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Antimicrobial Agents and Chemotherapy, January 2009, p. 81-85, Vol. 53, No. 1
0066-4804/09/$08.00+0 doi:10.1128/AAC.01177-08
Copyright © 2009, American Society for Microbiology. All Rights Reserved.

Division of Infectious Diseases, Oregon Health and Science University, and Department of Veterans Affairs Medical Center, Portland, Oregon
Received 4 September 2008/ Returned for modification 16 October 2008/ Accepted 24 October 2008
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Given the limited duration of drug administration and the few cases studied to date, there are not yet any reports of MBV resistance in CMV isolates from treated subjects. Because the antiviral mechanism of MBV differs from the mechanisms of the currently licensed systemic anti-CMV drugs ganciclovir, foscarnet, and cidofovir, all of which target the viral DNA polymerase, cross-resistance between MBV and the existing drugs is not expected and none has been reported. The CMV UL97 kinase is involved in the antiviral actions of both MBV and ganciclovir, since this kinase is responsible for the initial phosphorylation of ganciclovir that is essential for that drug to have antiviral activity (3). Well-known UL97 mutations that commonly confer ganciclovir resistance, located at codons 460, 592, 594, and 595, do not confer cross-resistance to MBV (9). The propagation of CMV isolates and strains in vitro under MBV results in UL97 mutations at or near the ATP-binding domain (codons 353, 397, 409, and 411) that confer moderate to high-level MBV resistance but not ganciclovir cross-resistance (1, 4, 7).
Separately, it has been reported that mutations in UL27, a CMV gene of unknown function, are selected after the in vitro propagation of CMV and confer a relatively lower level of MBV resistance than the known UL97 mutations. In one case, UL27 mutation L335P was identified in a viral strain resistant to other experimental drugs and further propagated under MBV (13). Three additional instances of UL27 mutations (R233S, A406V/C415stop, and W362R) were also found after the propagation of laboratory CMV strain AD169 under a carbocyclic analog of MBV, and these mutations were confirmed to confer low-grade MBV resistance by transfer to a reference CMV strain (5).
To increase the understanding of the relative frequency and diversity of UL27 mutations in CMV strains exposed to MBV in vitro and to assess the relative levels of drug resistance conferred, additional experiments were performed to propagate CMV cultures under MBV and characterize the resulting UL27 mutations. To distinguish whether UL27 mutations are a specific result of MBV exposure or whether it is an adaptation to loss of the UL97 kinase, two CMV strains that were genetically defective in UL97 were serially propagated without any added drug and were monitored for UL27 mutations.
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Propagation under MBV.
MBV (1263W94) was provided by GlaxoSmithKline and was diluted into cell culture medium from a 100 mM stock solution in dimethyl sulfoxide. Viral cultures were serially propagated in fibroblast cultures with initial MBV concentrations of 0.3 µM for clinical isolates and 0.1 µM for strain T2294; these concentrations match the baseline MBV 50% effective concentrations (EC50s) published previously (4, 7). Thereafter, the MBV concentrations were increased up to 10 µM when the viral growth appeared to improve under drug and the abnormal UL97-defective cytopathic effect lessened, as described previously (4, 7). Cultures were passed weekly to fresh fibroblast monolayers as
20% of the infected cells from the prior passage. Strains T2266 and T2819, which were defective in UL97, were serially propagated without the use of any MBV.
Genotypic analysis of viral strains.
Aliquots of infected cells were frozen at each viral passage. After every five passages, infected cell DNA extracts were amplified by PCR and checked for their UL97 and UL27 sequences. If changes from the baseline sequences were observed, extracts of infected cells from intermediate passages were analyzed to determine the earliest passage that showed a sequence change. Sequencing was performed by PCR amplification and automated dideoxy sequencing with a BigDye Terminator fluorescent dye kit (Applied Biosystems) and an automated sequencer instrument. This technology is expected to detect the presence of a mutated sequence in the population when it is present in
20% of the total population (20). Estimates of the percentage of viruses with a mutated sequence in a population were made by comparison of the peak heights in the chromatogram files generated by the sequencing system.
Transfer of UL27 mutations to strain T2394. The UL27 mutations observed were transferred to strain T2394 by using a contransfection method similar to that used to generate other strains with UL27 and UL97 mutations (4, 5, 7). Briefly, T2394 genomic viral DNA was extracted from the supernatant of infected cell cultures, digested with SwaI at a unique site within UL27 adjacent to the fluorescent reporter cassette, and cotransfected with a cloned DNA segment (AD169 nucleotides 31236 to 36674; GenBank accession number X17403) that contained the UL27 mutation(s) to be studied. Recombinant viruses were recognized by the absence of a fluorescent cytopathic effect. A small fraction of fluorescent infected cells (parental strain T2394) was sometimes seen after cotransfection, and plaque purification was performed at least one step beyond the stage at which fluorescence was no longer observed, followed by sequencing of the entire UL27 sequence to confirm the presence of the desired mutation and the absence of unintended ones.
Phenotypic assay of MBV sensitivity.
SEAP yield reduction assays were performed as described previously (6, 8). Cell-free virus stock was inoculated onto 6-day-old human embryonic lung fibroblast monolayers in 24-well culture plates at a multiplicity of infection (MOI) of 0.01 to 0.02 and cultured for 6 days under a range of MBV concentrations in six wells per assay. The drug concentration required to reduce the supernatant SEAP activity by 50% (EC50), assayed by using a chemiluminescent substrate, was determined by curve fitting and was used to compare the sensitivities of strains to the sensitivity of baseline strain T2211. To allow for variations in culture conditions and to provide statistical significance for relatively small differences in drug sensitivity, at least 12 total assay replicates performed on at least four separate assay dates were used to calculate a mean EC50 and the standard error. Simultaneous assays were performed with control strain T2211 on all setup dates to obtain appropriate EC50s for the combinations of cell cultures and drug concentrations used. Strain T2890 (UL97 mutation V353A) was used as a resistant control strain that was expected to confer an
15-fold increased MBV EC50 over that for strain T2211 (7).
Comparative growth rates of mutants with UL27 mutations. Multicycle viral growth curves were assessed by serial measurement of the SEAP activity in the supernatants of 24-well cultures of human embryonic lung fibroblasts at days 1, 4, 5, 6, 7, and 8 after the inoculation of a specific strain at an MOI of 0.01 to 0.02 (6, 7). Since the effective initial inoculum has an important influence on the subsequent growth curve and the SEAP activity at 24 h postinoculation is a measure of the MOI (6), care was taken to compare the growth curves of virus stocks that were inoculated into wells of the same batch of cultured fibroblasts and that showed similar SEAP activities at 24 h. Strain T2266 was used as a severely growth-attenuated UL97-deficient control strain and was inoculated at a slightly higher MOI. The mean SEAP activity and standard deviation in four replicate wells were used to construct the growth curves.
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50% of the sequence population eight passages later, by which time a UL97 mutation had evolved. For the fourth clinical isolate (experiment M18), UL97 mutation V353A appeared first and was among the mutations described in a previous report (7). This was followed three passages later by the appearance of a UL27 mutation when the drug concentration was increased from 4 µM to 10 µM. Mutants with this UL27 mutation remained
60% of the sequence population after six additional passages. |
View this table: [in a new window] |
TABLE 1. UL27 and UL97 mutations selected under MBV
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To assess whether a genetic deficiency in UL97 expression was sufficient to elicit UL27 mutations in the absence of MBV exposure, two UL97-knockout constructs were serially propagated. Strains T2266 and T2819 both have the expected UL97-defective cytopathic appearance (4) and evolved UL27 mutations after 21 to 30 passages without added drug. Ten passages later, mutants with UL27 mutations were estimated to be 40 to 50% of the sequence population.
Genotypic analysis of UL27 and UL97 mutations. The UL27 mutations detected in the nine experiments (Table 1) consisted of five point mutations, two stop mutations, and two frameshift mutations, with no individual mutation detected in more than one experiment; and they differed from all four previously reported UL27 mutations (5, 13). Each of the stop and frameshift mutations interrupted the translation of UL27 at or before codon 362, including one mutation (codon 22 stop) that essentially knocked out the entire UL27 gene. The diversity of UL27 mutations is in contrast to the UL97 mutations selected in vitro under MBV (1, 4, 7), which so far have been shown to involve only point mutations at codons 353, 397, 409, and 411. The two new instances of the UL97 T409M mutation reported here augment its status as the most common mutation selected under MBV under the cell culture conditions used in this study (4).
Recombinant phenotyping of UL27 mutations. To confirm that the nine UL27 mutations observed affect sensitivity to MBV, they were transferred to strain T2394, creating the mutant recombinant viruses listed in Table 2. Mutations were transferred individually, except in the case of experiment M17, in which seven common baseline amino acid changes in UL27 that occurred in the clinical isolate were transferred, with (strain T2898) and without (strain T2899) the addition of the UL27 mutation W362stop. After plaque purification and sequence verification, many yield-reduction phenotyping assays were performed with each recombinant virus and gave mean MBV EC50s for the mutants with UL27 mutations that were increased two- to threefold over those for control strains T2211 and T2899 (Table 2). This level of MBV resistance is consistent with that previously reported for mutants with UL27 mutations by use of a different yield reduction assay (5). Importantly, point mutations L193F and L426F, which resulted from the propagation of genetically UL97-defective strains without MBV, conferred similar levels of MBV resistance. The low-grade resistance conferred by UL27 mutations is considerably less than that conferred by UL97 mutations (9- to >200-fold), as exemplified by strain T2890 (4, 7). The seven UL27 amino acid changes seen in the baseline clinical isolates (5; unpublished data) and represented in strain T2899 did not confer any MBV resistance.
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View this table: [in a new window] |
TABLE 2. Genotypes and MBV sensitivities of recombinant CMV strains
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FIG. 1. SEAP growth curves for selected CMV mutant strains with UL27 mutations and controls. Calibrated viral inocula (6) were used to achieve 24-h SEAP readings of 590, 640, 773, 707, 725, and 1,340 for strains T2899, T2211, T2867, T2931, T2898, and T2266, respectively. Cultures of each strain were set up in quadruplicate, and supernatants were sampled at days 1 and 4 to 8. The mean SEAP activities and standard deviations on each day were plotted on the basis of light output from a chemiluminescent substrate (6). The rank order of the growth curves is not explainable by the relative 24-h SEAP readings that reflect the MOI of input virus. wt, wild type.
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There is no understanding of the biological role of UL27 mutations that emerge under conditions of UL97 kinase deficiency. The normal function of the human CMV UL27 gene remains unknown, despite the finding that the corresponding M27 gene in murine CMV appears to be an interferon antagonist (24); a similar function was not observed for UL27 (16). UL27 encodes a 608-residue protein with a putative nuclear localization signal near residue 500 (5) but little recognizable homology to proteins of known function. The observed abundance of UL27 stop and frameshift mutations suggests that the normal nuclear localization and expression of this gene product are mildly detrimental to viral growth in the absence of the UL97 kinase. UL27 possibly acts as a negative kinase modulator that becomes less desirable when the UL97 kinase is absent and cellular kinases must play compensatory roles in viral growth. A clearer understanding of compensatory changes for the loss of the UL97 kinase requires an assessment of the relative importance of its various known and potential substrates, such as the viral UL44 polymerase accessory protein (14, 17), the UL83 tegument protein (12), the cellular retinoblastoma protein (11, 19), and possibly, the UL27 protein on the basis of the sequence context of some if its serine residues (5). A lack of phosphorylation of the UL27 protein in the absence of UL97 kinase activity could also be a factor favoring UL27 mutations. The normal functions of UL27 are not essential in cell culture, since UL27-defective mutants grow relatively well.
The significance of UL27 mutations in the clinical use of MBV also remains uncertain. No CMV isolates from subjects who have received prolonged MBV treatment in clinical trials are yet available for study. By themselves, UL27 mutations probably do not confer enough MBV resistance to preclude therapeutic use of the drug, although such mutations may facilitate the subsequent emergence of UL97 mutations, as in experiments M12 and M20. UL27 mutations also appear to add to existing single UL97 mutations, such as V353A or T409M, which already confer 15- to 80-fold increased MBV resistance (experiments M18, M27, M28, and M30), possibly further increasing the level of drug resistance toward the very high levels (a >150-fold increase in the EC50) seen with certain UL97 mutations and combinations.
This study triples the number of UL27 mutations that have been documented to confer decreased sensitivity to MBV and which need to be included in the databases used for the genotypic analysis of resistance to this anti-CMV drug, which is in advanced-stage clinical trials. Further data collection and recombinant phenotyping are needed, especially with isolates from treated subjects, to refine the genetic basis for the detection of MBV resistance.
This work was supported by NIH grant AI39938 and U.S. Department of Veterans Affairs research funds.
Published ahead of print on 3 November 2008. ![]()
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signaling and antiviral responses. J. Exp. Med. 201:1543-1553.
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