ORCID Profile
0000-0003-0427-8029
Current Organisations
Universidad Señor de Sipán
,
Universidad Peruana Cayetano Heredia: Lima, PE
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Publisher: Cold Spring Harbor Laboratory
Date: 13-11-2021
DOI: 10.1101/2021.11.12.21266245
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), compatible with benchtop sequencers, allowing for high accuracy sequencing at higher coverage and lower cost than WGS, targeting genomic regions of interest. The novelty of the assay is in its high number of targets multiplexed in one easy workflow, combining population genetic markers with 13 near full-length resistance genes, applicable for many different use cases. We provide a first proof-of-principle for hrp2 and hrp3 deletion detection using licon 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 with a retrospective s le collection (n = 254) from the Peruvian Amazon between 2003 and 2018. By combining phenotypic markers and a within-country 28-SNP-barcode, we were able to distinguish different lineages with multiple resistant ( dhfr/dhps/crt/mdr1 ) haplotypes and hrp2 and hrp3 deletions, increasing in recent years. We found no evidence suggesting the emergence of ART-resistance in Peru. These findings indicate a parasite population under drug pressure, but susceptible to current antimalarials, and demonstrates the added value of a highly multiplexed molecular tool to inform malaria strategies and surveillance systems. While the power of next generation sequencing technologies to inform and guide malaria control programs has become broadly recognized, integration of genomic data for operational incorporation into malaria surveillance remains a challenge in most malaria endemic countries. The main obstacles include limited infrastructure and accessibility to high-throughput sequencing facilities and the need for local capacity to run 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 endemic countries, increasing ownership and ensuring timely results for informed decision and policy-making.
Publisher: American Society for Microbiology
Date: 13-04-2023
DOI: 10.1128/SPECTRUM.00960-22
Abstract: 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.
Location: Peru
No related grants have been discovered for Carlos Alberto Fernandez Miñope.