Complete genome sequence of a novel polerovirus infecting chickpea (Cicer arietinum L.).

The complete genome sequence of a novel polerovirus identified in chickpea (C. arietinum L.) is presented. Its sequence was assembled using small RNA sequencing and assembly (sRSA) and confirmed by RT-PCR, 5' and 3' RACE, and Sanger sequencing. According to the current ICTV sequence demarcation criterion of greater than 10% amino acid (aa) sequence divergence in all gene products when compared to other poleroviruses, the newly identified polerovirus should be classified as a member of a new species, and we propose the name "chickpea leafroll virus" (CpLRV) for this virus. The genome of CpLRV is 5,770 nucleotides (nt) long and is organized into seven open reading frames (ORFs), designated as ORF0, ORF1, ORF2, ORF3a, ORF3, ORF4, and ORF5, which code for putative P0, P1, P1-P2, P3a, P3, P4, and P3-P5 proteins, respectively. The 5' untranslated region (UTR) consists of 27 nt, starting with the conserved sequence 5'-ACAAAA-3', which is typical of poleroviruses, while the 3' UTR consists of 229 nt. Phylogenetic analysis based on the aa sequences of P0, P1, P1-P2, P3, P4, and P3-P5 showed that CpLRV clustered with members of the genus Polerovirus and is closely related to chickpea chlorotic stunt virus (CpCSV) and faba bean polerovirus 1 (FBPV1). Recombination analysis suggested that CpLRV is a recombinant of two unknown viruses that share the highest nucleotide sequence similarity with FBPV1 (76.9% identity) and suakwa aphid-borne yellows virus (SAbYV) (64.8% identity). The putative recombination event was identified in the 5' region of the CpLRV genome, the region that encodes proteins P0, P1, and P1-P2. This is the first report of a polerovirus infecting chickpea in Mexico.

Complete genome sequence of a novel comovirus infecting common bean.

The complete genome sequence of a novel comovirus identified in Guanajuato, Mexico, in a common bean plant (Phaseolus vulgaris L.) coinfected with Phaseolus vulgaris alphaendornavirus 1 (PvEV-1) and Phaseolus vulgaris alphaendornavirus 2 (PvEV-2) is presented. According to the current ICTV taxonomic criteria, this comovirus corresponds to a new species, and the name "Phaseolus vulgaris severe mosaic virus" (PvSMV) is proposed for this virus based on the observed symptoms of "severe mosaic" syndrome caused by comoviruses in common bean. PvSMV is closely related to bean pod mosaic virus (BPMV), and its genome consists of two polyadenylated RNAs. RNA-1 (GenBank accession number MN837498) is 5969 nucleotides (nt) long and encodes a single polyprotein of 1856 amino acids (aa), with an estimated molecular weight (MW) of 210 kDa, that contains putative proteins responsible for viral replication and proteolytic processing. RNA-2 (GenBank accession number MN837499) is 3762 nt long and encodes a single polyprotein of 1024 aa, with an estimated MW of 114 kDa, that contains putative movement and coat proteins. Cleavage sites were predicted based on similarities in size and homology to aa sequences of other comoviruses available in the GenBank database. Symptoms associated with PvSMV include mosaic, local necrotic lesions, and apical necrosis. This is the first report of a comovirus infecting common bean in Mexico.