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Molina-de la Fuente I, Pacheco MA, García L, González V, Riloha M, Oki C, Benito A, Escalante AA, Berzosa P. Evolution of pfhrp2 and pfhrp3 deletions in Equatorial Guinea between the pre- and post-RDT introduction. Malar J 2024; 23:215. [PMID: 39026276 PMCID: PMC11264669 DOI: 10.1186/s12936-024-05036-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Accepted: 07/05/2024] [Indexed: 07/20/2024] Open
Abstract
BACKGROUND Pfhrp2 and pfhrp3 deletions are threatening Plasmodium falciparum malaria diagnosis by rapid diagnostic tests (RDT) due to false negatives. This study assesses the changes in the frequencies of pfhrp2 and pfhrp3 deletions (pfhrp2Del and pfhrp3Del, respectively) and the genes in their flaking regions, before and after RDT introduction in Equatorial Guinea. METHODS A total of 566 P. falciparum samples were genotyped to assess the presence of pfhrp2 and pfhrp3 deletions and their flanking genes. The specimens were collected 18 years apart from two provinces of Equatorial Guinea, North Bioko (Insular Region) and Litoral Province (Continental Region). Orthologs of pfhrp2 and pfhrp3 genes from other closely related species were used to compare sequencing data to assess pfhrp2 and pfhrp3 evolution. Additionally, population structure was studied using seven neutral microsatellites. RESULTS This study found that pfhrp2Del and pfhrp3Del were present before the introduction of RDT; however, they increased in frequency after their use, reaching more than 15%. Haplotype networks suggested that pfhrp2Del and pfhrp3Del emerged multiple times. Exon 2 of pfhrp2 and pfhrp3 genes had high variability, but there were no significant changes in amino acid sequences. CONCLUSIONS Baseline sampling before deploying interventions provides a valuable context to interpret changes in genetic markers linked to their efficacy, such as the dynamic of deletions affecting RDT efficacy.
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Affiliation(s)
- Irene Molina-de la Fuente
- Biomedicine and biotechnology Department, University of Alcalá, Ctra.Madrid-Barcelona Km.33,600, 28871, Alcalá de Henares, Spain.
- National Centre of Tropical Medicine, Carlos III Institute of Health, C/ Sinesio Delgado 10, 28029, Madrid, Spain.
- Consorcio Centro de Investigación Biomédica en Red - CIBERINFEC ISCIII, C/ Sinesio Delgado 10, 28029, Madrid, Spain.
| | - M Andreína Pacheco
- Biology Department/Institute of Genomics and Evolutionary Medicine (iGEM), Temple University, (SERC - 645), 1925 N. 12 St, Philadelphia, PA, 19122-1801, USA
| | - Luz García
- National Centre of Tropical Medicine, Carlos III Institute of Health, C/ Sinesio Delgado 10, 28029, Madrid, Spain
- Consorcio Centro de Investigación Biomédica en Red - CIBERINFEC ISCIII, C/ Sinesio Delgado 10, 28029, Madrid, Spain
| | - Vicenta González
- National Centre of Tropical Medicine, Carlos III Institute of Health, C/ Sinesio Delgado 10, 28029, Madrid, Spain
- Consorcio Centro de Investigación Biomédica en Red - CIBERINFEC ISCIII, C/ Sinesio Delgado 10, 28029, Madrid, Spain
| | - Matilde Riloha
- Ministry of Health and Social Welfare (MINSABS), National Programne for Malaria Control, Malabo, Equatorial Guinea
| | - Consuelo Oki
- Ministry of Health and Social Welfare (MINSABS), National Programne for Malaria Control, Malabo, Equatorial Guinea
| | - Agustín Benito
- National Centre of Tropical Medicine, Carlos III Institute of Health, C/ Sinesio Delgado 10, 28029, Madrid, Spain
- Consorcio Centro de Investigación Biomédica en Red - CIBERINFEC ISCIII, C/ Sinesio Delgado 10, 28029, Madrid, Spain
| | - Ananias A Escalante
- Biology Department/Institute of Genomics and Evolutionary Medicine (iGEM), Temple University, (SERC - 645), 1925 N. 12 St, Philadelphia, PA, 19122-1801, USA
| | - Pedro Berzosa
- National Centre of Tropical Medicine, Carlos III Institute of Health, C/ Sinesio Delgado 10, 28029, Madrid, Spain
- Consorcio Centro de Investigación Biomédica en Red - CIBERINFEC ISCIII, C/ Sinesio Delgado 10, 28029, Madrid, Spain
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Cabrera-Sosa L, Nolasco O, Kattenberg JH, Fernandez-Miñope C, Valdivia HO, Barazorda K, Arévalo de Los Rios S, Rodriguez-Ferrucci H, Vinetz JM, Rosanas-Urgell A, Van Geertruyden JP, Gamboa D, Delgado-Ratto C. Genomic surveillance of malaria parasites in an indigenous community in the Peruvian Amazon. Sci Rep 2024; 14:16291. [PMID: 39009685 PMCID: PMC11250820 DOI: 10.1038/s41598-024-66925-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 07/05/2024] [Indexed: 07/17/2024] Open
Abstract
Hard-to-reach communities represent Peru's main challenge for malaria elimination, but information about transmission in these areas is scarce. Here, we assessed Plasmodium vivax (Pv) and P. falciparum (Pf) transmission dynamics, resistance markers, and Pf hrp2/3 deletions in Nueva Jerusalén (NJ), a remote, indigenous community in the Peruvian Amazon with high population mobility. We collected samples from November 2019 to May 2020 by active (ACD) and passive case detection (PCD) in NJ. Parasites were identified with microscopy and PCR. Then, we analyzed a representative set of positive-PCR samples (Pv = 68, Pf = 58) using highly-multiplexed deep sequencing assays (AmpliSeq) and compared NJ parasites with ones from other remote Peruvian areas using population genetics indexes. The ACD intervention did not reduce malaria cases in the short term, and persistent malaria transmission was observed (at least one Pv infection was detected in 96% of the study days). In Nueva Jerusalen, the Pv population had modest genetic diversity (He = 0.27). Pf population had lower diversity (He = 0.08) and presented temporal clustering, one of these clusters linked to an outbreak in February 2020. Moreover, Pv and Pf parasites from NJ exhibited variable levels of differentiation (Pv Fst = 0.07-0.52 and Pf Fst = 0.11-0.58) with parasites from other remote areas. No artemisin resistance mutations but chloroquine (57%) and sulfadoxine-pyrimethamine (35-67%) were detected in NJ's Pf parasites. Moreover, pfhrp2/3 gene deletions were common (32-50% of parasites with one or both genes deleted). The persistent Pv transmission and the detection of a Pf outbreak with parasites genetically distinct from the local ones highlight the need for tailored interventions focusing on mobility patterns and imported infections in remote areas to eliminate malaria in the Peruvian Amazon.
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Affiliation(s)
- Luis Cabrera-Sosa
- Laboratorio de Malaria: Parásitos y Vectores, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias e Ingeniería, Universidad Peruana Cayetano Heredia, Lima, Peru.
- Instituto de Medicina Tropical "Alexander Von Humboldt", Universidad Peruana Cayetano Heredia, Lima, Peru.
| | - Oscar Nolasco
- Laboratorio de Malaria: Parásitos y Vectores, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias e Ingeniería, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Johanna H Kattenberg
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Carlos Fernandez-Miñope
- Instituto de Medicina Tropical "Alexander Von Humboldt", Universidad Peruana Cayetano Heredia, Lima, Peru
- Malaria Research Group (MaRch), Global Health Institute (GHI), Family Medicine and Population Health Department (FAMPOP), Faculty of Medicine, University of Antwerp, Antwerp, Belgium
| | - Hugo O Valdivia
- Department of Parasitology, U.S. Naval Medical Research Unit SOUTH (NAMRU SOUTH), Lima, Peru
| | - Keare Barazorda
- Department of Parasitology, U.S. Naval Medical Research Unit SOUTH (NAMRU SOUTH), Lima, Peru
| | | | - Hugo Rodriguez-Ferrucci
- Facultad de Medicina Humana, Universidad Nacional de la Amazonía Peruana, Iquitos, Loreto, Peru
| | - Joseph M Vinetz
- Instituto de Medicina Tropical "Alexander Von Humboldt", Universidad Peruana Cayetano Heredia, Lima, Peru
- Section of Infectious Diseases, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Anna Rosanas-Urgell
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Jean-Pierre Van Geertruyden
- Malaria Research Group (MaRch), Global Health Institute (GHI), Family Medicine and Population Health Department (FAMPOP), Faculty of Medicine, University of Antwerp, Antwerp, Belgium
| | - Dionicia Gamboa
- Laboratorio de Malaria: Parásitos y Vectores, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias e Ingeniería, Universidad Peruana Cayetano Heredia, Lima, Peru
- Instituto de Medicina Tropical "Alexander Von Humboldt", Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Christopher Delgado-Ratto
- Instituto de Medicina Tropical "Alexander Von Humboldt", Universidad Peruana Cayetano Heredia, Lima, Peru.
- Malaria Research Group (MaRch), Global Health Institute (GHI), Family Medicine and Population Health Department (FAMPOP), Faculty of Medicine, University of Antwerp, Antwerp, Belgium.
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Villalobos G, Lopez-Escamilla E, Olivo-Diaz A, Romero-Valdovinos M, Martinez A, Maravilla P, Martinez-Hernandez F. Genetic Variation among the Partial Gene Sequences of the Ribosomal Protein Large-Two, the Internal Transcribed Spacer, and the Small Ribosomal Subunit of Blastocystis sp. from Human Fecal Samples. Microorganisms 2024; 12:1152. [PMID: 38930533 PMCID: PMC11205392 DOI: 10.3390/microorganisms12061152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 06/01/2024] [Accepted: 06/04/2024] [Indexed: 06/28/2024] Open
Abstract
In the present study, we compared the genetic variability of fragments from the internal transcribed spacer region (ITS) and the small subunit ribosomal DNA (SSUrDNA) as nuclear markers, in contrast with the ribosomal protein large two (rpl2) loci, placed in the mitochondrion-related organelles (MROs) within and among human fecal samples with Blastocystis. Samples were analyzed using polymerase chain reaction (PCR)-sequencing, phylogenies, and genetics of population structure analyses were performed. In total, 96 sequences were analyzed, i.e., 33 of SSUrDNA, 35 of rpl2, and 28 of ITS. Only three subtypes (STs) were identified, i.e., ST1 (11.4%), ST2 (28.6%), and ST3 (60%); in all cases, kappa indexes were 1, meaning a perfect agreement among ST assignations. The topologies of phylogenetic inferences were similar among them, clustering to each ST in its specific cluster; discrepancies between phylogeny and assignment of STs were not observed. The STRUCTURE v2.3.4 software assigned three subpopulations corresponding to the STs 1-3, respectively. The population indices were consistent with those previously reported by other groups. Our results suggest the potential use of the ITS and rpl2 genes as molecular markers for Blastocystis subtyping as an alternative approach for the study of the genetic diversity observed within and between human isolates of this microorganism.
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Affiliation(s)
- Guiehdani Villalobos
- Departamento de Produccion Agricola y Animal, Universidad Autonoma Metropolitana, Mexico City 04960, Mexico;
| | - Eduardo Lopez-Escamilla
- Departamento de Biologia Molecular e Histocompatibilidad, Hospital General “Dr. Manuel Gea Gonzalez”, Mexico City 14080, Mexico; (E.L.-E.); (A.O.-D.)
| | - Angelica Olivo-Diaz
- Departamento de Biologia Molecular e Histocompatibilidad, Hospital General “Dr. Manuel Gea Gonzalez”, Mexico City 14080, Mexico; (E.L.-E.); (A.O.-D.)
| | - Mirza Romero-Valdovinos
- Laboratorio de Patogenos Emergentes, Departamento de Biologia Molecular e Histocompatibilidad, Hospital General “Dr. Manuel Gea Gonzalez”, Mexico City 14080, Mexico;
| | - Arony Martinez
- Departamento de Ecologia de Agentes Patogenos, Hospital General “Dr. Manuel Gea Gonzalez”, Mexico City 14080, Mexico;
| | - Pablo Maravilla
- Departamento de Ecologia de Agentes Patogenos, Hospital General “Dr. Manuel Gea Gonzalez”, Mexico City 14080, Mexico;
| | - Fernando Martinez-Hernandez
- Departamento de Ecologia de Agentes Patogenos, Hospital General “Dr. Manuel Gea Gonzalez”, Mexico City 14080, Mexico;
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Cabrera-Sosa L, Nolasco O, Kattenberg JH, Fernandez-Miñope C, Valdivia HO, Barazorda K, Rios SADL, Rodriguez-Ferrucci H, Vinetz JM, Rosanas-Urgell A, Geertruyden JPV, Gamboa D, Delgado-Ratto C. Genomic surveillance of malaria parasites in an indigenous community in the Peruvian Amazon. RESEARCH SQUARE 2024:rs.3.rs-3979991. [PMID: 38464169 PMCID: PMC10925399 DOI: 10.21203/rs.3.rs-3979991/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Hard-to-reach communities represent Peru's main challenge for malaria elimination, but information about transmission in these areas is scarce. Here, we assessed Plasmodium vivax (Pv) and P. falciparum (Pf) transmission dynamics, resistance markers, and Pf hrp2/3 deletions in Nueva Jerusalén (NJ), a remote, indigenous community in the Peruvian Amazon with high population mobility. We collected samples from November 2019 to May 2020 by active (ACD) and passive case detection (PCD) in NJ. Parasites were identified with microscopy and PCR. Then, we analyzed a representative set of positive-PCR samples (Pv = 68, Pf = 58) using highly-multiplexed deep sequencing assays (AmpliSeq) and compared NJ parasites with ones from other remote Peruvian areas using population genetics indexes. The ACD intervention did not reduce malaria cases in the short term, and persistent malaria transmission was observed (at least one Pv infection was detected in 96% of the study days). In Nueva Jerusalen, the Pv population had modest genetic diversity (He = 0.27). Pf population had lower diversity (He = 0.08) and presented temporal clustering, one of these clusters linked to an outbreak in February 2020. Moreover, Pv and Pf parasites from NJ exhibited variable levels of differentiation (Pv Fst = -0.52 & Pf Fst = 0.11-0.58) with parasites from other remote areas. No artemisin resistance mutations but chloroquine (57%) and sulfadoxine-pyrimethamine (35-67%) were detected in NJ's Pf parasites. Moreover, pfhrp2/3 gene deletions were common (32-50% of parasites with one or both genes deleted). The persistent Pv transmission and the detection of a Pf outbreak with parasites genetically distinct from the local ones highlight the need for tailored interventions focusing on mobility patterns and imported infections in remote areas to eliminate malaria in the Peruvian Amazon.
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Affiliation(s)
- Luis Cabrera-Sosa
- Laboratorio de Malaria: Parásitos y Vectores, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias e Ingeniería, Universidad Peruana Cayetano Heredia
| | - Oscar Nolasco
- Laboratorio de Malaria: Parásitos y Vectores, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias e Ingeniería, Universidad Peruana Cayetano Heredia
| | | | - Carlos Fernandez-Miñope
- Malaria Research group (MaRch), Global Health Institute, Family Medicine and Population Health department, Faculty of Medicine, University of Antwerp
| | - Hugo O Valdivia
- Department of Parasitology, U.S. Naval Medical Research Unit SOUTH (NAMRU SOUTH)
| | - Keare Barazorda
- Department of Parasitology, U.S. Naval Medical Research Unit SOUTH (NAMRU SOUTH)
| | | | | | - Joseph M Vinetz
- Section of Infectious Diseases, Department of Internal Medicine, Yale School of Medicine
| | | | - Jean-Pierre Van Geertruyden
- Malaria Research group (MaRch), Global Health Institute, Family Medicine and Population Health department, Faculty of Medicine, University of Antwerp
| | - Dionicia Gamboa
- Laboratorio de Malaria: Parásitos y Vectores, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias e Ingeniería, Universidad Peruana Cayetano Heredia
| | - Christopher Delgado-Ratto
- Malaria Research group (MaRch), Global Health Institute, Family Medicine and Population Health department, Faculty of Medicine, University of Antwerp
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McCracken GR, Gaston D, Pettipas J, Loder A, Majer A, Grudeski E, Labbé G, Joy BK, Patriquin G, LeBlanc JJ. Neglected SARS-CoV-2 variants and potential concerns for molecular diagnostics: a framework for nucleic acid amplification test target site quality assurance. Microbiol Spectr 2023; 11:e0076123. [PMID: 37815347 PMCID: PMC10715164 DOI: 10.1128/spectrum.00761-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 06/02/2023] [Indexed: 10/11/2023] Open
Abstract
IMPORTANCE Molecular tests like polymerase chain reaction were widely used during the COVID-19 pandemic but as the pandemic evolved, so did SARS-CoV-2. This virus acquired mutations, prompting concerns that mutations could compromise molecular test results and be falsely negative. While some manufacturers may have in-house programs for monitoring mutations that could impact their assay performance, it is important to promptly report mutations in circulating viral strains that could adversely impact a diagnostic test result. However, commercial test target sites are proprietary, making independent monitoring difficult. In this study, SARS-CoV-2 test target sites were sequenced to monitor and assess mutations impact, and 29 novel mutations impacting SARS-CoV-2 detection were identified. This framework for molecular test target site quality assurance could be adapted to any molecular test, ensuring accurate diagnostic test results and disease diagnoses.
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Affiliation(s)
- Gregory R. McCracken
- Division of Microbiology, Department of Pathology and Laboratory Medicine, Nova Scotia Health (NSH), Halifax, Nova Scotia, Canada
| | - Daniel Gaston
- Department of Pathology, Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia, Canada
- Division of Hematopathology, Department of Pathology and Laboratory Medicine, Nova Scotia Health (NSH), Halifax, Nova Scotia, Canada
| | - Janice Pettipas
- Nova Scotia Provincial Public Health Laboratory Network (PPHLN), Halifax, Nova Scotia, Canada
| | - Allana Loder
- National Microbiology Laboratory (NML), Public Health Agency of Canada (PHAC), Winnipeg, Manitoba, Canada
| | - Anna Majer
- National Microbiology Laboratory (NML), Public Health Agency of Canada (PHAC), Winnipeg, Manitoba, Canada
| | - Elsie Grudeski
- National Microbiology Laboratory (NML), Public Health Agency of Canada (PHAC), Winnipeg, Manitoba, Canada
| | - Geneviève Labbé
- National Microbiology Laboratory (NML), Public Health Agency of Canada (PHAC), Winnipeg, Manitoba, Canada
| | - Bryn K. Joy
- Medical Sciences Program, Faculty of Sciences, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Glenn Patriquin
- Division of Microbiology, Department of Pathology and Laboratory Medicine, Nova Scotia Health (NSH), Halifax, Nova Scotia, Canada
- Department of Pathology, Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Jason J. LeBlanc
- Division of Microbiology, Department of Pathology and Laboratory Medicine, Nova Scotia Health (NSH), Halifax, Nova Scotia, Canada
- Department of Pathology, Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia, Canada
- Department of Medicine (Infectious Diseases), Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia, Canada
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