Nanopore sequencing for real-time genomic surveillance of<i>Plasmodium falciparum</i>

Girgis, Sophia T.; Adika, Edem; Nenyewodey, Felix E; Senoo, Dodzi Kwaku Jnr; Ngoi, Joyce M.; Bandoh, Kukua; Lorenz, Oliver; Steeg, Guus van de; Nsoh, Sebastian; Judge, Kim; Pearson, Richard D.; Almagro-Garcia, Jacob; Saiid, Samirah; Atampah, Solomon; Amoako, Enock K.; Morang’a, Collins M.; Asoala, Victor; Adjei, Elrmion S; Burden, William A. M.; Roberts-Sengier, William; Drury, Eleanor; Gonçalves, Sónia; Awandare, Gordon A.; Kwiatkowski, Dominic; Amenga-Etego, Lucas; Hamilton, William L.

doi:10.1101/2022.12.20.521122

Cited by 3 publications

(2 citation statements)

References 122 publications

(140 reference statements)

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“…DBS samples were transferred to the Wellcome Sanger Institute (WSI), UK, for DNA extraction and sequencing. DNA extraction from DBS was performed using the QIAamp Investigator Biorobot kit on the Qiagen Biorobot Universal instrument, protocol described in [45].…”

Section: Study Site and Samplesmentioning

confidence: 99%

A fourth locus in thePlasmodium falciparumgenome associated with sickle haemoglobin

Hamilton,

Band,

Aniweh

et al. 2023

Preprint

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Heterozygosity for sickle haemoglobin (HbS) confers protection against severe malaria caused by the parasite Plasmodium falciparum. Recent work suggests that this protective effect can depend on the parasite genotype. Here, we performed a genome-wide association analysis of P. falciparum against human beta-globin genotypes in a sample of 1,368 people with mild malaria in northern Ghana. We replicated the previously identified associations with HbS at two parasite loci. However, a newly identified locus within the serine/threonine kinase FIKK4.2, which we term Pfsa4, was also associated with HbS; this finding replicated in a published sample from Mali. The Pfsa1-4 mutations vary widely in frequencies across Africa, are absent from Asia, and are highly correlated with each-other across multiple populations. We found no strong associations with haemoglobin C. These findings add new complexity to the emerging picture of association between human and co-evolving malaria parasite genomes, suggesting new avenues for functional exploration.

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Section: Study Site and Samplesmentioning

confidence: 99%

A fourth locus in thePlasmodium falciparumgenome associated with sickle haemoglobin

Hamilton,

Band,

Aniweh

et al. 2023

Preprint

Self Cite

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“…The means can be minimalized significantly. For example, researchers demonstrated that Oxford Nanopore sequencing technology could be utilized via a gaming laptop, allowing for sequencing on the go [216].…”

Section: Genetic Engineeringmentioning

confidence: 99%

IoT Health Devices: Exploring Security Risks in the Connected Landscape

Affia

Finch

Jung

et al. 2023

IoT

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The concept of the Internet of Things (IoT) spans decades, and the same can be said for its inclusion in healthcare. The IoT is an attractive target in medicine; it offers considerable potential in expanding care. However, the application of the IoT in healthcare is fraught with an array of challenges, and also, through it, numerous vulnerabilities that translate to wider attack surfaces and deeper degrees of damage possible to both consumers and their confidence within health systems, as a result of patient-specific data being available to access. Further, when IoT health devices (IoTHDs) are developed, a diverse range of attacks are possible. To understand the risks in this new landscape, it is important to understand the architecture of IoTHDs, operations, and the social dynamics that may govern their interactions. This paper aims to document and create a map regarding IoTHDs, lay the groundwork for better understanding security risks in emerging IoTHD modalities through a multi-layer approach, and suggest means for improved governance and interaction. We also discuss technological innovations expected to set the stage for novel exploits leading into the middle and latter parts of the 21st century.

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Long-Read Sequencing and De Novo Genome Assembly Pipeline of Two Plasmodium falciparum Clones (Pf3D7, PfW2) Using Only the PromethION Sequencer from Oxford Nanopore Technologies without Whole-Genome Amplification

Delandre,

Lamer,

Loreau

et al. 2024

Biology

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Antimalarial drug resistance has become a real public health problem despite WHO measures. New sequencing technologies make it possible to investigate genomic variations associated with resistant phenotypes at the genome-wide scale. Based on the use of hemisynthetic nanopores, the PromethION technology from Oxford Nanopore Technologies can produce long-read sequences, in contrast to previous short-read technologies used as the gold standard to sequence Plasmodium. Two clones of P. falciparum (Pf3D7 and PfW2) were sequenced in long-read using the PromethION sequencer from Oxford Nanopore Technologies without genomic amplification. This made it possible to create a processing analysis pipeline for human Plasmodium with ONT Fastq only. De novo assembly revealed N50 lengths of 18,488 kb and 17,502 kb for the Pf3D7 and PfW2, respectively. The genome size was estimated at 23,235,407 base pairs for the Pf3D7 clone and 21,712,038 base pairs for the PfW2 clone. The average genome coverage depth was estimated at 787X and 653X for the Pf3D7 and PfW2 clones, respectively. This study proposes an assembly processing pipeline for the human Plasmodium genome using software adapted to large ONT data and the high AT percentage of Plasmodium. This search provides all the parameters which were optimized for use with the software selected in the pipeline.

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Nanopore sequencing for real-time genomic surveillance ofPlasmodium falciparum

Cited by 3 publications

References 122 publications

A fourth locus in thePlasmodium falciparumgenome associated with sickle haemoglobin

A fourth locus in thePlasmodium falciparumgenome associated with sickle haemoglobin

IoT Health Devices: Exploring Security Risks in the Connected Landscape

Long-Read Sequencing and De Novo Genome Assembly Pipeline of Two Plasmodium falciparum Clones (Pf3D7, PfW2) Using Only the PromethION Sequencer from Oxford Nanopore Technologies without Whole-Genome Amplification

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