Multiplex PCR-Based Nanopore Sequencing and Epidemiological Surveillance of Hantaan orthohantavirus in Apodemus agrarius, Republic of Korea
Abstract
:1. Introduction
2. Materials and Methods
2.1. Ethics Statement
2.2. Sample Collection
2.3. Mitochondrial DNA Analysis
2.4. Indirect Immunofluorescence Antibody Test
2.5. Reverse Transcription-Polymerase Chain Reaction
2.6. Quantitative PCR
2.7. Multiplex PCR-Based Enrichment
2.8. Library Preparation for Sequencing on MinION Platform
2.9. Library Preparation for Sequencing on MiSeq Platform
2.10. Phylogenetic Analysis
3. Results
3.1. Trapping Sites of Small Mammals from the ROK
3.2. Serological and Molecular Prevalence of HTNV Collected from the ROK
3.3. HTNV RNA Loads and Determination of Viral Copy Number from A. agrarius Lung Tissues
3.4. Multiplex PCR-Based NGS of HTNV Using MinION or MiSeq Platforms
3.5. Phylogeographic Analysis
4. Discussion
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Species | Small Mammal Trapping Location | Total (%) | ||||||
---|---|---|---|---|---|---|---|---|
Paju | Pocheon | Pyeongtaek | Yeoncheon | Cheorwon | Chuncheon | Hwacheon | ||
Apodemus agrarius | 7 | 18 | 41 | 48 | 105 | 38 | 46 | 303 (86.6) |
Crocidura lasiura | -a | - | - | 1 | 7 | 4 | 1 | 13 (3.7) |
Crocidura shantungensis | - | - | - | - | 1 | 1 | 1 | 3 (0.9) |
Mus musculus | - | - | 7 | - | 9 | - | 1 | 17 (4.9) |
Myodes regulus | 2 | - | - | 1 | 1 | - | - | 4 (1.1) |
Micromys minutus | - | - | 2 | - | 1 | 2 | - | 5 (1.4) |
Microtus fortis | - | - | - | - | 1 | - | - | 1 (0.3) |
Rattus norvegicus | - | - | 3 | - | - | - | - | 3 (0.9) |
Tscherskia triton | - | - | - | - | - | - | 1 | 1 (0.3) |
Total | 9 | 18 | 53 | 50 | 125 | 45 | 50 | 350 (100) |
Trapping Site | Number of Captured A. agrarius | Seropositivity for Anti-HTNV IgG (%) | HTNV RNA Positivity (%) | ||||
---|---|---|---|---|---|---|---|
Male | Female | Total | Male | Female | Total | ||
Paju | 7 | 0/2 | 0/5 | 0/7 | -a | - | - |
Pocheon | 18 | 1/9 (11.1) | 0/9 | 1/18 (5.6) | 1/1 (100) | - | 1/1 (100) |
Pyeongtaek | 41 | 0/23 | 0/18 | 0/41 | - | - | - |
Yeoncheon | 48 | 2/22 (9.1) | 3/26 (11.5) | 5/48 (10.4) | 1/2 (50) | 1/3 (33.3) | 2/5 (40) |
Cheorwon | 105 | 5/60 (8.3) | 2/45 (4.4) | 7/105 (6.7) | 4/5 (80) | 2/2 (100) | 6/7 (85.7) |
Chuncheon | 38 | 0/18 | 1/20 (5) | 1/38 (2.6) | - | 0/1 | 0/1 |
Hwacheon | 46 | 4/20 (20) | 2/26 (7.7) | 6/46 (13.0) | 3/4 (75) | 0/2 | 3/6 (50) |
Total | 303 | 12/154 (7.8) | 8/149 (5.4) | 20/303 (6.6) | 9/12 (75) | 3/8 (37.5) | 12/20 (60) |
Viral RNA Copy Number (Copies/µL) | Sample | Site | Anti-HTNV IgG Titer | Nested RT-PCR | Ct Value | HTNV Genomes, % Coverage (Minimum Read Depth, >10×) | ||
---|---|---|---|---|---|---|---|---|
L Segment | M Segment | S Segment | ||||||
104 to 105 | Aa19-233 | Cheorwon | 1:64 a | Pos | 20.5 | 96.8 | 98.5 | 100 |
Aa19-278 | Cheorwon | 1:32 a | Pos | 22.2 | 92.9 | 98.4 | 100 | |
102 to 103 | Aa19-236 | Cheorwon | 1:32 a | Pos | 29.4 | 95.3 | 98.4 | 100 |
Aa19-36 | Cheorwon | 1:512 b | Pos | 29.7 | 91.7 | 98.4 | 100 | |
10 to 102 | Aa19-89 | Yeoncheon | 1:64 a | Pos | 31.8 | 95.9 | 98.4 | 100 |
Aa19-57 | Pocheon | 1:8096 b | Pos | 32.7 | 95.8 | 98.4 | 100 | |
Aa19-167 | Yeoncheon | 1:256 a | Pos | 34.0 | 95.9 | 96.4 | 100 | |
Aa19-38 | Cheorwon | 1:16,384 b | Pos | 34.4 | 92.3 | 98.4 | 100 | |
Aa19-153 | Hwacheon | 1:4096 b | Pos | 34.5 | 92.7 | 98.4 | 100 | |
1 to 10 | Aa19-152 | Hwacheon | 1:512 a | Pos | 36.4 | 82.6 | 97.0 | 92.1 |
Aa19-144 | Hwacheon | 1:256 b | Pos | 37.3 | 88.8 | 96.4 | 95.1 | |
0 to 1 | Aa19-39 | Cheorwon | 1:512 b | Pos | 40.0 | 65.4 | 90.6 | 92.2 |
Viral RNA Copy Number (Copies/µL) | Sample | Site | Ct Value | L Segment | M Segment | S Segment | |||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Insertion | Deletion | Mismatch | Accuracy a | Insertion | Deletion | Mismatch | Accuracy | Insertion | Deletion | Mismatch | Accuracy | ||||
104 to 105 | Aa19-233 | Cheorwon | 20.5 | 0 | 3 | 12 | 99.8 | 0 | 5 | 2 | 99.9 | 0 | 1 | 4 | 99.8 |
Aa19-278 | Cheorwon | 22.2 | 0 | 4 | 9 | 99.9 | 0 | 6 | 2 | 99.9 | 0 | 1 | 0 | 100 | |
102 to 103 | Aa19-236 | Cheorwon | 29.4 | 0 | 5 | 9 | 99.9 | 0 | 6 | 3 | 99.9 | 0 | 1 | 1 | 99.9 |
Aa19-36 | Cheorwon | 29.7 | 0 | 3 | 12 | 99.8 | 0 | 5 | 2 | 99.9 | 0 | 1 | 1 | 99.9 | |
10 to 102 | Aa19-89 | Yeoncheon | 31.8 | 0 | 3 | 6 | 99.9 | 0 | 5 | 6 | 99.8 | 0 | 1 | 1 | 99.9 |
Aa19-57 | Pocheon | 32.7 | 0 | 4 | 9 | 99.9 | 0 | 5 | 4 | 99.9 | 0 | 1 | 2 | 99.9 | |
Aa19-167 | Yeoncheon | 34.0 | 0 | 4 | 8 | 99.9 | 0 | 4 | 4 | 99.9 | 0 | 1 | 0 | 100 | |
Aa19-38 | Cheorwon | 34.4 | 0 | 3 | 12 | 99.8 | 0 | 5 | 7 | 99.8 | 0 | 1 | 2 | 99.9 | |
Aa19-153 | Hwacheon | 34.5 | 0 | 5 | 14 | 99.8 | 0 | 4 | 3 | 99.9 | 0 | 1 | 3 | 99.8 | |
1 to 10 | Aa19-152 | Hwacheon | 36.4 | 0 | 5 | 18 | 99.7 | 0 | 2 | 11 | 99.7 | 0 | 1 | 7 | 99.6 |
Aa19-144 | Hwacheon | 37.3 | 0 | 4 | 14 | 99.8 | 0 | 4 | 11 | 99.7 | 0 | 1 | 7 | 99.6 | |
0 to 1 | Aa19-39 | Cheorwon | 40.0 | 0 | 2 | 59 | 99.1 | 0 | 2 | 36 | 99.0 | 0 | 1 | 28 | 98.3 |
Total | Average (%) | 0 | 3.8 | 15.2 | 99.8 | 0 | 4.4 | 7.6 | 99.8 | 0 | 1 | 4.7 | 99.7 |
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Park, K.; Lee, S.-H.; Kim, J.; Lee, J.; Lee, G.-Y.; Cho, S.; Lee, S.H.; Park, K.; No, J.S.; Budhathoki, S.; et al. Multiplex PCR-Based Nanopore Sequencing and Epidemiological Surveillance of Hantaan orthohantavirus in Apodemus agrarius, Republic of Korea. Viruses 2021, 13, 847. https://doi.org/10.3390/v13050847
Park K, Lee S-H, Kim J, Lee J, Lee G-Y, Cho S, Lee SH, Park K, No JS, Budhathoki S, et al. Multiplex PCR-Based Nanopore Sequencing and Epidemiological Surveillance of Hantaan orthohantavirus in Apodemus agrarius, Republic of Korea. Viruses. 2021; 13(5):847. https://doi.org/10.3390/v13050847
Chicago/Turabian StylePark, Kyungmin, Seung-Ho Lee, Jongwoo Kim, Jingyeong Lee, Geum-Young Lee, Seungchan Cho, Seung Ho Lee, Kkothanahreum Park, Jin Sun No, Shailesh Budhathoki, and et al. 2021. "Multiplex PCR-Based Nanopore Sequencing and Epidemiological Surveillance of Hantaan orthohantavirus in Apodemus agrarius, Republic of Korea" Viruses 13, no. 5: 847. https://doi.org/10.3390/v13050847
APA StylePark, K., Lee, S. -H., Kim, J., Lee, J., Lee, G. -Y., Cho, S., Lee, S. H., Park, K., No, J. S., Budhathoki, S., Kim, Y. -J., Kim, Y. -S., Kim, H. -C., Klein, T. A., Kim, W. -K., & Song, J. -W. (2021). Multiplex PCR-Based Nanopore Sequencing and Epidemiological Surveillance of Hantaan orthohantavirus in Apodemus agrarius, Republic of Korea. Viruses, 13(5), 847. https://doi.org/10.3390/v13050847