Can't work from home: Pooled nucleic acid testing of laboratory workers during covid

ABSTRACT

Background: Closing labs to decrease spread of COVID-19 has impacted research progress. Serial testing could supplement other measures to help provide a safe lab environment. Methods: Lab employees who came to work at an academic laboratory at the University of California San Diego (UCSD) were invited and consented to perform their own anterior nasal swab or have a swab collected by an on-site physician. Nasal swabs were combined into one pool for each work shift. Each pool underwent nucleic acid testing (NAT) via qRT-PCR to detect SARS-CoV-2 RNA (FluxErgy). Results were available within one hour. Positive pools were deconvoluted and tested individually. Cost evaluation of the pooling approach was compared to individual NAT and to institutional guidelines for lab occupancy. Results: From Apr 9 to Oct 26, 2020 (28 weeks), 1,199 nasal swab samples collected from lab workers were batched in 194 pools of median size 7 [95%I 3-11]. A median of 41 tests per week [95%I 22-67] were performed in a total of 77 participants (Fig 1). 19 core staff were tested a median 54 times [95%I13-95]. Of the 194 pools, 7 (3.6%, n=47 samples) were considered positive and required repeat testing of all participant samples in the pool as confirmation. One true positive was identified before work started. That participant was referred to their primary care provider. This early detection prevented a 2-week quarantine of 7 employees. Given ∼$65/hour salary per lab worker, this saved 420 hours of work and ∼$26,600 in wages. Current UCSD guidelines recommend decreasing staffing levels to 25% of pre-COVID-19 occupancy. Regular NAT allowed 100% staffing. Screening of lab technicians with the pooled NAT strategy over 6 months cost $25,740 but permitted 2,430 person-hours of additional work ($132,210 in wages), as compared to the recommended 75% reduction without testing. A similar approach with individual NAT would cost $124,020 (thus $98,280 saved by pooling). Conclusion: Regular pooled NAT for SARS-CoV-2 among lab personnel offers a cost-efficient way to maintain a safe lab environment without a reduction in staffing. This approach could be applied in other settings to help ensure safe work environments.