Complete genome sequence of bovine herpesvirus type 1.1 (BoHV-1.1) Los Angeles (LA) strain and its genotypic relationship to BoHV-1.1 Cooper and more recently isolated wild-type field strains.

The Cooper and Los Angeles (LA) strains were the two original respiratory strains of bovine herpesvirus type 1.1 (BoHV-1.1) isolated in the 1950s from cattle with infectious bovine rhinotracheitis. We report the complete genome sequence for the BoHV-1.1 LA strain and compare it to the prototype Cooper strain and six wild-type BoHV-1.1 isolates. A nucleotide sequence divergence of 0.74% was noted across the two complete genomes, caused by 19 single-nucleotide polymorphisms (SNPs) involving 12 genes and insertions/deletions that primarily affected the number of repeats within reiterated repeat regions of the genome. Phylogenetic analysis revealed that Cooper and LA strains are genetically the most ancient strains from which all of the more-recently isolated field strains of BoHV-1.1 evolved.

Sequence of the ateline alphaherpesvirus 1 (HVA1) genome.

Here, we report the genome sequence of a spider monkey alphaherpesvirus (ateline alphaherpesvirus 1, HVA1) and compare it with that of other primate alphaherpesviruses. The HVA1 genome is 147,346 bp long and contains 67 predicted ORFs. The genetic layout of the HVA1 genome is similar to that of the squirrel monkey alphaherpesvirus (saimirine alphaherpesvirus 1, HVS1) in that it lacks inverted repeat regions flanking the unique long region and homologues of the UL43, UL49.5, US8.5 and US10-12 genes. Unlike HVS1, HVA1 also lacks a homologue of the RL1 (γ34.5) gene and a replication origin near the end of the genome. Consistent with previous phylogenetic analyses, all predicted proteins of HVA1 are most closely related to those of HVS1.

Complete genomic sequence and comparative analysis of four genital and respiratory isolates of bovine herpesvirus subtype 1.2b (BoHV-1.2b), including the prototype virus strain K22.

Bovine herpesvirus subtype 1.2b (BoHV-1.2b) is associated primarily with bovine infectious pustular vulvovaginitis. We report here the complete genomic sequence of four BoHV-1.2b isolates. The DNA sequence identity of the four genomes is 98.9 %. Differences were primarily in regions containing direct repeats, specifically gene UL36 and the terminal repeat regions immediately flanking gene BICP22. BoHV-1.2b and BoHV-1.1 genomes are similar in size (~135 kb), completely orthologous with respect to regional structure and gene location, and have a 97.5 % DNA sequence homology. The most notable difference is the structure of the DNA replication origin of the two viruses.

Poisson factor models with applications to non-normalized microRNA profiling.

MOTIVATION: Next-generation (NextGen) sequencing is becoming increasingly popular as an alternative for transcriptional profiling, as is the case for micro RNAs (miRNA) profiling and classification. miRNAs are a new class of molecules that are regulated in response to differentiation, tumorigenesis or infection. Our primary motivating application is to identify different viral infections based on the induced change in the host miRNA profile. Statistical challenges are encountered because of special features of NextGen sequencing data: the data are read counts that are extremely skewed and non-negative; the total number of reads varies dramatically across samples that require appropriate normalization. Statistical tools developed for microarray expression data, such as principal component analysis, are sub-optimal for analyzing NextGen sequencing data. RESULTS: We propose a family of Poisson factor models that explicitly takes into account the count nature of sequencing data and automatically incorporates sample normalization through the use of offsets. We develop an efficient algorithm for estimating the Poisson factor model, entitled Poisson Singular Value Decomposition with Offset (PSVDOS). The method is shown to outperform several other normalization and dimension reduction methods in a simulation study. Through analysis of an miRNA profiling experiment, we further illustrate that our model achieves insightful dimension reduction of the miRNA profiles of 18 samples: the extracted factors lead to more accurate and meaningful clustering of the cell lines. AVAILABILITY: The PSVDOS software is available on request.

Genome sequence of a pathogenic isolate of monkey B virus (species Macacine herpesvirus 1).

The only genome sequence for monkey B virus (BV; species Macacine herpesvirus 1) is that of an attenuated vaccine strain originally isolated from a rhesus monkey (BVrh). Here we report the genome sequence of a virulent BV strain isolated from a cynomolgus macaque (BVcy). The overall genome organization is the same, although sequence differences exist. The greatest sequence divergence is located in non-coding areas of the long and short repeat regions. Like BVrh, BVcy has duplicated Ori elements and lacks an ORF corresponding to the γ34.5 gene of herpes simplex virus. Nine of ten miRNAs and the majority of ORFs are conserved between BVrh and BVcy. The most divergent genes are several membrane-associated proteins and those encoding immediate early proteins.

Complete genome sequence of the NVSL BoHV-1.1 Cooper reference strain.

The only complete genome sequence available for bovine herpesvirus 1 (BoHV-1) is a composite sequence derived from four different BoHV-1.1 strains and one BoHV-1.2 strain. Such a chimeric genome sequence is problematic for molecular genetic studies on this virus. We report here the complete genome sequence for the BoHV-1.1 NVSL reference strain Cooper. Although similar to the published chimeric genome sequence, there are a number of nucleotide substitutions and deletions/insertions across the genome, many of which affect coding sequences.

Genome sequence of a chimpanzee herpesvirus and its relation to other primate alphaherpesviruses.

This study reports the complete genome sequence of chimpanzee herpesvirus (ChHV), an alphaherpesvirus isolated from a chimpanzee. Although closely related to human herpes simplex virus type 2 (HSV2), the level of sequence diversity confirms that ChHV is sufficiently distinct to be considered a member of a different virus species rather than a variant strain of HSV2. Phylogenetic comparison with other simplexviruses at several levels supports the hypothesis that HSV2 and ChHV co-evolved with their respective human and chimpanzee hosts and raises questions regarding the evolutionary origins of HSV1.

Characterization of a spontaneous drug-resistant mutant of monkey B virus (Macacine herpesvirus 1).

Monkey B virus (Macacine herpesvirus 1; BV) is an alpha-herpesvirus of macaques that causes serious infections in humans. A spontaneous mutant resistant to penciclovir (PCV) was isolated. Several genes were sequenced to identify mutations potentially responsible for PCV resistance. A single nucleotide deletion in the thymidine kinase (TK) gene was identified. To confirm its role in PCV resistance, several TK recombinants were constructed. A TK-deletion virus and a recombinant carrying the mutation were both resistant to PCV, while a revertant was PCV-sensitive. These results demonstrate that spontaneous drug-resistant mutants of BV do occur and that the BV TK is responsible for sensitivity to PCV.

An approach to generate noncontact ACL-injury prone situations on a computer using kinematic data of non-injury situations and Monte Carlo simulation.

ACL-injuries are one of the most common knee injuries in noncontact sports. Kinematic data of injury prone situations provide important information to study the underlying ACL-injury mechanisms. However, these data are rare. In this work an approach is presented to generate injury prone situations for noncontact ACL-injuries on a computer. The injury prone situations are generated by a musculoskeletal simulation model using kinematic data of a non-injury situation and the method of Monte Carlo simulation. The approach is successfully applied to generate injury prone landings in downhill ski racing. The characteristics of the obtained injury prone landings are consistent with video recordings of injury cases.

Isolation of a naturally occurring vaccine/wild-type recombinant bovine herpesvirus type 1 (BoHV-1) from an aborted bovine fetus.

Bovine herpesvirus type 1 (BoHV-1) causes various disease syndromes in cattle including respiratory disease and abortions. During an investigation into the potential role of BoHV-1 modified-live vaccines (MLV) causing diseases in cattle, we performed whole genome sequencing on six BoHV-1 field strains isolated at Cornell Animal Health Diagnostic Center in the late 1970s. Three isolates (two respiratory and a fetal) were identified as vaccine-derived isolates, having SNP patterns identical to that of a previously sequenced MLV virus that exhibited a deleted US2 and truncated US1.67 genes. Two other isolates (a respiratory and a fetal) were categorized as wild-type (WT) viruses based on their unique SNP pattern that is distinct from MLV viruses. The sixth isolate from an aborted fetus was a recombinant virus with 62% of its genome exhibiting SNPs identical to one of the above-mentioned WT viruses also recovered from an aborted fetus. The remaining 38% consisted of two blocks of sequences derived from the MLV virus. The first block replaced the UL9-UL19 region, and the second vaccine-derived sequence block encompassed all the genes within the unique short region and the internal/terminal repeats containing the regulatory genes BICP4 and BICP22. This is confirmatory evidence that recombination between BoHV-1 MLV and WT viruses can occur under natural conditions and cause disease. It is important in that it underscores the potential for the glycoprotein E negative (gE-) marker vaccine used to eradicate BoHV-1 in some countries, to recombine with virulent field strains allowing them to capture the gE- marker, thereby endangering the control and eradication programs.

Questioning the Extreme Neurovirulence of Monkey B Virus (Macacine alphaherpesvirus 1).

Monkey B virus (Macacine alphaherpesvirus 1; BV) occurs naturally in macaques of the genus Macaca, which includes rhesus and long-tailed (cynomolgus) monkeys that are widely used in biomedical research. BV is closely related to the human herpes simplex viruses (HSV), and BV infections in its natural macaque host are quite similar to HSV infections in humans. Zoonotic BV is extremely rare, having been diagnosed in only a handful of North American facilities with the last documented case occurring in 1998. However, BV is notorious for its neurovirulence since zoonotic infections are serious, usually involving the central nervous system, and are frequently fatal. Little is known about factors underlying the extreme neurovirulence of BV in humans. Here we review what is actually known about the molecular biology of BV and viral factors affecting its neurovirulence. Based on what is known about related herpesviruses, areas for future research that may elucidate mechanisms underlying the neurovirulence of this intriguing virus are also reviewed.

Understanding Primate Herpesviruses.

Viruses related to the herpes simplex viruses of humans are present in all nonhuman primate (NHP) species tested and cross species transmission has been documented. The herpesvirus present in macaques, Herpes B virus (BV) rarely causes disease in its natural macaque host. However, when transmitted to a nonnative host, BV has occasionally caused severe and even fatal disease if not treated immediately. Here we present a comprehensive review of the taxonomy, molecular biology, physiology, epidemiology, diagnosis and treatment of BV. We also summarizes what is known about related herpesviruses of other NHP species and the zoonotic potential of these viruses.

Genome sequence variation among isolates of monkey B virus (Macacine alphaherpesvirus 1) from captive macaques.

Complete genome sequences of 19 strains of monkey B virus (Macacine alphaherpesvirus 1; BV) isolated from several macaque species were determined. A low level of sequence variation was present among BV isolates from rhesus macaques. Most variation among BV strains isolated from rhesus macaques was located in regions of repetitive or quasi-repetitive sequence. Variation in coding sequences (polypeptides and miRNAs) was minor compared to regions of non-coding sequences. Non-coding sequences in the long and short repeat regions of the genome did however exhibit islands of conserved sequence. Oral and genital isolates from a single monkey were identical in sequence and varied only in the number of iterations of repeat units in several areas of repeats. Sequence variation between BV isolates from different macaque species (different BV genotypes) was much greater and was spread across the entire genome, confirming the existence of different genotypes of BV in different macaque species.

Efficacy of the early administration of valacyclovir hydrochloride for the treatment of neuropathogenic equine herpesvirus type-1 infection in horses.

OBJECTIVE To determine whether prophylactic administration of valacyclovir hydrochloride versus initiation of treatment at the onset of fever would differentially protect horses from viral replication and clinical disease attributable to equine herpesvirus type-1 (EHV-1) infection. ANIMALS 18 aged mares. PROCEDURES Horses were randomly assigned to receive an oral placebo (control), treatment at detection of fever, or prophylactic treatment (initiated 1 day prior to viral challenge) and then inoculated intranasally with a neuropathogenic strain of EHV-1. Placebo or valacyclovir was administered orally for 7 or 14 days after EHV-1 inoculation or detection of fever (3 horses/group). Effects of treatment on viral replication and clinical disease were evaluated. Plasma acyclovir concentrations and viremia were assessed to determine inhibitory concentrations of valacyclovir. RESULTS Valacyclovir administration decreased shedding of virus and viremia, compared with findings for control horses. Rectal temperatures and clinical disease scores in horses that received valacyclovir prophylactically for 2 weeks were lower than those in control horses. The severity of but not the risk for ataxia was decreased by valacyclovir administration. Viremia was decreased when steady-state trough plasma acyclovir concentrations were > 0.8 µg/mL, supporting the time-dependent activity of acyclovir. CONCLUSIONS AND CLINICAL RELEVANCE Valacyclovir treatment significantly decreased viral replication and signs of disease in EHV-1-infected horses; effects were greatest when treatment was initiated before viral inoculation, but treatment was also effective when initiated as late as 2 days after inoculation. During an outbreak of equine herpesvirus myeloencephalopathy, antiviral treatment may be initiated in horses at various stages of infection, including horses that have not yet developed signs of viral disease.

Bovine herpesvirus-1: Genetic diversity of field strains from cattle with respiratory disease, genital, fetal disease and systemic neonatal disease and their relationship to vaccine strains.

Bovine herpesvirus-1 (BoHV-1) causes disease in cattle with varied clinical forms. In the U.S. there are two BoHV1 subtypes, BoHV-1.1 and BoHV-1.2b. Control programs in North America incorporate modified live (MLV) or killed (KV) viral vaccines. However, BoHV-1 strains continue to be isolated from diseased animals or fetuses after vaccination. It is possible to differentiate BoHV-1 wild-type from MLV vaccine strains by determining their single nucleotide polymorphism (SNP) patterns through either whole-genome sequencing or PCR sequencing of genomic regions containing vaccine-defining SNPs. To determine the BoHV-1 subtype in clinical isolates and their relationship to MLV strains, 8 isolates from varied clinical disease at three different laboratories in the U.S. were sequenced and phylogenetically analyzed. Five samples were isolated within the past 5 years from New York and 3 were archived samples recovered 35 years prior from Oklahoma and Louisiana. Based on phylogenetic analysis, four of the cases appeared to be due to an MLV vaccine: 3 cases of aborted fetuses and one neonate with systemic BoHV-1 disease. One aborted fetus was from a herd with no reported history of MLV vaccination in two years. The remaining four isolates did not group with any MLV vaccines: two were associated with bovine respiratory disease, one with vulvovaginitis, and a fourth was determined to be a BoHV-1.2b respiratory isolate. Recovery of BoHV-1.1 that is very closely related to an MLV vaccine virus from a herd not receiving vaccines in an extended period prior to its isolation suggests that MLV viruses may remain latent or circulate within herds for long periods.

Detection and characterization of viruses as field and vaccine strains in feedlot cattle with bovine respiratory disease.

This study investigated viruses in bovine respiratory disease (BRD) cases in feedlots, including bovine herpesvirus-1 (BoHV-1), bovine viral diarrhea virus (BVDV), bovine respiratory syncytial virus (BRSV), bovine coronaviruses (BoCV) and parainfluenza-3 virus (PI3V). Nasal swabs were collected from 114 cattle on initial BRD treatment. Processing included modified live virus (MLV) vaccination. Seven BRD necropsy cases were included for 121 total cases. Mean number of days on feed before first sample was 14.9 days. Swabs and tissue homogenates were tested by gel based PCR (G-PCR), quantitative-PCR (qPCR) and quantitative real time reverse transcriptase PCR (qRT-PCR) and viral culture. There were 87/114 (76.3%) swabs positive for at least one virus by at least one test. All necropsy cases were positive for at least one virus. Of 121 cases, positives included 18/121 (14.9%) BoHV-1; 19/121 (15.7%) BVDV; 76/121 (62.8%) BoCV; 11/121 (9.1%) BRSV; and 10/121 (8.3%) PI3V. For nasal swabs, G-PCR (5 viruses) detected 44/114 (38.6%); q-PCR and qRT-PCR (4 viruses) detected 81/114 (71.6%); and virus isolation detected 40/114 (35.1%). Most were positive for only one or two tests, but not all three tests. Necropsy cases had positives: 5/7 G-PCR, 5/7 q-PCR and qRT-PCR, and all were positive by cell culture. In some cases, G-PCR and both real time PCR were negative for BoHV-1, BVDV, and PI3V in samples positive by culture. PCR did not differentiate field from vaccines strains of BoHV-1, BVDV, and PI3V. However based on sequencing and analysis, field and vaccine strains of culture positive BoHV-1, BoCV, BVDV, and PI3V, 11/18 (61.1%) of BoHV-1 isolates, 6/17 (35.3%) BVDV isolates, and 1/10 (10.0%) PI3V identified as vaccine. BRSV was only identified by PCR testing. Interpretation of laboratory tests is appropriate as molecular based tests and virus isolation cannot separate field from vaccine strains. Additional testing using sequencing appears appropriate for identifying vaccine strains.

Temporal progression of viral replication and gross and histological lesions in Balb/c mice inoculated epidermally with Saimiriine herpesvirus 1 (SaHV-1).

Saimiriine herpesvirus 1 (SaHV-1), an alphaherpesvirus enzootic in squirrel monkeys, is genetically related to monkey B virus and human herpes simplex virus (HSV). To study the temporal progression of viral spread and associated lesions, Balb/c mice were inoculated epidermally by scarification with a green fluorescent protein (GFP)-expressing recombinant strain of SaHV-1 and killed sequentially. Pinpoint ulcerative lesions in the inoculated epidermis progressed over a few days to unilateral or bilateral hindlimb paresis or paralysis, urinary and faecal incontinence, abdominal distension, hunched posture and eventual depression warranting euthanasia. Viral replication was present within epidermal keratinocytes, neurons of the dorsal root ganglia and thoracolumbar spinal cord, regional autonomic ganglia, lower urinary tract epithelium and colonic myenteric plexuses, as indicated by histological lesions and GFP expression. Almost all mice inoculated with 10(5) or 10(6) plaque-forming units (PFU) of SaHV-1 developed rapidly progressive disease. Two of eight mice given 10(4)PFU developed disease, but no mice receiving less than 10(4)PFU gave evidence of infection. Mice that showed no clinical signs also failed to develop an antiviral IgG response, indicating absence of active viral infection. For SaHV-1 inoculated epidermally, the ID(50), CNSD(50) and LD(50) values were identical (10(4.38)), indicating that successful infection by this route invariably resulted in lethal CNS (central nervous system) disease. Consistently severe disease in all infected animals, with regionally extensive distribution of viral replication, constituted a marked difference from the disease produced by intramuscular inoculation.

Clinicopathological characterization of monkey B virus (Cercopithecine herpesvirus 1) infection in mice.

The purpose of this study was to establish a small animal model for monkey B virus (BV) infection. Mice were inoculated intramuscularly with several BV isolates. Comparisons were based upon the doses required to produce infection (ID50), non-central nervous system (CNS) clinical disease (CS50), CNS disease (CNSD50) and lethal effect (LD50). Strains differed in respect of the dose required to produce clinical disease in BALB/c mice. C57BL/6 mice were more resistant than BALB/c mice to CNS disease. Skin lesions at the inoculation site consisted of epidermal necrosis, ulceration, serocellular crusts and underlying dermatitis. CNS lesions included marked inflammation in the ipsilateral dorsal root ganglion and lumbar spinal cord (point of viral entry). The distribution of the lumbar spinal cord lesions suggested viral entry via sensory afferent neurons, ventral motor tracts, or both. The lesions in the more cranial spinal cord segments suggested ascension to the brain via bilateral spinothalamic and spinoreticular tracts. Brain lesions included encephalitis with neuronal necrosis and white matter destruction located consistently at the base of the brainstem, the reticular system, and rostrally to the thalamus and hypothalamus. Viral antigen was detected immunohistochemically in the lesions. The results indicated an ascending encephalomyelitis syndrome similar to that produced by BV in man.

Bovine herpesvirus-1: evaluation of genetic diversity of subtypes derived from field strains of varied clinical syndromes and their relationship to vaccine strains.

Bovine herpesvirus-1 (BoHV-1) causes significant disease in cattle. Control programs in North America incorporate vaccination with modified live viral (MLV) or killed (KV) vaccine. BoHV-1 strains are isolated from diseased animals or fetuses after vaccination. There are markers for differentiating MLV from field strains using whole-genome sequencing and analysis identifying single nucleotide polymorphisms (SNPs). Using multiple primer sets and sequencing of products permits association of BoHV-1 isolates with vaccines. To determine association between vaccine virus and strains isolated from clinical cases following vaccination, we analyzed 12 BoHV-1 isolates from animals with various clinical syndromes; 9 corresponded to BoHV-1.1 respiratory group. The remaining three corresponded to BoHV-1.2b, typically found in genital tracts of cattle. Four BoHV-1 isolates were identical to a vaccine strain; three were from post-vaccination abortion episodes with typical herpetic lesions whose dams had received MLV vaccine during pregnancy, and one from a heifer given a related MLV vaccine; Sequences of two respiratory isolates perfectly matched mutations characterizing RLB106 strain, a temperature sensitive mutant used in intranasal and parenteral vaccines. The last three respiratory strains clearly appeared related to a group of MLV vaccines. Previously the MLV vaccines were grouped into four groups based on SNPs patterns. In contrast with above-mentioned isolates that closely matched SNP patterns of their respective MLV vaccine virus, these 3 strains both lacked some and possessed a number of additional mutations compared to a group of MLV vaccine viral genome. Finding BoHV-1.2b in respiratory cases indicates focus should be given BoHV-1.2b as an emerging virus or a virus not recognized nor fully characterized in BRD.

Complex chromatid-isochromatid exchanges following irradiation with heavy ions?

We describe a peculiar and relatively rare type of chromosomal rearrangement induced in human peripheral lymphocytes that were ostensibly irradiated in G(0) phase of the cell cycle by accelerated heavy ions, and which, to the best of our knowledge, have not been previously described. The novel rearrangements which were detected using mFISH following exposure to 500 MeV/nucleon and 5 GeV/n 56Fe particles, but were not induced by either 137Cs gamma rays or 238Pu alpha particles, can alternatively be described as either complex chromatid-isochromatid or complex chromatid-chromosome exchanges. Different mechanisms potentially responsible for their formation are discussed.