Feasibility of using alternative swabs and storage solutions for paired SARS-CoV-2 detection and microbiome analysis in the hospital environment

Abstract

Background Determining the role of fomites in the transmission of SARS-CoV-2 is essential in the hospital setting and will likely be important outside of medical facilities as governments around the world make plans to ease COVID-19 public health restrictions and attempt to safely reopen economies. Expanding COVID-19 testing to include environmental surfaces would ideally be performed with inexpensive swabs that could be transported safely without concern of being a source of new infections. However, CDC-approved clinical-grade sampling supplies and techniques using a synthetic swab are expensive, potentially expose laboratory workers to viable virus and prohibit analysis of the microbiome due to the presence of antibiotics in viral transport media (VTM). To this end, we performed a series of experiments comparing the diagnostic yield using five consumer-grade swabs (including plastic and wood shafts and various head materials including cotton, synthetic, and foam) and one clinical-grade swab for inhibition to RNA. For three of these swabs, we evaluated performance to detect SARS-CoV-2 in twenty intensive care unit (ICU) hospital rooms of patients including COVID-19+ patients. All swabs were placed in 95% ethanol and further evaluated in terms of RNase activity. SARS-CoV-2 was measured both directly from the swab and from the swab eluent. Results Compared to samples collected in VTM, 95% ethanol demonstrated significant inhibition properties against RNases. When extracting directly from the swab head as opposed to the eluent, RNA recovery was approximately 2–4× higher from all six swab types tested as compared to the clinical standard of testing the eluent from a CDC-approved synthetic (SYN) swab. The limit of detection (LoD) of SARS-CoV-2 from floor samples collected using the consumer-grade plastic (CGp) or research-grade plastic The Microsetta Initiative (TMI) swabs was similar or better than the SYN swab, further suggesting that swab type does not impact RNA recovery as measured by the abundance of SARS-CoV-2. The LoD for TMI was between 0 and 362.5 viral particles, while SYN and CGp were both between 725 and 1450 particles. Lastly microbiome analyses (16S rRNA gene sequencing) of paired samples (nasal and floor from same patient room) collected using different swab types in triplicate indicated that microbial communities were not impacted by swab type, but instead driven by the patient and sample type. Conclusions Compared to using a clinical-grade synthetic swab, detection of SARS-CoV-2 from environmental samples collected from ICU rooms of patients with COVID was similar using consumer-grade swabs, stored in 95% ethanol. The yield was best from the swab head rather than the eluent and the low level of RNase activity and lack of antibiotics in these samples makes it possible to perform concomitant microbiome analyses.

SARS-CoV-2 detection status associates with bacterial community composition in patients and the hospital environment

“…Sample collection for SARS-CoV-2 RNA screening is typically performed using viral transport media containing fetal bovine serum and a cocktail of antibiotics, which could negatively influence studies of bacteria and other microbes [ 21 , 22 ]. For this study, swab samples were stored in 95% EtOH in order to inactivate the virus for safe transportation [ 23 ] while stabilizing the microbial community [ 24 ].…”

Occupational and environmental exposure to SARS-CoV-2 in and around infected mink farms

“…Another limitation is the unknown recovery efficiency of SARS-CoV-2 RNA from the environmental samples. A recent study by Minich et al 30 on SARS-CoV-2 RNA recovery from swabs reported overall good recovery rates, and many factors were found to play a role (including swab type, storage solution, molecular processing), but especially the sampling itself. In our study, these factors remained the same throughout the study period, including collection of samples, which was strictly performed according to protocol by the same fieldworker, preventing potential differential errors.…”

A Comprehensive Sampling Study on SARS-CoV-2 Contamination of Air and Surfaces in a Large Meat Processing Plant Experiencing COVID-19 Clusters in June 2020

“…If we consider low RNA loads in participating workers a proxy of viral excretion, 29–31 high shedding rates of SARS-CoV-2 for the majority are not to be expected; however, there might be individual differences and shedders among workers who were not tested. Most workers tested positive only pre-shift, which may be explained by physiological accumulation of respiratory tract secretions at the start of the day, 32 swabbing differences between testers, 33 and/or influence of stochastic processes especially at low viral loads (higher chance of false negatives). SARS-CoV-2 RNA level in the positive sewage sample was comparable with levels detected at urban sewage sites in the Netherlands in the early stage of the epidemic (March 2020) 34 .…”