Pooled Laboratory Testing for COVID -19
Journal of pathology informatics
; 12, 2021.
Article
in English
| EuropePMC | ID: covidwho-1560088
Keywords
Background:, SARS-COV-2, mass, diagnostic, screening, is, essential, to, disrupt, its, transmission, and, spread., Gold, standard, RT-qPCR, testing, capacity, is, limited, time, consuming, and, resource, intensive., Pooled, testing, or, group, testing, provides, a, solution., Pooled, testing, was, first, introduced, in, 1943, and, recently, applied, in, the, context, of, COVID, screening., Here, we, describe, a, novel, high, throughput, workflow, implemented, in, our, laboratory, to, screen, high, volumes, of, specimens, and, discuss, optimal, sample, size, selection.; Methods:, As, depicted, in, the, workflow, diagram, the, client, portal, generates, orders, with, patient, identifier, and, transmit, them, to, Epic, Beaker., A, human, readable, (Accession), and, machine-readable, (Instrument), IDs, are, transmitted, back, to, the, client, portal, which, creates, barcoded, labels., Three, robots, pool, specimens, on, 384, well, plates, containing, RT-qPCR, reagents, and, documents, the, relationship, of, pool, to, the, individual, specimens., RT-qPCR, is, performed, by, QuantStudio., If, a, pool, tests, positive, or, indeterminate, the, specimens, are, identified, and, run, individually., We, leveraged, the, formula, below, to, determine, the, likelihood, of, a, pool, being, positive, and, the, optimal, sample, size, for, our, pools.; P, (probability, of, pool, to, be, positive), =, 1, -, (1, -, prevalence, of, infection), ; Results:, From, Jan, 1, to, Mar, 8, 2021, our, laboratory, processed, 19,634, individual, samples, averaging, 59, pools/day, or, 297, samples/day., 3-5%, of, pools/day, test, intermittent/positive, requiring, individual, samples, to, be, retested., Using, a, pool, size, of, 5, our, laboratory, can, handle, more, than, 6,000, pooled/test, per, day, (30,000, individuals/day)., Assuming, 5%, of, pools, testing, positive, 1500, samples, would, require, individual, retesting, thus, 7500, reactions, to, test, 30,000, individual, samples., Currently, pooling, samples, in, batches, of, 5, provides, us, with, savings, of, ~74%, PCR, reactions/day.; Conclusions:, “Optimal, pool, size”, is, challenging, as, it, varies, with, infection, prevalence, testing, frequency, and, assay, sensitivity, of, the, assay., Pool, size, is, naturally, limited, due, to, increased, prevalence, of, false, negativity, and, low, viral, load, in, group, testing, combining, too, many, samples., Our, table, allows, laboratories, to, determine, the, optimal, pool, size, considering, the, prevalence, of, positive, swabs, in, their, community, and, confirmed, that, a, pool, of, 5, was, optimal, in, our, patient, population.
Full text:
Available
Collection:
Databases of international organizations
Database:
EuropePMC
Language:
English
Journal:
Journal of pathology informatics
Year:
2021
Document Type:
Article
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