ISLAMABAD: Wastewater flowing through nullahs may look unremarkable, but for public health researchers it can provide an early indication of the infectious diseases circulating in a community.
Dr Imran Nisar and his colleagues at the Aga Khan University are studying sewage samples to detect the genetic material of disease-causing organisms, sometimes before increases are visible through routine clinical reporting.
“By systematically collecting and testing wastewater samples, we can identify signals of pathogens circulating in a community, including those causing diarrhoeal, respiratory and vaccine-preventable diseases,” said Dr Nisar. “The aim is to complement existing surveillance and give health authorities an earlier indication of possible disease transmission”, he added.
The Infectious Diseases Research Laboratory at the Aga Khan University expanded its genomic surveillance capacity during the Covid-19 pandemic. The experience encouraged the team to explore whether wastewater testing could be applied more systematically to multiple diseases and eventually support surveillance beyond Karachi.
In that regard, the AKU and its partners, the National Institutes of Health, and experts from the Duke-NUS Medical School Singapore and ASIA Pathogen Genomics Initiative, launched Pakistan’s first national wastewater surveillance system, policy and dashboard in Islamabad.
NIH’s CEO Dr Mohammad Salman, Dr Afreenish Amir and Dr Rehan Zafar, Dr Vincent Pang of Duke-NUS and Nisar worked for three years to set it up. Federal Minister for National Health Services Syed Mustafa Kamal called wastewater surveillance an invaluable public health tool that complements clinical testing and supports early warning and outbreak detection.
The NIH CEO said that the strategy would help the country move from project-based initiatives to a coordinated, sustainable national programme. “The beauty of the dashboard is that it doesn’t reinvent the wheel. Pakistan is known to have one of the world’s strongest tracking systems dealing with polio.”
The NIH and WHO are already checking for the virus in 127 spots across the country. Teams are already trained to collect, transport and process sewage samples. It was just a matter of building on this network. During Covid-19, the polio platform quickly adjusted to detect SARS-CoV-2. But why stop at polio and Covid-19,” says Dr Nisar, adding that it is cheap to scale it up as well.
The AKU virus gene-detecting lab tests 95 bugs to spot drug-treatable cholera, typhoid-causing salmonella and TB, vaccine-preventable polio, measles and hepatitis, and pandemic-potential pathogens such as coronavirus, influenza and mpox, plus antibiotic-resistant genes, mosquito-borne viruses such as dengue and Zika.
During the event at NIH, the AKU team presented the first (but not final) Wastewater Environmental Surveillance (WES) results from Karachi testing on the dashboard. And as expected, there was a strong signal for cholera and diarrhoea-causing r. coli.
The lab teams collected samples every two weeks for seven months from all the city’s districts (Liaquatabad, Orangi 6, Rabia City, Malir’s Magsi Goth, Korangi’s Bhittai Colony, Hijrat Colony and Machhar Colony) that covered a population of 9.4 million people.
As the government has been involved, the WES will be plugged into the existing national Integrated Disease Surveillance and Response system as an early-warning radar. The partners have not just been working on getting the lab tests done, but have developed SOPs and strategies to make the data useful for the health providers after combining clinical, environmental, and veterinary data.
Published in Dawn, July 15th, 2026
