Ongoing mpox outbreak in Kamituga, South Kivu province, associated with monkeypox virus of a novel Clade I sub-lineage, Democratic Republic of the Congo, 2024

Abstract

Since the beginning of 2023, the number of people with suspected monkeypox virus (MPXV) infection have sharply increased in the Democratic Republic of the Congo (DRC). We report near-to-complete MPXV genome sequences derived from six cases from the South Kivu province. Phylogenetic analyses reveal that the MPXV affecting the cases belongs to a novel Clade I sub-lineage. The outbreak strain genome lacks the target sequence of the probe and primers of a commonly used Clade I-specific real-time PCR.

Sustained Human Outbreak of a New MPXV Clade I Lineage in Eastern Democratic Republic of the Congo

“…16 Although the proposed Clade Ib is currently only represented by genomes from the Kamituga outbreak, the short fragmentary sequences isolated from earlier zoonotic mpox cases in the area suggest that this lineage likely pre-existed in a local, non-human animal reservoir. 15 Of note, a large ~1kbp deletion in the MPXV genome (Δ19,128-20,270 coordinates relative to the Clade I reference genome, GenBank accession: NC_003310) has been reported in genome sequences from Kamituga linked to this outbreak, 14 interfering with the Clade I-specific diagnostic PCR originally developed by Li et al 17 The new genomes associated with the thus far exhibit this deletion and will not amplify with the specific diagnostic. Conversely, the other MPXV Clade Ia genomes we sampled from 2023/2024 did not contain this deletion.…”

“…Of note, a large ∼1kbp deletion in the MPXV genome (Δ19,128-20,270 coordinates relative to the Clade I reference genome, GenBank accession: NC_003310) has been reported in genome sequences from Kamituga linked to this outbreak, 14 interfering with the Clade I-specific diagnostic PCR originally developed by Li et al 17 The new genomes associated with the Kamituga outbreak also contain this deletion, implying that all genomes sampled from Clade Ib thus far exhibit this deletion and will not amplify with the specific diagnostic. Conversely, the other MPXV Clade Ia genomes we sampled from 2023/2024 did not contain this deletion.…”

U.S. Preparedness and Response to Increasing Clade I Mpox Cases in the Democratic Republic of the Congo — United States, 2024

“…Geographic differences in demographic characteristics and viral genetic diversity suggest various transmission drivers (i.e., zoonotic, household, or sexual) in different provinces, resulting in a complex epidemiologic picture. In South Kivu province, where sexual transmission has been reported, a distinct lineage of clade I MPXV was observed, including genetic markers suggesting sustained human-to-human transmission and a deletion in a nonessential segment of the genome that includes the C3 gene targeted by CDC’s clade I–specific polymerase chain reaction (PCR) test ( 5 , 6 ).…”

“…In addition, some Laboratory Response Network, state public health, and commercial laboratories offer laboratory-developed tests (LDTs) §§§§ and FDA emergency use–authorized tests that can differentially detect clade II (thereby ruling out clade I); a few offer LDTs that differentially detect clade I. However, because of concerns about potential genomic deletions affecting test efficacy ( 5 , 6 ), CDC recommends that the NVO test be used in addition to clade-specific testing, and that positive NVO or negative clade II test results be further investigated through sequence analysis. ¶¶¶¶ In addition, CDC conducts surveillance using clade-specific PCR testing and sequence analysis of NVO-positive specimens received from other U.S. laboratories.…”

Roundtable Report: Discussion on mpox in DRC and Social Science Considerations for Operational Response

“…Research was reported from South Kivu indicating the presence of a new mpox strain, which can also be tricky to detect with some testing methods. 5 Participants reported outbreak differences in the two major hotspots, one in the west and one in the east. In Équateur province, a densely forested region, cases are largely amongst children in hunting communities.…”