RT Journal Article
SR Electronic
T1 Building up a genomic surveillance platform for SARS-CoV-2 in the middle of a pandemic: a true North–South collaboration
JF BMJ Global Health
JO BMJ Global Health
FD BMJ Publishing Group Ltd
SP e012589
DO 10.1136/bmjgh-2023-012589
VO 8
IS 11
A1 Khan, Waqasuddin
A1 Kabir, Furqan
A1 Kanwar, Samiah
A1 Aziz, Fatima
A1 Muneer, Sahrish
A1 Kalam, Adil
A1 Rajab Ali, Mehdia Nadeem
A1 Ansari, Nadia
A1 Vanaerschot, Manu
A1 Ahyong, Vida
A1 Fahsbender, Liz
A1 Kalantar, Katrina
A1 Black, Allison
A1 Glascock, Abigail
A1 Gil, Juliana
A1 Ayscue, Patrick
A1 Tato, Cristina
A1 Jehan, Fyezah
A1 Nisar, Imran
YR 2023
UL http://gh.bmj.com/content/8/11/e012589.abstract
AB Next-generation sequencing technology has revolutionised pathogen surveillance over the last two decades. However, the benefits are not equitably distributed, with developing countries lagging far behind in acquiring the required technology and analytical capacity. Recent declines in the cost associated with sequencing—equipment and running consumables have created an opportunity for broader adoption. During the COVID-19 pandemic, rapid diagnostics development and DNA sequencing revolutionised the ability to diagnose and sequence SARS-CoV-2 rapidly. Socioeconomic inequalities substantially impact the ability to sequence SARS-CoV-2 strains and undermine a developing country’s pandemic preparedness. Low- and middle-income countries face additional challenges in establishing, maintaining and expanding genomic surveillance. We present our experience of establishing a genomic surveillance system at the Aga Khan University, Karachi, Pakistan. Despite being at a leading health sciences research institute in the country, we encountered significant challenges. These were related to collecting standardised contextual data for SARS-CoV-2 samples, procuring sequencing reagents and consumables, and challenges with library preparation, sequencing and submission of high-quality SARS-CoV-2 genomes. Several technical roadblocks ensued during the implementation of the genomic surveillance framework, which were resolved in collaboration with our partners. High-quality genome sequences were then deposited on open-access platforms per the best practices. Subsequently, these efforts culminated in deploying Pakistan’s first SARS-CoV-2 phyllo surveillance map as a Nextstrain build. Our experience offers lessons for the successful development of Genomic Surveillance Infrastructure in resource-limited settings struck by a pandemic.Data are available in a public, open access repository. Data sharing not applicable as no data sets generated and/or analysed for this study. The sequencing data is available under BioProject accession ID: PRJNA764553