scholarly journals Evaluation of Group Testing for SARS-CoV-2 RNA

Author(s):  
Nasa Sinnott-Armstrong ◽  
Daniel L. Klein ◽  
Brendan Hickey

AbstractDuring the current COVID-19 pandemic, testing kit and RNA extraction kit availability has become a major limiting factor in the ability to determine patient disease status and accurately quantify prevalence. Current testing strategies rely on individual tests of cases matching restrictive diagnostic criteria to detect SARS-CoV-2 RNA, limiting testing of asymptomatic and mild cases. Testing these individuals is one effective way to understand and reduce the spread of COVID-19.Here, we develop a pooled testing strategy to identify these low-risk individuals. Drawing on the well-studied group testing literature, modeling suggests practical changes to testing protocols which can reduce test costs and stretch a limited test kit supply. When most tests are negative, pooling reduces the total number of tests up to four-fold at 2% prevalence and eight-fold at 0.5% prevalence. At current SARS-CoV-2 prevalence, randomized group testing optimized per country could double the number of tested individuals from 1.85M to 3.7M using only 671k more tests.This strategy is well-suited to supplement testing for asymptomatic and mild cases who would otherwise go untested, and enable them to adopt behavioral changes to slow the spread of COVID-19.

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Julius Žilinskas ◽  
Algirdas Lančinskas ◽  
Mario R. Guarracino

AbstractDuring the COVID-19 pandemic it is essential to test as many people as possible, in order to detect early outbreaks of the infection. Present testing solutions are based on the extraction of RNA from patients using oropharyngeal and nasopharyngeal swabs, and then testing with real-time PCR for the presence of specific RNA filaments identifying the virus. This approach is limited by the availability of reactants, trained technicians and laboratories. One of the ways to speed up the testing procedures is a group testing, where the swabs of multiple patients are grouped together and tested. In this paper we propose to use the group testing technique in conjunction with an advanced replication scheme in which each patient is allocated in two or more groups to reduce the total numbers of tests and to allow testing of even larger numbers of people. Under mild assumptions, a 13 ×  average reduction of tests can be achieved compared to individual testing without delay in time.


Author(s):  
Julius Žilinskas ◽  
Algirdas Lančinskas ◽  
Mario R. Guarracino

AbstractIn absence of a vaccine or antiviral drugs for the COVID-19 pandemic, it becomes urgent to test for positiveness to the virus as many people as possible, in order to detect early outbreaks of the infection. Present testing solutions are based on the extraction of RNA from patients using oropharyngeal (OP) and nasopharyngeal (NP) swabs, and then testing with real-time PCR for the presence of specific RNA filaments identifying the virus. This approach is limited by the availability of reactants, trained technicians and laboratories. To speed up the testing procedures, some attempts have been done on group testing, which means that the swabs of multiple patients are grouped together and tested. Here we propose to use this technique in conjunction with a combinatorial replication scheme in which each patient is allocated in two or more groups to reduce total numbers of tests and to allow testing of even larger numbers of people. Under mild assumptions, a 13× average reduction of tests can be achieved.


2021 ◽  
Author(s):  
Xuhua Xia

Abstract The pooled testing strategy [1] misses two key parameters, the infection prevalence p and its variance mentioned many times in the paper as the key determinants of any pooled testing strategy. For illustrating their methods, the authors used p from other studies that employed individual tests. It turned that that no statistical estimators for p and its variance have ever been derived for testing data of pooled samples since the first formulation of testing strategies based on pooled sampled in 1943 [2]. Here I derive the maximum likelihood estimators for p and its variance based on tests of pooled samples. This should result in significant saving in time, resource, and costs.


2021 ◽  
Vol 6 (1) ◽  
Author(s):  
Alex Zhao ◽  
Kavin Kumaravel ◽  
Emanuele Massaro ◽  
Marta Gonzalez

AbstractGroup testing has recently become a matter of vital importance for efficiently and rapidly identifying the spread of Covid-19. In particular, we focus on college towns due to their density, observability, and significance for school reopenings. We propose a novel group testing strategy which requires only local information about the underlying transmission network. By using cellphone data from over 190,000 agents, we construct a mobility network and run extensive data-driven simulations to evaluate the efficacy of four different testing strategies. Our results demonstrate that our group testing method is more effective than three other baseline strategies for reducing disease spread with fewer tests.


2021 ◽  
pp. 217-249
Author(s):  
Matthew Aldridge ◽  
David Ellis

AbstractWhen testing for a disease such as COVID-19, the standard method is individual testing: we take a sample from each individual and test these samples separately. An alternative is pooled testing (or ‘group testing’), where samples are mixed together in different pools, and those pooled samples are tested. When the prevalence of the disease is low and the accuracy of the test is fairly high, pooled testing strategies can be more efficient than individual testing. In this chapter, we discuss the mathematics of pooled testing and its uses during pandemics, in particular the COVID-19 pandemic. We analyse some one- and two-stage pooling strategies under perfect and imperfect tests, and consider the practical issues in the application of such protocols.


2021 ◽  
Author(s):  
Shimba Henerico ◽  
Richard V. Makapa ◽  
Bernard C. Okamo ◽  
Benson R. Kidenya ◽  
Geoffrey Japhet ◽  
...  

Abstract Background: Tuberculosis (TB) is a global public health problem, with the highest burden occurring in low-income countries, wherein the use of more sensitive diagnostics, such as Xpert MTB/RIF (GeneXpert), is still limited by costs. Testing of pooled samples from various individuals has been thought and thus investigated as a cost saving strategy to diagnose some diseases including TB. Then in cases where a pool is positive, retesting of the individual samples in that pool is done to identify the positive sample. We assessed the utility of a pooled testing strategy to optimize the affordability of GeneXpert for the diagnosis of TB Mwanza Tanzania. Methods: Remainder of samples from presumptive TB patients submitted for routine TB diagnosis were used for pooled samples (5 per pool) testing. The agreement of the results between individual sample testing against pooled samples testing and cost-effectiveness were assessed.Results: A total of 250 individual routinely submitted samples for TB diagnosis were tested using the established protocols. The median age of study participants was 35 [IQR 27 – 40] years and 143 (57.2%) were males. Of the 250 samples, 28 (11.2%) were detected to have MTB whereas 222 (88.8%) samples, were negative. Of the 50 sputum pools made, MTB were detected in 17 (34.0%) pools. Following retesting of these 17 positive pools, all 28 (100%) individual MTB samples were detected with the overall agreement being 100% (With the sensitivity of 100% and specificity of 100%). The number of individual MTB positive ranged from 1 to 3 per pool. Using pooling of sputum samples, the technique saved 115 (46.0%) of the cartridges in running 250 samples. This is equivalent to saving US$ 1147.7. Conclusion: The pooled sputum testing strategy reduced cartridge costs by 46.0%. The use of the pooled testing strategy reduces costs and has the potential to increase the affordability of GeneXpert testing in countries with limited resources. Pooled sputum for Xpert MTB/RIF can be used as an affordable diagnostic and/or screening tool in resource limited settings, such as Tanzania.


Blood ◽  
2006 ◽  
Vol 108 (11) ◽  
pp. 606-606 ◽  
Author(s):  
Claudio G. Brunstein ◽  
Daniela Setubal ◽  
Marcie Tomblyn ◽  
Todd DeFor ◽  
Mukta Arora ◽  
...  

Abstract Allogeneic hematopoietic stem cell transplantation (HSCT) is a standard treatment for patients with high risk or advanced AML. However, older age and of co-morbidities frequently limit its use due to high risk of regimen related toxicities (RRT) after a myeloablative regimen. While the inception of RIC regimens has been very successful at reducing RRT, lack of available HLA matched sibling or unrelated donors has become the principal limiting factor. We hypothesized that UCB would increase the utilization of HSCT in patients with AML who lacked a HLA-matched, medically suitable sibling donor. Therefore, we evaluated the various transplant outcomes in 64 AML patients treated with RIC followed by transplantation with HLA-matched sibling PBSC (n=21) and 4–6/6 HLA matched UCB (n=43). All pts received Fludarabine (Flu, 200 mg/kg) and total body irradiation (TBI 200 cGy) with either cyclophosphamide (Cy 50 mg/kg, n=49) or Busulfan (Bu 8 mg/kg, n=15). All pts received cyclosporine A and mycophenolate mofetil GVHD prophylaxis. UCB grafts were composed of 1 (n=15) or 2 (n=28) units to achieve the minimum cell dose. Patients with good and intermediate risk cytogenetics in first complete remission (CR1) were classified as standard risk; others were classified as high risk. Multivariate models considered: donor type, age, disease status, weight, CMV serostatus, cytogenetic risk, disease risk, acute GVHD, conditioning regimen, and time from diagnosis to HSCT. The proportion of engraftment (88% vs. 100%, p=0.10), the incidence of grade II–IV GVHD at day 100 (51% vs. 62%, p=0.85) and TRM at 1 year (28% vs 38%, p=0.43) did not differ between UCB and PBSC recipients. Similarly, relapse at 2 years (UCB 35% vs SIB 35%, p=0.72) and 2 year survival (UCB 31% vs SIB 32%, p=0.62) were comparable. In multivariate analysis, only disease risk group was associated with increased relative risk (RR) of relapse (RR 2.9, 95%CI, 1.3–6.2, p<0.01) and death (RR 2.6, 95%CI, 1.1–5.5, p=0.02). These results demonstrate that partially HLA matched UCB after RIC markedly extends the availability of HSCT with results comparable to those observed with PBSC from HLA matched sibling donors. Variable UCB (n=43) SIB PBSC (n=21) p value * Cell doses of double UCB grafts=combined cell dose. Age in years - median (range) 53 (22–68) 54 (19–69) 0.77 Weight in kg - median (range) 75 (53–120) 72 (51–112) 0.24 Recipient/Donor CMV + 20 (47%)/− 13 (62%)/8 (38%) <0.01 HLA-match 6/6* 5 (7%) 21 (100%) HLA-match 4–5/6* 66 (93%) Zero Disease status CR1 18 (43%) 14 (67%) Cytogenetics good/intermediate 32 (84%) 10 (48%) 0.31 Cytogenetics poor risk 7 (16%) 10 (48%) TNC X10 7/kg median (range)* 3.6 (1.6–5.9) 93.4 (64.8–212.3) CD34 X105/kg median (range)* 4.9 (1.1–18.8) 52.2 (14.1–153.7) Median follow-up in years 2.7 (0.7–5.5) 1.3 (0.7–6.1)


2021 ◽  
Vol 5 ◽  
pp. 186 ◽  
Author(s):  
Charles N. Agoti ◽  
Martin Mutunga ◽  
Arnold W. Lambisia ◽  
Domtila Kimani ◽  
Robinson Cheruiyot ◽  
...  

Background. International recommendations for the control of the coronavirus disease 2019 (COVID-19) pandemic emphasize the central role of laboratory testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent, at scale. The availability of testing reagents, laboratory equipment and qualified staff are important bottlenecks to achieving this. Elsewhere, pooled testing (i.e. combining multiple samples in the same reaction) has been suggested to increase testing capacities in the pandemic period. Methods. We discuss our experience with SARS-CoV-2 pooled testing using real-time reverse transcription polymerase chain reaction (RT-PCR) on the Kenyan Coast. Results. In mid-May, 2020, our RT-PCR testing capacity for SARS-CoV-2 was improved by ~100% as a result of adoption of a six-sample pooled testing strategy. This was accompanied with a concomitant saving of ~50% of SARS-CoV-2 laboratory test kits at both the RNA extraction and RT-PCR stages. However, pooled testing came with a slight decline of test sensitivity. The RT-PCR cycle threshold value (ΔCt) was ~1.59 higher for samples tested in pools compared to samples tested singly. Conclusions. Pooled testing is a useful strategy to increase SARS-CoV-2 laboratory testing capacity especially in low-income settings.


2021 ◽  
Vol 2021 ◽  
pp. 1-6
Author(s):  
Mayank Gangwar ◽  
Alka Shukla ◽  
Virendra Kumar Patel ◽  
Pradyot Prakash ◽  
Gopal Nath

The study is aimed at establishing the optimal parameters for RNA purification of pooled specimens, in SARS-CoV-2 assay. This research work evaluates the difference of extracted RNA purity of pooled samples with and without treatment with isopropyl alcohol and its effect on real-time RT-PCR. As per the protocol of the Indian Council of Medical Research (ICMR), 5 sample pools were analysed using qRT-PCR. A total of 100 pooled samples were selected for the study by mixing 50 μL of one COVID-19 positive nasopharyngeal/oropharyngeal (NP/OP) specimen and 50 μL each of 4 known negative specimens. Pool RNA was extracted using the column-based method, and 1 set of pooled extracted RNA was tested as such, while RNA of the second set was treated additionally with chilled isopropyl alcohol (modified protocol). Further, the purity of extracted RNA in both the groups was checked using Microvolume Spectrophotometers (Nanodrop) followed by RT-PCR targeting E-gene and RNaseP target. The results showed that the purity index of extracted RNA of untreated pooled specimens was inferior to isopropyl alcohol-treated templates, which was observed to be 85% sensitivity and 100% specificity. The average Cq (E gene) in the unpurified and purified pool RNA group was 34.66 and 31.48, respectively. The nanodrop data suggested that purified RNA concentration was significantly increased with an average value of 24.73 ± 1.49   ng / uL , which might be the reason for high sensitivity and specificity. Thus, this group testing of SARS-CoV-2 cases using pools of 5 individual samples would be the best alternative for saving molecular reagents, personnel time, and can increase the overall testing capacity. However, purity of RNA is one of the important determinants to procure unfailing results, thus, this additional purification step must be included in the protocol after RNA has been extracted using commercially available kit before performing qRT-PCR.


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