, Bauchi, Oyo, Sokoto, Kano, Adamawa, and Kaduna states, while a second sub-lineage composed of strains from Adamawa, Bauchi, Lagos, Kaduna, Plateau, Niger, Oyo and Akwa-Ibom. Woma, et al (2016) also suggested the presence of a lineage group IV to be more important than the lineage II strain, which was until then the dominant lineage found in the country (Shamaki, 2002; Kwiatek, et al., 2007).
This study conducted in Nigeria on samples taken from local markets in 2017 and in 2018 has made it possible to explore, through a phylogenetic study of the PPRV N gene, the different lineages and subgroups of PPRV circulating in the country during this period. These results made it possible to complete and update the information obtained during the studies conducted previously. Thus, it has been established that two different lineages were still circulating in Nigeria between 2017 and 2018: lineage II and lineage IV. The unique sequence of lineage II was found in the state of Oyo. The geographic position of these sequences corroborates what was found previously. Strains of lineage II have already been isolated in this state and neighbouring states, located on the western border of Nigeria. These results remain consistent with what has been found so far, lineage II being still strongly present in West Africa (Tounkara, et al., 2018). The phylogenetic position of this new lineage II sequence is significantly different from the sequences described by Mantip and Woma. This result would suggest that lineage strain II harvested in 2018 could represent a new incursion of the lineage from a neighbouring country and not an evolution of a strain already circulating in the country. Isolation of more lineage II strains in the region and phylogenetic analyses based on longer PPRV sequences would confirm this hypothesis.
The large majority of sequences obtained during this sampling effort belonged to lineage IV, suggesting differences in circulation dynamics of lineage II and IV in Nigeria (possibly associated with hosts and season), or a strong overall dominance of lineage IV in the country. Further sampling, in different type of markets and ruminant populations and at different time would help unravel this issue. The two sub-lineages IV-NigA and IV-NigB could be identified again in our study. Only 4 out of 72 samples were infected with strains grouped within sub-lineage IV-NigA. However, recent strains clustering with sub-lineage IV-NigA differ from sequences presented in earlier studies. The sequences found in 2018 were phylogenetically closer to one strain found in Niger in 2013 (Tounkara, et al., 2018). It is difficult to make assumptions about this result. It may correspond to movement of the sub-lineage IV-NigA between Niger and Nigeria, as there are large cross-border transhumance/animal movements in this area, with Niger as the country of departure for most of the flow (Corniaux, 2014).
Furthermore, information on the life of the animal sampled before it arrived in the market would be an asset in a better knowledge of the commercial routes borrowed and therefore of potential movement interfaces of the disease. In addition, knowledge about trade existing between states of the same country but also between countries must be further investigated. The IV-NigA and IV-NigB sub-lineages seem to contain, as demonstrated by Woma and Mantip, statistically significant genetic clusters. In this study, four new genetic clusters were identified within the IV-NigB sub-lineage. These clusters gather samples of different but often neighbouring states, suggesting a circulation of PPR across states. Several of these clusters were found at the same time in the same market which implies a co-circulation of different strains of PPR in the markets. Due to the grouping of animals from different origins in the same markets, these main markets represent a significant risk of transmission and spread of the disease. The IV-NigB2 cluster grouped samples from states located along the border with Cameroon. Samples from Cameroon should be obtained to verify if this genetic group is found also on the other side of the border. This north-south axis is also a path of transhumance used seasonally by nomadic pastoralists (Shamaki, D., personal communication, May 2019, Montpellier). In contrast, the lineage IV-NigB4 cluster brings together very distant states, suggesting long-distances PPR spread, possibly associated with animal trade.
Presence of multiple clusters, but also of sequences that did not belonged to any of the two sub-lineages IV-Nig, suggest that the genetic diversity of the lineage IV in Nigeria is probably higher than shown by analyses based on partial N gene sequences. Analyzes based on larger sampling encompassing the entire region, using longer sequences and at best complete genomes of PPRV are necessary to better understand the phylogenetic relationships within PPRV and study the transmission dynamics of the virus in Nigeria and the African region from West. This high genetic diversity in Nigeria may be due to the strategical importance of the country in regional animal trade.
Phylogenetic analysis efforts such as those carried out for this project should continue and be improved. This improvement must take into account the size and the plan of sampling and the information collected from sampled individuals. It should therefore be possible to extend the sampling strategy to better understand the transmission and cross-border spread of the disease. This information may be important for developing appropriate and effective surveillance and control strategies against PPR.