Standard Operating Procedure for Lyssavirus Surveillance of the Bat Population in Taiwan

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Summary

This protocol introduces a standard laboratory operating procedure for diagnostic testing of lyssavirus antigens in bats in Taiwan.

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Hsu, W. C., Hsu, C. L., Tu, Y. C., Chang, J. C., Tsai, K. R., Lee, F., Hu, S. C. Standard Operating Procedure for Lyssavirus Surveillance of the Bat Population in Taiwan. J. Vis. Exp. (150), e59421, doi:10.3791/59421 (2019).

Abstract

Viruses within the genus Lyssavirus are zoonotic pathogens, and at least seven lyssavirus species are associated with human cases. Because bats are natural reservoirs of most lyssaviruses, a lyssavirus surveillance program of bats has been conducted in Taiwan since 2008 to understand the ecology of these viruses in bats. In this program, non-governmental bat conservation organizations and local animal disease control centers cooperated to collect dead bats or bats dying of weakness or illness. Brain tissues of bats were obtained through necropsy and subjected to direct fluorescent antibody test (FAT) and reverse transcription polymerase chain reaction (RT-PCR) for detection of lyssavirus antigens and nucleic acids. For the FAT, at least two different rabies diagnosis conjugates are recommended. For the RT-PCR, two sets of primers (JW12/N165-146, N113F/N304R) are used to amplify a partial sequence of the lyssavirus nucleoprotein gene. This surveillance program monitors lyssaviruses and other zoonotic agents in bats. Taiwan bat lyssavirus is found in two cases of the Japanese pipistrelle (Pipistrellus abramus) in 2016–2017. These findings should inform the public, health professionals, and scientists of the potential risks of contacting bats and other wildlife.

Introduction

Viruses within the genus Lyssavirus are zoonotic pathogens. There are at least seven lyssavirus species associated with human cases1. In addition to the 16 species in this genus1,2,3, Taiwan bat lyssavirus (TWBLV)4 and Kotalahti bat lyssavirus5 have been recently identified in bats, but their taxonomic statuses have yet to be determined.

Bats are the natural hosts of most lyssaviruses, with the exception of Mokola lyssavirus and Ikoma lyssavirus, which have yet not been identified in any bats1,2,3,6. The information on lyssaviruses in Asian bats is still limited. Two uncharacterized lyssaviruses in Asian bats (one in India and the other in Thailand)7,8 have been reported. One human rabies case associated with a bat bite in China was reported in 2002, but the diagnosis was made only by clinical observation9. In Central Asia, Aravan lyssavirus was identified in the lesser mouse-eared bat (Myotis blythi) in Kyrgyzstan in 1991, and Khujand lyssavirus was identified in the whiskered bat (Myotis mystacinus) in Tajikistan in 200110. In South Asia, Gannoruwa bat lyssavirus was identified in the Indian flying fox (Pteropus medius) in Sri Lanka in 20153. In Southeast Asia, several serological studies on bats in the Philippines, Thailand, Bangladesh, Cambodia, and Vietnam showed variable seroprevalence11,12,13,14,15. Although Irkut lyssavirus was identified in the greater tube-nosed bat (Murina leucogaster) in Jilin Province, China in 201216, the exact species and locations of lyssaviruses in East Asian bat populations remain unknown.

To assess the presence of lyssavirus in Taiwanese bat populations, a surveillance program employing both direct FAT and RT-PCR was initiated. Taiwan bat lyssavirus was identified in two cases of the Japanese pipistrelle (Pipistrellus abramus)4 in 2016–2017. In the present article, a laboratory standard operating procedure is introduced for lyssavirus surveillance of the bat population in Taiwan. The flow chart of bat lyssavirus diagnosis in our laboratory is presented in Figure 1.

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Protocol

1. Safety precautions when handling lyssaviruses

  1. Ensure that all laboratory workers handling bat specimens receive pre-exposure rabies prophylaxis17. Monitor the rabies antibody levels of the workers beforehand and re-examine them every 6 months17. Follow-up rabies vaccination is required for those whose antibody levels are lower than 0.5 IU/mL17.
  2. Depending on the biosafety regulations of the country where the laboratory is located, ensure that the following procedures are performed in suitable biosafety level laboratories (e.g., BSL-2 laboratories in Taiwan and BSL-3 laboratories in Australia), and that workers are currently qualified and wear proper personal protective equipment18.
    NOTE: Rabies vaccination provides little to no protection from lyssaviruses belonging to phylogroups II and III18. Workers must be informed that several zoonotic pathogens have been identified in bats19 and should handle samples under suitable biosafety level laboratory conditions with proper personal protective equipment.

2. Sample collection

  1. Use found weak or sick bats or carcasses.
    NOTE: Weak or sick bats are delivered to the Bat Conservation Society of Taipei for veterinary care or research, while carcasses are submitted directly to the Animal Health Research Institute. No healthy bats have been euthanized in this surveillance program.
  2. Have a bat ecologist identify bat species through morphological characteristics20.
  3. Perform DNA barcoding of the bat species when lyssavirus positive is diagnosed, using previously published procedures21.
  4. Submit an information sheet of each bat carcass (collection site, species, clinical signs, etc.).

3. Necropsy of bat specimens

  1. Prepare materials.
    1. Prepare a clean dissection board and place a sterile absorbent pad for necropsy.
    2. Prepare collection tubes for collecting bat organs.
    3. Prepare disposable tweezers and scalpels for necropsy. Change tools between each bat’s necropsy. Prepare cotton balls moistened with 70% ethanol for cleaning tweezers and scalpels during sampling.
    4. Prepare two microscope slides for the FAT. Collect fresh specimens and fix them in formalin solution for histopathological examination.
  2. Examine all external orifices before necropsy. Photograph the bat’s external features, especially the head, ears, and wings, for species differentiation.
  3. Collect an oral swab sample. Place the bat in ventral recumbency on the board and fix the bat’s head with tweezers. Cut the skin along the midline of the calvaria with a scalpel and pull the skin to the lateral sides. Cut the skull along the midline of the calvaria with a scalpel and open it with tweezers to expose the brain tissue.
  4. Remove the brain tissue from the skull and place it on a sterile tongue depressor, and make impression smears from the brain tissue (see step 4.2). Collect a small piece of fresh brain tissue and fix it in formalin for histopathological examination. Contain the remaining brain tissue in a tube for nucleic acid extraction.
  5. Clean tweezers and scalpel with cotton balls moistened with 70% ethanol to remove retained tissues between specimen collection.
  6. Place the bat on the board in dorsal recumbency and fix it on the board with needles at both sides of the axilla and tail heel.
  7. Incise the skin along the midline of the body from mandible to anus. Lift and separate the skin and underlying muscle tissues with tweezers. Collect the salivary glands, which are near the mandibular bone.
  8. Lift the sternum slightly with tweezers, and cut the sternum and abdominal wall along the midline with a scalpel. Cut the clavicles with a scalpel. Fix the left and right rib cages to the board with needles to open the thoracic cavity.
  9. Record the gross lesions and the degree of post-mortem change.
  10. Remove the visceral tissues (i.e., heart, lungs, liver, kidneys, intestines) from the carcass using tweezers and a scalpel. Collect the visceral specimens as needed for future research.
    NOTE: Collection of duplicate samples is recommended. One should be collected for molecular diagnosis, and the other should be frozen at -80 °C with or without viral transport medium for viral culture22.

4. Direct fluorescent antibody test (FAT)

  1. Make impression smears of the brain tissue for the FAT. Perform the FAT as previously described18,23 with the following modifications.
  2. Gently separate the brain tissue from the connected nerve tissue with tweezers and transfer the brain tissue to a sterile tongue depressor. Cut the cross-section of the brain, including the brain stem and cerebellum18,23. Make impression smears of the brain tissue by lightly touching the cut surface of the brain tissue, and press the slide on lens tissue to remove excess tissue.
  3. Fix the slides with acetone at -20 °C for 30 min. Dry the tested slides and the positive and negative controls before staining with conjugate.
  4. Using each of the two commercially available FITC-conjugated anti-rabies antibodies for staining lyssavirus antigen is highly recommended23. Determine the working concentration of the commercial conjugate before the first staining. Drop the diluted conjugates through a 0.45 μM syringe filter onto the slides and incubate the slides at 37 °C for 30 min within a wet chamber.
  5. Drain the excess conjugate from the slides and wash the slides with phosphate-buffered saline (PBS) after incubation.
  6. Drop a small amount of 10% glycerol on the slides and cover with cover slides.
  7. Examine the slides with a fluorescent microscope.

5. Nucleic acid extraction

  1. Add the proper volume of MEM-10 (minimum essential medium supplemented with 10% fetal bovine serum) to the brain tissue (10% w/v).
  2. Homogenate the brain tissue with a 5 mm steel bead in a homogenizer instrument and centrifuge at 825 x g for 10 min.
  3. Extract the nucleic acid, the final volume of which is 50 μL, within 200 μL of the supernatant using the commercially available total nucleic acid extraction kit with instrument.

6. RT-PCR and phylogenetic analysis

NOTE: Several primer sets have been published to detect all known lyssaviruses or specific lyssaviruses. The protocol described here is an example that our laboratory uses and may not fit all experimental needs. Select suitable primers according to laboratory needs.

  1. Prepare the one-step RT-PCR reagent as follows: add 5 μL of extracted nucleic acid to the reaction mixture containing 2.5 μL of 10x reaction buffer, 0.5 μL of forward and reverse primers (10 μM of each), 4 μL of 1.25 mM dNTP, 0.3 μL of RNase inhibitor (40 U/µL), 0.3 μL of reverse transcriptase (10 U/µL), 0.4 μL of DNA polymerase (5 U/µL), and 11.5 μL of DEPC-treated water.
    NOTE: The primer set used in this protocol is JW12 (5'-ATGTAACACCYCTACAATG-3') and N165-146 (5'-GCAGGGTAYTTRTACTCATA-3')24. Modify the preparation of reagents and cycling conditions according to the primer sets used.
  2. Perform the cycling under the following conditions: incubation at 42 °C for 40 min; initial denaturation at 94 °C for 10 min; 35 cycles of 94 °C for 30 s, 55 °C for 30 s, and 72 °C for 30 s; and finally, further extension at 72 °C for 10 min.
  3. Use another or more primer sets to increase the diagnostic sensitivity.
    1. Use N113F (5'-GTAGGATGCTATATGGG-3') and N304R (5'-TTGACGAAGATCTTGCTCAT-3')25,26 to prepare the one-step RT-PCR reagent as follows: add 5 μL of extracted nucleic acid to a reaction mixture containing 5 μL of 10x buffer, 5 μL of forward and reverse primers (4 μM of each), 5 μL of 1.25 mM dNTP, 0.5 μL of RNase inhibitor (40 U/µL), 0.2 μL of reverse transcriptase (10 U/µL), 1 μL of DNA polymerase (5 U/µL), and 23.3 μL of DEPC-treated water.
    2. Perform the cycling under the following conditions: incubation at 42 °C for 40 min; initial denaturation at 95 °C for 5 min; 35 cycles of 95 °C for 1 min, 55 °C for 1 min and 20 s, and 72 °C for 1 min; and finally, further extension at 72 °C for 10 min.
      NOTE: Depending on laboratory needs, choose suitable primers for diagnosis. N113F was originally designed for rabies virus amplification, but it may not work well for other lyssaviruses. The set of N113F and N304R works well for rabies virus (Taiwan ferret badger variant) and Taiwan bat lyssavirus. It will be easier to obtain whole nucleoprotein sequences by using the set of JW12 and N304R primers if the lyssavirus is amplified by both of the above two primer sets.
  4. Analyze the PCR product on 2% agarose gel electrophoresis and visualize by UV light illumination.
  5. Sequence the PCR product by commercial sequencing service.
  6. Enter or upload the sequence to the webpage of the Nucleotide Basic Local Alignment Search Tool (BLAST). Select the "others (nr etc.)" database and enter the organism as Lyssavirus. Select the MegaBlast algorithm and run the BLAST.

7. Virus isolation

NOTE: Perform virus isolation when either 1) the FAT or 2) the RT-PCR indicates positivity.

  1. Homogenize the brain specimen in a 10% (w/v) suspension in MEM-10. Centrifuge at 825 x g for 10 min.
  2. Inoculate 200 µL of supernatant with a suspension of 3 x 106 MNA (mouse neuroblastoma) cells in 1 mL of MEM-10 for 1 h at 37 °C with 1% CO2. Transfer the brain homogenate-cell suspension to a 25 cm2 flask and add 6 mL of MEM-10.
  3. Cultivate 1 mL of the brain homogenate-cell suspension in a 4 well Teflon-coated glass slide with 6 mm diameter at the same time.
  4. After 3–4 days of incubation at 37 °C with 1% CO2, fix the cells on the 4 well slide with 100% acetone (v/v).
  5. Stain the slides with two FITC-conjugated anti-rabies antibodies following steps 4.4–4.7. The cells are infected when the intracytoplasmic inclusions are investigated. Record the percentage of infected cells.
  6. Perform trypsinization and subculture of the inoculated cell culture when the slides are stained as negative:
    1. Remove medium and rinse the flask with 5 mL of PBS.
    2. Add 1 mL of trypsin to the flask and firmly strike the bottom of the flask.
    3. Add 6 mL of MEM-10 and resuspend the cells.
    4. Put the cell suspension into a new tissue flask (6 mL) and onto a 4 well slide (1 mL).
  7. Repeat steps 7.4–7.6 until 100% infectivity is reached.
  8. Collect the supernatant after 24 h of incubation.

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Representative Results

From 2014 to May 2017, 332 bat carcasses from 13 species were collected for surveillance. Two tested positive. In the first bat case, the brain impression tested negative using the FAT with one of the commercial FITC-conjugated anti-rabies antibodies (Figure 2), while the RT-PCRs employing each of the two primer sets (JW12/N165-146, N113F/N304R) yielded positive results (Figure 3). A 428 bp sequence of amplicon (amplified with N113F/N304R and containing the partial nucleoprotein gene) was obtained. Its sequence was subjected to BLAST querying by the GenBank database. The result showed that the sequence was similar to lyssaviruses with identities of less than 79% (Figure 4), supporting the identities of the detected lyssaviruses.

Later, two lyssaviruses were isolated successfully from these two brains, and the viruses were confirmed by FAT (Figure 5) and sequencing. The identified lyssavirus was designated as Taiwan bat lyssavirus (TWBLV) based on the sequence analysis4. In the second case, the results obtained from the FATs employing each of the two commercial FITC-conjugated anti-rabies antibodies were inconsistent, as described for the first case.

Figure 1
Figure 1: Bat lyssavirus diagnosis flow chart.
Flowchart showing the current process and diagnostic methods which our laboratory used now. Virus isolation should be performed when either the direct fluorescent antibody test or the reverse transcription polymerase chain reaction is positive. Please click here to view a larger version of this figure.

Figure 2
Figure 2: Direct FAT with two commercial FITC-conjugated anti-rabies antibodies of whole brain compression from a TWBLV-infected bat yielding inconsistent results.
Case number: 2016-2300: (A) The FAT with Reagent A (5x dilution), demonstrating apple green positive signals. (B) The FAT with Reagent B, showing a negative result (20x dilution). Please click here to view a larger version of this figure.

Figure 3
Figure 3: Products of RT-PCRs employing two primer sets.
The primer set used in lanes 1 to 3 was JW12/N165-146, and the expected product size was 111 base pairs. The primer set used in lanes 4 to 6 was N113F /N304R, and the expected product size was 521 base pairs. Both tests of the sample (lanes 1 and 4) were positive. M = 100 bp DNA ladder; lanes 1 and 4 = tested sample; lanes 2 and 5 = positive controls; lanes 3 and 6 = negative controls. Please click here to view a larger version of this figure.

Figure 4
Figure 4: BLAST result of N113F/N304R product of TWBLV infected bat.
BLAST results showed that the case was most similar to the lyssavirus, but the identity with the lyssavirus in the database was only 79%. Please click here to view a larger version of this figure.

Figure 5
Figure 5: Comparison of lyssavirus antigen distribution of virus isolation of TWBLV with two FITC-conjugated anti-rabies conjugates.
The 10% bat brain emulsion (TWBLV infected) was inoculated into mouse neuroblastoma cells for virus isolation. The FATs were performed at the tenth passage and stained with two FITC-conjugated anti-rabies antibodies. Antigen distribution of mouse neuroblastoma cells with two rabies conjugates showed significant differences. (A) The FAT with Reagent A (5x dilution). (B) The FAT with Reagent B (5x dilution). Please click here to view a larger version of this figure.

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Discussion

This laboratory standard operating procedure (SOP) provides a serial process for testing bat samples for the presence of lyssavirus antigens in Taiwan. The key steps include the employment of FAT and RT-PCR. The selection of suitable samples and successful isolation of the virus are also important. Additionally, some troubleshooting was conducted during the monitoring of bat lyssaviruses. The major difference was the target animals. Initially (2008–2009), the target animals of bat lyssavirus surveillance were live bats, which were trapped in Kinmen Island in Taiwan then tested for lyssavirus after euthanasia. Most of the trapped bats were healthy and unlikely to carry lyssavirus, and this approach to monitoring was not humane. Therefore, in the third year, only dead or dying bats were collected and expand the surveillance area from regional to national. After eight years of continuous monitoring, the first bat lyssavirus case was finally detected in Taiwan.

Although FAT is the most widely used method for rabies diagnosis and recommended by OIE and WHO18, few studies have demonstrated inconsistent results when different conjugates were used in the FAT5,27. Similar inconsistent results also appeared in TWBLV-infected cases. In the TWBLV-infected MNA cells, the results of FAT showed significant differences in 2 conjugates (Figure 5). One of the FITC-conjugated anti-rabies antibodies did not react well, even at higher concentrations. Because of the variation of lyssavirus antigen in the samples and the variation of the antibody avidity and affinity of antibodies in the conjugates, it is recommended that two different conjugates be used in FAT to prevent false negative results in lyssavirus diagnosis23,28,29.

RT-PCR can provide confirmatory diagnosis for inconsistent results of FAT. Due to the high genetic diversity of lyssavirus, it is recommended that more than one primer set in RT-PCR be used to increase the accuracy of lyssavirus screening29,30. A primer set designed from highly conserved nucleoprotein genes is the most commonly used set in lyssavirus detection29. RT-PCR can also be used for diagnosis in putrefactive samples when FAT cannot be performed31,32. To avoid false negativity preventing the discovery of a novel lyssavirus, more tools are recommended for detection. Two novel lyssaviruses4, Taiwan bat lyssavirus, were identified during this survey employing the SOP.

Additionally, one highly diverse TWBLV strain and a novel new species of lyssavirus were found in bats in Taiwan in 2018 (unpublished data). The findings proved that employment of both the FAT and RT-PCR to detect lyssaviruses in bats is useful. Some limitations of the RT-PCR primer set used in this SOP should be noted. In the primer set of N113F/N304R, N113F was originally designed for rabies virus amplification, but it may not work well for other lyssaviruses. Several primers for lyssavirus detection have been published by other researchers29,30 and can be chosen according to laboratory needs.

This article is a step-by-step introduction to bat lyssavirus surveillance in Taiwan. It is hoped that this SOP will be helpful to researchers who are interested in bat lyssavirus surveillance. As more researchers carry out surveys of bats, more lyssaviruses will be identified in the future. This SOP monitors not only lyssaviruses but also other zoonoses agents in bats. Such findings can inform the public, health professionals, and scientists of the potential risks of contact with bats and other wildlife. It will also help increase understanding of the evolution and origins of the lyssavirus and lead to substantial progress in scientific research.

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Disclosures

No conflicts of interest are declared.

Acknowledgments

We thank Tien-Cheng Li, Yi-Tang Lin, Chia-Jung Tsai, and Ya-Lan Li for their assistance during this study. This study was supported by grant no. 107AS-8.7.1-BQ-B2 (1) from the Bureau of Animal and Plant Health Inspection and Quarantine, Council of Agriculture, Executive Yuan, Taiwan.

Materials

Name Company Catalog Number Comments
2.5% Trypsin (10x) Gibco 15090046 Trypsin
25 cm2 flask Greiner bio-one 690160
Acetone Honeywell 32201-1L
Agarose I VWR Life Science 97062-250
Alcohol NIHON SHIYAKU REAGENT NS-32294
AMV Reverse Transcriptase Promega M5101
Antibiotic-Antimycotic(100X)  Gibco 15240-062 MEM-10
Blade Braun BA215
Centrifuge eppendorf 5424R
Chemilumineance system TOP BIO CO. MGIS-21-C2-1M
Collection tube Qiagen 990381
Collection tube SSI 2341-SO
Cover slide Muto Pure chemical Co., LTD. 24505
DNA analyzer Applied Biosystems 3700XL
Fetal bovine serum Gibco 10437028 MEM-10
FITC Anti-Rabies Monoclonal Globulin Fujirebio Diagnostic Inc. 800-092 FITC-conjugated anti-rabies antibodies: reagent B
Four-well Teflon-coating glass slide Thermo Fisher Scientific 30-86H-WHITE
Gel Electrophoresis System Major Science MJ-105-R
HBSS (1x) Gibco 14175095 Trypsin
Incubator ASTEC SCA-165DS
Inverted Microscope Olympus IX71
L-Glutamine 200 mM (100x) Gibco A2916801 MEM-10
LIGHT DIAGNOSTICS Rabies FAT reagent EMD Millipore Corporation 5100 FITC-conjugated anti-rabies antibodies: reagent A
MagNA Pure Compact Instrument Roche 03731146001
MagNA Pure Compact NA Isolation Kit 1 Roche 03730964001
MEM (10x) Gibco 11430030 MEM-10
MEM NEAA (100x) Gibco 11140050 MEM-10
MEM vitamin solution Gibco 11120052 MEM-10
NaHCO3 Merck 1.06329.0500 MEM-10
Needle Terumo NN*2332R9
PBS Medicago 09-8912-100
Primer synthesis Mission Biotech
RNasin ribonuclease inhibitor Promega N2111
Sequencing service Mission Biotech
Slide Thermo Scientific AA00008032E00MNT10
Sodium Pyruvate (100 mM) Gibco 11360070 MEM-10
Stainless Steel Beads QIAGEN 69989
Sterile absorbent pad 3M 1604T-2
Syringe filter Nalgene 171-0045
Taq polymerase JMR Holdings JMR-801
Thermal cycler Applied Biosystems 2720
TissueLyser II QIAGEN 85300
Tongue depressor HONJER CO., LTD. 122246
Tweezer Tennyson medical Instrument developing CO., LTD. A0601
Tylosin Tartrate Sigma T6271-10G MEM-10

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References

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