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Evaluation of SARS-CoV-2 diagnostics and risk factors associated with SARS-CoV-2 infection in Zambia

Tembo, John; Egbe, Nkongho Franklyn; Maluzi, Kwitaka; Mulonga, Kangwa; Chilufya, Moses; Kapata, Nathan; Mukonka, Victor; ... Bates, Matthew; + view all (2022) Evaluation of SARS-CoV-2 diagnostics and risk factors associated with SARS-CoV-2 infection in Zambia. International Journal of Infectious Diseases 10.1016/j.ijid.2022.04.017. (In press). Green open access

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Abstract

OBJECTIVES: To conduct a diagnostic validation study of SARS-CoV-2 diagnostic kits. METHODOLOGY: We compared SARS-CoV-2 diagnostic test results from three RT-PCR assays used by the Zambian government between Nov 2020 to Feb 2021 (the Panther Fusion® assay, Da An Gene's 2019-nCoV RNA kit and Maccura's PCR Kit) with the Altona RealStar RT-PCR kit which served as the gold standard. We also evaluated results from rapid antigen testing, and whether co-morbidities were linked with increased odds of infection. RESULTS: We recruited 244 participants, 61% (149/244) were positive by at least one PCR assay. Da An Gene, Maccura and Panther Fusion assays had sensitivities of 0.0% (95%CI 0-41%), 27.1% (95%CI 15-42%) and 76% (95%CI 65-85%) respectively but specificity was low (<85% for all three assays). HIV and TB were not associated with SARS-CoV-2, whereas female sex (OR 0.5 (0.3-0.9), p = 0.026) and Chronic Pulmonary Disease (0.1 (0.0-0.8), p = 0.031), were associated with lower odds of SARS-CoV-2 infection. 84% of 44 samples sequenced were Beta variant. CONCLUSIONS: The RT-PCR assays evaluated did not meet WHO recommended minimum sensitivity of 80%. Local diagnostic validation studies should be embedded within preparedness plans for future outbreaks to improve the public health response.

Type: Article
Title: Evaluation of SARS-CoV-2 diagnostics and risk factors associated with SARS-CoV-2 infection in Zambia
Open access status: An open access version is available from UCL Discovery
DOI: 10.1016/j.ijid.2022.04.017
Publisher version: https://doi.org/10.1016/j.ijid.2022.04.017
Language: English
Additional information: © 2022 Published by Elsevier Ltd on behalf of International Society for Infectious Diseases. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/)
Keywords: SARS-CoV-2, COVID-19, diagnostics, serology, real time- PCR, lateral flow test, RDTs, comorbidities
UCL classification: UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences > Div of Infection and Immunity
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL
URI: https://discovery.ucl.ac.uk/id/eprint/10147537
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