A novel CRISPR-based malaria diagnostic capable of Plasmodium detection, speciation, and drug-resistance genotyping

Abstract

CRISPR-based diagnostics are a new class of highly sensitive and specific assays with multiple applications in infectious disease diagnosis. SHERLOCK, or Specific High-Sensitivity Enzymatic Reporter UnLOCKing, is one such CRISPR-based diagnostic that combines recombinase polymerase pre-amplification, CRISPR-RNA base-pairing, and LwCas13a activity for nucleic acid detection. We developed SHERLOCK assays for malaria capable of detecting all Plasmodium species known to cause malaria in humans and species-specific detection of P. vivax and P. falciparum, the species responsible for the majority of malaria cases worldwide. We validated these assays against parasite genomic DNA and achieved analytical sensitivities ranging from 2.5-18.8 parasites per reaction. We further tested these assays using a diverse panel of 123 clinical samples from the Democratic Republic of the Congo, Uganda, and Thailand and pools of Anopheles mosquitoes from Thailand. When compared to real-time PCR, the P. falciparum assay achieved 94% sensitivity and 94% specificity in clinical samples. In addition, we developed a SHERLOCK assay capable of detecting the dihydropteroate synthetase (dhps) single nucleotide variant A581G associated with P. falciparum sulfadoxine-pyrimethamine resistance. Compared to amplicon-based deep sequencing, the dhps SHERLOCK assay achieved 73% sensitivity and 100% specificity when applied to a panel of 43 clinical samples, with false-negative calls only at lower parasite densities. These novel SHERLOCK assays have potential to spawn a new generation of molecular diagnostics for malaria and demonstrate the versatility of CRISPR-based diagnostic approaches. One-sentence summaryNovel malaria SHERLOCK assays enabled robust detection, speciation, and genotyping of Plasmodium spp. in diverse samples collected in Africa and Asia.