Improved limit of detection for zoonoticPlasmodium knowlesiandP. cynomolgisurveillance using reverse transcription for total nucleic acid preserved samples or dried blood spots
Authors: Braima Kamil A , Piera Kim A , Lubis Inke ND , Noviyanti Rintis , Rajahram Giri S , Kariodimedjo Pinkan , Nainggolan Irbah RA , Permatasari Ranti , Trianty Leily , Amalia Ristya , Saimah binti Sakam Sitti , Tan Angelica F , William Timothy , Westaway Jacob AF , Lee PingChin , Daim Sylvia , Surendra Henry , Christy Nathaniel , Letizia Andrew G , Peatey Christopher L , Moideen Mohd Arshil , Barber Bridget E , Sutherland Colin J , Anstey Nicholas M , Grigg Matthew J 
Published: April 2024

ABSTRACTBackgroundZoonoticP. knowlesiandP. cynomolgisymptomatic and asymptomatic infections occur across endemic areas of Southeast Asia. Most infections are low-parasitemia, with an unknown proportion below routine microscopy detection thresholds. Molecular surveillance tools optimizing the limit of detection (LOD) would allow more accurate estimates of zoonotic malaria prevalence.MethodsAn established ultra-sensitivePlasmodiumgenus quantitative-PCR (qPCR) assay targeting the 18S rRNA gene underwent LOD evaluation with and without reverse transcription (RT) forP. knowlesi,P. cynomolgiandP. vivaxusing total nucleic acid preserved (DNA/RNA ShieldTM) isolates and archived dried blood spots (DBS). LODs for selectedP. knowlesi-specific assays, and referenceP. vivax-andP. cynomolgi-specific assays were determined with RT. Assay specificities were assessed using clinical malaria samples and malaria-negative controls.ResultsThe use of reverse transcription improvedPlasmodiumspecies detection by up to 10,000-fold (Plasmodiumgenus), 2759-fold (P. knowlesi), 1000-fold (P. vivax) and 10-fold (P. cynomolgi). The median LOD with RT for the Kamau et al.Plasmodiumgenus RT-qPCR assay was ≤0.0002 parasites/µL forP. knowlesiand 0.002 parasites/µL for bothP. cynomolgiandP. vivax. The LODs with RT forP. knowlesi-specific PCRs were: Imwong et al. 18S rRNA (0.0007 parasites/µL); Divis et al. real-time 18S rRNA (0.0002 parasites/µL); Lubis et al. hemi-nestedSICAvar(1.1 parasites/µL) and Lee et al. nested 18S rRNA (11 parasites/µL). The LOD forP. vivax-andP. cynomolgi-specific assays with RT were 0.02 and 0.20 parasites/µL respectively. For DBSP. knowlesisamples the median LOD for thePlasmodiumgenus qPCR with RT was 0.08, and without RT was 19.89 parasites/uL (249-fold change); no LOD improvement was demonstrated in DBS archived beyond 6 years. ThePlasmodiumgenus andP. knowlesi-assays were 100% specific forPlasmodiumspecies andP. knowlesidetection, respectively, from 190 clinical infections and 48 healthy controls. ReferenceP. vivax-specific primers demonstrated known cross-reactivity withP. cynomolgi.ConclusionOur findings support the use of an 18S rRNAPlasmodiumgenus qPCR and species-specific nested PCR protocol with RT for highly-sensitive surveillance of zoonotic and humanPlasmodiumspecies infections.Author SummaryThe monkey malaria parasitePlasmodium knowlesihas been found to increasingly infect humans across Southeast Asia via the bite of it’s anopheline mosquito vectors. Human infections with a similar monkey parasite,Plasmodium cynomologi,have also been reported. The diagnostic tools commonly used to detect these malaria species are often unable to detect very low-level infections. We aimed to to improve surveillance detection tools and blood sample collection methods to detect these zoonotic malaria species and understand the extent of transmission and the burden of disease. This study validated and compared the use of molecular laboratory assays targeting these species. We found that with the use of reverse transcription, large improvements in the limit of detection were possible, by up to 10,000-fold for initial malaria screening, and up to 2759-fold for specificP. knowlesidetection. Findings from this study support the use of ultrasensitive detection tools to improve surveillance approaches to emerging zoonotic malaria species.