Molecular characterization of encephalomyocarditis virus strains isolated from an African elephant and rats in a French zoo

Abstract

In November 2013, a fatal encephalomyocarditis virus (EMCV) case in a captive African elephant (Loxodonta africana) occurred at the Réserve Africaine de Sigean, a zoo in the south of France. Here we report the molecular characterization of the EMCV strains isolated from samples collected from the dead elephant and from 3 rats (Rattus rattus) captured in the zoo at the same time. The EMCV infection was confirmed by reverse-transcription real-time PCR (RT-rtPCR) and genome sequencing. Complete genome sequencing and sequence alignment indicated that the elephant's EMCV strain was 98.1-99.9% identical to the rat EMCV isolates at the nucleotide sequence level. Phylogenetic analysis of the ORF, P1, VP1, and 3D sequences revealed that the elephant and rat strains clustered into lineage A of the EMCV 1 group. To our knowledge, molecular characterization of EMCV in France and Europe has not been reported previously in a captive elephant. The full genome analyses of EMCV isolated from an elephant and rats in the same outbreak emphasizes the role of rodents in EMCV introduction and circulation in zoos.

Keywords: Elephants; encephalomyocarditis virus; phylogenetic analysis; rats.

Figure 1.

Neighbor-joining tree based on the complete ORF sequence showing relationships between the encephalomyocarditis virus (EMCV) strains isolated at Sigean zoo and EMCV sequences available in GenBank. The evolutionary distances were computed using the Tamura–Nei method. The percentages of bootstrap values >70% of 1,000 replicates that support each branch node are shown next to the branches. The scale bar indicates nucleotide substitutions per site.