Abstract: Equine infectious anemia virus (EIAV) is a persistent lentivirus that causes equine infectious
anemia (EIA). In Brazil, EIAV is endemic in the Pantanal region, and euthanasia is not mandatory in
this area. All of the complete genomic sequences from field viruses are from North America, Asia,
and Europe, and only proviral genomic sequences are available. Sequences from Brazilian EIAV
are currently available only for gag and LTR regions. Thus, the present study aimed for the first
time to sequence the entire EIAV genomic RNA in naturally infected horses from an endemic area
in Brazil. RNA in plasma from naturally infected horses was used for next-generation sequencing
(NGS), and gaps were filled using Sanger sequencing methodology. Complete viral genomes of EIAV
from two horses were obtained and annotated (Access Number: MN560970 and MN560971). Putative
genes were analyzed and compared with previously described genes, showing conservation in gag
and pol genes and high variations in LTR and env sequences. Amino acid changes were identified in
the p26 protein, one of the most common targets used for diagnosis, and p26 molecular modelling
showed surface amino acid alterations in some epitopes. Brazilian genome sequences presented 88.6%
nucleotide identity with one another and 75.8 to 77.3% with main field strains, such as EIAV Liaoning,
Wyoming, Ireland, and Italy isolates. Furthermore, phylogenetic analysis suggested that this Brazilian
strain comprises a separate monophyletic group. These results may help to better characterize EIAV
and to overcome the challenges of diagnosing and controlling EIA in endemic regions
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