Evolutionary dynamics of viral attenuation

Abstract

The genetic trajectory leading to viral attenuation was studied in a canine parvovirus (CPV) strain grown on dog kidney cells for 115 transfers. Consensus sequences of viral populations at passages 0, 3, 30, 50, 80, and 115 were obtained from PCR products covering 86% of the genome; clones from each of the 80th and 115th passages were also sequenced, covering 69% of the genome. Sixteen changes were fixed in the 115th-passage virus sample. Levels of polymorphism were strikingly different over time, in part because of a plaque-cloning step at passage 112 that reduced variation: passage 80 had 19 variants common among the clones, but passage 115 had only a single common variant. Several mutations increased in the culture at the same time, with most reaching fixation only after the 80th passage. The pattern of evolution was consistent with recombination and not with separate selective sweeps of individual mutations. Thirteen of the changes observed were identical to or at the same positions as changes observed in other isolates of CPV or feline panleukopenia virus.

FIG. 1.

Sequence changes found in CPV during passage in dog cells between the wild-type virus (pass 0) and after 3, 30, 50, 80, and 115 passages in primary dog cells or after 103 passages in dog cells and 9 passages in cat cells (103/9). The left column (Changes detected) indicates the genomic nucleotide position(s) (24) and the gene affected. The next column gives the amino acid substitution(s) where those occurred (blank if the nucleotide change was noncoding). The residue number in the gene is given for each protein affected. The pass 0 column gives the ancestral base, and the new base is given in the 115 or 103/9 (cat) column. (Top) Twenty changes observed in PCR consensus sequences. Each of the variable sites that was detected in the PCR consensus sequence is shown as white (no change from pass 0), shaded (polymorphic signal in the PCR consensus sequence), or black (apparently fixed in that sequence). The number of variant nucleotides at each position in the nine clones of the 80th passage is shown as a ratio in parentheses for each position evaluated between bases 1099 and 4649 of that virus stock. The passage 115 data show the variation present at each position in eight clones of PCR products that were prepared as two segments and cloned into plasmids before sequencing. Virus isolate sequences (Virus isolates) were sequences obtained from GenBank or from other studies examining the sequences of natural isolates of CPV. (Bottom [Changes detected in p80 clones]) The lower seven changes were detected in only one to three of the nine clones prepared from the 80th-passage viruses, between nt 1099 and 4649 in the genome. The 115 column shows that only one of those passage 80 clone mutations was also seen in the eight clones from passage 115. Mutations found only in clones from passage 115 are not shown (all those not shown were present in just one of the eight clones). At the far right, those sequence changes observed in the passage 115 and 103/9 attenuation lineages are compared to the sequences of other viral isolates. Del or del, deletion; ins, insertion.

FIG. 2.

Polymorphic sites in the nine clones prepared from the 80th-passage virus. The nucleotide positions are ordered along the vertical axis corresponding to changes observed in the PCR consensus sequence (upper 15) and those that were not observed in the consensus sequence (lower 7). Each of columns 1 to 9 represents a different clone corresponding to a different viral isolate. A black square denotes the evolved (nonancestral) base, which changed as indicated in Fig. 1. All of the clones have unique sequences, which is suggestive of recombination.