Sequence analysis of the equid herpesvirus 2 chemokine receptor homologues E1, ORF74 and E6 demonstrates high sequence divergence between field isolates

Genomic diversity and natural recombination of equid gammaherpesvirus 5 isolates

BACKGROUND

Equid gammaherpesvirus 5 (EHV5) is closely related to equid gammaherpesvirus 2 (EHV2). Detection of EHV5 is frequent in horse populations worldwide, but it is often without a clear and significant clinical impact. Infection in horses can often present as subclinical disease; however, it has been associated with respiratory disease, including equine multinodular pulmonary fibrosis (EMPF). Genetic heterogeneity within small regions of the EHV5 glycoprotein B (gB) sequences have been reported and multiple genotypes of this virus have been identified within individual horses, but full genome sequence data for these viruses is limited. The primary focus of this study was to assess the genomic diversity and natural recombination among EHV5 isolates.

RESULTS

The genome size of EHV5 prototype strain and the five EHV5 isolates cultured for this study, including four isolates from the same horse, ranged from 181,929 to 183,428 base pairs (bp), with the sizes of terminal repeat regions varying from 0 to 10 bp. The nucleotide sequence identity between the six EHV5 genomes ranged from 95.5 to 99.1%, and the estimated average nucleotide diversity between isolates was 1%. Individual genes displayed varying levels of nucleotide diversity that ranged from 0 to 19%. The analysis of nonsynonymous substitution (Ka > 0.025) revealed high diversity in eight genes. Genome analysis using RDP4 and SplitsTree programs detected evidence of past recombination events between EHV5 isolates.

CONCLUSION

Genomic diversity and recombination hotspots were identified among EHV5 strains. Recombination can drive genetic diversity, particularly in viruses that have a low rate of nucleotide substitutions. Therefore, the results from this study suggest that recombination is an important contributing factor to EHV5 genomic diversity. The findings from this study provide additional insights into the genetic heterogeneity of the EHV5 genome.

Whole genome sequence analysis of equid gammaherpesvirus -2 field isolates reveals high levels of genomic diversity and recombination

Background

Equid gammaherpesvirus 2 (EHV2) is a gammaherpesvirus with a widespread distribution in horse populations globally. Although its pathogenic significance can be unclear in most cases of infection, EHV2 infection can cause upper respiratory tract disease in foals. Co-infection of different strains of EHV2 in an individual horse is common. Small regions of the EHV2 genome have shown considerable genetic heterogeneity. This could suggest genomic recombination between different strains of EHV2, similar to the extensive recombination networks that have been demonstrated for some alphaherpesviruses. This study examined natural recombination and genome diversity of EHV2 field isolates.

Results

Whole genome sequencing analysis of 18 EHV2 isolates, along with analysis of two publicly available EHV2 genomes, revealed variation in genomes sizes (from 173.7 to 184.8 kbp), guanine plus cytosine content (from 56.7 to 57.8%) and the size of the terminal repeat regions (from 17,196 to 17,551 bp). The nucleotide sequence identity between the genomes ranged from 86.2 to 99.7%. The estimated average inter-strain nucleotide diversity between the 20 EHV2 genomes was 2.9%. Individual gene sequences showed varying levels of nucleotide diversity and ranged between 0 and 38.1%. The ratio of nonsynonymous substitutions, Ka, to synonymous substitutions, Ks, (Ka/Ks) suggests that over 50% of EHV2 genes are undergoing diversifying selection. Recombination analyses of the 20 EHV2 genome sequences using the recombination detection program (RDP4) and SplitsTree revealed evidence of viral recombination.

Conclusions

Analysis of the 18 new EHV2 genomes alongside the 2 previously sequenced genomes revealed a high degree of genetic diversity and extensive recombination networks. Herpesvirus genome diversification and virus evolution can be driven by recombination, and our findings are consistent with recombination being a key mechanism by which EHV2 genomes may vary and evolve.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08789-x.

Recent advancements in our understanding of equid gammaherpesvirus infections

Equid gammaherpesviruses are ubiquitous and widespread in the equine population. Despite their frequent detection, their contribution to immune system modulation and the pathogenesis of several diseases remains unclear. Genetic variability and the combination of equid gammaherpesvirus strains a horse is infected with might be clinically significant. Initial gammaherpesvirus infection occurs in foals peripartum with latency then established in peripheral blood mononuclear cells. A novel EHV-5 study suggests that following inhalation equid gammaherpesviruses might obtain direct access to T and B lymphocytes via the tonsillar crypts to establish latency. EHV-5 is associated with equine multinodular pulmonary fibrosis, however, unlike with EHV-2 there is currently minimal evidence for its role in milder cases of respiratory disease and poor performance. Transmission is presumed to be via the upper respiratory tract with periodic reactivation of the latent virus in adult horses. Stress of transport has been identified as a risk factor for reactivation and shedding of equine gammaherpesviruses. There is currently a lack of evidence for the effectiveness of antiviral drugs in the treatment of equine gammaherpesvirus infections.

Prevalence and sequence analysis of equid herpesviruses from the respiratory tract of Polish horses

Background

Equid herpesviruses (EHVs) are widespread in equine populations worldwide. While the infection with equine α-herpesviruses (EHV-1 and EHV-4) has been linked to several clinical outcomes, the pathogenic potential for equine γ-herpesviruses (EHV-2 and EHV-5) is still unclear. The objective of the current study was to determine the prevalence of infection with EHVs among Polish horses, to investigate factors associated with EHV infections among horses sampled, and to determine genetic variability within Polish EHV-2 isolates.

Methods

Virus-specific real-time PCR assays were used for detection of EHV-1, EHV-2, EHV-4 and EHV-5 in nasal swabs collected from 540 horses from 13 national horse studs located throughout Poland. A proportion of EHV-2/5 positive samples were subjected to virus isolation followed by amplification and analysis of partial glycoprotein B sequence.

Results

Overall, 448/540 (83.0%) horses sampled were positive for at least one virus. The most prevalent was infection with EHV-2 (77.2%), followed by EHV-5 (47.0%), and EHV-4 (0.4%). None of the horses was positive for EHV-1. Approximately half of the virus-infected horses were positive for both EHV-2 and EHV-5. The proportion of EHV-2/5 positive horses varied by age, breed, and season. Only 8.0% of horses sampled, mostly Arabians, showed clinical signs of respiratory disease at the time of sampling. The viral load of both EHV-2 and EHV-5 DNA was highest in swabs from young horses, which was particularly evident for EHV-2 infected foals. Mean viral loads in nasal swabs collected from diseased horses were higher than in swabs from healthy horses. That was also true for EHV-2 when only diseased Arabian foals were considered, but the levels of EHV-5 DNA were lower in swabs from diseased than from healthy foals. In agreement with other studies, there was a considerable variability between Polish EHV-2 sequences, with no clustering of sequences from horses with different health status. The level of EHV-2 variability seemed to differ between different studs/breeds.

Conclusions

The presence of foals and yearlings on a property is likely to increase the risk of active EHV-2/5 infection among in-contact horses. The existence of breed-specific differences in susceptibility to EHV-2/5 infections should be further investigated, as it may provide one variable that needs to be considered in attempts to associate EHV-2/5 infections with disease. Overall, the data presented add to the existing knowledge of the epidemiology and biology of equine γ-herpesviruses, with the long-term goal of better understanding of the pathogenesis and the impact of infections with these viruses on the well-being of the horse.

Establishment and characterization of fetal equine kidney and lung cells with extended lifespan. Susceptibility to equine gammaherpesvirus infection and transfection efficiency

Due to the slow growth of equine gammaherpesviruses, isolation of these viruses requires cells that can be propagated long term and show clear cytopathy following infection. Equine cell lines with extended lifespan were established from primary cells originating from equine fetal kidney and lung by transfecting the cells with the retroviral vector LXSN116E6E7 containing the human papilloma virus oncogenes 16 E6 and E7. The transfected equine kidney cell line and equine lung cell line can be propagated for more than 40 passages, whereas the corresponding primary cells only for 10-12 passages. The primary cells and the derived cell lines can be infected with equine gammaherpesvirus 2 (EHV-2) with similar efficiency. However EHV-5 can be grown to a substantially higher titer in the kidney cell line than their primary counterpart, with cytopathic effect visible three days earlier than in the primary cells. Due to rapid cell growth the lung cell line is difficult to use for virus production. The kidney cell line was four times more susceptible to transfection as compared to the primary kidney cells. On the other hand no difference was between the lung cell line and the primary lung cells in transfection efficiency. The cell lines can be a valuable tool for investigating gammaherpesviruses, and possibly other viruses infecting horses.

Gammaherpesvirus infections in equids: a review

Although the first equine gammaherpesvirus was identified over 50 years ago, the isolation and characterization of other members of this virus group has been relatively recent. Even so, numerous clinical syndromes have been identified in equid species in association with these viruses. Equid gammaherpesviruses are a genetically heterogeneous viral subfamily, the function of which in host immune modulation and disease pathogenesis has not yet been elucidated. While they share similarities with gammaherpesviruses in humans, the role they play in their relationship with the host is the subject of continued interest and research. Their widespread presence in horses and other equid species provides a considerable challenge in linking them with particular clinical and pathological conditions and in defining their significance from a diagnostic and therapeutic viewpoint. The present review provides an update on the taxonomy, epidemiology, and clinical syndromes, especially respiratory, reported in association with gammaherpesvirus infection in horses, donkeys, and other equid species.

Genome sequences of equid herpesviruses 2 and 5

We resequenced the genome of equid herpesvirus 2 (EHV2) strain 86/67 and sequenced the genomes of EHV2 strain G9/92 and equid herpesvirus 5 (EHV5) strain 2-141/67. The most prominent genetic differences are the dissimilar locations of the interleukin-10 (IL-10)-like genes and the presence of an OX-2-like gene in EHV5 only.

Determinism and randomness in the evolution of introns and sine inserts in mouse and human mitochondrial solute carrier and cytokine receptor genes

In the homologous genes studied, the exons and introns alternated in the same order in mouse and human. We studied, in both species: corresponding short segments of introns, whole corresponding introns and complete homologous genes. We considered the total number of nucleotides and the number and orientation of the SINE inserts. Comparisons of mouse and human data series showed that at the level of individual relatively short segments of intronic sequences the stochastic variability prevails in the local structuring, but at higher levels of organization a deterministic component emerges, conserved in mouse and human during the divergent evolution, despite the ample re-editing of the intronic sequences and the fact that processes such as SINE spread had taken place in an independent way in the two species. Intron conservation is negatively correlated with the SINE occupancy, suggesting that virus inserts interfere with the conservation of the sequences inherited from the common ancestor.

Detection and quantitation of equid gammaherpesviruses (EHV-2, EHV-5) in nasal swabs using an accredited standardised quantitative PCR method

Equid gammaherpesviruses-2 and -5 are involved in respiratory problems, with potential clinical manifestations such as nasal discharge, pharyngitis and swollen lymph nodes. These viruses are sometimes associated with a poor-performance syndrome, which may result in a significant and negative economic impact for the horse industry. The aim of the present study was to develop and validate quantitative PCR methods for the detection and quantitation of EHV-2 and EHV-5 in equine respiratory fluids. Two distinct tests were characterised: (a) for the qPCR alone and (b) for the whole method (extraction and qPCR) according to the standard model AFNOR XP U47-600-2 (viz., specificity, quantifiable sensibility, linearity, accuracy, range of application, trueness, precision, repeatability and precision of reproducibility). EHV-2 and EHV-5 detection were performed on nasal swabs collected from 172 horses, all of which exhibited clinical signs of respiratory disease. The data revealed a high rate of EHV-2/EHV-5 co-detection that was correlated significantly with age. Viral load of EHV-2 was significantly higher in young horses whereas viral load of EHV-5 was not significantly different with age.

Equine gammaherpesviruses: perfect parasites?

The evolutionary success of the equine gammaherpesviruses (GHVs) is demonstrated by their consistent and widespread presence in horse populations worldwide. Equine GHVs establish infection in young foals and can be continually detected over the lifetime of the host either by recrudescence of latent infections or by re-infection. A definitive diagnosis of clinical disease in horses due to GHV infection remains challenging given the ubiquitous nature of the GHVs in horses without clinical signs, as well as in horses with clinical signs ranging from mild respiratory disease to severe equine multinodular pulmonary fibrosis. This review aims to examine what is known about equine GHV and explore the balance of the relationship that has evolved over millions of years between these viruses and their host.

A survey of respiratory viruses in New Zealand horses

AIMS

To determine which viruses circulate among selected populations of New Zealand horses and whether or not viral infections were associated with development of respiratory disease.

METHODS

Nasal swabs were collected from 33 healthy horses and 52 horses with respiratory disease and tested by virus isolation and/or PCR for the presence of equine herpesviruses (EHV) and equine rhinitis viruses.

RESULTS

Herpesviruses were the only viruses detected in nasal swab samples. When both the results of nasal swab PCR and virus isolation were considered together, a total of 41/52 (79%) horses with respiratory disease and 2/32 (6%) healthy horses were positive for at least one virus. As such, rates of virus detection were significantly higher (p<0.001) in samples from horses with respiratory disease than from healthy horses. More than half of the virus-positive horses were infected with multiple viruses. Infection with EHV-5 was most common (28 horses), followed by EHV-2 (27 horses), EHV-4 (21 horses) and EHV-1 (3 horses).

CONCLUSIONS

Herpesviruses were more commonly detected in nasal swabs from horses with respiratory disease than from healthy horses suggesting their aetiological involvement in the development of clinical signs among sampled horses. Further investigation to elucidate the exact relationships between these viruses and respiratory disease in horses is warranted.

CLINICAL RELEVANCE

Equine respiratory disease has been recognised as an important cause of wastage for the equine industry worldwide. It is likely multifactorial, involving complex interactions between different microorganisms, the environment and the host. Ability to control, or minimise, the adverse effects of equine respiratory disease is critically dependent on our understanding of microbial agents involved in these interactions. The results of the present study update our knowledge on the equine respiratory viruses currently circulating among selected populations of horses in New Zealand.

Genetic diversity of equine gammaherpesviruses (γ-EHV) and isolation of a syncytium forming EHV-2 strain from a horse in Iceland

The horse population in Iceland is a special breed, isolated from other equines for at least one thousand years. This provides an exceptional opportunity to investigate old and new pathogens in a genetically closed herd. Both types of equine gammaherpesviruses, EHV-2 and EHV-5, are common in Iceland. Genetic variation was examined by sequencing four genes, glycoprotein B (gB), glycoprotein H (gH), DNA polymerase and DNA terminase for 12 Icelandic and seven foreign EHV-2 strains. One Icelandic virus isolate, gEHV-Dv, induced syncytium formation, an uncharacteristic cytopathy for EHV-2 in equine kidney cells. When sequenced, the glycoprotein genes were different from both EHV-2 and EHV-5, but the polymerase and terminase genes had 98-99% identity to EHV-2. Therefore the gEHV-Dv strain can be considered a variant of EHV-2. Substantial genetic variability was seen within the EHV-2 glycoprotein genes but limited in the polymerase and terminase genes. The Icelandic EHV-2 strains do not seem to differ phylogenetically from the foreign viruses, despite isolation for over a thousand years.

Evidence for endogenous retroviruses in human chemokine receptor gene introns: possible evolutionary inferences and biological roles

The human chemokine receptor (CKR) genes CCR2, CCR6, CCR7, CCR9, CCR10, CXCR4, and CXCR5 harbor one or two introns. CCR7, CCR9, CCR10, and CXCR5 introns, (but not CCR2, CCR6, and CXCR4 introns) encompass retrovirus-like inserts with the characteristics of SINEs (short interspersed nuclear elements) up to 300 nucleotides (nt) long. Other characteristic elements of the retroviral genome, such as long terminal repeats and gag, pol, and env genes, are lacking. The inserts likely derived from one (or more) of the following retroviruses: XA34 (NCBI GenBank Nucleotides, U29659), HERV-P-T47D (AF087913), ERV FTD (U27241), HERV-K (Y17832), HML6p (U86698), HERV-H/env60 (AJ289710), XA38 (U37066). Virus-like inserts are remarkably homogeneous in all CKR introns, with nt identities of about 80%. Percentages of nt identities between the CKR inserts and the corresponding viral sequences are also about 80%. With reference to the CKR sequence, the viral sequence aligns in some instances Plus/Plus (XA34, HML6p, HERV-H/env60, and XA38) and in other instances Plus/Minus (HERV-P-T47D, ERV FTD, and HERV-K). Some aspects of the evolution of retroviruses and CKRs as well as hypotheses on the biological significance of the SINE inserts are discussed.

Detection and sequence analysis of equine gammaherpesviruses from horses with respiratory tract disease in Turkey

The equid herpesvirus 2 (EHV-2) and 5 (EHV-5), identified agents of respiratory infections and keratoconjunctivitis cases in some equids, comprise a high degree of antigenic heterogeneity. Prevalence and genetic characterization of EHV-2 and EHV-5 strains from Turkey were investigated in this study. A total of 73 nasal swabs and 54 blood specimens were sampled from horses with respiratory tract diseases characterized by mucopurulent nasal discharge and occasional coughing. Overall, EHV-2- and EHV-5-specific DNA amplicons were obtained from 19.2% (14/73) and 21.9% (16/73) of horses tested by multiplex nested PCR. Sequences of EHV-2 and EHV-5 glycoprotein B (gB) gene were used in a phylogenetic analysis that included six EHV-2 and three EHV-5 isolates, which showed that the Turkish EHV-2 and EHV-5 strains have marked sequence divergence from European strains and from each other. Turkish EHV-2 isolates were divided into two distinct subdivisions, and a few isolates were located on a separate branch. This study provides the first epidemiological and phylogenetical report about EHV-2 and EHV-5 infections in Turkey.

Equine gammaherpesviruses: pathogenesis, epidemiology and diagnosis

Equine gammaherpesviruses (γEHV) have been widely studied over the past 45 years and many isolates have been characterised. Despite this, the diagnosis of γEHV infection remains difficult to establish as its clinical manifestations lack specificity, ranging from mild respiratory signs in a small number of animals to outbreaks in large groups of young horses. This review focuses on the epidemiology, pathogenesis, clinical manifestations and diagnosis of equine herpesvirus (EHV)-2 and -5 infections, as well as on the genetic variation of these viruses. Study of these variations has resulted in hypotheses relating to viral re-infection and re-activation. Interestingly, the viruses were found to contain genetic sequences identical to those of eukaryotic cells which are considered central to the development of viral latency through interfering with host immune and inflammatory responses. Future molecular biological studies will further elucidate the virulence mechanisms of these equine pathogens.

Herpesviruses in respiratory liquids of horses: putative implication in airway inflammation and association with cytological features

The objectives of this study were to estimate the prevalence and the potential role of equine herpesviruses (EHVs) detection in both bronchoalveolar lavage (BAL) and tracheal wash (TW). The population included a control group (CTL; 37 TW and 25 BAL) and a pathological group (PAT; 259 TW and 387 BAL), including horses either suffering from respiratory diseases including syndrome of tracheal inflammation, inflammatory airway disease, recurrent airway obstruction, or submitted to respiratory investigation because of exercise intolerance or poor performance. Each respiratory liquid was submitted to a standardised cytological analysis, mentioning the morphological abnormalities of exfoliated epithelial cells (ECAb) and ciliocytophthoria (CCPh) as markers of potential viral infection, as well as PCR assays including a consensus PCR and virus-specific PCR for both equine alphaherpesviruses (EHV-1; EHV-4) and gammaherpesviruses (EHV-2; EHV-5). The EHV infections were more prevalent in the TW of PAT group (P=0.004), with the highest prevalence being for EHV-2 (P=0.006). The EHV detection in BALs was not significantly different between groups. The EHVs detection in TW was correlated to the polymorphonuclear neutrophil (PMN) counts in the respiratory liquid but not with CCPh or ECAb. CCPh or ECAb were associated with both consensus PCR and EHV-2 and EHV-5 virus-type PCR in the BAL only. The significant detection of EHVs in the TW of PAT group in association with the PMN increased counts could lead to further investigations about their putative role in equine syndrome of tracheal inflammation.

Isolation of a gammaherpesvirus similar to asinine herpesvirus-2 (AHV-2) from a mule and a survey of mules and donkeys for AHV-2 infection by real-time PCR

Equids are commonly infected by herpesviruses, but isolation of herpesviruses from mules has apparently not been previously reported. Furthermore, the genomic relationships among the various equid herpesviruses are poorly characterized. We describe the isolation and preliminary characterization of a mule gammaherpesvirus tentatively identified as asinine herpesvirus-2 (AHV-2; also designated equid herpesvirus-7 (EHV-7)) from the nasal secretions (NS) of a healthy mule in northern California. The virus was initially identified by transmission electron microscopic examination of lysates of cell culture inoculated with NS collected from the mule. A 913 nucleotide sequence of the DNA polymerase gene was amplified using degenerate primers, and comparison of this sequence with those of various other herpesviruses showed that the mule herpesvirus was most closely related to EHV-2 (AHV-2 sequences were not available for comparison). The sequence of a shorter portion (166 nucleotides) of the mule herpesvirus DNA polymerase gene was identical to that of the published sequence of an asinine gammaherpesvirus, previously designated as AHV-4-3 (AY054992). AHV-2 was detected by real-time polymerase chain reaction assay in the NS of approximately 8% of a cohort of 114 healthy mules and 13 donkeys.