DNA nucleotide sequence heterogeneity between the Towne and AD169 strains of cytomegalovirus

Human cytomegalovirus genomics and transcriptomics through the lens of next-generation sequencing: revision and future challenges

The human cytomegalovirus (HCMV) genome was sequenced by hierarchical shotgun almost 30 years ago. Over these years, low and high passaged strains have been sequenced, improving, albeit still far from complete, the understanding of the coding potential, expression dynamics and diversity of wild-type HCMV strains. Next-generation sequencing (NGS) platforms have enabled a huge advancement, facilitating the comparison of differentially passaged strains, challenging diagnostics and research based on a single or reduced gene set genotyping. In addition, it allowed to link genetic features to different viral phenotypes as for example, correlating large genomic re-arrangements to viral attenuation or different mutations to antiviral resistance and cell tropism. NGS platforms provided the first high-resolution experiments to HCMV dynamics, allowing the study of intra-host viral population structures and the description of rare transcriptional events. Long-read sequencing has recently become available, helping to identify new genomic re-arrangements, partially accounting for the genetic variability displayed in clinical isolates, as well as, in changing the understanding of the HCMV transcriptome. Better knowledge of the transcriptome resulted in a vast number of new splicing events and alternative transcripts, although most of them still need additional validation. This review summarizes the sequencing efforts reached so far, discussing its approaches and providing a revision and new nuances on HCMV sequence variability in the sequencing field.

Cytomegalovirus blocks intestinal stroma-induced down-regulation of macrophage HIV-1 infection

Intestinal macrophages, unlike macrophages from other tissues, do not support HIV-1 infection or produce proinflammatory cytokines. In vitro studies suggest this unique, functional phenotype is a result of the exposure of newly recruited blood monocytes to intestinal stromal products. However, in AIDS-related CMV colitis, mucosal macrophages express HIV-1 and proinflammatory cytokines. Therefore, we investigated the mechanism by which CMV confers permissiveness to HIV-1 and cytokine production on intestinal macrophages. We show that intestinal stroma-conditioned media (S-CM) down-regulated monocyte-derived macrophage infection by HIV-1 (pseudotyped with YU2 envelope or vesicular stomatitis virus glycoprotein) and production of TNF-alpha, but preinfection of the cells with CMV reversed this down-regulation, enhancing HIV-1 infection, p24 production, and TNF-alpha release. The ability of CMV to reverse S-CM down-regulation of macrophage HIV-1 infection was blocked by anti-TNF-alpha antibodies and over-ridden by exogenous TNF-alpha. Immunohistochemical analysis of monocyte-derived macrophages exposed to CMV and HIV-1 (YU2 pseudotype) revealed that the cells infrequently contained CMV and HIV-1 viral proteins. In addition, analysis of colon tissue sections from HIV-1-infected patients with CMV colitis showed that some macrophage-like cells contained CMV and TNF-alpha proteins, others contained HIV-1 and TNF-alpha proteins, but cells infrequently contained CMV and HIV-1 proteins. These results indicate that CMV blocks stromal product inhibition of HIV-1 infection in macrophages, and this inhibition is mediated, at least in part, by CMV-induced TNF-alpha acting in trans to enhance HIV-1 infection.

Human cytomegalovirus TRS1 and IRS1 gene products block the double-stranded-RNA-activated host protein shutoff response induced by herpes simplex virus type 1 infection

Human cytomegalovirus (HCMV) attachment and entry stimulates the expression of cellular interferon-inducible genes, many of which target important cellular functions necessary for viral replication. Double-stranded RNA-dependent host protein kinase (PKR) is an interferon-inducible gene product that limits viral replication by inhibiting protein translation in the infected cell. It was anticipated that HCMV encodes gene products that facilitate the evasion of this PKR-mediated antiviral response. Using a deltagamma1 34.5 herpes simplex virus type 1 (HSV-1) recombinant that triggers PKR-mediated protein synthesis shutoff, experiments identified an HCMV gene product expressed in the initial hours of infection that allows continued protein synthesis in the infected cell. Recombinant HSV-1 viruses expressing either the HCMV TRS1 or IRS1 protein demonstrate that either of these HCMV gene products allows the deltagamma1 34.5 recombinant viruses to evade PKR-mediated protein shutoff and maintain late viral protein synthesis.

A review of genetic differences between limited and extensively passaged human cytomegalovirus strains

The complete genetic content of human cytomegalovirus (HCMV) has been difficult to determine, since most strains studied in the laboratory have been extensively passaged in human fibroblast cultures which can change the genetic content as well as the biological properties of the virus. Approximately 13 kb of novel DNA sequences located near the right edge of the unique long (UL) component of the genome has been discovered in Toledo, clinical isolates and certain stocks of Towne. This region of novel sequence, designated the UL/b' region, encodes several interesting proteins including vCXC-1, a potent IL-8 homologue, and UL144, a member of the TNF receptor family. This region is missing from the prototypic laboratory variants of Towne and AD169. In contrast to Toledo and other low passage isolates which have relatively small repeats bracketing the UL component, the Towne and AD169 laboratory variants contain large (>10 kb) b/b' repeats. The large size of these repeats in AD169 and Towne appear to have arisen as compensation for the loss of sequences from the UL/b' region that existed in less passaged variants of these strains. Consequently, many of the haploid genes at the left edge of the prototypic wild-type (wt) UL component are diploid in AD169 and Towne. We hypothesise that this plasticity of the genome at the right edge of the UL component results from extensive passage and adaptation to replication in fibroblasts in vitro. Further work will be required to understand the complete genetic content of wt HCMV.

Quantitative PCR determination of human cytomegalovirus in blood cells

We evaluated a rapid and sensitive method to determine human cytomegalovirus (CMV) DNA levels in blood cells using a quantitative polymerase chain reaction (PCR) technique. This method is based on real-time detection of PCR using a dual fluorescence-labeled probe and a sequence detector. Ten copies of CMV DNA were detected, when 1 microg of DNA from blood samples was used with this method, and a good correlation was obtained between increased concentrations of copy numbers calculated and measured copy numbers of CMV DNA (r = 0.999). Forty normal subjects exhibited no copies of CMV DNA. On the other hand, a 6-month-old girl tested positive for increased levels 4 weeks after liver transplant. This method is simple, accurate, and sensitive for the quantitative detection of CMV DNA in vivo, indicating possible applications for the diagnosis and monitoring of CMV infection.

Quantitative evaluation of cytomegalovirus DNA in infantile hepatitis

We used a PCR method to develop a diagnostic assay for the detection of cytomegalovirus (CMV) DNA in infantile hepatitis, which has been suggested to be associated with CMV infection. CMV DNA was detected in 25 (58.1%) of 43 patients with elevated serum alanine aminotransferase (ALT) levels but no jaundice, and no hepatitis B or C as assessed by conventional PCR. None of the samples from 97 healthy infants tested positive for CMV DNA. We assayed CMV DNA quantitatively in blood using a real-time PCR system that allowed reproducible detection of at least 10 copies of CMV DNA. When 1 microg of DNA from each blood sample was used in this system, a good correlation was obtained between the calculated and measured copy numbers of CMV DNA. This system detected CMV DNA in 29 patients (67.4%) with liver dysfunction. Serial studies in patients with liver dysfunction revealed that CMV DNA copy number decreased, ultimately to below 10, as the ALT levels normalized. In contrast, no CMV DNA copies were detectable by the real-time system in any of the samples from control subjects. These results highlight the usefulness of detecting CMV DNA in the diagnosis of infantile hepatitis and indicate that the real-time quantitative PCR assay may be a valuable tool for monitoring CMV-associated infantile hepatitis.

Failure in detection of Epstein-Barr virus and cytomegalovirus in specimen obtained by fine needle aspiration biopsy of thyroid in patients with subacute thyroiditis

To study the possible role of viral infection in the etiology of subacute thyroiditis (SAT), we measured serum virus-specific antibodies to measles, rubella, mumps, type I herpes, chicken pox, human parvovirus B19 and cytomegalovirus (CMV) in 10 patients with SAT during the course of illness. In spite of the presence of IgG to each virus in more than 70% of patients, no significant changes in the IgG titers were observed except those to measles, rubella, chicken pox or CMV in only 10% of patients, respectively. Then we examined the presence of virus DNA in specimens of 9 patients with SAT obtained by fine-needle aspiration biopsy (FNAB) of the thyroid. DNA was amplified to detect that of Epstein-Barr virus and CMV by polymerase chain reaction. However, none of them were detected in all the specimens. Whereas previous studies suggest the involvement of viral infection in the pathogenesis of SAT, we failed to demonstrate significant changes in serum antiviral antibody titers or to detect viral DNA in the specimens obtained by FNAB of the thyroid. Thus further studies are clearly required to establish the definite role of viral infection in the pathogenesis of SAT.

Evaluation by polymerase chain reaction of cytomegalovirus reactivation in intensive care patients under mechanical ventilation

OBJECTIVE

The study was undertaken to determine if critically ill patients under mechanical ventilation could reactivate latent cytomegalovirus (CMV) in either lung or blood.

DESIGN

Prospective study in critically ill patients was performed in a multidisciplinary intensive care unit in a university hospital.

PATIENTS

23 non-immunocompromised, mechanically ventilated patients who were anti-CMV immunoglobulin G-positive. Ten immunocompromised patients with active CMV infection and 16 asymptomatic CMV seropositive non-immunocompromised patients constituted the positive and negative control groups.

MEASUREMENTS AND RESULTS

The presence of CMV in blood and bronchoalveolar lavage (BAL) was evaluated by both viral cultures and polymerase chain reaction (PCR). Thirty-seven blood and 22 BAL samples were investigated. Sequential samples were evaluated in 8 patients. For PCR, a 290 bp fragment in the first exon of the immediate early 1 gene was amplified. In order to exclude inhibitors of PCR amplification, a 268 bp fragment of the beta-globin gene was concurrently amplified in all samples. Viral cultures of blood and BAL were negative in all 23 non-immunocompromised, mechanically ventilated patients. Moreover, no CMV DNA could be amplified in blood BAL samples, whereas a beta-globin amplification was observed in all samples.

CONCLUSION

In a series of 23 critically ill patients under mechanical ventilation who were seropositive for CMV, no reactivation of CMV in blood or lung was demonstrated.

Strain-dependent differences in the human cytomegalovirus replication origin

The nucleotide sequence of the human cytomegalovirus replication origin of strain Towne (an AatII-SacI fragment corresponding to nt 90372-94637 of strain AD169) was determined and compared with AD169. Two differences were found in the nucleotide sequence level. One was the alteration of structural organization (a major difference): a 189-bp region of AD169 (nt 93337-93525) was directly repeated three times in Towne. The other was a change in the nucleotide residue level including substitution, insertion, or deletion (a minor difference). The divergent residues were predominantly localized within the nt 92591-92855 region of AD169. A replication assay revealed that replication ability remained after deletion of the 189-bp repeat but disappeared after either a 1.5-kb deletion from the AatII end or a 0.9-kb deletion from the SacI end. The 1.5- and 0.9-kb regions were relatively conserved. These results indicate that at least two regions essential for replication ability lie outside of both the relatively variable region and the 189-bp repeat and suggest that these essential regions support replication even with a spatial separation of either one (AD169) or three repeats (Towne) of the 189-bp region.

Cell types involved in replication and distribution of human cytomegalovirus

As the number of patients suffering from severe HCMV infections has steadily increased, there is a growing need to understand the molecular mechanisms by which the virus causes disease. The factors that control infection at one time and the events leading to virus multiplication at another time are only beginning to be understood. The interaction of HCMV with different host cells is one key for elucidating these processes. Through modern techniques, much has been learned about the biology of HCMV infections in culture systems. In addition to endothelial cells, epithelial cells, and smooth muscle cells, fibroblasts are one cell population preferentially infected in solid tissues in vivo. From these sites of multiplication, the virus may be carried by peripheral monocytes and circulating endothelial cells to reach distant sites of the body. This would explain the multiorgan involvement in acute HCMV infection and the modes of viral transmission. From what has been learned mainly from human fibroblast culture systems, future studies will focus on how HCMV regulates the expression of its putative 200 genes in different host cells at different stages of cell differentiation and activation to result in viral latency and pathogenesis.

Human cytomegalovirus clinical isolates carry at least 19 genes not found in laboratory strains

Nucleotide sequence comparisons were performed on a highly heterogeneous region of three human cytomegalovirus strains, Toledo, Towne, and AD169. The low-passage, virulent Toledo genome contained a DNA segment of approximately 13 kbp that was not found in the Towne genome and a segment of approximately 15 kbp that was not found in the AD169 genome. The Towne strain contained approximately 4.7 kbp of DNA that was absent from the AD169 genome, and only about half of this segment was present, arranged in an inverted orientation, in the Toledo genome. These additional sequences were located at the unique long (UL)/b' (IRL) boundary within the L component of the viral genome. A region representing nucleotides 175082 to 178221 of the AD169 genome was conserved in all three strains; however, substantial reduction in the size of the adjacent b' sequence was found. The additional DNA segment within the Toledo genome contained 19 open reading frames not present in the AD169 genome. The additional DNA segment within the Towne genome contained four new open reading frames, only one of which shared homology with the Toledo genome. This comparison was extended to five additional clinical isolates, and the additional Toledo sequence was conserved in all. These findings reveal a dramatic level of genome sequence complexity that may explain the differences that these strains exhibit in virulence and tissue tropism. Although the additional sequences have not altered the predicted size of the viral genome (230 to 235 kbp), a total of 22 new open reading frames (denoted UL133 to UL154), many of which have sequence characteristics of glycoproteins, are now defined as cytomegalovirus specific. Our work suggests that wild-type virus carries more than 220 genes, some of which are lost by large-scale deletion and rearrangement of the UL/b' region during laboratory passage.

Rapid epidemiologic analysis of cytomegalovirus by using polymerase chain reaction amplification of the L-S junction region

A technique based on polymerase chain reaction (PCR) amplification was developed to facilitate the study of the epidemiology of cytomegalovirus (CMV). Consensus oligonucleotide primers from repetitive DNA sequences were designed to amplify interspersed repetitive sequences in an area of heterogeneity within the L-S junction region of the CMV genome, and PCR products were detected by gel electrophoresis. Purified CMV DNAs from 25 CMV isolates, 13 from members of five families in which person-to-person transmission was documented, 9 random clinical isolates of CMV, and 3 laboratory reference strains of CMV (Towne, Davis, and AD169), were analyzed. The gel electrophoretic patterns of DNA bands, or PCR profiles, produced by amplification with the L-S primers were unique for epidemiologically unrelated strains and laboratory reference strains, yet similar patterns were observed for epidemiologically related strains isolated from members of the same family. This method of rapid fingerprinting of CMV DNA within the hypervariable L-S junction region by PCR to produce strain-specific, variably sized PCR products should simplify the molecular epidemiologic analysis of CMV.

Primer-mediated enzymatic amplification of cytomegalovirus (CMV) DNA. Application to the early diagnosis of CMV infection in marrow transplant recipients

A nucleic acid amplification procedure, the polymerase chain reaction (PCR), has been used to establish a diagnostic assay for the identification of cytomegalovirus (CMV) immediate-early sequences in clinical specimens. Preliminary testing against virus-infected cell cultures indicated that the PCR assay was highly CMV-specific, recognizing both wild-type and laboratory strains of CMV. There was no cross-reactivity with human DNA or with DNA from other herpes viruses. The sensitivity of the assay, using cloned CMV AD169 Eco RI fragment-J as template, was 1 viral genome per 40,000 cells. In a prospective study of CMV infection in bone marrow transplant recipients, the PCR assay correctly identified four patients with confirmed CMV infection. In three of these patients who were followed longitudinally, correlation of DNA reactivity with CMV culture and CMV antibody status over time indicated that DNA was the most sensitive marker for the diagnosis of CMV infection.

Mapping and expression of a human cytomegalovirus major viral protein

We constructed a DNA fragment map of low-passage Towne strain cytomegalovirus by analyzing cross-blot hybridization and hybridizations of isolated recombinant clones. The abundant late transcripts were located on this map by hybridization of labeled total RNA of virus-infected cells to blotted DNA fragments. The most abundant late transcript, carried by the 11.7-kilobase EcoRI fragment (EcoRI-G), was precisely mapped. The EcoRI fragment was fragmented and subcloned in a plasmid carrying simian virus 40 sequences (pSV-OH, constructed by Chi-Bom Chae, Department of Biochemistry, University of North Carolina, Chapel Hill). One resulting recombinant plasmid, pHD713SV2, was transferred to simian virus 40-transformed monkey kidney cells (COS-1) by DNA transfection. Synthesis of a cytomegalovirus-specific 67-kilodalton protein was detected in these cells by reaction of blotted proteins with virus-specific monoclonal antibody. The 67-kilodalton protein is a major phosphorylated protein found in virions; it is not glycosylated. The location of the gene for this 67-kilodalton protein is therefore assigned to the center of the L-unique region of human cytomegalovirus, at 0.37 to 0.39 map units.

Cytomegalovirus hepatitis in normal and immune compromised hosts

Liver biopsies of six previously normal hosts (Group I, NH), with recent or acute CMV infection, and autopsy liver samples of four immunocompromised hosts (Group II, ICH) with overwhelming CMV infection have been studied in an occasional survey. In both groups, portal tract involvement, bile duct inflammation, liver cell degeneration and parenchymal granulomas were present. In Group I, a randomly distributed hepatitis with predominant involvement of the periportal areas was present, including sinusoidal arrays of lymphocytes and lymphohistiocytic aggregates. In contrast, in Group II liver cell damage was more extensive and the inflammatory infiltration only scarce. Intracellular viral inclusion bodies were found only in Group II, both in liver cells and in bile duct epithelium. Morphologically, the presence of viral inclusion bodies correlated well with the immunohistologic demonstration of CMV specific "late" (CMV-LA) or structural antigens. In addition, CMV-specific "early" (CMV-EA) or non-structural antigens were present in liver cell nuclei of 2/6 NH and 2/4 ICH. The possible relations between the inflammation and the lack of structural antigenic viral expression are discussed. It is concluded that ICH with CMV infection have a prominent cytopathogenic effect and widespread lytic viral infection in the liver in the absence of adequate immunologic reactivity, whereas the opposite is found in NH.

A variant of human cytomegalovirus derived from a persistently infected culture

Infection of cells derived from an osteogenic sarcoma (HOS) with human cytomegalovirus (HCMV) resulted in persistent infection. It appears that persistent infection is due to a balance between release of virus and the growth of uninfected cells. Viruses derived from the persistently infected cultures were not temperature sensitive nor were they defective interfering particles. However, hybridization experiments using the Q-labeled probe from the XbaI Q fragment indicated that one copy of the repeat sequences contained in fragments Q and O of CMV, Towne DNA have been completely deleted from the virus DNA derived from the persistent culture. Thus the mechanism of persistent infection is probably due in part to a variant of CMV present in the cultures.

Structural organization of human herpesvirus DNA molecules

The herpesviruses are among the largest and most complex of all DNA viruses, and their genomes display an astonishing diversity in size, structure, and organization. In 1974, the features of large inverted repeats and structural isomerization were first discovered, and these proved to be characteristic properties of many herpesvirus genomes. Since then, research using the powerful techniques of modern molecular biology has revealed a great deal of comparative structural information about the arrangement of repetitive sequences and the location, structure, and primary nucleotide sequences of the genes for several easily assayed or abundantly expressed gene products. Extensive restriction enzyme cleavage maps and complete sets of cloned DNA fragments have been constructed for each of the five human herpesviruses, HSV-1, HSV-2, CMV, EBV, and VZV, and the entire 175,000-bp nucleotide sequence of EBV DNA has been determined. Based on these maps and reagents, the procedures of "DNA fingerprinting" and "dot hybridization" are proving useful at a clinical level for characterization of isolates and studying herpesvirus epidemiology. Strain differences, localized heterogeneity, tandem-repeat-defective genomes, and sites of cell-virus DNA homology have been described in some detail. The attention of basic researchers is now turning to equating structure with function, and rapid progress is expected in studies aimed at a better understanding of the mechanisms of viral DNA replication, maintenance of the latent state, reactivation, transformation, packaging, and regulation of the lytic cycle, etc using cloned functionally active DNA fragments, isolated intact genes and promoters, and DNA transfection and in vitro expression systems.

Structure of the transforming region of human cytomegalovirus AD169

The minimum size fragment of human cytomegalovirus AD169 required to initiate transformation was determined by transfection of primary rat embryo cells with deletion fragments constructed by digestion of a cloned fragment containing the transforming region (pCM4000) with exonuclease III and S1 nuclease. The results indicate that the left-hand boundary of the minimum size sequence for transformation must reside between 490 and 318 bases from the HindIII site of pCM4000. The right-hand boundary was defined by the EcoRI site which is 20 bases from the HindIII site. The nucleotide sequence of the transforming fragment of human cytomegalovirus was determined by the chemical degradation technique of Maxam and Gilbert and with the dideoxynucleoside triphosphate chain termination method. The sequence of pCM4000 comprises 2,848 base pairs and has an A X T composition of 59.5%. Reading frame analysis of the sequence indicated the longest open reading frame was 118 amino acids in length. Northern blot analysis of polyadenylated and non-polyadenylated RNA extracted from cells at immediate early and late times after infection with human cytomegalovirus indicate that one 5.0-kilobase RNA species hybridized to pCM4000 (Jahn et al., J. Virol, in press). The direction of transcription was determined by hybridization of this transcript with M13 single-stranded probes, and S1 analysis of this RNA did not detect introns.

Genome structure and virion polypeptides of the primate herpesviruses Herpesvirus aotus types 1 and 3: comparison with human cytomegalovirus

Two serologically distinguishable primate herpesviruses, Herpesvirus aotus type 1 and type 3, were examined with regard to their genomes and structural polypeptides. The duplex DNA genomes of these two viruses were found to be essentially identical in molecular weight (Mr approximately equal to 145 X 10(6)) and guanine plus cytosine composition (55%). Both contained unique and inverted repeat nucleotide sequences of the same size and arrangement, which, as judged by DNA-DNA hybridization and restriction enzyme analyses, were at least 95% homologous. In addition, no differences were observed in electrophoretic profiles of virion polypeptides. Because of their great similarity with respect to these criteria, the two viruses ought to be considered independent isolates (or strains) of a single virus, which should be designated H. aotus type 1. The elevated molecular weight and presence of two sets of inverted repeat sequences closely resemble the structure of the human cytomegalovirus genome. However, no sequence homology (less than 5%) nor similarity in virion polypeptides was detected between H. aotus type 1 and human cytomegalovirus.

Transformation of NIH 3T3 cells with cloned fragments of human cytomegalovirus strain AD169

NIH 3T3 cells were transfected with restriction endonuclease and cloned human cytomegalovirus DNA fragments to identify the transforming region(s). Cleavage of human cytomegalovirus strain AD169 DNA with XbaI and HindIII left a transforming region intact whereas EcoRI inactivated this function. Transfection of cells with cosmids containing human cytomegalovirus DNA spanning the entire genome resulted in transformation by one cosmid, pCM1058, with the AD169 HindIII DNA fragments E, R, T, and a'. Cells were selected for their growth in 1.2% methylcellulose. The clones isolated had a significant replating efficiency and were oncogenic in BALB/c nu/nu mice. Transfection of cosmids and plasmids containing subsets of the viral sequences in pCM1058 identified a common region possessed by all of the transforming recombinant molecules. This region was in the HindIII E fragment with the left boundary defined by the EcoRI d-R junction and the right boundary defined by the HindIII E-T junction. Further mapping and transfection experiments determined that the transforming region was contained without a 2.9-kilobase fragment between map units 0.123 and 0.14 on the prototype molecule of the AD169 strain.

Cloning of the human cytomegalovirus genome as endonuclease XbaI fragments

Restriction enzyme XbaI DNA fragments that represent 99% of the sequences from the long and short unique as well as the repeat sequences of the human cytomegalovirus (CMV) genome have been cloned into bacterial plasmid pACYC184. The viral DNA sequences associated with the recombinant plasmids were analyzed by restriction mapping and by hybridization to fragments of authentic viral DNA. The relationship of the cloned viral DNA fragments to the XbaI physical map of the viral genome is demonstrated. Even though large recombinant plasmids ranging from approx. 39 to 1.8 kb were isolated, most if not all of the viral DNA fragments were stable during propagation in Escherichia coli HB101.