Pathogen genomic surveillance, the ability to track changes in the genetic makeup of viruses, bacteria, and other microbes has become an indispensable tool in modern public health. While high-income countries have long used this technology to detect outbreaks, trace transmission chains, and guide interventions, many low- and middle-income countries (LMICs) have struggled to adopt it due to high costs, complex technical requirements, and limited bioinformatics capacity.

Prior to COVID-19, Pakistan had no in-country genomic sequencing capacity for public health purposes. The pandemic changed everything. It was not only a wake-up call but also a catalyst for a sweeping transformation. In response to the crisis, Pakistan rapidly established its first national genomic surveillance infrastructure at the National Institute of Health (NIH) enabling real-time tracking of SARS-CoV-2 variants for the first time in our history.

This blog reflects on how genomics reshaped Pakistan’s pandemic response, how we continue using it for emerging threats like Mpox and why embedding it in national policy is essential for future epidemic preparedness.

COVID-19: The Catalyst for Genomic Self-Reliance

Before 2020, genetic sequencing in Pakistan was largely confined to research institutions, with limited use in public health. The Virology Department at NIH had basic Sanger sequencing capacity, but this older technology lacked the throughput and speed needed for real-time surveillance of evolving pathogens. In many cases, clinical samples had to be shipped abroad causing delays, incurring costs, and raising biosecurity concerns.

The COVID-19 pandemic exposed this gap dramatically.

Recognizing the urgent need, NIH with technical support from the U.S. Centers for Disease Control and Prevention (CDC) established Pakistan’s first Next-Generation Sequencing (NGS) facility for public health in May 2020. I was fortunate to be part of the capacity-building journey, receiving training and helping operationalize this breakthrough.

The impact was immediate. In June 2020, the newly operational NGS facility detected the D614G mutation, an early indication of variant-driven transmission during Pakistan’s first COVID-19 wave. By the time the Alpha variant (B.1.1.7) emerged, our capacity had matured. Although national case numbers were declining, our sequencing data showed a sharp rise in Alpha cases. This early warning, reported to the National Command and Operation Centre (NCOC), allowed Pakistan to anticipate rather than simply react to the pandemic’s third wave.

This marked a turning point: for the first time, genomic evidence was shaping national policy in real time.

Subsequent waves driven by Delta, Omicron, and its sub-lineages were tracked in similar fashion. More than 7,000 SARS-CoV-2 genomes have since been submitted to GISAID, a number unimaginable just five years ago. But beyond numbers, this data informed decisions, guided testing and containment strategies, and cemented the role of genomics in Pakistan’s public health response.

Though most of these sequences were generated by the lab I lead, credit is due to our partners at Aga Khan University which had Sanger sequencing capacity before the pandemic and developed NGS capabilities during COVID-19—and the provincial public health labs in KP, Punjab, and Sindh, which established NGS capacity from scratch, having lacked even basic Sanger sequencers prior to the pandemic. This transformation proves that, with political will and investment, even complex systems can be built quickly and effectively.

Beyond COVID-19: Expanding Genomic Surveillance

Our genomic capacity is no longer limited to COVID-19.

In April 2023, during the global Mpox (monkeypox) public health emergency of international concern (PHEIC), NIH identified the first national case as Clade IIb, Lineage A.2.1. Later, in December 2024, NIH also reported the more virulent Clade Ib variant—an event made possible only through local sequencing.

These efforts provided timely answers to policymakers: identifying clades (critical for risk stratification), tracing virus importation routes through phylogenetics, and shaping national containment efforts.

Our work has since expanded to vector-borne diseases such as dengue virus and Crimean-Congo hemorrhagic fever virus (CCHFV). NIH is also leveraging genomics to study rotavirus, measles, mumps, influenza, and RSV, underscoring its broader utility for endemic and emerging threats.

Challenges on the Genomic Frontier

Despite this remarkable progress, several challenges remain:

1. Lack of sustained national ownership: Much of Pakistan’s genomic work has been supported by donors and development partners. Without federal and provincial governments investment, the current system risks collapse once external support fades.

2. Shortage of trained bioinformaticians: While NIH and AKU have built technical capacity, provincial labs still face acute human resource and infrastructure gaps in bioinformatics.

3. Delayed implementation of national strategy: Although Pakistan launched its National Genomic Surveillance Strategy in February 2023, implementation has been slow. To address this, I recently led a national revision process to incorporate a clear implementation plan and One Health lens, identifying priority pathogens and enabling cross-sector coordination.