| Literature DB >> 34175613 |
Evangeline Ann Daniel1, Bennett Henzeler Esakialraj L2, Anbalagan S2, Kannan Muthuramalingam2, Ramesh Karunaianantham2, Lucia Precilla Karunakaran2, Manohar Nesakumar2, Murugesan Selvachithiram2, Sathyamurthi Pattabiraman2, Sudhakar Natarajan2, Srikanth Prasad Tripathy2, Luke Elizabeth Hanna3.
Abstract
SARS-CoV-2 has surged across the globe causing the ongoing COVID-19 pandemic. Systematic testing to facilitate index case isolation and contact tracing is needed for efficient containment of viral spread. The major bottleneck in leveraging testing capacity has been the lack of diagnostic resources. Pooled testing is a potential approach that could reduce cost and usage of test kits. This method involves pooling individual samples and testing them 'en bloc'. Only if the pool tests positive, retesting of individual samples is performed. Upon reviewing recent articles on this strategy employed in various SARS-CoV-2 testing scenarios, we found substantial diversity emphasizing the requirement of a common protocol. In this article, we review various theoretically simulated and clinically validated pooled testing models and propose practical guidelines on applying this strategy for large scale screening. If implemented properly, the proposed approach could contribute to proper utilization of testing resources and flattening of infection curve.Entities:
Keywords: COVID-19; Diagnosis; Pooled testing; RT-PCR; SARS-CoV-2; Sensitivity
Year: 2021 PMID: 34175613 PMCID: PMC8127528 DOI: 10.1016/j.diagmicrobio.2021.115432
Source DB: PubMed Journal: Diagn Microbiol Infect Dis ISSN: 0732-8893 Impact factor: 2.803
Fig. 1Adaptive pooled testing strategies: (A) Dorfman Pooling: Population is divided into two pools of optimum size 8 and tested. The positively tested pool is then deconvoluted to identify the individual infected sample. (B) Column and row pooling: On a 96-well plate, rows and columns are pooled separately. The negative rows and columns are excluded. The individuals from positive rows and columns are then tested individually. In the above illustration, 5 positive samples are identified with 45 tests, compared to 96 tests if tested individually. (C) Household grouping: Pools are formed from each household in a locality and tested. Positive groups undergo individual testing.
Fig. 2Adaptive pooled testing strategy: Sample pooling based on Hypercube algorithm. For this example, the three sets of slices are shown in blue, red and green. If one infected individual is present, tests on each set of slices identify their coordinate in that direction. Hence only nine tests would uniquely identify them. (Colour version of figure is available online)
Summary of global pooled testing studies-Validation of pooled testing in different clinical settings. Pooling works with maximum efficiency in prevalence <3% with pool size <10)
| Study setting | Location | Sample size | Sample type | Prevalence (%) | Optimum Pool size | Reduction in tests (%) |
|---|---|---|---|---|---|---|
| Pooling samples before RNA extraction | ||||||
| ( | Nebraska, US | 60 | Nasopharyngeal swabs | 1 | 11 | 80 |
| ( | Tunisia, North Africa | 800 | Nasopharyngeal swabs | <1 | 10 | 80 |
| ( | Kilifi, Kenya | 1500 | Nasopharyngeal swabs | <4 | 6 | 53.3 |
| ( | Jerusalem, Israel | 133816 | Nasopharyngeal swabs | 1-6 | 5,8 | 76 |
| ( | Homburg, | 1191 | Nasopharyngeal and Oropharyngeal swabs | 1.93 | 30 | 78 |
| ( | San Francisco Bay Area, California, US | 2888 | Nasopharyngeal and bronchoalveolar lavage swabs | 0.07 | 9, 10 | 77 |
| ( | Jerusalem, Israel | 26576 | Nasopharyngeal swabs | 0.23 | 8 | 85 |
| ( | Spain | 3519 | Nasopharyngeal swabs | 6.86 | 10 | 61.57 |
| ( | Maryland, Washington D.C., US | 449 | Saliva | 5 | 5 | 40 |
| ( | Hong Kong, China | 55 | Deep throat saliva | 0.39 | 5 | - |
| ( | California, | 101 | Nasopharyngeal, midturbinate swabs | ≤10 | 4 | - |
| ( | Wuhan, China | 23 | Oropharyngeal swabs | - | 6,10 | - |
| ( | Chandigarh, India | 500 | Nasopharyngeal swabs | <2 | 10 | 69 |
| ( | Melbourne, Australia | 29000 | Nasopharyngeal swabs | <0.5 | 8 | 87.5 |
| ( | Massachusetts, US | 960 | Nasopharyngeal swabs | 3.1 | 48 | 65 |
| ( | Maryland, US | 7000 | Nasal mid-turbinate and nasopharyngeal swabs | 0.11 | 10 | 89 |
| ( | Melbourne, Australia | 31 | Nasopharyngeal swabs | <5 | 4,6 | >50 |
| ( | Tokyo, Japan | 555 | Nasopharyngeal swabs | 3.6 | 5,10 | 47 |
| ( | Seoul, Jeonju, South Korea | 350 | Nasopharyngeal and oropharyngeal swabs | - | 2-16 | - |
| ( | Hainan, China | 944 | Nasopharyngeal swabs | Airport | 10 | 87.6 |
| ( | Malaysia | 1745 | Nasopharyngeal and oropharyngeal swabs | <5 | 10 | 57 |
| ( | New York, US | 530 | Nasopharyngeal swabs | 1-2 | 3 | 67 |
| ( | Odisha, India | 7228 | Nasopharyngeal and oropharyngeal swabs | 3.5 | 4 | 64.2 |
| ( | Oklahoma, US | 630 | Nasopharyngeal swabs | <8 | 5 | 52.5 |
| 10 | 45 | |||||
| ( | Rwanda, East Africa | 1280 | Oropharyngeal swabs | 2 | 20 | - |
| ( | Seattle, US | 160 | Nasopharyngeal swabs | <8 | 4 | - |
| ( | India | 1000 | Nasopharyngeal and oropharyngeal swabs | - | 5 | - |
| ( | Ohio, US | 20 | Nasopharyngeal swabs | 0.5 | 10 | |
| ( | Detroit, US | 15 | Nasopharyngeal swabs | 2 | 6 | 70 |
| ( | Madhya Pradesh, India | 545 | Nasopharyngeal and oropharyngeal swabs | 4.8 | 5 | 70 |
| ( | Beer-Sheva, Israel | 1115 | Nasopharyngeal and oropharyngeal swabs | 1 | 48 | 87.1 |
| ( | Da Nang, Vietnam | 96123 | Nasopharyngeal swabs | <1 | 5 | 77 |
| ( | Valencia, Spain | 40 | Nasopharyngeal swabs | - | 5, 10 | - |
| ( | Porto Alegre, Brazil | 220 | Nasopharyngeal and oropharyngeal swabs | - | 10 | - |
| ( | San Francisco Bay, California, US | 1648 | Nasopharyngeal and oropharyngeal swabs | 19.1 | 4, 8 | |
| ( | New Haven, US | Saliva | >3 | 5, 10, 20 | - | |
| ( | Haifa, Israel | 388 | Nasopharyngeal and oropharyngeal swabs | - | 32 | - |
| ( | Duke University, Durham, North Carolina | 10265 | Nasopharyngeal swabs | ≤0.1 | 5 | 90 |
| ( | Homburg, Germany | 25978 | Nasopharyngeal and oropharyngeal swabs | 0.9 | 10 | 91 |
| Pooling extracted RNA | ||||||
| ( | Bangkok, Thailand | 200 | Saliva | 9 | 5 | 47.5 |
| ( | Uttarakhand, India | 102 | - | 4.1 | 20 | 40 |
| ( | Chile, South America | 63 | Nasopharyngeal swabs | 10 | 5 | - |
| ( | New Delhi, India | 280 | Nasopharyngeal and oropharyngeal swabs | - | ||
| ( | Freiburg, Bonn, Leipzig, Regensburg, Frankfurt (Germany) | 700 | Pharyngeal swabs, sputum, broncho-alveolar lavage fluid | - | 10 | 99.89 |
| ( | Spain | 100 | Nasopharyngeal swabs | 2 | 20 | 77 |
| Sub Pool 5 | 80 | |||||
| ( | New Delhi, | 55 | Nasopharyngeal and oropharyngeal swabs | 4 | 6 | 63 |
| ( | Galapagos, Equador | 114 | Nasopharyngeal swabs | <5 | 3 | - |
| Pooling at the time of collection in a single VTM tube | ||||||
| ( | Brazil | 19535 | Nasopharyngeal swabs | 1.26 | 16 | 77 |
| ( | Tenerif, Spain | 4475 | Nasopharyngeal swabs | 5 | 5 | 62 |
| ( | Lucknow, India | 19570 | Nasopharyngeal and Oropharyngeal swabs | <5 | 5 | 76 |
| 10 | 93 | |||||
| ( | New York, US | 20 | Upper respiratory swab | <1.5 | 5, 9 | 75 |
| ( | Delhi, | 230 | Nasopharyngeal swabs | - | 5 | 70 |
| Pooling directly into lysis buffer | ||||||
| ( | Frankfort, Germany | 100 | Nasopharyngeal and oropharyngeal swabs | 2 | 5, 10 | 40 |
| ( | Bangkok, Thailand | 99 | Nasopharyngeal and oropharyngeal swabs | 0.1-10 | 10 | 80 |
‘-’ indicates that studies that did not report prevalence rate at the time of testing and the resources saved
Fig. 3Pooling methods employed in clinical setups: (A) Sample pooling before RNA extraction (B) Pooling of extracted RNA (C) Sample pooling at the time of collection (D) Sample collected directly into the lysis buffer; VTM= viral transport media.
Fig. 4Diagnostic accuracy utilising pooled testing strategy: The size of the bubble depicts pool size, while the different colours code for different studies. The purple-shaded area represents areas with sensitivity and specificity combinations that meet the acceptable levels of Target Product Profile (TPP) put forth by WHO for COVID-19 diagnostics. The dashed square box within the purple-shaded area portrays the desirable level. Study bubbles clustered within the acceptable limits infer efficient diagnostic capability in detecting SARS-CoV-2 by pooling samples. (Colour version of figure is available online)