Complete Sequence and Comparative Analysis of the Genome of Herpes B Virus ( Cercopithecine Herpesvirus 1 ) from a Rhesus Monkey

Abstract

The complete DNA sequence of herpes B virus (Cercopithecine herpesvirus 1) strain E2490, isolated from a rhesus macaque, was determined. The total genome length is 156,789 bp, with 74.5% G؉C composition and overall genome organization characteristic of alphaherpesviruses. The first and last residues of the genome were defined by sequencing the cloned genomic termini. There were six origins of DNA replication in the genome due to tandem duplication of both oriL and oriS regions. Seventy-four genes were identified, and sequence homology to proteins known in herpes simplex viruses (HSVs) was observed in all cases but one. The degree of amino acid identity between B virus and HSV proteins ranged from 26.6% (US5) to 87.7% (US15). Unexpectedly, B virus lacked a homolog of the HSV ␥ 1 34.5 gene, which encodes a neurovirulence factor. Absence of this gene was verified in two low-passage clinical isolates derived from a rhesus macaque and a zoonotically infected human. This finding suggests that B virus most likely utilizes mechanisms distinct from those of HSV to sustain efficient replication in neuronal cells. Despite the considerable differences in G؉C content of the macaque and B virus genes (51% and 74.2%, respectively), codons used by B virus are optimal for the tRNA population of macaque cells. Complete sequence of the B virus genome will certainly facilitate identification of the genetic basis and possible molecular mechanisms of enhanced B virus neurovirulence in humans, which results in an 80% mortality rate following zoonotic infection.Comparative genome analyses of closely related viruses offer insight into the protein coding capacities of viral genomes (18, 69), a means to biologically classify viruses (2, 19) and identify viral genes involved in virulence and pathogenicity (1,37,67). The number of completely sequenced viral genomes has been increasing rapidly and now exceeds 1,000, including 29 herpesvirus genomes (GenBank data, http://www.ncbi.nlm.nih.gov /PMGifs/Genomes/viruses.html).B virus (Cercopithecine herpesvirus 1, monkey B virus) is a member of the subfamily Alphaherpesvirinae, which together with human herpes simplex virus types 1 and 2 (HSV-1 and HSV-2) constitutes the genus Simplexvirus. B virus generally causes only mild localized or asymptomatic infections in its natural hosts, Asian monkeys of the genus Macaca (33,34,74). In contrast, B virus infections in foreign hosts, humans or monkey species other than macaques, often result in encephalitis, encephalomyelitis, and death (53,73,74).The genome organization of B virus is similar to that of HSV-1 and HSV-2: the unique long (U L ) and unique short (U S ) segments flanked by inverted long (R L ) and short (R S ) repeat sequences are covalently joined in four possible isomeric configurations (26). Sequence analysis of the partial U S regions of B virus and simian agent 8 virus demonstrated that human and primate viruses are colinear in this genomic segment (51). However, only a limited number of B virus gene sequences from the U L region have b...

First genome analysis and molecular characterization of Chickpea chlorotic dwarf virus Egyptian isolate infecting squash

“…Or this could be explained as a silencing suppression activity to regain the replication fitness of non-host virus as it has been proved for Tobacco Mild Green Mosaic Virus [18]. It has been observed also through different sequencing trails that the RepA gene start codon was GTG rather than ATG this has been also described by Perelygina et al [37], that it was inferred that the B virus UL1 and UL2 genes use the GTG codon as a start codon at genomic sequence positions 9,072 and 9,814, respectively. Conservation of the UL1 GTG start codon was confirmed by sequence analysis of the 5 0 -region of the respected gene from two B virus clinical isolates.…”

Specific Detection and Identification of Herpes B Virus by a PCR-Microplate Hybridization Assay

“…In addition, herpes B virus shows strong serological cross-reactivity with HSV (5,18). The genetic arrangement is almost identical between herpes B virus and HSV (8,21,22,25), and the nucleotide sequences of the herpes B virus genes have been reported to show high homology with the corresponding HSV genes (1,21,22,25). These similarities suggest that a sample from a patient with herpes B virus infection also contains HSV and that misidentification occurs in a diagnosis of the infection.…”

“…A specific herpes B virus detection method is also necessary in order to distinguish herpes B virus from the closely related HSV. In the present study, we designed PCR to amplify the regions of the US5 gene encoding glycoprotein J, which was shown to be the most divergent of the protein-coding genes in HSV-1, HSV-2, and herpes B viruses (4,25) and the 3Ј-flanking noncoding intergenic region.…”

“…PCR was designed to amplify the herpes B virus target sequence, which is the most divergent in the genome sequence among HSV-1, HSV-2, and herpes B virus (4,25). Furthermore, the amplified region was shown to have a highly genetic polymorphism among herpes B virus isolates derived from different natural host species (33).…”

Varicella zoster virus infection

“…Because ICP34.5 is present in herpes simplex virus 1 and 2, but lacking in VZV and betaherpesviruses, the gene may have been acquired by herpes simplex viruses more recently than 30 million years ago (before the common ancestor of all these viruses) 200,201 . Alternatively, VZV could have lost the gene at a later time.…”