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Lancaster AK, Single RM, Mack SJ, Sochat V, Mariani MP, Webster GD. PyPop: a mature open-source software pipeline for population genomics. Front Immunol 2024; 15:1378512. [PMID: 38629078 PMCID: PMC11019567 DOI: 10.3389/fimmu.2024.1378512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 03/08/2024] [Indexed: 04/19/2024] Open
Abstract
Python for Population Genomics (PyPop) is a software package that processes genotype and allele data and performs large-scale population genetic analyses on highly polymorphic multi-locus genotype data. In particular, PyPop tests data conformity to Hardy-Weinberg equilibrium expectations, performs Ewens-Watterson tests for selection, estimates haplotype frequencies, measures linkage disequilibrium, and tests significance. Standardized means of performing these tests is key for contemporary studies of evolutionary biology and population genetics, and these tests are central to genetic studies of disease association as well. Here, we present PyPop 1.0.0, a new major release of the package, which implements new features using the more robust infrastructure of GitHub, and is distributed via the industry-standard Python Package Index. New features include implementation of the asymmetric linkage disequilibrium measures and, of particular interest to the immunogenetics research communities, support for modern nomenclature, including colon-delimited allele names, and improvements to meta-analysis features for aggregating outputs for multiple populations. Code available at: https://zenodo.org/records/10080668 and https://github.com/alexlancaster/pypop.
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Affiliation(s)
- Alexander K. Lancaster
- Amber Biology LLC, Cambridge, MA, United States
- Ronin Institute, Montclair, NJ, United States
- Institute for Globally Distributed Open Research and Education (IGDORE), Cambridge, MA, United States
| | - Richard M. Single
- Department of Mathematics and Statistics, University of Vermont, Burlington, VT, United States
| | - Steven J. Mack
- Department of Pediatrics, University of California, San Francisco, Oakland, CA, United States
| | - Vanessa Sochat
- Livermore Computing, Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Michael P. Mariani
- Department of Mathematics and Statistics, University of Vermont, Burlington, VT, United States
- Mariani Systems LLC, Hanover, NH, United States
| | - Gordon D. Webster
- Amber Biology LLC, Cambridge, MA, United States
- Ronin Institute, Montclair, NJ, United States
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2
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Kattenberg JH, Monsieurs P, De Meyer J, De Meulenaere K, Sauve E, de Oliveira TC, Ferreira MU, Gamboa D, Rosanas‐Urgell A. Population genomic evidence of structured and connected Plasmodium vivax populations under host selection in Latin America. Ecol Evol 2024; 14:e11103. [PMID: 38529021 PMCID: PMC10961478 DOI: 10.1002/ece3.11103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 02/15/2024] [Accepted: 02/20/2024] [Indexed: 03/27/2024] Open
Abstract
Pathogen genomic epidemiology has the potential to provide a deep understanding of population dynamics, facilitating strategic planning of interventions, monitoring their impact, and enabling timely responses, and thereby supporting control and elimination efforts of parasitic tropical diseases. Plasmodium vivax, responsible for most malaria cases outside Africa, shows high genetic diversity at the population level, driven by factors like sub-patent infections, a hidden reservoir of hypnozoites, and early transmission to mosquitoes. While Latin America has made significant progress in controlling Plasmodium falciparum, it faces challenges with residual P. vivax. To characterize genetic diversity and population structure and dynamics, we have analyzed the largest collection of P. vivax genomes to date, including 1474 high-quality genomes from 31 countries across Asia, Africa, Oceania, and America. While P. vivax shows high genetic diversity globally, Latin American isolates form a distinctive population, which is further divided into sub-populations and occasional clonal pockets. Genetic diversity within the continent was associated with the intensity of transmission. Population differentiation exists between Central America and the North Coast of South America, vs. the Amazon Basin, with significant gene flow within the Amazon Basin, but limited connectivity between the Northwest Coast and the Amazon Basin. Shared genomic regions in these parasite populations indicate adaptive evolution, particularly in genes related to DNA replication, RNA processing, invasion, and motility - crucial for the parasite's survival in diverse environments. Understanding these population-level adaptations is crucial for effective control efforts, offering insights into potential mechanisms behind drug resistance, immune evasion, and transmission dynamics.
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Affiliation(s)
| | - Pieter Monsieurs
- Malariology UnitInstitute of Tropical Medicine AntwerpAntwerpBelgium
| | - Julie De Meyer
- Malariology UnitInstitute of Tropical Medicine AntwerpAntwerpBelgium
- Present address:
Integrated Molecular Plant physiology Research (IMPRES) and Plants and Ecosystems (PLECO), Department of BiologyUniversity of AntwerpAntwerpBelgium
| | | | - Erin Sauve
- Malariology UnitInstitute of Tropical Medicine AntwerpAntwerpBelgium
| | - Thaís C. de Oliveira
- Department of Parasitology, Institute of Biomedical SciencesUniversity of São PauloSão PauloBrazil
| | - Marcelo U. Ferreira
- Department of Parasitology, Institute of Biomedical SciencesUniversity of São PauloSão PauloBrazil
- Global Health and Tropical Medicine, Institute of Hygiene and Tropical MedicineNova University of LisbonLisbonPortugal
| | - Dionicia Gamboa
- Instituto de Medicina Tropical “Alexander von Humboldt”Universidad Peruana Cayetano HerediaLimaPeru
- Laboratorio de Malaria: Parásitos y Vectores, Laboratorios de Investigación y Desarrollo, Departamento de Ciencias Celulares y Moleculares, Facultad de Ciencias e IngenieríaUniversidad Peruana Cayetano HerediaLimaPeru
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Torres K, Ferreira MU, Castro MC, Escalante AA, Conn JE, Villasis E, da Silva Araujo M, Almeida G, Rodrigues PT, Corder RM, Fernandes ARJ, Calil PR, Ladeia WA, Garcia-Castillo SS, Gomez J, do Valle Antonelli LR, Gazzinelli RT, Golenbock DT, Llanos-Cuentas A, Gamboa D, Vinetz JM. Malaria Resilience in South America: Epidemiology, Vector Biology, and Immunology Insights from the Amazonian International Center of Excellence in Malaria Research Network in Peru and Brazil. Am J Trop Med Hyg 2022; 107:168-181. [PMID: 36228921 PMCID: PMC9662219 DOI: 10.4269/ajtmh.22-0127] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 05/28/2022] [Indexed: 11/07/2022] Open
Abstract
The 1990s saw the rapid reemergence of malaria in Amazonia, where it remains an important public health priority in South America. The Amazonian International Center of Excellence in Malaria Research (ICEMR) was designed to take a multidisciplinary approach toward identifying novel malaria control and elimination strategies. Based on geographically and epidemiologically distinct sites in the Northeastern Peruvian and Western Brazilian Amazon regions, synergistic projects integrate malaria epidemiology, vector biology, and immunology. The Amazonian ICEMR's overarching goal is to understand how human behavior and other sociodemographic features of human reservoirs of transmission-predominantly asymptomatically parasitemic people-interact with the major Amazonian malaria vector, Nyssorhynchus (formerly Anopheles) darlingi, and with human immune responses to maintain malaria resilience and continued endemicity in a hypoendemic setting. Here, we will review Amazonian ICEMR's achievements on the synergies among malaria epidemiology, Plasmodium-vector interactions, and immune response, and how those provide a roadmap for further research, and, most importantly, point toward how to achieve malaria control and elimination in the Americas.
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Affiliation(s)
- Katherine Torres
- Institute of Tropical Medicine Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Marcelo U. Ferreira
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, Sao Paulo, Brazil
| | - Marcia C. Castro
- Department of Global Health and Population, Harvard T. H. Chan School of Public Health, Boston, Massachusetts
| | - Ananias A. Escalante
- Department of Biology and Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, Pennsylvania
| | - Jan E. Conn
- Department of Biomedical Sciences, School of Public Health, University at Albany, State University of New York, Albany, New York
- Wadsworth Center, New York State Department of Health, Albany, New York
| | - Elizabeth Villasis
- Institute of Tropical Medicine Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | | | - Gregorio Almeida
- Instituto de Pesquisas Rene Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Brazil
| | - Priscila T. Rodrigues
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, Sao Paulo, Brazil
| | - Rodrigo M. Corder
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, Sao Paulo, Brazil
| | - Anderson R. J. Fernandes
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, Sao Paulo, Brazil
| | - Priscila R. Calil
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, Sao Paulo, Brazil
| | - Winni A. Ladeia
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, Sao Paulo, Brazil
| | - Stefano S. Garcia-Castillo
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Joaquin Gomez
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | | | - Ricardo T. Gazzinelli
- Instituto de Pesquisas Rene Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Brazil
- Division of Infectious Disease and Immunology, Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Douglas T. Golenbock
- Division of Infectious Disease and Immunology, Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Alejandro Llanos-Cuentas
- Institute of Tropical Medicine Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Dionicia Gamboa
- Institute of Tropical Medicine Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Joseph M. Vinetz
- Institute of Tropical Medicine Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
- Section of Infectious Diseases, Department of Internal Medicine, Yale School of Medicine, New Haven, Connecticut
- Address correspondence to Joseph M. Vinetz, Section of Infectious Diseases, Department of Internal Medicine, Yale School of Medicine, 25 York St., Winchester 403D, PO Box 802022, New Haven, CT 06520. E-mail:
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4
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Brashear AM, Cui L. Population genomics in neglected malaria parasites. Front Microbiol 2022; 13:984394. [PMID: 36160257 PMCID: PMC9493318 DOI: 10.3389/fmicb.2022.984394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 08/22/2022] [Indexed: 11/13/2022] Open
Abstract
Malaria elimination includes neglected human malaria parasites Plasmodium vivax, Plasmodium ovale spp., and Plasmodium malariae. Biological features such as association with low-density infection and the formation of hypnozoites responsible for relapse make their elimination challenging. Studies on these parasites rely primarily on clinical samples due to the lack of long-term culture techniques. With improved methods to enrich parasite DNA from clinical samples, whole-genome sequencing of the neglected malaria parasites has gained increasing popularity. Population genomics of more than 2200 P. vivax global isolates has improved our knowledge of parasite biology and host-parasite interactions, identified vaccine targets and potential drug resistance markers, and provided a new way to track parasite migration and introduction and monitor the evolutionary response of local populations to elimination efforts. Here, we review advances in population genomics for neglected malaria parasites, discuss how the rich genomic information is being used to understand parasite biology and epidemiology, and explore opportunities for the applications of malaria genomic data in malaria elimination practice.
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5
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Wetzler EA, Marchesini P, Villegas L, Canavati S. Changing transmission dynamics among migrant, indigenous and mining populations in a malaria hotspot in Northern Brazil: 2016 to 2020. Malar J 2022; 21:127. [PMID: 35439994 PMCID: PMC9018056 DOI: 10.1186/s12936-022-04141-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 03/28/2022] [Indexed: 12/05/2022] Open
Abstract
Background Roraima state is the northernmost state in Brazil and the primary border-crossing point between Brazil and Venezuela. The uncontrolled surge of malaria in Venezuela, coupled with mass migration of Venezuelans to neighbouring countries and the upward trend in informal mining in the state, pose a serious threat to the broader region, especially to migrant, indigenous and mining populations, jeopardizing malaria elimination efforts. This study describes changes in the epidemiological profile of malaria in Roraima state related to time, place and populations at risk from 2016 to 2020. Methods De-identified malaria surveillance data were obtained from the Malaria Epidemiological Surveillance System from 2016 to 2020. Pearson’s chi-square tested differences between imported and autochthonous cases. Multivariable logistic regression was used to identify risk factors for imported versus autochthonous cases by demographic characteristics. Results Odds of being an imported case were higher for Plasmodium falciparum cases (AOR = 2.08). However, as the number of cases from Venezuela decreased in 2020 following closure of the border, the proportion of P. falciparum cases increased markedly, from 6.24% in 2019 to 18.50% in 2020. Over the 5-year period, the odds of being an imported case among miners were about nine times higher than the general population (AOR = 8.99). The proportion of total malaria cases that were among indigenous people increased from 33.09% in 2016 to 54.83% in 2020. Indigenous children had a higher burden of malaria with over 40% of cases in children 0 to 9 years old, compared to 8% in non-indigenous children 0 to 9 years old. In some municipalities, place of infection differed from place of notification, with a large proportion of cases in these municipalities reporting in Boa Vista. Conclusions Malaria remains a serious threat in Roraima state, especially among high-risk populations, such as miners, migrants, and indigenous people. As malaria cases have increased among indigenous people and miners, and the proportion of P. falciparum cases has increased, elimination efforts require understanding of these risk factors to tailor interventions appropriately. Furthermore, cross-border surveillance systems need to be urgently strengthened at formal and unofficial border points, especially since the border with Venezuela reopened in July 2021. Supplementary Information The online version contains supplementary material available at 10.1186/s12936-022-04141-6.
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Affiliation(s)
- Erica Anne Wetzler
- World Vision US, 34834 Weyerhaeuser Way South Federal Way, Washington, USA.
| | - Paola Marchesini
- Department of Surveillance for Zoonotic and Vector Borne Diseases, Ministry of Health, Brasilia, Federal District, Brazil
| | - Leopoldo Villegas
- Association for Social and Civil Impact (ASOCIS), Tumeremo, Venezuela.,Global Development One, Silver Spring, MD, USA
| | - Sara Canavati
- World Vision US, 34834 Weyerhaeuser Way South Federal Way, Washington, USA
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Hashemi M, Schneider KA. Bias-corrected maximum-likelihood estimation of multiplicity of infection and lineage frequencies. PLoS One 2021; 16:e0261889. [PMID: 34965279 PMCID: PMC8716058 DOI: 10.1371/journal.pone.0261889] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Accepted: 12/13/2021] [Indexed: 11/19/2022] Open
Abstract
Background The UN’s Sustainable Development Goals are devoted to eradicate a range of infectious diseases to achieve global well-being. These efforts require monitoring disease transmission at a level that differentiates between pathogen variants at the genetic/molecular level. In fact, the advantages of genetic (molecular) measures like multiplicity of infection (MOI) over traditional metrics, e.g., R0, are being increasingly recognized. MOI refers to the presence of multiple pathogen variants within an infection due to multiple infective contacts. Maximum-likelihood (ML) methods have been proposed to derive MOI and pathogen-lineage frequencies from molecular data. However, these methods are biased. Methods and findings Based on a single molecular marker, we derive a bias-corrected ML estimator for MOI and pathogen-lineage frequencies. We further improve these estimators by heuristical adjustments that compensate shortcomings in the derivation of the bias correction, which implicitly assumes that data lies in the interior of the observational space. The finite sample properties of the different variants of the bias-corrected estimators are investigated by a systematic simulation study. In particular, we investigate the performance of the estimator in terms of bias, variance, and robustness against model violations. The corrections successfully remove bias except for extreme parameters that likely yield uninformative data, which cannot sustain accurate parameter estimation. Heuristic adjustments further improve the bias correction, particularly for small sample sizes. The bias corrections also reduce the estimators’ variances, which coincide with the Cramér-Rao lower bound. The estimators are reasonably robust against model violations. Conclusions Applying bias corrections can substantially improve the quality of MOI estimates, particularly in areas of low as well as areas of high transmission—in both cases estimates tend to be biased. The bias-corrected estimators are (almost) unbiased and their variance coincides with the Cramér-Rao lower bound, suggesting that no further improvements are possible unless additional information is provided. Additional information can be obtained by combining data from several molecular markers, or by including information that allows stratifying the data into heterogeneous groups.
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Affiliation(s)
- Meraj Hashemi
- Department of Applied Computer- and Biosciences, University of Applied Sciences Mittweida, Mittweida, Germany
- * E-mail:
| | - Kristan A. Schneider
- Department of Applied Computer- and Biosciences, University of Applied Sciences Mittweida, Mittweida, Germany
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Auburn S, Cheng Q, Marfurt J, Price RN. The changing epidemiology of Plasmodium vivax: Insights from conventional and novel surveillance tools. PLoS Med 2021; 18:e1003560. [PMID: 33891580 PMCID: PMC8064506 DOI: 10.1371/journal.pmed.1003560] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Sarah Auburn and co-authors discuss the unique biology and epidemiology of P. vivax and current evidence on conventional and new approaches to surveillance.
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Affiliation(s)
- Sarah Auburn
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Australia
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Qin Cheng
- Department of Drug Resistance and Diagnostics, Australian Defence Force Malaria and Infectious Disease Institute, Brisbane, Australia
- The Australian Defence Force Malaria and Infectious Disease Institute Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Jutta Marfurt
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Australia
| | - Ric N. Price
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Australia
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
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Grillet ME, Moreno JE, Hernández-Villena JV, Vincenti-González MF, Noya O, Tami A, Paniz-Mondolfi A, Llewellyn M, Lowe R, Escalante AA, Conn JE. Malaria in Southern Venezuela: The hottest hotspot in Latin America. PLoS Negl Trop Dis 2021; 15:e0008211. [PMID: 33493212 PMCID: PMC7861532 DOI: 10.1371/journal.pntd.0008211] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 02/04/2021] [Accepted: 11/25/2020] [Indexed: 12/11/2022] Open
Abstract
Malaria elimination in Latin America is becoming an elusive goal. Malaria cases reached a historical ~1 million in 2017 and 2018, with Venezuela contributing 53% and 51% of those cases, respectively. Historically, malaria incidence in southern Venezuela has accounted for most of the country's total number of cases. The efficient deployment of disease prevention measures and prediction of disease spread to new regions requires an in-depth understanding of spatial heterogeneity on malaria transmission dynamics. Herein, we characterized the spatial epidemiology of malaria in southern Venezuela from 2007 through 2017 and described the extent to which malaria distribution has changed country-wide over the recent years. We found that disease transmission was focal and more prevalent in the southeast region of southern Venezuela where two persistent hotspots of Plasmodium vivax (76%) and P. falciparum (18%) accounted for ~60% of the total number of cases. Such hotspots are linked to deforestation as a consequence of illegal gold mining activities. Incidence has increased nearly tenfold over the last decade, showing an explosive epidemic growth due to a significant lack of disease control programs. Our findings highlight the importance of spatially oriented interventions to contain the ongoing malaria epidemic in Venezuela. This work also provides baseline epidemiological data to assess cross-border malaria dynamics and advocates for innovative control efforts in the Latin American region.
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Affiliation(s)
- Maria Eugenia Grillet
- Laboratorio de Biología de Vectores y Parásitos, Instituto de Zoología y Ecología Tropical, Facultad de Ciencias, Universidad Central de Venezuela. Caracas, Venezuela
- * E-mail: ,
| | - Jorge E. Moreno
- Centro de Investigaciones de Campo “Dr. Francesco Vitanza,” Servicio Autónomo Instituto de Altos Estudios “Dr. Arnoldo Gabaldón,” MPPS. Tumeremo, Bolívar, Venezuela
| | - Juan V. Hernández-Villena
- Laboratorio de Biología de Vectores y Parásitos, Instituto de Zoología y Ecología Tropical, Facultad de Ciencias, Universidad Central de Venezuela. Caracas, Venezuela
| | - Maria F. Vincenti-González
- Department of Medical Microbiology, University Medical Center Groningen, University of Groningen. Groningen, The Netherlands
| | - Oscar Noya
- Instituto de Medicina Tropical, Facultad de Medicina, Universidad Central de Venezuela. Caracas, Venezuela
- Centro para Estudios Sobre Malaria, Instituto de Altos Estudios “Dr. Arnoldo Gabaldón”, MPPS. Caracas, Venezuela
| | - Adriana Tami
- Department of Medical Microbiology, University Medical Center Groningen, University of Groningen. Groningen, The Netherlands
- Departamento de Parasitología, Facultad de Ciencias de la Salud, Universidad de Carabobo. Valencia, Venezuela
| | - Alberto Paniz-Mondolfi
- Incubadora Venezolana de la Ciencia-IDB. Barquisimeto, Venezuela
- Icahn School of Medicine at Mount Sinai. New York, United States of America
| | - Martin Llewellyn
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow. Glasgow, Scotland, United Kingdom
| | - Rachel Lowe
- Centre on Climate Change and Planetary Health, London School of Hygiene and Tropical Medicine. London, United Kingdom
- Barcelona Institute for Global Health-ISGlobal. Barcelona, Spain
| | - Ananías A. Escalante
- Institute for Genomics and Evolutionary Medicine, Temple University. Philadelphia, United States of America
| | - Jan E. Conn
- Griffin Laboratory, Wadsworth Center, New York State Department of Health. Albany, New York, United States of America
- Department of Biomedical Sciences, School of Public Health, University at Albany—State University of New York. Albany, New York, United States of America
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Gomes MFC, Codeço CT, Bastos LS, Lana RM. Measuring the contribution of human mobility to malaria persistence. Malar J 2020; 19:404. [PMID: 33176792 PMCID: PMC7659106 DOI: 10.1186/s12936-020-03474-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 10/31/2020] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND To achieve malaria elimination, it is important to determine the role of human mobility in parasite transmission maintenance. The Alto Juruá basin (Brazil) exhibits one of the largest vivax and falciparum malaria prevalence in the Amazon. The goal of this study was to estimate the contribution of human commutes to malaria persistence in this region, using data from an origin-destination survey. METHODS Data from an origin-destination survey were used to describe the intensity and motivation for commutations between rural and urban areas in two Alto Juruá basin (Brazil) municipalities, Mâncio Lima and Rodrigues Alves. The relative time-person spent in each locality per household was estimated. A logistic model was developed to estimate the effect of commuting on the probability of contracting malaria for a certain residence zone inhabitant commuting to another zone. RESULTS The main results suggest that the assessed population is not very mobile. A total of [Formula: see text] households reported spending over [Formula: see text] of their annual person-hour in areas within the same residence zone. Study and work were the most prevalent commuting motivations, calculated at [Formula: see text] and [Formula: see text] respectively. Spending person-hours in urban Rodrigues Alves conferred relative protection to urban Mâncio Lima residents. The opposite effect was observed for those spending time in rural areas of both municipalities. CONCLUSION Residence area is a stronger determinant for contracting malaria than commuting zones in the Alto Juruá region. As these municipalities are a hotspot for Plasmodium transmission, understanding the main local human fluxes is essential for planning control strategies, since the probability of contracting malaria is dependent on the transmission intensity of both the origin and the displacement area. The natural conditions for the circulation of certain pathogens, such as Plasmodium spp., combined with the Amazon human mobility pattern indicate the need for disease control perspective changes. Therefore, intersectoral public policies should become the basis for health mitigation actions.
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Affiliation(s)
- Marcelo F C Gomes
- Programa de Computação Científica, Fundação Oswaldo Cruz, Avenida Brasil, 4365, Manguinhos, 21040-900, Rio de Janeiro, Brazil.
| | - Cláudia T Codeço
- Programa de Computação Científica, Fundação Oswaldo Cruz, Avenida Brasil, 4365, Manguinhos, 21040-900, Rio de Janeiro, Brazil
| | - Leonardo S Bastos
- Programa de Computação Científica, Fundação Oswaldo Cruz, Avenida Brasil, 4365, Manguinhos, 21040-900, Rio de Janeiro, Brazil
| | - Raquel M Lana
- Programa de Computação Científica, Fundação Oswaldo Cruz, Avenida Brasil, 4365, Manguinhos, 21040-900, Rio de Janeiro, Brazil
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10
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Almeida-de-Oliveira NK, de Abreu-Fernandes R, Lima-Cury L, de Lavigne AR, de Pina-Costa A, Perce-da-Silva DDS, Catanho M, Rossi AD, Brasil P, Tadeu Daniel-Ribeiro C, Ferreira-da-Cruz MDF. Balancing selection and high genetic diversity of Plasmodium vivax circumsporozoite central region in parasites from Brazilian Amazon and Rio de Janeiro Atlantic Forest. PLoS One 2020; 15:e0241426. [PMID: 33166298 PMCID: PMC7652573 DOI: 10.1371/journal.pone.0241426] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 10/14/2020] [Indexed: 11/19/2022] Open
Abstract
Circumsporozoite protein (CSP) is the primary pre-erythrocytic vaccine target in Plasmodium species. Knowledge about their genetic diversity can help predict vaccine efficacy and the spread of novel parasite variants. Thus, we investigated pvcsp gene polymorphisms in 219 isolates (136 from Brazilian Amazon [BA], 71 from Rio de Janeiro Atlantic Forest [AF], and 12 from non-Brazilian countries [NB]). Forty-eight polymorphic sites were detected, 46 in the central repeat region (CR), and two in the C-terminal region. Also, the CR presents InDels and a variable number of repeats. All samples correspond to the VK210 variant, and 24 VK210 subtypes based on CR. Nucleotide diversity (π = 0.0135) generated a significant number of haplotypes (168) with low genetic differentiation between the Brazilian regions (Fst = 0.208). The haplotype network revealed similar distances among the BA and AF regions. The linkage disequilibrium indicates that recombination does not seem to be acting in diversity, reinforcing natural selection's role in accelerating adaptive evolution. The high diversity (low Fst) and polymorphism frequencies could be indicators of balancing selection. Although malaria in BA and AF have distinct vector species and different host immune pressures, consistent genetic signature was found in two regions. The immunodominant B-cell epitope mapped in the CR varies from seven to 19 repeats. The CR T-cell epitope is conserved only in 39 samples. Concerning to C-terminal region, the Th2R epitope presented nonsynonymous SNP only in 6% of Brazilian samples, and the Th3R epitope remained conserved in all studied regions. We conclude that, although the uneven distribution of alleles may jeopardize the deployment of vaccines directed to a specific variable locus, a unique vaccine formulation could protect populations in all Brazilian regions.
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Affiliation(s)
- Natália Ketrin Almeida-de-Oliveira
- Laboratório de Pesquisa em Malária, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, Brazil
- Centro de Pesquisa, Diagnóstico e Treinamento em Malária (CPD-Mal), Reference Laboratory for Malaria in the Extra-Amazonian Region for the Brazilian Ministry of Health, SVS & Fiocruz, Rio de Janeiro, Brazil
| | - Rebecca de Abreu-Fernandes
- Laboratório de Pesquisa em Malária, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, Brazil
- Centro de Pesquisa, Diagnóstico e Treinamento em Malária (CPD-Mal), Reference Laboratory for Malaria in the Extra-Amazonian Region for the Brazilian Ministry of Health, SVS & Fiocruz, Rio de Janeiro, Brazil
| | - Lidiane Lima-Cury
- Laboratório de Pesquisa em Malária, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, Brazil
- Centro de Pesquisa, Diagnóstico e Treinamento em Malária (CPD-Mal), Reference Laboratory for Malaria in the Extra-Amazonian Region for the Brazilian Ministry of Health, SVS & Fiocruz, Rio de Janeiro, Brazil
| | - Aline Rosa de Lavigne
- Laboratório de Pesquisa em Malária, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, Brazil
- Centro de Pesquisa, Diagnóstico e Treinamento em Malária (CPD-Mal), Reference Laboratory for Malaria in the Extra-Amazonian Region for the Brazilian Ministry of Health, SVS & Fiocruz, Rio de Janeiro, Brazil
| | - Anielle de Pina-Costa
- Centro de Pesquisa, Diagnóstico e Treinamento em Malária (CPD-Mal), Reference Laboratory for Malaria in the Extra-Amazonian Region for the Brazilian Ministry of Health, SVS & Fiocruz, Rio de Janeiro, Brazil
- Laboratório de Pesquisa Clínica em Doenças Febris Agudas, Instituto Nacional de Infectologia Evandro Chagas, Fiocruz, Rio de Janeiro, Brazil
- Centro Universitário Serra dos Órgãos (UNIFESO), Teresópolis, Rio de Janeiro, Brazil
| | - Daiana de Souza Perce-da-Silva
- Laboratório de Pesquisa em Malária, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, Brazil
- Centro de Pesquisa, Diagnóstico e Treinamento em Malária (CPD-Mal), Reference Laboratory for Malaria in the Extra-Amazonian Region for the Brazilian Ministry of Health, SVS & Fiocruz, Rio de Janeiro, Brazil
| | - Marcos Catanho
- Laboratório de Genética Molecular de Microrganismos, IOC, Fiocruz, Rio de Janeiro, Brazil
| | - Atila Duque Rossi
- Laboratório de Virologia Molecular, Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, RJ, Brazil
| | - Patrícia Brasil
- Centro de Pesquisa, Diagnóstico e Treinamento em Malária (CPD-Mal), Reference Laboratory for Malaria in the Extra-Amazonian Region for the Brazilian Ministry of Health, SVS & Fiocruz, Rio de Janeiro, Brazil
- Laboratório de Pesquisa Clínica em Doenças Febris Agudas, Instituto Nacional de Infectologia Evandro Chagas, Fiocruz, Rio de Janeiro, Brazil
| | - Cláudio Tadeu Daniel-Ribeiro
- Laboratório de Pesquisa em Malária, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, Brazil
- Centro de Pesquisa, Diagnóstico e Treinamento em Malária (CPD-Mal), Reference Laboratory for Malaria in the Extra-Amazonian Region for the Brazilian Ministry of Health, SVS & Fiocruz, Rio de Janeiro, Brazil
| | - Maria de Fátima Ferreira-da-Cruz
- Laboratório de Pesquisa em Malária, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, Brazil
- Centro de Pesquisa, Diagnóstico e Treinamento em Malária (CPD-Mal), Reference Laboratory for Malaria in the Extra-Amazonian Region for the Brazilian Ministry of Health, SVS & Fiocruz, Rio de Janeiro, Brazil
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11
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Taylor AR, Echeverry DF, Anderson TJC, Neafsey DE, Buckee CO. Identity-by-descent with uncertainty characterises connectivity of Plasmodium falciparum populations on the Colombian-Pacific coast. PLoS Genet 2020; 16:e1009101. [PMID: 33196661 PMCID: PMC7704048 DOI: 10.1371/journal.pgen.1009101] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 11/30/2020] [Accepted: 09/08/2020] [Indexed: 01/09/2023] Open
Abstract
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.
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Affiliation(s)
- Aimee R. Taylor
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Diego F. Echeverry
- Centro Internacional de Entrenamiento e Investigaciones Médicas (CIDEIM), Cali, Colombia
- Universidad Icesi, Calle 18 No. 122-135, Cali, Colombia
- Departamento de Microbiologia, Facultad de Salud, Universidad del Valle, Cali, Colombia
| | - Timothy J. C. Anderson
- Disease Intervention and Prevention Program, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Daniel E. Neafsey
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Caroline O. Buckee
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
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12
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Pacheco MA, Forero-Peña DA, Schneider KA, Chavero M, Gamardo A, Figuera L, Kadakia ER, Grillet ME, Oliveira-Ferreira J, Escalante AA. Malaria in Venezuela: changes in the complexity of infection reflects the increment in transmission intensity. Malar J 2020; 19:176. [PMID: 32380999 PMCID: PMC7206825 DOI: 10.1186/s12936-020-03247-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 04/26/2020] [Indexed: 01/07/2023] Open
Abstract
Background Malaria incidence has reached staggering numbers in Venezuela. Commonly, Bolívar State accounted for approximately 70% of the country cases every year. Most cases cluster in the Sifontes municipality, a region characterized by an extractive economy, including gold mining. An increase in migration to Sifontes, driven by gold mining, fueled a malaria spillover to the rest of the country and the region. Here samples collected in 2018 were compared with a previous study of 2003/2004 to describe changes in the parasites population structures and the frequency of point mutations linked to anti-malarial drugs. Methods A total of 88 Plasmodium falciparum and 94 Plasmodium vivax isolates were collected in 2018 and compared with samples from 2003/2004 (106 P. falciparum and 104 P. vivax). For P. falciparum, mutations linked to drug resistance (Pfdhfr, Pfdhps, and Pfcrt) and the Pfk13 gene associated with artemisinin delayed parasite clearance, were analysed. To estimate the multiplicity of infection (MOI), and perform P. falciparum and P. vivax population genetic analyses, the parasites were genotyped by using eight standardized microsatellite loci. Results The P. falciparum parasites are still harbouring drug-resistant mutations in Pfdhfr, Pfdhps, and Pfcrt. However, there was a decrease in the frequency of highly resistant Pfdhps alleles. Mutations associated with artemisinin delayed parasite clearance in the Pfk13 gene were not found. Consistent with the increase in transmission, polyclonal infections raised from 1.9% in 2003/2004 to 39% in 2018 in P. falciparum and from 16.3 to 68% in P. vivax. There is also a decrease in linkage disequilibrium. Bayesian clustering yields two populations linked to the time of sampling, showing that the parasite populations temporarily changed. However, the samples from 2003/2004 and 2018 have several alleles per locus in common without sharing multi-locus genotypes. Conclusions The frequency of mutations linked with drug resistance in P. falciparum shows only changes in Pfdhps. Observations presented here are consistent with an increase in transmission from the previously circulating parasites. Following populations longitudinally, using molecular surveillance, provides valuable information in cases such as Venezuela with a fluid malaria situation that is affecting the regional goals toward elimination.
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Affiliation(s)
- M Andreína Pacheco
- Biology Department/Institute of Genomics and Evolutionary Medicine (iGEM), Temple University, Philadelphia, PA, USA
| | - David A Forero-Peña
- Escuela de Ciencias de la Salud, Universidad de Oriente, Núcleo Bolívar, Ciudad Bolívar, Venezuela.,Departamento de Medicina Interna, Complejo Hospitalario Universitario "Ruíz y Páez", Ciudad Bolívar, Venezuela.,Biomedical Research and Therapeutic Vaccines Institute, Ciudad Bolívar, Venezuela
| | | | - Melynar Chavero
- Escuela de Ciencias de la Salud, Universidad de Oriente, Núcleo Bolívar, Ciudad Bolívar, Venezuela.,Departamento de Medicina Interna, Complejo Hospitalario Universitario "Ruíz y Páez", Ciudad Bolívar, Venezuela.,Biomedical Research and Therapeutic Vaccines Institute, Ciudad Bolívar, Venezuela
| | - Angel Gamardo
- Biomedical Research and Therapeutic Vaccines Institute, Ciudad Bolívar, Venezuela
| | - Luisamy Figuera
- Departamento de Medicina Interna, Complejo Hospitalario Universitario "Ruíz y Páez", Ciudad Bolívar, Venezuela.,Biomedical Research and Therapeutic Vaccines Institute, Ciudad Bolívar, Venezuela
| | - Esha R Kadakia
- Biology Department/Institute of Genomics and Evolutionary Medicine (iGEM), Temple University, Philadelphia, PA, USA
| | - María E Grillet
- Instituto de Zoología y Ecología Tropical, Universidad Central de Venezuela, Caracas, Venezuela
| | | | - Ananias A Escalante
- Biology Department/Institute of Genomics and Evolutionary Medicine (iGEM), Temple University, Philadelphia, PA, USA.
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13
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Li Y, Hu Y, Zhao Y, Wang Q, Ngassa Mbenda HG, Kittichai V, Lawpoolsri S, Sattabongkot J, Menezes L, Liu X, Cui L, Cao Y. Dynamics of Plasmodium vivax populations in border areas of the Greater Mekong sub-region during malaria elimination. Malar J 2020; 19:145. [PMID: 32268906 PMCID: PMC7140319 DOI: 10.1186/s12936-020-03221-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Accepted: 04/03/2020] [Indexed: 12/18/2022] Open
Abstract
Background Countries within the Greater Mekong Sub-region (GMS) of Southeast Asia have committed to eliminating malaria by 2030. Although the malaria situation has greatly improved, malaria transmission remains at international border regions. In some areas, Plasmodium vivax has become the predominant parasite. To gain a better understanding of transmission dynamics, knowledge on the changes of P. vivax populations after the scale-up of control interventions will guide more effective targeted control efforts. Methods This study investigated genetic diversity and population structures in 206 P. vivax clinical samples collected at two time points in two international border areas: the China-Myanmar border (CMB) (n = 50 in 2004 and n = 52 in 2016) and Thailand-Myanmar border (TMB) (n = 50 in 2012 and n = 54 in 2015). Parasites were genotyped using 10 microsatellite markers. Results Despite intensified control efforts, genetic diversity remained high (HE = 0.66–0.86) and was not significantly different among the four populations (P > 0.05). Specifically, HE slightly decreased from 0.76 in 2004 to 0.66 in 2016 at the CMB and increased from 0.80 in 2012 to 0.86 in 2015 at the TMB. The proportions of polyclonal infections varied significantly among the four populations (P < 0.05), and showed substantial decreases from 48.0% in 2004 to 23.7 at the CMB and from 40.0% in 2012 to 30.7% in 2015 at the TMB, with corresponding decreases in the multiplicity of infection. Consistent with the continuous decline of malaria incidence in the GMS over time, there were also increases in multilocus linkage disequilibrium, suggesting more fragmented and increasingly inbred parasite populations. There were considerable genetic differentiation and sub-division among the four tested populations. Temporal genetic differentiation was observed at each site (FST = 0.081 at the CMB and FST = 0.133 at the TMB). Various degrees of clustering were evident between the older parasite samples collected in 2004 at the CMB and the 2016 CMB and 2012 TMB populations, suggesting some of these parasites had shared ancestry. In contrast, the 2015 TMB population was genetically distinctive, which may reflect a process of population replacement. Whereas the effective population size (Ne) at the CMB showed a decrease from 4979 in 2004 to 3052 in 2016 with the infinite allele model, the Ne at the TMB experienced an increase from 6289 to 10,259. Conclusions With enhanced control efforts on malaria, P. vivax at the TMB and CMB showed considerable spatial and temporal differentiation, but the presence of large P. vivax reservoirs still sustained genetic diversity and transmission. These findings provide new insights into P. vivax transmission dynamics and population structure in these border areas of the GMS. Coordinated and integrated control efforts on both sides of international borders are essential to reach the goal of regional malaria elimination.
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Affiliation(s)
- Yuling Li
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, 110122, Liaoning, China.,Emergency Department, The First Affiliated Hospital of Dalian Medical University, Dalian, 116011, Liaoning, China
| | - Yubing Hu
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, 110122, Liaoning, China
| | - Yan Zhao
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, 110122, Liaoning, China
| | - Qinghui Wang
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, 110122, Liaoning, China
| | - Huguette Gaelle Ngassa Mbenda
- Division of Infectious Diseases and International Medicine, Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA
| | - Veerayuth Kittichai
- Mahidol Vivax Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Saranath Lawpoolsri
- Mahidol Vivax Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Jetsumon Sattabongkot
- Mahidol Vivax Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Lynette Menezes
- Division of Infectious Diseases and International Medicine, Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA
| | - Xiaoming Liu
- Center for Global Health and Infectious Disease Research, College of Public Health, University of South Florida, Tampa, FL, 33612, USA
| | - Liwang Cui
- Division of Infectious Diseases and International Medicine, Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA. .,Center for Global Health and Infectious Disease Research, College of Public Health, University of South Florida, Tampa, FL, 33612, USA.
| | - Yaming Cao
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, 110122, Liaoning, China.
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14
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Abstract
Malaria is a vector-borne disease that involves multiple parasite species in a variety of ecological settings. However, the parasite species causing the disease, the prevalence of subclinical infections, the emergence of drug resistance, the scale-up of interventions, and the ecological factors affecting malaria transmission, among others, are aspects that vary across areas where malaria is endemic. Such complexities have propelled the study of parasite genetic diversity patterns in the context of epidemiologic investigations. Importantly, molecular studies indicate that the time and spatial distribution of malaria cases reflect epidemiologic processes that cannot be fully understood without characterizing the evolutionary forces shaping parasite population genetic patterns. Although broad in scope, this review in the Microbiology Spectrum Curated Collection: Advances in Molecular Epidemiology highlights the need for understanding population genetic concepts when interpreting parasite molecular data. First, we discuss malaria complexity in terms of the parasite species involved. Second, we describe how molecular data are changing our understanding of malaria incidence and infectiousness. Third, we compare different approaches to generate parasite genetic information in the context of epidemiologically relevant questions related to malaria control. Finally, we describe a few Plasmodium genomic studies as evidence of how these approaches will provide new insights into the malaria disease dynamics. *This article is part of a curated collection.
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15
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González-Cerón L, Rodríguez MH, Ovilla-Muñoz MT, Santillán-Valenzuela F, Hernández-Ávila JE, Rodríguez MC, Martínez-Barnetche J, Villarreal-Treviño C. Ookinete-Specific Genes and 18S SSU rRNA Evidenced in Plasmodium vivax Selection and Adaptation by Sympatric Vectors. Front Genet 2020; 10:1362. [PMID: 32153625 PMCID: PMC7047961 DOI: 10.3389/fgene.2019.01362] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 12/12/2019] [Indexed: 01/26/2023] Open
Abstract
In the southern Pacific coast of Chiapas, Mexico (SM), the two most abundant vector species, Nyssorhynchus albimanus and Anopheles pseudopunctipennis, were susceptible to different Plasmodium vivax Pvs25/28 haplotypes. To broaden our understanding of the existing P. vivax in the area, genes encoding proteins relevant for ookinete development and the 18S rRNA were studied. P. vivax infectivity (percentage of infected mosquitoes and oocyst numbers) was evaluated by simultaneously feeding infected blood samples from patients to Ny. albimanus and An. pseudopunctipennis female mosquitoes. Three infectivity patterns were identified: one group of parasites were more infective to An. pseudopunctipennis than to Ny. albimanus, another group was more infective to Ny. albimanus, while a third group infected both vectors similarly. In 29 parasite isolates, the molecular variations of ookinete-specific genes and the 18S rRNA-type S were analyzed. Using concatenated sequences, phylogenetic trees, and Structure analysis, parasite clustering within SM isolates and between these and those from other geographical origins were investigated. A ML phylogenetic tree resolved two parasite lineages: PvSM-A and PvSM-B. They were associated to a different 18S rRNA variant. PvSM-A parasites had 18S rRNA variant rV2 and correspond to parasites causing high oocyst infection in Ny. albimanus. A new ML tree and Structure analysis, both comprising global sequences, showed PvSM-A clustered with Latin American parasites. Meanwhile, all isolates of PvSM-B had 18S rRNA variant rV1 and remained as unique genetic cluster comprising two subgroups: PvSM-Ba, producing high infection in An. pseudopunctipennis, and PvSM-Bb, causing similar oocyst infection in both vector species. PvSM-A parasites were genetically similar to parasites from South America. Meanwhile, PvSM-B were exclusive to southern Mexico and share ancestry with Asian parasites. The results suggest that these lineages evolved separately, likely by geographic and vector restriction.
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Affiliation(s)
- Lilia González-Cerón
- Regional Center of Research in Public Health, National Institute of Public Health, Ministry of Health, Tapachula, Mexico
| | - Mario H Rodríguez
- Vector Borne Diseases, Center for Research on Infectious Diseases, National Institute of Public Health, Ministry of Health, Cuernavaca, Mexico
| | - Marbella T Ovilla-Muñoz
- Chronic Infections and Cancer, Center for Research on Infectious Diseases, National Institute of Public Health, Ministry of Health, Cuernavaca, Mexico
| | - Frida Santillán-Valenzuela
- Regional Center of Research in Public Health, National Institute of Public Health, Ministry of Health, Tapachula, Mexico
| | - Juan E Hernández-Ávila
- Center of Information for Public Health Decisions, National Institute of Public Health, Ministry of Health, Mexico City, Mexico
| | - María Carmen Rodríguez
- Vector Borne Diseases, Center for Research on Infectious Diseases, National Institute of Public Health, Ministry of Health, Cuernavaca, Mexico
| | - Jesús Martínez-Barnetche
- Chronic Infections and Cancer, Center for Research on Infectious Diseases, National Institute of Public Health, Ministry of Health, Cuernavaca, Mexico
| | - Cuauhtémoc Villarreal-Treviño
- Regional Center of Research in Public Health, National Institute of Public Health, Ministry of Health, Tapachula, Mexico
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16
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Nelson CS, Sumner KM, Freedman E, Saelens JW, Obala AA, Mangeni JN, Taylor SM, O'Meara WP. High-resolution micro-epidemiology of parasite spatial and temporal dynamics in a high malaria transmission setting in Kenya. Nat Commun 2019; 10:5615. [PMID: 31819062 PMCID: PMC6901486 DOI: 10.1038/s41467-019-13578-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 11/14/2019] [Indexed: 01/03/2023] Open
Abstract
Novel interventions that leverage the heterogeneity of parasite transmission are needed to achieve malaria elimination. To better understand spatial and temporal dynamics of transmission, we applied amplicon next-generation sequencing of two polymorphic gene regions (csp and ama1) to a cohort identified via reactive case detection in a high-transmission setting in western Kenya. From April 2013 to July 2014, we enrolled 442 symptomatic children with malaria, 442 matched controls, and all household members of both groups. Here, we evaluate genetic similarity between infected individuals using three indices: sharing of parasite haplotypes on binary and proportional scales and the L1 norm. Symptomatic children more commonly share haplotypes with their own household members. Furthermore, we observe robust temporal structuring of parasite genetic similarity and identify the unique molecular signature of an outbreak. These findings of both micro- and macro-scale organization of parasite populations might be harnessed to inform next-generation malaria control measures. Here, Nelson et al. use amplicon next-generation sequencing of two P. falciparum polymorphic gene regions to investigate the genetic similarity of parasite populations across time and space in a pediatric cohort in Kenya. They identify both micro- and macro-scale structuring of malaria parasites in this high-transmission setting, which could inform future intervention strategies.
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Affiliation(s)
- Cody S Nelson
- Duke Global Health Institute, Duke University, Durham, North Carolina, USA.
| | - Kelsey M Sumner
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, USA.,Division of Infectious Diseases, Duke University School of Medicine, Durham, North Carolina, USA
| | - Elizabeth Freedman
- Division of Infectious Diseases, Duke University School of Medicine, Durham, North Carolina, USA
| | - Joseph W Saelens
- Division of Infectious Diseases, Duke University School of Medicine, Durham, North Carolina, USA
| | - Andrew A Obala
- School of Medicine, Moi University College of Health Sciences, Eldoret, Kenya
| | - Judith N Mangeni
- School of Nursing, Moi University College of Health Sciences, Eldoret, Kenya
| | - Steve M Taylor
- Duke Global Health Institute, Duke University, Durham, North Carolina, USA.,Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, USA.,Division of Infectious Diseases, Duke University School of Medicine, Durham, North Carolina, USA
| | - Wendy P O'Meara
- Duke Global Health Institute, Duke University, Durham, North Carolina, USA.,Division of Infectious Diseases, Duke University School of Medicine, Durham, North Carolina, USA
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17
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Manrique P, Miranda-Alban J, Alarcon-Baldeon J, Ramirez R, Carrasco-Escobar G, Herrera H, Guzman-Guzman M, Rosas-Aguirre A, Llanos-Cuentas A, Vinetz JM, Escalante AA, Gamboa D. Microsatellite analysis reveals connectivity among geographically distant transmission zones of Plasmodium vivax in the Peruvian Amazon: A critical barrier to regional malaria elimination. PLoS Negl Trop Dis 2019; 13:e0007876. [PMID: 31710604 PMCID: PMC6874088 DOI: 10.1371/journal.pntd.0007876] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 11/21/2019] [Accepted: 10/25/2019] [Indexed: 12/31/2022] Open
Abstract
Despite efforts made over decades by the Peruvian government to eliminate malaria, Plasmodium vivax remains a challenge for public health decision-makers in the country. The uneven distribution of its incidence, plus its complex pattern of dispersion, has made ineffective control measures based on global information that lack the necessary detail to understand transmission fully. In this sense, population genetic tools can complement current surveillance. This study describes the genetic diversity and population structure from September 2012 to March 2015 in three geographically distant settlements, Cahuide (CAH), Lupuna (LUP) and Santa Emilia (STE), located in the Peruvian Amazon. A total 777 P. vivax mono-infections, out of 3264, were genotyped. Among study areas, LUP showed 19.7% of polyclonal infections, and its genetic diversity (Hexp) was 0.544. Temporal analysis showed a significant increment of polyclonal infections and Hexp, and the introduction and persistence of a new parasite population since March 2013. In STE, 40.1% of infections were polyclonal, with Hexp = 0.596. The presence of four genetic clusters without signals of clonal expansion and infections with lower parasite densities compared against the other two areas were also found. At least four parasite populations were present in CAH in 2012, where, after June 2014, malaria cases decreased from 213 to 61, concomitant with a decrease in polyclonal infections (from 0.286 to 0.18), and expectedly variable Hexp. Strong signals of gene flow were present in the study areas and wide geographic distribution of highly diverse parasite populations were found. This study suggests that movement of malaria parasites by human reservoirs connects geographically distant malaria transmission areas in the Peruvian Amazon. The maintenance of high levels of parasite genetic diversity through human mobility is a critical barrier to malaria elimination in this region. Plasmodium vivax transmission is heterogeneous and discontinuous in the Peruvian Amazon. Such heterogeneity is the result of factors that include, but are not restricted to, the environment, public policies, and characteristics of the parasite, the vector, and human activities. All these factors make P. vivax transmission resilient to interventions. In order to achieve the goals of control and local elimination, P. vivax surveillance must inform how those factors sustain disease transmission in order to focalize and synchronize control strategies. In this study, we implemented molecular surveillance complemented with population genetic tools in the areas of Cahuide, Lupuna, and Santa Emilia located in the Peruvian Amazon. In particular, we characterize the transmission and the parasite genetic variation in these sites from September 2012 to March 2015. The changes in parasite diversity, the wide geographic dispersion of parasite subpopulation and the introduction of a new parasite clone or subpopulation in Lupuna documented in this study suggest that connectivity among the different endemic areas, likely due to human mobility, sustains disease transmission in the region hindering the success of control measures. This information must be considered in the design of current control strategies.
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Affiliation(s)
- Paulo Manrique
- Laboratorio ICEMR-Amazonia, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofa, Universidad Peruana Cayetano Heredia, Lima, Perú
- * E-mail:
| | - Julio Miranda-Alban
- Laboratorio ICEMR-Amazonia, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofa, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Jhonatan Alarcon-Baldeon
- Laboratorio ICEMR-Amazonia, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofa, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Roberson Ramirez
- Laboratorio ICEMR-Amazonia, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofa, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Gabriel Carrasco-Escobar
- Laboratorio ICEMR-Amazonia, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofa, Universidad Peruana Cayetano Heredia, Lima, Perú
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Henry Herrera
- Laboratorio ICEMR-Amazonia, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofa, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Mitchel Guzman-Guzman
- Laboratorio ICEMR-Amazonia, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofa, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Angel Rosas-Aguirre
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Perú
- Fund for Scientific Research FNRS, Brussels, Belgium
- Research Institute of Health and Society (IRSS), Université catholique de Louvain, Brussels, Belgium
| | - Alejandro Llanos-Cuentas
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Perú
- Facultad de Salud Pública y Administración, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Joseph M. Vinetz
- Laboratorio ICEMR-Amazonia, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofa, Universidad Peruana Cayetano Heredia, Lima, Perú
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Perú
- Yale School of Medicine, Section of Infectious Diseases, Department of Internal Medicine, New Haven, Connecticut, United States of America
- Departamento de Ciencias Celulares y Moleculares, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Ananias A. Escalante
- Institute for Genomics and Evolutionary Medicine (IGEM), Temple University, Philadelphia, Pennsylvania, United States of America
| | - Dionicia Gamboa
- Laboratorio ICEMR-Amazonia, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofa, Universidad Peruana Cayetano Heredia, Lima, Perú
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Perú
- Departamento de Ciencias Celulares y Moleculares, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
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