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Zhang M, Wang Y, Shen HM, Chen SB, Wang TY, Kassegne K, Chen JH. Genetic Diversity and Natural Selection of Plasmodium vivax Merozoite Surface Protein 8 in Global Populations. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 122:105605. [PMID: 38759940 DOI: 10.1016/j.meegid.2024.105605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 05/09/2024] [Accepted: 05/14/2024] [Indexed: 05/19/2024]
Abstract
Plasmodium vivax Merozoite Surface Protein 8 (PvMSP8) is a promising candidate target for the development of multi-component vaccines. Therefore, determining the genetic variation pattern of Pvmsp8 is essential in providing a reference for the rational design of the P. vivax malaria vaccines. This study delves into the genetic characteristics of the Pvmsp8 gene, specifically focusing on samples from the China-Myanmar border (CMB) region, and contrasts these findings with broader global patterns. The study uncovers that Pvmsp8 exhibits a notable level of conservation across different populations, with limited polymorphisms and relatively low nucleotide diversity (0.00023-0.00120). This conservation contrasts starkly with the high polymorphisms found in other P. vivax antigens such as Pvmsp1. A total of 25 haplotypes and 14 amino acid mutation sites were identified in the global populations, and all mutation sites were confined to non-functional regions. The study also notes that most CMB Pvmsp8 haplotypes are shared among Burmese, Cambodian, Thai, and Vietnamese populations, indicating less geographical variance, but differ notably from those found in Pacific island regions or the Panama. The findings underscore the importance of considering regional genetic diversity in P. vivax when developing targeted malaria vaccines. Non departure from neutral evolution were found by Tajima's D test, however, statistically significant differences were observed between the kn/ks rates. The study's findings are crucial in understanding the evolution and population structure of the Pvmsp8 gene, particularly during regional malaria elimination efforts. The highly conserved nature of Pvmsp8, combined with the lack of mutations in its functional domain, presents it as a promising candidate for developing a broad and effective P. vivax vaccine. This research thus lays a foundation for the rational development of multivalent malaria vaccines targeting this genetically stable antigen.
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Affiliation(s)
- Man Zhang
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research); National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases; National Health Commission of the People's Republic of China (NHC) Key Laboratory of Parasite and Vector Biology; World Health Organization (WHO) Collaborating Center for Tropical Diseases; National Center for International Research on Tropical Diseases, Shanghai 200025, People's Republic of China
| | - Yue Wang
- School of Basic Medical Sciences and Forensic Medicine, Hangzhou Medical College, Hangzhou 310013, People's Republic of China
| | - Hai-Mo Shen
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research); National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases; National Health Commission of the People's Republic of China (NHC) Key Laboratory of Parasite and Vector Biology; World Health Organization (WHO) Collaborating Center for Tropical Diseases; National Center for International Research on Tropical Diseases, Shanghai 200025, People's Republic of China
| | - Shen-Bo Chen
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research); National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases; National Health Commission of the People's Republic of China (NHC) Key Laboratory of Parasite and Vector Biology; World Health Organization (WHO) Collaborating Center for Tropical Diseases; National Center for International Research on Tropical Diseases, Shanghai 200025, People's Republic of China
| | - Tian-Yu Wang
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research); National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases; National Health Commission of the People's Republic of China (NHC) Key Laboratory of Parasite and Vector Biology; World Health Organization (WHO) Collaborating Center for Tropical Diseases; National Center for International Research on Tropical Diseases, Shanghai 200025, People's Republic of China
| | - Kokouvi Kassegne
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research); National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases; National Health Commission of the People's Republic of China (NHC) Key Laboratory of Parasite and Vector Biology; World Health Organization (WHO) Collaborating Center for Tropical Diseases; National Center for International Research on Tropical Diseases, Shanghai 200025, People's Republic of China; School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, People's Republic of China
| | - Jun-Hu Chen
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research); National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases; National Health Commission of the People's Republic of China (NHC) Key Laboratory of Parasite and Vector Biology; World Health Organization (WHO) Collaborating Center for Tropical Diseases; National Center for International Research on Tropical Diseases, Shanghai 200025, People's Republic of China; School of Basic Medical Sciences and Forensic Medicine, Hangzhou Medical College, Hangzhou 310013, People's Republic of China; School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, People's Republic of China; Hainan Tropical Diseases Research Center (Hainan Sub-Center, Chinese Center for Tropical Diseases Research), Haikou 571199, China.
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Hu Y, Li Y, Brashear AM, Zeng W, Wu Z, Wang L, Wei H, Soe MT, Aung PL, Sattabongkot J, Kyaw MP, Yang Z, Zhao Y, Cui L, Cao Y. Plasmodium vivax populations in the western Greater Mekong Subregion evaluated using a genetic barcode. PLoS Negl Trop Dis 2024; 18:e0012299. [PMID: 38959285 PMCID: PMC11251639 DOI: 10.1371/journal.pntd.0012299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 07/16/2024] [Accepted: 06/18/2024] [Indexed: 07/05/2024] Open
Abstract
An improved understanding of the Plasmodium vivax populations in the Great Mekong Subregion (GMS) is needed to monitor the progress of malaria elimination. This study aimed to use a P. vivax single nucleotide polymorphism (SNP) barcode to evaluate the population dynamics and explore the gene flow among P. vivax parasite populations in the western GMS (China, Myanmar and Thailand). A total of 315 P. vivax patient samples collected in 2011 and 2018 from four regions of the western GMS were genotyped for 42 SNPs using the high-throughput MassARRAY SNP genotyping technology. Population genetic analysis was conducted to estimate the genetic diversity, effective population size, and population structure among the P. vivax populations. Overall, 291 samples were successfully genotyped at 39 SNPs. A significant difference was observed in the proportion of polyclonal infections among the five P. vivax populations (P = 0.0012, Pearson Chi-square test, χ2 = 18.1), with western Myanmar having the highest proportion (96.2%, 50/52) in 2018. Likewise, the average complexity of infection was also highest in western Myanmar (1.31) and lowest in northeast Myanmar (1.01) in 2018. The older samples from western China in 2011 had the highest pairwise nucleotide diversity (π, 0.388 ± 0.046), expected heterozygosity (He, 0.363 ± 0.02), and the largest effective population size. In comparison, in the neighboring northeast Myanmar, the more recent samples in 2018 showed the lowest values (π, 0.224 ± 0.036; He, 0.220 ± 0.026). Furthermore, the 2018 northeast Myanmar parasites showed high and moderate genetic differentiation from other populations with FST values of 0.162-0.252, whereas genetic differentiation among other populations was relatively low (FST ≤ 0.059). Principal component analysis, phylogeny, and STRUCTURE analysis showed that the P. vivax population in northeast Myanmar in 2018 substantially diverged from other populations. Although the 42 SNP barcode is a valuable tool for tracking parasite origins of worldwide parasite populations, a more extended barcode with additional SNPs is needed to distinguish the more related parasite populations in the western GMS.
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Affiliation(s)
- Yubing Hu
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, Liaoning, China
| | - Yuling Li
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, Liaoning, China
- Emergency Department, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Awtum M. Brashear
- Division of Infectious Disease and International Medicine, Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, United States of America
| | - Weilin Zeng
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, China
| | - Zifang Wu
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, Liaoning, China
| | - Lin Wang
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, Liaoning, China
| | - Haichao Wei
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, Liaoning, China
| | - Myat Thu Soe
- Myanmar Health Network Organization, Yangon, Myanmar
| | | | - Jetsumon Sattabongkot
- Mahidol Vivax Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | | | - Zhaoqing Yang
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, China
| | - Yan Zhao
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, Liaoning, China
| | - Liwang Cui
- Division of Infectious Disease and International Medicine, Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, United States of America
| | - Yaming Cao
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, Liaoning, China
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Bradley L, Yewhalaw D, Hemming-Schroeder E, Jeang B, Lee MC, Zemene E, Degefa T, Lo E, King C, Kazura J, Yan G. Epidemiology of Plasmodium vivax in Duffy negatives and Duffy positives from community and health centre collections in Ethiopia. Malar J 2024; 23:76. [PMID: 38486245 PMCID: PMC10941426 DOI: 10.1186/s12936-024-04895-1] [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: 09/25/2023] [Accepted: 02/28/2024] [Indexed: 03/17/2024] Open
Abstract
BACKGROUND Malaria remains a significant cause of morbidity and mortality in Ethiopia with an estimated 3.8 million cases in 2021 and 61% of the population living in areas at risk of malaria transmission. Throughout the country Plasmodium vivax and Plasmodium falciparum are co-endemic, and Duffy expression is highly heterogeneous. The public health significance of Duffy negativity in relation to P. vivax malaria in Ethiopia, however, remains unclear. This study seeks to explore the prevalence and rates of P. vivax malaria infection across Duffy phenotypes in clinical and community settings. METHODS A total of 9580 and 4667 subjects from community and health facilities from a malaria endemic site and an epidemic-prone site in western Ethiopia were enrolled and examined for P. vivax infection and Duffy expression from February 2018 to April 2021. Association between Duffy expression, P. vivax and P. falciparum infections were examined for samples collected from asymptomatic community volunteers and symptomatic subjects from health centres. RESULTS Infection rate of P. vivax among Duffy positives was 2-22 fold higher than Duffy negatives in asymptomatic volunteers from the community. Parasite positivity rate was 10-50 fold higher in Duffy positives than Duffy negatives among samples collected from febrile patients attending health centres and mixed P. vivax and P. falciparum infections were significantly more common than P. vivax mono infections among Duffy negative individuals. Plasmodium vivax parasitaemia measured by 18sRNA parasite gene copy number was similar between Duffy positives and Duffy negatives. CONCLUSIONS Duffy negativity does not offer complete protection against infection by P. vivax, and cases of P. vivax in Duffy negatives are widespread in Ethiopia, being found in asymptomatic volunteers from communities and in febrile patients from health centres. These findings offer evidence for consideration when developing control and intervention strategies in areas of endemic P. vivax and Duffy heterogeneity.
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Affiliation(s)
- Lauren Bradley
- Department of Ecology and Evolutionary Biology, School of Biological Sciences, University of California Irvine, Irvine, CA, 92697, USA
| | - Delenasaw Yewhalaw
- Department of Medical Laboratory Sciences and Pathology, College of Health Sciences, Jimma University, 5195, Jimma, Ethiopia
- Tropical and Infectious Diseases Research Centre, Jimma University, Jimma, Ethiopia
| | - Elizabeth Hemming-Schroeder
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Brook Jeang
- Department of Ecology and Evolutionary Biology, School of Biological Sciences, University of California Irvine, Irvine, CA, 92697, USA
| | - Ming-Chieh Lee
- Department of Ecology and Evolutionary Biology, School of Biological Sciences, University of California Irvine, Irvine, CA, 92697, USA
| | - Endalew Zemene
- Tropical and Infectious Diseases Research Centre, Jimma University, Jimma, Ethiopia
| | - Teshome Degefa
- School of Medical Laboratory Sciences, Faculty of Health Sciences, Jimma University, Jimma, Ethiopia
| | - Eugenia Lo
- Department of Microbiology and Immunology, Drexel University, Philadelphia, PA, 19104, USA
| | - Christopher King
- Center for Global Health and Disease, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - James Kazura
- Center for Global Health and Disease, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Guiyun Yan
- Department of Ecology and Evolutionary Biology, School of Biological Sciences, University of California Irvine, Irvine, CA, 92697, USA.
- Program in Public Health, College of Health Sciences, University of California at Irvine, Irvine, CA, 92697, USA.
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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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5
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Hazzard B, Sá JM, Bogale HN, Pascini TV, Ellis AC, Amin S, Armistead JS, Adams JH, Wellems TE, Serre D. Single-cell analyses of polyclonal Plasmodium vivax infections and their consequences on parasite transmission. RESEARCH SQUARE 2024:rs.3.rs-3888175. [PMID: 38410426 PMCID: PMC10896380 DOI: 10.21203/rs.3.rs-3888175/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Most Plasmodium vivax infections contain genetically distinct parasites, but the consequences of this polyclonality on the development of asexual parasites, their sexual differentiation, and their transmission remain unknown. We describe infections of Saimiri monkeys with two strains of P. vivax and the analyses of 117,350 parasites characterized by single cell RNA sequencing and individually genotyped. In our model, consecutive inoculations fail to establish polyclonal infections. By contrast, simultaneous inoculations of two strains lead to sustained polyclonal infections, although without detectable differences in parasite regulation or sexual commitment. Analyses of sporozoites dissected from mosquitoes fed on coinfected monkeys show that all genotypes are successfully transmitted to mosquitoes. However, after sporozoite inoculation, not all genotypes contribute to the subsequent blood infections, highlighting an important bottleneck during pre-erythrocytic development. Overall, these studies provide new insights on the mechanisms regulating the establishment of polyclonal P. vivax infections and their consequences for disease transmission.
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Affiliation(s)
- Brittany Hazzard
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Juliana M. Sá
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Haikel N. Bogale
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Tales V. Pascini
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Angela C. Ellis
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Shuchi Amin
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Jennifer S. Armistead
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
- Center for Global Health and Inter-Disciplinary Research, College of Public Health, University of South Florida, Tampa, USA
| | - John H. Adams
- Center for Global Health and Inter-Disciplinary Research, College of Public Health, University of South Florida, Tampa, USA
| | - Thomas E. Wellems
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - David Serre
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Lead contact
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Gartner V, Redelings BD, Gaither C, Parr JB, Kalonji A, Phanzu F, Brazeau NF, Juliano JJ, Wray GA. Genomic insights into Plasmodium vivax population structure and diversity in central Africa. Malar J 2024; 23:27. [PMID: 38238806 PMCID: PMC10797969 DOI: 10.1186/s12936-024-04852-y] [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: 07/27/2023] [Accepted: 01/12/2024] [Indexed: 01/22/2024] Open
Abstract
BACKGROUND Though Plasmodium vivax is the second most common malaria species to infect humans, it has not traditionally been considered a major human health concern in central Africa given the high prevalence of the human Duffy-negative phenotype that is believed to prevent infection. Increasing reports of asymptomatic and symptomatic infections in Duffy-negative individuals throughout Africa raise the possibility that P. vivax is evolving to evade host resistance, but there are few parasite samples with genomic data available from this part of the world. METHODS Whole genome sequencing of one new P. vivax isolate from the Democratic Republic of the Congo (DRC) was performed and used in population genomics analyses to assess how this central African isolate fits into the global context of this species. RESULTS Plasmodium vivax from DRC is similar to other African populations and is not closely related to the non-human primate parasite P. vivax-like. Evidence is found for a duplication of the gene PvDBP and a single copy of PvDBP2. CONCLUSION These results suggest an endemic P. vivax population is present in central Africa. Intentional sampling of P. vivax across Africa would further contextualize this sample within African P. vivax diversity and shed light on the mechanisms of infection in Duffy negative individuals. These results are limited by the uncertainty of how representative this single sample is of the larger population of P. vivax in central Africa.
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Affiliation(s)
- Valerie Gartner
- Biology Department, Duke University, Durham, NC, 27708, USA
- University Program in Genetics and Genomics, Duke University, Durham, NC, 27708, USA
| | - Benjamin D Redelings
- Biology Department, Duke University, Durham, NC, 27708, USA
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, 66045, USA
- Ronin Institute, Durham, NC, 27705, USA
| | | | | | - Albert Kalonji
- SANRU Asbl, 149 A/B, Boulevard du 30 Juin, Kinshasa, Gombe, Democratic Republic of Congo
| | - Fernandine Phanzu
- SANRU Asbl, 149 A/B, Boulevard du 30 Juin, Kinshasa, Gombe, Democratic Republic of Congo
| | | | | | - Gregory A Wray
- Biology Department, Duke University, Durham, NC, 27708, USA.
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Kepple D, Ford CT, Williams J, Abagero B, Li S, Popovici J, Yewhalaw D, Lo E. Comparative transcriptomics reveal differential gene expression among Plasmodium vivax geographical isolates and implications on erythrocyte invasion mechanisms. PLoS Negl Trop Dis 2024; 18:e0011926. [PMID: 38285730 PMCID: PMC10901308 DOI: 10.1371/journal.pntd.0011926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 02/28/2024] [Accepted: 01/19/2024] [Indexed: 01/31/2024] Open
Abstract
The documentation of Plasmodium vivax malaria across Africa especially in regions where Duffy negatives are dominant suggests possibly alternative erythrocyte invasion mechanisms. While the transcriptomes of the Southeast Asian and South American P. vivax are well documented, the gene expression profile of P. vivax in Africa is unclear. In this study, we examined the expression of 4,404 gene transcripts belong to 12 functional groups and 43 erythrocyte binding gene candidates in Ethiopian isolates and compared them with the Cambodian and Brazilian P. vivax transcriptomes. Overall, there were 10-26% differences in the gene expression profile amongst geographical isolates, with the Ethiopian and Cambodian P. vivax being most similar. Majority of the gene transcripts involved in protein transportation, housekeeping, and host interaction were highly transcribed in the Ethiopian isolates. Members of the reticulocyte binding protein PvRBP2a and PvRBP3 expressed six-fold higher than Duffy binding protein PvDBP1 and 60-fold higher than PvEBP/DBP2 in the Ethiopian isolates. Other genes including PvMSP3.8, PvMSP3.9, PvTRAG2, PvTRAG14, and PvTRAG22 also showed relatively high expression. Differential expression patterns were observed among geographical isolates, e.g., PvDBP1 and PvEBP/DBP2 were highly expressed in the Cambodian but not the Brazilian and Ethiopian isolates, whereas PvRBP2a and PvRBP2b showed higher expression in the Ethiopian and Cambodian than the Brazilian isolates. Compared to Pvs25, gametocyte genes including PvAP2-G, PvGAP (female gametocytes), and Pvs47 (male gametocytes) were highly expressed across geographical samples.
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Affiliation(s)
- Daniel Kepple
- Biological Sciences, University of North Carolina, Charlotte, North Carolina, United States of America
| | - Colby T. Ford
- Bioinformatics and Genomics, University of North Carolina, Charlotte, North Carolina, United States of America
- School of Data Science, University of North Carolina, Charlotte, North Carolina, United States of America
| | - Jonathan Williams
- Biological Sciences, University of North Carolina, Charlotte, North Carolina, United States of America
| | - Beka Abagero
- Biological Sciences, University of North Carolina, Charlotte, North Carolina, United States of America
| | - Shaoyu Li
- Mathematics and Statistics, University of North Carolina, Charlotte, North Carolina, United States of America
| | - Jean Popovici
- Malaria Research Unit, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Delenasaw Yewhalaw
- Tropical and Infectious Diseases Research Center, Jimma University, Jimma, Ethiopia
- School of Medical Laboratory Sciences, Faculty of Health Sciences, Jimma University, Jimma, Ethiopia
| | - Eugenia Lo
- Biological Sciences, University of North Carolina, Charlotte, North Carolina, United States of America
- Microbiology and Immunology, College of Medicine, Drexel University, Philadelphia, Pennsylvania, United States of America
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Kebede AM, Sutanto E, Trimarsanto H, Benavente ED, Barnes M, Pearson RD, Siegel SV, Erko B, Assefa A, Getachew S, Aseffa A, Petros B, Lo E, Mohammed R, Yilma D, Rumaseb A, Nosten F, Noviyanti R, Rayner JC, Kwiatkowski DP, Price RN, Golassa L, Auburn S. Genomic analysis of Plasmodium vivax describes patterns of connectivity and putative drivers of adaptation in Ethiopia. Sci Rep 2023; 13:20788. [PMID: 38012191 PMCID: PMC10682486 DOI: 10.1038/s41598-023-47889-w] [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: 09/04/2023] [Accepted: 11/20/2023] [Indexed: 11/29/2023] Open
Abstract
Ethiopia has the greatest burden of Plasmodium vivax in Africa, but little is known about the epidemiological landscape of parasites across the country. We analysed the genomic diversity of 137 P. vivax isolates collected nine Ethiopian districts from 2012 to 2016. Signatures of selection were detected by cross-country comparisons with isolates from Thailand (n = 104) and Indonesia (n = 111), representing regions with low and high chloroquine resistance respectively. 26% (35/137) of Ethiopian infections were polyclonal, and 48.5% (17/35) of these comprised highly related clones (within-host identity-by-descent > 25%), indicating frequent co-transmission and superinfection. Parasite gene flow between districts could not be explained entirely by geographic distance, with economic and cultural factors hypothesised to have an impact on connectivity. Amplification of the duffy binding protein gene (pvdbp1) was prevalent across all districts (16-75%). Cross-population haplotype homozygosity revealed positive selection in a region proximal to the putative chloroquine resistance transporter gene (pvcrt-o). An S25P variant in amino acid transporter 1 (pvaat1), whose homologue has recently been implicated in P. falciparum chloroquine resistance evolution, was prevalent in Ethiopia (96%) but not Thailand or Indonesia (35-53%). The genomic architecture in Ethiopia highlights circulating variants of potential public health concern in an endemic setting with evidence of stable transmission.
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Affiliation(s)
| | | | - Hidayat Trimarsanto
- Menzies School of Health Research and Charles Darwin University, Casuarina, PO Box 41096, Darwin, NT, 0811, Australia
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia
| | - Ernest Diez Benavente
- Laboratory of Experimental Cardiology, Department of Cardiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Mariana Barnes
- Menzies School of Health Research and Charles Darwin University, Casuarina, PO Box 41096, Darwin, NT, 0811, Australia
| | | | | | - Berhanu Erko
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Ashenafi Assefa
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
- School of Public Health, Addis Ababa University, Addis Ababa, Ethiopia
| | - Sisay Getachew
- Armauer Hansen Research Unit (AHRI), Addis Ababa, Ethiopia
- Addis Ababa University, Addis Ababa, Ethiopia
- Millipore Sigma (Bioreliance), Rockville, USA
| | - Abraham Aseffa
- Armauer Hansen Research Unit (AHRI), Addis Ababa, Ethiopia
| | | | - Eugenia Lo
- Department of Microbiology and Immunology, College of Medicine, Drexel University, Philadelphia, USA
| | | | - Daniel Yilma
- Jimma University Clinical Trial Unit, Department of Internal Medicine, Jimma University, Jimma, Ethiopia
| | - Angela Rumaseb
- Menzies School of Health Research and Charles Darwin University, Casuarina, PO Box 41096, Darwin, NT, 0811, Australia
| | - Francois Nosten
- Shoklo Malaria Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Julian C Rayner
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | | | - Ric N Price
- Menzies School of Health Research and Charles Darwin University, Casuarina, PO Box 41096, Darwin, NT, 0811, Australia
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Lemu Golassa
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Sarah Auburn
- Menzies School of Health Research and Charles Darwin University, Casuarina, PO Box 41096, Darwin, NT, 0811, Australia.
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand.
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9
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Sutanto E, Pava Z, Echeverry DF, Lopera-Mesa TM, Montenegro LM, Yasnot-Acosta MF, Benavente ED, Pearson RD, Herrera S, Arévalo-Herrera M, Trimarsanto H, Rumaseb A, Noviyanti R, Kwiatkowski DP, Price RN, Auburn S. Genomics of Plasmodium vivax in Colombia reveals evidence of local bottle-necking and inter-country connectivity in the Americas. Sci Rep 2023; 13:19779. [PMID: 37957271 PMCID: PMC10643449 DOI: 10.1038/s41598-023-46076-1] [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: 07/03/2023] [Accepted: 10/27/2023] [Indexed: 11/15/2023] Open
Abstract
Colombia aims to eliminate malaria by 2030 but remains one of the highest burden countries in the Americas. Plasmodium vivax contributes half of all malaria cases, with its control challenged by relapsing parasitaemia, drug resistance and cross-border spread. Using 64 Colombian P. vivax genomes collected between 2013 and 2017, we explored diversity and selection in two major foci of transmission: Chocó and Córdoba. Open-access data from other countries were used for comparative assessment of drug resistance candidates and to assess cross-border spread. Across Colombia, polyclonal infections were infrequent (12%), and infection connectivity was relatively high (median IBD = 5%), consistent with low endemicity. Chocó exhibited a higher frequency of polyclonal infections (23%) than Córdoba (7%), although the difference was not significant (P = 0.300). Most Colombian infections carried double pvdhfr (95%) and single pvdhps (71%) mutants, but other drug resistance mutations were less prevalent (< 10%). There was no evidence of selection at the pvaat1 gene, whose P. falciparum orthologue has recently been implicated in chloroquine resistance. Global population comparisons identified other putative adaptations. Within the Americas, low-level connectivity was observed between Colombia and Peru, highlighting potential for cross-border spread. Our findings demonstrate the potential of molecular data to inform on infection spread and adaptation.
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Affiliation(s)
| | - Zuleima Pava
- Menzies School of Health Research and Charles Darwin University, Darwin, Australia
| | - Diego F Echeverry
- Departamento de Microbiología, Universidad del Valle, Cali, Colombia
- International Training and Medical Research Center (CIDEIM), Cali, Colombia
| | | | | | - Maria F Yasnot-Acosta
- Grupo de Investigaciones Microbiológicas y Biomédicas de Córdoba (GIMBIC), Universidad de Córdoba, Monteria, Colombia
| | - Ernest Diez Benavente
- Laboratory of Experimental Cardiology, Department of Cardiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | | | | | - Myriam Arévalo-Herrera
- Caucaseco Scientific Research Center, Cali, Colombia
- Centro Internacional de Vacunas, Cali, Colombia
| | - Hidayat Trimarsanto
- Menzies School of Health Research and Charles Darwin University, Darwin, Australia
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia
| | - Angela Rumaseb
- Menzies School of Health Research and Charles Darwin University, Darwin, Australia
| | | | | | - Ric N Price
- Menzies School of Health Research and Charles Darwin University, Darwin, Australia
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Sarah Auburn
- Menzies School of Health Research and Charles Darwin University, Darwin, Australia.
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand.
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
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10
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De Meulenaere K, Cuypers B, Gamboa D, Laukens K, Rosanas-Urgell A. A new Plasmodium vivax reference genome for South American isolates. BMC Genomics 2023; 24:606. [PMID: 37821878 PMCID: PMC10568799 DOI: 10.1186/s12864-023-09707-5] [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: 03/14/2023] [Accepted: 09/30/2023] [Indexed: 10/13/2023] Open
Abstract
BACKGROUND Plasmodium vivax is the second most important cause of human malaria worldwide, and accounts for the majority of malaria cases in South America. A high-quality reference genome exists for Papua Indonesia (PvP01) and Thailand (PvW1), but is lacking for South America. A reference genome specifically for South America would be beneficial though, as P. vivax is a genetically diverse parasite with geographical clustering. RESULTS This study presents a new high-quality assembly of a South American P. vivax isolate, referred to as PvPAM (P. vivax Peruvian AMazon). The genome was obtained from a low input patient sample from the Peruvian Amazon and sequenced using PacBio technology, resulting in a highly complete assembly with 6497 functional genes. Telomeric ends were present in 17 out of 28 chromosomal ends, and additional (sub)telomeric regions are present in 12 unassigned contigs. A comparison of multigene families between PvPAM and the PvP01 genome revealed remarkable variation in vir genes, and the presence of merozoite surface proteins (MSP) 3.6 and 3.7. Three dhfr and dhps drug resistance associated mutations are present in PvPAM, similar to those found in other Peruvian isolates. Mapping of publicly available South American whole genome sequencing (WGS) data to PvPAM resulted in significantly fewer variants and truncated reads compared to the use of PvP01 or PvW1 as reference genomes. To minimize the number of core genome variants in non-South American samples, PvW1 is most suited for Southeast Asian isolates, both PvPAM and PvW1 are suited for South Asian isolates, and PvPAM is recommended for African isolates. Interestingly, non-South American samples still contained the least subtelomeric variants when mapped to PvPAM, indicating high quality of the PvPAM subtelomeric regions. CONCLUSIONS Our findings show that the PvPAM reference genome more accurately represents South American P. vivax isolates in comparison to PvP01 and PvW1. In addition, PvPAM has a high level of completeness, and contains a similar number of annotated genes as PvP01 or PvW1. The PvPAM genome therefore will be a valuable resource to improve future genomic analyses on P. vivax isolates from the South American continent.
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Affiliation(s)
- Katlijn De Meulenaere
- Department of Biomedical Sciences, Institute of Tropical Medicine Antwerp, Antwerp, Belgium.
- Department of Computer Science, University of Antwerp, Antwerp, Belgium.
| | - Bart Cuypers
- Department of Computer Science, University of Antwerp, Antwerp, Belgium
| | - Dionicia Gamboa
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
- Departamento de Ciencias Celulares y Moleculares, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Kris Laukens
- Department of Computer Science, University of Antwerp, Antwerp, Belgium
| | - Anna Rosanas-Urgell
- Department of Biomedical Sciences, Institute of Tropical Medicine Antwerp, Antwerp, Belgium.
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11
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Bradley L, Yewhalaw D, Hemming-Schroeder E, Jeang B, Lee MC, Zemene E, Degefa T, Lo E, King C, Kazura J, Yan G. Comparison of Plasmodium Vivax Infections in Duffy Negatives From Community and Health Center Collections in Ethiopia. RESEARCH SQUARE 2023:rs.3.rs-3385916. [PMID: 37886593 PMCID: PMC10602065 DOI: 10.21203/rs.3.rs-3385916/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
Background Malaria remains a significant cause of morbidity and mortality in Ethiopia with an estimated 4.2 million annual cases and 61% of the population living in areas at risk of malaria transmission. Throughout the country Plasmodium vivax and P. falciparum are co-endemic, and Duffy expression is highly heterogeneous. The public health significance of Duffy negativity in relation to P. vivax malaria in Ethiopia, however, remains unclear. Methods A total of 9,580 and 4,667 subjects from community and health facilities from a malaria endemic site and an epidemic-prone site in western Ethiopia were enrolled and examined for P. vivax infection and Duffy expression. Association between Duffy expression, P. vivax and P. falciparum infections were examined for samples collected from asymptomatic community volunteers and symptomatic subjects from health centers. Results Among the community-based cross-sectional samples, infection rate of P. vivax among the Duffy positives was 2-22 fold higher than among the Duffy negatives. Parasite positivity rate was 10-50 fold higher in Duffy positive than Duffy negatives among samples collected from the health center settings and mixed P. vivax and P. falciparum infections were significantly more common than P. vivax mono infections among Duffy negative individuals. P. vivax parasitemia measured by 18sRNA parasite gene copy number was similar between Duffy positives and Duffy negatives. Conclusions Duffy negativity does not offer complete protection against infection by P. vivax, and cases of P. vivax in Duffy negatives are widespread in Ethiopia, being found in asymptomatic volunteers from communities and in febrile patients from health centers. These findings offer evidence for consideration when developing control and intervention strategies in areas of endemic P. vivax and Duffy heterogeneity.
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12
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Nicholas J, De SL, Thawornpan P, Brashear AM, Kolli SK, Subramani PA, Barnes SJ, Cui L, Chootong P, Ntumngia FB, Adams JH. Preliminary characterization of Plasmodium vivax sporozoite antigens as pre-erythrocytic vaccine candidates. PLoS Negl Trop Dis 2023; 17:e0011598. [PMID: 37703302 PMCID: PMC10519608 DOI: 10.1371/journal.pntd.0011598] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 09/25/2023] [Accepted: 08/15/2023] [Indexed: 09/15/2023] Open
Abstract
Plasmodium vivax pre-erythrocytic (PE) vaccine research has lagged far behind efforts to develop Plasmodium falciparum vaccines. There is a critical gap in our knowledge of PE antigen targets that can induce functionally inhibitory neutralizing antibody responses. To overcome this gap and guide the selection of potential PE vaccine candidates, we considered key characteristics such as surface exposure, essentiality to infectivity and liver stage development, expression as recombinant proteins, and functional immunogenicity. Selected P. vivax sporozoite antigens were surface sporozoite protein 3 (SSP3), sporozoite microneme protein essential for cell traversal (SPECT1), sporozoite surface protein essential for liver-stage development (SPELD), and M2 domain of MAEBL. Sequence analysis revealed little variation occurred in putative B-cell and T-cell epitopes of the PE candidates. Each antigen was tested for expression as refolded recombinant proteins using an established bacterial expression platform and only SPELD failed. The successfully expressed antigens were immunogenic in vaccinated laboratory mice and were positively reactive with serum antibodies of P. vivax-exposed residents living in an endemic region in Thailand. Vaccine immune antisera were tested for reactivity to native sporozoite proteins and for their potential vaccine efficacy using an in vitro inhibition of liver stage development assay in primary human hepatocytes quantified on day 6 post-infection by high content imaging analysis. The anti-PE sera produced significant inhibition of P. vivax sporozoite invasion and liver stage development. This report provides an initial characterization of potential new PE candidates for a future P. vivax vaccine.
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Affiliation(s)
- Justin Nicholas
- Center for Global Health and Interdisciplinary Research, College of Public Health, University of South Florida, Tampa, Florida, United States of America
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, United States of America
| | - Sai Lata De
- Center for Global Health and Interdisciplinary Research, College of Public Health, University of South Florida, Tampa, Florida, United States of America
| | - Pongsakorn Thawornpan
- Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand
| | - Awtum M. Brashear
- Center for Global Health and Interdisciplinary Research, College of Public Health, University of South Florida, Tampa, Florida, United States of America
- Division of Infectious Diseases, Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, United States of America
| | - Surendra Kumar Kolli
- Center for Global Health and Interdisciplinary Research, College of Public Health, University of South Florida, Tampa, Florida, United States of America
| | - Pradeep Annamalai Subramani
- Center for Global Health and Interdisciplinary Research, College of Public Health, University of South Florida, Tampa, Florida, United States of America
| | - Samantha J. Barnes
- Center for Global Health and Interdisciplinary Research, College of Public Health, University of South Florida, Tampa, Florida, United States of America
| | - Liwang Cui
- Center for Global Health and Interdisciplinary Research, College of Public Health, University of South Florida, Tampa, Florida, United States of America
- Division of Infectious Diseases, Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, United States of America
| | - Patchanee Chootong
- Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand
| | - Francis Babila Ntumngia
- Center for Global Health and Interdisciplinary Research, College of Public Health, University of South Florida, Tampa, Florida, United States of America
| | - John H. Adams
- Center for Global Health and Interdisciplinary Research, College of Public Health, University of South Florida, Tampa, Florida, United States of America
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13
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Rumaseb A, Moraes Barros RR, Sá JM, Juliano JJ, William T, Braima KA, Barber BE, Anstey NM, Price RN, Grigg MJ, Marfurt J, Auburn S. No Association between the Plasmodium vivax crt-o MS334 or In9 pvcrt Polymorphisms and Chloroquine Failure in a Pre-Elimination Clinical Cohort from Malaysia with a Large Clonal Expansion. Antimicrob Agents Chemother 2023; 67:e0161022. [PMID: 37314336 PMCID: PMC10353443 DOI: 10.1128/aac.01610-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 05/04/2023] [Indexed: 06/15/2023] Open
Abstract
Increasing reports of resistance to a frontline malaria blood-stage treatment, chloroquine (CQ), raises concerns for the elimination of Plasmodium vivax. The absence of an effective molecular marker of CQ resistance in P. vivax greatly constrains surveillance of this emerging threat. A recent genetic cross between CQ sensitive (CQS) and CQ resistant (CQR) NIH-1993 strains of P. vivax linked a moderate CQR phenotype with two candidate markers in P. vivax CQ resistance transporter gene (pvcrt-o): MS334 and In9pvcrt. Longer TGAAGH motif lengths at MS334 were associated with CQ resistance, as were shorter motifs at the In9pvcrt locus. In this study, high-grade CQR clinical isolates of P. vivax from a low endemic setting in Malaysia were used to investigate the association between the MS334 and In9pvcrt variants and treatment efficacy. Among a total of 49 independent monoclonal P. vivax isolates assessed, high-quality MS334 and In9pvcrt sequences could be derived from 30 (61%) and 23 (47%), respectively. Five MS334 and six In9pvcrt alleles were observed, with allele frequencies ranging from 2 to 76% and 3 to 71%, respectively. None of the clinical isolates had the same variant as the NIH-1993 CQR strain, and none of the variants were associated with CQ treatment failure (all P > 0.05). Multi-locus genotypes (MLGs) at 9 neutral microsatellites revealed a predominant P. vivax strain (MLG6) accounting for 52% of Day 0 infections. The MLG6 strain comprised equal proportions of CQS and CQR infections. Our study reveals complexity in the genetic basis of CQ resistance in the Malaysian P. vivax pre-elimination setting and suggests that the proposed pvcrt-o MS334 and In9pvcrt markers are not reliable markers of CQ treatment efficacy in this setting. Further studies are needed in other endemic settings, applying hypothesis-free genome-wide approaches, and functional approaches to understand the biological impact of the TGAAGH repeats linked to CQ response in a cross are warranted to comprehend and track CQR P. vivax.
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Affiliation(s)
- Angela Rumaseb
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Northern Territory, Australia
| | - Roberto R. Moraes Barros
- Department of Microbiology, Immunology and Parasitology, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Juliana M. Sá
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Jonathan J. Juliano
- Division of Infectious Diseases, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Timothy William
- Clinical Research Centre, Queen Elizabeth Hospital, Sabah, Malaysia
- Infectious Diseases Society Sabah-Menzies School of Health Research Clinical Research Unit, Kota Kinabalu, Sabah, Malaysia
| | - Kamil A. Braima
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Northern Territory, Australia
| | - Bridget E. Barber
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Northern Territory, Australia
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Nicholas M. Anstey
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Northern Territory, Australia
- Infectious Diseases Society Sabah-Menzies School of Health Research Clinical Research Unit, Kota Kinabalu, Sabah, Malaysia
| | - Ric N. Price
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Northern Territory, 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
| | - Matthew J. Grigg
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Northern Territory, Australia
- Infectious Diseases Society Sabah-Menzies School of Health Research Clinical Research Unit, Kota Kinabalu, Sabah, Malaysia
| | - Jutta Marfurt
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Northern Territory, Australia
- College of Medicine and Public Health, Flinders University, Darwin, Northern Territory, Australia
| | - Sarah Auburn
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Northern Territory, 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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14
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Kepple D, Ford CT, Williams J, Abagero B, Li S, Popovici J, Yewhalaw D, Lo E. Comparative transcriptomics reveal differential gene expression in Plasmodium vivax geographical isolates and implications on erythrocyte invasion mechanisms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.16.528793. [PMID: 36824754 PMCID: PMC9949051 DOI: 10.1101/2023.02.16.528793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Plasmodium vivax uses Duffy binding protein (PvDBP1) to bind to the Duffy Antigen-Chemokine Receptor (DARC) to invade human erythrocytes. Individuals who lack DARC expression (Duffy-negative) are thought to be resistance to P. vivax. In recent years, P. vivax malaria is becoming more prevalent in Africa with a portion of these cases detected in Duffy-negatives. Apart from DBP1, members of the reticulocyte binding protein (RBP) and tryptophan-rich antigen (TRAg) families may also play a role in erythrocyte invasion. While the transcriptomes of the Southeast Asian and South American P. vivax are well documented, the gene expression profile of P. vivax in Africa and more specifically the expression level of several erythrocyte binding gene candidates as compared to DBP1 are largely unknown. This paper characterized the first P. vivax transcriptome in Africa and compared with those from the Southeast Asian and South American isolates. The expression of 4,404 gene transcripts belong to 12 functional groups including 43 specific erythrocyte binding gene candidates were examined. Overall, there were 10-26% differences in the gene expression profile amongst the geographical isolates, with the Ethiopian and Cambodian P. vivax being most similar. Majority of the gene transcripts involved in protein transportation, housekeeping, and host interaction were highly transcribed in the Ethiopian P. vivax. Erythrocyte binding genes including PvRBP2a and PvRBP3 expressed six-fold higher than PvDBP1and 60-fold higher than PvEBP/DBP2. Other genes including PvRBP1a, PvMSP3.8, PvMSP3.9, PvTRAG2, PvTRAG14, and PvTRAG22 also showed relatively high expression. Differential expression was observed among geographical isolates, e.g., PvDBP1 and PvEBP/DBP2 were highly expressed in the Cambodian but not the Brazilian and Ethiopian isolates, whereas PvRBP2a and PvRBP2b showed higher expression in the Ethiopian and Cambodian than the Brazilian isolates. Compared to Pvs25, the standard biomarker for detecting female gametocytes, PvAP2-G (PVP01_1440800), GAP (PVP01_1403000), and Pvs47 (PVP01_1208000) were highly expressed across geographical samples. These findings provide an important baseline for future comparisons of P. vivax transcriptomes from Duffy-negative infections and highlight potential biomarkers for improved gametocyte detection.
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Affiliation(s)
- Daniel Kepple
- Biological Sciences, University of North Carolina, Charlotte, NC 28223, USA
| | - Colby T. Ford
- Bioinformatics and Genomics, University of North Carolina, Charlotte, NC 28223, USA
- School of Data Science, University of North Carolina, Charlotte, NC 28223, USA
| | - Jonathan Williams
- Biological Sciences, University of North Carolina, Charlotte, NC 28223, USA
| | - Beka Abagero
- Biological Sciences, University of North Carolina, Charlotte, NC 28223, USA
| | - Shaoyu Li
- Mathematics and Statistics, University of North Carolina, Charlotte, NC 28223, USA
| | - Jean Popovici
- Malaria Research Unit, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Delenasaw Yewhalaw
- Tropical and Infectious Diseases Research Center, Jimma University, Jimma, Ethiopia
- School of Medical Laboratory Sciences, Faculty of Health Sciences, Jimma University, Jimma, Ethiopia
| | - Eugenia Lo
- Biological Sciences, University of North Carolina, Charlotte, NC 28223, USA
- School of Data Science, University of North Carolina, Charlotte, NC 28223, USA
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15
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Liu Y, Zhang T, Chen SB, Cui YB, Wang SQ, Zhang HW, Shen HM, Chen JH. Retrospective analysis of Plasmodium vivax genomes from a pre-elimination China inland population in the 2010s. Front Microbiol 2023; 14:1071689. [PMID: 36846776 PMCID: PMC9948256 DOI: 10.3389/fmicb.2023.1071689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Accepted: 01/04/2023] [Indexed: 02/11/2023] Open
Abstract
Introduction In malaria-free countries, imported cases are challenging because interconnections with neighboring countries with higher transmission rates increase the risk of parasite reintroduction. Establishing a genetic database for rapidly identifying malaria importation or reintroduction is crucial in addressing these challenges. This study aimed to examine genomic epidemiology during the pre-elimination stage by retrospectively reporting whole-genome sequence variation of 10 Plasmodium vivax isolates from inland China. Methods The samples were collected during the last few inland outbreaks from 2011 to 2012 when China implemented a malaria control plan. After next-generation sequencing, we completed a genetic analysis of the population, explored the geographic specificity of the samples, and examined clustering of selection pressures. We also scanned genes for signals of positive selection. Results China's inland populations were highly structured compared to the surrounding area, with a single potential ancestor. Additionally, we identified genes under selection and evaluated the selection pressure on drug-resistance genes. In the inland population, positive selection was detected in some critical gene families, including sera, msp3, and vir. Meanwhile, we identified selection signatures in drug resistance, such as ugt, krs1, and crt, and noticed that the ratio of wild-type dhps and dhfr-ts increased after China banned sulfadoxine-pyrimethamine (SP) for decades. Discussion Our data provides an opportunity to investigate the molecular epidemiology of pre-elimination inland malaria populations, which exhibited lower selection pressure on invasion and immune evasion genes than neighbouring areas, but increased drug resistance in low transmission settings. Our results revealed that the inland population was severely fragmented with low relatedness among infections, despite a higher incidence of multiclonal infections, suggesting that superinfection or co-transmission events are rare in low-endemic circumstances. We identified selective signatures of resistance and found that the proportion of susceptible isolates fluctuated in response to the prohibition of specific drugs. This finding is consistent with the alterations in medication strategies during the malaria elimination campaign in inland China. Such findings could provide a genetic basis for future population studies, assessing changes in other pre-elimination countries.
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Affiliation(s)
- Ying Liu
- National Institute of Parasitic Diseases, Chinese Center for Diseases Control and Prevention (Chinese Center for Tropical Diseases Research), Shanghai, China,National Health Commission of the People’s Republic of China (NHC) Key Laboratory of Parasite and Vector Biology, Shanghai, China,World Health Organization (WHO) Collaborating Center for Tropical Diseases, Shanghai, China,National Center for International Research on Tropical Diseases, Shanghai, China,Henan Provincial Center for Disease Control and Prevention, Zhengzhou, China
| | - Tao Zhang
- Anhui Provincial Center for Disease Control and Prevention, Hefei, China
| | - Shen-Bo Chen
- National Institute of Parasitic Diseases, Chinese Center for Diseases Control and Prevention (Chinese Center for Tropical Diseases Research), Shanghai, China,National Health Commission of the People’s Republic of China (NHC) Key Laboratory of Parasite and Vector Biology, Shanghai, China,World Health Organization (WHO) Collaborating Center for Tropical Diseases, Shanghai, China,National Center for International Research on Tropical Diseases, Shanghai, China
| | - Yan-Bing Cui
- National Institute of Parasitic Diseases, Chinese Center for Diseases Control and Prevention (Chinese Center for Tropical Diseases Research), Shanghai, China,National Health Commission of the People’s Republic of China (NHC) Key Laboratory of Parasite and Vector Biology, Shanghai, China,World Health Organization (WHO) Collaborating Center for Tropical Diseases, Shanghai, China,National Center for International Research on Tropical Diseases, Shanghai, China
| | - Shu-Qi Wang
- Anhui Provincial Center for Disease Control and Prevention, Hefei, China
| | - Hong-Wei Zhang
- Henan Provincial Center for Disease Control and Prevention, Zhengzhou, China
| | - Hai-Mo Shen
- National Institute of Parasitic Diseases, Chinese Center for Diseases Control and Prevention (Chinese Center for Tropical Diseases Research), Shanghai, China,National Health Commission of the People’s Republic of China (NHC) Key Laboratory of Parasite and Vector Biology, Shanghai, China,World Health Organization (WHO) Collaborating Center for Tropical Diseases, Shanghai, China,National Center for International Research on Tropical Diseases, Shanghai, China,Hai-Mo Shen, ✉
| | - Jun-Hu Chen
- National Institute of Parasitic Diseases, Chinese Center for Diseases Control and Prevention (Chinese Center for Tropical Diseases Research), Shanghai, China,National Health Commission of the People’s Republic of China (NHC) Key Laboratory of Parasite and Vector Biology, Shanghai, China,World Health Organization (WHO) Collaborating Center for Tropical Diseases, Shanghai, China,National Center for International Research on Tropical Diseases, Shanghai, China,School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China,*Correspondence: Jun-Hu Chen, ✉
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16
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Dombrowski JG, Acford-Palmer H, Campos M, Separovic EPM, Epiphanio S, Clark TG, Campino S, Marinho CRF. Genetic diversity of Plasmodium vivax isolates from pregnant women in the Western Brazilian Amazon: a prospective cohort study. LANCET REGIONAL HEALTH. AMERICAS 2023; 18:100407. [PMID: 36844021 PMCID: PMC9950542 DOI: 10.1016/j.lana.2022.100407] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 09/16/2022] [Accepted: 11/11/2022] [Indexed: 12/03/2022]
Abstract
Background Each year, 92 million pregnant women are at risk of contracting malaria during pregnancy, with the underestimation of the mortality and morbidity burden associated with Plasmodium vivax. During pregnancy, P. vivax infection is associated with low birth weight, maternal anaemia, premature delivery, and stillbirth. In the State of Acre (Brazil), high transmission leaves pregnant women at greater risk of contracting malaria and having a greater number of recurrences. The study of genetic diversity and the association of haplotypes with adverse pregnancy effects is of great importance for the control of the disease. Here we investigate the genetic diversity of P. vivax parasites infecting pregnant women across their pregnancies. Methods P. vivax DNA was extracted from 330 samples from 177 women followed during pregnancy, collected in the State of Acre, Brazil. All samples were negative for Plasmodium falciparum DNA. Sequence data for the Pvmsp1 gene was analysed alongside data from six microsatellite (MS) markers. Allelic frequencies, haplotype frequencies, expected heterozygosity (HE) were calculated. Whole genome sequencing (WGS) was conducted on four samples from pregnant women and phylogenetic analysis performed with other samples from South American regions. Findings Initially, the pregnant women were stratified into two groups-1 recurrence and 2 or more recurrences-in which no differences were observed in clinical gestational outcomes or in placental histological changes between the two groups. Then we evaluated the parasites genetically. An average of 18.5 distinct alleles were found at each of the MS loci, and the HE calculated for each marker indicates a high genetic diversity occurring within the population. There was a high percentage of polyclonal infections (61.7%, 108/175), and one haplotype (H1) occurred frequently (20%), with only 9 of the haplotypes appearing in more than one patient. Interpretation Most pregnant women had polyclonal infections that could be the result of relapses and/or re-infections. The high percentage of H1 parasites, along with the low frequency of many other haplotypes are suggestive of a clonal expansion. Phylogenetic analysis shows that P. vivax population within pregnant women clustered with other Brazilian samples in the region. Funding FAPESP and CNPq - Brazil.
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Affiliation(s)
| | - Holly Acford-Palmer
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Monica Campos
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | | | - Sabrina Epiphanio
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Taane Gregory Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Susana Campino
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
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17
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Ibrahim A, Manko E, Dombrowski JG, Campos M, Benavente ED, Nolder D, Sutherland CJ, Nosten F, Fernandez D, Vélez-Tobón G, Castaño AT, Aguiar ACC, Pereira DB, da Silva Santos S, Suarez-Mutis M, Di Santi SM, Regina de Souza Baptista A, Dantas Machado RL, Marinho CR, Clark TG, Campino S. Population-based genomic study of Plasmodium vivax malaria in seven Brazilian states and across South America. LANCET REGIONAL HEALTH. AMERICAS 2023; 18:100420. [PMID: 36844008 PMCID: PMC9950661 DOI: 10.1016/j.lana.2022.100420] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 12/06/2022] [Accepted: 12/06/2022] [Indexed: 01/03/2023]
Abstract
Background Brazil is a unique and understudied setting for malaria, with complex foci of transmission associated with human and environmental conditions. An understanding of the population genomic diversity of P. vivax parasites across Brazil can support malaria control strategies. Methods Through whole genome sequencing of P. vivax isolates across 7 Brazilian states, we use population genomic approaches to compare genetic diversity within country (n = 123), continent (6 countries, n = 315) and globally (26 countries, n = 885). Findings We confirm that South American isolates are distinct, have more ancestral populations than the other global regions, with differentiating mutations in genes under selective pressure linked to antimalarial drugs (pvmdr1, pvdhfr-ts) and mosquito vectors (pvcrmp3, pvP45/48, pvP47). We demonstrate Brazil as a distinct parasite population, with signals of selection including ABC transporter (PvABCI3) and PHIST exported proteins. Interpretation Brazil has a complex population structure, with evidence of P. simium infections and Amazonian parasites separating into multiple clusters. Overall, our work provides the first Brazil-wide analysis of P. vivax population structure and identifies important mutations, which can inform future research and control measures. Funding AI is funded by an MRC LiD PhD studentship. TGC is funded by the Medical Research Council (Grant no. MR/M01360X/1, MR/N010469/1, MR/R025576/1, MR/R020973/1 and MR/X005895/1). SC is funded by Medical Research Council UK grants (MR/M01360X/1, MR/R025576/1, MR/R020973/1 and MR/X005895/1) and Bloomsbury SET (ref. CCF17-7779). FN is funded by The Shloklo Malaria Research Unit - part of the Mahidol Oxford Research Unit, supported by the Wellcome Trust (Grant no. 220211). ARSB is funded by São Paulo Research Foundation - FAPESP (Grant no. 2002/09546-1). RLDM is funded by Brazilian National Council for Scientific and Technological Development - CNPq (Grant no. 302353/2003-8 and 471605/2011-5); CRFM is funded by FAPESP (Grant no. 2020/06747-4) and CNPq (Grant no. 302917/2019-5 and 408636/2018-1); JGD is funded by FAPESP fellowships (2016/13465-0 and 2019/12068-5) and CNPq (Grant no. 409216/2018-6).
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Affiliation(s)
- Amy Ibrahim
- Faculty of Infectious & Tropical Diseases, London School of Hygiene
& Tropical Medicine, London, UK
| | - Emilia Manko
- Faculty of Infectious & Tropical Diseases, London School of Hygiene
& Tropical Medicine, London, UK
| | - Jamille G. Dombrowski
- Department of Parasitology, Institute of Biomedical Sciences, University
of São Paulo, São Paulo, Brazil
| | - Mónica Campos
- Faculty of Infectious & Tropical Diseases, London School of Hygiene
& Tropical Medicine, London, UK
| | - Ernest Diez Benavente
- Faculty of Infectious & Tropical Diseases, London School of Hygiene
& Tropical Medicine, London, UK
| | - Debbie Nolder
- Faculty of Infectious & Tropical Diseases, London School of Hygiene
& Tropical Medicine, London, UK
- Public Health England Malaria Reference Laboratory, London School of
Hygiene & Tropical Medicine, London, UK
| | - Colin J. Sutherland
- Faculty of Infectious & Tropical Diseases, London School of Hygiene
& Tropical Medicine, London, UK
- Public Health England Malaria Reference Laboratory, London School of
Hygiene & Tropical Medicine, London, UK
| | - Francois Nosten
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research
Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Tak,
Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of
Clinical Medicine Research Building, University of Oxford Old Road Campus,
Oxford, UK
| | - Diana Fernandez
- Grupo Malaria, Facultad de Medicina, Universidad de Antioquia, Antioquia,
Colombia
| | - Gabriel Vélez-Tobón
- Grupo Malaria, Facultad de Medicina, Universidad de Antioquia, Antioquia,
Colombia
| | | | | | | | - Simone da Silva Santos
- Laboratório de Doenças Parasitárias, Institute Oswaldo Cruz - Fiocruz-
Rio de Janeiro, Brazil
| | - Martha Suarez-Mutis
- Laboratório de Doenças Parasitárias, Institute Oswaldo Cruz - Fiocruz-
Rio de Janeiro, Brazil
| | | | - Andrea Regina de Souza Baptista
- Centro de Investigação de Microrganismos – CIM, Departamento de
Microbiologia e Parasitologia, Universidade Federal Fluminense,
Brazil
| | - Ricardo Luiz Dantas Machado
- Centro de Investigação de Microrganismos – CIM, Departamento de
Microbiologia e Parasitologia, Universidade Federal Fluminense,
Brazil
| | - Claudio R.F. Marinho
- Department of Parasitology, Institute of Biomedical Sciences, University
of São Paulo, São Paulo, Brazil
| | - Taane G. Clark
- Faculty of Infectious & Tropical Diseases, London School of Hygiene
& Tropical Medicine, London, UK
- Faculty of Epidemiology & Population Health, London School of Hygiene
& Tropical Medicine, London, UK
| | - Susana Campino
- Faculty of Infectious & Tropical Diseases, London School of Hygiene
& Tropical Medicine, London, UK
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18
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Trimarsanto H, Amato R, Pearson RD, Sutanto E, Noviyanti R, Trianty L, Marfurt J, Pava Z, Echeverry DF, Lopera-Mesa TM, Montenegro LM, Tobón-Castaño A, Grigg MJ, Barber B, William T, Anstey NM, Getachew S, Petros B, Aseffa A, Assefa A, Rahim AG, Chau NH, Hien TT, Alam MS, Khan WA, Ley B, Thriemer K, Wangchuck S, Hamedi Y, Adam I, Liu Y, Gao Q, Sriprawat K, Ferreira MU, Laman M, Barry A, Mueller I, Lacerda MVG, Llanos-Cuentas A, Krudsood S, Lon C, Mohammed R, Yilma D, Pereira DB, Espino FEJ, Chu CS, Vélez ID, Namaik-Larp C, Villegas MF, Green JA, Koh G, Rayner JC, Drury E, Gonçalves S, Simpson V, Miotto O, Miles A, White NJ, Nosten F, Kwiatkowski DP, Price RN, Auburn S. A molecular barcode and web-based data analysis tool to identify imported Plasmodium vivax malaria. Commun Biol 2022; 5:1411. [PMID: 36564617 PMCID: PMC9789135 DOI: 10.1038/s42003-022-04352-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 12/08/2022] [Indexed: 12/25/2022] Open
Abstract
Traditionally, patient travel history has been used to distinguish imported from autochthonous malaria cases, but the dormant liver stages of Plasmodium vivax confound this approach. Molecular tools offer an alternative method to identify, and map imported cases. Using machine learning approaches incorporating hierarchical fixation index and decision tree analyses applied to 799 P. vivax genomes from 21 countries, we identified 33-SNP, 50-SNP and 55-SNP barcodes (GEO33, GEO50 and GEO55), with high capacity to predict the infection's country of origin. The Matthews correlation coefficient (MCC) for an existing, commonly applied 38-SNP barcode (BR38) exceeded 0.80 in 62% countries. The GEO panels outperformed BR38, with median MCCs > 0.80 in 90% countries at GEO33, and 95% at GEO50 and GEO55. An online, open-access, likelihood-based classifier framework was established to support data analysis (vivaxGEN-geo). The SNP selection and classifier methods can be readily amended for other use cases to support malaria control programs.
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Affiliation(s)
- Hidayat Trimarsanto
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, NT, Australia
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia
| | - Roberto Amato
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | | | - Edwin Sutanto
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia
- Exeins Health Initiative, Jakarta, Indonesia
| | | | - Leily Trianty
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia
| | - Jutta Marfurt
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, NT, Australia
| | - Zuleima Pava
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, NT, Australia
| | - Diego F Echeverry
- International Training and Medical Research Center (CIDEIM), Cali, Colombia
- Departamento de Microbiología, Universidad del Valle, Cali, Colombia
- Universidad Icesi, Cali, Colombia
| | | | | | | | - Matthew J Grigg
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, NT, Australia
- Infectious Diseases Society Sabah-Menzies School of Health Research Clinical Research Unit, Kota Kinabalu, Sabah, Malaysia
| | - Bridget Barber
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, NT, Australia
- Infectious Diseases Society Sabah-Menzies School of Health Research Clinical Research Unit, Kota Kinabalu, Sabah, Malaysia
| | - Timothy William
- Infectious Diseases Society Sabah-Menzies School of Health Research Clinical Research Unit, Kota Kinabalu, Sabah, Malaysia
- Clinical Research Centre, Queen Elizabeth Hospital, Sabah, Malaysia
| | - Nicholas M Anstey
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, NT, Australia
| | - Sisay Getachew
- College of Natural Sciences, Addis Ababa University, Addis Ababa, Ethiopia
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Beyene Petros
- College of Natural Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Abraham Aseffa
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | | | - Awab G Rahim
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
- Nangarhar Medical Faculty, Nangarhar University, Ministry of Higher Education, Jalalabad, Afghanistan
| | - Nguyen H Chau
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Tran T Hien
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Mohammad S Alam
- Infectious Diseases Division, International Centre for Diarrheal Diseases Research, Dhaka, Bangladesh
| | - Wasif A Khan
- Infectious Diseases Division, International Centre for Diarrheal Diseases Research, Dhaka, Bangladesh
| | - Benedikt Ley
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, NT, Australia
| | - Kamala Thriemer
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, NT, Australia
| | - Sonam Wangchuck
- Royal Center for Disease Control, Department of Public Health, Ministry of Health, Thimphu, Bhutan
| | - Yaghoob Hamedi
- Infectious and Tropical Diseases Research Center, Hormozgan University of Medical Sciences, Bandar Abbas, Hormozgan Province, Iran
| | - Ishag Adam
- Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Yaobao Liu
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, China
- School of Public Health, Nanjing Medical University, Nanjing, China
| | - Qi Gao
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, China
| | - Kanlaya Sriprawat
- Shoklo Malaria Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Marcelo U Ferreira
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
- Global Health and Tropical Medicine, Institute of Hygiene and Tropical Medicine, NOVA University of Lisbon, Lisbon, Portugal
| | - Moses Laman
- Papua New Guinea Institute of Medical Research, Madang, Papua New Guinea
| | - Alyssa Barry
- Deakin University, Victoria, Australia
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Victoria, Australia
| | - Ivo Mueller
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Victoria, Australia
- Department of Parasites and Insect Vectors, Institut Pasteur, Paris, France
| | - Marcus V G Lacerda
- Fundação de Medicina Tropical, Manaus, Brazil
- Fundação Oswaldo Cruz, Manguinhos, Rio de Janeiro, Brazil
| | | | | | - Chanthap Lon
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | | | | | | | - Fe E J Espino
- Research Institute for Tropical Medicine, Manilla, Philippines
| | - Cindy S Chu
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
- Shoklo Malaria Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Iván D Vélez
- Malaria Group, Universidad de Antioquia, Medellin, Colombia
| | | | | | | | | | - Julian C Rayner
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Cambridge Institute for Medical Research, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Eleanor Drury
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Sónia Gonçalves
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Victoria Simpson
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Olivo Miotto
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Alistair Miles
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Nicholas J White
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Francois Nosten
- Shoklo Malaria Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Ric N Price
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, NT, Australia
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Sarah Auburn
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, NT, Australia.
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand.
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
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19
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Bouyssou I, Martínez FJ, Campagne P, Ma L, Doderer-Lang C, Chitnis CE, Ménard D. Plasmodium vivax blood stage invasion pathways: Contribution of omics technologies in deciphering molecular and cellular mechanisms. C R Biol 2022; 345:91-133. [PMID: 36847467 DOI: 10.5802/crbiol.95] [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: 10/26/2022] [Accepted: 10/27/2022] [Indexed: 11/25/2022]
Abstract
Vivax malaria is an infectious disease caused by Plasmodium vivax, a parasitic protozoan transmitted by female Anopheline mosquitoes. Historically, vivax malaria has often been regarded as a benign self-limiting infection due to the observation of low parasitemia in Duffy-positive patients in endemic transmission areas and the virtual absence of infections in Duffy-negative individuals in Sub Saharan Africa. However, the latest estimates show that the burden of the disease is not decreasing in many countries and cases of vivax infections in Duffy-negative individuals are increasingly reported throughout Africa. This raised questions about the accuracy of diagnostics and the evolution of interactions between humans and parasites. For a long time, our knowledge on P. vivax biology has been hampered due to the limited access to biological material and the lack of robust in vitro culture methods. Consequently, little is currently known about P. vivax blood stage invasion mechanisms. The introduction of omics technologies with novel and accessible techniques such as third generation sequencing and RNA sequencing at single cell level, two-dimensional electrophoresis, liquid chromatography, and mass spectrometry, has progressively improved our understanding of P. vivax genetics, transcripts, and proteins. This review aims to provide broad insights into P. vivax invasion mechanisms generated by genomics, transcriptomics, and proteomics and to illustrate the importance of integrated multi-omics studies.
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20
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Hazzard B, Sá JM, Ellis AC, Pascini TV, Amin S, Wellems TE, Serre D. Long read single cell RNA sequencing reveals the isoform diversity of Plasmodium vivax transcripts. PLoS Negl Trop Dis 2022; 16:e0010991. [PMID: 36525464 PMCID: PMC9803293 DOI: 10.1371/journal.pntd.0010991] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 12/30/2022] [Accepted: 11/28/2022] [Indexed: 12/23/2022] Open
Abstract
Plasmodium vivax infections often consist of heterogenous populations of parasites at different developmental stages and with distinct transcriptional profiles, which complicates gene expression analyses. The advent of single cell RNA sequencing (scRNA-seq) enabled disentangling this complexity and has provided robust and stage-specific characterization of Plasmodium gene expression. However, scRNA-seq information is typically derived from the end of each mRNA molecule (usually the 3'-end) and therefore fails to capture the diversity in transcript isoforms documented in bulk RNA-seq data. Here, we describe the sequencing of scRNA-seq libraries using Pacific Biosciences (PacBio) chemistry to characterize full-length Plasmodium vivax transcripts from single cell parasites. Our results show that many P. vivax genes are transcribed into multiple isoforms, primarily through variations in untranslated region (UTR) length or splicing, and that the expression of many isoforms is developmentally regulated. Our findings demonstrate that long read sequencing can be used to characterize mRNA molecules at the single cell level and provides an additional resource to better understand the regulation of gene expression throughout the Plasmodium life cycle.
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Affiliation(s)
- Brittany Hazzard
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Juliana M. Sá
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Angela C. Ellis
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Tales V. Pascini
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Shuchi Amin
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Thomas E. Wellems
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - David Serre
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
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21
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Development and Optimization of a Selective Whole-Genome Amplification To Study Plasmodium ovale Spp. Microbiol Spectr 2022; 10:e0072622. [PMID: 36098524 PMCID: PMC9602584 DOI: 10.1128/spectrum.00726-22] [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] [Indexed: 12/30/2022] Open
Abstract
Since 2010, the human-infecting malaria parasite Plasmodium ovale spp. has been divided into two genetically distinct species, P. ovale wallikeri and P. ovale curtisi. In recent years, application of whole-genome sequencing (WGS) to P. ovale spp. allowed to get a better understanding of its evolutionary history and discover some specific genetic patterns. Nevertheless, WGS data from P. ovale spp. are still scarce due to several drawbacks, including a high level of human DNA contamination in blood samples, infections with commonly low parasite density, and the lack of robust in vitro culture. Here, we developed two selective whole-genome amplification (sWGA) protocols that were tested on six P. ovale wallikeri and five P. ovale curtisi mono-infection clinical samples. Blood leukodepletion by a cellulose-based filtration was used as the gold standard for intraspecies comparative genomics with sWGA. We also demonstrated the importance of genomic DNA preincubation with the endonuclease McrBC to optimize P. ovale spp. sWGA. We obtained high-quality WGS data with more than 80% of the genome covered by ≥5 reads for each sample and identified more than 5,000 unique single-nucleotide polymorphisms (SNPs) per species. We also identified some amino acid changes in pocdhfr and powdhfr for which similar mutations in P. falciparum and P. vivax are associated with pyrimethamine or cycloguanil resistance. In conclusion, we developed two sWGA protocols for P. ovale spp. WGS that will help to design much-needed large-scale P. ovale spp. population studies. IMPORTANCE Plasmodium ovale spp. has the ability to cause relapse, defined as recurring asexual parasitemia originating from liver-dormant forms. Whole-genome sequencing (WGS) data are of importance to identify putative molecular markers associated with relapse or other virulence mechanisms. Due to low parasitemia encountered in P. ovale spp. infections and no in vitro culture available, WGS of P. ovale spp. is challenging. Blood leukodepletion by filtration has been used, but no technique exists yet to increase the quantity of parasite DNA over human DNA when starting from genomic DNA extracted from whole blood. Here, we demonstrated that selective whole-genome amplification (sWGA) is an easy-to-use protocol to obtain high-quality WGS data for both P. ovale spp. species from unprocessed blood samples. The new method will facilitate P. ovale spp. population genomic studies.
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22
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Genome-wide functional screening of drug-resistance genes in Plasmodium falciparum. Nat Commun 2022; 13:6163. [PMID: 36257944 PMCID: PMC9579134 DOI: 10.1038/s41467-022-33804-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 09/30/2022] [Indexed: 12/24/2022] Open
Abstract
The global spread of drug resistance is a major obstacle to the treatment of Plasmodium falciparum malaria. The identification of drug-resistance genes is an essential step toward solving the problem of drug resistance. Here, we report functional screening as a new approach with which to identify drug-resistance genes in P. falciparum. Specifically, a high-coverage genomic library of a drug-resistant strain is directly generated in a drug-sensitive strain, and the resistance gene is then identified from this library using drug screening. In a pilot experiment using the strain Dd2, the known chloroquine-resistant gene pfcrt is identified using the developed approach, which proves our experimental concept. Furthermore, we identify multidrug-resistant transporter 7 (pfmdr7) as a novel candidate for a mefloquine-resistance gene from a field-isolated parasite; we suggest that its upregulation possibly confers the mefloquine resistance. These results show the usefulness of functional screening as means by which to identify drug-resistance genes.
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23
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Lê HG, Naw H, Kang JM, Võ TC, Myint MK, Htun ZT, Lee J, Yoo WG, Kim TS, Shin HJ, Na BK. Molecular Profiles of Multiple Antimalarial Drug Resistance Markers in Plasmodium falciparum and Plasmodium vivax in the Mandalay Region, Myanmar. Microorganisms 2022; 10:2021. [PMID: 36296297 PMCID: PMC9612053 DOI: 10.3390/microorganisms10102021] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 10/05/2022] [Accepted: 10/08/2022] [Indexed: 09/21/2023] Open
Abstract
Emergence and spreading of antimalarial drug resistant malaria parasites are great hurdles to combating malaria. Although approaches to investigate antimalarial drug resistance status in Myanmar malaria parasites have been made, more expanded studies are necessary to understand the nationwide aspect of antimalarial drug resistance. In the present study, molecular epidemiological analysis for antimalarial drug resistance genes in Plasmodium falciparum and P. vivax from the Mandalay region of Myanmar was performed. Blood samples were collected from patients infected with P. falciparum and P. vivax in four townships around the Mandalay region, Myanmar in 2015. Partial regions flanking major mutations in 11 antimalarial drug resistance genes, including seven genes (pfdhfr, pfdhps, pfmdr-1, pfcrt, pfk13, pfubp-1, and pfcytb) of P. falciparum and four genes (pvdhfr, pvdhps, pvmdr-1, and pvk12) of P. vivax were amplified, sequenced, and overall mutation patterns in these genes were analyzed. Substantial levels of mutations conferring antimalarial drug resistance were detected in both P. falciparum and P. vivax isolated in Mandalay region of Myanmar. Mutations associated with sulfadoxine-pyrimethamine resistance were found in pfdhfr, pfdhps, pvdhfr, and pvdhps of Myanmar P. falciparum and P. vivax with very high frequencies up to 90%. High or moderate levels of mutations were detected in genes such as pfmdr-1, pfcrt, and pvmdr-1 associated with chloroquine resistance. Meanwhile, low frequency mutations or none were found in pfk13, pfubp-1, pfcytb, and pvk12 of the parasites. Overall molecular profiles for antimalarial drug resistance genes in malaria parasites in the Mandalay region suggest that parasite populations in the region have substantial levels of mutations conferring antimalarial drug resistance. Continuous monitoring of mutations linked with antimalarial drug resistance is necessary to provide useful information for policymakers to plan for proper antimalarial drug regimens to control and eliminate malaria in the country.
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Affiliation(s)
- Hương Giang Lê
- Department of Parasitology and Tropical Medicine, Institute of Health Sciences, Gyeongsang National University College of Medicine, Jinju 52727, Korea
- Department of Convergence Medical Science, Gyeongsang National University, Jinju 52727, Korea
| | - Haung Naw
- Department of Parasitology and Tropical Medicine, Institute of Health Sciences, Gyeongsang National University College of Medicine, Jinju 52727, Korea
- Department of Convergence Medical Science, Gyeongsang National University, Jinju 52727, Korea
| | - Jung-Mi Kang
- Department of Parasitology and Tropical Medicine, Institute of Health Sciences, Gyeongsang National University College of Medicine, Jinju 52727, Korea
- Department of Convergence Medical Science, Gyeongsang National University, Jinju 52727, Korea
| | - Tuấn Cường Võ
- Department of Parasitology and Tropical Medicine, Institute of Health Sciences, Gyeongsang National University College of Medicine, Jinju 52727, Korea
- Department of Convergence Medical Science, Gyeongsang National University, Jinju 52727, Korea
| | - Moe Kyaw Myint
- Department of Medical Research Pyin Oo Lwin Branch, Pyin Oo Lwin 05062, Myanmar
| | - Zaw Than Htun
- Department of Medical Research Pyin Oo Lwin Branch, Pyin Oo Lwin 05062, Myanmar
| | - Jinyoung Lee
- Department of Tropical Medicine, Inha Research Institute for Medical Sciences, Inha University College of Medicine, Incheon 22212, Korea
| | - Won Gi Yoo
- Department of Parasitology and Tropical Medicine, Institute of Health Sciences, Gyeongsang National University College of Medicine, Jinju 52727, Korea
- Department of Convergence Medical Science, Gyeongsang National University, Jinju 52727, Korea
| | - Tong-Soo Kim
- Department of Tropical Medicine, Inha Research Institute for Medical Sciences, Inha University College of Medicine, Incheon 22212, Korea
| | - Ho-Joon Shin
- Department of Microbiology, Ajou University College of Medicine, Suwon 16499, Korea
| | - Byoung-Kuk Na
- Department of Parasitology and Tropical Medicine, Institute of Health Sciences, Gyeongsang National University College of Medicine, Jinju 52727, Korea
- Department of Convergence Medical Science, Gyeongsang National University, Jinju 52727, Korea
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De Meulenaere K, Prajapati SK, Villasis E, Cuypers B, Kattenberg JH, Kasian B, Laman M, Robinson LJ, Gamboa D, Laukens K, Rosanas-Urgell A. Band 3–mediated Plasmodium vivax invasion is associated with transcriptional variation in PvTRAg genes. Front Cell Infect Microbiol 2022; 12:1011692. [PMID: 36250048 PMCID: PMC9563252 DOI: 10.3389/fcimb.2022.1011692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 09/09/2022] [Indexed: 11/13/2022] Open
Abstract
The Plasmodium vivax reticulocyte invasion process is still poorly understood, with only a few receptor-ligand interactions identified to date. Individuals with the Southeast Asian ovalocytosis (SAO) phenotype have a deletion in the band 3 protein on the surface of erythrocytes, and are reported to have a lower incidence of clinical P. vivax malaria. Based on this observation, band 3 has been put forward as a receptor for P. vivax invasion, although direct proof is still lacking. In this study, we combined functional ex vivo invasion assays and transcriptome sequencing to uncover a band 3–mediated invasion pathway in P. vivax and potential band 3 ligands. Invasion by P. vivax field isolates was 67%-71% lower in SAO reticulocytes compared with non-SAO reticulocytes. Reticulocyte invasion was decreased by 40% and 27%-31% when blocking with an anti-band 3 polyclonal antibody and a PvTRAg38 peptide, respectively. To identify new band 3 receptor candidates, we mRNA-sequenced schizont-stage isolates used in the invasion assays, and observed high transcriptional variability in multigene and invasion-related families. Transcriptomes of isolates with low or high dependency on band 3 for invasion were compared by differential expression analysis, which produced a list of band 3 ligand candidates with high representation of PvTRAg genes. Our ex vivo invasion assays have demonstrated that band 3 is a P. vivax invasion receptor and confirm previous in vitro studies showing binding between PvTRAg38 and band 3, although the lower and variable inhibition levels observed suggest the involvement of other ligands. By coupling transcriptomes and invasion phenotypes from the same isolates, we identified a list of band 3 ligand candidates, of which the overrepresented PvTRAg genes are the most promising for future research.
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Affiliation(s)
- Katlijn De Meulenaere
- Department of Biomedical Sciences, Institute of Tropical Medicine Antwerp, Antwerp, Belgium
- Department of Computer Science, University of Antwerp, Antwerp, Belgium
- *Correspondence: Anna Rosanas-Urgell, ; Katlijn De Meulenaere,
| | - Surendra Kumar Prajapati
- Department of Biomedical Sciences, Institute of Tropical Medicine Antwerp, Antwerp, Belgium
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Elizabeth Villasis
- Laboratorio de Malaria, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Bart Cuypers
- Department of Computer Science, University of Antwerp, Antwerp, Belgium
| | | | - Bernadine Kasian
- Vector-borne Diseases Unit, Papua New Guinea Institute for Medical Research, Madang, Papua New Guinea
| | - Moses Laman
- Vector-borne Diseases Unit, Papua New Guinea Institute for Medical Research, Madang, Papua New Guinea
| | - Leanne J. Robinson
- Vector-borne Diseases Unit, Papua New Guinea Institute for Medical Research, Madang, Papua New Guinea
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
- Health Security and Disease Elimination, Burnet Institute, Melbourne, VIC, Australia
| | - Dionicia Gamboa
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
- Departamento de Ciencias Celulares y Moleculares, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Kris Laukens
- Department of Computer Science, University of Antwerp, Antwerp, Belgium
| | - Anna Rosanas-Urgell
- Department of Biomedical Sciences, Institute of Tropical Medicine Antwerp, Antwerp, Belgium
- *Correspondence: Anna Rosanas-Urgell, ; Katlijn De Meulenaere,
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25
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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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Gill J, Sharma A. Genomic analysis of single nucleotide polymorphisms in malaria parasite drug targets. Parasit Vectors 2022; 15:309. [PMID: 36042490 PMCID: PMC9425944 DOI: 10.1186/s13071-022-05422-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 07/22/2022] [Indexed: 12/02/2022] Open
Abstract
Malaria is a life-threatening parasitic disease caused by members of the genus Plasmodium. The development and spread of drug-resistant strains of Plasmodium parasites represent a major challenge to malaria control and elimination programmes. Evaluating genetic polymorphism in a drug target improves our understanding of drug resistance and facilitates drug design. Approximately 450 and 19 whole-genome assemblies of Plasmodium falciparum and Plasmodium vivax, respectively, are currently available, and numerous sequence variations have been found due to the presence of single nucleotide polymorphism (SNP). In the study reported here, we analysed global SNPs in the malaria parasite aminoacyl-tRNA synthetases (aaRSs). Our analysis revealed 3182 unique SNPs in the 20 cytoplasmic P. falciparum aaRSs. Structural mapping of SNPs onto the three-dimensional inhibitor-bound complexes of the three advanced drug targets within aaRSs revealed a remarkably low mutation frequency in the crucial aminoacylation domains, low overall occurrence of mutations across samples and high conservation in drug/substrate binding regions. In contrast to aaRSs, dihydropteroate synthase (DHPS), also a malaria drug target, showed high occurrences of drug resistance-causing mutations. Our results show that it is pivotal to screen potent malaria drug targets against global SNP profiles to assess genetic variances to ensure success in designing drugs against validated targets and tackle drug resistance early on.
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Affiliation(s)
- Jasmita Gill
- ICMR-National Institute of Malaria Research, Sector 8, Dwarka, 110077, New Delhi, India
| | - Amit Sharma
- ICMR-National Institute of Malaria Research, Sector 8, Dwarka, 110077, New Delhi, India. .,International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, India.
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27
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Kattenberg JH, Nguyen HV, Nguyen HL, Sauve E, Nguyen NTH, Chopo-Pizarro A, Trimarsanto H, Monsieurs P, Guetens P, Nguyen XX, Esbroeck MV, Auburn S, Nguyen BTH, Rosanas-Urgell A. Novel highly-multiplexed AmpliSeq targeted assay for Plasmodium vivax genetic surveillance use cases at multiple geographical scales. Front Cell Infect Microbiol 2022; 12:953187. [PMID: 36034708 PMCID: PMC9403277 DOI: 10.3389/fcimb.2022.953187] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 07/19/2022] [Indexed: 11/17/2022] Open
Abstract
Although the power of genetic surveillance tools has been acknowledged widely, there is an urgent need in malaria endemic countries for feasible and cost-effective tools to implement in national malaria control programs (NMCPs) that can generate evidence to guide malaria control and elimination strategies, especially in the case of Plasmodium vivax. Several genetic surveillance applications (‘use cases’) have been identified to align research, technology development, and public health efforts, requiring different types of molecular markers. Here we present a new highly-multiplexed deep sequencing assay (Pv AmpliSeq). The assay targets the 33-SNP vivaxGEN-geo panel for country-level classification, and a newly designed 42-SNP within-country barcode for analysis of parasite dynamics in Vietnam and 11 putative drug resistance genes in a highly multiplexed NGS protocol with easy workflow, applicable for many different genetic surveillance use cases. The Pv AmpliSeq assay was validated using: 1) isolates from travelers and migrants in Belgium, and 2) routine collections of the national malaria control program at sentinel sites in Vietnam. The assay targets 229 amplicons and achieved a high depth of coverage (mean 595.7 ± 481) and high accuracy (mean error-rate of 0.013 ± 0.007). P. vivax parasites could be characterized from dried blood spots with a minimum of 5 parasites/µL and 10% of minority-clones. The assay achieved good spatial specificity for between-country prediction of origin using the 33-SNP vivaxGEN-geo panel that targets rare alleles specific for certain countries and regions. A high resolution for within-country diversity in Vietnam was achieved using the designed 42-SNP within-country barcode that targets common alleles (median MAF 0.34, range 0.01-0.49. Many variants were detected in (putative) drug resistance genes, with different predominant haplotypes in the pvmdr1 and pvcrt genes in different provinces in Vietnam. The capacity of the assay for high resolution identity-by-descent (IBD) analysis was demonstrated and identified a high rate of shared ancestry within Gia Lai Province in the Central Highlands of Vietnam, as well as between the coastal province of Binh Thuan and Lam Dong. Our approach performed well in geographically differentiating isolates at multiple spatial scales, detecting variants in putative resistance genes, and can be easily adjusted to suit the needs in other settings in a country or region. We prioritize making this tool available to researchers and NMCPs in endemic countries to increase ownership and ensure data usage for decision-making and malaria policy.
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Affiliation(s)
- Johanna Helena Kattenberg
- Biomedical Sciences Department, Institute of Tropical Medicine, Antwerp, Belgium
- *Correspondence: Johanna Helena Kattenberg, ; Anna Rosanas-Urgell,
| | - Hong Van Nguyen
- Department of Clinical Research, National Institute of Malariology, Parasitology and Entomology, Hanoi, Vietnam
| | - Hieu Luong Nguyen
- Department of Clinical Research, National Institute of Malariology, Parasitology and Entomology, Hanoi, Vietnam
| | - Erin Sauve
- Biomedical Sciences Department, Institute of Tropical Medicine, Antwerp, Belgium
| | - Ngoc Thi Hong Nguyen
- Department of Molecular Biology, National Institute of Malariology, Parasitology and Entomology, Hanoi, Vietnam
| | - Ana Chopo-Pizarro
- Biomedical Sciences Department, Institute of Tropical Medicine, Antwerp, Belgium
| | - Hidayat Trimarsanto
- Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
| | - Pieter Monsieurs
- Biomedical Sciences Department, Institute of Tropical Medicine, Antwerp, Belgium
| | - Pieter Guetens
- Biomedical Sciences Department, Institute of Tropical Medicine, Antwerp, Belgium
| | - Xa Xuan Nguyen
- Department of Epidemiology, National Institute of Malariology, Parasitology and Entomology, Hanoi, Vietnam
| | - Marjan Van Esbroeck
- Clinical Sciences Department, Institute of Tropical Medicine, Antwerp, Belgium
| | - Sarah Auburn
- Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
- Mahidol‐Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Binh Thi Huong Nguyen
- Department of Clinical Research, National Institute of Malariology, Parasitology and Entomology, Hanoi, Vietnam
| | - Anna Rosanas-Urgell
- Biomedical Sciences Department, Institute of Tropical Medicine, Antwerp, Belgium
- *Correspondence: Johanna Helena Kattenberg, ; Anna Rosanas-Urgell,
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Park JH, Kim MH, Sutanto E, Na SW, Kim MJ, Yeom JS, Nyunt MH, Abbas Elfaki MM, Abdel Hamid MM, Cha SH, Alemu SG, Sriprawat K, Anstey NM, Grigg MJ, Barber BE, William T, Gao Q, Liu Y, Pearson RD, Price RN, Nosten F, Yoon SI, No JH, Han ET, Auburn S, Russell B, Han JH. Geographical distribution and genetic diversity of Plasmodium vivax reticulocyte binding protein 1a correlates with patient antigenicity. PLoS Negl Trop Dis 2022; 16:e0010492. [PMID: 35737709 PMCID: PMC9258880 DOI: 10.1371/journal.pntd.0010492] [Citation(s) in RCA: 2] [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: 09/28/2021] [Revised: 07/06/2022] [Accepted: 05/12/2022] [Indexed: 01/12/2023] Open
Abstract
Plasmodium vivax is the most widespread cause of human malaria. Recent reports of drug resistant vivax malaria and the challenge of eradicating the dormant liver forms increase the importance of vaccine development against this relapsing disease. P. vivax reticulocyte binding protein 1a (PvRBP1a) is a potential vaccine candidate, which is involved in red cell tropism, a crucial step in the merozoite invasion of host reticulocytes. As part of the initial evaluation of the PvRBP1a vaccine candidate, we investigated its genetic diversity and antigenicity using geographically diverse clinical isolates. We analysed pvrbp1a genetic polymorphisms using 202 vivax clinical isolates from six countries. Pvrbp1a was separated into six regions based on specific domain features, sequence conserved/polymorphic regions, and the reticulocyte binding like (RBL) domains. In the fragmented gene sequence analysis, PvRBP1a region II (RII) and RIII (head and tail structure homolog, 152-625 aa.) showed extensive polymorphism caused by random point mutations. The haplotype network of these polymorphic regions was classified into three clusters that converged to independent populations. Antigenicity screening was performed using recombinant proteins PvRBP1a-N (157-560 aa.) and PvRBP1a-C (606-962 aa.), which contained head and tail structure region and sequence conserved region, respectively. Sensitivity against PvRBP1a-N (46.7%) was higher than PvRBP1a-C (17.8%). PvRBP1a-N was reported as a reticulocyte binding domain and this study identified a linear epitope with moderate antigenicity, thus an attractive domain for merozoite invasion-blocking vaccine development. However, our study highlights that a global PvRBP1a-based vaccine design needs to overcome several difficulties due to three distinct genotypes and low antigenicity levels.
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Affiliation(s)
- Ji-Hoon Park
- Department of Medical Environmental Biology and Tropical Medicine, School of Medicine, Kangwon National University, Chuncheon, Republic of Korea
| | - Min-Hee Kim
- Department of Medical Environmental Biology and Tropical Medicine, School of Medicine, Kangwon National University, Chuncheon, Republic of Korea
| | - Edwin Sutanto
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia
| | - Seok-Won Na
- Department of Medical Environmental Biology and Tropical Medicine, School of Medicine, Kangwon National University, Chuncheon, Republic of Korea
| | - Min-Jae Kim
- Department of Infectious Diseases, Asan Medical Center, Seoul, Republic of Korea
| | - Joon Sup Yeom
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | | | - Mohammed Mohieldien Abbas Elfaki
- Department of Parasitology and Medical Entomology, Institute of Endemic Diseases, University of Khartoum, Khartoum, Sudan
- Department of Microbiology and Parasitology, Faculty of Medicine, Jazan University, Jizan, Saudi Arabia
| | - Muzamil Mahdi Abdel Hamid
- Department of Parasitology and Medical Entomology, Institute of Endemic Diseases, University of Khartoum, Khartoum, Sudan
| | - Seok Ho Cha
- Department of Parasitology and Tropical Medicine, Inha University School of Medicine, Incheon, Republic of Korea
| | - Sisay Getachew Alemu
- College of Natural Sciences, Addis Ababa University, Addis Ababa, Ethiopia
- Armauer Hansen Research Institute, Jimma Road, Addis Ababa, Ethiopia
- Bioreliance, Rockville, Maryland, United States of America
| | - Kanlaya Sriprawat
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Tak, Thailand
| | - Nicholas M. Anstey
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Australia
| | - Matthew J. Grigg
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Australia
- Infectious Diseases Society Sabah-Menzies School of Health Research Clinical Research Unit, Sabah, Malaysia
| | - Bridget E. Barber
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Australia
- Infectious Diseases Society Sabah-Menzies School of Health Research Clinical Research Unit, Sabah, Malaysia
| | - Timothy William
- Infectious Diseases Society Sabah-Menzies School of Health Research Clinical Research Unit, Sabah, Malaysia
- Clinical Research Centre, Queen Elizabeth Hospital, Sabah, Malaysia
- Gleneagles Hospital, Sabah, Malaysia
| | - Qi Gao
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, China
| | - Yaobao Liu
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, China
- School of Public Health, Nanjing Medical University, Nanjing, China
| | | | - 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 Clinical Medicine Research Building, University of Oxford, Oxford, United Kingdom
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Francois Nosten
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Tak, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine Research Building, University of Oxford, Oxford, United Kingdom
| | - Sung-Il Yoon
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon, Republic of Korea
| | - Joo Hwan No
- Host-Parasite Research Laboratory, Institut Pasteur Korea, Seongnam, Republic of Korea
| | - Eun-Taek Han
- Department of Medical Environmental Biology and Tropical Medicine, School of Medicine, Kangwon National University, Chuncheon, Republic of Korea
| | - 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 Clinical Medicine Research Building, University of Oxford, Oxford, United Kingdom
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Bruce Russell
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Jin-Hee Han
- Department of Medical Environmental Biology and Tropical Medicine, School of Medicine, Kangwon National University, Chuncheon, Republic of Korea
- * E-mail:
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Zhang X, Wei H, Zhang Y, Zhao Y, Wang L, Hu Y, Nguitragool W, Sattabongkot J, Adams J, Cui L, Cao Y, Wang Q. Genetic diversity of Plasmodium vivax reticulocyte binding protein 2b in global parasite populations. Parasit Vectors 2022; 15:205. [PMID: 35698238 PMCID: PMC9191549 DOI: 10.1186/s13071-022-05296-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 04/23/2022] [Indexed: 11/19/2022] Open
Abstract
Background Plasmodium vivax reticulocyte binding protein 2b (PvRBP2b) plays a critical role in parasite invasion of reticulocytes by binding the transferrin receptor 1. PvRBP2b is a vaccine candidate based on the negative correlation between antibody titers against PvRBP2b recombinant proteins and parasitemia and risk of vivax malaria. The aim of this study was to analyze the genetic diversity of the PvRBP2b gene in the global P. vivax populations. Methods Near full-length PvRBP2b nucleotide sequences (190–8349 bp) were obtained from 88 P. vivax isolates collected from the China–Myanmar border (n = 44) and Thailand (n = 44). An additional 224 PvRBP2b sequences were retrieved from genome sequences from parasite populations worldwide. The genetic diversity, neutral selection, haplotype distribution and genetic differentiation of PvRBP2b were examined. Results The genetic diversity of PvRBP2b was distributed unevenly, with peak diversity found in the reticulocyte binding region in the N-terminus. Neutrality analysis suggested that this region is subjected to balancing selection or population bottlenecks. Several amino acid variants were found in all or nearly all P. vivax endemic regions. However, the critical residues responsible for reticulocyte binding were highly conserved. There was substantial population differentiation according to the geographical separation. The distribution of haplotypes in the reticulocyte binding region varied among regions; even the two major haplotypes Hap_6 and Hap_8 were found in only five populations. Conclusions Our data show considerable genetic variations of PvRBPb in global parasite populations. The geographic divergence may pose a challenge to PvRBP2b-based vaccine development. Graphical Abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s13071-022-05296-6.
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Affiliation(s)
- Xuexing Zhang
- Department of Immunology, College of Basic Medical Science, China Medical University, Shenyang, 110122, Liaoning, China
| | - Haichao Wei
- Department of Immunology, College of Basic Medical Science, China Medical University, Shenyang, 110122, Liaoning, China.,Department of Blood Transfusion Medicine, General Hospital of Northern Theater Command, Shenyang, 110015, Liaoning, China
| | - Yangminghui Zhang
- Department of Immunology, College of Basic Medical Science, China Medical University, Shenyang, 110122, Liaoning, China
| | - Yan Zhao
- Department of Immunology, College of Basic Medical Science, China Medical University, Shenyang, 110122, Liaoning, China
| | - Lin Wang
- Department of Immunology, College of Basic Medical Science, China Medical University, Shenyang, 110122, Liaoning, China.,Department of Blood Transfusion, Yantaishan Hospital, Yantai, 264000, Shandong, China
| | - Yubing Hu
- Department of Immunology, College of Basic Medical Science, China Medical University, Shenyang, 110122, Liaoning, China.,Central Laboratory, The First Hospital of China Medical University, Shenyang, 110001, Liaoning, China
| | - Wang Nguitragool
- 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
| | - John Adams
- College of Public Health, Global Health Infectious Disease Research (GHIDR) Program, Tampa, FL, USA
| | - Liwang Cui
- College of Public Health, Global Health Infectious Disease Research (GHIDR) Program, Tampa, FL, USA.,Department of Internal Medicine, Morsani College of Medicine, University of South Florida, 3720 Spectrum Boulevard, Suite 304, Tampa, FL, 33612, USA
| | - Yaming Cao
- Department of Immunology, College of Basic Medical Science, China Medical University, Shenyang, 110122, Liaoning, China.
| | - Qinghui Wang
- Department of Immunology, College of Basic Medical Science, China Medical University, Shenyang, 110122, Liaoning, China.
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30
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Ochoa R, Lunardelli VAS, Rosa DS, Laio A, Cossio P. Multiple-Allele MHC Class II Epitope Engineering by a Molecular Dynamics-Based Evolution Protocol. Front Immunol 2022; 13:862851. [PMID: 35572587 PMCID: PMC9094701 DOI: 10.3389/fimmu.2022.862851] [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: 01/26/2022] [Accepted: 03/28/2022] [Indexed: 11/13/2022] Open
Abstract
Epitopes that bind simultaneously to all human alleles of Major Histocompatibility Complex class II (MHC II) are considered one of the key factors for the development of improved vaccines and cancer immunotherapies. To engineer MHC II multiple-allele binders, we developed a protocol called PanMHC-PARCE, based on the unsupervised optimization of the epitope sequence by single-point mutations, parallel explicit-solvent molecular dynamics simulations and scoring of the MHC II-epitope complexes. The key idea is accepting mutations that not only improve the affinity but also reduce the affinity gap between the alleles. We applied this methodology to enhance a Plasmodium vivax epitope for multiple-allele binding. In vitro rate-binding assays showed that four engineered peptides were able to bind with improved affinity toward multiple human MHC II alleles. Moreover, we demonstrated that mice immunized with the peptides exhibited interferon-gamma cellular immune response. Overall, the method enables the engineering of peptides with improved binding properties that can be used for the generation of new immunotherapies.
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Affiliation(s)
- Rodrigo Ochoa
- Biophysics of Tropical Diseases, Max Planck Tandem Group, University of Antioquia UdeA, Medellin, Colombia
| | | | - Daniela Santoro Rosa
- Department of Microbiology, Immunology and Parasitology, Federal University of Sao Paulo, Sao Paulo, Brazil.,Institute for Investigation in Immunology (iii), Instituto Nacional de Ciência e Tecnologia (INCT), Sao Paulo, Brazil
| | - Alessandro Laio
- Physics Area, International School for Advanced Studies (SISSA), Trieste, Italy.,Condensed Matter and Statistical Physics Section, International Centre for Theoretical Physics (ICTP), Trieste, Italy
| | - Pilar Cossio
- Biophysics of Tropical Diseases, Max Planck Tandem Group, University of Antioquia UdeA, Medellin, Colombia.,Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany.,Center for Computational Mathematics, Flatiron Institute, New York, NY, United States.,Center for Computational Biology, Flatiron Institute, New York, NY, United States
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31
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Polymorphisms of potential drug resistant molecular markers in Plasmodium vivax from China–Myanmar border during 2008‒2017. Infect Dis Poverty 2022; 11:43. [PMID: 35462549 PMCID: PMC9036727 DOI: 10.1186/s40249-022-00964-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 03/21/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Plasmodium vivax remains the predominant species at the China–Myanmar border, imposing a major challenge to the recent gains in regional malaria elimination. To closely supervise the emerging of drug resistance in this area, we surveyed the variations in genes potentially correlated with drug resistance in P. vivax parasite and the possible drug selection with time.
Methods
A total of 235 P. vivax samples were collected from patients suffering uncomplicated malaria at Yingjiang, Tengchong, and Longling counties, and Nabang port in China, Yunnan province, and Laiza sub-township in Myanmar, from 2008 to 2017. Five potential drug resistance genes were amplified utilizing nested-PCR and analyzed, including pvdhfr, pvdhps, pvmdr1, pvcrt-o, and pvk12. The Pearson’s Chi-squared test or Fisher’s exact test were applied to determine the statistical frequency differences of mutations between categorical data.
Results
The pvdhfr F57I/L, S58R, T61M and S117T/N presented in 40.6%, 56.7%, 40.1%, and 56.0% of the sequenced P. vivax isolates, and these mutations significantly decreased with years. The haplotype formed by these quadruple mutations predominated in Yingjiang, Tengchong, Longling and Nabang. While a mutation H99S/R (56.6%) dominated in Laiza and increased with time. In pvdhps, the A383G prevailed in 69.2% of the samples, which remained the most prevalent haplotype. However, a significant decrease of its occurrence was also noticed over the time. The S382A/C and A553G existed in 8.4% and 30.8% of the isolates, respectively. In pvmdr1, the mutation Y976F occurred at a low frequency in 5/232 (2.2%), while T958M was fixed and F1076L was approaching fixed (72.4%). The K10 insertion was detected at an occurrence of 33.2% in pvcrt-o, whereas there was no significant difference among the sites or over the time. No mutation was identified in pvk12.
Conclusions
Mutations related with resistance to antifolate drugs are prevalent in this area, while their frequencies decrease significantly with time, suggestive of increased susceptibility of P. vivax parasite to antifolate drugs. Resistance to chloroquine (CQ) is possibly emerging. However, since the molecular mechanisms underneath CQ resistance is yet to be better understood, close supervision of clinical drug efficiency and continuous function investigation is urgently needed to alarm drug resistance.
Graphical abstract
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32
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Adam I, Alam MS, Alemu S, Amaratunga C, Amato R, Andrianaranjaka V, Anstey NM, Aseffa A, Ashley E, Assefa A, Auburn S, Barber BE, Barry A, Batista Pereira D, Cao J, Chau NH, Chotivanich K, Chu C, Dondorp AM, Drury E, Echeverry DF, Erko B, Espino F, Fairhurst R, Faiz A, Fernanda Villegas M, Gao Q, Golassa L, Goncalves S, Grigg MJ, Hamedi Y, Hien TT, Htut Y, Johnson KJ, Karunaweera N, Khan W, Krudsood S, Kwiatkowski DP, Lacerda M, Ley B, Lim P, Liu Y, Llanos-Cuentas A, Lon C, Lopera-Mesa T, Marfurt J, Michon P, Miotto O, Mohammed R, Mueller I, Namaik-larp C, Newton PN, Nguyen TN, Nosten F, Noviyanti R, Pava Z, Pearson RD, Petros B, Phyo AP, Price RN, Pukrittayakamee S, Rahim AG, Randrianarivelojosia M, Rayner JC, Rumaseb A, Siegel SV, Simpson VJ, Thriemer K, Tobon-Castano A, Trimarsanto H, Urbano Ferreira M, Vélez ID, Wangchuk S, Wellems TE, White NJ, William T, Yasnot MF, Yilma D. An open dataset of Plasmodium vivax genome variation in 1,895 worldwide samples. Wellcome Open Res 2022; 7:136. [PMID: 35651694 PMCID: PMC9127374 DOI: 10.12688/wellcomeopenres.17795.1] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/08/2022] [Indexed: 01/13/2023] Open
Abstract
This report describes the MalariaGEN Pv4 dataset, a new release of curated genome variation data on 1,895 samples of Plasmodium vivax collected at 88 worldwide locations between 2001 and 2017. It includes 1,370 new samples contributed by MalariaGEN and VivaxGEN partner studies in addition to previously published samples from these and other sources. We provide genotype calls at over 4.5 million variable positions including over 3 million single nucleotide polymorphisms (SNPs), as well as short indels and tandem duplications. This enlarged dataset highlights major compartments of parasite population structure, with clear differentiation between Africa, Latin America, Oceania, Western Asia and different parts of Southeast Asia. Each sample has been classified for drug resistance to sulfadoxine, pyrimethamine and mefloquine based on known markers at the dhfr, dhps and mdr1 loci. The prevalence of all of these resistance markers was much higher in Southeast Asia and Oceania than elsewhere. This open resource of analysis-ready genome variation data from the MalariaGEN and VivaxGEN networks is driven by our collective goal to advance research into the complex biology of P. vivax and to accelerate genomic surveillance for malaria control and elimination.
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Affiliation(s)
| | - Ishag Adam
- Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Mohammad Shafiul Alam
- Infectious Diseases Division, International Centre for Diarrheal Diseases Research, Bangladesh (ICDDR,B), Dhaka, Bangladesh
| | - Sisay Alemu
- Armauer Hansen Research Unit (AHRI), Addis Ababa, Ethiopia,Addis Ababa University, Addis Ababa, Ethiopia,MilliporeSigma (Bioreliance), Rockville, USA
| | - Chanaki Amaratunga
- National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, USA
| | | | | | - Nicholas M Anstey
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Australia
| | - Abraham Aseffa
- Armauer Hansen Research Unit (AHRI), Addis Ababa, Ethiopia
| | - Elizabeth Ashley
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - 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, UK,Mahidol‐Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Bridget E Barber
- Menzies School of Health Research, Darwin, Australia,QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Alyssa Barry
- Walter and Eliza Hall Institute, Parkville, Australia,Deakin University, Geelong, Australia,Burnet Institute, Melbourne, Australia
| | | | - Jun Cao
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, China,Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Nguyen Hoang Chau
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | | | - Cindy Chu
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Arjen M. Dondorp
- Mahidol‐Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | | | - Diego F. Echeverry
- Departamento de Microbiologia, Facultad de Salud, Universidad del Valle, Cali, Colombia
| | - Berhanu Erko
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Fe Espino
- Research Institute for Tropical Medicine, Department of Health, Manila, Philippines
| | | | | | | | - Qi Gao
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, China
| | - Lemu Golassa
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | | | - Matthew J Grigg
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Australia
| | - Yaghoob Hamedi
- Infectious and Tropical Diseases Research Center, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Tran Tinh Hien
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Ye Htut
- Department of Medical Research, Yangon, Myanmar
| | | | - Nadira Karunaweera
- University of Colombo, Colombo, Sri Lanka,School of Public Health, Harvard University, Boston, USA
| | - Wasif Khan
- Infectious Diseases Division, International Centre for Diarrheal Diseases Research, Bangladesh (ICDDR,B), Dhaka, Bangladesh
| | | | | | - Marcus Lacerda
- Instituto de Pesquisa Clínica Carlos Borborema, Fundação de Medicina Tropical Dr Heitor Vieira Dourado, Manaus, Brazil,Instituto Leônidas & Maria Deane, Fundação Oswaldo Cruz, Manaus, Brazil
| | - Benedikt Ley
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Australia
| | - Pharath Lim
- National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, USA,Parsons Corporation, Walter Reed Army Institute of Research (WRAIR), Silver Spring, USA
| | - Yaobao Liu
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, China,Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | | | - Chanthap Lon
- National Institute of Allergy and Infectious Diseases, Phnom Penh, Cambodia
| | | | - Jutta Marfurt
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Australia
| | | | - Olivo Miotto
- Wellcome Sanger Institute, Hinxton, UK,Mahidol‐Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Rezika Mohammed
- Department of Internal Medicine, University of Gondar, Gondar, Ethiopia
| | - Ivo Mueller
- Walter and Eliza Hall Institute, Parkville, Australia
| | | | - Paul N Newton
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Thuy-Nhien Nguyen
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK,Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Francois Nosten
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK,Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | | | - Zuleima Pava
- Centro Internacionale de Entrenamiento e Investigaciones Medicas, Cali, Colombia
| | | | | | - Aung P Phyo
- Mahidol‐Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand,Shoklo Malaria Research Unit, Bangkok, Thailand
| | - 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, UK,Mahidol‐Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | | | - Awab Ghulam Rahim
- Nangarhar Medical Faculty, Nangarhar University, Ministry of Higher Education, Jalalabad, Afghanistan
| | - Milijaona Randrianarivelojosia
- Institut Pasteur de Madagascar, Antananarivo, Madagascar,Universités d'Antananarivo et de Mahajanga, Antananarivo, Madagascar
| | - Julian C Rayner
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Angela Rumaseb
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Australia
| | | | | | - Kamala Thriemer
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Australia
| | | | | | - Marcelo Urbano Ferreira
- Universidade de São Paulo, São Paulo, Brazil,Institute of Hygiene and Tropical Medicine, NOVA University of Lisbon, Lisbon, Portugal
| | | | - Sonam Wangchuk
- Royal Center for Disease Control, Department of Public Health, Ministry of Health, Thimphu, Bhutan
| | - Thomas E Wellems
- National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, USA
| | - Nicholas J White
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK,Mahidol‐Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Timothy William
- Clinical Research Centre, Queen Elizabeth Hospital, Sabah, Malaysia,Infectious Diseases Society Sabah-Menzies School of Health Research Clinical Research Unit, Kota Kinabalu, Sabah, Malaysia
| | - Maria F Yasnot
- Grupo de Investigaciones Microbiológicas y Biomédicas de Córdoba-GIMBIC, Universidad de Córdoba, Monteria, Colombia
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33
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Späth GF, Bussotti G. GIP: an open-source computational pipeline for mapping genomic instability from protists to cancer cells. Nucleic Acids Res 2022; 50:e36. [PMID: 34928370 PMCID: PMC8989552 DOI: 10.1093/nar/gkab1237] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 11/01/2021] [Accepted: 12/03/2021] [Indexed: 11/25/2022] Open
Abstract
Genome instability has been recognized as a key driver for microbial and cancer adaptation and thus plays a central role in many diseases. Genome instability encompasses different types of genomic alterations, yet most available genome analysis software are limited to just one type of mutation. To overcome this limitation and better understand the role of genetic changes in enhancing pathogenicity we established GIP, a novel, powerful bioinformatic pipeline for comparative genome analysis. Here, we show its application to whole genome sequencing datasets of Leishmania, Plasmodium, Candida and cancer. Applying GIP on available data sets validated our pipeline and demonstrated the power of our tool to drive biological discovery. Applied to Plasmodium vivax genomes, our pipeline uncovered the convergent amplification of erythrocyte binding proteins and identified a nullisomic strain. Re-analyzing genomes of drug adapted Candida albicans strains revealed correlated copy number variations of functionally related genes, strongly supporting a mechanism of epistatic adaptation through interacting gene-dosage changes. Our results illustrate how GIP can be used for the identification of aneuploidy, gene copy number variations, changes in nucleic acid sequences, and chromosomal rearrangements. Altogether, GIP can shed light on the genetic bases of cell adaptation and drive disease biomarker discovery.
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Affiliation(s)
- Gerald F Späth
- Institut Pasteur, Université de Paris, INSERM U1201, Unité de Parasitologie moléculaire et Signalisation, Paris, France
| | - Giovanni Bussotti
- Institut Pasteur, Université de Paris, INSERM U1201, Unité de Parasitologie moléculaire et Signalisation, Paris, France
- Institut Pasteur, Université de Paris, Bioinformatics and Biostatistics Hub, F-75015 Paris, France
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34
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Ford A, Kepple D, Williams J, Kolesar G, Ford CT, Abebe A, Golassa L, Janies DA, Yewhalaw D, Lo E. Gene Polymorphisms Among Plasmodium vivax Geographical Isolates and the Potential as New Biomarkers for Gametocyte Detection. Front Cell Infect Microbiol 2022; 11:789417. [PMID: 35096643 PMCID: PMC8793628 DOI: 10.3389/fcimb.2021.789417] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 12/23/2021] [Indexed: 11/30/2022] Open
Abstract
The unique biological features of Plasmodium vivax not only make it difficult to control but also to eliminate. For the transmission of the malaria parasite from infected human to the vector, gametocytes play a major role. The transmission potential of a malarial infection is inferred based on microscopic detection of gametocytes and molecular screening of genes in the female gametocytes. Microscopy-based detection methods could grossly underestimate the reservoirs of infection as gametocytes may occur as submicroscopic or as micro- or macro-gametocytes. The identification of genes that are highly expressed and polymorphic in male and female gametocytes is critical for monitoring changes not only in their relative proportions but also the composition of gametocyte clones contributing to transmission over time. Recent transcriptomic study revealed two distinct clusters of highly correlated genes expressed in the P. vivax gametocytes, indicating that the male and female terminal gametocytogeneses are independently regulated. However, the detective power of these genes is unclear. In this study, we compared genetic variations of 15 and 11 genes expressed, respectively, in the female and male gametocytes among P. vivax isolates from Southeast Asia, Africa, and South America. Further, we constructed phylogenetic trees to determine the resolution power and clustering patterns of gametocyte clones. As expected, Pvs25 (PVP01_0616100) and Pvs16 (PVP01_0305600) expressed in the female gametocytes were highly conserved in all geographical isolates. In contrast, genes including 6-cysteine protein Pvs230 (PVP01_0415800) and upregulated in late gametocytes ULG8 (PVP01_1452800) expressed in the female gametocytes, as well as two CPW-WPC family proteins (PVP01_1215900 and PVP01_1320100) expressed in the male gametocytes indicated considerably high nucleotide and haplotype diversity among isolates. Parasite samples expressed in male and female gametocyte genes were observed in separate phylogenetic clusters and likely represented distinct gametocyte clones. Compared to Pvs25, Pvs230 (PVP01_0415800) and a CPW-WPC family protein (PVP01_0904300) showed higher expression in a subset of Ethiopian P. vivax samples. Thus, Pvs230, ULG8, and CPW-WPC family proteins including PVP01_0904300, PVP01_1215900, and PVP01_1320100 could potentially be used as novel biomarkers for detecting both sexes of P. vivax gametocytes in low-density infections and estimating transmission reservoirs.
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Affiliation(s)
- Anthony Ford
- Bioinformatics and Genomics, University of North Carolina, Charlotte, NC, United States
| | - Daniel Kepple
- Biological Sciences, University of North Carolina, Charlotte, NC, United States
| | - Jonathan Williams
- Biological Sciences, University of North Carolina, Charlotte, NC, United States
| | - Gabrielle Kolesar
- Biological Sciences, University of North Carolina, Charlotte, NC, United States
| | - Colby T Ford
- Bioinformatics and Genomics, University of North Carolina, Charlotte, NC, United States.,School of Data Science, University of North Carolina at Charlotte, Charlotte, NC, United States
| | - Abnet Abebe
- Department of Parasitology, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Lemu Golassa
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Daniel A Janies
- Bioinformatics and Genomics, University of North Carolina, Charlotte, NC, United States
| | - Delenasaw Yewhalaw
- Tropical and Infectious Disease Research Center, Jimma University, Jimma, Ethiopia.,School of Medical Laboratory Sciences, Faculty of Health Sciences, Jimma University, Jimma, Ethiopia
| | - Eugenia Lo
- Biological Sciences, University of North Carolina, Charlotte, NC, United States.,School of Data Science, University of North Carolina at Charlotte, Charlotte, NC, United States
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35
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Voinson M, Nunn CL, Goldberg A. Primate malarias as a model for cross-species parasite transmission. eLife 2022; 11:e69628. [PMID: 35086643 PMCID: PMC8798051 DOI: 10.7554/elife.69628] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 01/14/2022] [Indexed: 12/16/2022] Open
Abstract
Parasites regularly switch into new host species, representing a disease burden and conservation risk to the hosts. The distribution of these parasites also gives insight into characteristics of ecological networks and genetic mechanisms of host-parasite interactions. Some parasites are shared across many species, whereas others tend to be restricted to hosts from a single species. Understanding the mechanisms producing this distribution of host specificity can enable more effective interventions and potentially identify genetic targets for vaccines or therapies. As ecological connections between human and local animal populations increase, the risk to human and wildlife health from novel parasites also increases. Which of these parasites will fizzle out and which have the potential to become widespread in humans? We consider the case of primate malarias, caused by Plasmodium parasites, to investigate the interacting ecological and evolutionary mechanisms that put human and nonhuman primates at risk for infection. Plasmodium host switching from nonhuman primates to humans led to ancient introductions of the most common malaria-causing agents in humans today, and new parasite switching is a growing threat, especially in Asia and South America. Based on a wild host-Plasmodium occurrence database, we highlight geographic areas of concern and potential areas to target further sampling. We also discuss methodological developments that will facilitate clinical and field-based interventions to improve human and wildlife health based on this eco-evolutionary perspective.
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Affiliation(s)
- Marina Voinson
- Department of Evolutionary Anthropology, Duke UniversityDurhamUnited States
| | - Charles L Nunn
- Department of Evolutionary Anthropology, Duke UniversityDurhamUnited States
- Duke Global Health, Duke UniversityDurhamUnited States
| | - Amy Goldberg
- Department of Evolutionary Anthropology, Duke UniversityDurhamUnited States
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36
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Han J, Munro JE, Kocoski A, Barry AE, Bahlo M. Population-level genome-wide STR discovery and validation for population structure and genetic diversity assessment of Plasmodium species. PLoS Genet 2022; 18:e1009604. [PMID: 35007277 PMCID: PMC8782505 DOI: 10.1371/journal.pgen.1009604] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 01/21/2022] [Accepted: 12/14/2021] [Indexed: 11/18/2022] Open
Abstract
Short tandem repeats (STRs) are highly informative genetic markers that have been used extensively in population genetics analysis. They are an important source of genetic diversity and can also have functional impact. Despite the availability of bioinformatic methods that permit large-scale genome-wide genotyping of STRs from whole genome sequencing data, they have not previously been applied to sequencing data from large collections of malaria parasite field samples. Here, we have genotyped STRs using HipSTR in more than 3,000 Plasmodium falciparum and 174 Plasmodium vivax published whole-genome sequence data from samples collected across the globe. High levels of noise and variability in the resultant callset necessitated the development of a novel method for quality control of STR genotype calls. A set of high-quality STR loci (6,768 from P. falciparum and 3,496 from P. vivax) were used to study Plasmodium genetic diversity, population structures and genomic signatures of selection and these were compared to genome-wide single nucleotide polymorphism (SNP) genotyping data. In addition, the genome-wide information about genetic variation and other characteristics of STRs in P. falciparum and P. vivax have been available in an interactive web-based R Shiny application PlasmoSTR (https://github.com/bahlolab/PlasmoSTR).
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Affiliation(s)
- Jiru Han
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Australia
| | - Jacob E. Munro
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Australia
| | - Anthony Kocoski
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- Department of Mathematics and Statistics, The University of Melbourne, Melbourne, Australia
| | - Alyssa E. Barry
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Australia
- Disease Elimination Program, Burnet Institute, Melbourne, Australia
- IMPACT Institute for Innovation in Mental and Physical Health and Clinical Translation, Deakin University, Geelong, Australia
| | - Melanie Bahlo
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Australia
- * E-mail:
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37
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Marfurt J, Wirjanata G, Prayoga P, Chalfein F, Leonardo L, Sebayang BF, Apriyanti D, Sihombing MAEM, Trianty L, Suwanarusk R, Brockman A, Piera KA, Luo I, Rumaseb A, MacHunter B, Auburn S, Anstey NM, Kenangalem E, Noviyanti R, Russell B, Poespoprodjo JR, Price RN. Longitudinal ex vivo and molecular trends of chloroquine and piperaquine activity against Plasmodium falciparum and P. vivax before and after introduction of artemisinin-based combination therapy in Papua, Indonesia. Int J Parasitol Drugs Drug Resist 2021; 17:46-56. [PMID: 34193398 PMCID: PMC8358472 DOI: 10.1016/j.ijpddr.2021.06.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 06/09/2021] [Accepted: 06/11/2021] [Indexed: 01/13/2023]
Abstract
Drug resistant Plasmodium parasites are a major threat to malaria control and elimination. After reports of high levels of multidrug resistant P. falciparum and P. vivax in Indonesia, in 2005, the national first-line treatment policy for uncomplicated malaria was changed in March 2006, to dihydroartemisinin-piperaquine against all species. This study assessed the temporal trends in ex vivo drug susceptibility to chloroquine (CQ) and piperaquine (PIP) for both P. falciparum and P. vivax clinical isolates collected between 2004 and 2018, by using schizont maturation assays, and genotyped a subset of isolates for known and putative molecular markers of CQ and PIP resistance by using Sanger and next generation whole genome sequencing. The median CQ IC50 values varied significantly between years in both Plasmodium species, but there was no significant trend over time. In contrast, there was a significant trend for increasing PIP IC50s in both Plasmodium species from 2010 onwards. Whereas the South American CQ resistant 7G8 pfcrt SVMNT isoform has been fixed since 2005 in the study area, the pfmdr1 86Y allele frequencies decreased and became fixed at the wild-type allele in 2015. In P. vivax isolates, putative markers of CQ resistance (no pvcrt-o AAG (K10) insertion and pvmdr1 Y967F and F1076L) were fixed at the mutant alleles since 2005. None of the putative PIP resistance markers were detected in P. falciparum. The ex vivo drug susceptibility and molecular analysis of CQ and PIP efficacy for P. falciparum and P. vivax after 12 years of intense drug pressure with DHP suggests that whilst the degree of CQ resistance appears to have been sustained, there has been a slight decline in PIP susceptibility, although this does not appear to have reached clinically significant levels. The observed decreasing trend in ex vivo PIP susceptibility highlights the importance of ongoing surveillance.
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Affiliation(s)
- Jutta Marfurt
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, PO Box 41096, Casuarina, NT, 0811, Darwin, Australia.
| | - Grennady Wirjanata
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, PO Box 41096, Casuarina, NT, 0811, Darwin, Australia
| | - Pak Prayoga
- Papuan Health and Community Development Foundation (PHCDF), Jl. Caritas No. 1, 99961, Timika, Papua, Indonesia
| | - Ferryanto Chalfein
- Papuan Health and Community Development Foundation (PHCDF), Jl. Caritas No. 1, 99961, Timika, Papua, Indonesia
| | - Leo Leonardo
- Papuan Health and Community Development Foundation (PHCDF), Jl. Caritas No. 1, 99961, Timika, Papua, Indonesia
| | - Boni F Sebayang
- Eijkman Institute for Molecular Biology, Jl. Diponegoro 69, 10430, Jakarta, Indonesia
| | - Dwi Apriyanti
- Eijkman Institute for Molecular Biology, Jl. Diponegoro 69, 10430, Jakarta, Indonesia
| | - Maic A E M Sihombing
- Eijkman Institute for Molecular Biology, Jl. Diponegoro 69, 10430, Jakarta, Indonesia
| | - Leily Trianty
- Eijkman Institute for Molecular Biology, Jl. Diponegoro 69, 10430, Jakarta, Indonesia
| | - Rossarin Suwanarusk
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, PO Box 41096, Casuarina, NT, 0811, Darwin, Australia
| | - Alan Brockman
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, PO Box 41096, Casuarina, NT, 0811, Darwin, Australia
| | - Kim A Piera
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, PO Box 41096, Casuarina, NT, 0811, Darwin, Australia
| | - Irene Luo
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, PO Box 41096, Casuarina, NT, 0811, Darwin, Australia
| | - Angela Rumaseb
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, PO Box 41096, Casuarina, NT, 0811, Darwin, Australia
| | - Barbara MacHunter
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, PO Box 41096, Casuarina, NT, 0811, Darwin, Australia
| | - Sarah Auburn
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, PO Box 41096, Casuarina, NT, 0811, Darwin, Australia; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, UK; Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Nicholas M Anstey
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, PO Box 41096, Casuarina, NT, 0811, Darwin, Australia
| | - Enny Kenangalem
- Papuan Health and Community Development Foundation (PHCDF), Jl. Caritas No. 1, 99961, Timika, Papua, Indonesia; District Health Authority, Timika, Papua, Indonesia
| | - Rintis Noviyanti
- Eijkman Institute for Molecular Biology, Jl. Diponegoro 69, 10430, Jakarta, Indonesia
| | - Bruce Russell
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, PO Box 41096, Casuarina, NT, 0811, Darwin, Australia
| | - Jeanne R Poespoprodjo
- Papuan Health and Community Development Foundation (PHCDF), Jl. Caritas No. 1, 99961, Timika, Papua, Indonesia; Paediatric Research Office, Faculty of Medicine, Public Health and Nursing, Gadjah Mada University, Yogyakarta, Indonesia
| | - Ric N Price
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, PO Box 41096, Casuarina, NT, 0811, Darwin, Australia; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, UK; Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
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Zeng W, Zhao H, Zhao W, Yang Q, Li X, Li X, Duan M, Wang X, Li C, Xiang Z, Chen X, Cui L, Yang Z. Molecular Surveillance and Ex Vivo Drug Susceptibilities of Plasmodium vivax Isolates From the China-Myanmar Border. Front Cell Infect Microbiol 2021; 11:738075. [PMID: 34790586 PMCID: PMC8591282 DOI: 10.3389/fcimb.2021.738075] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 08/06/2021] [Indexed: 11/18/2022] Open
Abstract
Drug resistance in Plasmodium vivax may pose a challenge to malaria elimination. Previous studies have found that P. vivax has a decreased sensitivity to antimalarial drugs in some areas of the Greater Mekong Sub-region. This study aims to investigate the ex vivo drug susceptibilities of P. vivax isolates from the China–Myanmar border and genetic variations of resistance-related genes. A total of 46 P. vivax clinical isolates were assessed for ex vivo susceptibility to seven antimalarial drugs using the schizont maturation assay. The medians of IC50 (half-maximum inhibitory concentrations) for chloroquine, artesunate, and dihydroartemisinin from 46 parasite isolates were 96.48, 1.95, and 1.63 nM, respectively, while the medians of IC50 values for piperaquine, pyronaridine, mefloquine, and quinine from 39 parasite isolates were 19.60, 15.53, 16.38, and 26.04 nM, respectively. Sequence polymorphisms in pvmdr1 (P. vivax multidrug resistance-1), pvmrp1 (P. vivax multidrug resistance protein 1), pvdhfr (P. vivax dihydrofolate reductase), and pvdhps (P. vivax dihydropteroate synthase) were determined by PCR and sequencing. Pvmdr1 had 13 non-synonymous substitutions, of which, T908S and T958M were fixed, G698S (97.8%) and F1076L (93.5%) were highly prevalent, and other substitutions had relatively low prevalences. Pvmrp1 had three non-synonymous substitutions, with Y1393D being fixed, G1419A approaching fixation (97.8%), and V1478I being rare (2.2%). Several pvdhfr and pvdhps mutations were relatively frequent in the studied parasite population. The pvmdr1 G698S substitution was associated with a reduced sensitivity to chloroquine, artesunate, and dihydroartemisinin. This study suggests the possible emergence of P. vivax isolates resistant to certain antimalarial drugs at the China–Myanmar border, which demands continuous surveillance for drug resistance.
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Affiliation(s)
- Weilin Zeng
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, China
| | - Hui Zhao
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, China
| | - Wei Zhao
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, China
| | - Qi Yang
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, China
| | - Xinxin Li
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, China
| | - Xiaosong Li
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, China
| | - Mengxi Duan
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, China
| | - Xun Wang
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, China
| | - Cuiying Li
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, China
| | - Zheng Xiang
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, China
| | - Xi Chen
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, China
| | - Liwang Cui
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, United States
| | - Zhaoqing Yang
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, China
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Dia A, Jett C, Trevino SG, Chu CS, Sriprawat K, Anderson TJC, Nosten F, Cheeseman IH. Single-genome sequencing reveals within-host evolution of human malaria parasites. Cell Host Microbe 2021; 29:1496-1506.e3. [PMID: 34492224 DOI: 10.1016/j.chom.2021.08.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 06/17/2021] [Accepted: 08/13/2021] [Indexed: 02/06/2023]
Abstract
Population genomics of bulk malaria infections is unable to examine intrahost evolution; therefore, most work has focused on the role of recombination in generating genetic variation. We used single-cell sequencing protocol for low-parasitaemia infections to generate 406 near-complete single Plasmodium vivax genomes from 11 patients sampled during sequential febrile episodes. Parasite genomes contain hundreds of de novo mutations, showing strong signatures of selection, which are enriched in the ApiAP2 family of transcription factors, known targets of adaptation. Comparing 315 P. falciparum single-cell genomes from 15 patients with our P. vivax data, we find broad complementary patterns of de novo mutation at the gene and pathway level, revealing the importance of within-host evolution during malaria infections.
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Affiliation(s)
- Aliou Dia
- Host-Pathogen Interaction Program, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Catherine Jett
- Host-Pathogen Interaction Program, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Simon G Trevino
- Host-Pathogen Interaction Program, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Cindy S Chu
- Disease Intervention and Prevention, Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine Research building, University of Oxford, Old Road campus, Oxford, UK; Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Kanlaya Sriprawat
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Timothy J C Anderson
- Disease Prevention and Intervention Program, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - François Nosten
- Disease Intervention and Prevention, Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine Research building, University of Oxford, Old Road campus, Oxford, UK; Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Ian H Cheeseman
- Host-Pathogen Interaction Program, Texas Biomedical Research Institute, San Antonio, TX, USA.
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Minassian AM, Themistocleous Y, Silk SE, Barrett JR, Kemp A, Quinkert D, Nielsen CM, Edwards NJ, Rawlinson TA, Ramos Lopez F, Roobsoong W, Ellis KJ, Cho JS, Aunin E, Otto TD, Reid AJ, Bach FA, Labbé GM, Poulton ID, Marini A, Zaric M, Mulatier M, Lopez Ramon R, Baker M, Mitton CH, Sousa JC, Rachaphaew N, Kumpitak C, Maneechai N, Suansomjit C, Piteekan T, Hou MM, Khozoee B, McHugh K, Roberts DJ, Lawrie AM, Blagborough AM, Nugent FL, Taylor IJ, Johnson KJ, Spence PJ, Sattabongkot J, Biswas S, Rayner JC, Draper SJ. Controlled human malaria infection with a clone of Plasmodium vivax with high quality genome assembly. JCI Insight 2021; 6:152465. [PMID: 34609964 PMCID: PMC8675201 DOI: 10.1172/jci.insight.152465] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Controlled human malaria infection (CHMI) provides a highly informative means to investigate host-pathogen interactions and enable in vivo proof-of-concept efficacy testing of new drugs and vaccines. However, unlike Plasmodium falciparum, well-characterized P. vivax parasites that are safe and suitable for use in modern CHMI models are limited. Here, two healthy malaria-naïve UK adults with universal donor blood group were safely infected with a clone of P. vivax from Thailand by mosquito-bite CHMI. Parasitemia developed in both volunteers and, prior to treatment, each volunteer donated blood to produce a cryopreserved stabilate of infected red blood cells. Following stringent safety screening, the parasite stabilate from one of these donors ("PvW1") was thawed and used to inoculate six healthy malaria-naïve UK adults by blood-stage CHMI, at three different dilutions. Parasitemia developed in all volunteers, who were then successfully drug treated. PvW1 parasite DNA was isolated and sequenced to produce a high quality genome assembly by using a hybrid assembly method. We analysed leading vaccine candidate antigens and multigene families, including the Vivax interspersed repeat (VIR) genes of which we identified 1145 in the PvW1 genome. Our genomic analysis will guide future assessment of candidate vaccines and drugs, as well as experimental medicine studies.
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Affiliation(s)
| | | | - Sarah E Silk
- The Jenner Institute, University of Oxford, Oxford, United Kingdom
| | - Jordan R Barrett
- The Jenner Institute, University of Oxford, Oxford, United Kingdom
| | - Alison Kemp
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Doris Quinkert
- The Jenner Institute, University of Oxford, Oxford, United Kingdom
| | | | - Nick J Edwards
- The Jenner Institute, University of Oxford, Oxford, United Kingdom
| | | | | | | | | | - Jee-Sun Cho
- The Jenner Institute, University of Oxford, Oxford, United Kingdom
| | - Eerik Aunin
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Thomas D Otto
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Adam J Reid
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Florian A Bach
- Institute of Immunology and Infection Research, University of Edinburgh, Edinburgh, United Kingdom
| | | | - Ian D Poulton
- The Jenner Institute, University of Oxford, Oxford, United Kingdom
| | - Arianna Marini
- The Jenner Institute, University of Oxford, Oxford, United Kingdom
| | - Marija Zaric
- The Jenner Institute, University of Oxford, Oxford, United Kingdom
| | - Margaux Mulatier
- The Jenner Institute, University of Oxford, Oxford, United Kingdom
| | | | - Megan Baker
- The Jenner Institute, University of Oxford, Oxford, United Kingdom
| | - Celia H Mitton
- The Jenner Institute, University of Oxford, Oxford, United Kingdom
| | - Jason C Sousa
- Experimental Therapeutics Branch, Walter Reed Army Institute of Research, Maryland, United States of America
| | | | | | | | | | - Tianrat Piteekan
- Mahidol Vivax Research Unit, Mahidol University, Bangkok, Thailand
| | - Mimi M Hou
- The Jenner Institute, University of Oxford, Oxford, United Kingdom
| | - Baktash Khozoee
- The Jenner Institute, University of Oxford, Oxford, United Kingdom
| | - Kirsty McHugh
- The Jenner Institute, University of Oxford, Oxford, United Kingdom
| | - David J Roberts
- Nuffield Division of Clinical Laboratory Sciences, University of Oxford, Oxford, United Kingdom
| | - Alison M Lawrie
- The Jenner Institute, University of Oxford, Oxford, United Kingdom
| | | | - Fay L Nugent
- The Jenner Institute, University of Oxford, Oxford, United Kingdom
| | - Iona J Taylor
- The Jenner Institute, University of Oxford, Oxford, United Kingdom
| | | | - Philip J Spence
- Institute of Immunology and Infection Research, University of Edinburgh, Edinburgh, United Kingdom
| | | | - Sumi Biswas
- The Jenner Institute, University of Oxford, Oxford, United Kingdom
| | - Julian C Rayner
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Simon J Draper
- The Jenner Institute, University of Oxford, Oxford, United Kingdom
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41
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Rougeron V, Boundenga L, Arnathau C, Durand P, Renaud F, Prugnolle F. A population genetic perspective on the origin, spread and adaptation of the human malaria agents Plasmodium falciparum and Plasmodium vivax. FEMS Microbiol Rev 2021; 46:6373923. [PMID: 34550355 DOI: 10.1093/femsre/fuab047] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 09/06/2021] [Indexed: 01/20/2023] Open
Abstract
Malaria is considered one of the most important scourges that humanity has faced during its history, being responsible every year for numerous deaths worldwide. The disease is caused by protozoan parasites, among which two species are responsible of the majority of the burden, Plasmodium falciparum and Plasmodium vivax. For these two parasite species, the questions of their origin (how and when they appeared in humans), of their spread throughout the world, as well as how they have adapted to humans have long been of interest to the scientific community. Here, we review the current knowledge that has accumulated on these different questions, thanks in particular to the analysis of the genetic and genomic variability of these parasites and comparison with related Plasmodium species infecting other host species (like non-human primates). In this paper we review the existing body of knowledge, including current research dealing with these questions, focusing particularly on genetic analysis and genomic variability of these parasites and comparison with related Plasmodium species infecting other species of host (such as non-human primates).
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Affiliation(s)
- Virginie Rougeron
- Laboratory MIVEGEC, University of Montpellier, CNRS, IRD, 900 rue Jean François Breton, 34090 Montpellier, France.,CREES, Centre de Recherches en Écologie et Évolution de la Santé, Montpellier, France
| | - Larson Boundenga
- CIRMF, Centre Interdisciplinaire de Recherches Médicales de Franceville, Franceville, Gabon
| | - Céline Arnathau
- Laboratory MIVEGEC, University of Montpellier, CNRS, IRD, 900 rue Jean François Breton, 34090 Montpellier, France.,CREES, Centre de Recherches en Écologie et Évolution de la Santé, Montpellier, France
| | - Patrick Durand
- Laboratory MIVEGEC, University of Montpellier, CNRS, IRD, 900 rue Jean François Breton, 34090 Montpellier, France.,CREES, Centre de Recherches en Écologie et Évolution de la Santé, Montpellier, France
| | - François Renaud
- Laboratory MIVEGEC, University of Montpellier, CNRS, IRD, 900 rue Jean François Breton, 34090 Montpellier, France.,CREES, Centre de Recherches en Écologie et Évolution de la Santé, Montpellier, France
| | - Franck Prugnolle
- Laboratory MIVEGEC, University of Montpellier, CNRS, IRD, 900 rue Jean François Breton, 34090 Montpellier, France.,CREES, Centre de Recherches en Écologie et Évolution de la Santé, Montpellier, France
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Abstract
Almost 20 years have passed since the first reference genome assemblies were published for Plasmodium falciparum, the deadliest malaria parasite, and Anopheles gambiae, the most important mosquito vector of malaria in sub-Saharan Africa. Reference genomes now exist for all human malaria parasites and nearly half of the ~40 important vectors around the world. As a foundation for genetic diversity studies, these reference genomes have helped advance our understanding of basic disease biology and drug and insecticide resistance, and have informed vaccine development efforts. Population genomic data are increasingly being used to guide our understanding of malaria epidemiology, for example by assessing connectivity between populations and the efficacy of parasite and vector interventions. The potential value of these applications to malaria control strategies, together with the increasing diversity of genomic data types and contexts in which data are being generated, raise both opportunities and challenges in the field. This Review discusses advances in malaria genomics and explores how population genomic data could be harnessed to further support global disease control efforts.
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Affiliation(s)
- Daniel E Neafsey
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
- Infectious Disease and Microbiome Program, Broad Institute, Cambridge, MA, USA.
| | - Aimee R Taylor
- Infectious Disease and Microbiome Program, Broad Institute, Cambridge, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Bronwyn L MacInnis
- Infectious Disease and Microbiome Program, Broad Institute, Cambridge, MA, USA.
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43
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Tebben K, Bradwell K, Serre D. Variation in selective constraints along the Plasmodium life cycle. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2021; 92:104908. [PMID: 33975022 PMCID: PMC8205998 DOI: 10.1016/j.meegid.2021.104908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 05/04/2021] [Accepted: 05/07/2021] [Indexed: 11/16/2022]
Abstract
Plasmodium parasites, the cause of malaria, have a complex life cycle, infecting alternatively vertebrate hosts and female Anopheles mosquitoes and undergoing intra- and extra-cellular development in several organs of these hosts. Most of the ~5000 protein-coding genes present in Plasmodium genomes are only expressed at specific life stages, and different genes might therefore be subject to different selective pressures depending on the biological activity of the parasite and its microenvironment at this point in development. Here, we estimate the selective constraints on the protein-coding sequences of all annotated genes of rodent and primate Plasmodium parasites and, using data from scRNA-seq experiments spanning many developmental stages, analyze their variation with regard to when these genes are expressed in the parasite life cycle. Our study reveals extensive variation in selective constraints throughout the parasites' development and highlights stages that are evolving more rapidly than others. These findings provide novel insights into the biology of these parasites and could provide important information to develop better treatment strategies or vaccines against these medically-important organisms.
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Affiliation(s)
- Kieran Tebben
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Katie Bradwell
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - David Serre
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
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Abstract
African apes harbor at least twelve Plasmodium species, some of which have been a source of human infection. It is now well established that Plasmodium falciparum emerged following the transmission of a gorilla parasite, perhaps within the last 10,000 years, while Plasmodium vivax emerged earlier from a parasite lineage that infected humans and apes in Africa before the Duffy-negative mutation eliminated the parasite from humans there. Compared to their ape relatives, both human parasites have greatly reduced genetic diversity and an excess of nonsynonymous mutations, consistent with severe genetic bottlenecks followed by rapid population expansion. A putative new Plasmodium species widespread in chimpanzees, gorillas, and bonobos places the origin of Plasmodium malariae in Africa. Here, we review what is known about the origins and evolutionary history of all human-infective Plasmodium species, the time and circumstances of their emergence, and the diversity, host specificity, and zoonotic potential of their ape counterparts.
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Affiliation(s)
- Paul M Sharp
- Institute of Evolutionary Biology and Centre for Immunity, Infection and Evolution, University of Edinburgh, EH9 3FL, United Kingdom
| | - Lindsey J Plenderleith
- Institute of Evolutionary Biology and Centre for Immunity, Infection and Evolution, University of Edinburgh, EH9 3FL, United Kingdom
| | - Beatrice H Hahn
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA;
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45
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High Proportion of Genome-Wide Homology and Increased Pretreatment pvcrt Levels in Plasmodium vivax Late Recurrences: a Chloroquine Therapeutic Efficacy Study. Antimicrob Agents Chemother 2021; 65:e0009521. [PMID: 34031050 DOI: 10.1128/aac.00095-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Chloroquine (CQ) is the first-line treatment for Plasmodium vivax malaria in most countries where malaria is endemic. Monitoring P. vivax CQ resistance (CQR) is critical but remains challenged by the difficulty to distinguish real treatment failure from reinfection or liver relapse. The therapeutic efficacy of CQ against uncomplicated P. vivax malaria was evaluated in Gia Lai Province, Vietnam. Sixty-seven patients were enrolled and followed for 42 days using microscopy and quantitative PCR. Adequate clinical and parasitological response (ACPR) was 100% (66/66) on day 28 but 75.4% (49/65) on day 42. Eighteen recurrences (27.7%) were detected, with a median time to recurrence of 42 days (interquartile range [IQR], 35 to 42) and blood CQ concentration of <100 ng/ml. Primary infections leading to recurrence occurred in younger individuals (median age for ACPR = 25 years [IQR, 20 to 28]; recurrences = 18 [16 to 21]; P = 0.002) had a longer parasite clearance time (PCT for ACPR = 47.5 h [IQR, 36.2 to 59.8 h]; recurrences = 54.2 [48.4 to 62.0]; P = 0.035) and higher pvcrt gene expression (median relative expression ratio for ACPR = 0.09 [IQR, 0.05 to 0.22]; recurrences = 0.20 [0.15 to 0.56]; P = 0.002), but showed no differences in ex vivo CQ sensitivity. Parasite genotyping by microsatellites, single nucleotide polymorphism (SNP) barcoding, and whole-genome sequencing (WGS) identified a majority of homologous recurrences, with 80% (8/10) showing >98% identity by descent to paired day 0 samples. This study shows that CQ remained largely efficacious to treat P. vivax in Gia Lai; i.e., recurrences occurred late (>day 28) and in the presence of low blood CQ concentrations. However, the combination of both WGS and gene expression analysis (pvcrt) data with clinical data (PCT) allowed us to identify potential emergence of low-grade CQR, which should be closely monitored. (This study has been registered at ClinicalTrials.gov under identifier NCT02610686.).
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46
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Singh A, Kaushik R, Chaurasia DK, Singh M, Jayaram B. PvP01-DB: computational structural and functional characterization of soluble proteome of PvP01 strain of Plasmodium vivax. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2021; 2020:5857404. [PMID: 32542363 PMCID: PMC7296392 DOI: 10.1093/database/baaa036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 04/07/2020] [Accepted: 04/29/2020] [Indexed: 01/09/2023]
Abstract
Despite Plasmodium vivax being the main offender in the majority of malarial infections, very little information is available about its adaptation and development in humans. Its capability for activating relapsing infections through its dormant liver stage and resistance to antimalarial drugs makes it as one of the major challenges in eradicating malaria. Noting the immediate necessity for the availability of a comprehensive and reliable structural and functional repository for P. vivax proteome, here we developed a web resource for the new reference genome, PvP01, furnishing information on sequence, structure, functions, active sites and metabolic pathways compiled and predicted using some of the state-of-the-art methods in respective fields. The PvP01 web resource comprises organized data on the soluble proteome consisting of 3664 proteins in blood and liver stages of malarial cycle. The current public resources represent only 163 proteins of soluble proteome of PvP01, with complete information about their molecular function, biological process and cellular components. Also, only 46 proteins of P. vivax have experimentally determined structures. In this milieu of extreme scarcity of structural and functional information, PvP01 web resource offers meticulously validated structures of 3664 soluble proteins. The sequence and structure-based functional characterization led to a quantum leap from 163 proteins available presently to whole soluble proteome offered through PvP01 web resource. We believe PvP01 web resource will serve the researchers in identifying novel protein drug targets and in accelerating the development of structure-based new drug candidates to combat malaria. Database Availability: http://www.scfbio-iitd.res.in/PvP01
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Affiliation(s)
- Ankita Singh
- Supercomputing Facility for Bioinformatics & Computational Biology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India, 110016.,Centre of Evolution and Medicine, Arizona State University, Life Sciences C, 427 East Tyler Mall, Tempe, AZ 85281, United States
| | - Rahul Kaushik
- Supercomputing Facility for Bioinformatics & Computational Biology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India, 110016.,Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Dheeraj Kumar Chaurasia
- Supercomputing Facility for Bioinformatics & Computational Biology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India, 110016
| | - Manpreet Singh
- Supercomputing Facility for Bioinformatics & Computational Biology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India, 110016
| | - B Jayaram
- Supercomputing Facility for Bioinformatics & Computational Biology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India, 110016.,Kusuma School of Biological Sciences, Indian Institute of Technology, Delhi, Hauz Khas, New Delhi, India, 110016.,Department of Chemistry, Indian Institute of Technology, Delhi, Hauz Khas, New Delhi, India, 110016
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47
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Chaturvedi R, Chhibber-Goel J, Verma I, Gopinathan S, Parvez S, Sharma A. Geographical spread and structural basis of sulfadoxine-pyrimethamine drug-resistant malaria parasites. Int J Parasitol 2021; 51:505-525. [PMID: 33775670 DOI: 10.1016/j.ijpara.2020.12.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 11/24/2020] [Accepted: 12/03/2020] [Indexed: 12/22/2022]
Abstract
The global spread of sulfadoxine (Sdx, S) and pyrimethamine (Pyr, P) resistance is attributed to increasing number of mutations in DHPS and DHFR enzymes encoded by malaria parasites. The association between drug resistance mutations and SP efficacy is complex. Here we provide an overview of the geographical spread of SP resistance mutations in Plasmodium falciparum (Pf) and Plasmodium vivax (Pv) encoded dhps and dhfr genes. In addition, we have collated the mutation data and mapped it on to the three-dimensional structures of DHPS and DHFR which have become available. Data from genomic databases and 286 studies were collated to provide a comprehensive landscape of mutational data from 2005 to 2019. Our analyses show that the Pyr-resistant double mutations are widespread in Pf/PvDHFR (P. falciparum ∼61% in Asia and the Middle East, and in the Indian sub-continent; in P. vivax ∼33% globally) with triple mutations prevailing in Africa (∼66%) and South America (∼33%). For PfDHPS, triple mutations dominate South America (∼44%), Asia and the Middle East (∼34%) and the Indian sub-continent (∼27%), while single mutations are widespread in Africa (∼45%). Contrary to the status for P. falciparum, Sdx-resistant single point mutations in PvDHPS dominate globally. Alarmingly, highly resistant quintuple and sextuple mutations are rising in Africa (PfDHFR-DHPS) and Asia (Pf/PvDHFR-DHPS). Structural analyses of DHFR and DHPS proteins in complexes with substrates/drugs have revealed that resistance mutations map proximal to Sdx and Pyr binding sites. Thus new studies can focus on discovery of novel inhibitors that target the non-substrate binding grooves in these two validated malaria parasite drug targets.
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Affiliation(s)
- Rini Chaturvedi
- Molecular Medicine Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India; Department of Toxicology, Jamia Hamdard, New Delhi, India
| | - Jyoti Chhibber-Goel
- Molecular Medicine Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Ishika Verma
- Molecular Medicine Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Sreehari Gopinathan
- Molecular Medicine Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Suhel Parvez
- Department of Toxicology, Jamia Hamdard, New Delhi, India
| | - Amit Sharma
- Molecular Medicine Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India; National Institute of Malaria Research, Dwarka, New Delhi, India.
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48
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Pegoraro M, Weedall GD. Malaria in the 'Omics Era'. Genes (Basel) 2021; 12:genes12060843. [PMID: 34070769 PMCID: PMC8228830 DOI: 10.3390/genes12060843] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 05/24/2021] [Accepted: 05/27/2021] [Indexed: 12/26/2022] Open
Abstract
Genomics has revolutionised the study of the biology of parasitic diseases. The first Eukaryotic parasite to have its genome sequenced was the malaria parasite Plasmodium falciparum. Since then, Plasmodium genomics has continued to lead the way in the study of the genome biology of parasites, both in breadth—the number of Plasmodium species’ genomes sequenced—and in depth—massive-scale genome re-sequencing of several key species. Here, we review some of the insights into the biology, evolution and population genetics of Plasmodium gained from genome sequencing, and look at potential new avenues in the future genome-scale study of its biology.
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Benavente ED, Manko E, Phelan J, Campos M, Nolder D, Fernandez D, Velez-Tobon G, Castaño AT, Dombrowski JG, Marinho CRF, Aguiar ACC, Pereira DB, Sriprawat K, Nosten F, Moon R, Sutherland CJ, Campino S, Clark TG. Distinctive genetic structure and selection patterns in Plasmodium vivax from South Asia and East Africa. Nat Commun 2021; 12:3160. [PMID: 34039976 PMCID: PMC8154914 DOI: 10.1038/s41467-021-23422-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 04/28/2021] [Indexed: 12/30/2022] Open
Abstract
Despite the high burden of Plasmodium vivax malaria in South Asian countries, the genetic diversity of circulating parasite populations is not well described. Determinants of antimalarial drug susceptibility for P. vivax in the region have not been characterised. Our genomic analysis of global P. vivax (n = 558) establishes South Asian isolates (n = 92) as a distinct subpopulation, which shares ancestry with some East African and South East Asian parasites. Signals of positive selection are linked to drug resistance-associated loci including pvkelch10, pvmrp1, pvdhfr and pvdhps, and two loci linked to P. vivax invasion of reticulocytes, pvrbp1a and pvrbp1b. Significant identity-by-descent was found in extended chromosome regions common to P. vivax from India and Ethiopia, including the pvdbp gene associated with Duffy blood group binding. Our investigation provides new understanding of global P. vivax population structure and genomic diversity, and genetic evidence of recent directional selection in this important human pathogen.
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Affiliation(s)
- Ernest Diez Benavente
- Faculty of Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Emilia Manko
- Faculty of Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Jody Phelan
- Faculty of Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Monica Campos
- Faculty of Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Debbie Nolder
- Faculty of Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
- Public Health England Malaria Reference Laboratory, London School of Hygiene & Tropical Medicine, London, UK
| | - Diana Fernandez
- Grupo Malaria, Facultad de Medicina, Universidad de Antioquia, Antioquia, Colombia
| | - Gabriel Velez-Tobon
- Grupo Malaria, Facultad de Medicina, Universidad de Antioquia, Antioquia, Colombia
| | | | - Jamille G Dombrowski
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Claudio R F Marinho
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Anna Caroline C Aguiar
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | | | - Kanlaya Sriprawat
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Tak, Thailand
| | - Francois Nosten
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Tak, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine Research Building, University of Oxford Old Road Campus, Oxford, UK
| | - Robert Moon
- Faculty of Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Colin J Sutherland
- Faculty of Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
- Public Health England Malaria Reference Laboratory, London School of Hygiene & Tropical Medicine, London, UK
| | - Susana Campino
- Faculty of Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK.
| | - Taane G Clark
- Faculty of Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK.
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK.
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50
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Buyon LE, Elsworth B, Duraisingh MT. The molecular basis of antimalarial drug resistance in Plasmodium vivax. INTERNATIONAL JOURNAL FOR PARASITOLOGY-DRUGS AND DRUG RESISTANCE 2021; 16:23-37. [PMID: 33957488 PMCID: PMC8113647 DOI: 10.1016/j.ijpddr.2021.04.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 03/31/2021] [Accepted: 04/08/2021] [Indexed: 01/07/2023]
Abstract
Plasmodium vivax is the most geographically widespread cause of human malaria and is responsible for the majority of cases outside of the African continent. While great progress has been made towards eliminating human malaria, drug resistant parasite strains pose a threat towards continued progress. Resistance has arisen to multiple antimalarials in P. vivax, including to chloroquine, which is currently the first line therapy for P. vivax in most regions. Despite its importance, an understanding of the molecular mechanisms of drug resistance in this species remains elusive, in large part due to the complex biology of P. vivax and the lack of in vitro culture. In this review, we will cover the extent and challenges of measuring clinical and in vitro drug resistance in P. vivax. We will consider the roles of candidate drug resistance genes. We will highlight the development of molecular approaches for studying P. vivax biology that provide the opportunity to validate the role of putative drug resistance mutations as well as identify novel mechanisms of drug resistance in this understudied parasite. Validated molecular determinants and markers of drug resistance are essential for the rapid and cost-effective monitoring of drug resistance in P. vivax, and will be useful for optimizing drug regimens and for informing drug policy in control and elimination settings. Drug resistance is emerging in Plasmodium vivax, an important cause of malaria. The complex biology of P. vivax and the limited range of research tools make it difficult to identify drug resistance. The molecular mechanisms of drug resistance in P. vivax remain elusive. This review highlights the extent of drug resistance, the putative mechanisms of resistance and new technologies for the study of P. vivax drug resistance.
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Affiliation(s)
- Lucas E Buyon
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, 02115, MA, USA
| | - Brendan Elsworth
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, 02115, MA, USA
| | - Manoj T Duraisingh
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, 02115, MA, USA.
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