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Research Article
Joseph M Kungu
College of Veterinary Medicine Animal Resources and Biosecurity, Makerere University
Corresponding Author
License:
This work is licensed under a CC BY 4.0 License. Read Full License
Back ground: Corona Virus Disease 2019 (COVID 19) in Uganda was first reported in a male traveler from Dubai on 21st March, 2020 shortly after WHO had announced the condition as a global pandemic. Timely laboratory diagnosis of COVID -19 for all samples from both symptomatic and asymptomatic patients was observed as key in containing the pandemic and breaking the chain of transmission. However, there was a challenge of limited resources required for testing SARS-COV-2 in low and middle income countries. To mitigate this, a study was conducted to evaluate a sample pooling strategy for COVI-19 using real time PCR. The cost implication and the turn around time of pooled sample testing versus individual sample testing were also compared.
Methods: In this study, 1260 randomly selected samples submitted to Uganda Virus Research Institute for analysis were batched in pools of 5, 10, and 15. The pools were then extracted using a Qiagen kit. Both individual and pooled RNA were screened for the SARS-COV-2 E gene using a Berlin kit.
Results: Out of 1260 samples tested, 21 pools were positive in pools of 5 samples, 16 were positive in pools of 10 and 14 were positive in pools of 15 samples. The study also revealed that the pooling strategy helps to save a lot on resources, time and expands diagnostic capabilities without affecting the sensitivity of the test in areas with low SARS-COV-2 prevalence.
Conclusion: This study demonstrated that the pooling strategy for COVID-19 reduced on the turnaround time and there was a substantial increase in the overall testing capacity with limited resources as compared to individual testing.
Keywords
COVID-19, sample pooling, Uganda
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CURRENT STATUS: Under Review
Version 1
Posted 15 Mar, 2021
No community comments so far
Editorial decision: Major revision
On 23 Mar, 2021
Review #1 received
Received 21 Mar, 2021
Review #4 received
Received 21 Mar, 2021
Review #3 received
Received 21 Mar, 2021
Review #2 received
Received 21 Mar, 2021
Reviewer #4 agreed
On 16 Mar, 2021
Reviewer #5 agreed
On 16 Mar, 2021
Reviewer #8 agreed
On 16 Mar, 2021
Reviewer #7 agreed
On 16 Mar, 2021
Reviewer #1 agreed
On 16 Mar, 2021
Reviewer #2 agreed
On 16 Mar, 2021
Reviewer #3 agreed
On 16 Mar, 2021
Reviewer #6 agreed
On 16 Mar, 2021
Reviewers invited
Invitations sent on 16 Mar, 2021
Editor assigned
On 11 Mar, 2021
Editor invited
On 10 Mar, 2021
Submission checks complete
On 10 Mar, 2021
First submitted
On 02 Mar, 2021
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Subject Areas
Infectious Diseases
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This preprint is under consideration at BMC Infectious Diseases. A preprint is a preliminary version of a manuscript that has not completed peer review at a journal. Research Square does not conduct peer review prior to posting preprints. The posting of a preprint on this server should not be interpreted as an endorsement of its validity or suitability for dissemination as established information or for guiding clinical practice.
Learn more about In Review
Research Article
Joseph M Kungu
College of Veterinary Medicine Animal Resources and Biosecurity, Makerere University
Corresponding Author
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
Peer Review Timeline
CURRENT STATUS: Under Review
Version 1
Posted 15 Mar, 2021
No community comments so far
Editorial decision: Major revision
On 23 Mar, 2021
Review #1 received
Received 21 Mar, 2021
Review #4 received
Received 21 Mar, 2021
Review #3 received
Received 21 Mar, 2021
Review #2 received
Received 21 Mar, 2021
Reviewer #4 agreed
On 16 Mar, 2021
Reviewer #5 agreed
On 16 Mar, 2021
Reviewer #8 agreed
On 16 Mar, 2021
Reviewer #7 agreed
On 16 Mar, 2021
Reviewer #1 agreed
On 16 Mar, 2021
Reviewer #2 agreed
On 16 Mar, 2021
Reviewer #3 agreed
On 16 Mar, 2021
Reviewer #6 agreed
On 16 Mar, 2021
Reviewers invited
Invitations sent on 16 Mar, 2021
Editor assigned
On 11 Mar, 2021
Editor invited
On 10 Mar, 2021
Submission checks complete
On 10 Mar, 2021
First submitted
On 02 Mar, 2021
Subject Areas
Infectious Diseases
License:
This work is licensed under a CC BY 4.0 License. Read Full License
Back ground: Corona Virus Disease 2019 (COVID 19) in Uganda was first reported in a male traveler from Dubai on 21st March, 2020 shortly after WHO had announced the condition as a global pandemic. Timely laboratory diagnosis of COVID -19 for all samples from both symptomatic and asymptomatic patients was observed as key in containing the pandemic and breaking the chain of transmission. However, there was a challenge of limited resources required for testing SARS-COV-2 in low and middle income countries. To mitigate this, a study was conducted to evaluate a sample pooling strategy for COVI-19 using real time PCR. The cost implication and the turn around time of pooled sample testing versus individual sample testing were also compared.
Methods: In this study, 1260 randomly selected samples submitted to Uganda Virus Research Institute for analysis were batched in pools of 5, 10, and 15. The pools were then extracted using a Qiagen kit. Both individual and pooled RNA were screened for the SARS-COV-2 E gene using a Berlin kit.
Results: Out of 1260 samples tested, 21 pools were positive in pools of 5 samples, 16 were positive in pools of 10 and 14 were positive in pools of 15 samples. The study also revealed that the pooling strategy helps to save a lot on resources, time and expands diagnostic capabilities without affecting the sensitivity of the test in areas with low SARS-COV-2 prevalence.
Conclusion: This study demonstrated that the pooling strategy for COVID-19 reduced on the turnaround time and there was a substantial increase in the overall testing capacity with limited resources as compared to individual testing.
Figure 1
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