Microevolution of canine influenza virus in shelters and its molecular epidemiology in the United States

Abstract

Canine influenza virus (CIV) emerged around 2000 when an equine influenza virus (EIV) was transmitted to dogs in Florida. After 2003, the canine virus was carried by infected greyhounds to various parts of the United States and then became established in several large animal shelters, where it has continued to circulate. To better understand the evolution of CIV since its emergence, and particularly its microevolution in spatially restricted populations, we examined multiple gene segments of CIV from dogs resident in two large animal shelters in New York City during the period 2006 to 2009. In particular, we focused on viruses circulating in the two shelters in 2008 and 2009, which we found shared a common ancestor. While viruses in each shelter were generally monophyletic, we observed some gene flow between them. These shelter sequences were compared to earlier CIV isolates. The shelter viruses differed in 1 to 6 amino acids in each gene segment compared to viruses isolated in Florida between 2003 and 2005 and in Colorado in 2006 and 2008. A comparison of the sequences of equine and canine viruses revealed amino acid replacements that distinguished the viruses from the two hosts, but no clear evidence of positive selection indicative of host adaptation was detected, suggesting that any host range adaptation in CIV occurred early in the emergence of this virus or even before it transferred to dogs.

FIG. 1.

Phylogenetic trees of EIV (from 1963 to the present), CIV, and representative shelter sequences. CIV sequences are shown in blue; their detailed phylogenetic relationships are shown in the insets. Virus samples in black are equine sequences, and those in pink are canine sequences. Sequences of viruses from the dogs in the New York shelters are color coded and indicate the consensus sequence of the virus from an individual dog. All horizontal branches are drawn to a scale of nucleotide substitutions per site, and bootstrap values of >70% are shown. (A) HA1; (B) M; (C) NS.

FIG. 2.

Phylogenetic trees of cloned CIV sequences prepared after direct RT-PCR of virus in swabs of infected dogs sampled from the New York City shelters, as well as some other isolates. Samples were taken from shelter B in November 2008 (light pink boxes) and December 2009 (dark pink boxes) and from shelter A in March 2009 (light blue boxes) and September 2009 (dark blue boxes). Each colored circle represents a sequence, and sequences from the same dog are colored the same across all trees. All horizontal branches are drawn to a scale of nucleotide substitutions per site, and bootstrap values of >70% are shown. (A) HA1; (B) M; (C) NS.