key: cord-0758869-kkhdyadf
authors: Laguda Akingba, O.; Sprong, K.; Hardie, D. R.
title: Field performance evaluation of the PanBio rapid SARS-CoV-2 antigen assay in an epidemic driven by 501Y.v2 (lineage B.1.351) in the Eastern Cape, South Africa
date: 2021-02-05
journal: nan
DOI: 10.1101/2021.02.03.21251057
sha: fa96e2fbf43102a587cf6ad0831392d21459b115
doc_id: 758869
cord_uid: kkhdyadf

Background: South Africa was the African country most severely affected by the SARS-CoV-2 pandemic during 2020, experiencing 2 waves of infection. During the first wave, diagnostics were largely based on reverse transcription-linked PCR (RT-PCR). The Abbott PanBio antigen test was deployed during the 2nd wave which was driven by emergence of the 501Y.v2 variant. At the time of evaluation in mid-November 2020, 501Y.v2 was the dominant circulating virus in Nelson Mandela Bay, in the Eastern Cape Province. Methods: A prospective diagnostic evaluation study was undertaken, during a period of high community transmission, to evaluate the field performance of the PanBio antigen RTD. Testing was conducted at mobile community testing centres on 677 ambulant patients seeking SARS-CoV-2 testing. RT-PCR was performed on the original naso-pharyngeal antigen swabs to evaluate test performance. Results: Of 146 RT-PCR positive individuals, 101 were RTD positive in the clinic. The antigen RTD had an overall sensitivity of 69.2% (95%CI 61.4, 75.8) and specificity of 99.0% (95%CI 98.8, 99.3) in this clinical context. Sensitivity was strongly dependent on the amount of virus in clinical samples, as reflected by the PCR cycle threshold (CT) value, with 100% detection in samples where the CT was <20, 96% with CT between 20-25, 89% with CT between 26-30 and 64% when CT was 31-35. Conclusions: The assay reliably detected 501Y.v2 infections in ambulatory ill patients. Assay sensitivity was >90% in patients with high viral loads who are expected to be most infectious. Negative and positive predictive values were also >90%.

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is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint

The copyright holder for this this version posted February 5, 2021. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint

The copyright holder for this this version posted February 5, 2021. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint Verifying that used antigen swabs were suitable for PCR: is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint

The copyright holder for this this version posted February 5, 2021. ; https://doi.org/10.1101/2021.02.03.21251057 doi: medRxiv preprint is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint Sensitivity was strongly dependent on the quantity of virus in clinical samples, as reflected 128 by the CT value, with 100% detection by the antigen test in samples where the CT was <20, 129 95.5% with CT between 20-25, 89.3% with CT between 26-30 and 64,3% when CT was 31-35. 130 The CT values of antigen positive and negative samples are shown (Figures 2 a, is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint

The copyright holder for this this version posted February 5, 2021. ; https://doi.org/10.1101/2021.02.03.21251057 doi: medRxiv preprint

Cheryl Cohen2, Caroline Mudara1, THE 204 FIRST AND SECOND WAVE OF COVID-19 IN THREE DISTRICTS OF 205 SOUTH AFRICA, COVID-19 Spec

A, diagnosis of SARS-CoV-2 209 infection ( Review )

Antigen-detection in the diagnosis of SARS-CoV-2 infection 213 using rapid immunoassays Interim guidance

Panbio antigen 218 rapid test is reliable to diagnose SARS-CoV-2 infection in the first 219 7 days after the onset of symptoms

Comparison of 222 seven commercialSARS-CoV-2 rapid point of care antigen assays

Emergence and rapid spread of a new severe acute 230 respiratory syndrome-related coronavirus 2 (SARS-CoV-2) lineage 231 with multiple spike mutations in South Africa

CoV-2 501Y . V2 escapes neutralization by South African COVID-236 19 donor plasma

Assay specificity was similarly good at 99% and the predictive value of a positive test was 165 95%. This fulfils the WHO benchmark specificity requirements for deployment of this is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprintThe copyright holder for this this version posted February 5, 2021. ; https://doi.org/10.1101/2021.02.03.21251057 doi: medRxiv preprint It is made available under a perpetuity.is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprintThe copyright holder for this this version posted February 5, 2021. ; https://doi.org/10.1101/2021.02.03.21251057 doi: medRxiv preprint