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. 2003 Dec 9;100(25):14976-81.
doi: 10.1073/pnas.2136652100. Epub 2003 Dec 1.

Coding potential of laboratory and clinical strains of human cytomegalovirus

Eain Murphy  1 , Dong Yu, Jane Grimwood, Jeremy Schmutz, Mark Dickson, Michael A Jarvis, Gabriele Hahn, Jay A Nelson, Richard M Myers, Thomas E Shenk
Affiliations

Coding potential of laboratory and clinical strains of human cytomegalovirus

Eain Murphy et al. Proc Natl Acad Sci U S A. .

Abstract

Six strains of human cytomegalovirus have been sequenced, including two laboratory strains (AD169 and Towne) that have been extensively passaged in fibroblasts and four clinical isolates that have been passaged to a limited extent in the laboratory (Toledo, FIX, PH, and TR). All of the sequenced viral genomes have been cloned as infectious bacterial artificial chromosomes. A total of 252 ORFs with the potential to encode proteins have been identified that are conserved in all four clinical isolates of the virus. Multiple sequence alignments revealed substantial variation in the amino acid sequences encoded by many of the conserved ORFs.

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Figures

Fig. 1.
Fig. 1.
HCMV ORF organization. (A) Conventional ORF maps of the AD169 laboratory strain and clinical isolates. From the left, the AD169 genome contains TRL1-14 (green arrow), UL1-132 (dark blue arrow), IRL14-1 (green arrow), IRS1 (red arrow), US1-36 (light blue arrow), and TRS1 (red arrow). From the left, clinical isolates contain a unique domain including RL1-14 and UL1-151 (green plus dark blue arrow) followed by IRS1 (red arrow), US1-36 (light blue arrow), and TRS1 (red arrow). (B) ORF maps of the BAC clones whose sequences are reported in this article. Sequences were linearized at the position corresponding to nucleotide 1 of the original AD169 sequence. Arrows indicate the relative orientations of the repeated and unique ORF blocks. The RL region is not repeated in the clinical isolates (Toledo, PH, TR, and FIX); there is a single copy of the region (green segment appended to the unique long region). The Towne laboratory strain contains a block of ORFs (UL147–UL154, orange arrow) that is not present in AD169, and the clinical isolates contain a block of ORFs (UL133–UL151, orange arrow) that is not present in the AD169 laboratory strains. The BAC inserts are identified (B), and viral ORFs deleted during BAC insertions are listed in parentheses.
Fig. 2.
Fig. 2.
Variability of homologous ORFs. Global multiple sequence alignments were performed by using clustalw for all ORFs identified by blastp in the six HCMV isolates. For each ORF, the percentage identical (solid bar) plus percentage similar (cross-hatched bar) amino acids are presented for each FIX ORF in comparison to AD169 (light blue), Towne (dark blue), Toledo (yellow), PH (green), and TR (red). In cases where no bars are displayed, the FIX strain did not contain the ORF. ORFs marked with an asterisk do not have an AUG within 80 aa of their stop codon. The ORFs are presented in the order that they are found on the conventional AD169 map; the clinical strain-specific ORFs (UL133–UL151) are presented in the order in which they are found in FIX; the set of newly recognized ORFs (C-ORF1–C-ORF29) are presented after the previously recognized ORFs in the order in which they would occur on the map. Several ORFs, which are combined by splicing, have been analyzed as a single unit: UL21.5 (UL22a), UL36, UL37, UL89, UL111A, UL112-113, UL118-119, UL122, UL123, UL128, and UL131A. Comparisons are not presented for IRS1–US6, which are not present in the FIX BAC. UL154 is related to RL12, and UL153 is similar to RL14.
Fig. 3.
Fig. 3.
FIX ORF map. ORFs that are conserved in all four clinical isolates are presented in the order that they reside on the conventional clinical strain map displayed in Fig. 1 A. ORFs with an AUG that were recognized previously in AD169, Towne, or Toledo are oriented with dark blue arrows, previously recognized ORFs without an AUG are marked by light blue arrows, and newly recognized ORFs are shown with yellow arrows. Spliced ORFs are identified by caret symbols, and ORFs deleted by insertion of the BAC element are shown in a box. Two adjacent ORFs are present that were identified as RL6 homologues by blastp. UL141 contains a stop codon, and it is shown as two adjacent ORFs: UL141 and UL141.1.
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