Effective optimization of SARS-CoV-2 laboratory testing variables in an era of supply chain constraints

Optimizing testing regimes for the detection of COVID-19 in children and older adults

Introduction: Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection is a major pandemic and continuously emerging due to unclear prognosis and unavailability of reliable detection tools. Older adults are more susceptible to COVID-19 than children showing mature Angiotensin-Converting Enzyme 2 (ACE2), low concentration of immune targets, and comorbid conditions. Several detection platforms have been commercialized to date and more are in pipeline, however, the rate of false-positive results and rapid mutation of SARS-CoV-2 is increasing. Additionally, physiological, and geographical variations of affected individuals are also calling for diagnostic methods optimization.Areas Covered: Extensive information related to the optimization and usefulness of SARS-CoV-2 diagnostic methods based on sensitivity and specificity as definitive and feasible investigative tools is discussed. Moreover, an option of combining laboratory diagnostic methods to improve diagnostic strategies is also proposed and discussed in the comparative section of optimization studies.Expert Opinion: The review article explains the importance of optimization strategies for SARS-CoV-2 detection in children and older adults. There are advancements in COVID-19 detection including CRISPR-based, electrochemical, and optical-based sensing systems. However, the lack of sufficient studies on a comparative evaluation of standardized SARS-CoV-2 diagnostic methods among children and older adults, limit the authentication of commercialized kits.

Making a Difference: Adaptation of the Clinical Laboratory in Response to the Rapidly Evolving COVID-19 Pandemic

The COVID-19 pandemic, caused by severe acute respiratory syndrome coronavirus 2, led to unprecedented demands assigned to clinical diagnostic laboratories worldwide, forcing them to make significant changes to their regular workflow as they adapted to new diagnostic tests and sample volumes. Herein, we summarize the modifications/adaptation the laboratory had to exercise to cope with rapidly evolving situations in the current pandemic. In the first phase of the pandemic, the laboratory validated 2 reverse transcription polymerase chain reaction–based assays to test ∼1000 samples/day and rapidly modified procedures and validated various preanalytical and analytical steps to overcome the supply chain constraints that would have otherwise derailed testing efforts. Further, the pooling strategy was validated for wide-scale population screening using nasopharyngeal swab samples and saliva samples. The translational research arm of the laboratory pursued several initiatives to understand the variable clinical manifestations that this virus presented in the population. The phylogenetic evolution of the virus was investigated using next-generation sequencing technology. The laboratory has initiated the formation of a consortium that includes groups investigating genomes at the level of large structural variants, using genome optical mapping via this collaborative global effort. This article summarizes our journey as the laboratory has sought to adapt and continue to positively contribute to the unprecedented demands and challenges of this rapidly evolving pandemic.

Overcoming Supply Shortage for SARS-CoV-2 Detection by RT-qPCR

In February 2020, our laboratory started to offer a RT-qPCR assay for the qualitative detection of severe acute respiratory syndrome coronavirus 2. A few months after the assay was released to our patients, some materials, reagents, and equipment became in short supply. Alternative protocols were necessary in order to avoid stopping testing to the population. However, the suitability of these alternatives needs to be validated before their use. Here, we investigated if saliva is a reliable alternative specimen to nasopharyngeal swabs; if 0.45% saline is a reliable alternative to guanidine hydrochloride as a collection viral transport media; the stability of SARS-COV-2 in guanidine hydrochloride and in 0.45% saline for 10 and 50 days at room temperature; and if the primers/probe concentration and thermocycling times could be reduced so as to overcome the short supply of these reagents and equipment, without a significant loss of the assay performance. We found that saliva is not an appropriated specimen for our method-nasopharyngeal swabs perform better. Saline (0.45%) and guanidine hydrochloride have a similar SARS-CoV-2 diagnostic capability as tube additives. Reliable SARS-CoV-2 RNA detection can be performed after sample storage for 10 days at room temperature (18-23 °C) in both 0.45% saline and guanidine hydrochloride. Using synthetic RNA, and decreasing the concentration of primers by five-fold and probes by 2.5-fold, changed the assay limit of detection (LOD) from 7.2 copies/reaction to 23.7 copies/reaction and the subsequent reducing of thermocycling times changed the assay LOD from 23.7 copies/reaction to 44.2 copies/reaction. However, using real clinical samples with Cq values ranging from ~12.15 to ~36.46, the results of the three tested conditions were almost identical. These alterations will not affect the vast majority of diagnostics and increase the daily testing capability in 30% and increase primers and probe stocks in 500% and 250%, respectively. Taken together, the alternative protocols described here overcome the short supply of tubes, reagents and equipment during the SARS-CoV-2 pandemic, avoiding the collapse of test offering for the population: 105,757 samples were processed, and 25,156 SARS-CoV-2 diagnostics were performed from 9 May 2020 to 30 June 2020.