Molecular Characterization of the Cucumber Mosaic Virus and Cucumber Green Mottle Mosaic Virus Infecting Allium cepa in China

Onion (Allium cepa) belongs to the genus Allium in the family Liliaceae and is widely cultivated worldwide for its nutritional and medicinal value. However, in Hohhot, Inner Mongolia, China, many onion plants exhibited severe virus-like symptoms, including yellow stripes and leaf distortion. Symptomatic plants were collected, and virus identification was conducted through mechanical inoculation of Nicotiana benthamiana and transmission electron microscopy. Two types of virus particles, rod-shaped and spherical, were observed. Mixed infection of Cucumber mosaic virus (CMV) and Cucumber green mottle mosaic virus (CGMMV) was confirmed by high-throughput sequencing and RT-PCR. The detection rates of CMV and CGMMV in the samples were 8/161 and 1/161, respectively. Recombination analysis indicated that no recombination events were detected in the CGMMV, whereas one recombination event was identified in CMV, occurring on RNA1 from nt 59 to 171. The major parent was CMV DSMZ PV-1255 (ON013910) in Greece, and the minor parent was CMV Am (JX993909) in China. This study reports, for the first time, the complete genome sequences of CMV infecting onions in China and CGMMV infecting onions worldwide.