Emergence of mpox in Guinea: sporadic clade IIa cases and a clade IIb upsurge

Camara, J.; Petersen, N. P.; Koundouno, F. R.; Annibaldis, G.; Kourouma, K.; Soropogui, B.; Ryter, S.; Millimono, S. L.; Conde, M.; Nelson, E. V.; van Gelder, C.; Le, M.; Kolie, E.; Millimouno, T. E.; Tolno, F. M.; Kamano, F. M.; Keita, M. B.; Bongono, S. A.; Tolno, F.; Traore, O.; Conde, S.; Camara, A.; Lemey, P.; Günther, S.; Duraffour, S.; Boumbaly, S.

doi:10.64898/2026.03.03.709059

Home/Archive/bioRxiv

bioRxiv · 10.64898/2026.03.03.709059

Emergence of mpox in Guinea: sporadic clade IIa cases and a clade IIb upsurge

View original source ↗Export metadata ↓

Abstract

BackgroundMpox virus (MPXV) has caused recurrent outbreaks in West Africa. However, Guinea had not previously reported laboratory-confirmed cases or MPXV genomic data. MethodsSuspected cases were identified in the NZerekore region as well as in the Conakry (Sept 2024- Dec 2025) and confirmed by real-time PCR in regional and central laboratories, respectively. Whole-genome sequencing using nanopore technology was performed in-country, followed by phylogenetic and time-scaled evolutionary analyses. FindingsThe first mpox case was clinically diagnosed in September 2024 in the NZerekore region and laboratory-confirmed by the prefectural laboratory in Gueckedou. In total, seven cases were confirmed in Forest Guinea, of which five complete or almost complete MPXV genomes were recovered. All belonged to MPXV clade IIa. Genomic divergence, ancestral dating, and low APOBEC3-associated mutation frequencies were consistent with multiple independent zoonotic spillover events. In June 2025, one of the first mpox cases of an unfolding outbreak was confirmed in Conakry. Whole genome sequencing revealed MPXV clade IIb lineage G.1. By December 2025, the number of laboratory-confirmed mpox cases nationwide increased to 2,151. A total of nine outbreak strains were sequenced, all belonging to Clade IIb. The genomes clustered with contemporaneous genomes from Sierra Leone and showed high APOBEC3-associated mutation frequencies, suggesting sustained human-to-human transmission in the region. InterpretationThese data demonstrate simultaneous circulation of MPXV clade IIa and IIb strains in Guinea, likely resulting from zoonotic spillover and human-to-human transmission, respectively. Decentralised diagnostics and in-country sequencing facilitated rapid case confirmation and genomic surveillance, highlighting the importance of these critical capacities for outbreak preparedness and response. FundingGerman Federal Ministry of Health and the German Center for Infection Research (DZIF).

Explore related subjects

genomics Preprint

Keep this discovery

Explore connections, maps & timelines

BibTeX RIS

Camara, J., Petersen, N. P., Koundouno, F. R., Annibaldis, G., Kourouma, K., Soropogui, B., Ryter, S., Millimono, S. L., Conde, M., Nelson, E. V., van Gelder, C., Le, M., Kolie, E., Millimouno, T. E., Tolno, F. M., Kamano, F. M., Keita, M. B., Bongono, S. A., Tolno, F., Traore, O., Conde, S., Camara, A., Lemey, P., Günther, S., Duraffour, S., Boumbaly, S.. 2026-03-05. Emergence of mpox in Guinea: sporadic clade IIa cases and a clade IIb upsurge. https://doi.org/10.64898/2026.03.03.709059

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Structural variation in repeat elements is widespread in normal human tissues and in tumorigenesis

Somatic mosaicism contributes to genomic variation, yet postzygotic structural variants remain under-characterized. We performed long- and short-read WGS from multiple individuals (n=47 normal tissues; n=168 samples) and identified mosaic structural variants in all individuals and germ layers, impacting a median 285.2 kb/genome. Nearly half of breakpoints were independently validated, with tissue distributions reflecting both early and late developmental origins. Most mosaic variants were repeat-mediated and 8.3% overlapped functional elements, an enrichment compared to germline variants. To extend these analyses in samples where long-read sequencing is infeasible, we measured repeat alterations from short-read sequencing, recapitulating mosaic tissue-specific differences. We characterized tumor- and tissue- specific variation in repeats across 15 cancer types and found tumor-related repeat variation to be similar in scale to that of normal mosaic variation. Tracking repeat changes in cell-free DNA provided a noninvasive approach for tumor monitoring. Our analyses revealed widespread repeat-driven structural variation in health and disease.

genomics↗

bioRxiv2026

RNA isoform-resolved multiplexed sequencing with bioorthogonal barcoding

RNA isoform dysregulation drives disease pathogenesis and is the target of FDA-approved splice-switching therapeutics. However, multiplexed sequencing methods discard splice junction information because only 3' termini are barcoded and counted. Here, we repurpose acylation and click chemistries to conjugate bioorthogonal barcodes (bobcodes) directly onto multiple internal positions along cellular RNAs. Bobcoded RNAs from multiple samples are pooled for multiplexed cDNA synthesis, during which reverse transcriptase switches from each RNA template onto its tethered bobcode with greater than 99% accuracy in species mixing experiments. Bobcode attachment intervals set cDNA insert sizes without a library fragmentation step, and priming with poly(dT) or random hexamers selects between 3'-end counting and full-length isoform capture. A bioorthogonal barcode-sequencing (BOB-seq v0.1) drug screen identifies transcriptome-wide on- and off-target RNA splicing effects and outperforms existing multiplexing RNA sequencing methods in workflow simplicity, sample-to-sample variability, and barcoding accuracy. Bobcodes add isoform resolution to scalable multiplexed RNA sequencing.

genomics↗

bioRxiv2026

Structural polymorphism and population-variable coding capacity of HERV-K(HML-2) in human pangenomes

Approximately 8% of the human genome is derived from ancient retroviral infections. The most recently integrated of these endogenous retroviruses is the HERV-K(HML-2) clade, whose expression has been associated with cancer, amyotrophic lateral sclerosis, and embryogenesis. Studies of HERV expression, particularly HML-2, have relied predominantly on short-read sequencing. However, the high similarity among HML-2 proviruses prevents many short reads from being assigned uniquely to individual loci. We therefore compared haplotype-resolved long-read genome assemblies from 292 donors to resolve variation in proviral structure and coding capacity. Several loci previously thought to be fixed were structurally polymorphic. Tandem arrays occurred at 13 loci and contained up to six proviral copies in a single array. At 8q11.23, we identified a previously undescribed full-length provirus in one haplotype. All 583 other haplotypes carried a solo-LTR. We found that standard reference genomes failed to represent the coding capacity retained in many individuals, whose proviruses contained intact open reading frames despite disruptive mutations in the reference sequences. Short-read genotypes left 32.5% of the tested donor-variant pairs unresolved at sites associated with viral reading frames. These findings show why HML-2 expression must be interpreted in the context of the structural and coding alleles each individual carries.

genomics↗