Infection Rate Assay by Nested PCR and the Phylogenetic Analysis of Himetobi P Virus in the Main Pests of Rice-Wheat Cropping Systems.

Himetobi P virus (HiPV) is an ssRNA in the family Dicistroviridae that infects rice pests belonging to Hemiptera. To determine its host range, a nested PCR method was designed to detect HiPV in some of the main rice pests (Hemiptera) in eastern China. The incidence of infection in the grain aphid Sitobion avenae Fabricius (Hemiptera: Aphididae) was low (3%), while high incidences of infection occurred in the planthoppers Laodelphax striatellus (Fallén) (Hemiptera: Delphacidae) (100%) and Nilaparvata lugens (Hemiptera: Delphacidae) (51%) and in the leafhoppers Cicadella viridis (Hemiptera: Cicadellidae) (90%) and Nephotettix cincticeps (Hemiptera: Cicadellidae) (57%). Phylogenetic analysis by maximum likelihood tree and median-joining networks implied the HiPVs from the same hosts were genetically close. Neutral equilibrium evolution for the polymorphism data was tested by the Tajima's D test and by Fu and Li's D and F tests. Test values were negative, which indicates a selection on the HiPV haplotypes. We sequenced the complete genome sequence of HiPV to look for evidence of recombination. We identified a recombination event in which two genomes recombined in the region of ORF2. The two open reading frames of the HiPV had been selected with low Ka/Ks ratios compared with two previous genome sequences.