Comprehensive Analysis of Equid Herpesvirus Recombination: An Insight Into the Repeat Regions.

High-throughput sequencing of genomes has expanded our knowledge of the Alphaherpesvirinae, a widely extended subfamily of DNA viruses that recombine to increase their genetic diversity. It has been acknowledged that equid herpesvirus 1 (EHV-1) and equid herpesvirus 4 (EHV-4), two alphaherpesviruses with an economic impact on the horse industry, can recombine. This work aimed to analyze interspecific recombination between all equid alphaherpesvirus species, using genomes of EHV-1, EHV-3, EHV-4, EHV-6, EHV-8, and EHV-9 available in GenBank. 14 events of recombination by RDP4 and Simplot between EHV-1 x EHV-4, EHV-1 x EHV-9, EHV-8 x EHV-1, and EHV-8 x EHV-9 were identified. Ten out of 14 events involved ORF64, a double-copy gene located at the repeat regions that codifies for the infected cell protein 4 (ICP4). Among the ICP4, recombination can be found between EHV-1 X EHV-9, EHV-8 X EHV-9, and EHV-1 X EHV-4, the former affects zebra-borne genotypes, a type of EHV-1 that infect wild equids, and the latter match with previous breakpoints reported in fields isolates. Consequently, these findings strongly suggest that ICP4 is a hotspot for recombination. This work describes novel recombination events and is the first genome-wide recombination analysis using all available equid alphaherpesvirus species genomes.

Whole-genome analysis of natural interspecific recombinant between bovine alphaherpesviruses 1 and 5.

Bovine alphaherpesviruses 1 and 5 (BoHV-1 and BoHV-5) are closely related viruses that co-circulate in South America and recombine in the field. The complete genomes of three natural gB gene recombinant viruses between BoHV-1 and BoHV-5 were obtained by Illumina next-generation sequencing. Complete genome sequences of the three recombinant strains (RecA1, RecB2, and RecC2) have a similar size of approximately 138.3kb and a GC content of 75%. The genome structure corresponds to herpesvirus class D, with 69 open reading frames (ORFs) arranged in the same order as other bovine alphaherpesviruses related to BoHV-1. Their genomes were included in recombination network studies indicating statistically significant recombination evidence both based on the whole genome, as well as in the sub-regions. The novel recombinant region of 3074 nt of the RecB2 and RecC2 strains includes the complete genes of the myristylated tegument protein (UL11) and the glycoprotein M (UL10) and part of the helicase (UL9) gene, and it seems to have originated independently of the first recombinant event involving the gB gene. Phylogenetic analyzes performed with the amino acid sequences of UL9, UL 10, and UL11 indicated that RecB2 and RecC2 recombinants are closely related to the minor parental virus (BoHV-1.2b). On the contrary, RecA1 groups with the major parental (BoHV-5), thus confirming the absence of recombination in this region for this recombinant. One breakpoint in the second recombinant region lies in the middle of the UL9 reading frame, originating a chimeric enzyme half encoded by BoHV-5 and BoHV-1.2b parental strains. The chimeric helicases of both recombinants are identical and have 96.8 and 96.3% similarity with the BoHV-5 and BoHV-1 parents, respectively. In vitro characterization suggests that recombinants have delayed exit from the cell compared to parental strains. However, they produce the similar viral titer as their putative parents suggesting the accumulation of viral particles for the cell exit delayed on time. Despite in vitro different behavior, these natural recombinant viruses have been maintained in the bovine population for more than 30 years, indicating that recombination could be playing an important role in the biological diversity of these viral species. Our findings highlight the importance of studying whole genome diversity in the field and determining the role that homologous recombination plays in the structure of viral populations. A whole-genome recombinant characterization is a suitable tool to help understand the emergence of new viral forms with novel pathogenic features.

TLR activation, immune response and viral protection elicited in cattle by a commercial vaccine against Bovine Herpesvirus-1.

The innate and acquired immune response induced by a commercial inactivated vaccine against Bovine Herpesvirus-1 (BoHV-1) and protection conferred against the virus were analyzed in cattle. Vaccination induced high levels of BoHV-1 antibodies at 30, 60, and 90 days post-vaccination (dpv). IgG1 and IgG2 isotypes were detected at 90 dpv, as well as virus-neutralizing antibodies. An increase of anti-BoHV-1 IgG1 in nasal swabs was detected 6 days post-challenge in vaccinated animals. After viral challenge, lower virus excretion and lower clinical score were observed in vaccinated as compared to unvaccinated animals, as well as BoHV-1-specific proliferation of lymphocytes and production of IFNγ, TNFα, and IL-4. Downregulation of the expression of endosome Toll-like receptors 8-9 was detected after booster vaccination. This is the first thorough study of the immunity generated by a commercial vaccine against BoHV-1 in cattle.

Evidence of natural interspecific recombinant viruses between bovine alphaherpesviruses 1 and 5.

Closely related bovine alphaherpesviruses 1 (BoHV-1) and 5 (BoHV-5) co-circulate in certain countries, rendering cattle co-infection possible. This is a prerequisite for BoHV recombination. Here, we report the first identification of homologous recombination between field isolates of BoHV-1 and BoHV-5, two alphaherpesviruses belonging to two distinct species with an average genomic similarity of 82.3%. Three isolates of BoHV-5, previously classified as subtype "BoHV-5b", were phylogenetically studied and analyzed via eight PCR sequencing assays dispersed at regular intervals throughout the genome to discriminate between BoHV-1 and BoHV-5. In the phylogenetic analysis, differences of clustering were found in the UL27 gene which encodes the glycoprotein B (gB). We detected two recombination breakpoints in the open reading frame of the UL27 gene. We compared the amino acid sequences of the gB of BoHV-1.1 and 1.2, BoHV-5a and recombinant formerly named BoHV-5b (chimeric gB) and subsequently performed molecular modeling. All structures were alike and, simultaneously, similar to the chimeric gB. Neutralizing antibodies against BoHV-1, BoHV-5 and recombinant viruses were analyzed via serum virus neutralization test using polyclonal sera and a monoclonal antibody against gB to demonstrate an absence of viral escape for both assays. Our results show that homologous recombination between two related species of ruminant alphaherpesviruses can occur in natural field conditions. We found three recombinant field isolates, previously classified as BoHV-5b subtypes, between BoHV-1 and BoHV-5.

Protection induced by a glycoprotein E-deleted bovine herpesvirus type 1 marker strain used either as an inactivated or live attenuated vaccine in cattle.

BACKGROUND: Bovine herpesvirus type 1 (BoHV-1) is the causative agent of respiratory and genital tract infections; causing a high economic loss in all continents. Use of marker vaccines in IBR eradication programs is widely accepted since it allows for protection of the animals against the disease while adding the possibility of differentiating vaccinated from infected animals.The aim of the present study was the development and evaluation of safety and efficacy of a glycoprotein E-deleted (gE-) BoHV-1 marker vaccine strain (BoHV-1ΔgEßgal) generated by homologous recombination, replacing the viral gE gene with the ß-galactosidase (ßgal) gene. RESULTS: In vitro growth kinetics of the BoHV-1ΔgEßgal virus was similar to BoHV-1 LA. The immune response triggered by the new recombinant strain in cattle was characterized both as live attenuated vaccine (LAV) and as an inactivated vaccine. BoHV-1ΔgEßgal was highly immunogenic in both formulations, inducing specific humoral and cellular immune responses. Antibody titers found in animals vaccinated with the inactivated vaccine based on BoHV-1ΔgEßgal was similar to the titers found for the control vaccine (BoHV-1 LA). In the same way, titers of inactivated vaccine groups were significantly higher than any of the LAV immunized groups, independently of the inoculation route (p < 0.001). Levels of IFN-γ were significantly higher (p < 0.001) in those animals that received the LAV compared to those that received the inactivated vaccine. BoHV-1ΔgEßgal exhibited an evident attenuation when administered as a LAV; no virus was detected in nasal secretions of vaccinated or sentinel animals during the post-vaccination period. BoHV-1ΔgEßgal, when used in either formulation, elicited an efficient immune response that protected animals against challenge with virulent wild-type BoHV-1. Also, the deletion of the gE gene served as an immunological marker to differentiate vaccinated animals from infected animals. All animals vaccinated with the BoHV-1ΔgE ßgal strain were protected against disease after challenge and shed significantly less virus than control calves, regardless of the route and formulation they were inoculated. CONCLUSIONS: Based on its attenuation, immunogenicity and protective effect after challenge, BoHV-1ΔgEßgal virus is an efficient and safe vaccine candidate when used either as inactivated or as live attenuated forms.

Multiplex PCR followed by restriction length polymorphism analysis for the subtyping of bovine herpesvirus 5 isolates.

BACKGROUND: Several types and subtypes of bovine herpesviruses 1 and 5 (BoHV-1 and BoHV-5) have been associated to different clinical conditions of cattle, making type/subtype differentiation essential to understand the pathogenesis and epidemiology of BoHV infections. BoHV-5 subtyping is currently carried out by BstEII restriction enzyme analysis (REA) of the complete virus genome. This method allowed the description of three subtypes, one of which is the most widespread while the remaining two have so far only been found in South America. The present work describes a multiplex PCR followed by REA for BoHV-5 subtyping. RESULTS: The method consists in the simultaneous amplification of glycoprotein B and UL54 gene fragments of 534 and 669 base pairs (bp), respectively, BstEII digestion of amplicons, separation of products in 1% agarose gels, and analysis of fragment length polymorphims. The multiplex PCR detected up to 227 BoHV-5 genome copies and 9.2 × 105 BoHV-5 genome copies when DNA was extracted from purified virus or infected tissue homogenates, respectively. The applicability of multiplex PCR-REA was demonstrated on 3 BoHV-5 reference strains. In addition, subtyping of two new isolates and seventeen previously reported ones (17 BHV-5a and 2 BHV-5b) by this method gave coincident results with those obtained with the classic BstEII REA assay. CONCLUSIONS: Multiplex PCR-REA provides a new tool for the fast and simple diagnosis and subtyping of BoHV-5.

Effect of the US3 protein of bovine herpesvirus 5 on the actin cytoskeleton and apoptosis.

The US3 protein is a unique protein kinase only present in the Alphaherpesvirinae subfamily of the herpesviruses. Studies performed with several alphaherpesviruses demonstrated that the US3 protein is involved in cytoskeleton modifications during viral infection and displays anti-apoptotic activity. However, the US3 protein of BoHV-5 has not been studied up to now. As reported for other alphaherpesviruses, our results showed that BoHV-5 US3 confers resistance against apoptosis and induces cytoskeletal reorganization leading to cell rounding, actin stress fiber breakdown and cell projections that interconnect cells. The expression of a kinase-dead version of BoHV-5 US3 showed that the anti-apoptotic activity and the induction of cell projections are kinase-dependent whereas kinase activity is not absolutely required for actin stress fiber breakdown. Besides, the kinase-dead version of US3, but not the wild type protein, was found excluded from the nucleus. These results constitute the first report on the BoHV-5 US3 functions, and highlight that there are functional differences and similarities among US3 proteins of different alphaherpesviruses.

Characterization of interspecific recombinants generated from closely related bovine herpesviruses 1 and 5 through multiple PCR sequencing assays.

Bovine herpesviruses 1 (BoHV-1) and 5 (BoHV-5) are closely related alphaherpesviruses infecting cattle. In countries where both viruses circulate, co-infection of cattle is likely. It was shown that recombination occurs at a high frequency in cattle infected dually with two BoHV-1 mutants. In addition, interspecific recombinants are generated in cell culture co-infected with BoHV-1 and BoHV-5. Even if the process of interspecific recombination appears inefficient relative to intraspecific recombination, BoHV-1 and BoHV-5 may give rise to interspecific recombinants in co-infected cattle. Since molecular tools for differentiating BoHV-1 from BoHV-5 are limited and do not allow to localize recombination events between these closely related virus species, 13 PCR sequencing assays were developed to discriminate between BoHV-1 and BoHV-5 at regular intervals throughout the entire respective viral DNA genomes. These assays were used to determine the genetic background of two interspecific BoHV-1/-5 recombinants generated previously. The two crossover points where recombination events occurred between the parental strains were determined. This study provides a detailed analysis of two interspecific recombinant viruses generated in vitro from closely related alphaherpesviruses infecting the same natural host. It demonstrates that recombination can occur within very short fragments of sequence homology. This finding raises questions about the mechanisms involved in the strands exchange and resolution step of the homologous recombination used by herpesviruses. This method will allow monitoring generation of recombinants between closely related herpesvirus species both in vitro and in vivo.