FIG. 3.

Identification of mixed viral populations in cotton rat lungs. Lung samples were harvested (from rats A-2, A-3, A-4, B-1, B-2, C-1, C-2, C-3, and C-4) at 12 weeks postinfection, RNA was extracted, RT-PCR was performed, and nucleotide sequences were determined for the region from nucleotides 660 to 1210 in the F gene. For one sample, the A-4 regrown virus (MCRL5), virus was recovered in HEp-2 cells prior to characterization. The region shown is from nucleotides 810 to 833 in the F gene. Blue arrows indicate nucleotide 816 of the F gene. Base A (green) at position 816 is the parent A2 virus base. Lungs (A-2, A-4, and B-1) revealed mixtures at nucleotide 816, with both A and a mutation to T (red) present. The mutation to 816 T was also seen in the in vitro-derived escape mutant F212 (35). Red arrows indicate position 827 in the F gene. The A-4 regrown virus had the parental A2 virus base A instead of a mixed signal (A/T) at position 816; at position 827, the regrown virus revealed a mutation to C (blue) instead of the dominant base A (green) seen in the A-4 sample prior to recovery in cell culture.