Complete Genome Sequence of the English Isolate of Rat Cytomegalovirus ( Murid Herpesvirus 8 )

Abstract

fThe complete genome of the English isolate of rat cytomegalovirus (RCMV-E) was determined. RCMV-E has a 202,946-bp genome with noninverting repeats but without terminal repeats. Thus, it differs significantly in size and genomic arrangement from closely related rodent cytomegaloviruses (CMVs). To account for the differences between the rat CMV isolates of Maastricht and England, RCMV-E was classified as Murid herpesvirus 8 by the International Committee on Taxonomy of Viruses. The English isolate of rat cytomegalovirus (RCMV-E) is a member of the Betaherpesvirinae subfamily of the Herpesviridae. Two isolates of RCMV, the Maastricht isolate (RCMV-M) and RCMV-E, have been reported, and RCMV-M has been classified as Murid herpesvirus 2 (MuHV-2). RCMV-M was first described in 1982 by Bruggeman et al. (2), and in the same year, Priscott and Tyrrell (4) reported on the existence of another rat CMV that was later termed the "English" isolate (3). Both viruses had been isolated from Rattus norvegicus.The complete genome sequences of both MuHV-2 and MuHV-1 (MCMV Smith strain) have been published (NC_002512, 230,138 bp [ 7] and NC_004065, 230,278 bp [5]) as well as those of four very closely related isolates of MuHV-1 (6). The RCMV-M and RCMV-E genomes were shown to have significantly different restriction enzyme cleavage patterns, suggesting that they represent different betaherpesvirus species rather than different strains of the same virus (1,8).To analyze the viral genome, RCMV-E virion DNA was isolated from RCMV-E-infected rat embryo fibroblasts and analyzed by Sanger sequencing. In addition, shotgun sequencing (Macrogen, South Korea) with low coverage was performed. These data revealed substantial differences to MuHV-2 and served as a scaffold sequence. To confirm the data, RCMV-E virion DNA was subjected to 454 sequencing. The DNA was sheared with Covaris S2, and libraries were generated utilizing the rapid library kit and finally sequenced with Titanium chemistry on a 454 FLX instrument (Roche). Reads with a 26-fold coverage were mapped to our scaffold sequence data using Newbler 2.6 software. Analysis of the data showed that the RCMV-E genome comprises 202,946 bp. Results of a de novo assembly using Newbler 2.6 confirmed the results of the mapping. Therefore, from both physical analysis and the genome sequencing data, it is evident that the RCMV-E genome is considerably smaller than and thus differs significantly in size and gene content from both MuHV-1 and MuHV-2.Major criteria to identify open reading frames (ORFs) were a minimum length of 60 bp, an ATG start codon, and less than 60% overlap with adjacent ORFs. By this approach, 140 ORFs were identified using Lasergene 8 and Geneious 5.4 software packages. A total of 118 ORFs are homologous to MuHV-1 and MuHV-2, showing an E value of Ͻ0.001 in BLASTX analyses. Both at the nucleotide and protein levels, most RCMV genes are somewhat more closely related to MuHV-1, although they are almost equally divergent from both MuHV-1 and MuHV-2. However, RCMV-E encodes ...

Murine Cytomegalovirus Is Not Restricted to the House Mouse Mus musculus domesticus: Prevalence and Genetic Diversity in the European House Mouse Hybrid Zone

“…3). The root is placed at 21.33 Mya (95% HPD interval, 16.33 to 27.19 Mya) (this is the tMRCA of the two lineages of CMV proposed to have evolved separately in Murinae [36,37]). …”

“…The different MCMV variants were aligned at the amino acid level against other MCMV sequences and the rat CMV Maastricht strain (RCMV-M) sequence, available in GenBank, by using MUSCLE (35). The English strain of rat CMV (RCMV-E) was used as an outgroup, since it represents a distinct murine CMV lineage (36,37). Regions containing indels were removed from the final alignment, resulting in 716 nucleotides that were used in subsequent analyses.…”

Cytomegalovirus Expresses the Chemokine Homologue vXCL1 Capable of Attracting XCR1 + CD4 − Dendritic Cells

“…Our analysis of the MuHV8 genome (27) revealed the presence of a C chemokine, located at nucleotide positions 186261 to 186608 toward the right terminus, which to our knowledge is the first viral C chemokine to be reported. The gene product, desig-nated vXCL1, shares extensive homology with the C chemokine XCL1 of rat, mouse, and human.…”

Genetic Investigation of MHC-Independent Missing-Self Recognition by Mouse NK Cells Using an In Vivo Bone Marrow Transplantation Model

“…In rats, viral evasion of this system determines the outcome of viral titers during rat CMV-English infection (RCMV-E; Mhv-8) (20,21). Briefly, RCMV-infected cells lose surface expression of host Clr-b-like rat Clec2d11, yet RCMV-E encodes an NKR-P1B-specific decoy, RCTL, that functionally replaces Clec2d11 and inhibits NK cells.…”