Molecular characterization of equine infectious anaemia virus strains detected in England in 2010 and 2012

Abstract

Equine infectious anaemia virus (EIAV) is a retrovirus with worldwide distribution which is notifiable to the OIE. Despite its importance to the equine industry, most information regarding its biology have been obtained using only two strains (EIAVWYO and EIAVLIA) from the USA and China, respectively. Recently full genome sequences from Ireland, Italy and Japan have been published; however, this is still not representative of the number of EIAV outbreaks experienced globally each year. The limited availability of published sequences makes design of a universal EIAV PCR difficult, hence diagnosis is solely reliant on serology. Accordingly, it is important to further investigate the re‐emerging cases in other areas of the world. Here, we provide information regarding the outbreaks of EIA in England in 2010 and 2012 including the molecular characterization of strains. Full genome was obtained for two symptomatic cases but could not be resolved for the asymptomatic cases. The two British genomes from 2010 (EIAVDEV) and 2012 (EIAVCOR) each represent a new phylogenetic group, each differing genetically from the other available full genome sequences by 21.1%–25.5%. That the majority of new EIAV full genome sequences to be published adds another phylogenetic group indicates that the surface of EIAV global diversity is just being scratched. These data highlight that further work is needed to fully understand EIAV genetic diversity, namely the full genome sequencing of EIAV cases from a variety of locations and time points. This would aid both the use of phylogenetics in parallel with horse tracing as the epidemiological tool of disease tracking and the design of a universally applicable molecular diagnostic method.

Phylogeography of equine infectious anemia virus

“…This combined approach has been widely applied to explain virulence, spread, invasion and species establishment of pathogens worldwide (Magiorkinis et al, 2009; Auguste et al, 2015; Pigeault et al, 2015; Weaver and Forrester, 2015; Dellicour et al, 2016; Rogalski et al, 2017; S Dellicour et al, 2017; Forni et al, 2018; Fountain-Jones et al, 2018). However, these methodologies are still not commonly applied for food animal diseases and therefore, major evolution and global diversification of several infectious disease remain an important bottleneck for better and universally applicable molecular testing (Dorey-Robinson et al, 2019), especially in diseases affecting horse populations, such as EIAV (Antolin, 2008; Struchiner et al, 2008; Dorey-Robinson et al, 2019).…”

“…Phylogenetic relationships of EIAV have been previously assessed by the analysis of outbreak cases reported worldwide (Nagarajan and Simard, 2007; Cappelli et al, 2011; Capomaccio et al, 2012), mainly focused in the areas with high horse-related industry, such as Brazil (Bicout et al, 2006; Nogueira et al, 2017; Barzoni et al, 2018; Cursino et al, 2018). However, the evolutionary and spread history of EIAV is still unknown (Dorey-Robinson et al, 2019).…”

High Genomic Variability in Equine Infectious Anemia Virus Obtained from Naturally Infected Horses in Pantanal, Brazil: An Endemic Region Case

“…Full-length field sequences from other countries (except the Wyoming strain) have been described based on proviral DNA samples, but not genomic RNA. Although the EIAV LIA , EIAV IRE , EIAV MIY , and EIAV WY strains were sequenced using the Sanger method, NGS was employed to obtain the England sequences [10], and a partial sequence of EIAV ITA was obtained from amplification of 7841 bp of EIAV [11]. Both animals used in this study exhibited viremia at sample collection.…”

“…Characterization of viral populations in early HIV infection, analysis of viral evolution patterns, and identification of super-infective strains have been studied by next-generation sequencing (NGS), also known as high-throughput sequencing (HTS) [7]. Complete genomic sequences of field-isolated EIAV from five different countries have been published to date: EIAV WY (United States of America), EIAV LIA (China), EIAV MIY (Japan) [8], EIAV IRE (Ireland) [9], EIAV DEV and EIAV CORN (England) [10], and the incomplete sequence EIAV ITA (Italy) [11]. Only the last and most recently obtained sequences, EIAV ITA, EIAV DEV and EIAV CORN , were obtained by NGS.…”

“…The sequences from Italy and Ireland are very similar to each other. Sequences from China, Japan, the United States of America, England, and Italy/Ireland share approximately 80% identity, forming five separated clades and suggesting an independent evolution from a common ancestor [2,[10][11][12]. This fact indicates that the establishment of similar approaches for molecular diagnosis methods and control programs in different regions might be difficult [2].…”