Fig. 1: Primer set screening for the detection of SARS-CoV-2 E gene. | Communications Biology

Fig. 1: Primer set screening for the detection of SARS-CoV-2 E gene.

From: Vivid COVID-19 LAMP is an ultrasensitive, quadruplexed test using LNA-modified primers and a zinc ion and 5-Br-PAPS colorimetric detection system

Fig. 1: Primer set screening for the detection of SARS-CoV-2 E gene.

a Performance, measured as TTR, of the top three primer set candidates (E1, E2, E3) for SARS-CoV-2 E gene at the indicated number of synthetic SARS-CoV-2 RNA copies per reaction. b Comparison of E1, E2, and E3 primer sets containing LNA modifications near the 5’ end of their F3/B3 outer primers, labeled as E1L, E2L, E3L. Reaction conditions are identical with a. c An extended comparison of limits of detection of sets E1L and E2L. d Amplification improvements obtained by LNA modifications in all three primer set candidates displayed as changes in relative speed and higher amplification success rate. Based on data from a and b at 200 cp/rxn. Relative speed is mean TTR of base set divided by TTR of LNA-modified set. e Positions of LNA bases in sequences of F3/B3 outer primers in primer sets E1L, E2L, and E3L. Open symbols represent non-specific products, whereas closed symbols are specific as determined by melt curve analysis of amplification products. The highest time to reaction value on y-axis signifies the total duration of the reaction. Amplification success rate shows the number of samples that amplified over the course of the reaction. For NTC reactions, PCR-grade water was used as the input. All experiments were performed using “NEB WarmStart” reaction mix. “+N” signifies the presence of an LNA base. Error bars represent standard error of the mean. In all experiments, n = 8 technical replicates per group were used. TTR time to reaction, NTC no-template control.

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