Amplification of complete gag gene sequences from geographically distinct equine infectious anemia virus isolates

Development and evaluation of a real-time quantitative PCR for the detection of equine infectious anemia virus

IMPORTANCE

Equine infectious anemia (EIA) has a worldwide distribution and causes significant losses to the equine industry worldwide. A reliable detection method is necessary to control the transmission of EIA virus (EIAV). Currently, most of the available real-time PCR assays, including the qPCR of recommended by WOAH, are developed according to the sequences of European or American EIAV strains; however, the primers and probe sequences have low homology with Asian EIAV strains. To the best of our knowledge, no qPCR method capable of the well detection of Asian EIAV strains, especially Chinese EIAV strains, has been published to date. The development of a sensitive, specific, and rapid qPCR assay for the detection of the EIAV strains is therefore of great importance.

Molecular Characterization of the Major Open Reading Frames (ORFs) and Enhancer Elements From Four Geographically Distinct North American Equine Infectious Anemia Virus (EIAV) Isolates

Although the equine lentivirus (equine infectious anemia virus [EIAV]) poses a major threat to equid populations throughout most regions of the world, detailed knowledge concerning its molecular epidemiology is still in its infancy. Such information is important because the few studies conducted to date suggest there is extensive genetic variation between viral isolates that if confirmed has significant implications for future vaccine design and development of newer diagnostic procedures. Here, we avoid potential assembly artifacts inherent in composite sequencing techniques by using long-range PCR in conjunction with next-generation sequencing for the rapid molecular characterization of all major open reading frames (ORFs) and known transcription factor binding motifs within the long terminal repeats (LTRs) of four North American EIAV isolates from Pennsylvania (EIAV_PA), Tennessee (EIAV_TN), North Carolina (EIAV_NC), and Florida (EIAV_FL). These were compared with complete published EIAV field strain genomic sequences from Asia (EIAV_LIA, EIAV_MIY), Europe (EIAV_IRE), and North America (EIAV_WY) plus EIAV_UK a laboratory variant of EIAV_WY. Phylogenetic analysis using the long-range PCR products suggested all the New World EIAV isolates comprised a single monophyletic group associated with EIAV_IRE. This is distinct from the Asian isolates and so consistent with known historical details concerning the reintroduction of equids into North America by European settlers. Nonetheless nucleotide sequence identity for example between EIAV_PA and EIAV_TN, EIAV_NC, EIAV_FL, EIAV_WY, EIAV_UK plus EIAV_IRE was limited to 84.6%, 81.0%, 82.1%, 80.4%, 80.1%, and 77.6%, respectively, with some of these values being not too dissimilar to those between EIAV_PA and EIAV_LIA or EIAV_MIY at 78.0% and 75.4%, respectively. Overall, these results suggest substantial genetic diversity exists even within North American EIAV isolates. Comparative alignment of predicted amino acid sequences from all strains provides increased understanding concerning the extent of permitted substitutions in each viral ORF and known transcriptional LTR control elements.

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

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 (EIAV_WYO and EIAV_LIA ) 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 (EIAV_DEV ) and 2012 (EIAV_COR ) 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.