Background: 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. Methods: We developed SHERLOCK assays capable of detecting all Plasmodium species known to cause human malaria and species-specific detection of P. vivax and P. falciparum, the species responsible for the majority of malaria cases worldwide. We further tested these assays using a diverse panel of clinical samples from the Democratic Republic of the Congo, Uganda, and Thailand and pools of Anopheles mosquitoes from Thailand. In addition, we developed a prototype SHERLOCK assay capable of detecting the dihydropteroate synthetase (dhps) single nucleotide variant A581G associated with P. falciparum sulfadoxine resistance. Findings: The suite of Plasmodium assays achieved analytical sensitivities ranging from 25-188 parasites per reaction when tested against laboratory strain genomic DNA. When compared to real-time PCR, the P. falciparum assay achieved 94% sensitivity and 94% specificity during testing of 123 clinical samples. 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. Interpretation: These novel SHERLOCK assays demonstrate the versatility of CRISPR-based diagnostics and their potential as a new generation of molecular tools for malaria diagnosis and surveillance.

The majority of Plasmodium falciparum malaria diagnoses in Africa are made using rapid diagnostic tests (RDTs) that detect histidine-rich protein 2. Increasing reports of false-negative RDT results due to parasites with deletions of the pfhrp2 and/or pfhrp3 genes (pfhrp2/3) raise concern about existing malaria diagnostic strategies. We previously identified pfhrp2-negative parasites among asymptomatic children in the Democratic Republic of the Congo (DRC), but their impact on diagnosis of symptomatic malaria is unknown. We performed a cross-sectional study of false-negative RDTs in symptomatic subjects in 2017. Parasites were characterized by microscopy; RDT; pfhrp2/3 genotyping and species-specific PCR assays; a bead-based immunoassay for Plasmodium antigens; and/or whole-genome sequencing. Among 3627 symptomatic subjects, 427 (11.8%) had RDT-/microscopy + results. Parasites from eight (0.2%) samples were initially classified as putative pfhrp2/3 deletions by PCR, but antigen testing and whole-genome sequencing confirmed the presence of intact genes. 56.8% of subjects had PCR-confirmed malaria. Non-falciparum co-infection with P. falciparum was common (13.2%). Agreement between PCR and HRP2-based RDTs was satisfactory (Cohen’s kappa = 0.66) and superior to microscopy (0.33). Symptomatic malaria due to pfhrp2/3-deleted P. falciparum was not observed. Ongoing HRP2-based RDT use is appropriate for the detection of falciparum malaria in the DRC.

One-sentence summary: Novel malaria SHERLOCK assays enabled robust detection, 16 speciation, and genotyping of Plasmodium spp. in diverse samples collected in Africa Abstract word count: 228 20 Manuscript word count: 5291 21 # Corresponding author information: Jonathan B. Parr, MD, MPH; 130 Mason Farm 22Rd., Chapel HillABSTRACT 24 25 CRISPR-based diagnostics are a new class of highly sensitive and specific assays with 26 multiple applications in infectious disease diagnosis. SHERLOCK, Sensitivity Enzymatic Reporter UnLOCKing, is one such CRISPR-based diagnostic that 28 combines recombinase polymerase pre-amplification, CRISPR-RNA base-pairing, and 29LwCas13a activity for nucleic acid detection. We developed SHERLOCK assays for 30 malaria capable of detecting all Plasmodium species known to cause malaria in humans 31 and species-specific detection of P. vivax and P. falciparum, the species responsible for 32 the majority of malaria cases worldwide. We validated these assays against parasite 33 genomic DNA and achieved analytical sensitivities ranging from 2.5-18.8 parasites per 34 reaction. We further tested these assays using a diverse panel of 123 clinical samples 35 from the Democratic Republic of the Congo, Uganda, and Thailand and pools of 36 Anopheles mosquitoes from Thailand. When compared to real-time PCR, the P. 37 falciparum assay achieved 94% sensitivity and 94% specificity in clinical samples. In 38 addition, we developed a SHERLOCK assay capable of detecting the dihydropteroate 39 synthetase (dhps) single nucleotide variant A581G associated with P. falciparum 40 sulfadoxine-pyrimethamine resistance. Compared to amplicon-based deep sequencing, 41 the dhps SHERLOCK assay achieved 73% sensitivity and 100% specificity when 42 applied to a panel of 43 clinical samples, with false-negative calls only at lower parasite 43 densities. These novel SHERLOCK assays have potential to spawn a new generation of 44 molecular diagnostics for malaria and demonstrate the versatility of CRISPR-based 45 diagnostic approaches. 46 47 48 Newly developed technologies that utilize Clustered, Regularly-Interspaced Palindromic 49 Repeat (CRISPR) systems have the potential to revolutionize infectious disease 50 diagnostic testing.(1) SHERLOCK, or Specific High-Sensitivity Enzymatic Reporter 51UnLOCKing, is a CRISPR-based diagnostic assay that has now been used to detect 52 dengue and Zika viruses with excellent sensitivity and specificity.(2) Its simple workflow 53 and robust performance characteristics have enabled multiplexed detection and 54 genotyping of Zika and dengue viruses, with increasingly streamlined protocols that 55 facilitate use at the point-of-care.(3, 4) SHERLOCK's potential is perhaps greatest in 56 low-resource settings where improved, reliable diagnostics are urgently needed for 57 multiple pathogens and for malaria, in particular. 58 59 Timely and accurate diagnosis is an important component of malaria control and 60 elimination efforts. The current generation of rapid diagnostic tests (RDTs) that detect 61 ...

P. malariaeis found worldwide and causes chronic parasitism in its human hosts. We developed aP. malariae (Pm)diagnostic assay that uses rapid, isothermal recombinase polymerase amplification (RPA) and lateral-flow-strip detection. Using 18S rRNA plasmid DNA, the assay demonstrates a detection limit of 10 copies /µL (∼1.7 genome equivalents) and 100% analytical specificity. Testing in field samples showed 95% clinical sensitivity and 88% specificity compared to qPCR. Total assay time was 35 minutes. Combined with simplified DNA extraction methods, the assay has potential for future field-deployable point-of-care use to detect a parasite species that remains largely undiagnosed.

Background The majority of Plasmodium falciparum malaria diagnoses in Africa are made using rapid diagnostic tests (RDTs) that detect histidine-rich protein 2. Increasing reports of false-negative RDT results due to parasites with deletions of the pfhrp2 and/or pfhrp3 genes (pfhrp2/3) raise concern about existing malaria diagnostic strategies. We previously identified pfhrp2-negative parasites among asymptomatic children in the Democratic Republic of the Congo (DRC), but their impact on diagnosis of symptomatic malaria is unknown. Methods We performed a cross-sectional study of false-negative RDTs in symptomatic subjects in 2017. Parasites were characterized by microscopy; RDT; pfhrp2/3 genotyping and species-specific PCR assays; a multiplex bead-based immunoassay; and/or whole-genome sequencing. Results Among 3,627 symptomatic subjects, we identified 427 (11.8%) RDT-/microscopy+ cases. Parasites from eight (0.2%) samples were initially classified as putative pfhrp2/3 deletions by PCR, but antigen testing and whole-genome sequencing confirmed the presence of intact genes. Malaria prevalence was high (57%) and non-falciparum co-infection common (15%). HRP2-based RDT performance was satisfactory and superior to microscopy. Conclusions Symptomatic malaria due to pfhrp2/3-deleted P. falciparum was not observed in the DRC. Ongoing HRP2-based RDT use is appropriate for the detection of falciparum malaria in the DRC.

Plasmodium vivaxmalaria has not traditionally been a major concern in central Africa given the high prevalence of the human Duffy-negative phenotype that is believed to prevent infection. Increasing reports of asymptomatic and symptomatic infections in Duffy-negative individuals throughout Africa raise the possibility thatP. vivaxis evolving to evade host resistance, but there are few parasite samples with genomic data available from this part of the world. In this study, we perform whole genome sequencing of a newP. vivaxisolate from the Democratic Republic of the Congo (DRC) and assess how this central African isolate fits into the global context of this species. We use population genomics methods to show thatP. vivaxfrom DRC is similar to other African parasite populations and is not closely related to the non-human primate parasiteP. vivax-like.