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

PCR-RFLP analysis of cytomegalovirus infections associated with bone marrow transplantation in Japanese children

In order to investigate the longitudinal molecular epidemiology of cytomegalovirus (CMV) infections associated with bone marrow transplantation (BMT) in Japanese children, we analyzed 36 CMV strains from 11 cases. Three regions (DNA polymerase, glycoprotein H, and immediate-early regions) of CMV DNA were amplified by polymerase chain reaction (PCR), and amplified products were each digested with two restriction enzymes, followed by electrophoresis. These restriction fragment length polymorphism (RFLP) analyses allowed the differentiation of 36 strains into 13 genotypes. Each patient excreted his or her own CMV with distinct genotype over the study period of up to one year. CMVs of two different genotypes were recovered during a one-month study from one recipient, who received a peripheral blood stem cell transplantation. Although the majority of patients and donors were CMV-seropositive before BMT, multiple CMV infections might not be common and the reactivation of latently infected CMV might be prominent in Japanese children receiving transplants.

Cytomegalovirus (CMV) strain differences between the eye and blood in AIDS patients with CMV retinitis

OBJECTIVE

To investigate possible differences in cytomegalovirus (CMV) strain distribution between the eye and blood in AIDS patients with CMV retinitis.

METHODS

CMV DNA sequences from aqueous humour and peripheral blood leukocytes (PBL), obtained from 13 AIDS patients with CMV retinitis, were compared. DNA was isolated and the CMV IE-1 sequence (part of the immediate early-1 gene) and the a-sequence (located in the a-region) were amplified by polymerase chain reaction (PCR). The PCR products of the a-sequence were analysed by Southern blotting for amplified fragment-length polymorphisms. The level of divergence between the a-sequences of aqueous humour- and PBL-derived CMV was studied in two patients by cloning these sequences followed by sequence analysis.

RESULTS

CMV DNA could be detected in all aqueous humour samples and in 10 out of 13 paired blood samples. In the 10 patients, with CMV DNA detectable in both aqueous humour and PBL, seven cases showed differences between the amplified products of both compartments. Sequence analysis in two patients revealed that the aqueous humour and PBL of the same patient can harbour both identical, similar and highly divergent CMV a-sequences.

CONCLUSION

These results indicate that despite the haematogenous spread of CMV, the eye, being a relatively shielded organ, may contain CMV strains different from those found in the blood.

Structure of the rat cytomegalovirus genome termini

The lytic replication cycle of herpesviruses can be divided into the following three steps: (i) circularization, in which, after infection, the termini of the linear double-stranded viral genome are fused; (ii) replication, in which the circular DNA serves as template for DNA replication, which generates large DNA concatemers; and (iii) maturation, in which the concatemeric viral DNA is processed into unit-length genomes, which are packaged into capsids. Sequences at the termini of the linear virion DNA are thought to play a key role in both genome circularization and maturation. To investigate the mechanism of these processes in the replication of rat cytomegalovirus (RCMV), we cloned, sequenced, and characterized the genomic termini of this betaherpesvirus. Both RCMV genomic termini were found to contain a single copy of a direct terminal repeat (TR). The TR sequence is 504 bp in length, has a high GC content (76%), and is not repeated at internal sites within the RCMV genome. The TR comprises several small internal direct repeats as well as two sequences which are homologous to herpesvirus pac-1 and pac-2 sites, respectively. The organization of the RCMV TR is unique among cytomegaloviruses with respect to the position of the pac sequences: pac-1 is located near the left end of the TR, whereas pac-2 is present near the right end. Both RCMV DNA termini carry an extension of a single nucleotide at the 3' end. Since these nucleotides are complementary, circularization of the viral genome is likely to occur via a simple ligation reaction.

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.

Rapid molecular epidemiology of human immunodeficiency virus transmission

Close sequence homology between strains of HIV-1 have been used to corroborate cases of epidemiologically identified transmission. As an alternative to extensive DNA sequence analysis, genetic relateness between pairs of HIV quasispecies was estimated using the reduced electrophoretic mobilities of HIV-1 envelope DNA heteroduplexes through polyacrylamide gels. All six infections acquired in a dental practice in the late 1980s and four of six infections acquired through blood product transfusions and sexual contact in 1984-1985 could be rapidly identified. A rising level of genetic diversity within HIV-1 subtype B facilitated the detection of later transmission events. Transmission linkages could be detected up to 4 years following infection. The simple and rapid technique of DNA heteroduplex tracking can therefore assist epidemiological investigations of HIV transmission and potentially of other genetically variable infectious agents.

A polymorphic region of the human cytomegalovirus genome encoding putative glycoproteins

A region of the human cytomegalovirus genome (corresponding to nt 17973-19945 of strain AD169) was analyzed by restriction fragment length polymorphism. Rsa I digestion of the region showed 20 distinct patterns in agarose gel electrophoresis.

Analysis of acquired human cytomegalovirus infections by polymerase chain reaction

We used the polymerase chain reaction and primers corresponding to three regions of the human cytomegalovirus (HCMV) genome to study HCMVs isolated from 16 children attending a single day-care center and the father of two children in the same center. When we analyzed isolates with primers for the pp65 and major immediate-early genes, we observed nearly uniform amplification yielding products of predicted sizes. By contrast, primers for the a sequence demonstrated variability among HCMV strains, supporting the use of these primers as an epidemiologic tool. Analysis of a-sequence products from two isolates demonstrated 50 to 70% nucleotide homology with the a sequence of HCMV Towne strain DNA. We observed 95% nucleotide homology for the two a-sequence products derived from the father-child pair. Analysis of day-care center isolates indicated that two children excreted two distinct HCMV strains during the study interval.

Application of polymerase chain reaction to fingerprinting Aspergillus fumigatus by random amplification of polymorphic DNA

A new method for fingerprinting Aspergillus fumigatus by random amplification of polymorphic DNA (RAPD) by using single primers with arbitrary sequences is described. Five primers were examined with 19 isolates from six patients with aspergilloma as well as with A. fumigatus NCPF 2109. Two of the primers (GCT GGT GG and GCG CAC GG, 5' to 3') gave adequate discrimination between isolates, generating five and six types, respectively. Combination of the results obtained with each of these two primers generated 12 types. This compares very favorably with immunoblot fingerprinting and XbaI-generated restriction fragment length polymorphisms on the same isolates. Typeability and reproducibility were good with RAPD, and RAPD was less labor-intensive than immunoblot fingerprinting. RAPD typing results suggested that aspergillomas sometimes contain isolates of more than one type.