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Genomic analysis conducted by Indian virology laboratories has identified Clade Ib mpox in samples collected from Kerala over the last two years. As per information available with National Institute of Virology (NIV) in Pune, most of the cases were linked to recent international travel, while at least one case indicates probable local transmission.
Ten mpox samples collected in Kerala between September 2024 and March 2025 were genetically sequenced by laboratories associated with the Indian Council of Medical Research (ICMR) and NIV, Pune. All 10 samples were found to belong to Clade Ib, a lineage that has been circulating internationally since 2024, experts confirmed.
Laboratory data show that nine of the 10 patients had a recent history of foreign travel. Most had returned from the United Arab Emirates to Kerala, while one had travelled from Oman. One patient reported no travel history, suggesting likely household transmission following exposure to an infected contact.
Public health experts said the findings confirm that Clade Ib is already present in India and underline the role of international travel in introducing new mpox strains into the country.
“The Kerala cluster is small, but epidemiologically significant. It demonstrates importation of Clade Ib and limited local transmission. Without genomic sequencing, this information would not have been available,” observes Pragya Yadav, Rima R Sahay and Anita M Shete, researchers involved in the study.
Mpox is a viral disease transmitted through close physical contact, including contact with skin lesions and body fluids. It can also spread through contaminated materials such as bedding and clothing. Prolonged face-to-face exposure is another known route of transmission.
The disease was historically confined to parts of Central and West Africa. Global transmission expanded after 2022, with outbreaks reported across Europe, the Americas and Asia.
Clade Ib was first extensively documented during outbreaks in the Democratic Republic of Congo. It has since been reported in several countries, including the United Kingdom, Germany, Spain, the Netherlands and India. Global health agencies are monitoring the strain due to evidence of sustained human-to-human transmission and ongoing genetic mutations.
According to World Health Organization (WHO) situation reports, more than 20,000 mpox cases have been recorded globally since 2024. The highest mortality has been reported from African countries with limited access to healthcare. Fatality rates remain low in high-income and middle-income countries. Even so, the WHO has warned that mpox is now a permanently global public health concern.
In India, mpox surveillance relies mainly on PCR testing through government laboratories. Genomic sequencing is not routinely conducted for all confirmed cases and is limited to select centres, including NIV Pune and a small number of Virus Research and Diagnostic Laboratories under the ICMR network.
As a result, most mpox cases in India are diagnosed without strain identification. This makes it difficult to trace transmission pathways and limits the ability to monitor viral evolution. Authorities are often unable to determine whether infections are linked to international introductions or local spread.
“There is no dedicated national genomic surveillance programme for mpox or other emerging zoonotic diseases. The sequencing infrastructure created during COVID-19 was not institutionalised for long-term pathogen monitoring,” said S S Lal, a Kerala-based public health expert.
Following the reporting of imported mpox cases, Kerala’s health department issued revised state guidelines in October 2024. These mandate isolation of suspected patients, contact tracing and the use of personal protective equipment by healthcare workers. Samples are required to be referred to designated laboratories for testing and sequencing.
State officials said district hospitals have been instructed to maintain isolation facilities during peak travel seasons. Rapid response teams were also activated, particularly in districts with high volumes of international arrivals.
However, health workers said sequencing capacity has remained limited over the past two years, with slow turnaround times. Samples from some districts took several days to reach reference laboratories, and genomic results often took weeks.
“By the time sequencing data becomes available, the epidemiological window for intervention has often already passed,” said a district surveillance officer in northern Kerala.
Experts also pointed to major gaps in India’s vaccine preparedness. Globally, the primary mpox vaccine in use is MVA-BN, marketed as JYNNEOS or Imvanex. It is recommended for healthcare workers, laboratory staff and high-risk contacts. Vaccine availability remains limited, and India currently does not have a national mpox vaccination programme.
In 2024, the Serum Institute of India signed a manufacturing agreement with Bavarian Nordic, the developer of the vaccine, to produce doses for Indian and global markets. However, large-scale production has not yet begun, and no national policy has been announced on vaccine deployment.
“There is no operational framework on who should be vaccinated or under what conditions,” said an immunisation researcher based in Bengaluru. “There is also no clarity on whether India will adopt ring vaccination. Even if vaccines become available, we are not institutionally ready.”
The Kerala cluster has also highlighted public health risks associated with migration and international mobility. The state has more than 2.5 million expatriates working in Gulf countries and handles thousands of international arrivals daily through airports in Kochi, Kozhikode, Kannur and Thiruvananthapuram.
India currently has no systematic mpox screening or surveillance mechanism at airports or ports. Detection depends largely on symptomatic individuals seeking medical care after returning from abroad.
In the Kerala cluster, most patients developed symptoms several days after their return, suggesting that infections were imported undetected and identified only after clinical presentation.
“Travel-linked introduction is now the primary risk factor for mpox in India,” said a senior epidemiologist. “Without routine sequencing, we do not know how frequently this is happening.”
The WHO declared mpox a Public Health Emergency of International Concern in August 2024 and has since updated its emergency status based on evolving case trends. While case numbers have declined in some regions, Clade Ib continues to circulate internationally. The WHO has stressed the need for sustained surveillance and preparedness.
“Mpox is not causing a large outbreak in India today,” said Lal. “But it exposes serious weaknesses in genomic surveillance, vaccine policy and travel-related disease monitoring. These gaps will become far more dangerous when the next, more transmissible pathogen arrives.”
For now, the Clade Ib cases identified in Kerala remain limited and contained. Public health specialists argue that the episode underlines the urgent need for permanent national genomic surveillance, a clear vaccination strategy for emerging infections, and stronger monitoring of travel-linked disease risks.
“Kerala’s cluster is a signal,” said public health activist Dr Sylvia Karpagam. “The system has to be built before the next outbreak, not after it.”