Sequencing SARS-CoV-2 from antigen tests
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Abstract
Genomic surveillance empowers agile responses to SARS-CoV-2 by enabling scientists and public health analysts to issue recommendations aimed at slowing transmission, prioritizing contact tracing, and building a robust genomic sequencing surveillance strategy. Since the start of the pandemic, real time RT-PCR diagnostic testing from upper respiratory specimens, such as nasopharyngeal (NP) swabs, has been the standard. Moreover, respiratory samples in viral transport media are the ideal specimen for SARS-CoV-2 whole-genome sequencing (WGS). In early 2021, many clinicians transitioned to antigen-based SARS-CoV-2 detection tests, which use anterior nasal swabs for SARS-CoV-2 antigen detection. Despite this shift in testing methods, the need for whole-genome sequence surveillance remains. Thus, we developed a workflow for whole-genome sequencing with antigen test-derived swabs as an input rather than nasopharyngeal swabs. In this study, we use excess clinical specimens processed using the BinaxNOW™ COVID-19 Ag Card. We demonstrate that whole-genome sequencing from antigen tests is feasible and yields similar results from RT-PCR-based assays utilizing a swab in viral transport media.
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SciScore for 10.1101/2021.07.14.21260291: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics IRB: Excess clinical specimens were obtained under an institutional review board (IRB) exempt protocol (IRB reference number FWH20200103E). Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Table 2: Resources
Software and Algorithms Sentences Resources Specimen Acquisition: The BinaxNOW™ COVID-19 Ag Card (Abbott) was used to test basic medical trainees for SARS-CoV-2. Abbottsuggested: (Abbott, RRID:SCR_010477)Libraries with QRS > 1.0 were denatured and diluted to a final loading concentration of 10 pM following the Illumina MiSeq System Denature and Dilute Libraries Guide (Document # 15039740 v10), and then sequenced on the MiSeq … SciScore for 10.1101/2021.07.14.21260291: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics IRB: Excess clinical specimens were obtained under an institutional review board (IRB) exempt protocol (IRB reference number FWH20200103E). Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Table 2: Resources
Software and Algorithms Sentences Resources Specimen Acquisition: The BinaxNOW™ COVID-19 Ag Card (Abbott) was used to test basic medical trainees for SARS-CoV-2. Abbottsuggested: (Abbott, RRID:SCR_010477)Libraries with QRS > 1.0 were denatured and diluted to a final loading concentration of 10 pM following the Illumina MiSeq System Denature and Dilute Libraries Guide (Document # 15039740 v10), and then sequenced on the MiSeq system at 2 x 151 bp using the MiSeq v3, (600 cycle) kit (Illumina, Cat. MS-102-3003) MiSeqsuggested: (A5-miseq, RRID:SCR_012148)Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:Antigen card specimens present a few limitations when compared to NP swabs collected in viral transport media (VTM). First, in the workflow presented here, antigen test swabs are stored in 500 µL of DNA/RNA shield while NP swabs are stored in up to 3 mL of VTM. Multiple RNA extractions can be carried out from VTM specimens after the initial round RT-PCR testing but, antigen swab-derived viral RNA can only be extracted once. Next, variants with novel or interesting mutations can be cultured from VTM; enabling downstream biochemical or viral neutralization assays. In contrast, antigen tests immediately expose the specimen to an extraction buffer which disrupts the viral membrane, releases viral RNA, and enables the presentation of viral nucleocapsid antigens to anti-nucleocapsid antibodies on the LFA positive line. Thus, viruses collected post antigen-test are most likely non-culturable, however we did not evaluate cultivability. Here we only attempted to sequence from the BinaxNOW™ antigen test, but other antigen tests may also yield viable specimens for whole-genome sequencing. This work is a first step for future studies examining the sequencing utility of specimens collected for other antigen or rapid molecular tests.
Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- No protocol registration statement was detected.
Results from scite Reference Check: We found no unreliable references.
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