Limited intra-host diversity and background evolution accompany 40 years of canine parvovirus host adaptation and spread

Canine parvovirus (CPV) is a highly successful pathogen that has sustained pandemic circulation in dogs for more than 40 years. Here, integrating full-genome and deep sequencing analyses, structural information, and in vitro experimentation, we describe the macro- and micro-scale features that have accompanied CPV’s evolutionary success. Despite 40 years of viral evolution, all CPV variants are >∼99% identical in nucleotide sequence, with only a limited number (<40) of mutations becoming fixed or widespread during this time. Notably, most changes in the major capsid protein (VP2) are nonsynonymous and fall within, or adjacent to, the overlapping receptor footprint or antigenic regions, suggesting competitive selective pressures have played a key role in CPV evolution and likely constrained its evolutionary trajectory. Moreover, among the limited number of variable sites, CPV genomes exhibit complex patterns of variation that likely include parallel evolution, reversion, and recombination, making phylogenetic inference difficult. Additionally, deep sequencing of viral DNA in original clinical samples collected from dogs and other host species sampled between 1978 and 2018 revealed few sub-consensus single nucleotide variants (SNVs) above ∼0.5%, and experimental passages demonstrate that substantial pre-existing genetic variation is not necessarily required for rapid host receptor driven adaptation. Together, these findings suggest that although CPV is capable of rapid host adaptation, relatively low mutation rate, pleiotropy, and/or a lack of selective challenges since its initial emergence have reduced the long-term genetic diversity accumulation and evolutionary rate. Hence, continuously high levels of inter- and intra-host diversity are not intrinsic to highly adaptable viruses. IMPORTANCE Rapid mutation rates and correspondingly high levels of standing intra-host diversity and accumulated inter-host diversity over epidemic scales are often cited as key features of viruses with the capacity for emergence and sustained transmission in a new host species. However, most of this information comes from studies of RNA viruses, with relatively little being known about that evolutionary processes that occur for viruses with DNA genomes. Here we provide a unique model of virus evolution, integrating both long-term global-scale and short-term intra-host evolutionary processes of a virus in a new host animal. Our analysis reveals that successful host jumping and sustained onward transmission does not necessarily depend on a high level of intra-host diversity or result in the continued accumulation of high levels of long-term evolution change. These findings indicate that all aspects of a virus’s biology and ecology are relevant when considering their adaptability.