Tracking the spread of a naturally occurring Leishmania (L.) infantum mutant: a qPCR-based investigation in strains and clinical samples
12 affiliations
- 1Laboratório de Pesquisa em Leishmanioses, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Fiocruz, Rio de Janeiro, RJ Brazil
- 2Communicable Diseases and Environmental Determinants of Health (CDE), Neglected, Tropical and Vector Borne Diseases (VT), Pan American Health Organization, World Health Organization (PAHO/WHO), Rio de Janeiro, Brazil
- 3Laboratório de Pesquisa Clínica em Dermatozoonoses em Animais Domésticos-Instituto Nacional de Infectologia Evandro Chagas, Fundação Oswaldo Cruz, Fiocruz, Rio de Janeiro, RJ Brazil
- 4Laboratório de Biologia de Tripanosomatídeos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Fiocruz, Rio de Janeiro, RJ Brazil
- 5Universidade Católica Dom Bosco, Campo Grande, MS Brazil
- 6Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Fiocruz, Salvador, BA Brazil
- 7Escola de Medicina Veterinária e Zootecnia, Universidade Federal da Bahia, Salvador, BA Brazil
- 8Departamento de Patologia, Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, São Paulo, SP Brazil
- 9Centro de Parasitologia e Micologia, Instituto Adolfo Lutz, São Paulo, SP Brazil
- 10Laboratory of Pathology of Infectious Diseases, Medical School, São Paulo University, São Paulo, SP Brazil
- 11Laboratorio de Interacciones Hospedero-Patógeno-UBM, Institut Pasteur de Montevideo, Montevideo, Uruguay
- 12Laboratory of Molecular Virology and Parasitology, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
Abstract
Background: The co-circulation of Leishmania (Leishmania) infantum strains carrying a naturally occurring 12 kb genomic deletion (DEL) and the wild-type (NonDEL) parasites in the Americas raises important challenges for epidemiological surveillance, molecular diagnostics, and the interpretation of infection dynamics in visceral leishmaniasis (VL). In this study, we aimed to develop and apply a robust molecular approach to discriminate and quantify DEL and NonDEL genotypes and to assess their distribution, frequency, and patterns of co-infection across endemic regions.
Methods: We established a qPCR-based genotyping strategy combining a constitutive genomic target, present in all Leishmania (L.) infantum strains, with a NonDEL-specific target, enabling simultaneous genotype discrimination and parasite quantification.
Results: After validation using cultured parasites, the assay was applied to a large and diverse panel of strains isolates from humans and dogs preserved in a biobank, as well as clinical samples from dogs, cats, coatis, and sand flies across South and Central America. DEL parasites predominated (69.8%) and showed a wide geographic distribution in both strains and clinical samples, indicating their major contribution to transmission cycles. No significant association was observed between host type (human vs. canine) and genotype frequency. Notably, mixed-genotype infections were frequently detected, revealing within-host complexity not captured by conventional diagnostic methods. Quantification based on the constitutive target strongly correlated with kDNA-based parasite load estimates, supporting its simultaneous use for genotyping and quantification of L. (L.) infantum variants directly from clinical material.
Conclusions: This approach thus provides new insights into parasite population structure and infection dynamics and supports improved molecular surveillance and interpretation of diagnostic and epidemiological data in VL.
Graphical Abstract:
Supplementary Information: The online version contains supplementary material available at https://doi.org/10.1186/s13071-026-07571-2.
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BibTeX
@article{chagas2026tracking,
title = {{Tracking the spread of a naturally occurring Leishmania (L.) infantum mutant: a qPCR-based investigation in strains and clinical samples}},
author = {Marne Coimbra das Chagas and Ana Nilce Silveira Elkhoury and Samantha Valadas and Bruna Dias das Chagas and Camilly Enes and Artur Augusto Velho Mendes Junior and Sandro Antonio Pereira and Gabriel Carvalho de Macedo and André Luiz Rodrigues Roque and Manuela da Silva Solcà and Claudia Brodskyn and Deborah Bittencourt Mothé and Juliana Mariotti Guerra and José Eduardo Tolezano and Luiz Fabio Batista and Marcia Dalastra Laurenti and Lisvane Paes-Vieira and Carlos Robello and Otacilio C. Moreira and Elisa Cupolillo and Mariana Côrtes Boité},
journal = {Parasites \& Vectors},
year = {2026},
month = aug,
doi = {10.1186/s13071-026-07571-2},
url = {https://doi.org/10.1186/s13071-026-07571-2},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Tracking the spread of a naturally occurring Leishmania (L.) infantum mutant: a qPCR-based investigation in strains and clinical samples
AU - Marne Coimbra das Chagas
AU - Ana Nilce Silveira Elkhoury
AU - Samantha Valadas
AU - Bruna Dias das Chagas
AU - Camilly Enes
AU - Artur Augusto Velho Mendes Junior
AU - Sandro Antonio Pereira
AU - Gabriel Carvalho de Macedo
AU - André Luiz Rodrigues Roque
AU - Manuela da Silva Solcà
AU - Claudia Brodskyn
AU - Deborah Bittencourt Mothé
AU - Juliana Mariotti Guerra
AU - José Eduardo Tolezano
AU - Luiz Fabio Batista
AU - Marcia Dalastra Laurenti
AU - Lisvane Paes-Vieira
AU - Carlos Robello
AU - Otacilio C. Moreira
AU - Elisa Cupolillo
AU - Mariana Côrtes Boité
PY - 2026
DA - 2026/08/11
JO - Parasites & Vectors
DO - 10.1186/s13071-026-07571-2
UR - https://doi.org/10.1186/s13071-026-07571-2
AB - Background: The co-circulation of Leishmania (Leishmania) infantum strains carrying a naturally occurring 12 kb genomic deletion (DEL) and the wild-type (NonDEL) parasites in the Americas raises important challenges for epidemiological surveillance, molecular diagnostics, and the interpretation of infection dynamics in visceral leishmaniasis (VL). In this study, we aimed to develop and apply a robust molecular approach to discriminate and quantify DEL and NonDEL genotypes and to assess their distribution, frequency, and patterns of co-infection across endemic regions. Methods: We established a qPCR-based genotyping strategy combining a constitutive genomic target, present in all Leishmania (L.) infantum strains, with a NonDEL-specific target, enabling simultaneous genotype discrimination and parasite quantification. Results: After validation using cultured parasites, the assay was applied to a large and diverse panel of strains isolates from humans and dogs preserved in a biobank, as well as clinical samples from dogs, cats, coatis, and sand flies across South and Central America. DEL parasites predominated (69.8%) and showed a wide geographic distribution in both strains and clinical samples, indicating their major contribution to transmission cycles. No significant association was observed between host type (human vs. canine) and genotype frequency. Notably, mixed-genotype infections were frequently detected, revealing within-host complexity not captured by conventional diagnostic methods. Quantification based on the constitutive target strongly correlated with kDNA-based parasite load estimates, supporting its simultaneous use for genotyping and quantification of L. (L.) infantum variants directly from clinical material. Conclusions: This approach thus provides new insights into parasite population structure and infection dynamics and supports improved molecular surveillance and interpretation of diagnostic and epidemiological data in VL. Graphical Abstract: Supplementary Information: The online version contains supplementary material available at https://doi.org/10.1186/s13071-026-07571-2.
SN - 1756-3305
ER -