J. F. Young studied genetic variation in Influenza A virus. In a 1979 paper with P. Palese, RNA oligonucleotide fingerprints and peptide mapping were used to compare circulating strains.[ref]
The important comparison was between individual genetic segments, not just whole-strain labels. Different inferred parental origins within A/Cal/10/78 supported reassortment rather than explaining every difference by successive mutations. The evidence was comparative: the paper inferred ancestry from molecular patterns, rather than directly filming the historical exchange inside a cell.[ref]
Evolution of human influenza A viruses in nature: recombination contributes to genetic variation of H1N1 strains by J. F. Young and P. Palese. Abstract; oligonucleotide and peptide maps and inferred H1N1/H3N2 ancestry
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