Implementing parasite genotyping into national surveillance frameworks: feedback from control programmes and researchers in the Asia–Pacific region

[1]  J. Bailey,et al.  Sensitive, Highly Multiplexed Sequencing of Microhaplotypes From the Plasmodium falciparum Heterozygome , 2020, bioRxiv.

[2]  C. Buckee,et al.  Resolving the cause of recurrent Plasmodium vivax malaria probabilistically , 2019, Nature Communications.

[3]  M. Gatton,et al.  A review of the WHO malaria rapid diagnostic test product testing programme (2008–2018): performance, procurement and policy , 2019, Malaria Journal.

[4]  A. Lerch,et al.  Amplicon deep sequencing improves Plasmodium falciparum genotyping in clinical trials of antimalarial drugs , 2019, Scientific Reports.

[5]  D. Kwiatkowski,et al.  An open dataset of Plasmodium falciparum genome variation in 7,000 worldwide samples , 2019, bioRxiv.

[6]  Diego F. Echeverry,et al.  A molecular barcode and online tool to identify and map imported infection with Plasmodium vivax , 2019, bioRxiv.

[7]  A. Djimde,et al.  Targeted Next Generation Sequencing for malaria research in Africa: current status and outlook , 2019, Malaria Journal.

[8]  Juliana M. Sá,et al.  Plasmodium vivax chloroquine resistance links to pvcrt transcription in a genetic cross , 2019, Nature Communications.

[9]  B. Greenhouse,et al.  Applying next-generation sequencing to track falciparum malaria in sub-Saharan Africa , 2019, Malaria Journal.

[10]  Queen Saidi,et al.  Deployment and utilization of next-generation sequencing of Plasmodium falciparum to guide anti-malarial drug policy decisions in sub-Saharan Africa: opportunities and challenges , 2019, Malaria Journal.

[11]  O. Lund,et al.  Proof of concept: used malaria rapid diagnostic tests applied for parallel sequencing for surveillance of molecular markers of anti-malarial resistance in Bissau, Guinea-Bissau during 2014–2017 , 2019, Malaria Journal.

[12]  O. Lund,et al.  Proof of concept: used malaria rapid diagnostic tests applied for parallel sequencing for surveillance of molecular markers of anti-malarial resistance in Bissau, Guinea-Bissau during 2014–2017 , 2019, Malaria Journal.

[13]  D. Kwiatkowski,et al.  Emergence of artemisinin-resistant Plasmodium falciparum with kelch13 C580Y mutations on the island of New Guinea , 2019, bioRxiv.

[14]  Richard J Maude,et al.  Evolution and expansion of multidrug-resistant malaria in southeast Asia: a genomic epidemiology study , 2019, bioRxiv.

[15]  T. Kwan-Gett,et al.  Use cases for genetic epidemiology in malaria elimination , 2019, Malaria Journal.

[16]  Amy Wesolowski,et al.  Using parasite genetic and human mobility data to infer local and cross-border malaria connectivity in Southern Africa , 2019, eLife.

[17]  A. Tatem,et al.  Changing epidemiology and challenges of malaria in China towards elimination , 2019, Malaria journal.

[18]  A. Rosanas-Urgell,et al.  Longitudinal tracking and quantification of individual Plasmodium falciparum clones in complex infections , 2019, Scientific Reports.

[19]  Amy Wesolowski,et al.  Mapping imported malaria in Bangladesh using parasite genetic and human mobility data , 2019, eLife.

[20]  J. Grimsby,et al.  Detection of low-density Plasmodium falciparum infections using amplicon deep sequencing , 2019, Malaria Journal.

[21]  D. Serre,et al.  Recrudescence, Reinfection, or Relapse? A More Rigorous Framework to Assess Chloroquine Efficacy for Plasmodium vivax Malaria , 2018, The Journal of infectious diseases.

[22]  F. Ramos Report 2019 , 2019, Brazilian Business Review.

[23]  Susana Campino,et al.  Genomic analysis of a pre-elimination Malaysian Plasmodium vivax population reveals selective pressures and changing transmission dynamics , 2018, Nature Communications.

[24]  G. Yan,et al.  Molecular approaches to determine the multiplicity of Plasmodium infections , 2018, Malaria Journal.

[25]  Caroline O Buckee,et al.  Mapping malaria by combining parasite genomic and epidemiologic data , 2018, bioRxiv.

[26]  Melanie Bahlo,et al.  Identity-by-descent analyses for measuring population dynamics and selection in recombining pathogens , 2018, PLoS genetics.

[27]  P. Siba,et al.  Nationwide genetic surveillance of Plasmodium vivax in Papua New Guinea reveals heterogeneous transmission dynamics and routes of migration amongst subdivided populations. , 2018, Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases.

[28]  M. Bahlo,et al.  Increasingly inbred and fragmented populations of Plasmodium vivax associated with the eastward decline in malaria transmission across the Southwest Pacific , 2018, PLoS neglected tropical diseases.

[29]  J. Bailey,et al.  SeekDeep: single-base resolution de novo clustering for amplicon deep sequencing , 2017, Nucleic acids research.

[30]  Caroline O Buckee,et al.  Quantifying connectivity between local Plasmodium falciparum malaria parasite populations using identity by descent , 2017, PLoS genetics.

[31]  S. Schaffner,et al.  hmmIBD: software to infer pairwise identity by descent between haploid genotypes , 2017, bioRxiv.

[32]  R. Price,et al.  Passively versus Actively Detected Malaria: Similar Genetic Diversity but Different Complexity of Infection , 2017, The American journal of tropical medicine and hygiene.

[33]  Mehul Dhorda,et al.  The spread of artemisinin-resistant Plasmodium falciparum in the Greater Mekong subregion: a molecular epidemiology observational study , 2017, The Lancet. Infectious diseases.

[34]  K. Battle,et al.  Challenges for achieving safe and effective radical cure of Plasmodium vivax: a round table discussion of the APMEN Vivax Working Group , 2017, Malaria Journal.

[35]  A. Lerch,et al.  Development of amplicon deep sequencing markers and data analysis pipeline for genotyping multi-clonal malaria infections , 2017, bioRxiv.

[36]  R. Price,et al.  VivaxGEN: An open access platform for comparative analysis of short tandem repeat genotyping data in Plasmodium vivax populations , 2017, PLoS neglected tropical diseases.

[37]  Gil McVean,et al.  Deconvolution of multiple infections in Plasmodium falciparum from high throughput sequencing data , 2017, bioRxiv.

[38]  Sesh A. Sundararaman,et al.  Selective Whole-Genome Amplification Is a Robust Method That Enables Scalable Whole-Genome Sequencing of Plasmodium vivax from Unprocessed Clinical Samples , 2017, mBio.

[39]  D. Fidock,et al.  A surrogate marker of piperaquine-resistant Plasmodium falciparum malaria: a phenotype–genotype association study , 2017, The Lancet. Infectious diseases.

[40]  A. Barry,et al.  Dissecting malaria biology and epidemiology using population genetics and genomics. , 2017, International journal for parasitology.

[41]  D. Kwiatkowski,et al.  Genetic markers associated with dihydroartemisinin-piperaquine failure in Plasmodium falciparum malaria in Cambodia: a genotype-phenotype association study. , 2017, The Lancet. Infectious diseases.

[42]  R. Price,et al.  Molecular Epidemiology of P. vivax in Iran: High Diversity and Complex Sub-Structure Using Neutral Markers, but No Evidence of Y976F Mutation at pvmdr1 , 2016, PloS one.

[43]  D. Kwiatkowski,et al.  Whole genome sequencing of Plasmodium falciparum from dried blood spots using selective whole genome amplification , 2016, bioRxiv.

[44]  D. Kwiatkowski,et al.  Genomic Analysis Reveals a Common Breakpoint in Amplifications of the Plasmodium vivax Multidrug Resistance 1 Locus in Thailand , 2016, The Journal of infectious diseases.

[45]  Alistair Miles,et al.  Genomic analysis of local variation and recent evolution in Plasmodium vivax , 2016, Nature Genetics.

[46]  Adele M. Lehane,et al.  Globally prevalent PfMDR1 mutations modulate Plasmodium falciparum susceptibility to artemisinin-based combination therapies , 2016, Nature Communications.

[47]  R. Price,et al.  Efficacy of Artesunate-mefloquine for Chloroquine-resistant Plasmodium vivax Malaria in Malaysia: An Open-label, Randomized, Controlled Trial , 2016, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

[48]  R. Price,et al.  Where chloroquine still works: the genetic make-up and susceptibility of Plasmodium vivax to chloroquine plus primaquine in Bhutan , 2016, Malaria Journal.

[49]  Thomas A. Smith,et al.  The Incidence and Differential Seasonal Patterns of Plasmodium vivax Primary Infections and Relapses in a Cohort of Children in Papua New Guinea , 2016, PLoS neglected tropical diseases.

[50]  Paul J. McMurdie,et al.  DADA2: High resolution sample inference from Illumina amplicon data , 2016, Nature Methods.

[51]  R. Price,et al.  Further Evidence of Increasing Diversity of Plasmodium vivax in the Republic of Korea in Recent Years , 2016, PloS one.

[52]  Qin Cheng,et al.  Targeting vivax malaria in the Asia Pacific: The Asia Pacific Malaria Elimination Network Vivax Working Group , 2015, Malaria Journal.

[53]  R. Price,et al.  Expression of Plasmodium vivax crt-o Is Related to Parasite Stage but Not Ex Vivo Chloroquine Susceptibility , 2015, Antimicrobial Agents and Chemotherapy.

[54]  Duo-quan Wang,et al.  Transmission Risk from Imported Plasmodium vivax Malaria in the China–Myanmar Border Region , 2015, Emerging infectious diseases.

[55]  J. Bailey,et al.  Using Amplicon Deep Sequencing to Detect Genetic Signatures of Plasmodium vivax Relapse. , 2015, The Journal of infectious diseases.

[56]  Saorin Kim,et al.  Evidence of Plasmodium falciparum Malaria Multidrug Resistance to Artemisinin and Piperaquine in Western Cambodia: Dihydroartemisinin-Piperaquine Open-Label Multicenter Clinical Assessment , 2015, Antimicrobial Agents and Chemotherapy.

[57]  S. Schaffner,et al.  Modeling malaria genomics reveals transmission decline and rebound in Senegal , 2015, Proceedings of the National Academy of Sciences.

[58]  R. Price,et al.  Contrasting Transmission Dynamics of Co-endemic Plasmodium vivax and P. falciparum: Implications for Malaria Control and Elimination , 2015, PLoS neglected tropical diseases.

[59]  Juliana M. Sá,et al.  Development of a Single Nucleotide Polymorphism Barcode to Genotype Plasmodium vivax Infections , 2015, PLoS neglected tropical diseases.

[60]  Gilean McVean,et al.  Genetic architecture of artemisinin-resistant Plasmodium falciparum , 2015, Nature Genetics.

[61]  Pardis C Sabeti,et al.  COIL: a methodology for evaluating malarial complexity of infection using likelihood from single nucleotide polymorphism data , 2015, Malaria Journal.

[62]  W. Monteiro,et al.  Expression Levels of pvcrt-o and pvmdr-1 Are Associated with Chloroquine Resistance and Severe Plasmodium vivax Malaria in Patients of the Brazilian Amazon , 2014, PloS one.

[63]  D. Saunders,et al.  Dihydroartemisinin-piperaquine failure in Cambodia. , 2014, The New England journal of medicine.

[64]  D. Kwiatkowski,et al.  Spread of artemisinin resistance in Plasmodium falciparum malaria. , 2014, The New England journal of medicine.

[65]  Peter Chiodini,et al.  Plasmodium falciparum parasites lacking histidine-rich protein 2 and 3: a review and recommendations for accurate reporting , 2014, Malaria Journal.

[66]  R. Price,et al.  Genetic diversity and population structure of Plasmodium vivax in Central China , 2014, Malaria Journal.

[67]  Samuel A. Assefa,et al.  A barcode of organellar genome polymorphisms identifies the geographic origin of Plasmodium falciparum strains , 2014, Nature Communications.

[68]  J. Alves,et al.  Using mitochondrial genome sequences to track the origin of imported Plasmodium vivax infections diagnosed in the United States. , 2014, The American journal of tropical medicine and hygiene.

[69]  E. Winzeler,et al.  A High Resolution Case Study of a Patient with Recurrent Plasmodium vivax Infections Shows That Relapses Were Caused by Meiotic Siblings , 2014, PLoS neglected tropical diseases.

[70]  D. Wirth,et al.  The Sri Lankan paradox: high genetic diversity in Plasmodium vivax populations despite decreasing levels of malaria transmission , 2014, Parasitology.

[71]  B. Genton,et al.  A molecular marker of artemisinin-resistant Plasmodium falciparum malaria , 2013, Nature.

[72]  Q. Gao,et al.  Malaria in overseas labourers returning to China: an analysis of imported malaria in Jiangsu Province, 2001–2011 , 2014, Malaria Journal.

[73]  Timothy William,et al.  Plasmodium vivax Population Structure and Transmission Dynamics in Sabah Malaysia , 2013, PloS one.

[74]  R. Price,et al.  Nonlinear Mixed-Effects Modelling of In Vitro Drug Susceptibility and Molecular Correlates of Multidrug Resistant Plasmodium falciparum , 2013, PloS one.

[75]  François Nosten,et al.  Population genetic correlates of declining transmission in a human pathogen , 2012, Molecular ecology.

[76]  D. Ménard,et al.  Efficacy of Dihydroartemisinin-Piperaquine for Treatment of Uncomplicated Plasmodium falciparum and Plasmodium vivax in Cambodia, 2008 to 2010 , 2012, Antimicrobial Agents and Chemotherapy.

[77]  R. Price,et al.  Phenotypic and genotypic characterisation of drug-resistant Plasmodium vivax. , 2012, Trends in parasitology.

[78]  N. Fullman,et al.  Malaria elimination gaining ground in the Asia Pacific , 2012, Malaria Journal.

[79]  Taane G. Clark,et al.  Characterization of Within-Host Plasmodium falciparum Diversity Using Next-Generation Sequence Data , 2012, PloS one.

[80]  N. White,et al.  Chapter Two - Relapse , 2012 .

[81]  Shin-Hyeong Cho,et al.  Study of the genetic discrimination between imported and autochthonous cases of malaria in South Korea. , 2011, Journal of travel medicine.

[82]  S. Hay,et al.  Malaria distribution, prevalence, drug resistance and control in Indonesia. , 2011, Advances in parasitology.

[83]  S. Kano,et al.  Geographical origin of Plasmodium vivax in the Republic of Korea: haplotype network analysis based on the parasite's mitochondrial genome , 2010, Malaria Journal.

[84]  D. Hartl,et al.  Geographic structure of Plasmodium vivax: microsatellite analysis of parasite populations from Sri Lanka, Myanmar, and Ethiopia. , 2010, The American journal of tropical medicine and hygiene.

[85]  K. Silamut,et al.  Artemisinin resistance in Plasmodium falciparum malaria. , 2009, The New England journal of medicine.

[86]  B. Genton,et al.  Evaluation of Plasmodium vivax genotyping markers for molecular monitoring in clinical trials. , 2009, The Journal of infectious diseases.

[87]  M. U. Ferreira,et al.  A closer look at multiple-clone Plasmodium vivax infections: detection methods, prevalence and consequences. , 2009, Memorias do Instituto Oswaldo Cruz.

[88]  N. D. Djadid,et al.  Molecular characterization of antifolates resistance-associated genes, (dhfr and dhps) in Plasmodium vivax isolates from the Middle East , 2009, Malaria Journal.

[89]  M. Fukuda,et al.  Evidence of artemisinin-resistant malaria in western Cambodia. , 2008, The New England journal of medicine.

[90]  R. Price,et al.  Amplification of pvmdr1 associated with multidrug-resistant Plasmodium vivax. , 2008, The Journal of infectious diseases.

[91]  Pardis C Sabeti,et al.  A general SNP-based molecular barcode for Plasmodium falciparum identification and tracking , 2008 .

[92]  B. Genton,et al.  Molecular markers of in vivo Plasmodium vivax resistance to amodiaquine plus sulfadoxine-pyrimethamine: mutations in pvdhfr and pvmdr1. , 2008, The Journal of infectious diseases.

[93]  P. Newton,et al.  Gene Amplification of the Multidrug Resistance 1 Gene of Plasmodium vivax Isolates from Thailand, Laos, and Myanmar , 2008, Antimicrobial Agents and Chemotherapy.

[94]  C. Sibley,et al.  Geographical distribution of amino acid mutations in Plasmodium vivax DHFR and DHPS from malaria endemic areas of Thailand. , 2008, The American journal of tropical medicine and hygiene.

[95]  H. Tinto,et al.  Chloroquine‐resistance molecular markers (Pfcrt T76 and Pfmdr‐1 Y86) and amodiaquine resistance in Burkina Faso , 2008, Tropical medicine & international health : TM & IH.

[96]  R. Price,et al.  Chloroquine Resistant Plasmodium vivax: In Vitro Characterisation and Association with Molecular Polymorphisms , 2007, PloS one.

[97]  R. Price,et al.  Therapeutic response of multidrug-resistant Plasmodium falciparum and P. vivax to chloroquine and sulfadoxine–pyrimethamine in southern Papua, Indonesia , 2007, Transactions of the Royal Society of Tropical Medicine and Hygiene.

[98]  J. Carlton,et al.  Relapses of Plasmodium vivax infection usually result from activation of heterologous hypnozoites. , 2007, The Journal of infectious diseases.

[99]  Danny W. Wilson,et al.  Amino acid mutations in Plasmodium vivax DHFR and DHPS from several geographical regions and susceptibility to antifolate drugs. , 2006, The American journal of tropical medicine and hygiene.

[100]  J. Carlton,et al.  Microsatellite variation, repeat array length, and population history of Plasmodium vivax. , 2006, Molecular biology and evolution.

[101]  Q. Cheng,et al.  Limited Polymorphism in the Dihydropteroate Synthetase Gene (dhps) of Plasmodium vivax Isolates from Thailand , 2005, Antimicrobial Agents and Chemotherapy.

[102]  Manoj T Duraisingh,et al.  Contribution of the pfmdr1 gene to antimalarial drug-resistance. , 2005, Acta tropica.

[103]  C. Plowe,et al.  Mechanisms of Resistance of Malaria Parasites to Antifolates , 2005, Pharmacological Reviews.

[104]  J. Baird,et al.  Novel Plasmodium vivax dhfr Alleles from the Indonesian Archipelago and Papua New Guinea: Association with Pyrimethamine Resistance Determined by a Saccharomyces cerevisiae Expression System , 2005, Antimicrobial Agents and Chemotherapy.

[105]  L. Gradoni,et al.  Identification of the Plasmodium vivax mdr-like gene (pvmdr1) and analysis of single-nucleotide polymorphisms among isolates from different areas of endemicity. , 2005, The Journal of infectious diseases.

[106]  L. Gradoni,et al.  Risk of Plasmodium vivax malaria reintroduction in Uzbekistan: genetic characterization of parasites and status of potential malaria vectors in the Surkhandarya region. , 2004, Transactions of the Royal Society of Tropical Medicine and Hygiene.

[107]  François Nosten,et al.  Mefloquine resistance in Plasmodium falciparum and increased pfmdr1 gene copy number , 2004, The Lancet.

[108]  J. Baker,et al.  Sulfadoxine Resistance in Plasmodium vivax Is Associated with a Specific Amino Acid in Dihydropteroate Synthase at the Putative Sulfadoxine-Binding Site , 2004, Antimicrobial Agents and Chemotherapy.

[109]  Peter Beerli,et al.  Early Origin and Recent Expansion of Plasmodium falciparum , 2003, Science.

[110]  Hilde van der Togt,et al.  Publisher's Note , 2003, J. Netw. Comput. Appl..

[111]  J. Baker,et al.  Therapeutic Efficacies of Artesunate-Sulfadoxine-Pyrimethamine and Chloroquine-Sulfadoxine-Pyrimethamine in Vivax Malaria Pilot Studies: Relationship to Plasmodium vivax dhfr Mutations , 2002, Antimicrobial Agents and Chemotherapy.

[112]  L. Gradoni,et al.  Use of the Plasmodium vivax merozoite surface protein 1 gene sequence analysis in the investigation of an introduced malaria case in Italy. , 2002, Acta tropica.

[113]  J. E. Hyde,et al.  Mechanisms of resistance of Plasmodium falciparum to antimalarial drugs. , 2002, Microbes and infection.

[114]  D. Warhurst A molecular marker for chloroquine-resistant falciparum malaria. , 2001, The New England journal of medicine.

[115]  D. Conway,et al.  Origin of Plasmodium falciparum malaria is traced by mitochondrial DNA. , 2000, Molecular and biochemical parasitology.

[116]  J. T. Williams,et al.  Microsatellite markers reveal a spectrum of population structures in the malaria parasite Plasmodium falciparum. , 2000, Molecular biology and evolution.

[117]  K. Kirk,et al.  Pgh1 modulates sensitivity and resistance to multiple antimalarials in Plasmodium falciparum , 2000, Nature.

[118]  X. Su,et al.  Twelve microsatellite markers for characterization of Plasmodium falciparum from finger-prick blood samples , 1999, Parasitology.

[119]  G. Snounou,et al.  The use of PCR genotyping in the assessment of recrudescence or reinfection after antimalarial drug treatment. , 1998, Parasitology today.

[120]  A. Cowman,et al.  Selection for mefloquine resistance in Plasmodium falciparum is linked to amplification of the pfmdr1 gene and cross-resistance to halofantrine and quinine. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[121]  S. Wright,et al.  Isolation by Distance. , 1943, Genetics.