Second Recombinant Mpox Virus Merging Clades Ib and IIb Found in India

Genomic surveillance has once again caught evolution in the act. Researchers at the Indian Council of Medical Research—National Institute of Virology in Pune, working with clinical partners in Kerala and Puducherry, have characterized a travel-associated mpox case in India caused by a monkeypox virus (MPXV) genome that is a mosaic of two distinct viral clades, Ib and IIb. The finding, published in Nature Microbiology, represents only the second documented inter-clade recombinant MPXV in the world, following a virus detected in England in a traveller recently returned from Asia. The convergence of two independently discovered recombinants with strikingly similar genomic architecture suggests that recombination between circulating mpox lineages is not a one-off curiosity but a recurring feature of the ongoing global epidemic that surveillance systems must now be equipped to detect.

Poxviruses are large double-stranded DNA viruses, and recombination has long been recognized as a fundamental engine of their evolution. Laboratory studies dating back to the late 1980s demonstrated high levels of genetic exchange among poxvirus DNAs in infected cells, and comparative genomics of variola, the smallpox virus, revealed signatures of past recombination events in its evolutionary history. Recombination requires co-infection of a single cell by two genetically distinct viruses, after which the cellular and viral machinery can copy alternating templates, stitching together segments from each parent. In principle, mpox viruses from different clades could recombine wherever their transmission chains overlap — in a co-infected individual or, more plausibly given the epidemiology, in an animal reservoir host where viruses from distinct phylogeographic lineages might meet.

The Indian case came to light through the country’s mpox diagnostic network, which the Indian Council of Medical Research has been strengthening since the global outbreak of clade IIb virus began in 2022. The patient, who acquired the infection through travel, was managed clinically while specimens were forwarded for molecular testing and whole-genome sequencing. Initial real-time PCR screening could not have distinguished this virus from any other mpox infection, since standard assays target conserved genes shared across clades. Only when the researchers assembled the complete genome did the mosaic structure become apparent: stretches of sequence unambiguously derived from clade Ib, the lineage that emerged in Central Africa and spread internationally in 2024, alternating with stretches characteristic of clade IIb, the West African lineage behind the 2022 worldwide epidemic.

Detailed comparative analysis showed that the recombinant genome carries clade-defining mutations from both parental lineages. Clade-defining mutations are the fixed single-nucleotide changes that distinguish the major mpox clades Ia, Ib, IIa and IIb from one another; their simultaneous presence in a single genome, arranged in a block-like pattern along the chromosome, is the molecular fingerprint of recombination rather than convergent mutation. The team mapped 34 recombinant tracts — continuous segments of the genome inherited from one or the other parental clade — and identified 21 mutations that define the recombinant lineage itself. This pattern mirrors that of the UK recombinant virus, which likewise displayed 34 recombinant tracts and 21 recombinant lineage-associated mutations, a coincidence of architecture that points to a shared ancestry.

Phylogenetic analysis reinforced that conclusion. When individual recombinant tracts were extracted and placed on separate phylogenetic trees, each tract clustered with reference genomes from its parental clade, alternating between Ib and IIb positions depending on the segment examined. When whole recombinant genomes were compared with representative sequences from all four clades, the Indian and UK viruses formed a distinct group positioned intermediate between clades Ib and IIb. A phylogenetic network constructed with SplitsTree placed the recombinants in a characteristic box-like structure, a visual signature of reticulate evolution that arises when sequence relationships cannot be explained by a single branching tree. Statistical testing supported the inference of recombination among these viruses.

Beyond the phylogenetics, the team went a step further than most surveillance studies by isolating live virus. Clinical material was propagated in Vero CCL-81 cells, and cytopathic effects were observed by the third day after infection at the second passage, with the experiment repeated three times with consistent results. Virus isolation matters because it confirms that the recombinant genome was not an artefact of mixed sequencing reads from a co-infected patient but a viable, replicating virus. It also provides reagents for phenotypic characterization — growth kinetics, drug susceptibility, antigenicity — that sequence data alone cannot deliver. Both the clinical sample sequence and the isolate sequence were deposited publicly in the Pathoplexus database and the International Nucleotide Sequence Database Collaboration, under accession numbers that allow any laboratory to verify or extend the analysis.

The practical consequences for diagnostics are among the most important implications of the work. Several multiplex real-time PCR assays have been developed to differentiate mpox clades, exploiting clade-specific mutations to classify infections rapidly, and targeted assays exist specifically to detect the novel clade Ib lineage. A recombinant virus that combines genetic material from two clades can scramble such classifications: depending on which primer and probe sets are used, a single specimen might be typed as Ib, as IIb, or yield discordant results across targets. In the worst case, a diagnostic algorithm keyed to a clade Ib-specific mutation that falls inside a clade IIb-derived tract of the recombinant genome could produce a false negative for clade Ib classification. The authors outline a diagnostic workflow for the preliminary identification of suspected recombinant MPXV isolates, emphasizing that clade-typing assays should be interpreted alongside whole-genome sequencing whenever results are discordant or epidemiologically unexpected.

The broader epidemiological question raised by the finding is where and how these recombination events occurred. The Indian virus was imported through travel, and the UK virus was likewise detected in a traveller returning from Asia, yet both genomes cluster together, implying a common recombinant ancestor rather than two independent recombination events. That places the origin of this lineage in a location where clade Ib and clade IIb viruses circulate in proximity — a region where the 2024 clade Ib outbreak overlapped geographically with lingering clade IIb transmission. If such co-circulation is sustained, further recombinants can be expected. The properties of any recombinant cannot be assumed in advance: recombination can combine, dilute, or disrupt adaptive mutations affecting transmissibility, immune evasion, or antiviral susceptibility, and only phenotypic study of isolated viruses will resolve those questions.

For surveillance programmes, the lesson is that clade-labelled snapshots are no longer sufficient. The 2022 global mpox epidemic demonstrated how quickly a localized zoonotic spillover can become an international epidemic once a virus adapts to sustained human transmission, and the emergence of clade Ib in 2024 with higher reported severity underscored the cost of delayed recognition. Recombination adds a third dimension of unpredictability on top of mutation and geographic spread. Wastewater surveillance, which has successfully detected mpox in environmental samples, offers one complementary channel for tracking viral diversity at the population level, but it too depends on downstream sequencing to reveal recombinant structure. What the Indian and UK detections prove is that the global sequencing network, when properly resourced and connected to rapid data-sharing platforms such as Pathoplexus, can catch these events and alert the international community within the timeframe that matters for public health response.

The Indian study also illustrates the value of linking clinical care, laboratory diagnostics and research sequencing under a single coordinated response. State health authorities in Kerala coordinated disease control activities, clinical teams managed the patient, and the virology team at ICMR–NIV Pune performed molecular testing, genome sequencing, phylogenetic analysis and virus isolation as an integrated pipeline, supported by intramural funding and by the Department of Health Research’s programme to expand the national mpox laboratory network. The result is a complete characterization of a rare viral entity within weeks of detection — from bedside to genome to viable isolate to publicly shared sequence data. As mpox continues to circulate in humans and presumably in animal reservoirs, recombinant lineages such as this Ib/IIb mosaic will serve as markers of where distinct viral populations meet, and continued genomic surveillance, backed by standardized diagnostics capable of recognizing their mosaic genomes, will determine whether the world spots the next such virus before it spreads.

Subject of Research: Recombinant Clade Ib and IIb monkeypox virus identified in an imported mpox case in India

Article Title: Genomic surveillance of an imported recombinant Clade Ib and IIb monkeypox virus case in India

Article References: Sahay, R. R., Khurana, J., Moorkoth, A. P., PP, B., Shete, A. M., Yadav, S., Majumdar, T., Rani, S., Vijay, N., Mali, D., Kamble, S., Gavari, S., Gawande, P., Marathe, H., Acharya, A. K., Gupta, N., & Yadav, P. D. (2026). Genomic surveillance of an imported recombinant Clade Ib and IIb monkeypox virus case in India. Nature Microbiology. https://doi.org/10.1038/s41564-026-02508-y

Image Credits: AI Generated

DOI: 10.1038/s41564-026-02508-y

Keywords: mpox, monkeypox virus, recombination, Clade Ib, Clade IIb, genomic surveillance, whole-genome sequencing, phylogenetics, virus isolation, diagnostics, India, public health