ABSTRACT
Mpox virus from Clade I exhibits high virulence and poses significant mortality risks, especially among children. We isolated a strain of the mpox virus (hMpxV/Uganda/MUWRP-H1922SL/2025) from an adult woman in Uganda. Using phylogenetic tree analysis and PoxServer evaluation, we determined that this strain belongs to Clade/Lineage Ib.
KEYWORDS: mpox, Poxviridae, Orthopoxvirus
ANNOUNCEMENT
Mpox virus, previously known as monkeypox virus (MPXV), is a double-stranded DNA virus in the genus Orthopoxvirus and family Poxviridae (1). MPXV is divided into two clades: the virulent Central African Clade I and the less virulent West African Clade II (2). Transmission occurs by contact with wild mammals and person-to-person spread via respiratory secretions, skin contact, and contaminated fomites. Symptoms include fever, papular and vesiculopustular lesions, and lymphadenopathy (2). Severe infection can result in pneumonitis, encephalitis, keratitis, bacterial superinfection, and sometimes death (3). This study reports the genome of the mpox virus isolated from the skin lesion of an adult female at General Military Hospital Bombo (latitude:0.586389; longitude:32.536111) in Uganda.
A sample collected from a skin lesion was put in viral transport medium. DNA extraction from the sample was done using QIAamp MinElute Virus Spin Kit (50) (Qiagen, Cat No. 57704). An in-house real-time RT-PCR assay was used as previously described (4) to confirm the sample as positive for MPXV with a Ct value of 18. RT-PCR amplification was performed according to the SISPA Long-Fragment Superscript IV Reverse Transcriptase Protocol. The library was prepared according to the Rapid Sequencing DNA V14 Barcoding (SQK-RBK114.24 or SQK-RBK114.96) MinION Protocol and purified with AMPure XP beads to remove unwanted fragments. The final library was quantified using the Qubit dsDNA High-Sensitivity Assay, Qubit 4 fluorometer (Thermo Fisher Scientific, Waltham, United States). Sequencing of the prepared library was done on R10 MinION flow cells (FLO-MIN114, Oxford Nanopore Technologies, England) using MinION Mk1D sequencer with MinKNOW 25.03.9 software for 24 h. Base calling during sequencing was conducted using Dorado v1.1.1 (5). The sequencing produced 6,422,894 reads with an N50 value of 604 bp. Sequence read quality filtering was performed using fastp v0.23.2 to remove adapter sequences and short reads (6). An in-house tool (Virnano v001) built using Minimap2 v2.30-r1287 (7), Racon v1.4.13 (8), and Medaka v1.7.3 was used to map raw reads to the reference PQ178862 (9) and generate a consensus assembly. This assembly produced a consensus sequence with a coverage of 99.64× and an average depth of 90.26 reads. Clade assignment was done by matching consensus to related sequences in PoxSurver in GISAID (https://gisaid.org/). Contemporary sequences (2024–2025) from both clades I and II were retrieved from GISAID for comparison. Multiple sequence alignment was done with Mafft v7.526 (10), and a phylogenetic tree was constructed using IQtree v2.0.7 (11). The tree was annotated in ITOL (12). Default parameters for software were used, except where otherwise noted.
The partial genome was 195,619 bp in length and had a guanine-cytosine (GC) content of 33.06% and 179 predicted genes. PoxServer classified the clade/lineage of this genome as Ib. The genome matches closely to strain hMpxV/DRC/005/1978 in PoxServer. Phylogenetic tree analysis grouped this strain alongside clade Ib sequences from various geographic regions (Fig. 1). This information is crucial for ongoing surveillance of the mpox virus and its evolution and spread across the East and Central Africa region.
Fig 1.
Phylogenetic tree showing the mpox virus clade with strain hMpxV/Uganda/MUWRP-H1922SL/2025 from Uganda clusters.
ACKNOWLEDGMENTS
This work was funded by the Armed Forces Health Surveillance Branch (AFHSB), Global Emerging Infections Surveillance (GEIS) Section under ProMIS ID P0139_24_KY and P0118-24-RD.
The funders had no role in study design, data collection, and analysis, decision to publish, or preparation of the manuscript. The views expressed are those of the authors and do not reflect the official policy or position of the Department of Defense or the US Government.
Contributor Information
Denis K. Byarugaba, Email: denis.byarugaba@mak.ac.ug.
John J. Dennehy, Queens College Department of Biology, Queens, New York, USA
DATA AVAILABILITY
The genome sequence has been deposited in GenBank and can be retrieved using accession number PX711335. The raw sequence reads are available in the Sequence Read Archive (SRA) under BioProject PRJNA1331542 and can be retrieved with accession SRR35645093.
ETHICS APPROVAL
The study was approved by Makerere University School of Public Health Higher Degrees and Research Ethics Committee (HDREC087).
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Associated Data
This section collects any data citations, data availability statements, or supplementary materials included in this article.
Data Availability Statement
The genome sequence has been deposited in GenBank and can be retrieved using accession number PX711335. The raw sequence reads are available in the Sequence Read Archive (SRA) under BioProject PRJNA1331542 and can be retrieved with accession SRR35645093.