Repeated passage of soil-borne wheat mosaic virus (SBWMV; wild-type Oklahoma field isolate; designated Okl-0) by manual inoculation resulted in deletion of part of SBWMV RNA2. Deletion was apparent in the population of RNA2 molecules after only 11 weeks in primary inoculated wheat plants (called Okl-1) and after 5 passages (Okl-5; 20 weeks) no full-length RNA2 remained. The extent of deletion in the Oklahoma isolate was compared with that in the previously studied Lab 1 (Nebraska) isolate. RNA2 from Okl-1, Okl-7, and Lab 1 were analyzed by RT-PCR amplification using sets of primer pairs which spanned all portions of the intact molecule. Lab 1 and the new stable isolate, Okl-7, were found to be deleted for 1058 and 759 nt, respectively, within the region encoding the coat protein-readthrough domain. However, the Okl-7 deletion was in a different position from the Lab 1 deletion. This suggests that deletions of SBWMV RNA2 which occur during serial manual inoculation are not directed toward production of a conserved, truncated form of the 84-kDa extended coat protein, but might reflect an RNA sequence-dependent event.