Evolution of equine influenza virus in vaccinated horses

Abstract

Influenza A viruses are characterized by their ability to evade host immunity, even in vaccinated individuals. To determine how prior immunity shapes viral diversity in vivo, we studied the intra- and interhost evolution of equine influenza virus in vaccinated horses. Although the level and structure of genetic diversity were similar to those in naïve horses, intrahost bottlenecks may be more stringent in vaccinated animals, and mutations shared among horses often fall close to putative antigenic sites.

Fig 1

Intra- and interhost genetic variation of EIV in vaccinated horses. (A) Layout of the transmission chain (see main text). S, seeder; V1 to V5, vaccinated horses. The number refers to the order in which animals were introduced into the transmission chain. No virus was detected in horse V5 (shown with a stop sign). (B) Median joining networks derived from the horses included in the study. Each network was inferred by compiling sequences from all available days. The size of each circle is proportional to the frequency of identical sequences in the data set, and the number of sequences that constitute the consensus is indicated. The identification number of each horse is indicated at the bottom of each panel. Colors indicate the day in which the sample was taken relative to the day of contact. (C) Estimation of viral copy numbers from individual swabs by real-time PCR.