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Utility of the Onchocerca volvulus mitochondrial genome for delineation of parasite transmission zones

https://doi.org/10.1101/732446
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Outgoing claims: the papers this work cites, builds on, or argues with.

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Dating of the human-ape splitting by a molecular clock of mitochondrial DNA
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Onchocerciasis and its control. Report of a WHO Expert Committee on onchocerciasis control
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Helminthic Diseases: Onchocerciasis and Loiasis
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River Blindness
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Recrudescence of onchocerciasis in the Comoé valley in Southwest Burkina Faso
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Modelling the elimination of river blindness using long-term epidemiological and programmatic data from Mali and Senegal
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Population genetics of complex life-cycle parasites: an illustration with trematodes
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Whence river blindness? The domestication of mammals and host-parasite co-evolution in the nematode genus Onchocerca
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Harvesting the fruit of the human mtDNA tree
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Life history determines genetic structure and evolutionary potential of host–parasite interactions
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Infecting epidemiology with genetics: a new frontier in disease ecology
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Reduced genetic variation of an Onchocerca volvulus ABC transporter gene following treatment with ivermectin
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Prevalence and intensity of Onchocerca volvulus infection and efficacy of ivermectin in endemic communities in Ghana: a two-phase epidemiological study
inferredcites →https://doi.org/10.1016/s0166-6851(98)00102-9openalex-snapshot
The mitochondrial genome of Onchocerca volvulus: Sequence, structure and phylogenetic analysis
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Studies of winds and weather during migrations of Simulium damnosum Theobald (Diptera: Simuliidae), the vector of onchocerciasis in West Africa
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The pattern and speed of displacement of females ofSimulium damnosumTheobald s.l. (Diptera: Simuliidae) across the Onchocerciasis Control Programme area of West Africa in 1977 and 1978
inferredcites →https://doi.org/10.1017/s0016672300014634openalex-snapshot
The hitch-hiking effect of a favourable gene
inferredcites →https://doi.org/10.1017/s0016672300029827openalex-snapshot
Inbreeding coefficients and coalescence times
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Patterns of epidemiology and control of onchocerciasis in West Africa
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Genetic structure in natural populations of flukes and snails: a practical approach and review
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Cattle Before Crops: The Beginnings of Food Production in Africa
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Mitochondrial genome variation and the origin of modern humans
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A framework for variation discovery and genotyping using next-generation DNA sequencing data
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Genomic diversity in Onchocerca volvulus and its Wolbachia endosymbiont
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Onchocerca-Simuliumcomplexes
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The Discovery of Single-Nucleotide Polymorphisms—and Inferences about Human Demographic History
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adegenet : a R package for the multivariate analysis of genetic markers
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DnaSP v5: a software for comprehensive analysis of DNA polymorphism data
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The Sequence Alignment/Map format and SAMtools
inferredcites →https://doi.org/10.1093/bioinformatics/btr330openalex-snapshot
The variant call format and VCFtools
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A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data
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adegenet 1.3-1 : new tools for the analysis of genome-wide SNP data
inferredcites →https://doi.org/10.1093/bioinformatics/btr642openalex-snapshot
PGDSpider: an automated data conversion tool for connecting population genetics and genomics programs
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Does Increasing Treatment Frequency Address Suboptimal Responses to Ivermectin for the Control and Elimination of River Blindness?
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Maximum likelihood estimation of population parameters.
inferredcites →https://doi.org/10.1093/genetics/141.3.1007openalex-snapshot
Host movement and the genetic structure of populations of parasitic nematodes.
inferredcites →https://doi.org/10.1093/genetics/147.2.915openalex-snapshot
Statistical Tests of Neutrality of Mutations Against Population Growth, Hitchhiking and Background Selection
inferredcites →https://doi.org/10.1093/inthealth/ihx047openalex-snapshot
Diagnostics for onchocerciasis in the era of elimination
inferredcites →https://doi.org/10.1093/inthealth/ihx052openalex-snapshot
Onchocerciasis: shifting the target from control to elimination requires a new first-step—elimination mapping
inferredcites →https://doi.org/10.1093/inthealth/ihx058openalex-snapshot
Cross-border issues: an important component of onchocerciasis elimination programmes
inferredcites →https://doi.org/10.1093/inthealth/ihx066openalex-snapshot
Refocusing vector assessment towards the elimination of onchocerciasis from Africa: a review of the current status in selected countries
inferredcites →https://doi.org/10.1093/molbev/msw260openalex-snapshot
PartitionFinder 2: New Methods for Selecting Partitioned Models of Evolution for Molecular and Morphological Phylogenetic Analyses
inferredcites →https://doi.org/10.1093/nar/19.14.4008openalex-snapshot
‘Touchdown’ PCR to circumvent spurious priming during gene amplification
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040023openalex-snapshot
Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees.
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040114openalex-snapshot
Recent evolutionary history of American Onchocerca volvulus, based on analysis of a tandemly repeated DNA sequence family.
inferredcites →https://doi.org/10.1093/sysbio/syp081openalex-snapshot
When Trees Grow Too Long: Investigating the Causes of Highly Inaccurate Bayesian Branch-Length Estimates
inferredcites →https://doi.org/10.1093/sysbio/syq010openalex-snapshot
New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0
inferredcites →https://doi.org/10.1093/sysbio/syy032openalex-snapshot
Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7
inferredcites →https://doi.org/10.1098/rsif.2007.1041openalex-snapshot
Spatial dynamics and genetics of infectious diseases on heterogeneous landscapes
inferredcites →https://doi.org/10.1098/rstb.1990.0141openalex-snapshot
Progress in controlling the reinvasion of windborne vectors into the western area of the Onchocerciasis Control Programme in West Africa
inferredcites →https://doi.org/10.1111/2041-210x.12410openalex-snapshot
popart : full‐feature software for haplotype network construction
inferredcites →https://doi.org/10.1111/j.0014-3820.2004.tb01587.xopenalex-snapshot
LIFE CYCLES SHAPE PARASITE EVOLUTION: COMPARATIVE POPULATION GENETICS OF SALMON TREMATODES
inferredcites →https://doi.org/10.1111/j.1365-294x.2005.02587.xopenalex-snapshot
Molecular ecology of parasites: elucidating ecological and microevolutionary processes
inferredcites →https://doi.org/10.1111/j.1755-0998.2010.02847.xopenalex-snapshot
Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows
inferredcites →https://doi.org/10.1111/jbi.14281openalex-snapshot
The detection of disease clustering and a generalized regression approach.
inferredcites →https://doi.org/10.1126/science.289.5488.2342openalex-snapshot
High Direct Estimate of the Mutation Rate in the Mitochondrial Genome of Caenorhabditis elegans
inferredcites →https://doi.org/10.1146/annurev.es.18.110187.002421openalex-snapshot
INTRASPECIFIC PHYLOGEOGRAPHY: The Mitochondrial DNA Bridge Between Population Genetics and Systematics
inferredcites →https://doi.org/10.1179/000349802125000637openalex-snapshot
Rapid epidemiological mapping of onchocerciasis (REMO): its application by the African Programme for Onchocerciasis Control (APOC)
inferredcites →https://doi.org/10.1179/000349804225003253openalex-snapshot
An investigation of persistent microfilaridermias despite multiple treatments with ivermectin, in two onchocerciasis-endemic foci in Ghana
inferredcites →https://doi.org/10.1179/000349804225003415openalex-snapshot
Identification of variant ABC-transporter genes amongOnchocerca volvuluscollected from ivermectin-treated and untreated patients in Ghana, West Africa
inferredcites →https://doi.org/10.1186/1471-2156-11-94openalex-snapshot
Discriminant analysis of principal components: a new method for the analysis of genetically structured populations
inferredcites →https://doi.org/10.1186/1756-3305-5-28openalex-snapshot
Impact of long-term treatment of onchocerciasis with ivermectin in Kaduna State, Nigeria: first evidence of the potential for elimination in the operational area of the African Programme for Onchocerciasis Control
inferredcites →https://doi.org/10.1186/1756-3305-6-205openalex-snapshot
Stability and change in the distribution of cytospecies of the Simulium damnosum complex (Diptera: Simuliidae) in southern Ghana from 1971 to 2011
inferredcites →https://doi.org/10.1186/s13071-015-1159-9openalex-snapshot
Required duration of mass ivermectin treatment for onchocerciasis elimination in Africa: a comparative modelling analysis
inferredcites →https://doi.org/10.1186/s13071-019-3290-5openalex-snapshot
Entomological assessment of the transmission following recrudescence of onchocerciasis in the Comoé Valley, Burkina Faso
inferredcites →https://doi.org/10.1186/s40249-016-0160-7openalex-snapshot
Progress towards onchocerciasis elimination in the participating countries of the African Programme for Onchocerciasis Control: epidemiological evaluation results
inferredcites →https://doi.org/10.1186/s40249-018-0446-zopenalex-snapshot
Is onchocerciasis elimination in Africa feasible by 2025: a perspective based on lessons learnt from the African control programmes
inferredcites →https://doi.org/10.1371/journal.pcbi.1003537openalex-snapshot
BEAST 2: A Software Platform for Bayesian Evolutionary Analysis
inferredcites →https://doi.org/10.1371/journal.pntd.0000497openalex-snapshot
Feasibility of Onchocerciasis Elimination with Ivermectin Treatment in Endemic Foci in Africa: First Evidence from Studies in Mali and Senegal
inferredcites →https://doi.org/10.1371/journal.pntd.0001825openalex-snapshot
Proof-of-Principle of Onchocerciasis Elimination with Ivermectin Treatment in Endemic Foci in Africa: Final Results of a Study in Mali and Senegal
inferredcites →https://doi.org/10.1371/journal.pntd.0003542openalex-snapshot
Managing the Fight against Onchocerciasis in Africa: APOC Experience
inferredcites →https://doi.org/10.1371/journal.pntd.0005816openalex-snapshot
Genome-wide analysis of ivermectin response by Onchocerca volvulus reveals that genetic drift and soft selective sweeps contribute to loss of drug sensitivity
inferredcites →https://doi.org/10.1590/0074-02760150350openalex-snapshot
The mitogenome of Onchocerca volvulus from the Brazilian Amazonia focus
inferredcites →https://doi.org/10.2307/3283821openalex-snapshot
Microevolution and the Genetic Structure of Parasite Populations
inferredcites →https://doi.org/10.3389/fgene.2019.01282openalex-snapshot
Genomic Epidemiology in Filarial Nematodes: Transforming the Basis for Elimination Program Decisions
inferredcites →https://doi.org/10.4161/fly.19695openalex-snapshot
A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff
inferredcites →https://doi.org/10.48550/arxiv.1207.3907openalex-snapshot
Haplotype-based variant detection from short-read sequencing
inferredcites →https://doi.org/10.5281/zenodo.18192410openalex-snapshot
The principles of disease elimination and eradication
inferredcites →https://doi.org/10.6084/m9.figshare.963153.v1openalex-snapshot
Aligning sequence reads, clone sequences and assembly con*gs with BWA-MEM

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1016/bs.apar.2021.01.002openalex-snapshot
Taking the strain out of onchocerciasis? A reanalysis of blindness and transmission data does not support the existence of a savannah blinding strain of onchocerciasis in West Africa
inferred← citeshttps://doi.org/10.1101/2023.02.14.23285937openalex-snapshot
Synthesising environmental, epidemiological, and genetic data to assist decision making for onchocerciasis elimination
inferred← citeshttps://doi.org/10.3389/fgene.2019.01282openalex-snapshot
Genomic Epidemiology in Filarial Nematodes: Transforming the Basis for Elimination Program Decisions
inferred← citeshttps://doi.org/10.51585/gjm.2023.2.0023openalex-snapshot
Emergence and genetic diversity of zoonotic Onchocerca species among human populations in Taraba State, Nigeria
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