Use of a Novel Detection Tool to Survey Orthohantaviruses in Wild-Caught Rodent Populations
Abstract
:1. Introduction
2. Materials and Methods
2.1. Primer Design
2.2. Plasmid Construction and Cultured Viruses
2.3. Trapping and Sample Collection
2.4. RNA Extraction
2.5. Reverse Transcriptase-Quantitative Polymerase Chain Reaction (RT-qPCR) and Nested PCR
2.6. DNA gel Electrophoresis
2.7. Sanger Sequencing
2.8. Software Programs
3. Results
3.1. Primer Design for Pan-Orthohantaviruses Detection
3.2. Validation of Pan-Orthohantavirus Primers for Detection of Both New and Old World Orthohantaviruses
3.3. Screening Wild-Caught Rodents Using Pan-Orthohantavirus Primers
3.4. Sequencing PCR Fragments of Positive Rodents to Confirm Orthohantavirus Infection
4. Discussion
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Acknowledgments
Conflicts of Interest
References
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Primer | Sequence (5′-3′) | Target Segment (Gene) | Size (bp) | TM | |
---|---|---|---|---|---|
PanHS1 | Forward | GGRCARACHGCWGAYTGG | S (N) | 248 | 62 °C |
Reverse | CCDGGHGTBADYTCHTCDGCYTTCAT | ||||
PanHS2 | Forward | GAYATGMGDAAYACNATHATGGC | S (N) | 207 | 61 °C |
Reverse | CWGGRTCCATRTCATCHCC | ||||
PanHS7 | Forward | GGVCARACMGCWGAYTGG | S (N) | 248 | 57 °C |
Reverse | CCWGGTGTNADYTCWTCDGC | ||||
PanHS8 | Forward | CAGGAYATGVGRAAYACVATHATGGC | S (N) | 210 | 63 °C |
Reverse | CTCWGGRTCCATRTCATCMCC |
Genus Species | # Screened (%) | Sex M/F (% +) | Lung Tissue |
---|---|---|---|
PanHS8 + (%) | |||
Peromyscus maniculatus | 28 (28%) | 16 (50%)/12 (42%) | 13 (46%) |
Peromyscus leucopus | 14 (14%) | 8 (38%)/6 (67%) | 7 (50%) |
Peromyscus truei | 29 (29%) | 13 (38%)/16 (63%) | 15 (52%) |
Peromyscus boylii | 10 (10%) | 6 (33%)/4 (50%) | 4 (40%) |
Peromyscus nasutus | 3 (3%) | 1 (0%)/2 (50%) | 1 (33%) |
Mus musculus | 7 (7%) | 5 (40%)/2 (0%) | 2 (29%) |
Thomomys bottae | 4 (4%) | 2 (100%)/2 (0%) | 2 (50%) |
Neotomas albigula | 4 (4%) | 2 (100%)/2 (50%) | 3 (75%) |
Reithrodontomys megalotis | 1 (1%) | 0 (0%)/1 (0%) | 0 (0%) |
Total(s) | 100 (100%) | 53 (45%)/47 (49%) | 47 (47%) |
| ||
Repeated RT-qPCR Samples | Positive Percentage Accuracy | Negative Percentage Accuracy |
Total (n = 73) | 82.6% | 90.0% |
Rodent Samples Results | Number (%) of Hantavirus-Negative or Positive Rodents |
---|---|
Negatives | 53 (53%) |
False positives | 2 (2%) |
Positives | 45 (45%) |
Total | 100 (100%) |
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Goodfellow, S.M.; Nofchissey, R.A.; Ye, C.; Dunnum, J.L.; Cook, J.A.; Bradfute, S.B. Use of a Novel Detection Tool to Survey Orthohantaviruses in Wild-Caught Rodent Populations. Viruses 2022, 14, 682. https://doi.org/10.3390/v14040682
Goodfellow SM, Nofchissey RA, Ye C, Dunnum JL, Cook JA, Bradfute SB. Use of a Novel Detection Tool to Survey Orthohantaviruses in Wild-Caught Rodent Populations. Viruses. 2022; 14(4):682. https://doi.org/10.3390/v14040682
Chicago/Turabian StyleGoodfellow, Samuel M., Robert A. Nofchissey, Chunyan Ye, Jonathan L. Dunnum, Joseph A. Cook, and Steven B. Bradfute. 2022. "Use of a Novel Detection Tool to Survey Orthohantaviruses in Wild-Caught Rodent Populations" Viruses 14, no. 4: 682. https://doi.org/10.3390/v14040682