Phylogenomic relationship and evolutionary insights of sweet potato viruses from the western highlands of Kenya

Sweet potato is a major food security crop within sub-Saharan Africa where 90 % of Africa’s sweet potato production occurs. One of the major limitations of sweet potato production are viral infections. In this study, we used a combination of whole genome sequences from a field isolate from Kenya and those available in GenBank. Sequences of four sweet potato viruses: sweet potato feathery mottle virus (SPFMV) , sweet potato virus C (SPVC) , sweet potato chlorotic stunt viru s ( SPCSV ), sweet potato chlorotic fleck virus ( SPCFV) were obtained from the Kenyan sample. SPFMV sequences both from this study and from GenBank were found to be recombinant. Recombination breakpoints were found within the Nla-Pro, coat protein and P1 genes. The SPCSV, SPVC and SPCFV viruses from this study were non-recombinant. Bayesian phylogenomic relationships across whole genome trees showed variation in the number of well-supported clades; within SPCSV (RNA1 and RNA2) and SPFMV two well-supported clades (I and II) were resolved. The SPCFV tree resolved three well-supported clades (I-III) while four well-supported clades were resolved in SPVC (I-IV). Similar clades were resolved within the coalescent species trees. However, there were disagreements between the clades resolved in the gene trees compared to those from the whole genome tree and coalescent species trees. However the coat protein gene tree of SPCSV and SPCFV resolved similar clades to genome and coalescent species tree while this was not the case in SPFMV and SPVC. In addition, we report variation in selective pressure within sites of the individual genes across all four viruses; overall all viruses were under purifying selection. We report the first complete genomes of SPFMV, SPVC, SPCFV and a partial SPCSV from Kenya as a mixed infection in one sample. In addition, we reveal their phylogenomic relationships and provide evolutionary insights into these viruses. Our findings demonstrate the need for clean planting materials as the first line of control for these viruses, in particular for smallholder farmers within eastern Africa region.