A genomic platform for surveillance and antigen discovery in Plasmodium spp. using long-read amplicon sequencing.
CP: Biotechnology
CP: Microbiology
antigen discovery
circumsporozoite protein
genomic surveillance
glutamate-rich protein
long-read sequencing
malaria epidemiology
merozoite surface protein 1
merozoite surface protein 2
Journal
Cell reports methods
ISSN: 2667-2375
Titre abrégé: Cell Rep Methods
Pays: United States
ID NLM: 9918227360606676
Informations de publication
Date de publication:
25 09 2023
25 09 2023
Historique:
received:
14
07
2022
revised:
18
06
2023
accepted:
07
08
2023
medline:
28
9
2023
pubmed:
27
9
2023
entrez:
26
9
2023
Statut:
ppublish
Résumé
Many vaccine candidate proteins in the malaria parasite Plasmodium falciparum are under strong immunological pressure and confer antigenic diversity. We present a sequencing and data analysis platform for the genomic surveillance of the insertion or deletion (indel)-rich antigens merozoite surface protein 1 (MSP1), MSP2, glutamate-rich protein (GLURP), and CSP from P. falciparum using long-read circular consensus sequencing (CCS) in multiclonal malaria isolates. Our platform uses 40 PCR primers per gene to asymmetrically barcode and identify multiclonal infections in pools of up to 384 samples. With msp2, we validated the method using 235 mock infections combining 10 synthetic variants at different concentrations and infection complexities. We applied this strategy to P. falciparum isolates from a longitudinal cohort in Tanzania. Finally, we constructed an analysis pipeline that streamlines the processing and interpretation of epidemiological and antigenic diversity data from demultiplexed FASTQ files. This platform can be easily adapted to other polymorphic antigens of interest in Plasmodium or any other human pathogen.
Identifiants
pubmed: 37751696
pii: S2667-2375(23)00218-7
doi: 10.1016/j.crmeth.2023.100574
pmc: PMC10545912
pii:
doi:
Substances chimiques
Glutamic Acid
3KX376GY7L
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
100574Informations de copyright
Copyright © 2023 The Author(s). Published by Elsevier Inc. All rights reserved.
Déclaration de conflit d'intérêts
Declaration of interests The authors declare no competing interests.
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