1
|
Khan W, Kabir F, Kanwar S, Aziz F, Muneer S, Kalam A, Rajab Ali MN, Ansari N, Vanaerschot M, Ahyong V, Fahsbender L, Kalantar K, Black A, Glascock A, Gil J, Ayscue P, Tato C, Jehan F, Nisar I. Building up a genomic surveillance platform for SARS-CoV-2 in the middle of a pandemic: a true North-South collaboration. BMJ Glob Health 2023; 8:e012589. [PMID: 37984892 PMCID: PMC10660681 DOI: 10.1136/bmjgh-2023-012589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 09/09/2023] [Indexed: 11/22/2023] Open
Abstract
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.
Collapse
Affiliation(s)
- Waqasuddin Khan
- Pediatrics and Child Health, The Aga Khan University, Karachi, Sindh, Pakistan
- Biorepository and Omics Research Group, Medical College Pakistan, The Aga Khan University, Karachi, Sindh, Pakistan
| | - Furqan Kabir
- Pediatrics and Child Health, The Aga Khan University, Karachi, Sindh, Pakistan
- Biorepository and Omics Research Group, Medical College Pakistan, The Aga Khan University, Karachi, Sindh, Pakistan
| | - Samiah Kanwar
- Pediatrics and Child Health, The Aga Khan University, Karachi, Sindh, Pakistan
| | - Fatima Aziz
- Pediatrics and Child Health, The Aga Khan University, Karachi, Sindh, Pakistan
| | - Sahrish Muneer
- Pediatrics and Child Health, The Aga Khan University, Karachi, Sindh, Pakistan
| | - Adil Kalam
- Pediatrics and Child Health, The Aga Khan University, Karachi, Sindh, Pakistan
| | | | - Nadia Ansari
- Pediatrics and Child Health, The Aga Khan University, Karachi, Sindh, Pakistan
| | | | - Vida Ahyong
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Liz Fahsbender
- The Chan Zuckerberg Initiative, Palo Alto, California, USA
| | | | - Allison Black
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | | | - Juliana Gil
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | | | - Cristina Tato
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Fyezah Jehan
- Pediatrics and Child Health, The Aga Khan University, Karachi, Sindh, Pakistan
- Biorepository and Omics Research Group, Medical College Pakistan, The Aga Khan University, Karachi, Sindh, Pakistan
| | - Imran Nisar
- Pediatrics and Child Health, The Aga Khan University, Karachi, Sindh, Pakistan
- Biorepository and Omics Research Group, Medical College Pakistan, The Aga Khan University, Karachi, Sindh, Pakistan
| |
Collapse
|
2
|
Raj A, Ramirez K, Young KM, Stone N, Shankles P, Ali MNR, Compton AM, Lam W, Alexeev A, Sulchek T. Label-free microfluidic isolation of functional and viable lymphocytes from peripheral blood mononuclear cells. Biomicrofluidics 2023; 17:054102. [PMID: 37736019 PMCID: PMC10511259 DOI: 10.1063/5.0161047] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 08/28/2023] [Indexed: 09/23/2023]
Abstract
The separation of peripheral blood mononuclear cells (PBMCs) into constituent blood cell types is a vital step to obtain immune cells for autologous cell therapies. The ability to separate PBMCs using label-free microfluidic techniques, based on differences in biomechanical properties, can have a number of benefits over other conventional techniques, including lower cost, ease of use, and avoidance of animal-derived labeling antibodies. Here, we report a microfluidic device that uses compressive diagonal ridges to separate PBMCs into highly pure samples of viable and functional lymphocytes. The technique utilizes the differences in the biophysical properties of PBMC sub-populations to direct the lymphocytes and monocytes into separate outlets. The biophysical properties of the monocytes and lymphocytes from healthy donors were first characterized using atomic force microscopy. Lymphocytes were found to be significantly stiffer than monocytes, with a mean cell stiffness of 1495 and 931 Pa, respectively. The differences in biophysical properties resulted in distinct trajectories through the microchannel terminating at different outlets, resulting in a lymphocyte sample with purity and viability both greater than 96% with no effect on the cells' ability to produce interferon gamma, a cytokine crucial for innate and adaptive immunity.
Collapse
Affiliation(s)
- Abhishek Raj
- George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, 801 Ferst Drive, Atlanta, Georgia 30332-0405, USA
| | - Katily Ramirez
- School of Chemistry & Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive, Atlanta, Georgia 30332-0400, USA
| | - Katherine M. Young
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, 313 Ferst Drive, Atlanta, Georgia 30332-0535, USA
| | - Nicholas Stone
- George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, 801 Ferst Drive, Atlanta, Georgia 30332-0405, USA
| | - Peter Shankles
- George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, 801 Ferst Drive, Atlanta, Georgia 30332-0405, USA
| | - Mehdia Nadeem Rajab Ali
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, 313 Ferst Drive, Atlanta, Georgia 30332-0535, USA
| | - Anthony Malik Compton
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, 313 Ferst Drive, Atlanta, Georgia 30332-0535, USA
| | | | - Alexander Alexeev
- George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, 801 Ferst Drive, Atlanta, Georgia 30332-0405, USA
| | - Todd Sulchek
- Author to whom correspondence should be addressed:
| |
Collapse
|