Volume 31, Number 11—November 2025
Research
Monkeypox Virus Partial-Genome Amplicon Sequencing for Improvement of Genomic Surveillance during Mpox Outbreaks
Table 3
Characteristics of formalin-fixed (nos. 41–45) or inconclusive (nos. 46–48) MPXV specimens from the United States and sequencing read depths over the 10-kb and 15-kb regions or the whole genome of MPXV for study of partial-genome amplicon sequencing for improvement of genomic surveillance during mpox outbreaks*
| Specimen no. | Source | Year | DNA concentration, ng/μL | Ct | 10-kb | 15-kb | Genome |
|---|---|---|---|---|---|---|---|
| 41 | Tissue | 2022 | 39.4 | 17.1 | 576 | 347 | 9.6 |
| 42 | Tissue | 2022 | 6.3 | 17.1 | 981 | 1,065 | 0.1 |
| 43 | Rectum | 2023 | 56.4 | 17.4 | 794 | 977 | 17.9 |
| 44 | Lung | 2023 | 3.0 | 30.4 | 869 | 382 | 0.07 |
| 45 | Tissue | 2024 | 7.4 | 17.3 | 741 | 698 | 28.4 |
| 46 | Swab | 2024 | 0.0 | 37.1 | 69 | 1,391 | NA |
| 47 | Swab | 2024 | 0.0 | 37.3 | 15 | 691 | NA |
| 48 | Swab | 2024 | 0.0 | 37.2 | 359 | 1,092 | NA |
| 49 | Swab | 2024 | 0.0 | 38.4 | 25 | 155 | NA |
*Total DNA was extracted from formalin-fixed MPXV tissue specimens from different body sources of patients in the United States during 2022–2024 (nos. 41–45) or inconclusive specimens (nos. 46–49) with MPXV Ct >37. DNA concentrations (ng/µL), MPXV Ct values, and read depths over the 2 genomic regions (10-kb and 15-kb) derived from amplicon sequencing or over the whole genome (genome) of MPXV derived from metagenomic sequencing on DNA samples included. Whole-genome sequencing was not performed on 3 inconclusive specimens (nos. 46–48) or failed on specimen no.49; sequencing read depths over the whole genome of MPXV were not available. Ct, cycle threshold; MPXV, monkeypox virus; NA, not available.