Mosaic diseases of sugarcane caused by various viruses have been reported in most sugarcane planting countries and threaten global sugar production. There is a lack of extensive, systematic investigation of mosaic diseases and their causal viruses in China. In this study, a total of 901 leaf samples showing mosaic symptoms were collected from commercial fields in eight provincial regions in China and tested for sorghum mosaic virus (SrMV), sugarcane mosaic virus (SCMV), sugarcane streak mosaic virus (SCSMV), and maize yellow mosaic virus (MaYMV) using RT-PCR with four specific primer pairs. Of 901 tested samples, 38.5% (347/901) of samples were infected with one of the four viruses alone. Infection by two or more viruses was seen for 42.6% (384/901) of samples. The highest incidence of virus-causing sugarcane mosaic disease was SrMV (70.1%), followed by SCMV (33.4%) and SCSMV (30.3%), and the lowest incidence was seen for MaYMV (5.1%). Three viruses (SrMV, SCMV, and SCSMV) were found in eight sugarcane-planting provinces, whereas MaYMV was only found in Fujian, Guangxi, and Sichuan provinces. Mixed infections of the three main viruses, particularly for SrMV + SCMV and SrMV + SCSMV, were commonly found in the sugarcane samples. Our systematic determination of the occurrence and distribution of four RNA viruses associated with sugarcane mosaic diseases can provide evidence to guide the development of strategies for the prevention and control of sugarcane mosaic diseases in China.

Yellow leaf disease caused by sugarcane yellow leaf virus (SCYLV) is one of the most prevalent diseases worldwide. In this study, six near-complete genome sequences of SCYLV were determined to be 5775–5881 bp in length. Phylogenetic analysis revealed that the two SCYLV isolates from Réunion Island, France, and four from China were clustered into REU and CUB genotypes, respectively, based on 50 genomic sequences (this study = 6, GenBank = 44). Meanwhile, all 50 isolates were clustered into three phylogroups (G1–G3). Twelve significant recombinant events occurred in intra- and inter-phylogroups between geographical origins and host crops. Most recombinant hotspots were distributed in coat protein read-through protein (RTD), followed by ORF0 (P0) and ORF1 (P1). High genetic divergences of 12.4% for genomic sequences and 6.0–24.9% for individual genes were determined at nucleotide levels. The highest nucleotide diversity (π) was found in P0, followed by P1 and RdRP. In addition, purifying selection was a main factor restricting variability in SCYLV populations. Infrequent gene flow between Africa and the two subpopulations (Asia and America) were found, whereas frequent gene flow between Asia and America subpopulations was observed. Taken together, our findings facilitate understanding of genetic diversity and evolutionary dynamics of SCYLV.

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