Genetic composition and complexity of virus populations at tungro-endemic and outbreak rice sites

We have recently demonstrated the geographic isolation of rice tungro bacil liform virus (RTBV) populations in the tungro-endemic provinces of Isabela and North Cotabato, Philippines. In this study, we examined the genetic str ucture of the virus populations at the tungro-outbreak sites of Lanao del N orte, a province adjacent to North Cotabalo. We also analyzed the virus pop ulations at the tungro-endemic sites of Subang, Indonesia, and Dien Khanh, Vietnam. Total DNA extracts from 274 isolates were digested with EcoRV rest riction enzyme and hybridized with a full-length probe of RTBV. In the tota l population, 22 EcoRV-restricted genome profiles (genotypes) were identifi ed. Although overlapping genotypes could be observed, the outbreak sites of Lanao del Norte had a genotype combination distinct from that of Subang or Dien Khanh but a genotype combination similar to that identified earlier f rom North Cotabato, the adjacent endemic province. Sequence analysis of the intergenic region and part of the ORF1 RTBV genome from randomly selected genotypes confirms the geographic clustering of RTBV genotypes and, combine d with restriction analysis, the results suggest a fragmented spatial distr ibution of RTBV local populations in the three countries. Because RTBV depe nds on rice tungro spherical virus (RTSV) for transmission, the population dynamics of both tungro viruses were then examined at the endemic and outbr eak sites within the Philippines. The RTBV genotypes and the coat protein R TSV genotypes were used as indicators for virus diversity. A shift in popul ation structure of both viruses was observed at the outbreak sites with a r educed RTBV but increased RTSV gene diversity.