Pooled testing conserves SARS-CoV-2 laboratory resources and improves test turn-around time: experience on the Kenyan Coast

Agoti, Charles N.; Mutunga, Martin; Lambisia, Arnold W.; Kimani, Domtila; Cheruiyot, Robinson; Kiyuka, Patience K.; Lewa, Clement; Gicheru, Elijah; Tendwa, Metrine; Mohammed, Khadija Said; Osoti, Victor; Makale, Johnstone; Tawa, Brian; Odundo, Calleb; Cheruiyot, Wesley; Nyamu, Wilfred; Gumbi, Wilson; Mwacharo, Jedidah; Nyamako, Lydia; Otieno, Edward; Amadi, David; Thoya, Janet; Karani, Angela; Mugo, Daisy; Musyoki, Jennifer; Gumba, Horace; Mwarumba, Salim; Gichuki, Bonface M.; Njuguna, Susan; Riako, Debra; Mutua, Shadrack; Gitonga, John N.; Sein, Yiakon; Bartilol, Brian; Mwangi, Shaban; Omuoyo, Donwilliams O.; Morobe, John M.; Laurent, Zaydah R. de; Bejon, Philip; Ochola‐Oyier, Lynette Isabella; Tsofa, Benjamin

doi:10.12688/wellcomeopenres.16113.1

Cited by 14 publications

(14 citation statements)

References 22 publications

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“…A study in Kenya also showed that the cycle threshold values were higher for samples which were pooled then tested individually. 17 The study in Spain also showed that sample dilution in pooling strategy resulted in a median loss of 2.8 to 3.3 Ct and thereby drop in sensitivity. 18…”

Section: Discussionmentioning

confidence: 95%

“…A lot of factors affect the sensitivity of RT-PCR, like the sensitivity of the kit, dilution used, the techniques of sample collection, type of samples (NPS vs oropharyngeal vs nasal etc), sample transport temperature, viral load in the sample which varies according to the stage of infection. 22,23 Therefore RT-PCR of sample pooling strategy has its own limitations, it cannot ensure the diagnostic integrity of the individual sample, 24 it can mask the technical errors like insufficient sampling, 19,25 it has higher percentage of false negatives, 10 reduces sensitivity 26 and sample dilution has led to the risk of missing weak viral load or borderline positive samples 17,21 Although pooling of samples facilitates rational use of resources, it might miss individuals who might be positive for COVID-19. 27,28…”

Section: Discussionmentioning

confidence: 99%

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Evaluation of pooling of samples for testing SARS-COV- 2 for mass screening of COVID-19

Mahmoud

Ibrahim

Thakre

et al. 2021

Preprint

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Background The current pandemic of SARS- COV- 2 virus, widely known as COVID-19 has affected millions of people around the world. The World Health Organization (WHO) has recommended vigorous testing to differentiate SARS-CoV-2 from other respiratory infections to aid in guiding appropriate care and management. Situations like this have demanded robust testing strategies and pooled testing of samples for SARS- COV- 2 virus has provided the solution to mass screening of people. The pooled testing strategy can be very effective in testing with limited resources, yet it comes with its own limitations. These limitations need critical consideration when it comes to testing of highly infectious disease like COVID -19. Methods The study evaluated the pooled testing of nasopharyngeal swabs for SARS- COV- 2 by comparing sensitivity of individual sample testing with 4 and 8 pool sample testing. Median cycle threshold (Ct) values were compared. The precision of pooled testing was assessed by doing an inter and intra assay of pooled samples. Coefficient of variance was calculated for inter and intra assay variability. Results The sensitivity becomes considerably low when the samples are pooled, there is a higher percentage of false negatives with higher pool size and when the patient viral load is low or weak positive samples. High variability was seen in the intra and inter assay, especially in weak positive samples and larger pool size. Conclusion As COVID - 19 numbers are still high and testing capacity needs to be high, we have to meticulously evaluate the testing strategy for each country depending on its testing capacity, infrastructure, economic strength, and need to make a serious call on cost effective strategy of resource saving and risk/ cost of missing positive patients.

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Section: Discussionmentioning

confidence: 95%

Section: Discussionmentioning

confidence: 99%

Evaluation of pooling of samples for testing SARS-COV- 2 for mass screening of COVID-19

Mahmoud

Ibrahim

Thakre

et al. 2021

Preprint

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“…Nasopharyngeal (NP) and oropharyngeal (OP) swabs were collected into a single tube and transported to KEMRI-Wellcome Trust Research Programme (KWTRP) for SARS-CoV-2 diagnosis. Briefly, the positive infections were RNA purified using a QIAGEN extraction kit followed by real-time reverse-transcription PCR (RT-PCR) (Agoti et al, 2020; Said et al, 2020).…”

Section: Methodsmentioning

confidence: 99%

Tracking the introduction and spread of SARS-CoV-2 in coastal Kenya

Githinji

Laurent

Mohammed

et al. 2020

Preprint

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We generated 274 SARS-CoV-2 genomes from samples collected during the early phase of the Kenyan pandemic. Phylogenetic analysis identified 8 global lineages and at least 76 independent SARS-CoV-2 introductions into Kenyan coast. The dominant B.1 lineage (European origin) accounted for 82.1% of the cases. Lineages A, B and B.4 were detected from screened individuals at the Kenya-Tanzania border or returning travellers but did not lead to established transmission. Though multiple lineages were introduced in coastal Kenya within three months following the initial confirmed case, none showed extensive local expansion other than cases characterised by lineage B.1, which accounted for 45 of the 76 introductions. We conclude that the international points of entry were important conduits of SARS-CoV-2 importations. We speculate that early public health responses prevented many introductions leading to established transmission, but nevertheless a few undetected introductions were sufficient to give rise to an established epidemic.

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“…Laboratory arrangements for testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has been hampered due to the considerable strain on global supply chains for equipment reagents, personal protective equipment and other consumables. Many countries are experiencing an acute shortage of important reagents required for the polymerase chain reaction (PCR) assay for SARS-CoV-2 [ 4 ]. It is clearly understood that the rapid diagnosis of COVID-19 in both symptomatic and asymptomatic patients can shed light on transmission patterns and facilitate contact tracing for adopting a strategy for containment.…”

Section: Introductionmentioning

confidence: 99%

Evaluating the efficiency of specimen (sample) pooling for real-time PCR based diagnosis of COVID-19

Shukla¹,

Upadhyay²,

Maurya³

2021

Indian Journal of Medical Microbiology

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Purpose This study is aims at evaluating the efficacy and sensitivity of specimen pooling for testing of SARS-CoV-2 virus to determine the accuracy, resource savings, and identification of borderline positive cases without impacting the accuracy of the testing. Method This study was conducted between August and October 2020, we performed COVID-19 testing by RT-PCR on the samples from varying prevalence of rural population (non-hot spot) referred to COVID laboratory, in the first step, the samples were collated into pools of 5 or 10. These pools were tested by RT-PCR. Negative pools were reported as negative whereas positive pools of 5 and 10 were then de-convoluted and each sample was tested individually. Results In the present study, we tested 1580 samples in 158 pools of 10 and 17,515 samples in 3503 pools of 5. Among 10 samples pool, 11 (13%) pools flagged positive in the first step. In the second step, among 11 pools (110 samples) de-convoluted strategy was followed in which 10 individual samples came positive. Among 5 samples pool, 164 (13%) pools flagged positive in the first step. In the second step, among 164 pools (820 samples) de-convoluted strategy was followed in which 171 individual samples came positive. The pooled sample testing strategy saves substantial resources and time during surge testing and enhanced pandemic surveillance. This approach requires around 76%–93% fewer tests in low to moderate prevalence settings and group sizes up to 5–10 in a population, compared to individual testing. Conclusion Pooled sample RT- PCR analysis strategies can save substantial resources and time for COVID-19 mass testing in comparison with individual testing without compromising the quality of outcome of the test. In particular, the pooled sample approach can facilitate mass screening in the early asymptomatic stages of COVID-19 infections.

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Pooled testing conserves SARS-CoV-2 laboratory resources and improves test turn-around time: experience on the Kenyan Coast

Cited by 14 publications

References 22 publications

Evaluation of pooling of samples for testing SARS-COV- 2 for mass screening of COVID-19

Evaluation of pooling of samples for testing SARS-COV- 2 for mass screening of COVID-19

Tracking the introduction and spread of SARS-CoV-2 in coastal Kenya

Evaluating the efficiency of specimen (sample) pooling for real-time PCR based diagnosis of COVID-19

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