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Paschalidis A, Watson OJ, Aydemir O, Verity R, Bailey JA. coiaf: Directly estimating complexity of infection with allele frequencies. PLoS Comput Biol 2023; 19:e1010247. [PMID: 37294835 PMCID: PMC10310041 DOI: 10.1371/journal.pcbi.1010247] [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: 05/23/2022] [Revised: 06/29/2023] [Accepted: 05/01/2023] [Indexed: 06/11/2023] Open
Abstract
In malaria, individuals are often infected with different parasite strains. The complexity of infection (COI) is defined as the number of genetically distinct parasite strains in an individual. Changes in the mean COI in a population have been shown to be informative of changes in transmission intensity with a number of probabilistic likelihood and Bayesian models now developed to estimate the COI. However, rapid, direct measures based on heterozygosity or FwS do not properly represent the COI. In this work, we present two new methods that use easily calculated measures to directly estimate the COI from allele frequency data. Using a simulation framework, we show that our methods are computationally efficient and comparably accurate to current approaches in the literature. Through a sensitivity analysis, we characterize how the distribution of parasite densities, the assumed sequencing depth, and the number of sampled loci impact the bias and accuracy of our two methods. Using our developed methods, we further estimate the COI globally from Plasmodium falciparum sequencing data and compare the results against the literature. We show significant differences in the estimated COI globally between continents and a weak relationship between malaria prevalence and COI.
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Affiliation(s)
- Aris Paschalidis
- Department of Pathology and Laboratory Medicine, Brown University, Providence, Rhode Island, United States of America
| | - Oliver J. Watson
- Department of Pathology and Laboratory Medicine, Brown University, Providence, Rhode Island, United States of America
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - Ozkan Aydemir
- Department of Pathology and Laboratory Medicine, Brown University, Providence, Rhode Island, United States of America
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts, United States of America
| | - Robert Verity
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - Jeffrey A. Bailey
- Department of Pathology and Laboratory Medicine, Brown University, Providence, Rhode Island, United States of America
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2
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Kümpornsin K, Kochakarn T, Yeo T, Okombo J, Luth MR, Hoshizaki J, Rawat M, Pearson RD, Schindler KA, Mok S, Park H, Uhlemann AC, Jana GP, Maity BC, Laleu B, Chenu E, Duffy J, Moliner Cubel S, Franco V, Gomez-Lorenzo MG, Gamo FJ, Winzeler EA, Fidock DA, Chookajorn T, Lee MCS. Generation of a mutator parasite to drive resistome discovery in Plasmodium falciparum. Nat Commun 2023; 14:3059. [PMID: 37244916 DOI: 10.1038/s41467-023-38774-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 05/12/2023] [Indexed: 05/29/2023] Open
Abstract
In vitro evolution of drug resistance is a powerful approach for identifying antimalarial targets, however, key obstacles to eliciting resistance are the parasite inoculum size and mutation rate. Here we sought to increase parasite genetic diversity to potentiate resistance selections by editing catalytic residues of Plasmodium falciparum DNA polymerase δ. Mutation accumulation assays reveal a ~5-8 fold elevation in the mutation rate, with an increase of 13-28 fold in drug-pressured lines. Upon challenge with the spiroindolone PfATP4-inhibitor KAE609, high-level resistance is obtained more rapidly and at lower inocula than wild-type parasites. Selections also yield mutants with resistance to an "irresistible" compound, MMV665794 that failed to yield resistance with other strains. We validate mutations in a previously uncharacterised gene, PF3D7_1359900, which we term quinoxaline resistance protein (QRP1), as causal for resistance to MMV665794 and a panel of quinoxaline analogues. The increased genetic repertoire available to this "mutator" parasite can be leveraged to drive P. falciparum resistome discovery.
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Affiliation(s)
- Krittikorn Kümpornsin
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- Calibr, Division of the Scripps Research Institute, La Jolla, CA, USA
| | - Theerarat Kochakarn
- The Laboratory for Molecular Infection Medicine Sweden and Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Tomas Yeo
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - John Okombo
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Madeline R Luth
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | | | - Mukul Rawat
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | | | - Kyra A Schindler
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Sachel Mok
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
- Center for Malaria Therapeutics and Antimicrobial Resistance, Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Heekuk Park
- Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Anne-Catrin Uhlemann
- Center for Malaria Therapeutics and Antimicrobial Resistance, Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
- Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Gouranga P Jana
- TCG Lifesciences Private Limited, Salt-lake Electronics Complex, Kolkata, India
| | - Bikash C Maity
- TCG Lifesciences Private Limited, Salt-lake Electronics Complex, Kolkata, India
| | - Benoît Laleu
- Medicines for Malaria Venture, International Centre Cointrin, Geneva, Switzerland
| | - Elodie Chenu
- Medicines for Malaria Venture, International Centre Cointrin, Geneva, Switzerland
| | - James Duffy
- Medicines for Malaria Venture, International Centre Cointrin, Geneva, Switzerland
| | | | - Virginia Franco
- Global Health Medicines R&D, GlaxoSmithKline, Tres Cantos, Madrid, Spain
| | | | | | - Elizabeth A Winzeler
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - David A Fidock
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
- Center for Malaria Therapeutics and Antimicrobial Resistance, Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Thanat Chookajorn
- The Laboratory for Molecular Infection Medicine Sweden and Department of Molecular Biology, Umeå University, Umeå, Sweden
- Genomics and Evolutionary Medicine Unit, Centre of Excellence in Malaria Research, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Marcus C S Lee
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
- Biological Chemistry and Drug Discovery, Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee, UK.
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3
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Pharmacokinetics and antimalarial activities of reduction-responsive releasing dihydroartemisinin prodrug self-assembled nanoparticles in rodents. J Drug Deliv Sci Technol 2021. [DOI: 10.1016/j.jddst.2021.102515] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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4
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Tandoh KZ, Wilson MD, Quashie NB, Duah-Quashie NO. Implicating extracellular vesicles in Plasmodium falciparum artemisinin resistance development. Traffic 2021; 22:194-200. [PMID: 33860593 DOI: 10.1111/tra.12787] [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: 10/24/2020] [Revised: 04/10/2021] [Accepted: 04/13/2021] [Indexed: 01/08/2023]
Abstract
Plasmodium falciparum malaria remains a disease of significant public health impact today. With the risk of emerging artemisinin resistance stalling malaria control efforts, the need to deepen our understanding of the parasite's biology is dire. Extracellular vesicles (EVs) are vital to the biology of P. falciparum and play a role in the pathogenesis of malaria. Recent studies have also shown that EVs may play a role in the development of artemisinin resistance in P. falciparum. Here, we highlight evidence on EVs in P. falciparum biology and malaria pathogenesis and argue that there is sufficient ground to propose a role for EVs in the development of P. falciparum artemisinin resistance. We suggest that EVs are actively secreted functional organelles that contribute to cellular homeostasis in P. falciparum-infected red blood cells under artemisinin pressure. Further exploration of this hypothesized EVs-based molecular mechanism of artemisinin resistance will aid the discovery of novel antimalarial therapies.
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Affiliation(s)
- Kwesi Z Tandoh
- West African Centre for Cell Biology of Infectious Pathogens, Department of Biochemistry, Cell and Molecular Biology, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
| | - Michael D Wilson
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Neils B Quashie
- Department of Epidemiology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana.,Centre for Tropical Clinical Pharmacology and Therapeutics, School of Medicine and Dentistry, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Nancy O Duah-Quashie
- Department of Epidemiology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
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5
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Joonlasak K, Batty EM, Kochakarn T, Panthan B, Kümpornsin K, Jiaranai P, Wangwiwatsin A, Huang A, Kotanan N, Jaru-Ampornpan P, Manasatienkij W, Watthanachockchai T, Rakmanee K, Jones AR, Fernandez S, Sensorn I, Sungkanuparph S, Pasomsub E, Klungthong C, Chookajorn T, Chantratita W. Genomic surveillance of SARS-CoV-2 in Thailand reveals mixed imported populations, a local lineage expansion and a virus with truncated ORF7a. Virus Res 2020; 292:198233. [PMID: 33227343 PMCID: PMC7679658 DOI: 10.1016/j.virusres.2020.198233] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 09/07/2020] [Accepted: 11/12/2020] [Indexed: 12/20/2022]
Abstract
There were multiple introduction events of SARS-CoV-2 into Thailand. One lineage, designated A/Thai-1, has expanded and has become a predominant and unique lineage in Thailand. A major frame-shift mutation was found at the gene encoding ORF7a, a putative host antagonizing factor of the virus.
Coronavirus Disease 2019 (COVID-19) is a global public health threat. Genomic surveillance of SARS-CoV-2 was implemented in March of 2020 at a major diagnostic hub in Bangkok, Thailand. Several virus lineages supposedly originated in many countries were found, and a Thai-specific lineage, designated A/Thai-1, has expanded to be predominant in Thailand. A virus sample in the SARS-CoV-2 A/Thai-1 lineage contains a frame-shift deletion at ORF7a, encoding a putative host antagonizing factor of the virus.
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Affiliation(s)
- Khajohn Joonlasak
- COVID-19 Network Investigations Alliance (CONI), Bangkok, Thailand; Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Elizabeth M Batty
- COVID-19 Network Investigations Alliance (CONI), Bangkok, Thailand; Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Theerarat Kochakarn
- COVID-19 Network Investigations Alliance (CONI), Bangkok, Thailand; Genomics and Evolutionary Medicine Unit (GEM), Center of Excellence in Malaria Research, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand; Faculty of Medicine Ramathibodi Hospital, Mahidol University Bangkok, Thailand
| | - Bhakbhoom Panthan
- COVID-19 Network Investigations Alliance (CONI), Bangkok, Thailand; Center for Medical Genomics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Krittikorn Kümpornsin
- COVID-19 Network Investigations Alliance (CONI), Bangkok, Thailand; Wellcome Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Poramate Jiaranai
- COVID-19 Network Investigations Alliance (CONI), Bangkok, Thailand; Center for Medical Genomics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Arporn Wangwiwatsin
- COVID-19 Network Investigations Alliance (CONI), Bangkok, Thailand; Department of Biology, Faculty of Science, Khon Kaen University, Khon Kaen, Thailand
| | - Angkana Huang
- COVID-19 Network Investigations Alliance (CONI), Bangkok, Thailand; Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Namfon Kotanan
- COVID-19 Network Investigations Alliance (CONI), Bangkok, Thailand; Genomics and Evolutionary Medicine Unit (GEM), Center of Excellence in Malaria Research, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Peera Jaru-Ampornpan
- Virology and Cell Technology Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Wudtichai Manasatienkij
- COVID-19 Network Investigations Alliance (CONI), Bangkok, Thailand; Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Treewat Watthanachockchai
- Division of Virology, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Kingkan Rakmanee
- Division of Virology, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Anthony R Jones
- COVID-19 Network Investigations Alliance (CONI), Bangkok, Thailand; Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Stefan Fernandez
- COVID-19 Network Investigations Alliance (CONI), Bangkok, Thailand; Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Insee Sensorn
- COVID-19 Network Investigations Alliance (CONI), Bangkok, Thailand; Center for Medical Genomics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Somnuek Sungkanuparph
- Chakri Naruebodindra Medical Institute, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Samut Prakan, Thailand
| | - Ekawat Pasomsub
- COVID-19 Network Investigations Alliance (CONI), Bangkok, Thailand; Division of Virology, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Chonticha Klungthong
- COVID-19 Network Investigations Alliance (CONI), Bangkok, Thailand; Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Thanat Chookajorn
- COVID-19 Network Investigations Alliance (CONI), Bangkok, Thailand; Genomics and Evolutionary Medicine Unit (GEM), Center of Excellence in Malaria Research, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
| | - Wasun Chantratita
- COVID-19 Network Investigations Alliance (CONI), Bangkok, Thailand; Center for Medical Genomics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand.
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