4.8 Article

Multiplexed ddPCR-amplicon sequencing reveals isolated Plasmodium falciparum populations amenable to local elimination in Zanzibar, Tanzania

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Public, Environmental & Occupational Health

Spatiotemporal dynamics of malaria in Zanzibar, 2015-2020

Donal Bisanzio et al.

Summary: Despite high coverage of malaria interventions, malaria elimination in Zanzibar remains elusive, with the annual number of cases increasing gradually over the last 3 years. This study aimed to assess the spatiotemporal dynamics of malaria in Zanzibar between 2015 and 2020 and identify malaria hotspots for targeted interventions. The analyses revealed stable hotspots in certain areas, suggesting the need for more tailored approaches.

BMJ GLOBAL HEALTH (2023)

Article Multidisciplinary Sciences

Modelling the impact of interventions on imported, introduced and indigenous malaria infections in Zanzibar, Tanzania

Aatreyee M. Das et al.

Summary: This study used a stochastic metapopulation model to test the impact of new interventions on malaria transmission in Zanzibar. They found that despite high case importation rates, the majority of new cases were indigenous. Increasing the coverage of interventions such as reactive case detection can lead to substantial decreases in malaria incidence, but transmission reduction in both Zanzibar and mainland Tanzania is necessary for elimination within the next 40 years.

NATURE COMMUNICATIONS (2023)

Article Immunology

Sensitive, Highly Multiplexed Sequencing of Microhaplotypes From the Plasmodium falciparum Heterozygome

Sofonias K. Tessema et al.

Summary: A novel bioinformatics pipeline was developed to select and characterize diverse and tractable short-range sequences in the Plasmodium falciparum genome, and a robust multiplexing method was used to amplify and sequence these sequences simultaneously. The method achieved high coverage, specificity, and sensitivity, making it a flexible tool for efficient and high-throughput studies in different epidemiological settings.

JOURNAL OF INFECTIOUS DISEASES (2022)

Article Infectious Diseases

Tenfold difference in DNA recovery rate: systematic comparison of whole blood vs. dried blood spot sample collection for malaria molecular surveillance

Aurel Holzschuh et al.

Summary: This study compared the effect of different blood sample preservation methods on the limit of detection and DNA recovery for molecular diagnosis. The results showed that whole blood had higher DNA recovery and lower limit of detection compared to dried blood spots. Magnetic bead-based and Tween-Chelex methods were found to be effective for DNA extraction.

MALARIA JOURNAL (2022)

Article Biochemistry & Molecular Biology

Design and implementation of multiplexed amplicon sequencing panels to serve genomic epidemiology of infectious disease: A malaria case study

Emily LaVerriere et al.

Summary: Multiplexed PCR amplicon sequencing (AmpSeq) is a valuable tool for monitoring threatened species and managing wildlife populations, as well as for understanding the genomic epidemiology of infectious diseases. The study describes the design and evaluation of two new AmpSeq assays for Plasmodium falciparum malaria parasites, and provides guidance on panel design and implementation for infectious disease research.

MOLECULAR ECOLOGY RESOURCES (2022)

Article Infectious Diseases

The impact of reactive case detection on malaria transmission in Zanzibar in the presence of human mobility

Aatreyee M. Das et al.

Summary: This study uses a metapopulation model to examine the role of human mobility and reactive case detection in the persistence of malaria on Zanzibar. The findings suggest that malaria would likely cease to persist on the island without imported cases from mainland Tanzania. The study also explores potential intervention scenarios but finds that none of them are sufficient to eliminate malaria.

EPIDEMICS (2022)

Article Multidisciplinary Sciences

Decreased susceptibility of Plasmodium falciparum to both dihydroartemisinin and lumefantrine in northern Uganda

Patrick K. Tumwebaze et al.

Summary: This study found that the partial resistance to artemisinin may lead to the selection of Plasmodium falciparum that is resistant to combination therapy partner drugs. The susceptibility to lumefantrine and dihydroartemisinin was lower in northern Uganda where resistance-associated mutations have emerged, compared to eastern Uganda. Multiple genetic polymorphisms were associated with altered drug susceptibility in Plasmodium falciparum.

NATURE COMMUNICATIONS (2022)

Article Genetics & Heredity

Dcifer: an IBD-based method to calculate genetic distance between polyclonal infections

Inna Gerlovina et al.

Summary: Dcifer is a method for calculating genetic distance between polyclonal infections, designed for unphased data, and provides reliable inference. It delivers accurate and interpretable results, with statistical power that is 2-4 times greater than existing approaches.

GENETICS (2022)

Article Biochemistry & Molecular Biology

Describing the current status of Plasmodium falciparum population structure and drug resistance within mainland Tanzania using molecular inversion probes

Kara A. Moser et al.

Summary: The study utilized high-throughput Plasmodium genomic data to analyze parasite population structure and geographic distribution of drug resistance mutations in Tanzania nationwide. The results indicated clear genetic separation between parasites from the northern and southern regions, with more drug resistance mutations found in the northern districts. The Malaria Indicator Survey data corresponded with genetic findings, providing insights into local genetic diversity and transmission patterns of malaria parasites.

MOLECULAR ECOLOGY (2021)

Review Infectious Diseases

Spatial and molecular mapping of Pfkelch13 gene polymorphism in Africa in the era of emerging Plasmodium falciparum resistance to artemisinin: a systematic review

Nadine K. Kayiba et al.

Summary: The systematic review reveals that Africa, previously thought to not have established artemisinin resistance, has reported resistance-related mutants in the past five years. Surveillance using molecular markers of artemisinin resistance in Plasmodium falciparum can offer valuable decision-making information to maintain the effectiveness of artemisinin in Africa.

LANCET INFECTIOUS DISEASES (2021)

Review Genetics & Heredity

Advances and opportunities in malaria population genomics

Daniel E. Neafsey et al.

Summary: Nearly 20 years have passed since the first reference genome assemblies for Plasmodium falciparum and Anopheles gambiae were published. Having reference genomes for human malaria parasites and important mosquito vectors has advanced our understanding in disease biology, drug resistance, and vaccine development. Population genomics data are increasingly used to assess malaria epidemiology and intervention efficacy, presenting both opportunities and challenges in malaria control strategies.

NATURE REVIEWS GENETICS (2021)

Review Multidisciplinary Sciences

Systematic review of Plasmodium falciparum and Plasmodium vivax polyclonal infections: Impact of prevalence, study population characteristics, and laboratory procedures

Luis Lopez et al.

Summary: Multiple infections of genetically distinct clones of the same Plasmodium species are common in malaria endemic settings. However, the association between multiplicity and prevalence is weak.

PLOS ONE (2021)

Article Biology

Genetic surveillance in the Greater Mekong subregion and South Asia to support malaria control and elimination

Christopher G. Jacob et al.

Summary: GenRe-Mekong is a platform for genetic surveillance of malaria in the Greater Mekong Subregion, providing valuable insights and aiding decision-making for NMCPs. It offers detailed knowledge about drug resistance, facilitates data sharing, and enables cross-border resistance monitoring, benefiting the malaria community as a whole.
Article Immunology

Changing Prevalence of Potential Mediators of Aminoquinoline, Antifolate, and Artemisinin Resistance Across Uganda

Victor Asua et al.

Summary: This study identified concerning spread of mutations that may limit the efficacies of key antimalarial drugs in multiple sites in Uganda.

JOURNAL OF INFECTIOUS DISEASES (2021)

Article Public, Environmental & Occupational Health

Operational Coverage and Timeliness of Reactive Case Detection for Malaria Elimination in Zanzibar, Tanzania

Tina van der Horst et al.

AMERICAN JOURNAL OF TROPICAL MEDICINE AND HYGIENE (2020)

Article Multidisciplinary Sciences

The impact of antimalarial resistance on the genetic structure of Plasmodium falciparum in the DRC

Robert Verity et al.

NATURE COMMUNICATIONS (2020)

Article Infectious Diseases

Malaria infection prevalence and sensitivity of reactive case detection in Zanzibar

Logan Stuck et al.

INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES (2020)

Article Infectious Diseases

Genetic diversity of Plasmodium falciparum in Grande Comore Island

Nasserdine Papa Mze et al.

MALARIA JOURNAL (2020)

Article Genetics & Heredity

Estimating Relatedness Between Malaria Parasites

Aimee R. Taylor et al.

GENETICS (2019)

Review Infectious Diseases

Antimalarial drug resistance in Africa: the calm before the storm?

Melissa D. Conrad et al.

LANCET INFECTIOUS DISEASES (2019)

Article Multidisciplinary Sciences

Major subpopulations of Plasmodium falciparum in sub-Saharan Africa

Alfred Amambua-Ngwa et al.

SCIENCE (2019)

Article Multidisciplinary Sciences

Amplicon deep sequencing improves Plasmodium falciparum genotyping in clinical trials of antimalarial drugs

Maria Gruenberg et al.

SCIENTIFIC REPORTS (2019)

Article Biochemistry & Molecular Biology

Microhaplotypes provide increased power from short-read DNA sequences for relationship inference

Diana S. Baetscher et al.

MOLECULAR ECOLOGY RESOURCES (2018)

Article Infectious Diseases

hmmIBD: software to infer pairwise identity by descent between haploid genotypes

Stephen F. Schaffner et al.

MALARIA JOURNAL (2018)

Article Medicine, General & Internal

Mapping malaria by combining parasite genomic and epidemiologic data

Amy Wesolowski et al.

BMC MEDICINE (2018)

Review Parasitology

Malaria Epidemiology at the Clone Level

Cristian Koepfli et al.

TRENDS IN PARASITOLOGY (2017)

Article Microbiology

Molecular Profile of Malaria Drug Resistance Markers of Plasmodium falciparum in Suriname

Stella M. Chenet et al.

ANTIMICROBIAL AGENTS AND CHEMOTHERAPY (2017)

Article Genetics & Heredity

Estimating the Number of Subpopulations (K) in Structured Populations

Robert Verity et al.

GENETICS (2016)

Article Biology

Genomic epidemiology of artemisinin resistant malaria

Roberto Amato et al.

Article Genetics & Heredity

Estimating the Number of Subpopulations (K) in Structured Populations

Robert Verity et al.

GENETICS (2016)

Article Multidisciplinary Sciences

VSEARCH: a versatile open source tool for metagenomics

Torbjorn Rognes et al.

Article Genetics & Heredity

Genetic architecture of artemisinin-resistant Plasmodium falciparum

Olivo Miotto et al.

NATURE GENETICS (2015)

Article Medicine, General & Internal

Genetic Diversity and Protective Efficacy of the RTS, S/AS01 Malaria Vaccine

D. E. Neafsey et al.

NEW ENGLAND JOURNAL OF MEDICINE (2015)

Article Multidisciplinary Sciences

Modeling malaria genomics reveals transmission decline and rebound in Senegal

Rachel F. Daniels et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2015)

Article Medicine, General & Internal

Ultra-Sensitive Detection of Plasmodium falciparum by Amplification of Multi-Copy Subtelomeric Targets

Natalie Hofmann et al.

PLOS MEDICINE (2015)

Article Multidisciplinary Sciences

Swarm v2: highly-scalable and high-resolution amplicon clustering

Frederic Mahe et al.

Article Computer Science, Software Engineering

UpSet: Visualization of Intersecting Sets

Alexander Lex et al.

IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS (2014)

Article Biochemistry & Molecular Biology

Population genetic correlates of declining transmission in a human pathogen

Standwell C. Nkhoma et al.

MOLECULAR ECOLOGY (2013)

Editorial Material Medicine, General & Internal

Hitting Hotspots: Spatial Targeting of Malaria for Control and Elimination

Teun Bousema et al.

PLOS MEDICINE (2012)

Article Biochemical Research Methods

adegenet 1.3-1: new tools for the analysis of genome-wide SNP data

Thibaut Jombart et al.

BIOINFORMATICS (2011)

Review Biochemistry & Molecular Biology

Assessing population structure: F-ST and related measures

Patrick G. Meirmans et al.

MOLECULAR ECOLOGY RESOURCES (2011)

Article Multidisciplinary Sciences

Travel risk, malaria importation and malaria transmission in Zanzibar

Arnaud Le Menach et al.

SCIENTIFIC REPORTS (2011)

Article Biochemical Research Methods

BEDTools: a flexible suite of utilities for comparing genomic features

Aaron R. Quinlan et al.

BIOINFORMATICS (2010)

Article Biochemical Research Methods

The Sequence Alignment/Map format and SAMtools

Heng Li et al.

BIOINFORMATICS (2009)

Article Biochemistry & Molecular Biology

GST and its relatives do not measure differentiation

Lou Jost

MOLECULAR ECOLOGY (2008)

Article Computer Science, Interdisciplinary Applications

The ade4 package: Implementing the duality diagram for ecologists

Stephane Dray et al.

JOURNAL OF STATISTICAL SOFTWARE (2007)

Article Genetics & Heredity

A genome-wide map of diversity in Plasmodium falciparum

Sarah K. Volkman et al.

NATURE GENETICS (2007)

Review Pharmacology & Pharmacy

Mechanisms of resistance of malaria parasites to antifolates

A Gregson et al.

PHARMACOLOGICAL REVIEWS (2005)