Temporal and spatial analysis of Plasmodium falciparum genomics reveals patterns of parasite connectivity in a low-transmission district in Southern Province, Zambia

被引：1

作者：

Fola, Abebe A. ^{[1
]}

Moser, Kara A. ^{[2
]}

Aydemir, Ozkan ^{[1
]}

Hennelly, Chris ^{[2
]}

Kobayashi, Tamaki ^{[3
]}

Shields, Timothy ^{[3
]}

Hamapumbu, Harry ^{[4
]}

Musonda, Michael ^{[4
]}

Katowa, Ben ^{[4
]}

Matoba, Japhet C. ^{[4
]}

Stevenson, Jennifer C. E. ^{[4
]}

Norris, Douglas E. E. ^{[5
]}

Thuma, Philip E. ^{[4
]}

Wesolowski, Amy J. ^{[3
]}

Moss, William J. A. ^{[3
,5
]}

Bailey, Jeffrey A. J. ^{[1
]}

Juliano, Jonathan J. ^{[2
,6
,7
,8
]}

机构：

[1] Brown Univ, Dept Pathol & Lab Med, 55 Claverick St, Providence, RI 02906 USA

[2] Univ North Carolina Chapel Hill, Univ North Carolina, Inst Global Hlth & Infect Dis, Chapel Hill, NC 27599 USA

[3] Johns Hopkins Bloomberg Sch Publ Hlth, Dept Epidemiol, Baltimore, MD 21205 USA

[4] Macha Res Trust, Choma, Zambia

[5] Johns Hopkins Bloomberg Sch Publ Hlth, Johns Hopkins Malaria Res Inst, Dept Mol Microbiol & Immunol, Baltimore, MD 21205 USA

[6] Univ North Carolina Chapel Hill, Sch Med, Div Infect Dis, Chapel Hill, NC 27599 USA

[7] Univ North Carolina Chapel Hill, Gillings Sch Global Publ Hlth, Dept Epidemiol, Chapel Hill, NC 27599 USA

[8] Univ North Carolina Chapel Hill, Sch Med, Curriculum Genet & Mol Biol, Chapel Hill, NC 27599 USA

来源：

MALARIA JOURNAL | 2023年 / 22卷 / 01期

基金：

美国国家卫生研究院;

关键词：

Plasmodium falciparum; Transmission; Zambia; Genomics; MALARIA; VIVAX;

D O I：

10.1186/s12936-023-04637-9

中图分类号：

R51 [传染病];

学科分类号：

100401 ;

摘要：

BackgroundUnderstanding temporal and spatial dynamics of malaria transmission will help to inform effective interventions and strategies in regions approaching elimination. Parasite genomics are increasingly used to monitor epidemiologic trends, including assessing residual transmission across seasons and importation of malaria into these regions.MethodsIn a low and seasonal transmission setting of southern Zambia, a total of 441 Plasmodium falciparum samples collected from 8 neighbouring health centres between 2012 and 2018 were genotyped using molecular inversion probes (MIPs n = 1793) targeting a total of 1832 neutral and geographically informative SNPs distributed across the parasite genome. After filtering for quality and missingness, 302 samples and 1410 SNPs were retained and used for downstream population genomic analyses.ResultsThe analyses revealed most (67%, n = 202) infections harboured one clone (monogenomic) with some variation at local level suggesting low, but heterogenous malaria transmission. Relatedness identity-by-descent (IBD) analysis revealed variable distribution of IBD segments across the genome and 6% of pairs were highly-related (IBD & GE; 0.25). Some of the highly-related parasite populations persisted across multiple seasons, suggesting that persistence of malaria in this low-transmission region is fueled by parasites "seeding" across the dry season. For recent years, clusters of clonal parasites were identified that were dissimilar to the general parasite population, suggesting parasite populations were increasingly fragmented at small spatial scales due to intensified control efforts. Clustering analysis using PCA and t-SNE showed a lack of substantial parasite population structure.ConclusionLeveraging both genomic and epidemiological data provided comprehensive picture of fluctuations in parasite populations in this pre-elimination setting of southern Zambia over 7 years.

引用

页数：11