Emergence and co-circulation of Clade Ib and Clade IIb Mpox viruses in Khyber Pakhtunkhwa Pakistan, 2024–2026: clinical, genomic, and public health insights from a non-endemic region

Mpox remains a global public health concern, with increasing reports of travel-associated and locally acquired infections outside historically endemic regions. Pakistan is particularly vulnerable to repeated introductions because of extensive labor migration to Gulf countries and limited decentralized diagnostics. We aimed to characterize the clinical, epidemiological, and genomic features of Mpox cases detected in Pakistan during 2024-26 and assess evidence of local transmission. We conducted a descriptive cross-sectional study of all patients meeting WHO Mpox suspected-case criteria and reported through the Khyber Pakhtunkhwa-Integrated Disease Surveillance and Response System between August 1, 2024 and April 16, 2026. Clinical and epidemiological data were retrieved via standardized surveillance forms. Diagnostic confirmation used real-time PCR, and whole-genome sequencing (WGS; Illumina iSeq) was performed on samples with Ct ≤ 23. Among 137 suspected cases, 29 were laboratory-confirmed. Median age was 31 years (range 0.6–80 years); 20 (68.9%) were male, eight (27.6%) female, and one (3.4%) transgender. Thirteen (44.8%) infections were imported, five (17.2%) were secondary transmission cases, six (20.7%) were locally acquired, and five (17.2%) were classified as probable local infections. Vesiculopustular rash was present in all cases (100%), followed by fever (82.8%), musculoskeletal pain (37.9%), genital or perianal lesions (34.5%) and sore throat (24.1%). Clinical illness was generally mild, and with most patients recovered completely; however, two patients died during the course of illness. Whole-genome sequencing of four representative cases identified both Clade IIb (lineage A.2.1) and Clade Ib viruses. Phylogenetic analysis showed close genetic relationships of the Pakistani genomes with sequences reported from Pakistan, the United States, Nepal, and Thailand. A locally acquired case was assigned to Clade Ib, providing the first genomic detection of Clade Ib in Pakistan. The first genomic detection of Clade Ib, alongside detection of Clade IIb, highlights the genetic diversity of MPXV detected in Pakistan. Epidemiological investigation identified both imported and locally acquired infections, underscoring the need for strengthened genomic surveillance, decentralized diagnostics, and improved access to vaccines and therapeutics.