DSpace Repository

Malaria Molecular Surveillance in the Peruvian Amazon with a Novel Highly Multiplexed Plasmodium falciparum AmpliSeq Assay.

Show simple item record

dc.contributor.author Kattenberg, Johanna Helena
dc.contributor.author Fernandez Miñope, Carlos Alberto
dc.contributor.author van Dijk, Norbert J.
dc.contributor.author Llacsahuanga Allca, Lidia Elena
dc.contributor.author Guetens, Pieter
dc.contributor.author Valdivia, Hugo O.
dc.contributor.author Van Geertruyden, Jean-Pierre
dc.contributor.author Rovira-Vallbona, Eduard
dc.contributor.author Monsieurs, Pieter
dc.contributor.author Delgado Ratto, Richard Christopher
dc.contributor.author Gamboa Vilela, Dionicia Baziliza
dc.contributor.author Rosanas-Urgell, Anna
dc.coverage.spatial Mazán, Loreto, Perú
dc.coverage.spatial Punchana, Loreto, Perú
dc.coverage.spatial San Juan Bautista, Loreto, Perú
dc.coverage.spatial Pastaza, Loreto, Perú
dc.date.accessioned 2023-04-16T04:38:15Z
dc.date.available 2023-04-16T04:38:15Z
dc.date.issued 2023
dc.identifier.uri https://hdl.handle.net/20.500.12866/13390
dc.description.abstract Molecular surveillance for malaria has great potential to support national malaria control programs (NMCPs). To bridge the gap between research and implementation, several applications (use cases) have been identified to align research, technology development, and public health efforts. For implementation at NMCPs, there is an urgent need for feasible and cost-effective tools. We designed a new highly multiplexed deep sequencing assay (Pf AmpliSeq), which is compatible with benchtop sequencers, that allows high-accuracy sequencing with higher coverage and lower cost than whole-genome sequencing (WGS), targeting genomic regions of interest. The novelty of the assay is its high number of targets multiplexed into one easy workflow, combining population genetic markers with 13 nearly full-length resistance genes, which is applicable for many different use cases. We provide the first proof of principle for hrp2 and hrp3 deletion detection using amplicon sequencing. Initial sequence data processing can be performed automatically, and subsequent variant analysis requires minimal bioinformatic skills using any tabulated data analysis program. The assay was validated using a retrospective sample collection (n = 254) from the Peruvian Amazon between 2003 and 2018. By combining phenotypic markers and a within-country 28-single-nucleotide-polymorphism (SNP) barcode, we were able to distinguish different lineages with multiple resistance haplotypes (in dhfr, dhps, crt and mdr1) and hrp2 and hrp3 deletions, which have been increasing in recent years. We found no evidence to suggest the emergence of artemisinin (ART) resistance in Peru. These findings indicate a parasite population that is under drug pressure but is susceptible to current antimalarials and demonstrate the added value of a highly multiplexed molecular tool to inform malaria strategies and surveillance systems. IMPORTANCE While the power of next-generation sequencing technologies to inform and guide malaria control programs has become broadly recognized, the integration of genomic data for operational incorporation into malaria surveillance remains a challenge in most countries where malaria is endemic. The main obstacles include limited infrastructure, limited access to high-throughput sequencing facilities, and the need for local capacity to run an in-country analysis of genomes at a large-enough scale to be informative for surveillance. In addition, there is a lack of standardized laboratory protocols and automated analysis pipelines to generate reproducible and timely results useful for relevant stakeholders. With our standardized laboratory and bioinformatic workflow, malaria genetic surveillance data can be readily generated by surveillance researchers and malaria control programs in countries of endemicity, increasing ownership and ensuring timely results for informed decision- and policy-making. en_US
dc.language.iso eng
dc.publisher American Society for Microbiology
dc.relation.ispartofseries Microbiology Spectrum
dc.rights info:eu-repo/semantics/restrictedAccess
dc.rights.uri https://creativecommons.org/licenses/by-nc-nd/4.0/deed.es
dc.subject DNA sequencing en_US
dc.subject drug resistance en_US
dc.subject genetic epidemiology en_US
dc.subject hrp2 and hrp3 deletions en_US
dc.subject malaria en_US
dc.subject Plasmodium falciparum en_US
dc.subject surveillance studies en_US
dc.title Malaria Molecular Surveillance in the Peruvian Amazon with a Novel Highly Multiplexed Plasmodium falciparum AmpliSeq Assay. en_US
dc.type info:eu-repo/semantics/article
dc.identifier.doi https://doi.org/10.1128/spectrum.00960-22
dc.subject.ocde https://purl.org/pe-repo/ocde/ford#1.06.01
dc.relation.issn 2165-0497


Files in this item

Files Size Format View

There are no files associated with this item.

This item appears in the following Collection(s)

Show simple item record

info:eu-repo/semantics/restrictedAccess Except where otherwise noted, this item's license is described as info:eu-repo/semantics/restrictedAccess

Search DSpace


Browse

My Account

Statistics