Volume 31, Number 11—November 2025
Research
Monkeypox Virus Partial-Genome Amplicon Sequencing for Improvement of Genomic Surveillance during Mpox Outbreaks
Jiusheng Deng, Daisy McGrath, Kimberly Wilkins, Luis A. Haddock, Whitni Davidson, Demi B. Rabeneck, Joseph Madden, Vaughn Wicker, Adrienne Amuri-Aziza, Tony Wawina-Bokalanga, Placide Mbala-Kingebeni, Christina L. Hutson, Yu Li, and Crystal Gigante
Table 1
Characteristics of MPXV specimens with Ct <30 and amplicon sequencing read depths over the 10-kb and 15-kb genomic region of MPXV for study of partial-genome amplicon sequencing for improvement of genomic surveillance during mpox outbreaks*
| Specimen no. | Source/sample type | Country/year | DNA concentration, ng/μL | Ct | 10-kb | 15-kb |
|---|---|---|---|---|---|---|
| 1 | Back/lesion | USA/2024 | 4.7 | 19.8 | 1,279 | 554 |
| 2 | Swab drag | USA/2024 | 5.6 | 22.7 | 840 | 408 |
| 3 | Chest lesion | USA/2024 | 1.2 | 21.0 | 3,800 | 465 |
| 4 | Lesion | USA/2024 | 4.3 | 22.6 | 1,455 | 324 |
| 5 | Back/lesion | USA/2024 | 1.0 | 21.1 | 3,046 | 449 |
| 6 | Leg/skin swab | USA/2024 | 8.4 | 20.1 | 1,625 | 328 |
| 7 | Skin swab | USA/2024 | 1.0 | 22.0 | 1,417 | 487 |
| 8 | Eye/swab drag | USA/2024 | 4.0 | 21.2 | 1,019 | 345 |
| 9 | Penis/swab | USA/2024 | 10.7 | 19.2 | 1,097 | 464 |
| 10 | Penis/skin swab | USA/2024 | 1.4 | 21.7 | 1,750 | 584 |
| 11 | Penis/skin swab | USA/2024 | 9.3 | 19.9 | 2,760 | 479 |
| 12 | Chest/skin swab | USA/2024 | 9.1 | 21.9 | 950 | 116 |
| 13 | Back/skin swab | USA/2024 | 4.6 | 19.6 | 2,365 | 557 |
| 14 | Hand/skin swab | USA/2024 | 22.0 | 20.5 | 1,870 | 461 |
| 15 | Perianal/swab | USA/2024 | 2.9 | 21.3 | 1,259 | 432 |
| 16 | Penis/skin swab | USA/2024 | 2.1 | 19.6 | 2,363 | 281 |
| 17 | Perianal/swab | USA/2024 | 23.0 | 23.3 | 2,764 | 264 |
| 18 | Penis/skin swab | USA/2024 | 1.0 | 20.8 | 1,673 | 652 |
| 19 | Penis/lesion | USA/2024 | 10.9 | 21.5 | 932 | 241 |
| 20 | Lesion | USA/2024 | 2.5 | 23.8 | 3,095 | 272 |
| 21 | Crusts | DRC/2017 | 2.3 | 16.0 | 3,612 | 329 |
| 22 | Vesicles | DRC/2017 | 1.9 | 16.0 | 1,819 | 1,231 |
| 23 | Vesicles | DRC/2016 | 8.1 | 15.2 | 1,361 | 1,653 |
| 24 | Vesicles | DRC/2017 | 16.0 | 16.7 | 1,421 | 1,607 |
| 25 | Vesicles | DRC/2017 | 9.1 | 15.6 | 1,778 | 2,169 |
| 26 | Crusts | DRC/2016 | 89.0 | 13.0 | 142 | 1,469 |
| 27 | Vesicles | DRC/2017 | 62.0 | 18.0 | 797 | 1,056 |
| 28 | Vesicles | DRC/2017 | 30.0 | 17.0 | 212 | 670 |
| 29 | Vesicles | DRC/2017 | 28.0 | 22.3 | 1,180 | 762 |
| 30 | Vesicles | DRC/2016 | 20.0 | 20.7 | 783 | 698 |
| 31 | Swab | DRC/2024 | 0.8 | 22.6 | 2,022 | 1,520 |
| 32 | Swab | DRC/2024 | 0.2 | 25.2 | 2,300 | 1,835 |
| 33 | Swab | DRC/2024 | 6.0 | 17.7 | 1,856 | 1,339 |
| 34 | Swab | DRC/2024 | 9.0 | 17.8 | 1,147 | 895 |
| 35 | Swab | DRC/2024 | 0.2 | 25.1 | 1,907 | 1,532 |
| 36 | Swab | DRC/2024 | 4.9 | 19.0 | 1,718 | 1,254 |
*Total DNA was extracted from MPXV specimens (n = 36) from different body sources of patients in USA in 2024 (nos. 1–20) or in DRC during 2016–2024 (nos. 21–36). DNA concentrations (ng/µL), MPXV Ct values, and read depths over the 2 genomic regions of MPXV genomes (10-kb and 15-kb) derived from amplicon sequencing on DNA samples included. Ct, cycle threshold; DRC, Democratic Republic of the Congo; MPXV, monkeypox virus; USA, United States.
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