Impact of viral load on sample pooling for reverse-transcription polymerase chain reaction detection-based diagnosis of coronavirus disease 2019 in Nigeria
Background: The coronavirus disease 2019 (COVID-19) pandemic strained diagnostic testing capacities globally, particularly in low- and middle-income countries like Nigeria. Reverse-transcription polymerase chain reaction (RT-PCR) remains the gold standard for COVID-19 detection, but limited testing...
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| Format: | Article |
| Language: | English |
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AOSIS
2025-02-01
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| Series: | African Journal of Laboratory Medicine |
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| Online Access: | https://ajlmonline.org/index.php/ajlm/article/view/2514 |
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| author | Timan T. Eliya Elvis E. Isere Bassey Emmana Chukwuebuka Ugwu Jonathan Kushim Precious Ishaku Aisha E. Ibrahim John S. Bimba |
| author_facet | Timan T. Eliya Elvis E. Isere Bassey Emmana Chukwuebuka Ugwu Jonathan Kushim Precious Ishaku Aisha E. Ibrahim John S. Bimba |
| author_sort | Timan T. Eliya |
| collection | DOAJ |
| description | Background: The coronavirus disease 2019 (COVID-19) pandemic strained diagnostic testing capacities globally, particularly in low- and middle-income countries like Nigeria. Reverse-transcription polymerase chain reaction (RT-PCR) remains the gold standard for COVID-19 detection, but limited testing resources caused bottlenecks in Nigeria’s response during the pandemic. Sample pooling offers a cost-effective strategy to enhance testing capacity during future outbreaks.
Objective: This study determined the maximum number of COVID-19 samples that can be pooled for RT-PCR testing in Nigeria without compromising the detection sensitivity of a single positive sample.
Methods: A total of 1222 nasopharyngeal samples from symptomatic COVID-19 patients in Nasarawa State, Nigeria, collected between March 2021 and August 2022, were retrieved from the laboratory biorepository and analysed from November 2022 to February 2023. These included five positive samples with cycle threshold (Ct) values ranging from ≤ 20 to 40, and 1217 negative samples. Positive samples were pooled with negative ones at increasing dilution ratios (1:4–1:64), to assess detection sensitivity on the GeneXpert platform.
Results: A positive sample with a Ct value ≤ 25 could be pooled with up to 64 negative samples while maintaining a detectable positive result. However, samples with Ct values of 36–40 could only be pooled with a maximum of eight negative samples. Higher Ct values reduced pooling effectiveness.
Conclusion: Sample pooling is a feasible method for scaling up COVID-19 RT-PCR testing in resource-limited settings like Nigeria. The Ct value is critical in determining optimal pool sizes for accurate detection.
What this study adds: The findings provide critical guidelines for determining the optimal pool sizes based on Ct values, aiding in effective COVID-19 testing strategies. By optimising sample pooling based on viral load, health authorities can improve their response to future COVID-19 outbreaks and similar public health emergencies. |
| format | Article |
| id | doaj-art-a98de256d1e14ea69c1df4753eddd5e5 |
| institution | Kabale University |
| issn | 2225-2002 2225-2010 |
| language | English |
| publishDate | 2025-02-01 |
| publisher | AOSIS |
| record_format | Article |
| series | African Journal of Laboratory Medicine |
| spelling | doaj-art-a98de256d1e14ea69c1df4753eddd5e52025-02-11T13:21:50ZengAOSISAfrican Journal of Laboratory Medicine2225-20022225-20102025-02-01141e1e610.4102/ajlm.v14i1.2514490Impact of viral load on sample pooling for reverse-transcription polymerase chain reaction detection-based diagnosis of coronavirus disease 2019 in NigeriaTiman T. Eliya0Elvis E. Isere1Bassey Emmana2Chukwuebuka Ugwu3Jonathan Kushim4Precious Ishaku5Aisha E. Ibrahim6John S. Bimba7Zankli Research Centre, Bingham University, Karu, Nasarawa StateZankli Research Centre, Bingham University, Karu, Nasarawa StateZankli Research Centre, Bingham University, Karu, Nasarawa StateZankli Research Centre, Bingham University, Karu, Nasarawa StateZankli Research Centre, Bingham University, Karu, Nasarawa StateZankli Research Centre, Bingham University, Karu, Nasarawa StateDepartment of Biological Sciences, Faculty of Sciences, Bingham University, Karu, Nasarawa StateZankli Research Centre, Bingham University, Karu, Nasarawa State, Nigeria; and, Department of Community Medicine, Bingham University, Karu, Nasarawa State, Nigeria; and, Department of Clinical Sciences, Liverpool School of Tropical Medicine, LiverpoolBackground: The coronavirus disease 2019 (COVID-19) pandemic strained diagnostic testing capacities globally, particularly in low- and middle-income countries like Nigeria. Reverse-transcription polymerase chain reaction (RT-PCR) remains the gold standard for COVID-19 detection, but limited testing resources caused bottlenecks in Nigeria’s response during the pandemic. Sample pooling offers a cost-effective strategy to enhance testing capacity during future outbreaks. Objective: This study determined the maximum number of COVID-19 samples that can be pooled for RT-PCR testing in Nigeria without compromising the detection sensitivity of a single positive sample. Methods: A total of 1222 nasopharyngeal samples from symptomatic COVID-19 patients in Nasarawa State, Nigeria, collected between March 2021 and August 2022, were retrieved from the laboratory biorepository and analysed from November 2022 to February 2023. These included five positive samples with cycle threshold (Ct) values ranging from ≤ 20 to 40, and 1217 negative samples. Positive samples were pooled with negative ones at increasing dilution ratios (1:4–1:64), to assess detection sensitivity on the GeneXpert platform. Results: A positive sample with a Ct value ≤ 25 could be pooled with up to 64 negative samples while maintaining a detectable positive result. However, samples with Ct values of 36–40 could only be pooled with a maximum of eight negative samples. Higher Ct values reduced pooling effectiveness. Conclusion: Sample pooling is a feasible method for scaling up COVID-19 RT-PCR testing in resource-limited settings like Nigeria. The Ct value is critical in determining optimal pool sizes for accurate detection. What this study adds: The findings provide critical guidelines for determining the optimal pool sizes based on Ct values, aiding in effective COVID-19 testing strategies. By optimising sample pooling based on viral load, health authorities can improve their response to future COVID-19 outbreaks and similar public health emergencies.https://ajlmonline.org/index.php/ajlm/article/view/2514coronavirus disease 2019pandemicreal-time polymerase chain reaction testingcycle thresholdsample poolingnigeria |
| spellingShingle | Timan T. Eliya Elvis E. Isere Bassey Emmana Chukwuebuka Ugwu Jonathan Kushim Precious Ishaku Aisha E. Ibrahim John S. Bimba Impact of viral load on sample pooling for reverse-transcription polymerase chain reaction detection-based diagnosis of coronavirus disease 2019 in Nigeria African Journal of Laboratory Medicine coronavirus disease 2019 pandemic real-time polymerase chain reaction testing cycle threshold sample pooling nigeria |
| title | Impact of viral load on sample pooling for reverse-transcription polymerase chain reaction detection-based diagnosis of coronavirus disease 2019 in Nigeria |
| title_full | Impact of viral load on sample pooling for reverse-transcription polymerase chain reaction detection-based diagnosis of coronavirus disease 2019 in Nigeria |
| title_fullStr | Impact of viral load on sample pooling for reverse-transcription polymerase chain reaction detection-based diagnosis of coronavirus disease 2019 in Nigeria |
| title_full_unstemmed | Impact of viral load on sample pooling for reverse-transcription polymerase chain reaction detection-based diagnosis of coronavirus disease 2019 in Nigeria |
| title_short | Impact of viral load on sample pooling for reverse-transcription polymerase chain reaction detection-based diagnosis of coronavirus disease 2019 in Nigeria |
| title_sort | impact of viral load on sample pooling for reverse transcription polymerase chain reaction detection based diagnosis of coronavirus disease 2019 in nigeria |
| topic | coronavirus disease 2019 pandemic real-time polymerase chain reaction testing cycle threshold sample pooling nigeria |
| url | https://ajlmonline.org/index.php/ajlm/article/view/2514 |
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