Within-host genetic diversity of endemic and emerging parvoviruses of dogs and cats

Abstract

Viral emergence can result from the adaptation of endemic pathogens to new or altered host environments, a process that is strongly influenced by the underlying sequence diversity. To determine the extent and structure of intrahost genetic diversity in a recently emerged single-stranded DNA virus, we analyzed viral population structures during natural infections of animals with canine parvovirus (CPV) or its ancestor, feline panleukopenia virus (FPV). We compared infections that occurred shortly after CPV emerged with more recent infections and examined the population structure of CPV after experimental cross-species transmission to cats. Infections with CPV and FPV showed limited genetic diversity regardless of the analyzed host tissue or year of isolation. Coinfections with genetically distinct viral strains were detected in some cases, and rearranged genomes were seen in both FPV and CPV. The sporadic presence of some sequences with multiple mutations suggested the occurrence of either particularly error-prone viral replication or coinfection by more distantly related strains. Finally, some potentially organ-specific host effects were seen during experimental cross-species transmission, with many of the mutations located in the nonstructural protein NS2. These included residues with evidence of positive selection at the population level, which is compatible with a role of this protein in host adaptation.

FIG. 1.

Overview of natural virus samples analyzed. The host from which the sample was collected, the virus type, and year of collection are indicated. The likely natural host range and year of global spread are indicated. Viruses used for inoculation of kittens are marked.

FIG. 2.

Mutations in the consensus sequences. The isolate consensus sequences from clinical samples of FPV (A) and CPV (B) infections were compared by using the oldest FPV and CPV samples as reference sequences in each case. The nucleotide position is indicated at the top, and the character state of individual nucleotides is indicated below each sequence. Changes in amino acid sequence are characterized above the sequence, where appropriate. Synonymous changes are indicated by black boxes, and nonsynonymous changes are indicated by red boxes, while the location in the viral genome can be inferred by referring to the genome map shown below the sequences.

FIG. 3.

Intrahost diversity in FPV and CPV samples. (A) The gene regions covered by PCR amplification and a corresponding translation map of the parvovirus genome are indicated. (B and C) Divergent viral sequences detected in animals naturally infected with FPV (B) or CPV (C) are shown. The location of mutations in the parvovirus genome and the type of nucleotide substitution are indicated for each divergent sequence, the number of individual clones analyzed for each sample and the gene product affected by nonsynonymous mutations are indicated, and the year of isolation is identified. For comparison, in the case of the CPV-infected cat described previously by Battilani et al. (4), 10 out of 14 clones analyzed for the VP2 gene harbored one or more mutations each, which distinguished the clone from the consensus sequence.

FIG. 4.

Analysis of the sequence recovered from experimental CPV-13.us.81 infection of cats. (A) Summary of the expected pathogenesis of FPV in cats, including the viral location at various days postinfection (p.i.) and organs infected. (B) Characterization of viral sequences recovered from different organs, including the type of nucleotide substitution and the attained protein (for nonsynonymous changes) of each infected cats.