1) you really have infection by 2 isolates, and such idea is supported by the observed recombinations in RTBV sequence, see:
Sharma S, Rabindran R, Robin S, Dasgupta I. Analysis of the complete DNA
sequence of rice tungro bacilliform virus from southern India indicates it to be
a product of recombination. Arch Virol. 2011 Dec;156(12):2257-62
2) your plants have endogenous rice tungro bacilliform virus-like sequences, see:
Kunii M, Kanda M, Nagano H, Uyeda I, Kishima Y, Sano Y. Reconstruction of putative DNA virus from endogenous rice tungro bacilliform virus-like sequences in the rice genome: implications for integration and evolution. BMC Genomics. 2004 Oct 18;5:80.