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Sekine S, Chan CW, Kalkoa M, Yamar S, Iata H, Taleo G, Kc A, Kagaya W, Kido Y, Kaneko A. Tracing the origins of Plasmodium vivax resurgence after malaria elimination on Aneityum Island in Vanuatu. COMMUNICATIONS MEDICINE 2024; 4:91. [PMID: 38762604 PMCID: PMC11102431 DOI: 10.1038/s43856-024-00524-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 05/08/2024] [Indexed: 05/20/2024] Open
Abstract
BACKGROUND Five years after successful malaria elimination, Aneityum Island in Vanuatu experienced an outbreak of Plasmodium vivax of unknown origin in 2002. Epidemiological investigations revealed several potential sources of P. vivax. We aimed to identify the genetic origin of P. vivax responsible for the resurgence. METHODS Five P. vivax microsatellite markers were genotyped using DNA extracted from archived blood samples. A total of 69 samples from four P. vivax populations was included: 29 from the outbreak in 2002, seven from Aneityum in 1999 and 2000, 18 from visitors to Aneityum in 2000, and 15 from nearby Tanna Island in 2002. A neighbour-joining phylogenetic tree was constructed to elucidate the relationships among P. vivax isolates. STRUCTURE and principal component analysis were used to assess patterns of genetic structure. RESULTS Here we show distinct genetic origins of P. vivax during the outbreak on Aneityum. While the origin of most P. vivax lineages found during the outbreak remains unidentified, limited genetic diversity among these lineages is consistent with a rapid expansion from a recent common ancestor. Contemporaneous P. vivax from neighboring Tanna and potential relapse of P. vivax acquired from other islands in 1999 and 2000 are also identified as minor contributors to the outbreak. CONCLUSIONS Multiple reintroductions of P. vivax after elimination highlight the high receptivity and vulnerability to malaria resurgence in island settings of Vanuatu, despite robust surveillance and high community compliance to control measures.
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Affiliation(s)
- Sho Sekine
- Department of Virology, Graduate School of Medicine, and Osaka International Research Center for Infectious Diseases, Osaka Metropolitan University, Osaka, Japan
- Department of Medical Technology, Morinomiya University of Medical Sciences, Osaka, Japan
| | - Chim W Chan
- Department of Virology, Graduate School of Medicine, and Osaka International Research Center for Infectious Diseases, Osaka Metropolitan University, Osaka, Japan
| | - Morris Kalkoa
- National Malaria and other Vector Borne Diseases Control Program (NVBDCP), Ministry of Health, Port Vila, Vanuatu
| | - Sam Yamar
- National Malaria and other Vector Borne Diseases Control Program (NVBDCP), Ministry of Health, Port Vila, Vanuatu
| | - Harry Iata
- National Malaria and other Vector Borne Diseases Control Program (NVBDCP), Ministry of Health, Port Vila, Vanuatu
| | - George Taleo
- National Malaria and other Vector Borne Diseases Control Program (NVBDCP), Ministry of Health, Port Vila, Vanuatu
| | - Achyut Kc
- Department of Virology, Graduate School of Medicine, and Osaka International Research Center for Infectious Diseases, Osaka Metropolitan University, Osaka, Japan
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Wataru Kagaya
- Department of Virology, Graduate School of Medicine, and Osaka International Research Center for Infectious Diseases, Osaka Metropolitan University, Osaka, Japan
- Department of Eco-epidemiology, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Yasutoshi Kido
- Department of Virology, Graduate School of Medicine, and Osaka International Research Center for Infectious Diseases, Osaka Metropolitan University, Osaka, Japan
| | - Akira Kaneko
- Department of Virology, Graduate School of Medicine, and Osaka International Research Center for Infectious Diseases, Osaka Metropolitan University, Osaka, Japan.
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.
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Sohail A, Barry A, Auburn S, Cheng Q, Lau CL, Lee R, Price RN, Furuya-Kanamori L, Bareng P, McGuinness SL, Leder K. Imported malaria into Australia: surveillance insights and opportunities. J Travel Med 2024; 31:taad164. [PMID: 38127641 PMCID: PMC10998534 DOI: 10.1093/jtm/taad164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 12/14/2023] [Accepted: 12/18/2023] [Indexed: 12/23/2023]
Abstract
BACKGROUND Malaria continues to pose a significant burden in endemic countries, many of which lack access to molecular surveillance. Insights from malaria cases in travellers returning to non-endemic areas can provide valuable data to inform endemic country programmes. To evaluate the potential for novel global insights into malaria, we examined epidemiological and molecular data from imported malaria cases to Australia. METHODS We analysed malaria cases reported in Australia from 2012 to 2022 using National Notifiable Disease Surveillance System data. Molecular data on imported malaria cases were obtained from literature searches. RESULTS Between 2012 and 2022, 3204 malaria cases were reported in Australia. Most cases (69%) were male and 44% occurred in young adults aged 20-39 years. Incidence rates initially declined between 2012 and 2015, then increased until 2019. During 2012-2019, the incidence in travellers ranged from 1.34 to 7.71 per 100 000 trips. Cases were primarily acquired in Sub-Saharan Africa (n = 1433; 45%), Oceania (n = 569; 18%) and Southern and Central Asia (n = 367; 12%). The most common countries of acquisition were Papua New Guinea (n = 474) and India (n = 277). Plasmodium falciparum accounted for 58% (1871/3204) of cases and was predominantly acquired in Sub-Saharan Africa, and Plasmodium vivax accounted for 32% (1016/3204), predominantly from Oceania and Asia. Molecular studies of imported malaria cases to Australia identified genetic mutations and deletions associated with drug resistance and false-negative rapid diagnostic test results, and led to the establishment of reference genomes for P. vivax and Plasmodium malariae. CONCLUSIONS Our analysis highlights the continuing burden of imported malaria into Australia. Molecular studies have offered valuable insights into drug resistance and diagnostic limitations, and established reference genomes. Integrating molecular data into national surveillance systems could provide important infectious disease intelligence to optimize treatment guidelines for returning travellers and support endemic country surveillance programmes.
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Affiliation(s)
- Asma Sohail
- School of Public Health and Preventive Medicine, Monash University, Melbourne 3004, Australia
- Department of Infectious Diseases, Grampians Health, Ballarat 3350, Australia
| | - Alyssa Barry
- Institute for Physical and Mental Health and Clinical Translation (IMPACT) and School of Medicine, Deakin University, Geelong 3220, Australia
- Disease Elimination Program, Burnet Institute, Melbourne 3004, Australia
| | - Sarah Auburn
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin 0800, Australia
| | - Qin Cheng
- Drug Resistance and Diagnostics, Australian Defence Force Malaria and Infectious Disease Institute, Brisbane 4051, Australia
| | - Colleen L Lau
- School of Public Health, Faculty of Medicine, The University of Queensland, Herston 4006, Australia
| | - Rogan Lee
- Parasitology Unit, Institute of Clinical Pathology and Medical Research, Sydney 2145, Australia
| | - Ric N Price
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin 0800, Australia
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX1 2JD, UK
| | - Luis Furuya-Kanamori
- School of Public Health, Faculty of Medicine, The University of Queensland, Herston 4006, Australia
| | - Paolo Bareng
- Institute for Physical and Mental Health and Clinical Translation (IMPACT) and School of Medicine, Deakin University, Geelong 3220, Australia
| | - Sarah L McGuinness
- School of Public Health and Preventive Medicine, Monash University, Melbourne 3004, Australia
- Department of Infectious Diseases, Alfred Health, Melbourne 3004, Australia
| | - Karin Leder
- School of Public Health and Preventive Medicine, Monash University, Melbourne 3004, Australia
- Victorian Infectious Diseases Service, Melbourne Health, Melbourne 3052, Australia
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Ishengoma DS, Mandara CI, Madebe RA, Warsame M, Ngasala B, Kabanywanyi AM, Mahende MK, Kamugisha E, Kavishe RA, Muro F, Mandike R, Mkude S, Chacky F, Njau R, Martin T, Mohamed A, Bailey JA, Fola AA. Microsatellites reveal high polymorphism and high potential for use in anti-malarial efficacy studies in areas with different transmission intensities in mainland Tanzania. Malar J 2024; 23:79. [PMID: 38491359 PMCID: PMC10943981 DOI: 10.1186/s12936-024-04901-6] [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: 12/09/2023] [Accepted: 03/04/2024] [Indexed: 03/18/2024] Open
Abstract
BACKGROUND Tanzania is currently implementing therapeutic efficacy studies (TES) in areas of varying malaria transmission intensities as per the World Health Organization (WHO) recommendations. In TES, distinguishing reinfection from recrudescence is critical for the determination of anti-malarial efficacy. Recently, the WHO recommended genotyping polymorphic coding genes, merozoite surface proteins 1 and 2 (msp1 and msp2), and replacing the glutamate-rich protein (glurp) gene with one of the highly polymorphic microsatellites in Plasmodium falciparum to adjust the efficacy of antimalarials in TES. This study assessed the polymorphisms of six neutral microsatellite markers and their potential use in TES, which is routinely performed in Tanzania. METHODS Plasmodium falciparum samples were obtained from four TES sentinel sites, Kibaha (Pwani), Mkuzi (Tanga), Mlimba (Morogoro) and Ujiji (Kigoma), between April and September 2016. Parasite genomic DNA was extracted from dried blood spots on filter papers using commercial kits. Genotyping was done using six microsatellites (Poly-α, PfPK2, TA1, C3M69, C2M34 and M2490) by capillary method, and the data were analysed to determine the extent of their polymorphisms and genetic diversity at the four sites. RESULTS Overall, 83 (88.3%) of the 94 samples were successfully genotyped (with positive results for ≥ 50.0% of the markers), and > 50.0% of the samples (range = 47.6-59.1%) were polyclonal, with a mean multiplicity of infection (MOI) ranging from 1.68 to 1.88 among the four sites. There was high genetic diversity but limited variability among the four sites based on mean allelic richness (RS = 7.48, range = 7.27-8.03, for an adjusted minimum sample size of 18 per site) and mean expected heterozygosity (He = 0.83, range = 0.80-0.85). Cluster analysis of haplotypes using STRUCTURE, principal component analysis, and pairwise genetic differentiation (FST) did not reveal population structure or clustering of parasites according to geographic origin. Of the six markers, Poly-α was the most polymorphic, followed by C2M34, TA1 and C3M69, while M2490 was the least polymorphic. CONCLUSION Microsatellite genotyping revealed high polyclonality and genetic diversity but no significant population structure. Poly-α, C2M34, TA1 and C3M69 were the most polymorphic markers, and Poly-α alone or with any of the other three markers could be adopted for use in TES in Tanzania.
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Affiliation(s)
- Deus S Ishengoma
- National Institute for Medical Research, Dar es Salaam, Tanzania.
- Faculty of Pharmaceutical Sciences, Monash University, Melbourne, Australia.
- Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA.
| | - Celine I Mandara
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Rashid A Madebe
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | | | - Billy Ngasala
- Department of Parasitology, School of Public Health, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
- Department of Women's and Children's Health, International Maternal and Child Health (IMCH), Uppsala University, Uppsala, Sweden
| | | | | | - Erasmus Kamugisha
- Bugando Medical Centre, Catholic University of Health and Allied Sciences, Mwanza, Tanzania
| | - Reginald A Kavishe
- Kilimanjaro Christian Medical Centre, Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Florida Muro
- Kilimanjaro Christian Medical Centre, Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Renata Mandike
- National Malaria Control Programme, Ministry of Health, Dodoma, Tanzania
| | - Sigsbert Mkude
- National Malaria Control Programme, Ministry of Health, Dodoma, Tanzania
| | - Frank Chacky
- National Malaria Control Programme, Ministry of Health, Dodoma, Tanzania
| | - Ritha Njau
- Malariologist and Public Health Specialist, Dar es Salaam, Tanzania
| | - Troy Martin
- HIV Vaccine Trials Network, Fred Hutch Cancer Research Centre, Seattle, WA, USA
| | - Ally Mohamed
- National Malaria Control Programme, Ministry of Health, Dodoma, Tanzania
| | - Jeffrey A Bailey
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI, USA
| | - Abebe A Fola
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI, 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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Ruybal-Pesántez S, McCann K, Vibin J, Siegel S, Auburn S, Barry AE. Molecular markers for malaria genetic epidemiology: progress and pitfalls. Trends Parasitol 2024; 40:147-163. [PMID: 38129280 DOI: 10.1016/j.pt.2023.11.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 11/13/2023] [Accepted: 11/14/2023] [Indexed: 12/23/2023]
Abstract
Over recent years, progress in molecular markers for genotyping malaria parasites has enabled informative studies of epidemiology and transmission dynamics. Results have highlighted the value of these tools for surveillance to support malaria control and elimination strategies. There are many different types and panels of markers available for malaria parasite genotyping, and for end users, the nuances of these markers with respect to 'use case', resolution, and accuracy, are not well defined. This review clarifies issues surrounding different molecular markers and their application to malaria control and elimination. We describe available marker panels, use cases, implications for different transmission settings, limitations, access, cost, and data accuracy. The information provided can be used as a guide for molecular epidemiology and surveillance of malaria.
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Affiliation(s)
- Shazia Ruybal-Pesántez
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK; Institute of Microbiology, Universidad San Francisco de Quito, Quito, Ecuador
| | - Kirsty McCann
- Life Sciences Discipline, Burnet Institute, Melbourne, Victoria, Australia; Centre for Innovation in Infectious Disease and Immunology Research (CIIDIR), Institute for Mental and Physical Health and Clinical Translation (IMPACT) and School of Medicine, Deakin University, Geelong, Victoria, Australia
| | - Jessy Vibin
- Life Sciences Discipline, Burnet Institute, Melbourne, Victoria, Australia; Centre for Innovation in Infectious Disease and Immunology Research (CIIDIR), Institute for Mental and Physical Health and Clinical Translation (IMPACT) and School of Medicine, Deakin University, Geelong, Victoria, Australia
| | | | - Sarah Auburn
- Menzies School of Health Research and Charles Darwin University, Darwin, Northern Territory, Australia; Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Alyssa E Barry
- Life Sciences Discipline, Burnet Institute, Melbourne, Victoria, Australia; Centre for Innovation in Infectious Disease and Immunology Research (CIIDIR), Institute for Mental and Physical Health and Clinical Translation (IMPACT) and School of Medicine, Deakin University, Geelong, Victoria, Australia.
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6
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Fola AA, Moser KA, Aydemir O, Hennelly C, Kobayashi T, Shields T, Hamapumbu H, Musonda M, Katowa B, Matoba J, Stevenson JC, Norris DE, Thuma PE, Wesolowski A, Moss WJ, Bailey JA, Juliano JJ. Temporal and spatial analysis of Plasmodium falciparum genomics reveals patterns of parasite connectivity in a low-transmission district in Southern Province, Zambia. Malar J 2023; 22:208. [PMID: 37420265 PMCID: PMC10327325 DOI: 10.1186/s12936-023-04637-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 06/30/2023] [Indexed: 07/09/2023] Open
Abstract
BACKGROUND Understanding temporal and spatial dynamics of malaria transmission will help to inform effective interventions and strategies in regions approaching elimination. Parasite genomics are increasingly used to monitor epidemiologic trends, including assessing residual transmission across seasons and importation of malaria into these regions. METHODS In a low and seasonal transmission setting of southern Zambia, a total of 441 Plasmodium falciparum samples collected from 8 neighbouring health centres between 2012 and 2018 were genotyped using molecular inversion probes (MIPs n = 1793) targeting a total of 1832 neutral and geographically informative SNPs distributed across the parasite genome. After filtering for quality and missingness, 302 samples and 1410 SNPs were retained and used for downstream population genomic analyses. RESULTS The analyses revealed most (67%, n = 202) infections harboured one clone (monogenomic) with some variation at local level suggesting low, but heterogenous malaria transmission. Relatedness identity-by-descent (IBD) analysis revealed variable distribution of IBD segments across the genome and 6% of pairs were highly-related (IBD ≥ 0.25). Some of the highly-related parasite populations persisted across multiple seasons, suggesting that persistence of malaria in this low-transmission region is fueled by parasites "seeding" across the dry season. For recent years, clusters of clonal parasites were identified that were dissimilar to the general parasite population, suggesting parasite populations were increasingly fragmented at small spatial scales due to intensified control efforts. Clustering analysis using PCA and t-SNE showed a lack of substantial parasite population structure. CONCLUSION Leveraging both genomic and epidemiological data provided comprehensive picture of fluctuations in parasite populations in this pre-elimination setting of southern Zambia over 7 years.
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Affiliation(s)
- Abebe A. Fola
- Department of Pathology and Laboratory Medicine, Brown University, 55 Claverick Street, Providence, RI 02906 USA
| | - Kara A. Moser
- University of North Carolina Institute for Global Health and Infectious Diseases, University of North Carolina Chapel Hill, Chapel Hill, NC 27599 USA
| | - Ozkan Aydemir
- Department of Pathology and Laboratory Medicine, Brown University, 55 Claverick Street, Providence, RI 02906 USA
| | - Chris Hennelly
- University of North Carolina Institute for Global Health and Infectious Diseases, University of North Carolina Chapel Hill, Chapel Hill, NC 27599 USA
| | - Tamaki Kobayashi
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205 USA
| | - Timothy Shields
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205 USA
| | | | | | - Ben Katowa
- Macha Research Trust, Choma District, Choma, Zambia
| | | | | | - Douglas E. Norris
- Department of Molecular Microbiology and Immunology, The Johns Hopkins Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205 USA
| | | | - Amy Wesolowski
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205 USA
| | - William J. Moss
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205 USA
- Department of Molecular Microbiology and Immunology, The Johns Hopkins Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205 USA
| | - Jeffrey A. Bailey
- Department of Pathology and Laboratory Medicine, Brown University, 55 Claverick Street, Providence, RI 02906 USA
| | - Jonathan J. Juliano
- University of North Carolina Institute for Global Health and Infectious Diseases, University of North Carolina Chapel Hill, Chapel Hill, NC 27599 USA
- Division of Infectious Diseases, School of Medicine, University of North Carolina Chapel Hill, Chapel Hill, NC 27599 USA
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina Chapel Hill, Chapel Hill, NC 27599 USA
- Curriculum in Genetics and Molecular Biology, School of Medicine, University of North Carolina Chapel Hill, Chapel Hill, NC 27599 USA
| | - the Southern, Central Africa International Center of Excellence for Malaria Research (ICEMR)
- Department of Pathology and Laboratory Medicine, Brown University, 55 Claverick Street, Providence, RI 02906 USA
- University of North Carolina Institute for Global Health and Infectious Diseases, University of North Carolina Chapel Hill, Chapel Hill, NC 27599 USA
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205 USA
- Macha Research Trust, Choma District, Choma, Zambia
- Department of Molecular Microbiology and Immunology, The Johns Hopkins Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205 USA
- Division of Infectious Diseases, School of Medicine, University of North Carolina Chapel Hill, Chapel Hill, NC 27599 USA
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina Chapel Hill, Chapel Hill, NC 27599 USA
- Curriculum in Genetics and Molecular Biology, School of Medicine, University of North Carolina Chapel Hill, Chapel Hill, NC 27599 USA
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Mueller I, Vantaux A, Karl S, Laman M, Witkowski B, Pepey A, Vinit R, White M, Barry A, Beeson JG, Robinson LJ. Asia-Pacific ICEMR: Understanding Malaria Transmission to Accelerate Malaria Elimination in the Asia Pacific Region. Am J Trop Med Hyg 2022; 107:131-137. [PMID: 36228917 PMCID: PMC9662229 DOI: 10.4269/ajtmh.21-1336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Accepted: 07/06/2022] [Indexed: 01/31/2023] Open
Abstract
Gaining an in-depth understanding of malaria transmission requires integrated, multifaceted research approaches. The Asia-Pacific International Center of Excellence in Malaria Research (ICEMR) is applying specifically developed molecular and immunological assays, in-depth entomological assessments, and advanced statistical and mathematical modeling approaches to a rich series of longitudinal cohort and cross-sectional studies in Papua New Guinea and Cambodia. This is revealing both the essential contribution of forest-based transmission and the particular challenges posed by Plasmodium vivax to malaria elimination in Cambodia. In Papua New Guinea, these studies document the complex host-vector-parasite interactions that are underlying both the stunning reductions in malaria burden from 2006 to 2014 and the significant resurgence in transmission in 2016 to 2018. Here we describe the novel analytical, surveillance, molecular, and immunological tools that are being applied in our ongoing Asia-Pacific ICEMR research program.
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Affiliation(s)
- Ivo Mueller
- Population Health & Immunity Division, Walter + Eliza Hall Institutes, Melbourne, Australia;,University of Melbourne, Melbourne, Australia;,Address correspondence to Ivo Mueller, Population Health & Immunity Division, Walter + Eliza Hall Institutes, 1G Royal Parade, Parkville, Victoria, Australia 3052. E-mail:
| | | | - Stephan Karl
- Australian Institute of Tropical Health & Medicine, James Cook University, Cairns, Australia;,PNG Institute of Medical Research, Madang, Papua New Guinea
| | - Moses Laman
- PNG Institute of Medical Research, Madang, Papua New Guinea
| | | | - Anais Pepey
- Institute Pasteur Cambodia, Phnom Penh, Cambodia
| | - Rebecca Vinit
- PNG Institute of Medical Research, Madang, Papua New Guinea
| | | | - Alyssa Barry
- Deakin University, Geelong, Australia;,Burnet Institute, Melbourne, Australia
| | - James G. Beeson
- University of Melbourne, Melbourne, Australia;,Burnet Institute, Melbourne, Australia;,Monash University, Victoria, Australia
| | - Leanne J. Robinson
- Population Health & Immunity Division, Walter + Eliza Hall Institutes, Melbourne, Australia;,PNG Institute of Medical Research, Madang, Papua New Guinea;,Burnet Institute, Melbourne, Australia;,Monash University, Victoria, Australia
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8
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Adderley J, Boulet C, McCann K, McHugh E, Ioannidis LJ, Yeoh LM. Advances in Plasmodium research, an update: highlights from the Malaria in Melbourne 2021 conference. Mol Biochem Parasitol 2022; 250:111487. [DOI: 10.1016/j.molbiopara.2022.111487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 05/05/2022] [Accepted: 05/18/2022] [Indexed: 11/28/2022]
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9
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Argyropoulos DC, Ruybal‐Pesántez S, Deed SL, Oduro AR, Dadzie SK, Appawu MA, Asoala V, Pascual M, Koram KA, Day KP, Tiedje KE. The impact of indoor residual spraying on Plasmodium falciparum microsatellite variation in an area of high seasonal malaria transmission in Ghana, West Africa. Mol Ecol 2021; 30:3974-3992. [PMID: 34143538 PMCID: PMC8456823 DOI: 10.1111/mec.16029] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 05/26/2021] [Accepted: 06/01/2021] [Indexed: 01/16/2023]
Abstract
Here, we report the first population genetic study to examine the impact of indoor residual spraying (IRS) on Plasmodium falciparum in humans. This study was conducted in an area of high seasonal malaria transmission in Bongo District, Ghana. IRS was implemented during the dry season (November-May) in three consecutive years between 2013 and 2015 to reduce transmission and attempt to bottleneck the parasite population in humans towards lower diversity with greater linkage disequilibrium. The study was done against a background of widespread use of long-lasting insecticidal nets, typical for contemporary malaria control in West Africa. Microsatellite genotyping with 10 loci was used to construct 392 P. falciparum multilocus infection haplotypes collected from two age-stratified cross-sectional surveys at the end of the wet seasons pre- and post-IRS. Three-rounds of IRS, under operational conditions, led to a >90% reduction in transmission intensity and a 35.7% reduction in the P. falciparum prevalence (p < .001). Despite these declines, population genetic analysis of the infection haplotypes revealed no dramatic changes with only a slight, but significant increase in genetic diversity (He : pre-IRS = 0.79 vs. post-IRS = 0.81, p = .048). Reduced relatedness of the parasite population (p < .001) was observed post-IRS, probably due to decreased opportunities for outcrossing. Spatiotemporal genetic differentiation between the pre- and post-IRS surveys (D = 0.0329 [95% CI: 0.0209 - 0.0473], p = .034) was identified. These data provide a genetic explanation for the resilience of P. falciparum to short-term IRS programmes in high-transmission settings in sub-Saharan Africa.
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Affiliation(s)
- Dionne C. Argyropoulos
- School of BioSciencesBio21 InstituteThe University of MelbourneMelbourneVic.Australia
- Department of Microbiology and ImmunologyBio21 Institute and Peter Doherty InstituteThe University of MelbourneMelbourneVic.Australia
| | - Shazia Ruybal‐Pesántez
- School of BioSciencesBio21 InstituteThe University of MelbourneMelbourneVic.Australia
- Present address:
Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical ResearchMelbourneVic.Australia
- Present address:
Department of Medical Biology and Bio21 InstituteThe University of MelbourneMelbourneVic.Australia
- Present address:
Burnet InstituteMelbourneVic.Australia
| | - Samantha L. Deed
- School of BioSciencesBio21 InstituteThe University of MelbourneMelbourneVic.Australia
- Department of Microbiology and ImmunologyBio21 Institute and Peter Doherty InstituteThe University of MelbourneMelbourneVic.Australia
| | - Abraham R. Oduro
- Navrongo Health Research CentreGhana Health ServiceNavrongoGhana
| | - Samuel K. Dadzie
- Noguchi Memorial Institute for Medical ResearchUniversity of GhanaLegonGhana
| | - Maxwell A. Appawu
- Noguchi Memorial Institute for Medical ResearchUniversity of GhanaLegonGhana
| | - Victor Asoala
- Navrongo Health Research CentreGhana Health ServiceNavrongoGhana
| | - Mercedes Pascual
- Department of Ecology and EvolutionUniversity of ChicagoChicagoUSA
| | - Kwadwo A. Koram
- Noguchi Memorial Institute for Medical ResearchUniversity of GhanaLegonGhana
| | - Karen P. Day
- School of BioSciencesBio21 InstituteThe University of MelbourneMelbourneVic.Australia
- Department of Microbiology and ImmunologyBio21 Institute and Peter Doherty InstituteThe University of MelbourneMelbourneVic.Australia
| | - Kathryn E. Tiedje
- School of BioSciencesBio21 InstituteThe University of MelbourneMelbourneVic.Australia
- Department of Microbiology and ImmunologyBio21 Institute and Peter Doherty InstituteThe University of MelbourneMelbourneVic.Australia
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10
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Auburn S, Cheng Q, Marfurt J, Price RN. The changing epidemiology of Plasmodium vivax: Insights from conventional and novel surveillance tools. PLoS Med 2021; 18:e1003560. [PMID: 33891580 PMCID: PMC8064506 DOI: 10.1371/journal.pmed.1003560] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Sarah Auburn and co-authors discuss the unique biology and epidemiology of P. vivax and current evidence on conventional and new approaches to surveillance.
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Affiliation(s)
- Sarah Auburn
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Australia
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Qin Cheng
- Department of Drug Resistance and Diagnostics, Australian Defence Force Malaria and Infectious Disease Institute, Brisbane, Australia
- The Australian Defence Force Malaria and Infectious Disease Institute Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Jutta Marfurt
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Australia
| | - Ric N. Price
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Australia
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
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11
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Fola AA, Kattenberg E, Razook Z, Lautu-Gumal D, Lee S, Mehra S, Bahlo M, Kazura J, Robinson LJ, Laman M, Mueller I, Barry AE. SNP barcodes provide higher resolution than microsatellite markers to measure Plasmodium vivax population genetics. Malar J 2020; 19:375. [PMID: 33081815 PMCID: PMC7576724 DOI: 10.1186/s12936-020-03440-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 10/03/2020] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Genomic surveillance of malaria parasite populations has the potential to inform control strategies and to monitor the impact of interventions. Barcodes comprising large numbers of single nucleotide polymorphism (SNP) markers are accurate and efficient genotyping tools, however may need to be tailored to specific malaria transmission settings, since 'universal' barcodes can lack resolution at the local scale. A SNP barcode was developed that captures the diversity and structure of Plasmodium vivax populations of Papua New Guinea (PNG) for research and surveillance. METHODS Using 20 high-quality P. vivax genome sequences from PNG, a total of 178 evenly spaced neutral SNPs were selected for development of an amplicon sequencing assay combining a series of multiplex PCRs and sequencing on the Illumina MiSeq platform. For initial testing, 20 SNPs were amplified in a small number of mono- and polyclonal P. vivax infections. The full barcode was then validated by genotyping and population genetic analyses of 94 P. vivax isolates collected between 2012 and 2014 from four distinct catchment areas on the highly endemic north coast of PNG. Diversity and population structure determined from the SNP barcode data was then benchmarked against that of ten microsatellite markers used in previous population genetics studies. RESULTS From a total of 28,934,460 reads generated from the MiSeq Illumina run, 87% mapped to the PvSalI reference genome with deep coverage (median = 563, range 56-7586) per locus across genotyped samples. Of 178 SNPs assayed, 146 produced high-quality genotypes (minimum coverage = 56X) in more than 85% of P. vivax isolates. No amplification bias was introduced due to either polyclonal infection or whole genome amplification (WGA) of samples before genotyping. Compared to the microsatellite panels, the SNP barcode revealed greater variability in genetic diversity between populations and geographical population structure. The SNP barcode also enabled assignment of genotypes according to their geographic origins with a significant association between genetic distance and geographic distance at the sub-provincial level. CONCLUSIONS High-throughput SNP barcoding can be used to map variation of malaria transmission dynamics at sub-national resolution. The low cost per sample and genotyping strategy makes the transfer of this technology to field settings highly feasible.
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Affiliation(s)
- Abebe A Fola
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA
| | - Eline Kattenberg
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Vector Borne Diseases Unit, Papua New Guinea Institute of Medical Research, Madang, Papua New Guinea
- Malariology Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | - Zahra Razook
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- IMPACT Institute for Innovation in Mental and Physical Health and Clinical Translation, Deakin University, 75 Pigdons Road, Waurn Ponds, Geelong, VIC, 3216, Australia
| | - Dulcie Lautu-Gumal
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
- Vector Borne Diseases Unit, Papua New Guinea Institute of Medical Research, Madang, Papua New Guinea
- Disease Elimination Program, Burnet Institute, Melbourne, VIC, Australia
- IMPACT Institute for Innovation in Mental and Physical Health and Clinical Translation, Deakin University, 75 Pigdons Road, Waurn Ponds, Geelong, VIC, 3216, Australia
| | - Stuart Lee
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
| | - Somya Mehra
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Disease Elimination Program, Burnet Institute, Melbourne, VIC, Australia
- IMPACT Institute for Innovation in Mental and Physical Health and Clinical Translation, Deakin University, 75 Pigdons Road, Waurn Ponds, Geelong, VIC, 3216, Australia
| | - Melanie Bahlo
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
| | - James Kazura
- Disease Elimination Program, Burnet Institute, Melbourne, VIC, Australia
- Centre for Global Health and Diseases, Case Western Reserve University, Cleveland, Ohio, USA
| | - Leanne J Robinson
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
- Vector Borne Diseases Unit, Papua New Guinea Institute of Medical Research, Madang, Papua New Guinea
- Disease Elimination Program, Burnet Institute, Melbourne, VIC, Australia
| | - Moses Laman
- Vector Borne Diseases Unit, Papua New Guinea Institute of Medical Research, Madang, Papua New Guinea
| | - Ivo Mueller
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
- Department of Parasites and Insect Vectors, Institut Pasteur, Paris, France
| | - Alyssa E Barry
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia.
- Disease Elimination Program, Burnet Institute, Melbourne, VIC, Australia.
- IMPACT Institute for Innovation in Mental and Physical Health and Clinical Translation, Deakin University, 75 Pigdons Road, Waurn Ponds, Geelong, VIC, 3216, Australia.
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