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ABSTRACT |
 TOP ABSTRACT INTRODUCTIONMATERIALS AND METHODSRESULTSDISCUSSIONREFERENCES |
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INTRODUCTION |
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TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTSDISCUSSIONREFERENCES |
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From previous studies conducted from 1995 to 2000, mosquitoes collected from the Amazon Basin region of Peru yielded more than 180 viral isolates from three different viral families: Togaviridae, Flaviviridae, and Bunyaviridae (Klein T and others, unpublished data).9,10 From the previously collected data on mosquito abundance, seasonality, and distribution coupled with knowledge of virus and vector relationships (Klein T and others, unpublished data), Culex (Melanoconion) pedroi mosquitoes and EEEV virus (family Togaviridae, genus Alphavirus) were selected as targets for the first field evaluation of an RT-PCR system developed for use in the field. Alphaviruses are known to cause disease in humans and are considered to be medically relevant arthropod-borne pathogens.11 They contain positive-sense single-stranded RNA genomes encapsidated by a single type of capsid protein. The nucleocapsid is surrounded by a lipid bi-layer containing virus-encoded glycoproteins. The Alphavirus genome contains a 5'-methylguanosine cap and a 3'-polyadenosine tail.
During November 2000, a field laboratory was set up in the Amazon Basin region of Peru, near the city of Iquitos, to conduct the field evaluation of the RT-PCR field system. The system was designed to provide a rapid, highly sensitive, and deployable pathogen-detection system for augmentation into military field laboratories. Conducting molecular diagnostics in the field under non-optimal laboratory conditions (extreme temperature and humidity, generator-supplied electrical power, non-filtered air, and a minimal cold chain) required development of processes and procedures to compensate for the harsh field conditions. For this technology to work in the field, standardized, reliable, and easily performed procedures were developed and tested first under optimal laboratory conditions, then by evaluation under harsh environmental field conditions. The RT-PCR assays were designed as generic assays that could be used with any number of PCR primer sets to detect any number of viruses. The primer annealing temperatures were not optimized in favor of a single set of reaction conditions that would simplify use of the assays and prevent mistakes in the field. The use of RT-PCR in the field is a powerful tool for determining risk assessments in real time. Within one day, mosquitoes can be trapped, processed, and evaluated for the presence of any number of medically relevant pathogens. We have shown that RT-PCR diagnostics can be accomplished in the field under harsh environmental conditions.
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MATERIALS AND METHODS |
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To compare the efficiency of the extracting medium, mosquitoes were also triturated in 0.75 mL of Trizol®-LS (Invitrogen Corp., Carlsbad, CA) by using a copper BB. After trituration, the mosquito homogenate was clarified by centrifugation in a microcentrifuge at 4°C and 12,000 rpm for five minutes. The supernatant was transferred to a clean 1.5-mL microcentrifuge tube containing 0.25 mL of PBS and RNA was isolated as described in this report starting with the addition of chloroform.
Isolation of RNA and synthesis of cDNA. Clarified mosquito-PBS homogenate or virus infected cell culture supernatant (250 µL) was combined with 0.75 mL of Trizol®-LS in a microcentrifuge tube, vortexed briefly, and incubated at room temperature for five minutes. Chloroform (200 µL) was added to the tube, vortexed or shaken for 10 seconds, and incubated for 10 minutes at room temperature. The aqueous phase containing the viral RNA was separated from the organic phase by centrifugation at 4°C and 12,000 rpm for 10 minutes in a microcentrifuge. After centrifugation, 500–550 µL of the clear aqueous solution was removed and transferred to a clean RNase-free 1.5-mL microcentrifuge tube containing 1 µL of glycogen (20 mg/mL). Isopropanol (500 µL) was added, and the tube was vortexed briefy. The RNA was pelleted on the bottom of the tube by centrifugation at 4°C and 12,000 rpm for 10 minutes. The clear supernatant was decanted, leaving a white pellet at the bottom of the tube. Ethanol (500 µL, 75%) was added to the tube containing the pellet. The tube was inverted several times and then centrifuged at 4°C and 12,000 rpm for two minutes. The clear supernatant was decanted, and the tube was briefly centrifuged to collect the residual alcohol into the bottom. The residual alcohol was removed from the RNA pellet with a pipet. The RNA pellet was dissolved in 12–25 µL of nuclease-free water at room temperature for 5–10 minutes. After vortexing, the RNA was collected into the bottom of the tube by brief centrifugation and then stored on ice or frozen at -70°C.
The presence of inhibitors co-isolated during the RNA purification step was evaluated by subjecting the RNA to a second round of purification. RNA isolated from mosquitoes triturated in PBS or in Trizol®-LS was further purified using the RNeasy Mini Kit (Qiagen, Inc., Valencia, CA) according to the manufacturer’s instructions.
The RNA extracted from the mosquito homogenate was converted into cDNA as follows. RNA (10 µL) and 2 µL of random hexamer (100 nmol) were combined in a dome-topped PCR tube and placed in a thermal cycler programmed as follows: 70°C for 10 minutes, 4°C for five minutes, 25°C for 15 minutes, 42°C for 50 minutes, 70°C for 15 minutes, and then 4°C for storage. At the beginning of the 25°C step, the thermal cycler program was paused and 4 µL of 5x RT buffer (Invitrogen, Inc.), 2 µL of 0.1M dithiotheitol, 1 µL of deoxynucleotide triphosphate mixture (10 mM each), and 1 µL of SuperscriptTMII (Invitrogen, Inc.) was added to each tube. Random hexamer was used instead of a reverse primer specific to EEEV to allow for the reverse transcription of any viral RNA genome present in the mosquito homogenates. This procedure was designed to allow for the detection of any possible viruses circulating in the same region as EEEV (i.e., VEEV or western equine encephalitis virus) by using the same cDNA with different PCR primer sets. The tubes were inverted several times to mix the contents, centrifuged to collected the material into the bottoms of the tubes, and then placed back into the thermal cycler to complete the program. Once completed, the cDNAs were stored on ice or frozen at -20°C.
PCR amplification and gel electrophoresis.
The sequences of the PCR primers are listed in Table 1
.13–16 The PCR amplification of targeted viral sequences present in the cDNA prepared from the RNA isolated from the mosquitoes was accomplished as follows. For a 25-µL reaction, 1–2 µL of cDNA, 1 µL of forward primer (10 µM), 1 µL of reverse primer (10 µM), and 21TM22 µL of water was added to each PCR tube containing one puRe TaqTMReady-To-GoTM PCR bead (Amersham Biosciences, Corp., Piscataway, NJ). The PCR amplification was preformed as follows: 95°C for two minutes, followed by 35 cycles at 95°C for 30 seconds, 50°C for 30 seconds, and 72°C for 45 seconds, followed by 72°C for seven minutes and a final hold at 4°C.
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Field site location and mosquito collections. Mosquitoes were collected from a secondary jungle site near the village of Puerto Almendras, located approximately 25 km from the city of Iquitos, in the Amazon Basin region of Peru. The field laboratory was setup in a village hut with a tin roof, dirt floors, and open windows. Electricity was supplied from a small 240-volt, gasoline-powered generator that was step-down transformed to 110 volts. Mosquito light traps baited with CO2 (American Biophysics Corp., North Kingstown, RI) were set at dusk and collected at dawn. The mosquitoes collected in the traps were immobilized with TEA, identified to species, and pooled into groups of 25–30. Culex (Mel.) pedroi mosquito pools were separated from all other pools, processed as outlined earlier, and tested for the presence of EEEV by RT-PCR. The remaining pools were returned to United States Army Medical Research Institute of Infectious Diseases (Fort Detrick, Frederick, MD) for other testing.
Field equipment. A commercially available mobile molecular laboratory kit (model MML-0150; MJ Research, Inc., Waltham, MA) designed for field use was evaluated in the field. The components of the laboratory kit consisted of a 25-well thermocycler (model PTC-150HB), a microcentrifuge (7,000 x g maximum), a compact ultraviolet transilluminator, and a Polaroid® camera with an ethidium bromide filter. The gel electrophoresis supplied with the kit was replaced with E-gel® agarose gels and E-gel® power bases. A second 25-well thermocycler (model PTC-150HB; MJ Research, Inc.), a 96-well thermocycler (model PTC-100–96V, MJ Research, Inc.) and a microcentifuge (16,000 x g Eppendorf model 5415C; Brinkman Instruments, Inc., Westbury, NY) were added to the kit to support the processing of more field samples. In subsequent field evaluations, the Eppendorf 5415C was replaced with a refrigerated microcentrifuge (16,100 x g Eppendorf model 5415R; Brinkman Instruments, Inc.). Styrofoam boxes containing wet ice were used to keep the reagents cold during the day and boxes containing dry ice were used to store the reagents overnight or for long-term storage of specimens. Dry ice and wet ice were locally available.
Laboratory sequencing and phylogenetic analysis. The RT-PCR amplification product (15 µL) from processed mosquito pools that tested positive for EEEV was purifed using the Qiaquick® PCR purification kit (Qiagen, Inc.) according to the manufacturer’s instructions. Automated sequencing was performed on an ABI 310 genetic analyzer using a Big-DyeTMsequencing kit (PE Biosystems, Inc., Foster City, CA) according to the manufacturer’s instructions. Primer, excess nucleotides, and buffer were removed from the Big-DyeTM sequencing reaction by eluting the material from a SephadexTMG-50 (Amersham Biosciences Corp.) column equilibrated with water. Sequences were aligned using the MegaAlign program (Lasergene analysis software; DNASTAR, Inc., Madison, WI) and sequence ends were trimmed to a uniform length. Phylogenetic analyses of aligned sequences were performed with the ClustalW method with a gap penalty of 15 and a gap length of 6.66. The phylogenetic tree generated by MegaAlign is a rooted tree with the number of substitution events indicated at the bottom of the tree.
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RESULTS |
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TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTSDISCUSSIONREFERENCES |
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). The selected primer sets targeted different regions of the Alphavirus genome. The results of six different primers sets used in the amplifying EEEV isolated from a single infected mosquito are shown in Figure 1. The PCR cycle times and temperatures used for the amplification of EEEV were generalized for an amplification product (amplicon) of 1,000 base pairs or less with low primer annealing temperatures. The low annealing temperature would also compensate for minor changes in the primer binding sites due to genetic drift. Even though the PCR assay was not optimized for any given primer set, the E-9657/E-10004 primer set14 produced the most abundant amplicon with the appropriate number of basepairs. The E-9657/E-10004 primer set also targeted conserved envelope sequences where the variable bases were replaced with degenerate bases. The primer sets E1 (+)/(-),13 VEE 0091/00092 (Oberste M and others, unpublished data), and M2W/cM3W16 produced adequate amounts of amplicon with the appropriate number of basepairs and could serve as additional primer sets for confirmational testing of presumed positive samples in the field. The primer set C (+)/(-)13 produced a small amount of amplicon with the wrong number of basepairs, while VEE 115/11615 failed to produce an amplicon with the appropriate number of basepairs.
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). St. Louis encephalitis virus, a flavivirus, was used as an unrelated control virus for the experiment. Eastern equine encephalitis virus was specifically amplified using the E-9657/E-10004 primer set while VEEV IA/B and SLEV were not amplified. Marginal amplification of VEEV IIIC was noted and probably resulted from sequence homology between the alphaviruses. The primer set E-9657/E-10004 was also used in the RT-PCR assay of other cell culture-passed alphaviruses, bunyaviruses, and flaviviruses isolated from Peru. For alphaviruses, Una was weakly amplified whereas Oriboca and Trocara were not amplified, for the bunyaviruses, Caraparu and Itaqui were not amplified, and the flavivirus Ilheus was also not amplified. Additional PCR assays were conducted on all samples that tested negative with the E-9657/E-10004 primer set by using other primer sets to confirm the presence of the appropriate viruses.
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The ability to detect one virus-infected mosquito in pooled mosquitoes was investigated by triturating one EEEV-infected mosquito with increasing numbers of uninfected mosquitoes (Figure 3). Trituration of one infected mosquito with up to 49 uninfected mosquitoes yielded RNA that was efficiently converted into cDNA. The PCR amplification of the cDNA resulted in approximately the same amount of amplicon for each pool containing one infected mosquito and either 0, 4, 9, 14, 24, or 49 uninfected mosquitoes. A standard plaque assay of each of the homogenates in Vero cells produced between 5.42 x 104 PFU/mL and 1.85 x 106 PFU/mL except for the pools containing only uninfected mosquitoes and those resulted in no plaques. Even though the amount of virus present in the infected mosquitoes varied by more than one log, the amount of amplicon produced after PCR amplification was approximately the same.
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Detection of EEEV in field-processed mosquitoes.
In the course of a two-week field evaluation, 3,227 Cx. (Mel.) pedroi mosquitoes were captured in CO2 baited light traps, pooled into groups of 25–30, and assayed by the RT-PCR for the presence of EEEV. All steps were completed at the field site, and the results after repeating the RNA extraction, RT assay, and after using 2 µL of cDNA in the PCR assay are shown in Figure 4. Presumptive positive and negative pools were reprocessed in the field and used to confirm the initial field results that included only 1 µL of cDNA. The EEEV amplicon generated in the field with the E-9657/E-10004 primer set co-migrated with a sample prepared in the laboratory from cell culture-derived EEEV. Pools 59, 60, 74, 110, and 153 tested positive for the presence of EEEV while the remaining 112 pools tested negative. Even though pools 59 and 60 were sequential, they were initially prepared and found to be positive by RT-PCR on two different days, thus making cross-contamination of pool 60 with pool 59 unlikely. The infection rate was calculated to be approximately 1.6 EEEV infected per 1,000 Cx. (Mel.) pedroi. This infection rate was similar to that determined by others in previous years for mosquitoes collected during November and assayed by plaque assay (Klein T and others, unpublished data).
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shows the relationship between the different viral isolates and between the Brazil-Peru (lineage II) and the Argentina-Panama (lineage III) subtype of EEEV.14,17 North American EEEV is also shown for comparison. Virus from pools 59, 60, 110, and 153 were found to be phylogenetically related to the Argentina-Panama subtype and virus from pool 74 was found to be related to the Brazil-Peru subtype. We noted no difference in the amplicon sequences among viruses from pools 59, 60, 110, and 153.
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DISCUSSION |
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TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTSDISCUSSIONREFERENCES |
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Several methods exist for detecting virus in arthropod samples.18,19 Agglutination or inhibition of agglutination-based assays, either using latex particles or red blood cells, require antisera specific for all the different viruses under investigation. The need for antisera, the temperature sensitivity of the assays, and the potential lack of specificity due to shared antigen-epitopes between viruses within the same families make this technique less desirable for use in the field. Other assay such as complement fixation, direct or indirect immunofluorescence assay (IFA) or enzyme immunoassay (EIA) analysis,20,21 ELISA,22 dipstick assays (discussed earlier), and time-resolved fluorometry23 also require antisera or antibodies specific to each virus. Some procedures such as an ELISA require large amounts of buffer for washing the plates, which is not practical in the field. Direct IFA and EIA also requires the preparation and maintenance of conjugated antibodies or antisera specific for each virus. This requires either a commercial source or in-house facilities to prepare the high quality antibodies and antisera needed for the assays and may be cost prohibitive. Also, nonspecific binding of the antibodies to the different proteins present in the triturated arthropod samples encountered in the field may diminish the effectiveness of the assays for detecting virus antigen in the presence of nonspecific background staining. The most specific immunologic test for the presence of a specific virus is the neutralization test. This test also requires antibodies specific for each virus and also requires the use of cultured cells, which is not feasible in the field. Biosensor-based methods, those that can detect the binding of an antigen to an antibody adsorbed onto the surface of a transducer, may have utility in the field but are currently restricted to the laboratory due to the size or fragile state of the analysis instrument.24,25 Other techniques useful in the laboratory, but not in the field, for identifying viruses are plaque assays, host range restriction analysis by growth in cultured cells, electron microscopy for determining the size, shape, and density of the viral particles, and sequence analysis.
Non-immunologic methods that are capable of detecting viruses present in arthropods are based on the amplification and detection of the viral genomes present in the sample by a PCR.26,27 A multitude of PCR methods exist (to include but not limited to conventional PCR and RT-PCR, real-time PCR, ligation-activated transcription PCR, in situ PCR, multiplex PCR, and nested PCR) that when coupled with multiple probe amplification procedures and detections methods make the PCR a versatile diagnostic tool. The advantages and disadvantages of the different PCR methods for detecting viruses have been reviewed elsewhere.26,27 This report describes our efforts at designing protocols and procedures that would minimize the problems normally associated with the detection of viruses in arthropods in the field using conventional RT-PCR.
We simplified specimen processing by eliminating the need for wet ice or a chill table for specimen identification. Chill tables and wet ice can cause condensation build-up on specimens that degrades the quality of the arthropod. For the purpose of this study, it was important to process specimens in an efficient and timely manner to allow for virus detection. Use of TEA as an immobilizing agent eliminated the condensation build-up associated with chill tables while keeping the specimens physiologically alive for an extended period of time. This provided the taxonomist with more time to make proper identifications.
To address the issue of virus containment, we modified our method of triturating specimens from using a battery-operated tissue homogenizer, which can splatter material outside of a microcentrifuge tube, to vortexing specimens within a sealed microcentrifuge tube containing a copper BB. Triturating mosquitoes in a chaotropic buffer (e.g., Trizol®-LS) neutralizes any viruses present and minimizes the safety concerns surrounding processing of virus-infected mosquitoes in the field, but has several drawbacks. We showed that triturating mosquitoes directly in Trizol®-LS requires an additional purification step, and that additional step require more time and money. More importantly, triturating mosquitoes directly in chaotropic buffers results in the loss of that viral species for further characterization. The virus cannot be returned to the laboratory, grown in culture, characterized, and preserved for future research. The procedures reported here were developed to minimize safety concerns while retaining any possible viral isolates for future characterization and identity confirmation.
Incorporating temperature-stable, pre-assembled products into the RT-PCR protocols provided two benefits, in addition to temperature stability. First, use of the Ready-To-GoTMPCR beads simplified the PCR protocol so that anyone with basic laboratory skills could successfully complete the assay. The product required fewer manipulations, thereby reducing the probability of cross-contamination. One goal of the research was to develop procedures that could be augmented into the United States Army’s Theater Army Medical Laboratory and could be completed by soldiers with basic laboratory skills. Second, using E-gel® agarose gels for analyzing PCR products in the field did not require a microwave to melt the agarose, did not require gel casting time (which would have been difficult in the tropical environment), and did not require liquid agarose gel electrophoresis buffer (which would have contributed to excess weight and possible transport spillage). The plastic sealed gels also facilitated gel handling and minimized exposure to ethidium bromide. In addition, the E-gel® power bases provided a light-weight electrophoresis power supply with a built-in timer.
Other commercially available products that were considered but not used in the field included RNA extraction kits and a product similar to the Ready-To-GoTM PCR beads but incorporated RT-PCR into one temperature stable bead. Since the aim of this project was to develop low-cost, simplified procedures, the addition of extraction kits, although extremely effective for RNA isolation, would have significantly increased the total cost of the process. Even though Trizol®-LS extraction uses volatile reagents, it is a very cost-effective procedure but could be replaced with an RNA isolation kit that does not use volatile reagents when the cost is comparable. The use of RT-PCR beads requires adding a virus-specific primer to initiate priming of the RT reaction. Therefore, a separate RT-PCR bead would be necessary for each and every virus under investigation and would rely on the isolated RNA (an enzymatically and chemically unstable nucleic acid) as the source of the nucleic acid used in the RT-PCR assay. Using random hexamer to primer the RT reaction produces cDNA that is more enzymatically and chemically stable, more resistant to freeze-thaw degradation, and that can be used as necessary with any primer set in the PCR assay. The costs associated with the use of the RT-PCR beads for one, two, or three or more assays is less, the same, or more, respectively, than the costs associated with our reported RT-PCR assay, yet the easy of use and temperature stability of the RT-PCR beads warrants additional testing and field evaluation. Research that is currently ongoing is focusing on developing PCR primers sets that can detect, for example, all alphaviruses present in a mosquito pool. This approach would allow for rapid screening of large numbers of mosquito pools. After detecting an alphavirus, specific primers would be used to identify the viral species.
The reported mosquito processing, RNA isolation and cDNA synthesis, and PCR amplification can detect EEEV in the field under extreme environmental conditions. Select military laboratories have the mission to identify and evaluate health hazards in the areas where deployed personnel operate. Incorporating the reported protocols and techniques into the Theater Army Medical Laboratory’s capabilities will enable personnel in the field to detect arthropod-borne viruses and to perform health-associated risk assessments in a timely manner. Currently, we are expanding the RT-PCR diagnostic protocols to include procedures for detecting malaria and other parasites found in mosquitoes and other arthropods in the field.
Received March 23, 2003. Accepted for publication November 6, 2003.
Acknowledgments: We thank Dr. Michael Turell for inoculating select mosquitoes, Angela Hadjipanayis for plaque assaying select viruses, Michael Delgado and Dieter Schachner for rearing of the laboratory mosquitoes, and the United States Navy Medical Research Center Detachment (Lima and Iquitos, Peru) for the logistical support provided during the field evaluation.
Disclaimer: The views in this report are those of the authors and should not be considered as positions of the Department of the Army.
Authors’ addresses: Monica L. O’Guinn, Command, USACHPPM-Pac, ATTN: MCHB-AJ-TEM (MAJ O’Guinn), APO, AP 96343-5006, Telephone: 81-3117-63-4478, Fax: 81-3117-63-8597. John S. Lee, Virology Division, United States Army Medical Research Institute of Infectious Diseases, 1425 Porter Street, Fort Detrick, Frederick, MD 21702, Telephone: 301 619-4912, Fax: 301-619-2290, E-mail: john.lee{at}det.amedd.army.mil. John P. Kondig, Diagnostics Systems Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, Telephone: 301-619-4781, Fax: 301-619-2290. Roberto Fernandez, United States Naval Medical Research Center Detachment, Unit 3800, APO, AA 34031, Telephone: 51-1-561-2882 extension 139, Fax: 51-1-561-304. Faustino Carbajal, 4301 Columbia Pike # 515, Arlington, VA, 22204, Telephone: 703-521-2118.
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REFERENCES |
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TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTSDISCUSSIONREFERENCES |
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This article has been cited by other articles:
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  J. P. KONDIG, M. J. TURELL, J. S. LEE, M. L. O'GUINN, and L. P. WASIELOSKI JR GENETIC ANALYSIS OF SOUTH AMERICAN EASTERN EQUINE ENCEPHALOMYELITIS VIRUSES ISOLATED FROM MOSQUITOES COLLECTED IN THE AMAZON BASIN REGION OF PERU Am J Trop Med Hyg, March 1, 2007; 76(3): 408 - 416. [Abstract] [Full Text] [PDF]
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