Molecular and biological characterization of <i> <scp>C</scp> owpea mild mottle virus </i> isolates infecting soybean in <scp>B</scp> razil and evidence of recombination

Abstract

The biological and molecular characterization of six isolates of a new Cowpea mild mottle virus strain ( CPMMV ; C arlavirus, B etaflexiviridae ) are reported. Soybean plants with mosaic and stem necrosis were collected in B ahia, G oiás, M ato G rosso and M inas G erais states, B razil. Complete genomes of the CPMMV isolates are 8180–8198 nucleotides (nt) long, excluding the 3′‐polyadenylated tail, and have 67–68% nt sequence identity with a G hana isolate of CPMMV , the only CPMMV isolate for which the genome has previously been sequenced. The replicase has only 60–61% nt sequence identity with the G hana CPMMV isolate, and the coat protein ( CP ) is highly conserved (79% nt sequence identity and 95–96% amino acid sequence identity). The high CP identity and the phylogenetic analyses supported the classification of the B razilian isolates as CPMMV . Biological and molecular differences with the G hana CPMMV isolate were found and indicated that the six isolates represent a distinct CPMMV strain denominated as CPMMV ‐ BR . Furthermore, it is shown that recombination occurred mainly in the polymerase gene, and may occur less frequently in other regions of the CPMMV genome.