Near-complete genome sequence of cowpea severe mosaic virus in South America and reduced yardlong bean production due to the viral infection

The sequence of a near-complete genome (two RNA segments) of cowpea severe mosaic virus (CpSMV) in the Comovirus genus is revealed in South America. High-throughput sequencing (HTS) was performed using total RNA extracted from partially purified virus preparations obtained from infected yardlong bean leaves ( Vigna unguiculata subsp. sesquipedalis ), collected in Santa Izabel, state of Pará, Brazil. The YLB (yardlong bean) isolate has an RNA-1 with 5896 nucleotides (nt) and an RNA-2 with 3515 nt, showing 74.2% and 67.9% identity, respectively, with the CpSMV-DG isolate sequences from the USA, the only complete genome available so far. Despite the low percentage in nt identity, the amino acid (aa) sequence of the viral protease together with the RNA-dependent RNA polymerase (Pro/RdRp) and the large and small coat proteins (CP-L/CP-S), used as species demarcation criteria of the Secoviridae family, showed 92.2% (Pro-RdRp) and 85.6% (CP-L/CL-S) identities between DG and YLB isolates sequences. The nucleotide identity of partial RNA-1 sequences of 2199 nt (part of the helicase, VPg, Pro, and 2/3 of the RdRP) varied from 95.1 to 95.3% among YLB and eleven isolates from Brazil available on GenBank. Phylogenetic analysis based on this 2199 nt sequence revealed that the YLB isolate was positioned in a different clade compared to other CpSMV isolates. An estimate of damage caused by CpSMV under experimental conditions revealed a reduction of 39.4% in the total number of pods and 54.3% in the total number of grains, regardless of the yardlong bean cultivar evaluated. The reduction of total weight of the grains by CpSMV infection was dependent on the cultivar and was higher in cv. De metro (66.2%) than in cv. Slin (38.9%).