Evolution and diversity in human herpes simplex virus genomes.

Herpes simplex virus 1 (HSV-1) causes a chronic, lifelong infection in >60% of adults. Multiple recent vaccine trials have failed, with viral diversity likely contributing to these failures. To understand HSV-1 diversity better, we comprehensively compared 20 newly sequenced viral genomes from China, Japan, Kenya, and South Korea with six previously sequenced genomes from the United States, Europe, and Japan.

Patterns of divergence in the vCXCL and vGPCR gene clusters in primate cytomegalovirus genomes.

Primate cytomegalovirus (CMV) genomes contain tandemly repeated gene clusters putatively encoding divergent CXC chemokine ligand-like proteins (vCXCLs) and G protein-coupled receptor-like proteins (vGPCRs). In human, chimpanzee and rhesus CMVs, respectively, the vCXCL cluster contains two, three and six genes, and the vGPCR cluster contains two, two and five genes. We report that (i) green monkey CMV strains fall into two groups, containing either eight and five genes or seven and six genes in the respective clusters, and (ii) owl monkey CMV has two and zero genes.

Novel cytomegaloviruses in free-ranging and captive great apes: phylogenetic evidence for bidirectional horizontal transmission.

Wild great apes often suffer from diseases of unknown aetiology. This is among the causes of population declines. Because human cytomegalovirus (HCMV) is an important pathogen, especially in immunocompromised individuals, a search for cytomegaloviruses (CMVs) in deceased wild and captive chimpanzees, gorillas and orang-utans was performed.

The genome of Epstein-Barr virus type 2 strain AG876.

Two Epstein-Barr virus (EBV) types are known, EBV1 and EBV2, which possess substantially diverged alleles for latency genes EBNA-2, EBNA-3A, EBNA-3B and EBNA-3C but are thought to be otherwise similar. We report the first complete EBV2 genome sequence, for strain AG876, as 172,764 bp. The sequence was interpreted as containing at least 80 protein coding genes.

On phylogenetic relationships among major lineages of the Gammaherpesvirinae.

Phylogenetic relationships within the subfamily Gammaherpesvirinae of the family Herpesviridae were investigated for three species in the genus Lymphocryptovirus (or gamma1 group) and nine in the genus Rhadinovirus (or gamma2 group). Alignments of amino acid sequences from up to 28 genes were used to derive trees by maximum-likelihood and Bayesian Monte Carlo Markov chain methods. Two problem areas were identified involving an unresolvable multifurcation for a clade within the gamma2 group, and a high divergence for Murid herpesvirus 4 (MHV4).

Genetic content of wild-type human cytomegalovirus.

The genetic content of wild-type human cytomegalovirus was investigated by sequencing the 235 645 bp genome of a low passage strain (Merlin). Substantial regions of the genome (genes RL1-UL11, UL105-UL112 and UL120-UL150) were also sequenced in several other strains, including two that had not been passaged in cell culture. Comparative analyses, which employed the published genome sequence of a high passage strain (AD169), indicated that Merlin accurately reflects the wild-type complement of 165 genes, containing no obvious mutations other than a single nucleotide substitution that truncates gene UL128.

Phylogenetic relationships in the Lymphocryptovirus genus of the Gammaherpesvirinae.

Complete DNA sequences were determined for the glycoprotein B (gB) genes of four viruses from the genus Lymphocryptovirus, whose hosts had been assigned as baboon, orangutan, chimpanzee and gorilla. Together with published sequences for the gB genes of three lymphocryptoviruses, namely the human pathogen Epstein-Barr virus (EBV), a rhesus monkey virus and a marmoset virus, the sequences were used to investigate evolutionary relationships in the genus. The chimpanzee and orangutan viruses' sequences were found to be so close that it is unlikely both represent natural infections in these hosts.

Two novel spliced genes in human cytomegalovirus.

Two novel spliced genes (UL131A and UL128) flanking UL130 were predicted from sequence comparisons between human cytomegalovirus (HCMV) and its closest known relative, chimpanzee cytomegalovirus (CCMV), and the splicing patterns were confirmed by mRNA mapping experiments. Both genes were transcribed with late kinetics and shared a polyadenylation site. Comparisons with wild-type HCMV in infected human tissues showed that three of five isolates passaged in cell culture contained disruptions of UL128, one was frameshifted in UL131A and one exhibited a deletion affecting UL131A and UL130.

Homology between the human cytomegalovirus RL11 gene family and human adenovirus E3 genes.

A significant proportion of the human cytomegalovirus (HCMV) genome comprises 12 multigene families that probably arose by gene duplication. One, the RL11 family, contains 12 members, most of which are predicted to encode membrane glycoproteins. Comparisons of sequences near the left end of the genome in several HCMV strains revealed two adjacent open reading frames that potentially encode related proteins: RL6, which is hypervariable, and RL5A, which has not been recognized previously.

The human cytomegalovirus genome revisited: comparison with the chimpanzee cytomegalovirus genome.

The gene complement of wild-type human cytomegalovirus (HCMV) is incompletely understood, on account of the size and complexity of the viral genome and because laboratory strains have undergone deletions and rearrangements during adaptation to growth in culture. We have determined the sequence (241 087 bp) of chimpanzee cytomegalovirus (CCMV) and have compared it with published HCMV sequences from the laboratory strains AD169 and Toledo, with the aim of clarifying the gene content of wild-type HCMV. The HCMV and CCMV genomes are moderately diverged and essentially collinear.