Molecular Characterization of Maize Streak Virus Reveals the First Occurrence of Strain H in Burkina Faso

Abstract

Aims: Maize is a major staple food in Sub-Saharan Africa but its production is severely affected by maize streak disease caused by Maize streak virus (MSV). Despite the importance of the disease for food security, information on the genetic diversity of MSV isolates in West Africa remains limited. This study aimed to characterize the genetic diversity of MSV isolates collected from maize and wild grasses in Burkina Faso and to determine their phylogenetic relationships, with particular emphasis on identifying previously unreported virus strains. Study Design: This was a molecular characterization study based on PCR detection, DNA sequencing, and phylogenetic analysis of MSV isolates. Place and Duration of Study: The study was conducted in Burkina Faso using MSV isolates collected from maize and wild grasses during field surveys over two years. Methodology: Leaf samples exhibiting symptoms of maize streak disease were collected from maize and wild grasses. MSV was detected by polymerase chain reaction (PCR), and six PCR products of sufficient quality were subjected to Sanger sequencing. The obtained sequences were analyzed for nucleotide composition and pairwise nucleotide identity. Principal component analysis (PCA) was performed to assess genetic relationships among isolates, and phylogenetic relationships were inferred using the Maximum Likelihood (ML) method together with reference MSV sequences retrieved from GenBank. Results: Six MSV isolates were successfully sequenced and analyzed. Pairwise nucleotide identity and phylogenetic analyses revealed a clear genetic structure, separating the isolates into distinct evolutionary groups. Most isolates clustered within MSV lineages previously described in the country. Interestingly, isolates obtained from Brachiaria lata (Schumach.) C.E. Hubb. formed a well-supported cluster belonging to MSV strain H, representing the first report of this strain in Burkina Faso. PCA further confirmed the genetic differentiation among the identified groups. Conclusion: This study provides the first molecular evidence of Maize streak virus strain H in Burkina Faso and expands current knowledge of the genetic diversity of MSV in the country. The detection of strain H in Brachiaria lata emphasizes the epidemiological importance of wild grasses as reservoirs of emerging MSV variants and provides valuable information for strengthening virus surveillance and developing sustainable maize disease management strategies.