Comparison of analytical performance and economic value of two biosurveillance methods for tracking SARS-COV-2 variants of concern

The development of biosurveillance programs with strong analytical performance and economically accessible protocols is essential for monitoring viral pathogens. Throughout the COVID-19 pandemic, whole-genome sequencing (WGS) has been the prevailing technology for SARS-CoV-2 variant of concern (VOC)...

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Published in:	Microbiology spectrum Vol. 12; no. 2; p. e0348423
Main Authors:	Pinkhover, Nicholas P, Pontbriand, Kerriann M, Fletcher, Kelli P, Sanchez, Eduardo, Okello, Kenneth, Garvey, Liam M, Pum, Alex, Li, Kurvin, DeOliveira, Gabriel, Proctor, Teddie, Feenstra, Jelena D M, Sorel, Océane, Gandhi, Manoj, Auclair, Jared R
Format:	Journal Article
Language:	English
Published:	United States American Society for Microbiology 06-02-2024
Subjects:	genotyping NGS PCR Public Health Research Article SARS-CoV-2 sequencing surveillance SARS-CoV-2 variants of concern genotyping NGS surveillance PCR sequencing
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Summary:	The development of biosurveillance programs with strong analytical performance and economically accessible protocols is essential for monitoring viral pathogens. Throughout the COVID-19 pandemic, whole-genome sequencing (WGS) has been the prevailing technology for SARS-CoV-2 variant of concern (VOC) detection. While WGS offers benefits, it is a lengthy process, financially and technically straining for scalable viral tracking. The aim of this study was to compare the analytical performance and economic feasibility of WGS and PCR mutation panels for distinguishing six known VOCs: Alpha (B.1.1.7 and Q.4), Gamma (P.1), Delta (B.1.617.2 and AY.4.2), and Omicron. (B.1.1.529.1). In all, 78 SARS-CoV-2-positive samples were collected from April to December 2021 at Northeastern University (Cabot Testing Site, Boston, MA, USA) for genotyping PCR and WGS analysis. MagMax Viral/Pathogen II Nucleic Acid Isolation and TaqPath COVID-19 Combo Kits were used for RNA extraction and SARS-CoV-2 confirmation. VOC discrimination was assessed using two TaqMan SARS-CoV-2 single nucleotide polymorphism (SNP) assay layouts, and Ion Torrent WGS. In November 2021, the mutation panel demonstrated marked versatility by detecting the emerging Omicron variant reported by South Africa. SNP panel analysis yielded the following 78 VOC identifications: Alpha B.1.1.7 ( = 20), Alpha Q.4 ( = 3), Gamma P.1 ( = 1), Delta B.1.617.2 ( = 30), Delta AY.4.2 ( = 3), and Omicron B.1.1.529.1 ( = 20) with one undetermined ( = 1) sample. Genotyping mutation panels designated lineages in 77 of 78 samples, 46/78 were confirmed by WGS, while 32 samples failed WGS lineage assignment. RT-PCR genotyping panels offer pronounced throughput and sensitivity and provide an economically advantageous technique for SARS-CoV-2 biosurveillance.IMPORTANCEThe results presented in our manuscript demonstrate how the value of simplistic and reliable molecular assays coupled with the core scientific principle of standardization can be overlooked by the charm of more sophisticated assays and instrumentation. This effect can often be amplified during tumultuous public health events, such as the COVID-19 pandemic. By adapting standardized PCR mutation panels to detect prominently circulating SARS-CoV-2 variants, we were able to better assess the potential health impacts of rising positivity rates and transmission clusters within the Northeastern University population. While several literature publications utilizing genotyping PCR and NGS have a similar scope to ours, many investigations lack sufficiently standardized genotyping PCR and NGS bioinformatics inclusionary/exclusionary criteria for SARS-CoV-2 variant identification. Finally, the economic benefits of standardized PCR mutation panels would allow for global implementation of biosurveillance, rather than reserving biosurveillance to more economically developed nations.
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 Present address: University of Massachusetts, Lowell, Massachusetts, USA Present address: LabCorp, Southborough, Massachusetts, USA Present address: University of New England, Biddeford, Maine, USA Present address: University of California, Los Angeles, California, USA Present address: Abbott Laboratories Inc., Santa Clara, California, USA Present address: Sarepta Therapeutics Inc., Cambridge, Massachusetts, USA The authors declare no conflict of interest.
ISSN:	2165-0497 2165-0497
DOI:	10.1128/spectrum.03484-23