Identity-by-descent with uncertainty characterises connectivity of Plasmodium falciparum populations on the Colombian-Pacific coast


Autoři: Aimee R. Taylor aff001;  Diego F. Echeverry aff003;  Timothy J. C. Anderson aff006;  Daniel E. Neafsey aff002;  Caroline O. Buckee aff001
Působiště autorů: Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA aff001;  Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA aff002;  Centro Internacional de Entrenamiento e Investigaciones Médicas (CIDEIM), Cali, Colombia aff003;  Universidad Icesi, Calle 18 No. 122-135, Cali, Colombia aff004;  Departamento de Microbiologia, Facultad de Salud, Universidad del Valle, Cali, Colombia aff005;  Disease Intervention and Prevention Program, Texas Biomedical Research Institute, San Antonio, Texas, USA aff006;  Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA aff007
Vyšlo v časopise: Identity-by-descent with uncertainty characterises connectivity of Plasmodium falciparum populations on the Colombian-Pacific coast. PLoS Genet 16(11): e1009101. doi:10.1371/journal.pgen.1009101
Kategorie: Research Article
doi: 10.1371/journal.pgen.1009101

Souhrn

Characterising connectivity between geographically separated biological populations is a common goal in many fields. Recent approaches to understanding connectivity between malaria parasite populations, with implications for disease control efforts, have used estimates of relatedness based on identity-by-descent (IBD). However, uncertainty around estimated relatedness has not been accounted for. IBD-based relatedness estimates with uncertainty were computed for pairs of monoclonal Plasmodium falciparum samples collected from five cities on the Colombian-Pacific coast where long-term clonal propagation of P. falciparum is frequent. The cities include two official ports, Buenaventura and Tumaco, that are separated geographically but connected by frequent marine traffic. Fractions of highly-related sample pairs (whose classification using a threshold accounts for uncertainty) were greater within cities versus between. However, based on both highly-related fractions and on a threshold-free approach (Wasserstein distances between parasite populations) connectivity between Buenaventura and Tumaco was disproportionally high. Buenaventura-Tumaco connectivity was consistent with transmission events involving parasites from five clonal components (groups of statistically indistinguishable parasites identified under a graph theoretic framework). To conclude, P. falciparum population connectivity on the Colombian-Pacific coast abides by accessibility not isolation-by-distance, potentially implicating marine traffic in malaria transmission with opportunities for targeted intervention. Further investigations are required to test this hypothesis. For the first time in malaria epidemiology (and to our knowledge in ecological and epidemiological studies more generally), we account for uncertainty around estimated relatedness (an important consideration for studies that plan to use genotype versus whole genome sequence data to estimate IBD-based relatedness); we also use threshold-free methods to compare parasite populations and identify clonal components. Threshold-free methods are especially important in analyses of malaria parasites and other recombining organisms with mixed mating systems where thresholds do not have clear interpretation (e.g. due to clonal propagation) and thus undermine the cross-comparison of studies.

Klíčová slova:

Cities – Colombia – DNA recombination – Malaria – Malarial parasites – Parasitic diseases – Plasmodium – Single nucleotide polymorphisms


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2020 Číslo 11

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