Nepal’s First Whole Genome Sequencing of the Monkeypox Virus: Imported Cases from Saudi Arabia with Evidences of Secondary Transmission

Abstract

Monkeypox (Mpox) is an infection caused by a zoonotic orthopoxvirus that is being reported in non-endemic regions. We present here 4 confirmed and probable cases managed at Sukraraj Tropical and Infectious Disease Hospital, Teku, Kathmandu. Three patients were Nepalese men returning from Saudi Arabia with fever, malaise, and papulopustular rashes. The fourth case, the wife of one patient, developed fever, myalgia, lethargy, headache, and later vaginal pustular lesions progressing to ulcers, indicating secondary transmission. Lesion swabs and crust samples underwent real-time PCR at the National Public Health Laboratory (NPHL), Teku, Kathmandu, Nepal targeting G2R and F3L genes, all testing positive (Ct ?35). Positive samples were sequenced in-country at NPHL for the first time using the PrimalSeq protocol on an Illumina MiSeq platform. Genome analysis confirmed Clade IIb A.2, matching strains circulating in Europe and the Middle East. NPHL’s clade identification was concordant with WHO reference laboratories, validating Nepal’s genomic capacity.
Keywords: Clade IIb A.2; genome sequencing; Monkeypox; Mpox; Nepal