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. On the basis of conservation of potential proteincoding regions and other sequence features, we have discounted 51 previously proposed HCMV ORFs, modified the interpretations for 24 (including assignments of multiple exons) and proposed ten novel genes. Several errors were detected in the published HCMV sequences. We presently recognize 165 genes in CCMV and 145 in AD169; this compares with an estimate of 189 unique genes for AD169 made in 1990. Our best estimate for the complement of wild-type HCMV is 164 to 167 genes. INTRODUCTIONHuman cytomegalovirus (HCMV; human herpesvirus 5) is ubiquitous and largely inapparent, but poses a risk of serious disease to those lacking a competent immune system, such as neonates, transplant patients and sufferers from AIDS (reviewed in Pass, 2001). HCMV is the prototype of subfamily Betaherpesvirinae, and is the most complex of the eight human herpesvirus species. HCMV is isolated routinely on human fibroblast cell lines, and several strains in common laboratory use, such as AD169 and Towne, were derived by multiple passages on such cells (reviewed in Mocarski & Tan Courcelle, 2001).The linear, double-stranded DNA genome of AD169 comprises two covalently linked segments (L and S), each consisting of a unique region (U L and U S ) flanked by an inverted repeat (TR L and IR L , TR S and IR S ), yielding the overall genome configuration TR L -U L -IR L -IR S -U S -TR S (reviewed in Mocarski & Tan Courcelle, 2001). In addition, the genome is terminally redundant, possessing a short region (the a sequence) as a direct repeat at the termini and also in inverse orientation at the IR L -IR S junction. Some genomes contain tandemly reiterated copies of the a sequence at these locations. U L and U S can invert relative to each other by recombination between inverted repeats in replicating DNA, resulting in four equimolar genome arrangements in virion DNA. The complete DNA sequence of AD169 was published in a seminal paper by Chee et al. (1990), and at that time was the largest viral genome sequence available. The total genome size was 229 354 bp, with U L being 166 972 bp, U S 35 418 bp, R L (a collective term for TR L and IR L ) 11 247 bp, R S (TR S and IR S ) 2524 bp and the a sequence (part of R L and R S in the sizes given above) 578 bp.As a primary criterion for identifying protein-coding regions, Chee et al. (1990) focused on open reading frames (ORFs) of 100 or more contiguous amino acidencoding codons that ov...

Type I interferon (IFN) induction is an immediate response to virus infection

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. CCMV and the Colburn strain of simian cytomegalovirus, which have been passaged in cell culture, also exhibit disruptions of UL128. These observations indicate that expression of either one of UL128 and UL131A is deleterious to growth of primate cytomegaloviruses in cell culture. Although the functions of these genes are unknown, sequence comparisons suggest that UL128 encodes a b-chemokine.The genome of the AD169 strain of human cytomegalovirus (HCMV; human herpesvirus 5) was characterized by Chee et al. (1990) as containing 189 putative protein-coding open reading frames (ORFs), some duplicated in an inverted repeat. An additional genome region was subsequently discovered in the Toledo strain (Cha et al., 1996). A recent comparison of these sequences with that of chimpanzee cytomegalovirus (CCMV) indicated that wild-type HCMV has 166-169 genes (Davison et al., 2003a, b). The present work concerns two of the eleven newly predicted genes in this redefined set.The upper part of Fig. 1(A) depicts the arrangement of ORFs UL131-UL128 as predicted by Chee et al. (1990), and the lower parts show alternative predictions based on comparisons between the AD169 and CCMV sequences. UL130 is unaltered, while spliced genes replace UL131 upstream and UL129 plus UL128 downstream. One of these genes is named UL131A because it occupies the same region as UL131 but does not share any encoded amino acid sequence, since the first exon is in a different reading frame from UL131. The other spliced gene retains the designation UL128 because it shares amino acid sequence with the original UL128 but not with UL129. Fig. 1(B, C) shows detailed alignments of the AD169 and CCMV sequences in these regions. Protein-coding regions were proposed from conservation of encoded amino acid sequences, and conceptually linked together via candidate splice donor and acceptor sites. This led to the hypothesis that UL131A and UL128 comprise two and three exons, respectively.In order to sustain this interpretation, it is necessary to propose that AD169 has a frameshift mutation (an additional residue making a tract of eight A residues) in UL131A exon 1 (Fig. 1B) and that CCMV has a frameshift mutation (an additional residue making a tract of eight C residues) in UL128 exon 1 (Fig. 1C). Davison et al. (2003a) confirmed the former lesion by resequencing the relevant AD169 region and comparing it with sequence obtained directly from clinical material. The proposed mutation in...

Fig. 7. The legend was incomplete in the print version of this article; the full legend is given below.

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. These genes potentially encode a domain that is the hallmark of proteins encoded by the RL11 family, and thus constitute two new members. A homologous domain is also present in a subset of human adenovirus E3 membrane glycoproteins. Evolution of genes specifying the shared domain in cytomegaloviruses and adenoviruses is characterized by extensive divergence, gene duplication and selective sequence loss. These features prompt speculation about the roles of these genes in the two virus families.Human cytomegalovirus (HCMV; human herpesvirus 5) is the most complex human herpesvirus. The 229 354 bp genome of a high passage laboratory strain (AD169) was characterized by Chee et al. (1990) and predicted to contain 189 putative protein-coding genes, some duplicated in the inverted repeats. Subsequent revisions, based largely on comparisons with chimpanzee cytomegalovirus (CCMV), the closest known relative of HCMV, indicated that the wild-type HCMV genome contains 164-167 genes (Davison et al., 2003). Chee et al. (1990) identified nine multigene families in AD169, and an additional three were recognized in low passage isolates (Davison et al., 2003). One, the RL11 family, consists of 12 genes (RL11, RL12, RL13, UL1, UL4, UL5, UL6, UL7, UL8, UL9, UL10 and UL11) oriented left to right near the left terminus of the genome and arranged contiguously but for the presence on the opposing strand of two unrelated genes (UL2 and UL3). RL11, RL12 and the 59-portion of RL13 are present twice in the AD169 genome by virtue of their location in an inverted repeat. This repeat is much smaller in low passage strains, which consequently contain single copies of these genes (Prichard et al., 2001). RL13 is also disrupted by a frameshift in AD169 (Yu et al., 2002). All members of the RL11 family (generically termed 'RL11 genes') are dispensable for virus growth in cell culture (Ripalti & Mocarski, 1991;Hobom et al., 2000;Yu et al., 2002; Atalay et al., 2002). RL11 genes are also present in CCMV, which has counterparts of all but UL1 (Davison et al., 2003). Cytomegaloviruses of mouse, rat and tupaia lack RL11 genes (Rawlinson et al., 1996;Vink et al., 2000;Bahr & Darai, 2001).The present work involved sequence analysis of the region near the left genome terminus in six HCMV strains. Four had been grown in human fibroblast cell lines, three of these (Merlin, 3157 and 6397) derived in Cardiff by three passages from urine samples from congenitally infected infants and one a widely used low passage strain (Toledo; Quinnan et al., 1984). DNA from the Cardiff st...

Chotpoti is a popular street food in the major areas of Bangladesh. Street foods play an important role in people's daily food options as well as their regular nutritional requirements are dependent on these foods, as their ever-growing busy schedule takes away the opportunity to eat of homemade food. Due to the expedient availability, these street foods are one of the primary food options for city peoples. The present study was undertaken to investigate the microbiological quality of Chotpoti sold by different street vendor at Savar area, Dhaka, Bangladesh. Microbial quality was assessed by total viable count (TVC), total coliform count (TCC); samples were inoculated into various selective media such as Nutrient agar, Eosin Methylene Blue (EMB) agar, Salmonella Shigella (SS) agar, Thiosulfate Citrate Bile Salts Sucrose (TCBS) agar and Mac Conkey's agar. Gram negative bacteria were isolated and identified from the samples. The TVC in Chotpoti sample was ranged from 6 × 10 5 CFU/g to TNTC and TCC was ranged from 6 × 10 5 CFU/g to 3 × 10 6 CFU/g. Antibiotic sensitivity test showed that the isolates were sensitive to antibiotics such as antibiotic against Streptomycin, Chloramphenicol.

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