As several countries across Southeast Asia and beyond report a sharp rise in Covid-19 cases driven by new variants, health authorities in Nepal are on high alert, despite detecting only a single case so far in 2025. With neighboring nations like India, Thailand, Singapore, and Hong Kong grappling with outbreaks linked to the JN.1 and XEC variants, experts warn that Nepal’s geographic proximity and porous borders could soon lead to a fresh wave of infections.
Regional Surge Raises Alarm
A resurgence of Covid-19 cases has swept through parts of Asia, with the JN.1 variant—a descendant of the Omicron BA.2.86 lineage—driving infections in countries such as India and Singapore. According to the World Health Organization, JN.1 carries around 30 mutations, including sub-variants like LF.7 and NB.1.8, which are fueling the current spike. Symptoms mirror those of earlier variants, including fever, dry cough, and loss of taste or smell, though studies suggest JN.1 may cause more severe diarrhea. 
In Thailand, media reports indicate 71,067 infections and 19 deaths between January 1 and May 14, 2025. Singapore recorded 14,200 cases by May 3, while Hong Kong reported 30 deaths over the past four weeks. India, meanwhile, has 257 active cases, predominantly mild, though two deaths in Mumbai were linked to patients with underlying health conditions rather than the virus itself. Adding to the complexity, a newly emerged recombinant strain known as XEC—a hybrid of Omicron sub-variants KS.1.1 and KP.3.3—has been identified as a key driver in Thailand. First detected in Germany in June 2024, XEC’s multiple mutations enable faster transmission.
Dr. Sher Bahadur Pun, chief of the Clinical Research Unit at Sukraraj Tropical and Infectious Disease Hospital in Kathmandu, highlighted the risk of cross-border transmission. “Virus could enter Nepal at any time due to geographic proximity with, and the movement of people from, countries that are seeing a spike in infections” he said. Nepal has previously experienced outbreaks following surges in neighboring regions, a pattern that underscores the urgency of current preparations.
Nepal’s Current Situation: A Fragile Calm
Despite the regional uptick, Nepal’s health authorities report a relatively calm situation domestically. Only one Covid-19 case has been detected since the start of 2025, according to Dr. Ranjan Raj Bhatta, director at the National Public Health Laboratory. The low case count has limited opportunities for detailed analysis, with Dr. Bhatta noting, “We don’t even have enough swab samples from Covid-infected persons to carry out whole-genome sequencing.” Such sequencing, a method to analyze the entire DNA sequence of the virus, is critical for understanding its severity and mutations.
In 2024, Nepal recorded 421 infections, a significant drop from the peak of earlier waves. The country has faced outbreaks of Omicron BA.2.86 and its sub-lineages, including JN.1, in the past. However, waning immunity from prior infections and vaccinations has left the population vulnerable, experts warn. With only one active case, the immediate threat appears minimal, but the lack of testing and sequencing capacity raises concerns about undetected spread.
Stepping Up Surveillance
In response to the regional crisis, Nepal’s Epidemiology and Disease Control Division convened a meeting with stakeholders on May 23, 2025, to bolster preparedness. Dr. Chandra Bhal Jha, director at the division, outlined plans to enhance surveillance at key entry points. “We have decided to step up surveillance measures at the Tribhuvan International Airport, as it is an entry point for travelers from countries witnessing a Covid surge—Singapore, Thailand, Hong Kong, and India” he said. Health workers at land border points have also been instructed to remain vigilant.
Health facilities across the country are on alert for a potential influx of cases. The division has requested Covid-19 test kits from the World Health Organization’s Nepal office, citing a limited stockpile and procurement challenges. “We have a limited number of testing kits in our stock, and they cannot be purchased immediately by following due process” Dr. Jha explained. At Sukraraj Tropical and Infectious Disease Hospital, preparations are underway to treat patients exhibiting Covid-like symptoms, particularly those returning from affected countries. Dr. Yuba Nidhi Basaula, the hospital’s director, urged the public to adhere to familiar safety measures. “As cases are rising in neighboring countries, everyone must follow safety measures, about which we are all aware of” he said.
Experts are also calling for increased testing of patients with influenza-like symptoms and a renewed emphasis on public health basics—wearing masks, washing hands, and avoiding crowded spaces. These measures, while simple, remain effective in curbing transmission, especially as new variants demonstrate heightened transmissibility.
Variants and Vulnerabilities: A Global Challenge
The emergence of variants like JN.1 and XEC underscores the evolving nature of the Covid-19 pandemic, now in its fifth year. JN.1, with its numerous mutations, has been linked to mild but widespread infections across Southeast Asia. XEC, meanwhile, represents a new frontier in the virus’s adaptability, combining traits from two Omicron sub-variants to spread more efficiently. While hospitalizations remain low in most affected regions—India, for instance, reports no need for hospital care in nearly all active cases—the death toll in places like Thailand and Hong Kong serves as a grim reminder of the virus’s potential lethality, particularly for vulnerable populations.
For Nepal, the challenge lies not only in managing potential outbreaks but also in addressing systemic gaps in healthcare infrastructure. Limited testing capacity, as evidenced by the inability to conduct whole-genome sequencing, hampers the country’s ability to track and respond to new variants. The reliance on international aid for test kits further highlights resource constraints, a recurring issue for low-income nations navigating global health crises. If a surge materializes, Nepal’s hospitals—already strained during previous waves—may struggle to cope without swift intervention and support.
Public Health Lessons and Regional Cooperation
The current situation in Southeast Asia offers a stark reminder of the interconnectedness of global health. Nepal’s porous borders with India, coupled with frequent travel to and from countries like Thailand and Singapore, create multiple pathways for viral transmission. Past outbreaks in the region have often preceded spikes in Nepal, a trend that health officials are keen to mitigate through proactive measures. Surveillance at airports and border crossings, while a critical first step, must be complemented by robust testing and contact tracing to prevent undetected community spread.
Regional cooperation could play a pivotal role in managing the crisis. Sharing data on variant spread, coordinating vaccine booster campaigns, and ensuring equitable access to testing and treatment resources are essential strategies for containing outbreaks. Nepal’s request for test kits from the WHO signals a willingness to engage with international partners, but sustained collaboration with neighboring countries—particularly India, which has a significant influence on Nepal’s health landscape—will be crucial.
Public awareness also remains a cornerstone of prevention. The familiarity of safety protocols—mask-wearing, hand hygiene, and social distancing—offers a low-cost, high-impact defense against the virus. Yet, compliance has waned in many communities as pandemic fatigue sets in. Reinforcing these habits through targeted campaigns could help Nepal avoid the worst of a potential surge, even as new variants test the limits of immunity.
Looking Ahead: Preparedness Over Panic
As Nepal monitors the unfolding situation in Southeast Asia, the balance between preparedness and panic is delicate. With just one confirmed case in 2025, the country has a window of opportunity to strengthen its defenses before a larger outbreak takes hold. Enhanced surveillance, international support for testing, and renewed public health messaging are critical steps in this effort. Yet, the specter of new variants like JN.1 and XEC looms large, a reminder that Covid-19 remains an unpredictable foe.
For now, health officials and citizens alike are bracing for what may come, drawing on lessons from past waves to navigate an uncertain future. As Dr. Pun aptly noted, the virus respects no borders—a reality that Nepal, and the broader region, must confront with vigilance and solidarity.
