Is COVID surveillance collapsing in low-income countries? WHO raises early red flags

The World Health Organization (WHO), in its late June 2025 update, expressed concern that genomic surveillance of COVID‑19 is faltering in low- and middle-income countries. The organization cited declining sequencing activity, reduced international funding, and donor fatigue as key contributors to growing blind spots in global variant monitoring—despite test positivity rising to 11 percent in several regions.

What did the WHO say in its June 2025 warning about COVID surveillance inequity?

According to WHO’s most recent risk assessment, published in the second half of June 2025, test positivity across 73 reporting countries has returned to levels last seen in mid-2024. However, WHO flagged what it described as “alarming surveillance gaps,” particularly in lower-income nations. The organization noted that fewer than half of positive samples in these settings are undergoing genomic sequencing, limiting early detection of emerging variants like NB.1.8.1, KP.2, and XFG. By contrast, high-income countries are maintaining near 0.5 percent sequencing coverage across confirmed cases.

Why does COVID-19 genomic surveillance still matter in the endemic phase of the virus?

While COVID-19 has officially entered the endemic phase, the virus continues to evolve. Genomic sequencing remains vital to detect significant mutations, guide vaccine updates, and assess potential impacts on transmission and severity. WHO’s Global Influenza Programme, which now integrates COVID-19 monitoring under its Respiratory Pathogens umbrella, has repeatedly warned that sustained variant tracking is critical to future outbreak preparedness.

The agency’s World Health Statistics 2025 report added that disruptions caused by the pandemic—including delays in essential health services—have set back routine surveillance systems in many countries, undermining real-time pandemic intelligence.

Which regions are experiencing the most severe COVID genomic surveillance drop-offs?

WHO data suggest that African, Southeast Asian, and Latin American countries continue to experience the largest drop-offs in COVID-19 genomic sequencing. Some laboratories have fully suspended SARS-CoV-2 surveillance due to expired funding or shifting national health priorities. North African countries, as well as certain island nations in the Caribbean, have also recorded low sequencing volumes despite experiencing upticks in COVID-19 positivity rates.

In contrast, countries like the United States, Australia, and parts of Europe have maintained partial sequencing networks, although even in these locations, volumes have declined from peak pandemic levels.

What recent updates from India and South Africa show about variant surveillance capacity?

In South Africa, the National Institute for Communicable Diseases (NICD) confirmed earlier in June that the NB.1.8.1 variant had not yet been detected. Officials attributed this to a combination of robust surveillance and the variant’s limited regional spread. In India, where several states have recently seen a rise in COVID-like symptoms, experts at AIIMS Bhopal reported the local dominance of the XFG variant—further reinforcing the importance of genomic monitoring.

Additionally, Indian researchers and public health groups are advocating for the rapid deployment of wastewater-based epidemiology as a supplementary tool to catch early signals of outbreak clusters, especially in urban zones with low clinical testing rates.

How are WHO and regional health agencies working to rebuild surveillance networks?

WHO has expanded its support through the International Pathogen Surveillance Network (IPSN), based at its Berlin hub. As of mid-2025, the initiative is funding over 235 organizations across low- and middle-income countries with technical support and more than US$4 million in infrastructure grants. The program aims to transition pandemic-era labs into long-term respiratory surveillance hubs.

On the African continent, initiatives like AFROSCREEN, CERI (Centre for Epidemic Response and Innovation), and the Africa Pathogen Genomics Initiative—run jointly by Africa CDC and the World Bank—have sequenced thousands of samples and trained hundreds of regional scientists. These programs are helping build a permanent workforce and ensure data pipelines are standardized and interoperable.

What are virologists and global health experts saying about reduced surveillance?

In June, Belinda Ngongo, Director of Global Health at Illumina, emphasized the company’s ongoing collaboration with the Africa Centres for Disease Control and Prevention to expand genomic surveillance infrastructure across the continent. Although Ngongo did not specify a formal deadline, the Africa CDC has publicly announced its objective to enable all 55 African Union member states to access next-generation sequencing capacity by the end of 2025. In a separate context, Dr. Tulio de Oliveira, director of the Centre for Epidemic Response and Innovation, has described Africa’s transformation into a global leader in genomic surveillance—highlighting its early detection of Beta and Omicron variants and the successful training of hundreds of local scientists as foundational milestones.

Public health advocates have also warned that delays in releasing sequencing data, due to fears of stigma or international travel bans, may discourage transparency unless strong global health governance mechanisms are put in place.

What solutions are being proposed to restore global COVID variant detection?

Global health institutions are calling for renewed and predictable financing to sustain surveillance efforts beyond short-term grants. This includes long-term budget support from the Pandemic Fund, Gavi, and bilateral donors. Another key recommendation is the integration of wastewater epidemiology and metagenomics as a low-cost, scalable early-warning mechanism in urban areas and transport hubs. Studies also recommend expanding traveler-based sequencing at international airports to track variants at their points of entry. Experts continue to stress the importance of strong international data-sharing frameworks that not only encourage transparency but also protect scientists from retaliation or travel sanctions tied to early variant reporting.

WHO has further advocated for embedding SARS-CoV-2 genomic surveillance within a broader respiratory pathogen monitoring network. This allows countries to pivot efficiently between COVID-19, influenza, RSV, and future pandemic threats, without the need to rebuild infrastructure with every emerging crisis.

Could the failure of genomic surveillance delay global response to dangerous variants?

According to the WHO Hub for Pandemic and Epidemic Intelligence in Berlin, even a single undetected variant emerging in an under-sequenced region could trigger months of uncontrolled transmission. This would undermine vaccine update timelines, delay clinical preparedness, and impair travel risk modeling. Public health officials now consider surveillance equity to be as critical as vaccine equity—particularly in fragile health systems where reactive strategies often arrive too late to prevent harm.

Ministers from Kenya, Bangladesh, and Peru echoed this concern at a Gavi-hosted panel earlier in June, warning that time lags in variant detection could once again disadvantage low-income countries during the next global health emergency.

What is the long-term outlook for global COVID-19 variant monitoring systems?

Rebuilding global surveillance capacity is emerging as a critical challenge for public health systems in the endemic phase of COVID-19. While sequencing technology is more widely available than ever before, the main obstacles are no longer scientific—they are political, financial, and institutional. WHO plans to continue funding regional hubs in Africa, Latin America, and Southeast Asia through at least 2028. Additional support from private donors such as the Gates Foundation and Wellcome Trust is expected to reinforce these programs.

Unless these efforts succeed, public health experts warn the world could soon enter a dangerous “variant blind spot.” In such a scenario, by the time a new variant is detected and understood, it may already have seeded global outbreaks. For countries without robust early warning systems, the costs could be immediate and severe—delayed booster campaigns, overwhelmed hospitals, and diminished public trust.