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SARS-CoV-2 Whole Genome Amplification and Sequencing for Effective Population-Based Surveillance and Control of Viral Transmission

Divinlal Harilal, Sathishkumar Ramaswamy, Tom Loney, Hanan Al Suwaidi, Hamda Khansaheb, Abdulmajeed Alkhaja, Rupa Varghese, Zulfa Deesi, Norbert Nowotny, Alawi Alsheikh-Ali, View ORCID ProfileAhmad Abou Tayoun
doi: https://doi.org/10.1101/2020.06.06.138339
Divinlal Harilal
1Al Jalila Genomics Center, Al Jalila Children’s Hospital, Dubai, United Arab Emirates
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Sathishkumar Ramaswamy
1Al Jalila Genomics Center, Al Jalila Children’s Hospital, Dubai, United Arab Emirates
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Tom Loney
2College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
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Hanan Al Suwaidi
2College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
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Hamda Khansaheb
3Medical Education & Research Department, Dubai Health Authority, Dubai, United Arab Emirates
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Abdulmajeed Alkhaja
3Medical Education & Research Department, Dubai Health Authority, Dubai, United Arab Emirates
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Rupa Varghese
4Microbiology and Infection Control Unit, Pathology and Genetics Department, Latifa Women and Children Hospital, Dubai Health Authority, Dubai, United Arab Emirates
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Zulfa Deesi
4Microbiology and Infection Control Unit, Pathology and Genetics Department, Latifa Women and Children Hospital, Dubai Health Authority, Dubai, United Arab Emirates
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Norbert Nowotny
2College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
5Institute of Virology, University of Veterinary Medicine Vienna, Vienna, Austria
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Alawi Alsheikh-Ali
2College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
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Ahmad Abou Tayoun
1Al Jalila Genomics Center, Al Jalila Children’s Hospital, Dubai, United Arab Emirates
2College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
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  • ORCID record for Ahmad Abou Tayoun
  • For correspondence: Ahmad.Tayoun@ajch.ae
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Abstract

Background With the gradual reopening of economies and resumption of social life, robust surveillance mechanisms should be implemented to control the ongoing COVID-19 pandemic. Unlike RT-qPCR, SARS-CoV-2 Whole Genome Sequencing (cWGS) has the added advantage of identifying cryptic origins of the virus, and the extent of community-based transmissions versus new viral introductions, which can in turn influence public health policy decisions. However, practical and cost considerations of cWGS should be addressed before it can be widely implemented.

Methods We performed shotgun transcriptome sequencing using RNA extracted from nasopharyngeal swabs of patients with COVID-19, and compared it to targeted SARS-CoV-2 full genome amplification and sequencing with respect to virus detection, scalability, and cost-effectiveness. To track virus origin, we used open-source multiple sequence alignment and phylogenetic tools to compare the assembled SARS-CoV-2 genomes to publicly available sequences.

Results We show a significant improvement in whole genome sequencing data quality and viral detection using amplicon-based target enrichment of SARS-CoV-2. With enrichment, more than 99% of the sequencing reads mapped to the viral genome compared to an average of 0.63% without enrichment. Consequently, a dramatic increase in genome coverage was obtained using significantly less sequencing data, enabling higher scalability and significant cost reductions. We also demonstrate how SARS-CoV-2 genome sequences can be used to determine their possible origin through phylogenetic analysis including other viral strains.

Conclusions SARS-CoV-2 whole genome sequencing is a practical, cost-effective, and powerful approach for population-based surveillance and control of viral transmission in the next phase of the COVID-19 pandemic.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • Included more samples and revised text

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted June 18, 2020.
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SARS-CoV-2 Whole Genome Amplification and Sequencing for Effective Population-Based Surveillance and Control of Viral Transmission
Divinlal Harilal, Sathishkumar Ramaswamy, Tom Loney, Hanan Al Suwaidi, Hamda Khansaheb, Abdulmajeed Alkhaja, Rupa Varghese, Zulfa Deesi, Norbert Nowotny, Alawi Alsheikh-Ali, Ahmad Abou Tayoun
bioRxiv 2020.06.06.138339; doi: https://doi.org/10.1101/2020.06.06.138339
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SARS-CoV-2 Whole Genome Amplification and Sequencing for Effective Population-Based Surveillance and Control of Viral Transmission
Divinlal Harilal, Sathishkumar Ramaswamy, Tom Loney, Hanan Al Suwaidi, Hamda Khansaheb, Abdulmajeed Alkhaja, Rupa Varghese, Zulfa Deesi, Norbert Nowotny, Alawi Alsheikh-Ali, Ahmad Abou Tayoun
bioRxiv 2020.06.06.138339; doi: https://doi.org/10.1101/2020.06.06.138339

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