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Deprecated: Implicit conversion from float 300.79999999999995 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534 J+Clin+Microbiol 2021 ; 59 (12): e0144621 Nephropedia Template TP
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Single-Amplicon Multiplex Real-Time Reverse Transcription-PCR with Tiled Probes To Detect SARS-CoV-2 spike Mutations Associated with Variants of Concern #MMPMID34432488
Babiker A; Immergluck K; Stampfer SD; Rao A; Bassit L; Su M; Nguyen V; Stittleburg V; Ingersoll JM; Bradley HL; Mavigner M; Schoof N; Kraft CS; Chahroudi A; Schinazi RF; Martin GS; Piantadosi A; Lam WA; Waggoner JJ
J Clin Microbiol 2021[Nov]; 59 (12): e0144621 PMID34432488show ga
To provide an accessible and inexpensive method to surveil for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) mutations, we developed a multiplex real-time reverse transcription-PCR (rRT-PCR) assay, the Spike single-nucleotide polymorphism (SNP) assay, to detect specific mutations in the spike receptor binding domain. A single primer pair was designed to amplify a 348-bp region of spike, and probes were initially designed to detect K417, E484K, and N501Y. The assay was evaluated using characterized variant sample pools and residual nasopharyngeal samples. Variant calls were confirmed by SARS-CoV-2 genome sequencing in a subset of samples. Subsequently, a fourth probe was designed to detect L452R. The lower limit of 95% detection was 2.46 to 2.48 log(10) genome equivalents (GE)/ml for the three initial targets ( approximately 1 to 2 GE/reaction). Among 253 residual nasopharyngeal swabs with detectable SARS-CoV-2 RNA, the Spike SNP assay was positive in 238 (94.1%) samples. All 220 samples with threshold cycle (C(T)) values of <30 for the SARS-CoV-2 N2 target were detected, whereas 18/33 samples with N2 C(T) values of >/=30 were detected. Spike SNP results were confirmed by sequencing in 50/50 samples (100%). Addition of the 452R probe did not affect performance for the original targets. The Spike SNP assay accurately identifies SARS-CoV-2 mutations in the receptor binding domain, and it can be quickly modified to detect new mutations that emerge.