A case for pooled testing of SARS-CoV-2

In a large-scale study, researchers at Hebrew University in Jerusalem have shown that pooled testing for SARS-CoV-2 can be highly efficient, with sufficient diagnostic accuracy despite lower sensitivity. The team tested 133,816 nose and throat samples in pool sizes of five or eight. If a group tested positive, every sample within the pool was retested. Negative testing groups were not retested. Using this approach enabled them to perform just one-quarter of the tests they would have needed to perform to assay every sample individually. “We spared 76% of RNA extraction and RT-PCR tests, despite the reality of frequently changing prevalence rate (0.5%-6%),” the researchers said. This was because people tend to get tested with other family members, roommates or coworkers, making it more likely that positive samples will be in the same group. “We propose that the better-than-expected performance of pooling in both efficiency and sensitivity aspects is rooted in a single factor: the non-random distribution of positive samples in pools,” they wrote. A practical implication of their findings is the importance of using preexisting knowledge of incoming samples to improve co-assignment. The researchers also cited the need for pooled testing to be “manageable at large-scale in a diagnostic lab.” The study was published as a preprint Oct. 26, 2020, at medRxiv.

FIT as effective as colonoscopy in ruling out suspected colorectal cancer

Results of a large international study found that a fecal immunochemical test (FIT) ruled out bowel cancer in patients with high-risk symptoms nearly 100% of the time. The NICE FIT study was led by Croydon University Hospital, U.K., and supported by RM Partners, the West London Cancer Alliance hosted by the Royal Marsden NHS Foundation Trust, with funding from NHS England’s cancer transformation fund. Close to 10,000 patients with colonoscopy outcomes were included in the data analysis, which was completed in January. The goal was to determine FIT’s diagnostic accuracy in symptomatic patients referred with suspected colorectal cancer (CRC) under current National Institute for Health and Care Excellence (NICE) guidelines. According to the team’s findings, published in the October 2020 issue of Gut, FIT was 99.8% effective in ruling out CRC, sparing about 60% of patients with a negative FIT result from a hospital visit and invasive biopsy. “FIT can appropriately triage these patients off urgent pathways for investigation,” the authors wrote. “Importantly, a negative FIT result can be used to reassure patients that their symptoms are unlikely to be due to CRC.” They now are examining the data to assess FIT’s sensitivity at diagnosing other bowel conditions.

Looking to comparative genomics analysis to explain COVID-19 susceptibility

San Diego-based Bionano Genomics Inc. said Erich Jarvis, a Howard Hughes Medical Institute investigator at Rockefeller University and chair of the Vertebrate Genome Project (VGP), is bringing his expertise in comparative genomics to the COVID-19 Host Genome SV Consortium as a co-investigator. The consortium is focused on the analysis with Saphyr of structural variants (SVs) in the human genome that predisposed people to the novel coronavirus or protect against it. The animal species in the study include the Chinese horseshoe bat and Chinese pangolin, both natural reservoirs of the virus, the clouded leopard, an animal that tested positive for SARS-CoV-2 at the Bronx Zoo and four domestic species thought to be vulnerable to the virus – sheep, Arabian camel, horse and Chinese hamster. For the human arm, the study will analyze the genomes of 10 patients who were hospitalized and/or died from COVID-19, as well as 10 people who did not get sick following exposure. According to Bionano, the VGP’s genome assembly team has developed and optimized a pipeline using long-reading sequencing, Bionano optical maps and a method called Hi-C to build reference-quality genomes. Using Bionano data in this comparative genomics analysis may identify biomarkers for COVID-19 risk and how to treat it, the company said.