The XEC variant of SARS-CoV-2, a recombinant sublineage of the Omicron strain, has emerged as a significant concern in Southeast Asia in 2025, particularly due to its high transmissibility. First identified in Germany in June 2024, XEC is a hybrid of two Omicron subvariants, KS.1.1 (FLiRT) and KP.3.3 (FLuQE), and carries mutations that enhance its spread, raising alarms across the region.
Characteristics of the XEC Variant
XEC is classified as a Variant Under Monitoring (VUM) by the World Health Organization (WHO) as of September 24, 2024, due to its genetic profile and rapid spread. It features mutations in the spike protein, notably T22N and Q493E, which confer a slight transmission advantage over other Omicron subvariants. Preliminary studies suggest XEC may exhibit increased immune evasion compared to its parent lineage, KP.3, though it does not appear to cause more severe disease. Symptoms remain consistent with previous Omicron strains, including fever, cough, sore throat, nasal congestion, diarrhea, and loss of taste or smell.
The variant’s effective reproduction number is higher than other circulating variants, indicating its potential to dominate globally. By January 2025, XEC accounted for 45% of SARS-CoV-2 sequences submitted to GISAID worldwide, underscoring its rapid rise. In Southeast Asia, limited testing and genomic sequencing capacities have made it challenging to track its prevalence accurately, but confirmed cases and genetic sequences indicate its presence across multiple countries.
Spread in Southeast Asia
- Thailand:
Thailand has been the epicenter of XEC’s spread in Southeast Asia, reporting a significant surge in COVID-19 cases in 2025. Between January 1 and May 14, 2025, the country recorded 71,067 infections and 19 deaths, with cases escalating post-Songkran holiday (April 13–15, 2025). By late May, weekly cases reached 43,213, a 35.5% increase from the previous week, with 108,891 total infections and 27 deaths attributed to XEC by some sources. However, data from Thailand’s Department of Medical Sciences indicates XEC comprised only 3.07% of sequenced cases in May 2025, with JN.1 remaining dominant at 63.92%. This discrepancy suggests XEC’s role may be overstated in some reports, but its rapid transmission—described as seven times faster than seasonal flu—has prompted heightened vigilance.
The Thai Department of Disease Control noted that XEC primarily affects vulnerable groups, including the elderly, pregnant women, and those with chronic illnesses. Schools in provinces like Kanchanaburi, Sukhothai, and Bangkok Noi have reported clusters, raising concerns about transmission in educational settings. Authorities have urged mask-wearing, hand hygiene, and symptom monitoring to curb the spread. - Singapore:
Singapore reported a rise in COVID-19 cases, with weekly infections increasing from 11,100 to 14,200 between April 27 and May 3, 2025, and hospitalizations rising from 102 to 133 daily. While variants LF.7 and NB.1.8 (both JN.1 descendants) dominate, accounting for over two-thirds of sequenced cases, XEC has been detected and is contributing to the uptick. The surge is attributed to waning population immunity and increased social gatherings. Singapore’s health authorities emphasize booster vaccinations, particularly for high-risk groups like those over 65, and maintain robust surveillance systems. - Other Southeast Asian Countries:
Data on XEC in other Southeast Asian nations is sparse due to limited genomic sequencing. Posts on X and web reports indicate XEC’s presence in at least 15 Asian countries, including some in Southeast Asia, with over 550 genetic sequences documented globally. However, specific confirmations in countries like Indonesia, Malaysia, Vietnam, or the Philippines are lacking as of May 2025. Earlier detection of another variant, BA.2.87.1, in wastewater samples from Southeast Asia (December 2023–January 2024) suggests the region’s vulnerability to new variants, but XEC’s spread remains underreported due to reduced testing.
Public Health Responses
Southeast Asian countries have adopted varied strategies to address XEC’s spread:
- Thailand: The Public Health Ministry has intensified surveillance, particularly after identifying two significant cluster outbreaks. Recommendations include frequent handwashing, mask-wearing in crowded areas, and monitoring respiratory symptoms. Schools have been advised to implement hybrid learning models to balance education and safety.
- Singapore: The Ministry of Health promotes booster shots with updated 2024–2025 vaccines targeting JN.1 and KP.2, which offer cross-protection against XEC. Rapid testing and public awareness campaigns are also prioritized.
- Regional Challenges: Limited testing and sequencing capacities across Southeast Asia hinder real-time tracking of XEC. The WHO has urged member states to strengthen influenza-like illness (ILI) and severe acute respiratory infection (SARI) surveillance to monitor SARS-CoV-2 variants.
Vaccination remains a cornerstone of the response. The 2024–2025 COVID-19 vaccines (Pfizer, Moderna, and Novavax), designed to target JN.1 or KP.2, are expected to protect against severe outcomes from XEC, despite slightly reduced neutralization efficacy. The WHO recommends booster doses every 6–12 months, particularly for high-risk groups.
Implications and Challenges
The rapid spread of XEC in Southeast Asia highlights several challenges:
- High Transmissibility: XEC’s mutations enable faster transmission, potentially outpacing other variants like KP.3.1.1 and LP.8.1. This is particularly concerning in densely populated urban areas and during festive periods like Songkran.
- Waning Immunity: Declining herd immunity, as noted in Singapore and Thailand, exacerbates the spread, especially among unvaccinated or under-vaccinated populations.
- Limited Surveillance: Reduced testing and sequencing in countries like Indonesia and Vietnam limit the ability to assess XEC’s true prevalence, potentially delaying response measures.
- Misinformation: Posts on X have occasionally exaggerated XEC’s impact, such as claims of 30,000 cases in five days in Thailand, which were debunked as misleading. Accurate communication is critical to avoid public panic.
Future Outlook
While XEC does not appear to cause more severe disease, its high transmissibility could strain healthcare systems, particularly in countries with limited resources. The WHO and regional health authorities emphasize the importance of maintaining genomic surveillance and sharing data through platforms like GISAID to track XEC’s evolution.
Southeast Asia’s experience with previous variants, such as Delta in 2021, underscores the need for proactive measures. Green-zoning strategies, travel restrictions, and enhanced vaccination campaigns could mitigate XEC’s impact. Hybrid education models and targeted protection for vulnerable groups, as suggested in Thailand, may serve as models for the region.
Conclusion
The XEC variant poses a significant public health challenge in Southeast Asia, particularly in Thailand, where it has driven a surge in cases, and in Singapore, where it contributes to rising infections. Its high transmissibility, coupled with waning immunity and limited surveillance, underscores the need for robust public health measures. Vaccination, rapid testing, and adherence to preventive protocols like mask-wearing remain critical to controlling XEC’s spread. As the region navigates this evolving pandemic, timely data sharing and coordinated responses will be essential to protect communities and prevent further escalation.
Note: This article is based on data and reports available up to May 27, 2025. Due to limited genomic sequencing in some Southeast Asian countries, the full extent of XEC’s spread may be underreported. For the latest updates, consult reputable sources like the WHO or national health authorities.
