Building up a genomic surveillance platform for SARS-CoV-2 in the middle of a pandemic: a true North–South collaboration
| Title: | Building up a genomic surveillance platform for SARS-CoV-2 in the middle of a pandemic: a true North–South collaboration |
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| Authors: | Fyezah Jehan, Patrick Ayscue, Waqasuddin Khan, Furqan Kabir, Imran Nisar, Allison Black, Samiah Kanwar, Fatima Aziz, Sahrish Muneer, Adil Kalam, Mehdia Nadeem Rajab Ali, Nadia Ansari, Manu Vanaerschot, Vida Ahyong, Liz Fahsbender, Katrina Kalantar, Abigail Glascock, Juliana Gil, Cristina Tato |
| Source: | BMJ Global Health, Vol 8, Iss 11 (2023) |
| Publisher Information: | BMJ Publishing Group, 2023. |
| Publication Year: | 2023 |
| Collection: | LCC:Medicine (General) LCC:Infectious and parasitic diseases |
| Subject Terms: | Medicine (General), R5-920, Infectious and parasitic diseases, RC109-216 |
| More Details: | 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. |
| Document Type: | article |
| File Description: | electronic resource |
| Language: | English |
| ISSN: | 2023-0125 2059-7908 |
| Relation: | https://gh.bmj.com/content/8/11/e012589.full; https://doaj.org/toc/2059-7908 |
| DOI: | 10.1136/bmjgh-2023-012589 |
| Access URL: | https://doaj.org/article/104801a489db4920b20e82f9fb7acc4b |
| Accession Number: | edsdoj.104801a489db4920b20e82f9fb7acc4b |
| Database: | Directory of Open Access Journals |
| ISSN: | 20230125 20597908 |
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| DOI: | 10.1136/bmjgh-2023-012589 |
| Published in: | BMJ Global Health |
| Language: | English |