An ICMR-led study combined clinical data with full genome sequencing to trace how the virus entered and evolved in India.
Published Jan 22, 2026 | 9:39 AM ⚊ Updated Jan 22, 2026 | 9:39 AM
Synopsis: A detailed genetic study by Indian researchers uncovered evidence of a hidden mpox Clade Ib outbreak in the Gulf region. Cases of Clade Ib were being imported from the UAE to India since September 2024; yet, the emergence of the first official case of Clade Ib in the UAE was in February 2025. The study combined clinical data with full genome sequencing to trace how the virus entered and evolved in India.
Kerala was importing mpox Clade Ib cases from the United Arab Emirates since September 2024. However, the UAE’s first “official” case wasn’t reported until February 2025, according to a detailed genetic study by Indian researchers who uncovered evidence of a hidden outbreak in the Gulf region.
The peer-reviewed study, published in the journal Virology, analysed ten laboratory-confirmed cases of mpox Clade Ib reported in Kerala between September 2024 and March 2025. Researchers found that nine patients had recently travelled abroad, mostly to the United Arab Emirates, while one case showed local transmission through close household contact with a returning traveller.
The study’s most striking finding centres on the timeline of infections. Cases of Clade Ib were being imported from the UAE since September 2024; yet, the emergence of the first official case of Clade Ib in the UAE was in February 2025, as reported by the World Health Organisation.
“Such a case underscores the presence of undetected and likely underreported mpox cases in the UAE,” the authors wrote in their discussion of the findings.
The research was led by scientists from the Indian Council of Medical Research’s National Institute of Virology in Pune, along with teams from Kerala government medical colleges and surveillance units. The study combined clinical data with full genome sequencing to trace how the virus entered and evolved in India.
The analysis revealed that the Kerala virus samples clustered genetically with mpox Clade Ib strains reported from Oman, Pakistan and Thailand, suggesting a shared regional transmission network rather than a single imported case. This pattern, the researchers said, points to repeated introductions linked to international travel and wider regional circulation.
“The identification of ten Clade Ib cases in India, with nine linked to international travel, predominantly to the UAE, strongly underscores the role of global connectivity in the rapid dissemination of emerging infectious diseases,” the authors noted.
Of the ten Indian cases, eight individuals had travelled to the UAE and one to Oman. One case, from Kerala, had no direct international travel but was a close contact of her husband, who had recently returned from Dubai, suggesting a probable instance of secondary transmission.
“This epidemiological link underscores the role of international travel in the introduction of Clade Ib into India,” the study stated.
Crucially, the study detected strong APOBEC3 mutation signatures across the Kerala samples. These mutations arise when the human immune system edits viral genetic material and are considered a marker of sustained human-to-human transmission. Compared to older mpox variants, Clade Ib showed a higher burden of such mutations, indicating active viral evolution.
“The higher APOBEC3-associated mutations in Clade Ib support sustained human-to-human transmission,” the researchers wrote. “APOBEC3 enzymes are part of the host’s innate immune response, inducing mutations in viral genomes during replication, which typically displays a mutation pattern of ‘TC → TT’ and ‘GA → AA’. The accumulation of these mutations serves as a genomic signature of repeated cycles of human-to-human transmission, leading to increased viral genetic diversity,” the study noted.
Six of the ten Kerala cases carried a newly identified mutation in a gene associated with immune system interaction. Researchers said this finding suggests the virus continues to adapt as it spreads, although the clinical impact of this specific mutation remains under investigation.
“A key observation is the identification of a new, unique non-synonymous mutation (G3703A) in the OPG003 gene found in six of the ten Indian viral sequences analysed,” the authors explained. “OPG003, which encodes an Ankyrin repeat-containing protein, plays a role in modulating the host’s immune response. This newly discovered mutation may represent a recent evolutionary adaptation that specifically affects viral properties in the Indian population, possibly altering how the virus interacts with the host’s immune defences.”
Clinically, all patients experienced fever, lymph node swelling and widespread vesiculo-pustular lesions, with a high proportion reporting genital involvement. All ten recovered without complications.
The median age of the cases was 34 years, with a male predominance at 80 percent. Among the patients, five individuals reported heterosexual contact in the foreign country approximately three weeks before symptom onset, while the remaining five denied any sexual contact.
Viral load measurements showed peak infectivity during the first two weeks of illness, reinforcing concerns about early transmission risk. “The early acute phase is crucial for transmission, particularly in high-viremia cases like Case-10,” the researchers noted, referring to a patient who had the highest viral load at 1.2 × 10⁸ copies/ml at day 10.
“Depending on the specimen type and collection time, peak viral loads among the ten cases were typically found between POD 6 and 13, ranging from roughly 10² to 10⁸ copies/ml,” the study found. “In most cases, viral DNA is cleared by POD 20–28; however, in some cases, prolonged detection was observed up to POD-34 or beyond.”
The authors warned that the combination of frequent international travel, efficient human transmission and ongoing genetic change makes mpox Clade Ib a public health concern.
“The findings highlight several key points, including the majority of cases were in young males, which is consistent with the ongoing global mpox outbreak epidemiology,” they wrote. “The presence of genital and oral lesions in a high proportion of cases underscores the importance of considering sexual transmission in the spread of this outbreak of mpox Clade Ib.”
They called for enhanced genomic surveillance, rapid case detection and close monitoring of travellers from affected regions to prevent further spread within India.
“This clustering indicates that the introductions into India are likely part of a broader spread within Asia, potentially originating from or circulating through common hubs like the UAE,” the researchers concluded. “The single case of probable secondary transmission within India further highlights the potential for localised spread upon introduction, emphasising the need for robust surveillance and contact tracing measures.”
The study represents the first in-depth analysis of the clinical and genomic characteristics of mpox Clade Ib identified in India, highlighting the critical role of international travel in virus introduction and indicating local transmission following introduction, with regional linkage inferred from epidemiological evidence.
(Edited by Muhammed Fazil.)
