TY - JOUR
T1 - Global diversity of soil-transmitted helminths reveals population-biased genetic variation that impacts diagnostic targets
AU - Papaiakovou, Marina
AU - Waeschenbach, Andrea
AU - Ajibola, Olumide
AU - Ajjampur, Sitara S.R.
AU - Anderson, Roy M.
AU - Bailey, Robin
AU - Benjamin-Chung, Jade
AU - Cambra-Pellejà, Maria
AU - Caro, Nicolas R.
AU - Chaima, David
AU - Cimino, Rubén O.
AU - Cools, Piet
AU - Cossa, Anélsio
AU - Dunn, Julia
AU - Galagan, Sean
AU - Gandasegui, Javier
AU - Grau-Pujol, Berta
AU - Houlder, Emma L.
AU - Ibikounlé, Moudachirou
AU - Jenkins, Timothy P.
AU - Kalua, Khumbo
AU - Kjetland, Eyrun F.
AU - Krolewiecki, Alejandro J.
AU - Levecke, Bruno
AU - Luty, Adrian J.F.
AU - MacDonald, Andrew S.
AU - Mandomando, Inácio
AU - Manuel, Malathi
AU - Martínez-Valladares, Maria
AU - Mejia, Rojelio
AU - Mekonnen, Zeleke
AU - Messa, Augusto
AU - Mpairwe, Harriet
AU - Muchisse, Osvaldo
AU - Muñoz, Jose
AU - Mwinzi, Pauline
AU - Novela, Valdemiro
AU - Odiere, Maurice R.
AU - Sacoor, Charfudin
AU - Walson, Judd L.
AU - Williams, Steven A.
AU - Witek-McManus, Stefan
AU - Littlewood, D. Timothy J.
AU - Cantacessi, Cinzia
AU - Doyle, Stephen R.
N1 - Funding Information:
The authors would like to thank John M Colford Jr for the support providing the samples from Bangladesh, Marisa Juarez and Paola A. Vargas for their help with egg collection and logistical support during the field sample processing in Or\u00E1n, Argentina, the NHM Molecular Labs, especially Ranbir Bailey, Elena Lugli and Claire Griffin, for access and logistical support, Stefano Colombo for help with DNA extractions on the samples from Uganda, and the Helminth Genomics group at the Wellcome Sanger Institute for insightful discussions throughout this project. Sequencing of samples was supported by the Bill & Melinda Gates Foundation (USA; OPP1129535) and the Wellcome Trust (UK; 206194). MP is supported by a Harding Distinguished Postgraduate Scholarship held at the University of Cambridge (UK). JBC is a Chan Zuckerberg Biohub Investigator. MM was supported, under the guidance of SRA, by a PhD studentship at The Tamil Nadu Dr. M.G.R. Medical University, Chennai. SRD is supported by a UKRI Future Leaders Fellowship (UK; MR/T020733/1) and the Wellcome Trust (UK; 206194). Samples provided by Ghent University (Belgium) were part of field trials supported by the Bill & Melinda Gates Foundation (USA; OPP1120972). Samples from Kenya were collected with financial support from the University of Georgia Research Foundation, Inc., which was funded by the Bill & Melinda Gates Foundation (USA; INV-010428) for the SCORE Project. Samples from Mozambique were collected by the Centro de Investiga\u00E7\u00E3o em Sa\u00FAde de Manhi\u00E7a (CISM), which is supported by the Government of Mozambique and the Spanish Agency for International Development Cooperation (AECID) and Institut de Salut Global de Barcelona (ISGlobal), which receives support from the grant CEX2018-000806-S funded by MCIN/AEI/10.13039/501100011033, and support from the Generalitat de Catalunya through the CERCA Program. For the purpose of Open Access, the authors have applied a CC BY public copyright Licence to any Author Accepted Manuscript version arising from this submission.
Publisher Copyright:
© The Author(s) 2025.
PY - 2025/12
Y1 - 2025/12
N2 - Soil-transmitted helminths (STHs) are intestinal parasites that affect over a billion people worldwide. STH control relies on microscopy-based diagnostics to monitor parasite prevalence and enable post-treatment surveillance; however, molecular diagnostics are rapidly being developed due to increased sensitivity, particularly in low-STH-prevalence settings. The genetic diversity of helminths and its potential impact on molecular diagnostics remain unclear. Using low-coverage genome sequencing, we assess the genetics of STHs within worm, faecal, and purified egg samples from 27 countries, identifying differences in the genetic connectivity and diversity of STH-positive samples across regions and cryptic diversity between closely related human- and pig-infective species. We define substantial copy number and sequence variants in current diagnostic target regions and validate the impact of genetic variation on qPCR diagnostics using in vitro assays. Our study provides insights into the diversity and genomic epidemiology of STHs, highlighting both the challenges and opportunities for developing molecular diagnostics needed to support STH control efforts.
AB - Soil-transmitted helminths (STHs) are intestinal parasites that affect over a billion people worldwide. STH control relies on microscopy-based diagnostics to monitor parasite prevalence and enable post-treatment surveillance; however, molecular diagnostics are rapidly being developed due to increased sensitivity, particularly in low-STH-prevalence settings. The genetic diversity of helminths and its potential impact on molecular diagnostics remain unclear. Using low-coverage genome sequencing, we assess the genetics of STHs within worm, faecal, and purified egg samples from 27 countries, identifying differences in the genetic connectivity and diversity of STH-positive samples across regions and cryptic diversity between closely related human- and pig-infective species. We define substantial copy number and sequence variants in current diagnostic target regions and validate the impact of genetic variation on qPCR diagnostics using in vitro assays. Our study provides insights into the diversity and genomic epidemiology of STHs, highlighting both the challenges and opportunities for developing molecular diagnostics needed to support STH control efforts.
UR - https://www.scopus.com/pages/publications/105010529657
U2 - 10.1038/s41467-025-61687-0
DO - 10.1038/s41467-025-61687-0
M3 - Article
C2 - 40640199
AN - SCOPUS:105010529657
SN - 2041-1723
VL - 16
JO - Nature Communications
JF - Nature Communications
IS - 1
M1 - 6374
ER -