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Article ; Online: coiaf

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

PLoS Computational Biology, Vol 19, Iss 6, p e

Directly estimating complexity of infection with allele frequencies.

2023 Volume 1010247

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.
Keywords	Biology (General) ; QH301-705.5
Subject code	310
Language	English
Publishing date	2023-06-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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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

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

Emerging Infectious Diseases, Vol 28, Iss 4, Pp 759-

2022 Volume 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.
Keywords	COVID-19 ; coronavirus disease ; severe acute respiratory syndrome coronavirus 2 ; SARS-CoV-2 ; infection attack rate ; infection fatality ratio ; Medicine ; R ; Infectious and parasitic diseases ; RC109-216
Language	English
Publishing date	2022-04-01T00:00:00Z
Publisher	Centers for Disease Control and Prevention
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Modelling population-level impact to inform target product profiles for childhood malaria vaccines

Alexandra B. Hogan / Peter Winskill / Robert Verity / Jamie T. Griffin / Azra C. Ghani

BMC Medicine, Vol 16, Iss 1, Pp 1-

2018 Volume 11

Abstract: Abstract Background The RTS,S/AS01 vaccine for Plasmodium falciparum malaria demonstrated moderate efficacy in 5–17-month-old children in phase 3 trials, and from 2018, the vaccine will be evaluated through a large-scale pilot implementation program. ... ...

Abstract	Abstract Background The RTS,S/AS01 vaccine for Plasmodium falciparum malaria demonstrated moderate efficacy in 5–17-month-old children in phase 3 trials, and from 2018, the vaccine will be evaluated through a large-scale pilot implementation program. Work is ongoing to optimise this vaccine, with higher efficacy for a different schedule demonstrated in a phase 2a challenge study. The objective of our study was to investigate the population-level impact of a modified RTS,S/AS01 schedule and dose amount in order to inform the target product profile for a second-generation malaria vaccine. Methods We used a mathematical modelling approach as the basis for our study. We simulated the changing anti-circumsporozoite antibody titre following vaccination and related the titre to vaccine efficacy. We then implemented this efficacy profile within an individual-based model of malaria transmission. We compared initial efficacy, duration and dose timing, and evaluated the potential public health impact of a modified vaccine in children aged 5–17 months, measuring clinical cases averted in children younger than 5 years. Results In the first decade of delivery, initial efficacy was associated with a higher reduction in childhood clinical cases compared to vaccine duration. This effect was more pronounced in high transmission settings and was due to the efficacy benefit occurring in younger ages where disease burden is highest. However, the low initial efficacy and long duration schedule averted more cases across all age cohorts if a longer time horizon was considered. We observed an age-shifting effect due to the changing immunological profile in higher transmission settings, in scenarios where initial efficacy was higher, and the fourth dose administered earlier. Conclusions Our findings indicate that, for an imperfect childhood malaria vaccine with suboptimal efficacy, it may be advantageous to prioritise initial efficacy over duration. We predict that a modified vaccine could outperform the current RTS,S/AS01, although ...
Keywords	RTS,S/AS01 ; Target product profile ; Plasmodium falciparum ; Malaria ; Efficacy ; Second-generation malaria vaccine ; Medicine ; R
Language	English
Publishing date	2018-07-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Epidemiological drivers of transmissibility and severity of SARS-CoV-2 in England

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

Nature Communications, Vol 14, Iss 1, Pp 1-

2023 Volume 9

Abstract: Abstract As the SARS-CoV-2 pandemic progressed, distinct variants emerged and dominated in England. These variants, Wildtype, Alpha, Delta, and Omicron were characterized by variations in transmissibility and severity. We used a robust mathematical model ...

Abstract	Abstract As the SARS-CoV-2 pandemic progressed, distinct variants emerged and dominated in England. These variants, Wildtype, Alpha, Delta, and Omicron were characterized by variations in transmissibility and severity. We used a robust mathematical model and Bayesian inference framework to analyse epidemiological surveillance data from England. We quantified the impact of non-pharmaceutical interventions (NPIs), therapeutics, and vaccination on virus transmission and severity. Each successive variant had a higher intrinsic transmissibility. Omicron (BA.1) had the highest basic reproduction number at 8.4 (95% credible interval (CrI) 7.8-9.1). Varying levels of NPIs were crucial in controlling virus transmission until population immunity accumulated. Immune escape properties of Omicron decreased effective levels of immunity in the population by a third. Furthermore, in contrast to previous studies, we found Alpha had the highest basic infection fatality ratio (3.0%, 95% CrI 2.8-3.2), followed by Delta (2.1%, 95% CrI 1.9–2.4), Wildtype (1.2%, 95% CrI 1.1–1.2), and Omicron (0.7%, 95% CrI 0.6-0.8). Our findings highlight the importance of continued surveillance. Long-term strategies for monitoring and maintaining effective immunity against SARS-CoV-2 are critical to inform the role of NPIs to effectively manage future variants with potentially higher intrinsic transmissibility and severe outcomes.
Keywords	Science ; Q
Subject code	360
Language	English
Publishing date	2023-07-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Author Correction

Nature Communications, Vol 14, Iss 1, Pp 1-

Epidemiological drivers of transmissibility and severity of SARS-CoV-2 in England

2023 Volume 4

Keywords	Science ; Q
Language	English
Publishing date	2023-12-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Estimating the COVID-19 infection fatality ratio accounting for seroreversion using statistical modelling

Communications Medicine, Vol 2, Iss 1, Pp 1-

2022 Volume 13

Abstract: Brazeau et al. use a statistical modelling approach to estimate COVID-19 infection fatality ratios from seroprevalence data. The authors’ model accounts for seroreversion over the course of the pandemic, as well as other important uncertainties such as ... ...

Abstract	Brazeau et al. use a statistical modelling approach to estimate COVID-19 infection fatality ratios from seroprevalence data. The authors’ model accounts for seroreversion over the course of the pandemic, as well as other important uncertainties such as serologic test characteristics.
Keywords	Medicine ; R
Language	English
Publishing date	2022-05-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: The use of jackknifing for the evaluation of geographic profiling reliability

Papini, Alessio / D. Kim Rossmo / Mark D. Stevenson / Robert Verity / Stephen C. Le Comber / Ugo Santosuosso

Ecological informatics. 2017 Mar., v. 38

2017

Abstract: The use of geographic profiling (GP), based on “Rossmo's formula”, a technique derived from criminology, has been previously proven to be effective in assessing the origin of invading species. The application on Caulerpa taxifolia showed the most ... ...

Abstract	The use of geographic profiling (GP), based on “Rossmo's formula”, a technique derived from criminology, has been previously proven to be effective in assessing the origin of invading species. The application on Caulerpa taxifolia showed the most probable center of spread of the invasion. This article discusses a method of assessing the degree of robustness of the results obtained with Rossmo's method.To provide an evaluation of the reliability of geographic profiling results we used the jackknife technique, randomly eliminating part of the data set for a given number of replicates (500) in order to analyze the obtained result for each replicate. In GP the results are a series of images with geoprofiling prioritization, each produced with one of the replicates. These images can be summarized in three different ways: (1) OR, depicting all the high probability pixels from the series of replicates; (2) AND, depicting only those high probability pixels present in every replicate; and (3) MEAN, depicting the mean color value for each pixel calculated from all the replicates. We show that jackknifing can be a useful method to increase robustness of GP analysis in criminology, epidemiology and biological invasions. Summarizing jackknifing results with the OR logical operator yields the highest sensitivity and worst specificity, while the use of the AND operator increases specificity but reduces sensitivity. Using the mean of the pixel values maintains the visualization of the areas of highest priority (specificity), while also showing the surrounding area with varying colors, analogous to confidence limits.
Keywords	Caulerpa taxifolia ; color ; criminology ; data collection ; ecological invasion ; epidemiology ; prioritization ; probability
Language	English
Dates of publication	2017-03
Size	p. 76-81.
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	2212016-6
ISSN	1878-0512 ; 1574-9541
ISSN (online)	1878-0512
ISSN	1574-9541
DOI	10.1016/j.ecoinf.2017.02.001
Database	NAL-Catalogue (AGRICOLA)

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Article: Vaccine approaches to malaria control and elimination: Insights from mathematical models

White, Michael T / Azra C. Ghani / Robert Verity / Thomas S. Churcher

Vaccine. 2015 Dec. 22, v. 33, no. 52

2015

Abstract: A licensed malaria vaccine would provide a valuable new tool for malaria control and elimination efforts. Several candidate vaccines targeting different stages of the malaria parasite's lifecycle are currently under development, with one candidate, RTS,S/ ...

Abstract	A licensed malaria vaccine would provide a valuable new tool for malaria control and elimination efforts. Several candidate vaccines targeting different stages of the malaria parasite's lifecycle are currently under development, with one candidate, RTS,S/AS01 for the prevention of Plasmodium falciparum infection, having recently completed Phase III trials. Predicting the public health impact of a candidate malaria vaccine requires using clinical trial data to estimate the vaccine's efficacy profile—the initial efficacy following vaccination and the pattern of waning of efficacy over time. With an estimated vaccine efficacy profile, the effects of vaccination on malaria transmission can be simulated with the aid of mathematical models.Here, we provide an overview of methods for estimating the vaccine efficacy profiles of pre-erythrocytic vaccines and transmission-blocking vaccines from clinical trial data. In the case of RTS,S/AS01, model estimates from Phase II clinical trial data indicate a bi-phasic exponential profile of efficacy against infection, with efficacy waning rapidly in the first 6 months after vaccination followed by a slower rate of waning over the next 4 years. Transmission-blocking vaccines have yet to be tested in large-scale Phase II or Phase III clinical trials so we review ongoing work investigating how a clinical trial might be designed to ensure that vaccine efficacy can be estimated with sufficient statistical power. Finally, we demonstrate how parameters estimated from clinical trials can be used to predict the impact of vaccination campaigns on malaria using a mathematical model of malaria transmission.
Keywords	clinical trials ; malaria ; malaria vaccines ; mathematical models ; parasites ; Plasmodium falciparum ; prediction ; public health ; vaccination
Language	English
Dates of publication	2015-1222
Size	p. 7544-7550.
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	605674-x
ISSN	1873-2518 ; 0264-410X
ISSN (online)	1873-2518
ISSN	0264-410X
DOI	10.1016/j.vaccine.2015.09.099
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Impact of seasonal variations in Plasmodium falciparum malaria transmission on the surveillance of pfhrp2 gene deletions

Oliver John Watson / Robert Verity / Azra C Ghani / Tini Garske / Jane Cunningham / Antoinette Tshefu / Melchior K Mwandagalirwa / Steven R Meshnick / Jonathan B Parr / Hannah C Slater

eLife, Vol

2019 Volume 8

Abstract: Ten countries have reported pfhrp2/pfhrp3 gene deletions since the first observation of pfhrp2-deleted parasites in 2012. In a previous study (Watson et al., 2017), we characterised the drivers selecting for pfhrp2/3 deletions and mapped the regions in ... ...

Abstract	Ten countries have reported pfhrp2/pfhrp3 gene deletions since the first observation of pfhrp2-deleted parasites in 2012. In a previous study (Watson et al., 2017), we characterised the drivers selecting for pfhrp2/3 deletions and mapped the regions in Africa with the greatest selection pressure. In February 2018, the World Health Organization issued guidance on investigating suspected false-negative rapid diagnostic tests (RDTs) due to pfhrp2/3 deletions. However, no guidance is provided regarding the timing of investigations. Failure to consider seasonal variation could cause premature decisions to switch to alternative RDTs. In response, we have extended our methods and predict that the prevalence of false-negative RDTs due to pfhrp2/3 deletions is highest when sampling from younger individuals during the beginning of the rainy season. We conclude by producing a map of the regions impacted by seasonal fluctuations in pfhrp2/3 deletions and a database identifying optimum sampling intervals to support malaria control programmes.
Keywords	radid diagnostic tests ; pfhrp2-deletion ; mapping ; mathematical modelling ; Medicine ; R ; Science ; Q ; Biology (General) ; QH301-705.5
Language	English
Publishing date	2019-05-01T00:00:00Z
Publisher	eLife Sciences Publications Ltd
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Spatial and epidemiological drivers of Plasmodium falciparum malaria among adults in the Democratic Republic of the Congo

Jonathan J Juliano / Jonathan B Parr / Steven R Meshnick / Molly Deutsch-Feldman / Nicholas F Brazeau / Kyaw L Thwai / Jeremie Muwonga / Melchior Kashamuka / Antoinette Tshefu Kitoto / Ozkan Aydemir / Jeffrey A Bailey / Jessie K Edwards / Robert Verity / Michael Emch / Emily W Gower

BMJ Global Health, Vol 5, Iss

2020 Volume 6

Abstract: Background Adults are frequently infected with malaria and may serve as a reservoir for further transmission, yet we know relatively little about risk factors for adult infections. In this study, we assessed malaria risk factors among adults using ... ...

Abstract	Background Adults are frequently infected with malaria and may serve as a reservoir for further transmission, yet we know relatively little about risk factors for adult infections. In this study, we assessed malaria risk factors among adults using samples from the nationally representative, cross-sectional 2013–2014 Demographic and Health Survey (DHS) conducted in the Democratic Republic of the Congo (DRC). We further explored differences in risk factors by urbanicity.Methods Plasmodium falciparum infection was determined by PCR. Covariates were drawn from the DHS to model individual, community and environmental-level risk factors for infection. Additionally, we used deep sequencing data to estimate the community-level proportions of drug-resistant infections and included these estimates as potential risk factors. All identified factors were assessed for differences in associations by urbanicity.Results A total of 16 126 adults were included. Overall prevalence of malaria was 30.3% (SE=1.1) by PCR; province-level prevalence ranged from 6.7% to 58.3%. Only 17% of individuals lived in households with at least one bed-net for every two people, as recommended by the WHO. Protective factors included increasing within-household bed-net coverage (Prevalence Ratio=0.85, 95% CI=0.76–0.95) and modern housing (PR=0.58, 95% CI=0.49–0.69). Community-level protective factors included increased median wealth (PR=0.87, 95% CI=0.83–0.92). Education, wealth, and modern housing showed protective associations in cities but not in rural areas.Conclusions The DRC continues to suffer from a high burden of malaria; interventions that target high-risk groups and sustained investment in malaria control are sorely needed. Areas of high prevalence should be prioritised for interventions to target the largest reservoirs for further transmission.
Keywords	Medicine (General) ; R5-920 ; Infectious and parasitic diseases ; RC109-216
Subject code	610
Language	English
Publishing date	2020-06-01T00:00:00Z
Publisher	BMJ Publishing Group
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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