tetano
Editor, Senior Moderator
J Virol Methods
. 2023 Sep 29;114827.
doi: 10.1016/j.jviromet.2023.114827. Online ahead of print. Evaluation of Illumina® COVIDSeq™ as a Tool for Omicron SARS-CoV-2 Characterisation
Kym Lowry[SUP] 1 [/SUP], Michelle J Bauer[SUP] 2 [/SUP], Cameron Buckley[SUP] 3 [/SUP], Claire Wang[SUP] 4 [/SUP], Amanda Bordin[SUP] 4 [/SUP], Steven Badman[SUP] 5 [/SUP], Patrick N A Harris[SUP] 6 [/SUP], Ian Mackay[SUP] 6 [/SUP], David Whiley[SUP] 4 [/SUP]
Affiliations
The continued emergence and transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants requires ongoing genetic surveillance to support public health responses. The expansion of reliable next generation sequence (NGS) platforms has enabled the rapid characterisation of the constant emergence of new SARS-CoV-2 variants using nasopharyngeal swab specimens. Several studies have assessed the ability of COVIDSeq to type earlier SARS-CoV-2 strains (pre-Delta) rapidly and successfully, however, there is limited data showing suitability against Omicron variants. In the present study, we evaluated the performance of the Illumina COVIDSeq Assay as a streamlined amplicon-based NGS platform for detection and typing of Omicron variants. Our results demonstrate the high performance of SARS-CoV-2 sequencing using the COVIDSeq approach, with good repeatability, reproducibility and sensitivity for samples approaching C[SUB]T[/SUB] 31. The COVIDSeq approach was 100% concordant with samples previously characterized by sequencing methods. The quick library preparation process and high throughput kit made it ideal for reflex testing, with a total time required for sequencing and analysis of approximately two days. This study demonstrates the effectiveness and versatility of the amplicon-based NGS characterisation method for SARS-CoV-2, providing a foundation for further research and development of custom-designed amplicon panels targeting different microorganisms.
Keywords: COVID-19; SARS-CoV-2; amplicon-based; genotyping; next generation sequencing; variant.
. 2023 Sep 29;114827.
doi: 10.1016/j.jviromet.2023.114827. Online ahead of print. Evaluation of Illumina® COVIDSeq™ as a Tool for Omicron SARS-CoV-2 Characterisation
Kym Lowry[SUP] 1 [/SUP], Michelle J Bauer[SUP] 2 [/SUP], Cameron Buckley[SUP] 3 [/SUP], Claire Wang[SUP] 4 [/SUP], Amanda Bordin[SUP] 4 [/SUP], Steven Badman[SUP] 5 [/SUP], Patrick N A Harris[SUP] 6 [/SUP], Ian Mackay[SUP] 6 [/SUP], David Whiley[SUP] 4 [/SUP]
Affiliations
- PMID: 37778540
- DOI: 10.1016/j.jviromet.2023.114827
The continued emergence and transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants requires ongoing genetic surveillance to support public health responses. The expansion of reliable next generation sequence (NGS) platforms has enabled the rapid characterisation of the constant emergence of new SARS-CoV-2 variants using nasopharyngeal swab specimens. Several studies have assessed the ability of COVIDSeq to type earlier SARS-CoV-2 strains (pre-Delta) rapidly and successfully, however, there is limited data showing suitability against Omicron variants. In the present study, we evaluated the performance of the Illumina COVIDSeq Assay as a streamlined amplicon-based NGS platform for detection and typing of Omicron variants. Our results demonstrate the high performance of SARS-CoV-2 sequencing using the COVIDSeq approach, with good repeatability, reproducibility and sensitivity for samples approaching C[SUB]T[/SUB] 31. The COVIDSeq approach was 100% concordant with samples previously characterized by sequencing methods. The quick library preparation process and high throughput kit made it ideal for reflex testing, with a total time required for sequencing and analysis of approximately two days. This study demonstrates the effectiveness and versatility of the amplicon-based NGS characterisation method for SARS-CoV-2, providing a foundation for further research and development of custom-designed amplicon panels targeting different microorganisms.
Keywords: COVID-19; SARS-CoV-2; amplicon-based; genotyping; next generation sequencing; variant.