Massab Umair
When high-fatality pathogens such as Nipah virus appear in regional headlines,
public attention naturally shifts toward travel screening, border controls, and worst-case
scenarios. Yet, history has repeatedly shown that the cornerstone of effective outbreak
response is not panic: it is laboratory preparedness.
For diseases like Nipah virus, clinical diagnosis alone is insufficient. The early symptoms,
fever, headache, respiratory illness, or altered consciousness, overlap with a wide range
of infectious conditions common in South Asia. Accurate and timely laboratory
confirmation therefore becomes essential for patient management, outbreak detection,
and public health decision-making.
However, testing for Nipah virus is not routine. Because of the virus’s high-risk profile,
laboratory work requires high-containment biosafety facilities (BSL-3 or higher), validated
molecular assays, and a workforce trained in advanced biosafety and biosecurity
practices. Globally, only a limited number of laboratories possess this capability.
Pakistan’s national diagnostic capacity
In Pakistan, the Department of Virology at the National Institute of Health (NIH) serves as
the sole national reference laboratory equipped to safely test suspected Nipah virus
samples. This capacity, including a functional BSL-3 laboratory, trained personnel, and a
CDC-validated real-time PCR assay, has been in place since 2021, well before recent
regional alerts.
This preparedness ensures that any suspected Nipah case in the country can be rapidly
and safely confirmed or ruled out, allowing public health authorities to act decisively while
avoiding unnecessary alarm.
Beyond diagnosis: the power of pathogen genomics
Modern outbreak response does not end with a positive or negative test. Pathogen
genomics now plays a central role in understanding where a virus came from, how it is
evolving, and whether cases are linked.
The NIH Virology Department hosts a pathogen genomic sequencing facility capable of
sequencing any viral pathogen, emerging, re-emerging, or novel, within days. Since its
establishment, this facility has contributed more than 5,500 complete viral genomes to
global databases such as GISAID and NCBI. Of these, approximately 5,000 are SARS-
CoV-2 genomes, in addition to over 200 influenza genomes, more than 70 Crimean-
Congo haemorrhagic fever virus genomes, and over 50 dengue virus genomes.
These genomic data have played a central role in tracking viral evolution, identifying
introductions into Pakistan, and informing national public health responses. Importantly,
they have also ensured that Pakistan remains an active contributor to global pathogen
surveillance rather than a passive recipient of external data.
Genomics in action: lessons from recent outbreaks
The practical value of this genomic capacity was first demonstrated at scale during the
COVID-19 pandemic, when real-time sequencing of SARS-CoV-2 was used to monitor
which variants were circulating in the country during successive waves. Genomic findings
generated at NIH were regularly shared with national decision-makers, including the
National Command and Operation Center, where they informed risk assessment and
public health decisions in the context of variant-driven transmission. This close linkage
between genomic evidence and policy response played an important role in
understanding the dynamics of COVID-19 outbreaks in Pakistan and in guiding timely,
evidence-based interventions.
A similar role for genomics was evident during the August–September 2024 dengue
outbreak, when an increase in severe cases was reported from Rawalpindi and
surrounding areas. During this period, a major tertiary care hospital in Rawalpindi referred
samples to NIH for genomic investigation, driven by concerns that the surge in disease
severity might be linked to the introduction of a new dengue genotype or genetic changes
associated with increased virulence.
Genomic sequencing and analysis of the samples were completed within two days. The
results showed no change in the circulating dengue genotypes and no novel or unusual
genetic mutations when compared with dengue virus strains previously reported from
Pakistan. These findings were promptly shared with the hospital leadership and clinical
teams.
By ruling out viral genetic changes as a contributing factor, genomic evidence helped
redirect attention from a hypothetical viral evolution scenario toward clinical management,
patient triage, and health-system factors, where interventions could have immediate
impact. This example illustrates an often underappreciated value of genomics: its ability
not only to detect new threats, but also to provide reassurance and refocus response
efforts when the virus itself has not changed.
This capacity was again clearly demonstrated during the mpox outbreak in 2024, when
Pakistan detected its first imported case amid widespread public concern. The virus was
sequenced within 48 hours, enabling rapid risk assessment and informed public
communication. Subsequent genomic surveillance documented the introduction of mpox
clade 1b in Pakistan. Of the 10 complete mpox genomes from Pakistan currently available
on GISAID, nine were generated at NIH, including all three clade 1b detections.
Another important demonstration of the value of genomic capacity came during the
August–September 2023 surge of acute haemorrhagic conjunctivitis (AHC) reported
across Punjab and several other parts of the country. At the time, thousands of cases
were being reported, yet the etiological agent remained unknown, creating uncertainty for
clinicians and public health authorities alike. To address this gap, samples were collected
from patients with AHC and analysed using a metagenomic sequencing approach, a
pathogen-agnostic method specifically designed to identify unknown or unexpected
infectious agents. Using this approach, complete genomes of Coxsackievirus A24 variant
(CVA24v) were successfully recovered from eye swab samples. This virus is a well-
known cause of epidemic AHC globally.
These genomic findings were promptly shared with relevant health authorities, providing
critical clarity at a time when speculation and misinformation were widespread. Identifying
the causative agent helped place the outbreak in proper context, reassured clinicians
about its expected clinical course, and reinforced the importance of basic infection
prevention measures rather than unnecessary escalation. This episode highlighted how
advanced sequencing is not only valuable for rare or exotic pathogens, but also for rapidly
resolving common outbreaks when routine diagnostics fall short.
Rational testing: an often-overlooked pillar of preparedness
Laboratory preparedness is not only about having advanced facilities; it also depends on
using them wisely. Experience from previous public health emergencies in Pakistan,
including the early COVID-19 response and the mpox outbreak, demonstrated how fear-
driven testing can overwhelm laboratories with samples that do not meet suspected case
definitions.
For high-risk pathogens like Nipah virus, indiscriminate testing is not only inefficient but
potentially hazardous, given the biosafety requirements involved. Testing must therefore
remain targeted, risk-based, and guided by clear clinical and epidemiological criteria.
To support this approach, NIH has already developed and disseminated technical
guidance for Nipah virus, defining suspected case definitions, appropriate sample types,
and biosafety requirements for collection and transport. These documents have been
formally shared with federal and provincial health authorities to ensure a standardized
national approach.
The need for local ownership and sustainability
An equally important issue is local ownership and sustainability. The establishment and
early growth of Pakistan’s pathogen genomic sequencing capacity has benefited from the
support of international partners, particularly for high-cost sequencing reagents and
consumables. While such partnerships have been invaluable in accelerating capacity
development, they are by nature time-limited and not a substitute for domestic
investment.
Advanced genomic surveillance cannot remain dependent on external support if it is to
function reliably during future public health emergencies. Sustaining and expanding this
capacity now requires clear ownership and financial commitment from within the country,
led by the Ministry of National Health Services Regulations and Coordination at the
federal level and the provincial health departments across Pakistan. Dedicated budget
lines for public health laboratories, particularly for genomic surveillance, biosafety, and
skilled human resources, are essential if these facilities are to move from pilot successes
to permanent national infrastructure.
Investing in genomics is not an optional add-on; it is a core function of modern public
health systems and a prerequisite for timely, evidence-based outbreak response.
Preparedness is the real headline
The emergence of new pathogens will continue to test health systems. The true measure
of preparedness is not how loudly we react, but how quickly and accurately we can detect,
characterize, and respond.
For Nipah virus and for the next emerging threat, Pakistan’s growing laboratory and
genomic capacity provides reassurance that the country is better prepared today than
ever before. Preserving and strengthening this foundation through sustained national
investment should remain a public health priority.
Dr. Massab Umair is a virologist and public health expert working at the National Institute of
Health (NIH), Pakistan. His work focuses on infectious disease surveillance, laboratory
preparedness, and pathogen genomics to support evidence-based public health decision-
making in Pakistan.