Challenges and issues of SARS-CoV-2 pool testing

Eberhardt, Jens Niklas; Breuckmann, Nikolas P.; Eberhardt, Christiane

doi:10.1016/s1473-3099(20)30467-9

Cited by 16 publications

(16 citation statements)

References 4 publications

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“…Eberhardt and colleagues suggest forming subgroups if a pool yields a positive result [20]. SARS-CoV-2-infected individuals need to be rapidly detected in order to apply quarantine measures and perform contact tracing.…”

Section: Discussionmentioning

confidence: 99%

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Safe and effective pool testing for SARS-CoV-2 detection

Wunsch

Aschemeier

Heger

et al. 2021

Preprint

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Background / Objectives: The global spread of SARS-CoV-2 is a serious public health issue. Large-scale surveillance screenings are crucial but can exceed diagnostic test capacities. We set out to optimize test conditions and implemented high throughput pool testing of respiratory swabs into SARS-CoV-2 diagnostics. Study design: In preparation for pool testing, we determined the optimal pooling strategy and pool size. In addition, we measured the impact of vortexing prior to sample processing, compared pipette- and swab-pooling method as well as the sensitivity of three different PCR assays. Results: Using optimized strategies for pooling, we systematically pooled 55,690 samples in a period of 44 weeks resulting in a reduction of 47,369 PCR reactions. In a low prevalence setting, we defined a preferable pool size of ten in a two-stage hierarchical pool testing strategy. Vortexing of the swabs increased cellular yield by a factor of 2.34, and sampling at or shortly after symptom onset was associated with higher viral loads. By comparing different pooling strategies, pipette-pooling was more efficient compared to swab-pooling. Conclusions: For implementing pooling strategies into high throughput diagnostics, we recommend to apply a pipette-pooling method, using pool sizes of ten samples, performing sensitivity validation of the PCR assays used, and vortexing swabs prior to analyses. Our data shows, that pool testing for SARS-CoV-2 detection is feasible and highly effective in a low prevalence setting.

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Section: Discussionmentioning

confidence: 99%

“…To our knowledge, this is the first systematic investigation addressing various aspects of pool testing for SARS-CoV-2 detection. However, reports on this topic have recently been published [17][18][19][20][21][22][23][24][25][26][27][28][29][30][31].…”

Section: Discussionmentioning

confidence: 99%

Safe and effective pool testing for SARS-CoV-2 detection

Wunsch

Aschemeier

Heger

et al. 2021

Preprint

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“…Due to the effect of dilution, the detection rate decreases if more samples are included in a single pool [17,19,29,30]. However, pooling fewer specimens would incur a higher cost.…”

Section: Comparison With Other Studiesmentioning

confidence: 99%

Evaluation of an Automated High-Throughput Liquid-Based RNA Extraction Platform on Pooled Nasopharyngeal or Saliva Specimens for SARS-CoV-2 RT-PCR

Chu

Yip

Chan

et al. 2021

Viruses

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SARS-CoV-2 RT-PCR with pooled specimens has been implemented during the COVID-19 pandemic as a cost- and manpower-saving strategy for large-scale testing. However, there is a paucity of data on the efficiency of different nucleic acid extraction platforms on pooled specimens. This study compared a novel automated high-throughput liquid-based RNA extraction (LRE) platform (PHASIFYTM) with a widely used magnetic bead-based total nucleic acid extraction (MBTE) platform (NucliSENS® easyMAG®). A total of 60 pools of nasopharyngeal swab and 60 pools of posterior oropharyngeal saliva specimens, each consisting of 1 SARS-CoV-2 positive and 9 SARS-CoV-2 negative specimens, were included for the comparison. Real-time RT-PCR targeting the SARS-CoV-2 RdRp/Hel gene was performed, and GAPDH RT-PCR was used to detect RT-PCR inhibitors. No significant differences were observed in the Ct values and overall RT-PCR positive rates between LRE and MBTE platforms (92.5% (111/120] vs 90% (108/120]), but there was a slightly higher positive rate for LRE (88.3% (53/60]) than MBTE (81.7% (49/60]) among pooled saliva. The automated LRE method is comparable to a standard MBTE method for the detection of SAR-CoV-2 in pooled specimens, providing a suitable alternative automated extraction platform. Furthermore, LRE may be better suited for pooled saliva specimens due to more efficient removal of RT-PCR inhibitors.

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“…Besides human resources, limited laboratory capacity for RT-PCR analysis may be a major barrier for the realization of monitoring concepts, especially if mass individual testing would be envisaged. Testing multiple samples in one approach (pooling) to screen asymptomatic people is an important strategy to consider -even if associated with challenges -when testing capacity is low and laboratory infrastructure overwhelmed [32][33][34][35][36]. It is also a more socially responsible strategy in regard to limited testing capacity globally [37].…”

Section: Implications For Future Monitoring Conceptsmentioning

confidence: 99%

Monitoring for COVID-19 by universal testing in a homeless shelter in Germany: a prospective feasibility cohort study

Lindner

Sarma

Rust³

et al. 2020

Preprint

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Background: Living conditions in homeless shelters may facilitate the transmission of COVID-19. Social determinants and pre-existing health conditions place homeless people at increased risk of severe disease. Described outbreaks in homeless shelters resulted in high proportions of infected residents and staff members. In addition to other infection prevention strategies, regular shelter-wide (universal) testing for COVID-19 may be valuable, depending on the level of community transmission and when resources permit. Methods: This was a prospective feasibility cohort study to evaluate universal testing for COVID-19 at a homeless shelter with 106 beds in Berlin, Germany. Co-researchers were recruited from the shelter staff. A PCR analysis of saliva or self-collected nasal/oral swab was performed weekly over a period of 3 weeks in July 2020. Acceptability and implementation barriers were analyzed by process evaluation using mixed methods including evaluation sheets, focus group discussion and a structured questionnaire. Results: Ninety-three out of 124 (75%) residents were approached to participate in the study. Fifty-one out of the 93 residents (54.8%) gave written informed consent. High retention rates (88.9% - 93.6%) of a weekly respiratory specimen were reached, but repeated collection attempts, as well as assistance were required. A self-collected nasal/oral swab was considered easier and more hygienic to collect than a saliva specimen. No resident was tested positive. Language barriers were the main reason for non-participation. Flexibility of sample collection schedules, the use of video and audio materials, and concise written information were the main recommendations of the co-researchers for future implementation. Conclusion: Voluntary universal testing for COVID-19 is feasible in homeless shelters. Universal testing of high-risk facilities will require flexible approaches, considering the level of the community transmission, the available resources, and the local recommendations. Lack of human resources and laboratory capacity may be a major barrier for implementation of universal testing, requiring adapted approaches compared to standard individual testing. Assisted self-collection of specimens and barrier free communication may facilitate implementation in homeless shelters. Program planning must consider needs and life situation of homeless people, and guarantee confidentiality and autonomy.

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Challenges and issues of SARS-CoV-2 pool testing

Cited by 16 publications

References 4 publications

Safe and effective pool testing for SARS-CoV-2 detection

Safe and effective pool testing for SARS-CoV-2 detection

Evaluation of an Automated High-Throughput Liquid-Based RNA Extraction Platform on Pooled Nasopharyngeal or Saliva Specimens for SARS-CoV-2 RT-PCR

Monitoring for COVID-19 by universal testing in a homeless shelter in Germany: a prospective feasibility cohort study

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