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, Simulundu, Edgar, Zumla, Alimuddin, Fwoloshi, Sombo, Mulenga, Lloyd, Pallerla, Srinivas Reddy, Velavan, Thirumalaisamy P. and Bates, Matthew (2022) Evaluation of SARS-CoV-2 diagnostics and risk factors associated with SARS-CoV-2 infection in Zambia. International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases, 120 . pp. 150-157. ISSN 1201-9712

Full content URL: https://doi.org/10.1016/j.ijid.2022.04.017

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

OBJECTIVES

To conduct a diagnostic validation study of SARS-CoV-2 diagnostic kits.

METHODS

We compared SARS-CoV-2 diagnostic test results from 3 RT-PCR assays used by the Zambian government between November 2020 and February 2021 (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 comorbidities were linked with increased odds of infection.

RESULTS

We recruited 244 participants, 61% (149/244) were positive by at least 1 PCR assay. Da An Gene, Maccura, and Panther Fusion assays had sensitivities of 0.0% (95% confidence interval [CI] 0%-41%), 27.1% (95% CI 15%-42%), and 76% (95% CI 65%-85%), respectively, but specificity was low (<85% for all 3 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. Of 44 samples, 84% 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.

Keywords:SARS-CoV-2, COVID-19, Diagnostics
Subjects:C Biological Sciences > C540 Virology
A Medicine and Dentistry > A300 Clinical Medicine
C Biological Sciences > C521 Medical Microbiology
Divisions:College of Science > School of Life Sciences
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ID Code:50078
Deposited On:11 Jul 2022 08:00

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