Table 1.
Strains of Orientia tsutsugamushi used in this study
| Cluster* | Strain | Source (when available) | Geographical origin | GenBank accession no. | Reference |
|---|---|---|---|---|---|
| Karp | 402I | Human | Japan | AF173047 | 14 |
| Karp | Kamimoto | Human | Japan | AF173046 | 14 |
| Karp | Mori | Human | Japan | AF173044 | 14 |
| Karp | Okazaki | Human | Japan | AF173045 | 14 |
| Karp | CMM1 | Rodent | Japan | AF302986 | 15 |
| Karp | KNP1 | Rodent | Japan | AF302987 | 15 |
| Karp | KNP2 | Rodent | Japan | AF302988 | 15 |
| Karp | Hirahata | Chiggers | Japan | AF173176 | 16 |
| Karp | R39 | Chiggers | Japan | AF201836 | 16 |
| Karp | R9 | Chiggers | Japan | AF201837 | 16 |
| Karp | Jecheon | Human | Korea | AF430143 | Unpublished |
| Karp | TW261 | Rodent | Taiwan | AY222636 | 17 |
| Karp | Karp | Human | New Guinea | AY956315 | Direct Submission |
| Karp | Matsuzawa | Human | Japan | AF173043 | 14 |
| Karp | Yeojoo | Human | Korea | AF430144 | Unpublished |
| TW73R | Rodent | Taiwan | AY222628 | 17 | |
| Saitama | TW121 | Rodent | Taiwan | AY222639 | 17 |
| Saitama | TW141 | Rodent | Taiwan | AY222638 | 17 |
| Saitama | TW441 | Rodent | Taiwan | AY222634 | 17 |
| Saitama | FAR1 | Rodent | Japan | AF302989 | 15 |
| Saitama | HSB1 | Rodent | Japan | AF302983 | 15 |
| Saitama | HSB2 | Rodent | Japan | AF302984 | 15 |
| Saitama | UAP1 | Rodent | Japan | AF302991 | 15 |
| Saitama | UAP2 | Rodent | Japan | AF302992 | 15 |
| Saitama | UAP4 | Rodent | Japan | AF302993 | 15 |
| Saitama | UAP7 | Rodent | Japan | AF302995 | 15 |
| Saitama | Pajoo | Human | Korea | AF430142 | Direct Submission |
| Saitama | Yongworl | Human | Korea | AF430141 | Direct Submission |
| LA-1 | Chiggers | Thailand | AF173049 | 14 | |
| TW45R | Rodent | Taiwan | AY222632 | 17 | |
| TW201 | Rodent | Taiwan | AY222637 | 17 | |
| TWyu81 | Chiggers | Taiwan | AY222640 | 17 | |
| Boryong | Kuroki | Human | Japan | M63380 | 7 |
| Boryong | Nishino | Human | Japan | AF173048 | 14 |
| Boryong | Boryong | Human | Korea | AM494475 | 18 |
| Kato | Kato | Human | Japan | M63382 | 7 |
| Kato | Akita-7 | Rodent | Japan | AF173041 | 14 |
| Kato | Omagari | Rodent | Japan | AF173040 | 14 |
| LF-1 | Chiggers | Thailand | AF173050 | 14 | |
| Kawasaki | Kawasaki | Human | Japan | M63383 | 7 |
| Kawasaki | Kanda | Human | Japan | AF173039 | 14 |
| Kawasaki | Oishi | Human | Japan | AF173037 | 14 |
| Kawasaki | Taguchi | Human | Japan | AF173038 | 14 |
| Gilliam | Gilliam | Taiwan | DQ485289 | Unpublished | |
| Gilliam | Neimeng-65 | China | AF140143 | Unpublished | |
| Gilliam | TW461 | Rodent | Taiwan | AY222631 | 17 |
| Gilliam | 405S | Human | Japan | AF173036 | 14 |
| Gilliam | Ikeda | Human | Japan | AF173033 | 14 |
| Gilliam | Iwataki-1 | Rodent | Japan | AF173035 | 14 |
| Gilliam | LP-1 | Chiggers | Japan | AF173034 | 14 |
| Gilliam | FAR2 | Rodent | Japan | AF302990 | 15 |
| Gilliam | HSB3 | Rodent | Japan | AF302985 | 15 |
| Gilliam | UAP6 | Rodent | Japan | AF302994 | 15 |
| Gilliam | Yonchon | Human | Korea | U19903 | 19 |
| Gilliam | SXH951 | Human | China | AF050669 | Unpublished |
| Shimokoshi | Human | Japan | M63381 | 7 | |
| Fuji | Chiggers | Japan | AF201834 | 16 | |
| LX-1 | Chiggers | Japan | AF173042 | 14 | |
| TA678 | Rodent | Thailand | U19904 | 20 | |
| TW381 | Rodent | Taiwan | AY222635 | 17 | |
| TW521 | Rodent | Taiwan | AY222630 | 17 | |
| TA763 | Rodent | Thailand | U80636 | 20 | |
| TA686 | Rodent | Thailand | U80635 | 20 | |
| TA716 | Rodent | Thailand | U19905 | 20 | |
| TW44R | Rodent | Taiwan | AY222633 | 17 | |
| TW62R | Rodent | Taiwan | AY222629 | 17 | |
| TWyu11 | Chiggers | Taiwan | AY222641 | 17 |