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, the practical and cost considerations of cWGS should be addressed before it is 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 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 found considerable 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, an increase in genome coverage was obtained using substantially less sequencing data, enabling higher scalability and sizable cost reductions. We also demonstrated 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.
journal_name
Clin Chemjournal_title
Clinical chemistryauthors
Harilal D,Ramaswamy S,Loney T,Suwaidi HA,Khansaheb H,Alkhaja A,Varghese R,Deesi Z,Nowotny N,Alsheikh-Ali A,Abou Tayoun Adoi
10.1093/clinchem/hvaa187subject
Has Abstractpub_date
2020-11-01 00:00:00pages
1450-1458issue
11eissn
0009-9147issn
1530-8561pii
5876628journal_volume
66pub_type
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更新日期:1987-06-01 00:00:00
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更新日期:1978-01-01 00:00:00
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更新日期:1991-07-01 00:00:00
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更新日期:1986-10-01 00:00:00
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