COVID-19 screening at the Pakistan Institute of Medical Science
By collecting and analysing data from a variety of well-established cohorts across the world, END-VOC hopes to rapidly identify and characterize emerging SARS-CoV-2 variants. In this interview, our partners in Pakistan (the DOPASI Foundation) explain the work they have been doing on COVID-19 and why their cohort is quite unique.
Can you briefly explain who you are and what you do?
The DOPASI Foundation is a non-profit organisation seeking to improve the quality of life of marginalised populations in Pakistan, through the implementation of integrated and innovative solutions. Our organisation aspires to aid social justice by promoting health and fighting hunger, illiteracy, and gender inequality. While doing so, we have emerged as a leader in the fight against communicable diseases.
What types of cohorts have you established during the COVID-19 pandemic?
DOPASI has not yet undertaken any cohort study on COVID-19 since the start of the pandemic. However, we did carry out certain cross-sectional studies at Islamabad’s Pakistan Institute of Medical Sciences – the largest public healthcare facility in the country, where we established a COVID-19 health screening camp. The camp was equipped with ultra portable X-ray device enabled with Artificial Intelligence (AI) technology to identify any signs of COVID-19 or any other lung abnormalities. For all those individuals presenting symptoms suggestive of chest diseases, we performed molecular diagnosis (RT-PCR/GeneXpert) to confirm the results for either COVID-19 or tuberculosis (TB).
As part of the END-VOC project, we are starting a novel study that involves sequencing SARS-CoV-2 samples from HIV and/or TB patients who test positive for COVID-19. This study will be the first of its sort in Pakistan.
What would you say is the added value of your cohort?
We believe that being able to trace the genetic changes of the virus in a sufficiently large cohort of HIV/AIDS and TB patients is a unique contribution of Pakistan to the project. Our cohort includes people from different socio-economic and ethnic backgrounds and particularly targets immunocompromised populations, where the risk of new variants emerging may be higher. Our work with this diverse cohort will also provide an effective information and communication platform for countering the spread of existing and new variants of COVID-19, especially among persons with HIV and TB, who are more vulnerable to COVID-19. Finally, we hope that, together with other project partners, we will help to standardise global health protocols, methods, bioinformatics tools, and best practices with other COVID-19 networks and with the World Health Organization (WHO).
How will your work in Pakistan contribute to END-VOC’s goal?
The END-VOC Pakistan cohort will allow to explore the occurrence and characteristics of current and emerging variants of concern (VOC) in patients with HIV, TB and/or TB/HIV coinfection, many of whom are immunocompromised. We will specifically look at the sequences, phylogenetics, transmissibility, pathogenicity, and treatment outcomes for these patients. In our view, the Pakistan cohort study will contribute to the END-VOC project through short- and long-term goals. In the short-term, it will allow us to i) elucidate the circulation of COVID-19 variants in Pakistan, as well as their transmissibility, pathogenicity and propensity to cause reinfection. This will guide best control and diagnostic strategies; ii) evaluate the impact of these variants on vaccine effectiveness and vaccination strategies; iii) choose optimal treatment strategies and iv) monitor the emergence and spread of new VOCs.
In the long-term, it will also allow us to understand the impact of different VOC on long-term post-infection sequelae (or Long Covid); identify the populations that pose a higher risk for the emergence of new VOCs; and extrapolate what we learn into regional and international pandemic preparedness networks, including WHO’s Emergency Preparedness Plan, the Coalition for Epidemic Preparedness Innovations (CEPI) and ECDC, to better respond to similar pandemics in the future.
Inversely, how will DOPASI benefit from participating in the END-VOC project?
The END-VOC consortium is aligned with our mission to empower people and communities that are traditionally underserved and live on the verge of poverty, while contending with several social injustices, health inequities and gender barriers. This cohort study will help us to reach those very groups of HIV and TB patients that are at high risk of contracting and suffering from COVID-19. The information we collect during this study will thus be useful in updating the national and global surveillance systems for quick mitigation responses. We also hope that the data systems and tools created through this project will enable our Foundation to strengthen collaboration and networking with international research networks in the future.
Interview by Adelaida Sarukhan
Photo: COVID-19 screening at the Pakistan Institute of Medical Science, by DOPASI Foundation
