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Building up a genomic surveillance platform for SARS-CoV-2 in the middle of a pandemic: a true North–South collaboration

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 associ...

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Autores principales: Khan, Waqasuddin, Kabir, Furqan, Kanwar, Samiah, Aziz, Fatima, Muneer, Sahrish, Kalam, Adil, Rajab Ali, Mehdia Nadeem, Ansari, Nadia, Vanaerschot, Manu, Ahyong, Vida, Fahsbender, Liz, Kalantar, Katrina, Black, Allison, Glascock, Abigail, Gil, Juliana, Ayscue, Patrick, Tato, Cristina, Jehan, Fyezah, Nisar, Imran
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BMJ Publishing Group 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10660681/
https://www.ncbi.nlm.nih.gov/pubmed/37984892
http://dx.doi.org/10.1136/bmjgh-2023-012589
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author Khan, Waqasuddin
Kabir, Furqan
Kanwar, Samiah
Aziz, Fatima
Muneer, Sahrish
Kalam, Adil
Rajab Ali, Mehdia Nadeem
Ansari, Nadia
Vanaerschot, Manu
Ahyong, Vida
Fahsbender, Liz
Kalantar, Katrina
Black, Allison
Glascock, Abigail
Gil, Juliana
Ayscue, Patrick
Tato, Cristina
Jehan, Fyezah
Nisar, Imran
author_facet Khan, Waqasuddin
Kabir, Furqan
Kanwar, Samiah
Aziz, Fatima
Muneer, Sahrish
Kalam, Adil
Rajab Ali, Mehdia Nadeem
Ansari, Nadia
Vanaerschot, Manu
Ahyong, Vida
Fahsbender, Liz
Kalantar, Katrina
Black, Allison
Glascock, Abigail
Gil, Juliana
Ayscue, Patrick
Tato, Cristina
Jehan, Fyezah
Nisar, Imran
author_sort Khan, Waqasuddin
collection PubMed
description 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.
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spelling pubmed-106606812023-11-19 Building up a genomic surveillance platform for SARS-CoV-2 in the middle of a pandemic: a true North–South collaboration Khan, Waqasuddin Kabir, Furqan Kanwar, Samiah Aziz, Fatima Muneer, Sahrish Kalam, Adil Rajab Ali, Mehdia Nadeem Ansari, Nadia Vanaerschot, Manu Ahyong, Vida Fahsbender, Liz Kalantar, Katrina Black, Allison Glascock, Abigail Gil, Juliana Ayscue, Patrick Tato, Cristina Jehan, Fyezah Nisar, Imran BMJ Glob Health Practice 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. BMJ Publishing Group 2023-11-19 /pmc/articles/PMC10660681/ /pubmed/37984892 http://dx.doi.org/10.1136/bmjgh-2023-012589 Text en © Author(s) (or their employer(s)) 2023. Re-use permitted under CC BY. Published by BMJ. https://creativecommons.org/licenses/by/4.0/This is an open access article distributed in accordance with the Creative Commons Attribution 4.0 Unported (CC BY 4.0) license, which permits others to copy, redistribute, remix, transform and build upon this work for any purpose, provided the original work is properly cited, a link to the licence is given, and indication of whether changes were made. See: https://creativecommons.org/licenses/by/4.0/.
spellingShingle Practice
Khan, Waqasuddin
Kabir, Furqan
Kanwar, Samiah
Aziz, Fatima
Muneer, Sahrish
Kalam, Adil
Rajab Ali, Mehdia Nadeem
Ansari, Nadia
Vanaerschot, Manu
Ahyong, Vida
Fahsbender, Liz
Kalantar, Katrina
Black, Allison
Glascock, Abigail
Gil, Juliana
Ayscue, Patrick
Tato, Cristina
Jehan, Fyezah
Nisar, Imran
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
title_full Building up a genomic surveillance platform for SARS-CoV-2 in the middle of a pandemic: a true North–South collaboration
title_fullStr Building up a genomic surveillance platform for SARS-CoV-2 in the middle of a pandemic: a true North–South collaboration
title_full_unstemmed Building up a genomic surveillance platform for SARS-CoV-2 in the middle of a pandemic: a true North–South collaboration
title_short Building up a genomic surveillance platform for SARS-CoV-2 in the middle of a pandemic: a true North–South collaboration
title_sort building up a genomic surveillance platform for sars-cov-2 in the middle of a pandemic: a true north–south collaboration
topic Practice
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10660681/
https://www.ncbi.nlm.nih.gov/pubmed/37984892
http://dx.doi.org/10.1136/bmjgh-2023-012589
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