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Article ; Online: Sampling for malaria molecular surveillance.

Mayor, Alfredo / Ishengoma, Deus S / Proctor, Joshua L / Verity, Robert

2023 Volume 39, Issue 11, Page(s) 954–968

Abstract: Strategic use of Plasmodium falciparum genetic variation has great potential to inform public health actions for malaria control and elimination. Malaria molecular surveillance (MMS) begins with a strategy to identify and collect parasite samples, guided ...

Abstract	Strategic use of Plasmodium falciparum genetic variation has great potential to inform public health actions for malaria control and elimination. Malaria molecular surveillance (MMS) begins with a strategy to identify and collect parasite samples, guided by public-health priorities. In this review we discuss sampling design practices for MMS and point out epidemiological, biological, and statistical factors that need to be considered. We present examples for different use cases, including detecting emergence and spread of rare variants, establishing transmission sources and inferring changes in malaria transmission intensity. This review will potentially guide the collection of samples and data, serve as a starting point for further methodological innovation, and enhance utilization of MMS to support malaria elimination.
MeSH term(s)	Humans ; Antimalarials/pharmacology ; Drug Resistance ; Malaria ; Plasmodium falciparum/genetics ; Malaria, Falciparum/epidemiology ; Malaria, Falciparum/prevention & control ; Malaria, Falciparum/drug therapy
Chemical Substances	Antimalarials
Language	English
Publishing date	2023-09-19
Publishing country	England
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	2036227-4
ISSN	1471-5007 ; 1471-4922
ISSN (online)	1471-5007
ISSN	1471-4922
DOI	10.1016/j.pt.2023.08.007
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Article ; Online: coiaf: Directly estimating complexity of infection with allele frequencies.

Paschalidis, Aris / Watson, Oliver J / Aydemir, Ozkan / Verity, Robert / Bailey, Jeffrey A

PLoS computational biology

2023 Volume 19, Issue 6, Page(s) e1010247

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 ... ...

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.
MeSH term(s)	Humans ; Malaria, Falciparum/epidemiology ; Malaria, Falciparum/genetics ; Malaria, Falciparum/parasitology ; Bayes Theorem ; Plasmodium falciparum/genetics ; Gene Frequency/genetics ; Malaria/parasitology
Language	English
Publishing date	2023-06-09
Publishing country	United States
Document type	Journal Article
ZDB-ID	2193340-6
ISSN	1553-7358 ; 1553-734X
ISSN (online)	1553-7358
ISSN	1553-734X
DOI	10.1371/journal.pcbi.1010247
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Article ; Online: Estimating the Number of Subpopulations (K) in Structured Populations.

Verity, Robert / Nichols, Richard A

Genetics

2016 Volume 203, Issue 4, Page(s) 1827–1839

Abstract: A key quantity in the analysis of structured populations is the parameter K, which describes the number of subpopulations that make up the total population. Inference of K ideally proceeds via the model evidence, which is equivalent to the likelihood of ... ...

Abstract	A key quantity in the analysis of structured populations is the parameter K, which describes the number of subpopulations that make up the total population. Inference of K ideally proceeds via the model evidence, which is equivalent to the likelihood of the model. However, the evidence in favor of a particular value of K cannot usually be computed exactly, and instead programs such as Structure make use of heuristic estimators to approximate this quantity. We show-using simulated data sets small enough that the true evidence can be computed exactly-that these heuristics often fail to estimate the true evidence and that this can lead to incorrect conclusions about K Our proposed solution is to use thermodynamic integration (TI) to estimate the model evidence. After outlining the TI methodology we demonstrate the effectiveness of this approach, using a range of simulated data sets. We find that TI can be used to obtain estimates of the model evidence that are more accurate and precise than those based on heuristics. Furthermore, estimates of K based on these values are found to be more reliable than those based on a suite of model comparison statistics. Finally, we test our solution in a reanalysis of a white-footed mouse data set. The TI methodology is implemented for models both with and without admixture in the software MavericK1.0.
MeSH term(s)	Animals ; Computer Simulation ; Genetics, Population ; Mice ; Models, Statistical ; Pigments, Biological/genetics ; Probability ; Software
Chemical Substances	Pigments, Biological
Language	English
Publishing date	2016-08
Publishing country	United States
Document type	Journal Article
ZDB-ID	2167-2
ISSN	1943-2631 ; 0016-6731
ISSN (online)	1943-2631
ISSN	0016-6731
DOI	10.1534/genetics.115.180992
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Article ; Online: Reassessing Reported Deaths and Estimated Infection Attack Rate during the First 6 Months of the COVID-19 Epidemic, Delhi, India.

Pons-Salort, Margarita / John, Jacob / Watson, Oliver J / Brazeau, Nicholas F / Verity, Robert / Kang, Gagandeep / Grassly, Nicholas C

Emerging infectious diseases

2022 Volume 28, Issue 4, Page(s) 759–766

Abstract: India reported >10 million coronavirus disease (COVID-19) cases and 149,000 deaths in 2020. To reassess reported deaths and estimate incidence rates during the first 6 months of the epidemic, we used a severe acute respiratory syndrome coronavirus 2 ... ...

Abstract	India reported >10 million coronavirus disease (COVID-19) cases and 149,000 deaths in 2020. To reassess reported deaths and estimate incidence rates during the first 6 months of the epidemic, we used a severe acute respiratory syndrome coronavirus 2 transmission model fit to data from 3 serosurveys in Delhi and time-series documentation of reported deaths. We estimated 48.7% (95% credible interval 22.1%-76.8%) cumulative infection in the population through the end of September 2020. Using an age-adjusted overall infection fatality ratio based on age-specific estimates from mostly high-income countries, we estimated that just 15.0% (95% credible interval 9.3%-34.0%) of COVID-19 deaths had been reported, indicating either substantial underreporting or lower age-specific infection-fatality ratios in India than in high-income countries. Despite the estimated high attack rate, additional epidemic waves occurred in late 2020 and April-May 2021. Future dynamics will depend on the duration of natural and vaccine-induced immunity and their effectiveness against new variants.
MeSH term(s)	COVID-19 ; Epidemics ; Humans ; Incidence ; India/epidemiology ; SARS-CoV-2
Language	English
Publishing date	2022-02-25
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1380686-5
ISSN	1080-6059 ; 1080-6040
ISSN (online)	1080-6059
ISSN	1080-6040
DOI	10.3201/eid2804.210879
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Article ; Online: What is genetic differentiation, and how should we measure it--GST, D, neither or both?

Verity, Robert / Nichols, Richard A

Molecular ecology

2014 Volume 23, Issue 17, Page(s) 4216–4225

Abstract: Estimates of the fixation index, F(ST), have been used as measures of population differentiation for many decades. However, there have been persistent voices in the literature suggesting that these statistics do not measure true differentiation. In ... ...

Abstract	Estimates of the fixation index, F(ST), have been used as measures of population differentiation for many decades. However, there have been persistent voices in the literature suggesting that these statistics do not measure true differentiation. In particular, the statistics Nei's G(ST) and Wier and Cockerham's θ have been criticized for being 'constrained' to not equal one in some situations that seem to represent maximal differentiation. Here, we address the issue of how to evaluate exactly how much information a particular statistic contains about the process of differentiation. This criterion can be used to counter most concerns about the performance of G(ST) (and related statistics), while also being reconciled with the insights of those who have proposed alternative measures of differentiation. In particular, the likelihood-based framework that we put forward can justify the use of G(ST) as an effective measure of differentiation, but also shows that in some situations G(ST) is insufficient on its own and needs supplementing by another measure such as Jost's D or Hedrick's G'(ST). This approach will become increasingly important in the future, as greater emphasis is placed on analysing large data sets.
MeSH term(s)	Gene Frequency ; Genetic Drift ; Genetics, Population/methods ; Heterozygote ; Likelihood Functions ; Models, Genetic ; Models, Statistical ; Mutation
Language	English
Publishing date	2014-09
Publishing country	England
Document type	Journal Article
ZDB-ID	1126687-9
ISSN	1365-294X ; 0962-1083
ISSN (online)	1365-294X
ISSN	0962-1083
DOI	10.1111/mec.12856
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Article: Substitution therapy service provision into older age.

Verity, Robert

Addiction (Abingdon, England)

2004 Volume 99, Issue 5, Page(s) 649–650

MeSH term(s)	Adult ; Delivery of Health Care/standards ; Drug and Narcotic Control/economics ; England ; Female ; Heroin Dependence/rehabilitation ; Humans ; Male ; Middle Aged
Language	English
Publishing date	2004-05
Publishing country	England
Document type	Letter
ZDB-ID	1141051-6
ISSN	1360-0443 ; 0965-2140
ISSN (online)	1360-0443
ISSN	0965-2140
DOI	10.1111/j.1360-0443.2004.00732.x
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Article: What is genetic differentiation, and how should we measure it—GST, D, neither or both?

Verity, Robert / Nichols, Richard A

Molecular ecology. 2014 Sept., v. 23, no. 17

2014

Abstract: Estimates of the fixation index, FST, have been used as measures of population differentiation for many decades. However, there have been persistent voices in the literature suggesting that these statistics do not measure true differentiation. In ... ...

Abstract	Estimates of the fixation index, FST, have been used as measures of population differentiation for many decades. However, there have been persistent voices in the literature suggesting that these statistics do not measure true differentiation. In particular, the statistics Nei's GST and Wier and Cockerham's θ have been criticized for being ‘constrained’ to not equal one in some situations that seem to represent maximal differentiation. Here, we address the issue of how to evaluate exactly how much information a particular statistic contains about the process of differentiation. This criterion can be used to counter most concerns about the performance of GST (and related statistics), while also being reconciled with the insights of those who have proposed alternative measures of differentiation. In particular, the likelihood‐based framework that we put forward can justify the use of GST as an effective measure of differentiation, but also shows that in some situations GST is insufficient on its own and needs supplementing by another measure such as Jost's D or Hedrick's G′ST. This approach will become increasingly important in the future, as greater emphasis is placed on analysing large data sets.
Keywords	data collection ; genetic variation ; statistics
Language	English
Dates of publication	2014-09
Size	p. 4216-4225.
Publishing place	Blackwell Science
Document type	Article
ZDB-ID	1126687-9
ISSN	1365-294X ; 0962-1083
ISSN (online)	1365-294X
ISSN	0962-1083
DOI	10.1111/mec.12856
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Article ; Online: Flexible and cost-effective genomic surveillance of P. falciparum malaria with targeted nanopore sequencing.

de Cesare, Mariateresa / Mwenda, Mulenga / Jeffreys, Anna E / Chirwa, Jacob / Drakeley, Chris / Schneider, Kammerle / Mambwe, Brenda / Glanz, Karolina / Ntalla, Christina / Carrasquilla, Manuela / Portugal, Silvia / Verity, Robert J / Bailey, Jeffrey A / Ghinai, Isaac / Busby, George B / Hamainza, Busiku / Hawela, Moonga / Bridges, Daniel J / Hendry, Jason A

Nature communications

2024 Volume 15, Issue 1, Page(s) 1413

Abstract: Genomic surveillance of Plasmodium falciparum malaria can provide policy-relevant information about antimalarial drug resistance, diagnostic test failure, and the evolution of vaccine targets. Yet the large and low complexity genome of P. falciparum ... ...

Abstract	Genomic surveillance of Plasmodium falciparum malaria can provide policy-relevant information about antimalarial drug resistance, diagnostic test failure, and the evolution of vaccine targets. Yet the large and low complexity genome of P. falciparum complicates the development of genomic methods, while resource constraints in malaria endemic regions can limit their deployment. Here, we demonstrate an approach for targeted nanopore sequencing of P. falciparum from dried blood spots (DBS) that enables cost-effective genomic surveillance of malaria in low-resource settings. We release software that facilitates flexible design of amplicon sequencing panels and use this software to design two target panels for P. falciparum. The panels generate 3-4 kbp reads for eight and sixteen targets respectively, covering key drug-resistance associated genes, diagnostic test antigens, polymorphic markers and the vaccine target csp. We validate our approach on mock and field samples, demonstrating robust sequencing coverage, accurate variant calls within coding sequences, the ability to explore P. falciparum within-sample diversity and to detect deletions underlying rapid diagnostic test failure.
MeSH term(s)	Humans ; Plasmodium falciparum/genetics ; Nanopore Sequencing ; Cost-Benefit Analysis ; Malaria, Falciparum/diagnosis ; Malaria/epidemiology ; Genomics ; Vaccines
Chemical Substances	Vaccines
Language	English
Publishing date	2024-02-15
Publishing country	England
Document type	Journal Article
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-024-45688-z
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Article: Strong isolation by distance and evidence of population microstructure reflect ongoing

Connelly, Sean V / Brazeau, Nicholas F / Msellem, Mwinyi / Ngasala, Billy E / Aydemir, Özkan / Goel, Varun / Niaré, Karamoko / Giesbrecht, David J / Popkin-Hall, Zachary R / Hennelly, Christopher M / Park, Zackary / Moormann, Ann M / Ong'echa, John Michael / Verity, Robert / Mohammed, Safia / Shija, Shija J / Mhamilawa, Lwidiko E / Morris, Ulrika / Mårtensson, Andreas /

Lin, Jessica T / Björkman, Anders / Juliano, Jonathan J / Bailey, Jeffrey A

medRxiv : the preprint server for health sciences

2024

Abstract: The Zanzibar archipelago of Tanzania has become a low-transmission area ... ...

Abstract	The Zanzibar archipelago of Tanzania has become a low-transmission area for
Language	English
Publishing date	2024-02-13
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.02.15.23285960
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Article ; Online: Author Correction: Epidemiological drivers of transmissibility and severity of SARS-CoV-2 in England.

Perez-Guzman, Pablo N / Knock, Edward / Imai, Natsuko / Rawson, Thomas / Elmaci, Yasin / Alcada, Joana / Whittles, Lilith K / Thekke Kanapram, Divya / Sonabend, Raphael / Gaythorpe, Katy A M / Hinsley, Wes / FitzJohn, Richard G / Volz, Erik / Verity, Robert / Ferguson, Neil M / Cori, Anne / Baguelin, Marc

Nature communications

2023 Volume 14, Issue 1, Page(s) 8099

Language	English
Publishing date	2023-12-07
Publishing country	England
Document type	Published Erratum
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-023-44062-9
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