Fig. 2: Comprehensive identification of HVs with CARMEN–Cas13.
From: Massively multiplexed nucleic acid detection with Cas13
a, The development and testing of a panel for all 169 HVs with at least 10 available genome sequences. b, Experimental design using pooled PCR amplification. c, Testing a comprehensive HV panel with synthetic targets using CARMEN–Cas13. PCR primer pools 1–15 and viral families are below and to the left of the heat map, respectively. Grey lines, crRNAs not tested. d, Multiplexed coronavirus panel, comprising human coronaviruses 229E, NL63 and HKU1 Middle East respiratory syndrome (MERS) coronavirus; severe acute respiratory syndrome (SARS) coronavirus; novel coronavirus SARS-CoV-2 (nCoV); and negative control (−). e, Testing the HV panel with patient samples (additional data in Extended Data Fig. 8a). Heat maps indicate background-subtracted fluorescence after 1 h (c) or 30 min (d), or fold change over background (e). NI, not interpretable. f, Concordance of CARMEN and NGS in patient sample testing. Each box displays the number of tests and the percentage of the total. g, Identification by NGS or CARMEN of any viral sequence from the known infections in patient samples (for example, detection of HIV in samples from patients with HIV). h, Identification by NGS or CARMEN of the crRNA target for each known infection. i, Positive test results in patient samples for viruses other than the known infections. DENV, dengue virus; ZIKV, Zika virus; HCV, hepatitis C virus; TLMV, Torque teno-like mini virus; Pegi A, pegivirus A; HPV4, human papillomavirus 4; KIPyV, KI polyomavirus; MCV, Merkel cell polyomavirus; SINV, Sindbis virus; γHPV, gamma human papillomavirus; βHPV, beta human papillomavirus 2; AROAV, aroa virus. CARMEN does not test for γHPV or AROAV because fewer than 10 γHPV or AROAV genomes had been published before 24 October 2018.
