An EIAV field isolate reveals much higher levels of subtype variability than currently reported for the equine lentivirus family

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 Anemia Viruses using targeted sequence enrichment and next generation sequencing

Equine infectious anemia virus (EIAV) is responsible of acute disease episodes characterized by fever, anemia, thrombocytopenia and anorexia in equids. The high mutation rate in EIAV genome limited the number of full genome sequences availability. In the present study, we used the SureSelect target enrichment system with Illumina Next Generation Sequencing to characterize the proviral DNA of Equine Infectious Anemia Virus (EIAV) from asymptomatic horses. This approach allows a direct sequencing of the EIAV whole genome without cloning or amplification steps and we could obtain for the first time the complete genomic DNA sequences of French EIAV strains. We analyzed their phylogenetic relationship and genetic variability by comparison with 17 whole EIAV genome sequences from different parts of the world. The results obtained provide new insights into the molecular detection of EIAV and genetic diversity of European viral strains.

Validation of an immunoblot assay employing an objective reading system and used as a confirmatory test in equine infectious anaemia surveillance programs

Equine infectious anaemia (EIA) is a blood borne disease that is listed among the notifiable diseases of the World Organisation for Animal Health (OIE). EIA is also regulated by the OIE for the international trading provisions and is generally subject to control programmes. Since 2011, Italy has been conducting a surveillance plan based on a three-tier diagnostic system, using a serological ELISA as screening test, an agar gel immunodiffusion test (AGIDT) as a confirmatory method, and an immunoblot (IB) as an alternative confirmatory assay for discordant results between the first two tests. As for the in-house competitive ELISA (c-ELISA) and the AGIDT, the Italian National Reference Laboratory for EIA (NRL) validated the IB according to the OIE guidelines, employing eight panels containing positive sera, including those from EIA virus (EIAV) proven infected horses, and negative horse, mule and donkey sera collected from different geographical areas. In addition, two international reference image panels were employed for the optimization and the validation of the digital image reading system adopted that allows an impartial measurement of the serum reactivity in the IB assay. The immunological reactivity to EIAV antigens, p26, gp45 and gp90 adsorbed on the IB membrane, determines the serological status of the animal and for EIA, a p26 positive band together with at least one of the other antigen defines a subject as serologically positive for EIAV. For validation, the parameters assessed were threshold values, analytical and diagnostic sensitivity and specificity, repeatability and reproducibility. These parameters were evaluated for each antigen as well as in combination, according to the diagnostic algorithm established above. The validation data defined the IB as having a satisfactory sensitivity, specificity, repeatability and reproducibility for all antigens and species tested. An instrumental recording of the results improves the confidence in using IB as a confirmatory test for EIAV, differently from the AGIDT that is read by an operator. The advantages of using the IB are its higher sensitivity, to that of the AGIDT, which allows an earlier detection of infection that reduces the risk of transmission and therefore the incidence of the EIA, and its higher specificity to that of the ELISA which is based on the discrimination of subjects reacting only against the p26, the antigen used by all ELISAs available, which are not considered as infected by EIAV. In particular, when this assay is used in outbreaks it can detect new cases earlier than the AGIDT, and therefore reduce the restriction period with an economic benefit for the animal owners and the public veterinary sanitary system.

Horses naturally infected with EIAV harbor 2 distinct SU populations but are monophyletic with respect to IN

Equine infectious anemia virus (EIAV) causes lifelong infections ranging from acutely fatal, to chronic, to asymptomatic. Within infected animals, EIAV is found as a quasispecies. Many experimental studies on EIAV, carried out in the U.S. over the past 70 years, have used either the highly virulent Wyoming (EIAVWYO) field strain or various derivatives of that strain. These infections have provided insights into the variety of genetic changes that accumulate in the env gene and LTR in experimentally infected horses. In the current study, we obtained EIAV sequences from blood samples collected from naturally infected Texas horses between 2000 and 2002. We found surface (SU) and long terminal repeat (LTR) sequences clearly related to EIAVWYO and its cell culture-adapted derivatives. Some blood samples yielded SU or LTR sequences belonging to 2 discrete clusters. In these cases, SU and LTR variation between animals was no greater than sequence variation within animals. In contrast, a portion of integrase (IN) was more homogeneous within animals than between animals. These results suggest that specific selective pressures are applied to SU and LTR sequences, potentially driving generation of two distinct sequence clusters within a horse. We speculate that viruses in one cluster may be more highly expressed and easily transmitted while those in the second cluster support long-term inapparent infection. The presence of homogeneous IN sequences within a horse supports the hypothesis that SU and LTR sequences diverged after the initial infection.

Infection of equine monocyte-derived macrophages with an attenuated equine infectious anemia virus (EIAV) strain induces a strong resistance to the infection by a virulent EIAV strain

The Chinese attenuated equine infectious anemia virus (EIAV) vaccine has successfully protected millions of equine animals from EIA disease in China. Given that the induction of immune protection results from the interactions between viruses and hosts, a better understanding of the characteristics of vaccine strain infection and host responses would be useful for elucidating the mechanism of the induction of immune protection by the Chinese attenuated EIAV strain. In this study, we demonstrate in equine monocyte-derived macrophages (eMDM) that EIAV_FDDV13, a Chinese attenuated EIAV strain, induced a strong resistance to subsequent infection by a pathogenic strain, EIAV_UK3. Further experiments indicate that the expression of the soluble EIAV receptor sELR1, Toll-like receptor 3 (TLR3) and interferon β (IFNβ) was up-regulated in eMDM infected with EIAV_FDDV13 compared with eMDM infected with EIAV_UK3. Stimulating eMDM with poly I:C resulted in similar resistance to EIAV infection as induced by EIAV_FDDV13 and was correlated with enhanced TLR3, sELR1 and IFNβ expression. The knock down of TLR3 mRNA significantly impaired poly I:C-stimulated resistance to EIAV, greatly reducing the expression of sELR1 and IFNβ and lowered the level of infection resistance induced by EIAV_FDDV13. These results indicate that the induction of restraining infection by EIAV_FDDV13 in macrophages is partially mediated through the up-regulated expression of the soluble viral receptor and IFNβ, and that the TLR3 pathway activation plays an important role in the development of an EIAV-resistant intracellular environment.

Envelope determinants of equine lentiviral vaccine protection

Lentiviral envelope (Env) antigenic variation and associated immune evasion present major obstacles to vaccine development. The concept that Env is a critical determinant for vaccine efficacy is well accepted, however defined correlates of protection associated with Env variation have yet to be determined. We reported an attenuated equine infectious anemia virus (EIAV) vaccine study that directly examined the effect of lentiviral Env sequence variation on vaccine efficacy. The study identified a significant, inverse, linear correlation between vaccine efficacy and increasing divergence of the challenge virus Env gp90 protein compared to the vaccine virus gp90. The report demonstrated approximately 100% protection of immunized ponies from disease after challenge by virus with a homologous gp90 (EV0), and roughly 40% protection against challenge by virus (EV13) with a gp90 13% divergent from the vaccine strain. In the current study we examine whether the protection observed when challenging with the EV0 strain could be conferred to animals via chimeric challenge viruses between the EV0 and EV13 strains, allowing for mapping of protection to specific Env sequences. Viruses containing the EV13 proviral backbone and selected domains of the EV0 gp90 were constructed and in vitro and in vivo infectivity examined. Vaccine efficacy studies indicated that homology between the vaccine strain gp90 and the N-terminus of the challenge strain gp90 was capable of inducing immunity that resulted in significantly lower levels of post-challenge virus and significantly delayed the onset of disease. However, a homologous N-terminal region alone inserted in the EV13 backbone could not impart the 100% protection observed with the EV0 strain. Data presented here denote the complicated and potentially contradictory relationship between in vitro virulence and in vivo pathogenicity. The study highlights the importance of structural conformation for immunogens and emphasizes the need for antibody binding, not neutralizing, assays that correlate with vaccine protection.

Genetic characterization by composite sequence analysis of a new pathogenic field strain of equine infectious anemia virus from the 2006 outbreak in Ireland

Equine infectious anemia virus (EIAV), the causative agent of equine infectious anaemia (EIA), possesses the least-complex genomic organization of any known extant lentivirus. Despite this relative genetic simplicity, all of the complete genomic sequences published to date are derived from just two viruses, namely the North American EIAVWYOMING (EIAVWY) and Chinese EIAVLIAONING (EIAVLIA) strains. In 2006, an outbreak of EIA occurred in Ireland, apparently as a result of the importation of contaminated horse plasma from Italy and subsequent iatrogenic transmission to foals. This EIA outbreak was characterized by cases of severe, sometimes fatal, disease. To begin to understand the molecular mechanisms underlying this pathogenic phenotype, complete proviral genomic sequences in the form of 12 overlapping PCR-generated fragments were obtained from four of the EIAV-infected animals, including two of the index cases. Sequence analysis of multiple molecular clones produced from each fragment demonstrated the extent of diversity within individual viral genes and permitted construction of consensus whole-genome sequences for each of the four viral isolates. In addition, complete env gene sequences were obtained from 11 animals with differing clinical profiles, despite exposure to a common EIAV source. Although the overall genomic organization of the Irish EIAV isolates was typical of that seen in all other strains, the European viruses possessed ≤80 % nucleotide sequence identity with either EIAVWY or EIAVLIA. Furthermore, phylogenetic analysis suggested that the Irish EIAV isolates developed independently of the North American and Chinese viruses and that they constitute a separate monophyletic group.

Identification of a novel equine infectious anemia virus field strain isolated from feral horses in southern Japan

Although equine infectious anemia (EIA) was described more than 150 years ago, complete genomic sequences have only been obtained from two field strains of EIA virus (EIAV), EIAVWyoming and EIAVLiaoning. In 2011, EIA was detected within the distinctive feral Misaki horse population that inhabits the Toi-Cape area of southern Japan. Complete proviral sequences comprising a novel field strain were amplified directly from peripheral blood of one of these EIAV-infected horses and characterized by nucleotide sequencing. The complete provirus of Miyazaki2011-A strain is 8208 bp in length with an overall genomic organization typical of EIAV. However, this field isolate possesses just 77.2 and 78.7 % nucleotide sequence identity with the EIAVWyoming and EIAVLiaoning strains, respectively, while similarity plot analysis suggested all three strains arose independently. Furthermore, phylogenetic studies using sequences obtained from all EIAV-infected Misaki horses against known viral strains strongly suggests these Japanese isolates comprise a separate monophyletic group.

Development of a high throughput, semi-automated, infectious center cell-based ELISA for equine infectious anemia virus

A faster semi-automated 96-well microtiter plate assay to determine viral infectivity titers, or viral focal units (vfu), of equine infectious anemia virus (EIAV) stocks is described. Optimization of the existing method modernizes a classic virological technique for viral titer determination by quantitating EIAV in experimentally infected cells via a cell-based ELISA. To allow for automation, multiple parameters of the current assay procedures were modified resulting in an assay that required only one quarter the original amount of virus and/or serum for infectivity or neutralization assays, respectively. Equivalent reductions in the required volumes of tissue culture, cell processing, and protein detection reagents were also achieved. Additionally, the new assay decreased the time required from start to finish from 10 days to 6 days (viral titer) or 7 days (viral neutralization), while increasing the number of samples that can be processed concurrently by transition to a 96-well microtiter plate format and by automated counting.

Unique evolution characteristics of the envelope protein of EIAV(LN₄₀), a virulent strain of equine infectious anemia virus

The Chinese equine infectious anemia virus (EIAV) virulent strain EIAV(LN40) is derived from a naturally occurring virus by continuously passing in horses for 16 generations. Its genome sequence is 23% different from that of the American strains or the Japanese strains, and the variation of envelope gp90 surface unit (SU) is as high as 41%. In this study, evolutions of the EIAV(LN40) gp90 gene in four infected horses were analyzed. Results showed that new quasispecies arose in the early stage of infection in all EIAV(LN40)-infected horses. These quasispecies belonged to branches different from EIAV(LN40) in a phylogenetic tree. In contrast, the gp90 sequences of viruses isolated after disease onset remained in the same phylogenetic branch as EIAV(LN40), with some having exactly the same sequences. The glycosylation sites 191NSSN and 237NNTW in the V3 and V4 region present or absent simultaneously in most of the predicted amino acid sequences. Changes in the glycosylation sites within V3, V4, and V5 regions are usually associated with the disease status. Glycosylation sites (191NSSN, 237NNTW, and 280NDTS) within these three regions were present in EIAV(LN40) and most of the quasispecies isolated after, but not before disease onset. These unique evolutionary characteristics of SU have not been reported for EIAV and other lentiviruses. Our results provide a reference for a further understanding of the mechanism underlying the persistent infection and escape from immune surveillance of EIAV.

Divergence, not diversity of an attenuated equine lentivirus vaccine strain correlates with protection from disease

We recently reported an attenuated EIAV vaccine study that directly examined the effect of lentiviral envelope sequence variation on vaccine efficacy. The study [1] demonstrated for the first time the failure of an ancestral vaccine to protect and revealed a significant, inverse, linear relationship between envelope divergence and protection from disease. In the current study we examine in detail the evolution of the attenuated vaccine strain utilized in this previous study. We demonstrate here that the attenuated strain progressively evolved during the six-month pre-challenge period and that the observed protection from disease was significantly associated with divergence from the original vaccine strain.