Molecular characterization reveals that squash chlorosis mottling virus and zucchini tigré mosaic virus are the same newly emerging potyvirus

In 2013, we published the first report of a novel potyvirus isolate, which was tentatively named squash chlorosis mottling virus (SqCMV), from an infected squash plant (Cucurbita pepo) collected in the Homestead area of Florida. The purpose of the current work was to further characterize the virus isolate based on molecular properties, and to determine its relationship to other potyviruses. The complete genome sequence of the virus was 10,292 nucleotides (nt), consisting of a 5’-UTR (182 nt), a complete ORF (10,098 nt) encoding a polyprotein of 3,365 amino acids, a motif for the PIPO protein and a 3’-UTR (112 nt), but excluding the poly-(A) tail. Phylogenetic analysis based on the complete genome and amino acid sequences revealed that the virus from Florida clustered with the type isolate of the newly described potyvirus zucchini tigré mosaic virus (ZTMV) sharing 82-90% nucleotide and 83-86% amino acid identities, respectively. Recombination analysis confirmed one major recombination event in the putative P1 coding region of the virus with the putative parental sequences predicted to resemble to ZTMV-Venezuela and France isolates. In addition, genetic diversity analysis indicated that the CP gene was under the highest selection pressure compared to other genes. Together, these results suggest that SqCMV and ZTMV are both representative isolates of the same species, Zucchini tiger mosaic virus. We present the first complete genome sequence of the ZTMV-HFL isolate from the USA.