Genetic structure of populations of sugarcane streak mosaic virus in China: Comparison with the populations in India

• We studied population structure in SCSMV isolates from China using genomic sequences.
• Quasispecies and mixed-infections were found to be frequent in SCSMV-infected plants.
• Genetic recombination was detected in SCSMV, although the frequency was low.
• We found at least nine phylogenetical lineages in SCSMV isolates from China.
• Gene flow between SCSMV isolates from China and India was found to be infrequent.

Sugarcane streak mosaic virus (SCSMV) causes mosaic and streak symptoms on sugarcane and sorghum crops, and has a broad host range. SCSMV is a member of the genus Poacevirus in the family Potyviridae.Ten SCSMV isolates were collected from sugarcane plants showing mosaic and streaking in Southern China from 2009–2011. Sequence-based phylogenetic and population genetic analyses were conducted using four partial genomic sequences covering the full genomes. These analyses were used to estimate the subpopulation differentiation and divergence within the Chinese virus population, and were compared with isolates from India. SCSMV-infected sugarcane plants in the field commonly harbor virus quasispecies (mutant cloud), and often have mixed infections with the same virus isolates. Inter- and intra-lineage recombination sites were identified in the protein 1, helper-component proteinase, coat protein and 3′ non-coding regions of the Chinese isolates. All the Chinese non-recombinant isolates fell into at least nine lineages, and many clustered with Indian isolates. However, estimates of genetic differentiation and gene flow indicated that the SCSMV populations in China and India are genetically independent. Our genetic study of a poacevirus population in South Asia regions indicates the importance of the evolutionary-based design to control viruses.