Genetic variation of rice tungro bacilliform virus in the Philippines

Restriction fragment length polymorphisms (RFLPs) were found in 27 full genome length clones from a glasshouse isolate of rice tungro bacilliform pararetrovirus (RTBV) from the International Rice Research Institute (IRRI), the Philippines and from clones from 5 field isolates from different parts of the Philippines. There was much less variation between the IRRI clones than between the field isolate clones. The RFLPs were due to single base changes and represented about 10% of the potential sites. Sequencing across the region between nt 7772 and 7989 confirmed that the field isolates differed from the published sequence more than did the IRRI clones. The most common substitutions were G > A, A > G and T > C. Sequence heterogeneity was also noted in PCR products from RTBV DNA from the isolates. These observations are discussed in relation to the quasispecies population concept of viruses.