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1 From the Department of Ophthalmology, Graduate School of Medicine, The University of Tokyo, Japan; 2 Miyata Eye Hospital, Miyakonojo Miyazaki, Japan; 3 Kawasaki City Public Health Laboratory, Kawasaki, Japan; and the 4 Department of Developmental Medical Sciences, Graduate School of Medicine, The University of Tokyo, Japan.
| Abstract |
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METHODS. A new PCR method using primer pairs of AF2/AR2, which are specific for the fiber genes, were developed to amplify 1150-bp products from nine oculopathogenic prototypes of subgenus D adenoviruses. Amplicons were cleaved with three restriction enzymes: DdeI, HinfI, and RsaI. Clinical specimens of 102 conjunctival scrapings were also evaluated by this PCR method. Restriction patterns of prototypes were used for the typing of clinical samples. Detection limit was determined by the PCR amplification of a known amount of purified adenovirus serotype 8 DNA.
RESULTS. A novel PCR method based on the fiber genes allowed the amplification of nine oculopathogenic serotypes of subgenus D (Ad8, Ad9, Ad15, Ad17, Ad19, Ad22, Ad28, Ad37, and Ad39). As little as 38.4 fg of adenovirus type 8 could be detected by this method. Positive results were obtained from 48 of 102 samples (47%) by both hexon- and fiber-based PCR, whereas only 29 of 102 (28.4%) yielded positive results by culture isolation/neutralization test (NT). All positive specimens (29 samples) of culture isolation and PCR-RFLP methods showed positive results by our new fiber-based PCR method, and no positive products were detected from other subgenus of adenovirus or nonadenoviral DNA.
CONCLUSIONS. A newly developed fiber-based PCR-REA method for the detection and typing of adenoviruses is faster than any former PCR methods. This all-in-1-day detection and typing method will be quite useful to the rapid diagnosis of subgenus D adenovirus infection.
| Introduction |
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Human adenovirus consists of a large family of 51 described serotypes, classified into 6 subgenera (AF) on the basis of biochemical, immunologic, and morphologic criteria.4 5 Thirty-two serotypes constitute subgenus D, and several of these have been significantly associated with ocular infections.6 For example, serotypes 8, 19, and 37 are the most common causative agents of EKC. Occasionally, Ad9, Ad15, and Ad22 have also been reported as a cause.7 On the other hand, Ad9, Ad15, Ad17, and Ad28 are known to induce relatively mild follicular conjunctivitis.4 Ad3, Ad4, and Ad7, which belong to other subgenus, also cause conjunctivitis and pharyngoconjunctival fever.4 Even though an antivirals medicine, Cidofovir (Baush and Lomb Pharmaceuticals, Inc., Tampa, FL), is in a preclinical trial and has been found to be a promising medicine against subgenus C adenoviruses (Ad1, Ad2, and Ad5), it is not clinically available at this moment.8 9 Clinical diagnosis are usually made based on the patients history, clinical examination, and if needed, a laboratory test detecting the viral antigen in an ocular swab sample or by culture and neutralization test (NT).10
For detection of adenovirus directly from conjunctival swab, a new test kit (immunochromatography; SAS Adenotest; SA Scientific Inc., San Antonio, TX) is currently available in developed countries. Yet, the sensitivity of this test is approximately 54.7%, and a negative test result does not always rule out the possibility of adenoviral infection.11 As long as 2 to 4 weeks are needed for the identification by culture isolation NT. Recent development of PCR-based rapid serotype identification methods such as hexon-based PCR restriction fragment length polymorphism (RFLP), type-specific PCR, and PCR with direct sequencing of products offer a sensitive and specific laboratory test similar to culture isolation and NT. They are only good for the detection of common EKC strains (Ad8, Ad19, and Ad37) from subgenus D, and 2 to 3 days are required for the whole procedure. Therefore, a more simple, more rapid, and more sensitive method was in demand to identify these oculopathogenic serotypes of subgenus D.
In this study, we developed a new PCR method based on the fiber gene for rapid, accurate detection and typing of the subgenus D adenoviruses directly from conjunctival scrapings.
| Materials and Methods |
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For the clinical study, ocular samples were collected in an eye clinic in South Kyushu, Japan, between March 1998 and February 2000 from patients diagnosed with EKC or acute conjunctivitis. Specimens were scraped from the lower palpebral conjunctiva and collected, respectively, in 1 ml of phosphate-buffered saline for PCR and in 1 ml of viral transport medium (1% fetal calf serum in Eagles MEM, 60 mg/l penicillin G, and 40 mg/l gentamicin) for culture isolation. These samples were preserved at -30°C until the analyses. This study was approved by the Ethical Committee of the University of Tokyo, School of Medicine. The research plan followed the tenets of the Declaration of Helsinki.
Preparation of Viral DNA
Prototypes.
Viral DNA was prepared by phenol/chloroform extraction and ethanol
precipitation. Briefly, 200 µl of culture fluid and the same volume
of lysis buffer [10 mM Tris-HCl (pH 7.6) 5 mM EDTA, 1% sodium dodecyl
sulfate (SDS), and 200 µg/ml Proteinase K] were mixed in a
microcentrifugation tube and incubated for 1 hour at 37°C. Then 20
µg of RNase A (Boehringer-Mannheim, Mannheim, Germany) was added to
the tube and incubated at 37°C for another hour. Then, the
same volume of phenol-chloroform (phenol, 100 µl; chloroform, 100
µl) was added to the mixture for 10 minutes and centrifuged at
8000g for 10 minutes. This extraction process was repeated
again. Finally, the supernatant containing genomic DNA was precipitated
in 500 µl of 100% ethanol. After drying, the pellet was dissolved in
30 µl of TE buffer.
Clinical Samples.
DNA from clinical samples was prepared for PCR by two protocols.
In the first protocol, DNA was prepared by guanidine thiocyanate glass powder methods as described previously.12 Briefly, 200 µl of clinical sample and the same volume of 1,2,2-trichloro-1,2,2-trifluoroethane were mixed in a microcentrifugation tube. After vortexing for 20 minutes, the mixture was centrifuged at 5500g for 10 minutes. Two hundred microliters of 6 M guanidine thiocyanate was added to 200 µl of the supernatant and vortexed for 5 minutes. Glass powder (4.8 µl; Asahi Glass Co Ltd., Tokyo, Japan) was added to the tube and mixed well for 20 minutes After centrifugation at 220g for 2 minutes, the supernatant was removed, and the pellet was washed three times with 800 µl washing buffer (Asahi Glass Co., Ltd.). After the last wash, 400 µl of 100% ethanol was added, and the pellet was dissolved and then further centrifuged at 8000g for 5 minutes. The supernatant was removed, and the pellet was dried in a vacuum centrifuge at 55°C to remove all the residual 100% ethanol. Then 24 µl distilled water was added to dissolve the pellet. The sample was heated in a heating block at 65°C for 10 minutes and then centrifuged at 8000g for 10 minutes. Supernatant that contained genomic DNA was stored at -30°C until use.
In the second protocol, 10 µl of clinical sample collected in phosphate-buffered saline was heated directly at 97°C for 15 minutes in a thermal cycler before adding PCR reagent.
Detection of Adenovirus
Primers.
Primers were selected for PCR on the basis of the alignment of the
fiber gene sequences (GenBank accession number for fiber gene X74660
[Ad8], U69130 [Ad19], U69132 [Ad37], X74659 [Ad9], and X72934
[Ad15]) from human adenovirus serotypes Ad8, Ad19, Ad37 Ad9, and
Ad15, respectively. The pair of primers AF2/AR2 was used to amplify
approximately 1150 bp in the general PCR. The primer positions
corresponded to 66 to 83 bp (AF2) and 1188 to 1205 bp (AR2) of Ad8
fiber gene (Table 1)
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Specificity of Detection.
Specificity of the test was determined using other subgenus of
adenoviruses and nonadenoviral DNA from other agents of conjunctivitis.
These agents included herpes simplex type I and type II, enterovirus,
and Chlamydia trachomatis.
Limits of Detection.
A known amount of Ad8 purified DNA was amplified after serial dilution
to obtain a theoretical range of virus particle
1010 to 101 per reaction
mixture; 0.384 fg of Ad DNA corresponds to a single copy of linear
double-stranded DNA that is approximately 35,000 bp. After PCR
amplification, 5 µl of product was electrophoresed in a 1.5% agarose
gel and stained with ethidium bromide.
Culture Isolation.
All clinical samples were seeded to a confluent monolayer of Hep2 or
CaCo2 cells that had grown in a 24-well plate and examined for 10 days
before the next passage. Samples were passaged four times in a 24-well
plate. If there was no cytopathic effect (CPE) after four passages,
samples were considered to be cell culture negative.
Typing of Adenovirus
Restriction Enzyme Analysis (REA).
REAs were performed using positive PCR products with three restriction
enzymes: DdeI, HinfI, and RsaI
(Boehringer-Mannheim). Briefly, 5 µl of PCR-amplified DNA product was
incubated with 10 units of restriction endonucleases in 15 µl of
reaction mixture and at a designated temperature (recommended by
manufacturer for each restriction endonuclease) for 3 hours. After
digestion, 10 µl of the reaction mixture was mixed with 3 µl of
loading buffer (60% glycerol, 0.25% bromphenol blue, and 0.25%
xylene cyanol) and then run in 1.5% horizontal agarose gel at 100 V
for 50 minutes in a 50 mM Tris-borate-EDTA buffer (pH 8.0). After
electrophoresis, the gel was stained with ethidium bromide. The bands
were visualized under UV light.
Hexon-based PCR-RFLP.
For hexon-based, PCR-RFLP after nested PCR, 956-bp positive PCR
products were digested with three restriction enzymes:
HaeIII, HinfI, and EcoT14I, and
restriction patterns were compared with a prototype pattern for typing.
Neutralization Test.
Cell culturepositive samples were typed by using antiadenoviral
serum.
| Results |
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Specificity and Limits of Detection
The primer pair AF2/AR2 amplified approximately 1150-bp products
from nine prototypes of subgenus D (Ad8, Ad9, Ad15, Ad17, Ad19, Ad22,
Ad28, Ad37, and Ad39 in fiber gene-based PCR; Fig. 1A
). The specificity of the PCR was tested against DNA from other subgenus
of adenovirus and nonadenoviral DNA (see Materials and Methods). No
amplified products were identified, indicating a high specificity of
the test.
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Ad Detection
Our PCR gave a positive result in 48 of 102 clinical samples
(47%; Fig. 1C
), whereas only 29 of 102 (28.4%) were identified
positive by culture isolation and NT. Hexon-based PCR produced the same
results as fiber gene-based PCR.
Ad Typing by REA
Nine prototypes were digested with three restriction enzymes
(DdeI, HinfI, and RsaI), and all
prototypes except Ad22 for RsaI were completely digested
(Fig. 2A)
. Polymorphic restriction patterns of three enzymes could be clearly
differentiated the nine prototypes. DdeI discriminated well
all the serotypes except Ad8 and Ad9. In these two serotypes, the upper
and lower restriction fragments are very close to each other, making it
difficult to tell the position. In case of Ad8, the upper and lower
restriction fragments are 584 and 551 bp, respectively. In case of Ad9,
the fragments are 584 and 557 bp, respectively. HinfI
discriminate all the serotypes except Ad19 and Ad37. Both have the same
restriction pattern for HinfI. Ad19 and Ad37 have same
restriction sites for RsaI as well. The upper two fragments
are 492 and 477 bp, respectively, and they appear to be a single
fragment. Ad22 do not have any restriction site for RsaI.
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| Discussion |
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Culture-NT is considered to be the "gold standard" for the identification of adenovirus. However, 2 to 4 weeks are required for the whole procedure. Furthermore, a successful cell culture heavily depends on a careful transport and storage procedure. Occasional cross-reaction among the serotypes often leads to a wrong identification of isolates. Therefore, PCR-based identifications of common serotypes, such as type-specific PCR, PCR-RFLF, and PCR with direct DNA sequencing, were in demand as a rapid, alternative methods to culture-NT.16 17 18 Type-specific PCR targets type-specific sites in the hypervariable region of the hexon gene. Because of the genetic variation of the target region among the different strains of the same serotype, this approach is prone to false-negative failure. For hexon-based PCR-RFLP, a nested PCR procedure is required. Identification of serotype is done by PCR and DNA sequencing that targets the hypervariable region of the hexon, where sequence of the prototypes and clinical samples are aligned to type the clinical samples. Because there are genetic variation in the hypervariable region, this method tends to be unrefined and requires expensive instrumentation and technical skill. Furthermore, these methods above only identify common EKC strains (Ad8, Ad19, and Ad37). Three days are required to yield a result. If less common serotypes (Ad9, Ad15, Ad22, and Ad39) are causing an outbreak of EKC, rapid agent identification and epidemic control may be difficult through these procedures. Our new method offers some advantages over previously described rapid identification methods, regarding its simplicity, rapidity, and cost-effectiveness. It could identify a wide range of nine serotypes that includes not only common and less-common agents of EKC, but also other serotypes associated with nonspecific follicular conjunctivitis.
Heat-mediated rupture of viral capsids to expose viral DNA for enzymatic action has been described.20 Direct heat treatment of clinical samples at 97°C for 15 minutes was found to be equally effective as the guanidine thiocyanate glass powder method, which is rather expensive and time consuming. The higher success rate of the heat method may be due to the less inhibitory substances found in conjunctival swabs.10 Therefore, our study used the direct heat method for all clinical samples. Very sensitive results of our fiber gene-based PCR using DNA extracted by the direct heat method indicate that this simple extraction method is quite useful.
Fiber genes of subgenus D are targeted for designation of the primers that are not significantly homologous among other subgenus.21 The nucleotide sequence of the fiber gene contains 5' noncoding region, fiber-coding region, and a 3' noncoding region. Regarding designation of the primers, the fiber gene sequences of Ad8, Ad9, Ad15, Ad19, and Ad37 derived from GenBank were compared. The forward and reverse primers, AF2/AR2 are located in the 5' coding and the 3' noncoding regions and are found to be conserved among the serotypes described here. Lengths of the fiber gene between the primers vary among the serotypes. The amplified product is approximately 1150 bp long and yields very little variation in lengths among the serotypes, although these differences do not help visual recognition of serotypes by PCR.
This long amplicon has multiple restriction sites for different restriction enzymes. We chose the most appropriate three restriction enzymes. When the amplified product is digested with three restriction enzymes (DdeI, HinfI, and RsaI), different serotypes could be discriminated by their polymorphic patterns. All serotypes were digested well except Ad22, which has no restriction site for RsaI.
The reliability of this new method was evaluated using clinical specimens. In comparison with culture isolation and hexon-based PCR method, our PCR method has a sensitivity of almost 100%. REA was performed on PCR positive samples, and the results were completely identical with those obtained by NT after cell culture isolation and hexon-based RFLP method.
The specificity of the PCR method was determined against other subgenus of adenovirus and nonadenoviral DNA. The lack of amplified products indicated a high level of specificity of the test.
The minimum limit of the detection level of our PCR was 102 copies of viral DNA. It is not known how many copies of viral DNA are needed to induce conjunctivitis. However, the minimum limit of 102 copy level is more sensitive than culture isolation.17
DNA preparation by heating and a single-round PCR enabled us to prepare a result in 1 day. Our new fiber-based PCR-REA method could detect and type nine serotypes of subgenus D adenoviruses within 1 day compared with the need of 2 to 4 weeks for conventional cell culture isolation-NT and 3 days with the hexon-based PCR-RFLP method. Our method, thus, can provide a faster, more sensitive, cost-effective tool for detecting several types of subgenus D adenoviruses.
| Acknowledgements |
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| Footnotes |
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Submitted for publication January 12, 2001; revised March 20, 2001; accepted March 29, 2001.
Commercial relationships policy: N.
The publication costs of this article were defrayed in part by page
charge payment. This article must therefore be marked
"advertisement" in accordance with 18 U.S.C.
1734
solely to indicate this fact.
Corresponding author: Jiro Numaga, 3-2-1-214, Nishigahara Kita-ku, Tokyo 114-0024, Japan. jnumaga{at}mub.biglobe.ne.jp
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