Identification and Genetic Evolution of Viruses Infecting Chili Peppers at Chifeng, Inner Mongolia

  Objective  Viruses that infected chili pepper crops in Chifeng City, Inner Mongolia were identified, and their genetic relationship analyzed.

  Methods  The 47 infected chili pepper plants at 4 major producing areas in Chifeng City were diagnosed, and viruses identified by sRNA high-throughput sequencing with bioinformatic analysis and RT-PCR. Fragments of RT-PCR were sequenced using the Sanger method to conduct a phylogenetic analysis with the MEGA software.

  Results  Six viruses were identified by sRNA high-throughput sequencing. Of which, 4 were re-verified by RT-PCR. The dominant viruses infecting the 4 regions differed significantly. They were Broad bean wilt virus 2(BBWV2) and Potato virus Y(PVY) in Chengzi County of Songshang District, PVY and Pepper mild mottle virus(PMMoV) in Jinshan County of Kalaqin District, and BBWV2 in Ningcheng County and Xiqiao County of kalaqin District. When the infection was caused by multiple viruses, it was mostly by two major pathogens and had the highest rate of occurrence at 61.54%. The phylogenetic analysis on the sequenced nucleotides of the viruses showed distinctive genetic differences between PMMoV and BBWV2 and, possibly, PVY of a novel genetic type.

  Conclusion  There are significant differences in the types of viruses, detection rates, and types of virus co-infections that occur in different chili production areas of Chifeng City in Inner Mongolia .