CLN - The Sample

Sample Pooling Effectively Expands SARS-CoV-2 Testing Capacity

The Sample: June 2020

Researchers at Saarland University in Saarbrücken, Germany, report that sample pooling for SARS-CoV-2 testing in asymptomatic individuals when the rate of community infection is low significantly expands testing capacity and saves test kits while appropriately detecting positive cases (Lancet Infect Disease 2020; doi.org/10.1016/S1473-3099(20)30362-5).

The authors’ procedure involves pooling samples before reverse transcriptase-polymerase chain reaction (RT-PCR) amplification, then only conducting individual tests when the pooled sample yields positive results. They evaluated the effect of this approach on the sensitivity of RT-PCR by comparing cycle threshold (Ct) values of pools that tested positive with Ct values of individual samples that tested positive.

In pool sizes from 4 to 30 samples per pool, the Ct values of positive pools ranged from 22 to 29 for the E-gene (envelope protein) assay, and from 21 to 29 for the S-gene (spike protein) assay. The Ct values were lower for both assays in retested individual positive samples. In both pooled and individual samples the Ct values were below 30 and “easily categorized as positive,” according to the authors.

The authors also successfully created sub-pools to further reduce the number of individual tests performed after a positive pool result. For example, by breaking 30-sample pools into 3 sub-pools of 10 samples each, in an 8-day period 1,191 samples required just 267 tests to detect 23 positive cases, a prevalence of 1.93% at a time when the rate of positive tests in their institution was 4.24%.

The investigators cautioned that borderline positive single samples might not be detected in large pools. This normally occurs in samples from convalescent patients 14–21 days after they become symptomatic.

The authors are now using this method to screen residents and staff in nursing and residential care homes in Saarland.

Preanalytics Matter in Diagnosing Gestational Diabetes Mellitus

Researchers at Australian Capital Territory (ACT) Pathology demonstrated that preanalytical blood sample processing protocols have “critical importance” in accurately diagnosing gestational diabetes mellitus (GDM) (Diabetes Care 2020; doi.org/10.2337/dc20-0304). Their findings, comparing two large groups of women whose blood was processed under different procedures, confirm modeling predictions and prior small studies that investigated the effect of preanalytical procedures on GDM diagnoses.

Until 2017, preanalytical processing requirements for one-step, three-point 75-g oral glucose tolerance testing (OGTT) in much of Australia involved collecting the three samples (fasting, 1-hr, 2-hr) and sending them together to a lab for processing. In 2017, ACT Pathology implemented stricter protocols that required all samples to be centrifuged within 10 minutes of collection.

The authors compared the effect of this change by examining fasting, 1-hr, and 2-hr sample results in 7,509 women tested under the old protocol (January 2015 to May 2017), and 4,808 tested under the new protocol (June 2017 to October 2018).

They found that early centrifugation of samples led to a significant, almost double, increase in the GDM diagnosis rate, from 11.6% to 20.6%. GDM diagnosis rates based on values from fasting and 1-hr samples increased by 127% and 66%, respectively; the diagnosis rate based on 2-hr samples increased a statistically insignificant 15%. The mean fasting, 1-hr, and 2-hr values in mmol/L under the old protocol were 4.41, 6.99, and 6.05, respectively, versus 4.65, 7.33, and 6.21, respectively, under the new early centrifugation protocol.

“It is clear that the preanalytical blood sampling protocol for OGTTs during pregnancy needs attention and standardization,” concluded the authors.

Polygenic Risk Score Identifies Men at Elevated Risk for Abdominal Aortic Aneurysm

A polygenic risk score (PRS) based on 29 mutations identified more men at risk of abdominal aortic aneurysm (AAA) than would be identified under current screening recommendations. Extending current guidelines to include testing for those with high PRS “would significantly increase the yield of current screening,” said the authors of a study presented at the American Heart Association’s Vascular Discovery: From Genes to Medicine Scientific Sessions 2020 (Presentation 170).

Current AAA screening recommendations call for a one-time ultrasound in men ages 65–75 with a history of smoking. The survival rate once an AAA ruptures is only about 20%, so better identifying individuals at risk remains a priority.

The authors used electronic health data to identify participants with and without AAA in the Million Veteran Program (MVP), a national genomic research initiative. They tested 18 million genotyped and imputed DNA variants for association with AAA using logistic regression modeling, then used external datasets to replicate these findings. Finally, they tested and validated a series of AAA PRSs using an independent set of MVP participants.

From 7,642 AAA cases and 172,172 controls, the researchers identified 14 novel AAA loci implicating already established risk factors like lipids (LPA, PCSK9) and smoking (CHRNA3). A one standard deviation increase in the 29-variant PRS was associated with a 32% increased risk of AAA. Men older than age 50 with the 5% highest PRS had an AAA prevalence of 7.8%, which is higher than that observed in AAA screening trials upon which current guidelines were based.

The researchers acknowledged the need for more investigation to understand how well the PRS captures risk in diverse ethnic groups, as Caucasian men predominate in the MVP.

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