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Journal of Clinical Microbiology, May 2007, p. 1523-1527, Vol. 45, No. 5
0095-1137/07/$08.00+0 doi:10.1128/JCM.00209-07
Copyright © 2007, American Society for Microbiology. All Rights Reserved.

Laura D. Kramer,1,3 and
Kristen A. Bernard1,3
Wadsworth Center, New York State Department of Health, Albany, New York,1 Upstate Infectious Diseases Associates, Albany, New York,2 School of Public Health, SUNY Albany, Albany, New York3
Received 26 January 2007/ Returned for modification 14 February 2007/ Accepted 14 March 2007
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Dengue infections are rare in individuals living in the United States but do occur in persons who have traveled to regions of the world where dengue is endemic. The patient discussed in this paper had traveled from Thailand, where dengue virus is endemic. Dengue fever has been reported in an increasing number of international travelers and is thought to be the second most frequent cause of hospitalization after malaria (17, 20). Acute infection by dengue virus can cause dengue fever, which is characterized by biphasic fever, headache, myalgia, eye pain, arthralgia, rash, prostration, lymphadenopathy, and leukopenia. In general, clinical findings include neutropenia followed by lymphocytosis, presence of atypical lymphocytes, and occasionally elevated levels of aspartate aminotransferase in serum (19). Virus can be detected in blood for 4 or 5 days after the onset of symptoms and then disappears as antibody (immunoglobulin M [IgM]) production increases. In primary infections, IgG antibody appears within a few days, whereas in secondary infections, the IgG level rises immediately after the onset of symptoms and remains high in most patients (18). In the early phases of the disease, because the symptoms are usually nonspecific, it is hard to distinguish the disease from West Nile, Japanese, and Saint Louis encephalitis and influenza, yellow fever (YF), measles, scrub typhus, malaria, and leptospirosis. This problem is exacerbated by the serologic cross-reactivity among flaviviruses, including West Nile virus (WNV), Japanese encephalitis (JE) virus, Saint Louis encephalitis (SLE) virus, dengue virus, and YF virus.
In the absence of either a vaccine or an effective therapy for dengue fever, timely diagnosis is critical to prevent the spread of disease, enhance preparedness, and exclude other viral etiologies of infection. Current methods for diagnosis of dengue infection and typing of dengue virus include virus isolation, serology, antigen detection, and molecular detection (4, 7). Serological evidence of virus infection is based on capture IgM and IgG enzyme-linked immunosorbent assay (ELISA) but has little impact on patient management and control measures because it requires documentation of a rise in antibody concentration from an acute-phase sample to a convalescent-phase sample. A further disadvantage of these tests is that there is a strong cross-reaction with other flavivirus-specific IgG antibodies. The plaque reduction neutralization technique, although it allows typing of the virus, is costly and difficult to perform. It is most effective in testing for primary dengue infections and less effective in testing for secondary dengue infections. An ELISA based on changes in the avidity of IgG during the infectious period has been developed (13). This test discriminates between primary and secondary dengue virus infections during the acute phase of dengue infection. Virus isolation by cell culture remains the gold standard for virus detection but has the disadvantage of taking over 7 days to complete. Both conventional and real-time reverse transcription-PCR (RT-PCR) methods have been used for molecular detection (2, 5, 10, 11). These methods are rapid, specific, and sensitive. In addition, under some conditions when virus infectivity is compromised and the virus does not grow in cell culture, viral RNA can still be detected by these methods. While blood specimens are traditionally used for diagnostic testing, epidemiologic and primate studies suggest that dengue virus is present in the respiratory tract (1, 8, 12), and therefore, respiratory specimens may be alternative specimens for diagnostic testing. Here, we used conventional RT-PCR, real-time RT-PCR, ELISA, a microsphere immunoassay (MIA), and viral culture for detection of the viral agents in the patient's blood and respiratory tract specimens.
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(This work was presented in part at the 54th Annual Meeting of the American Society of Tropical Medicine and Hygiene in December 2005.)
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Virus isolation and identification. Virus isolation was attempted on the acute-phase serum and respiratory samples (nasal, pharyngeal, and the two NPS swabs) from the patient. A 0.1-ml portion of each sample was added to duplicate wells of Vero (African green monkey kidney cells) and C6/36 (Aedes albopictus) cell monolayers. Vero and C6/36 cells were maintained at 37°C and 28°C, respectively. Cultures were blind passaged onto a second round of Vero and C6/36 cells after 7 days. Dengue virus does not cause a cytopathic effect (CPE) in C6/36 cells; therefore, all C6/36 cultures grown were passaged onto Vero cell culture monolayers for evidence of CPE. Immunofluorescence assays (IFAs) were performed on the infected-cell culture monolayers from all samples. Briefly, 10-well slides were spotted with 0.025 ml of the cell suspension of each sample culture and allowed to air dry. DEN-1, -2, -3, and -4-specific mouse monoclonal antibodies (MAbs) were as follows: DEN-1-specific MAb (Chemicon International Inc., Temecula, CA), DEN-2-specific MAb (Chemicon International Inc.), DEN-3-specific MAb (U.S. Biological, Swampscott, MA), and DEN-4-specific MAb (Chemicon International Inc.). The DEN-1, -2, -3, and -4-specific MAbs were diluted 1:100, added to duplicate wells for each sample, and incubated for 1 h at 37°C. After incubation, the slides were washed for 15 min in phosphate-buffered saline. A secondary antibody conjugated to fluorescein isothiocyanate (KPL, Gaithersburg, MD) was then added to each well, and slides were incubated for 1 h at 37°C. After incubation, the slides were again washed for 15 min in phosphate-buffered saline, and coverslips were added. Fluorescence was evaluated using a Zeiss Axiovert microscope equipped with a fluorescein isothiocyanate filter set.
Nucleic acid extraction and RT-PCR. Nucleic acid was extracted using the NucliSens miniMAG extraction method (bioMérieux, Marcy l'Etoile, France). Two hundred fifty microliters of each specimen was extracted and resuspended in a total volume of 50 µl. Flavivirus heminested RT-PCR using universal primers was modified from the method of Scaramozzino et al. (15) as follows. After amplification, 5 µl of the total nucleic acid was the template for RT-PCR, with 0.5 µM of primers CFD2 and MAMD and the QIAGEN one-step RT-PCR kit (QIAGEN Inc., Valencia, CA). The amplification reaction for the first round was performed under the following conditions: 30 min at 50°C; 15 min at 95°C; 35 cycles, with 1 cycle consisting of 1 min at 94°C, 1 min at 53°C, and 1 min at 72°C; and a final extension step (10 min at 72°C). Five microliters of the product from the first round of PCR was amplified in a second round of PCR using primers CFD2 and FS778 (1x PCR buffer with a final [MgCl2] of 1.5 mM, 0.5 µM of each primer, 10 µM deoxynucleoside triphosphate mix, 0.25 µl HotStarTaq DNA polymerase [QIAGEN Inc.]). Second-round thermocycler conditions were 15 min at 95°C; 35 cycles, with 1 cycle consisting of 1 min at 94°C, 1 min at 52°C, and 1 min at 72°C; and a final extension step (10 min at 72°C). Following RT-PCR, the product was run on a 2% agarose gel. The first-round PCR should generate a product of approximately 250 bp, and the second-round PCR should generate a product of approximately 220 bp. Bands of the expected size were cut from the gel and purified using an Ultrafree-DA centrifugal filter unit (Millipore, Billerica, MA). Sequencing reactions on the PCR products were performed using 3.2 pmol of the CFD2 and FS778 primers at the Wadsworth Center Molecular Genetics Core facility on an automated DNA sequencer model 3100 (Applied Biosystems, Foster City, CA).
Real-time RT-PCR detection. The real-time RT-PCR assay for DEN-1 is adapted from the method of Houng et al. (6). The forward primer for DEN-1 was modified to 5'-GGGAAGCTGTATCCTGGTGGTAA-3'. For this method, the assay was optimized to run as a one-step real-time RT-PCR using the SuperScript III platinum one-step quantitative RT-PCR system (Invitrogen, Carlsbad, CA) on an ABI 7500 sequence detection system instrument (Applied Biosystems). The 25-µl reaction mixture contained 0.5 µl of SuperScript III reverse transcriptase/platinum Taq mix, 12.5 µl of 2x reaction mix, 0.3 µM of each primer, 0.2 µM of probe, 0.5x Rox reference dye, 5.45 µl diethyl pyrocarbonate-treated H2O (Ambion, Austin, TX), and 5 µl of template. RT-PCR amplification, which includes an initial RT step, was performed as follows: 30 min at 48°C, followed by 45 cycles, with 1 cycle consisting of 10 s at 95°C, 15 s at 95°C, and 1 min at 60°C. Data were collected each cycle after the 1-min step at 60°C. Results were analyzed using the ABI 7500 software.
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View this table: [in a new window] |
TABLE 1. Serological results of acute- and convalescent-phase sera from the patienta
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View this table: [in a new window] |
TABLE 2. Results of RT-PCR and culture for various specimens from the patient
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The conventional RT-PCR method targets a conserved region of the NS5 gene, using a primer pair proposed by Kuno (9) and adapted by Scaramozzino et al. (15). We further adapted the assay and performed it as a one-step RT-PCR. The assay is a heminested, genus-specific RT-PCR which amplifies genomes from the pathogenic flaviviruses: YF virus, DEN1 to -4, JE virus, SLE virus, and WNV, among others. We determined that the PCR assay detects Powassan virus, a North American tick-borne encephalitis virus (data not shown). Sequencing of the PCR product and comparison of the amplified NS5 sequence with the sequences currently in the databases will aid in the identification of the flavivirus. Sequencing will also aid in eliminating false-positive results arising from generation of nonspecific PCR products of the expected size. The procedure can be used as a first-line diagnostic PCR screening method for pathogenic flaviviruses.
The real-time RT-PCR procedure is a 5' nuclease assay, which targets the 3' noncoding sequence (6). The 3' noncoding region contains the most conserved sequence in the four dengue virus serotypes and is thought to be involved in viral replication, transcription, and virulence (16, 23). The original protocol for the real-time assay entailed a two-step assay requiring separate RT and PCRs. We adapted this procedure to a one-step reaction, and we redesigned the forward primer. A number of real-time RT-PCR master mixes were compared, and the one that gave the most efficient reaction and best sensitivity and specificity was selected. Modification of the assay made it less prone to cross-contamination and also decreased the turnaround time for obtaining results.
Serum IgM against the virus envelope protein is generally produced within 5 days of onset of infection, with subsequent production of IgG (14). However, identification of the specific serotype, via IgG and IgM ELISAs, can be problematic. Cross-reactivity is frequently observed among all four serotypes of dengue virus, when ELISA using whole-virus antigen for the detection of dengue virus-specific antibody is used; this is especially true for secondary dengue infection. Although culture is the gold standard for identification of dengue infections, the virus grows slowly, and timely results are not available. In addition, growth in culture is dependent on the recovery of viable virus from a specimen from the patient.
In the case reported here, laboratory diagnosis was based on IgM and IgG ELISAs, virus isolation, and RT-PCR. The ELISAs exhibited cross-reactivity but indicated flavivirus infection. Viral culture showed CPE indicative of virus growth, and the conventional RT-PCR, sequencing, and real-time RT-PCR confirmed and clarified the subtype of dengue virus that was present. This multimethod analysis led to the reliable detection of dengue virus in the patient's specimens. Interestingly, virus was detected by conventional RT-PCR, real-time RT-PCR, and culture in the nasal specimen collected 1 day prior to the other specimens (Table 2). This may indicate the importance of timing in the collection of specimens during the course of the disease, or it may indicate that nasal swabs are better specimen types for testing. Follow-up studies are warranted to determine the timing and applicability of nasal swabs for dengue patients.
Our interest in investigating the presence of dengue virus in the respiratory tract was severalfold. NPS specimens are relatively easy to obtain and transport and are the specimens of choice for rapid detection of influenza virus. Indeed, illness from influenza and dengue infections may be difficult to distinguish on clinical grounds, and the differentiation has major epidemiologic implications. Wesselsbron virus, which is a flavivirus of the YF virus subgroup, has been reported to be found in the throat wash fluid of a laboratory worker (8). Studies of dengue virus infections in monkeys have shown virus to be present in the upper respiratory tract at the end, or just after termination, of viremia (12). An outbreak of dengue virus infection in health care workers raised the possibility that aerosol transmission can occur (V. Gupta, S. Bhoi, and P. Aggarwal, presented at the 54th Annual Meeting of the American Society of Tropical Medicine and Hygiene, December 2005).
We have shown that a multipronged laboratory approach can be used to diagnose dengue infection and differentiate dengue virus serotypes. Furthermore, the modified real-time RT-PCR assay that we use has the advantage of being less prone to cross-contamination while displaying reduced turnaround time for results. To our knowledge, ours is the first study to have identified dengue virus in respiratory tract specimens. Whether NPS specimens represent a useful alternative to blood specimens for the diagnosis of dengue infection will require additional study.
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The contents of this publication are solely the responsibility of the authors and do not necessarily represent the official views of CDC.
We thank the Molecular Genetics Core at the Wadsworth Center for performing the sequencing reactions and Charles Trimarchi for valuable comments on the manuscript.
Published ahead of print on 21 March 2007. ![]()
Present address: Rensselaer Polytechnic Institute, Rensselaer, NY. ![]()
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