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Fig. 1 | Microbiome

Fig. 1

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

Fig. 1

Validation of alternative swabs and storage buffer (95% EtOH and 91% isopropanol) in RNA recovery and detection of COVID-19. a Human RNAse P gene (Rp) amplification was used to compare nucleic acid extraction efficiency across sample processing methods. Clinical gold-standard synthetic-tipped plastic-shaft NP swabs stored in VTM and extracted from 200 μL of eluent (left, n = 39) have significantly higher copy numbers compared to 200 μL EtOH eluent from SYN nares swabs (middle, n = 22), but not when extracted from the EtOH-preserved swab head (right, n = 18). One-way ANOVA with Tukey’s multiple comparison VTM eluent vs EtOH eluent p ≤ 0.001, EtOH eluent vs EtOH swab p < 0.001, and VTM vs EtOH swab p = 0.266. b Extrapolated viral RNA copy number from COVID-19-positive nares samples collected with BD synthetic swabs in the hospital stored in 95% EtOH and extracted from either the eluent or swab from the same sample (n = 24, one-tailed paired Student’s t test p = 0.032). c Proportion of RNA recovered across three storage buffers: None, 95% EtOH, and 91% isopropanol using commercial human RNA added to storage buffers (ns, one-way ANOVA p > 0.05). d Evaluation of RNaseA inhibition by 95% EtOH (grey) and 91% isopropanol (blue) using either the human Rp or SARS-CoV-2 N1 primer set on control RNA added to each solution (unpaired t tests of 95% EtOH vs 91% Iso per marker at 0, 2500, and 25000 ng RNaseA). e Comparison human RNA recovery across six swab types (SYN, synthetic rayon “commercial”; BDF, BD foam “commercial”; TMI, BD TMI “commercial”; CGp, plastic “consumer-grade”; Pu, puritan “commercial”; CGw, wood “consumer-grade”), extracted from 200 μL eluent (blank bar) or the swab head. Recovery for each swab type is normalized to the CDC-recommended method (eluent from PE swab). A “2” would indicate there was 2× more RNA recovered whereas a 0.5 would indicate a 50% reduction in RNA recovery. f Total RNA copies per extraction for all samples which are grouped by sample type (eluent or swab head) and storage buffer (95% EtOH or 91% isopropanol). Pairwise comparisons performed within sample type (not significant) and across sample type controlling for storage buffer (Mann-Whitney, U = test statistic)

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