Imperial College London

DrRobJohnson

Faculty of MedicineSchool of Public Health

Research Associate
 
 
 
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Contact

 

robert.johnson11

 
 
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Location

 

VB11Norfolk PlaceSt Mary's Campus

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Summary

 

Publications

Publication Type
Year
to

6 results found

Haw D, Forchini G, Doohan P, Christen P, Pianella M, Johnson R, Bajaj S, Hogan A, Winskill P, Miraldo M, White P, Ghani A, Ferguson N, Smith P, Hauck Ket al., 2022, Optimizing social and economic activity while containing SARS-CoV-2 transmission using DAEDALUS, Nature Computational Science, ISSN: 2662-8457

Journal article

Jackson C, Johnson R, de Nazelle A, Goel R, de Sá TH, Tainio M, Woodcock Jet al., 2021, A guide to value of information methods for prioritising research in health impact modelling, Epidemiologic Methods, Vol: 10, Pages: 1-22, ISSN: 2194-9263

Health impact simulation models are used to predict how a proposed policy or scenario will affect population health outcomes. These models represent the typically-complex systems that describe how the scenarios affect exposures to risk factors for disease or injury (e.g. air pollution or physical inactivity), and how these risk factors are related to measures of population health (e.g. expected survival). These models are informed by multiple sources of data, and are subject to multiple sources of uncertainty. We want to describe which sources of uncertainty contribute most to uncertainty about the estimate or decision arising from the model. Furthermore, we want to decide where further research should be focused to obtain further data to reduce this uncertainty, and what form that research might take. This article presents a tutorial in the use of Value of Information methods for uncertainty analysis and research prioritisation in health impact simulation models. These methods are based on Bayesian decision-theoretic principles, and quantify the expected benefits from further information of different kinds. The expected value of partial perfect information about a parameter measures sensitivity of a decision or estimate to uncertainty about that parameter. The expected value of sample information represents the expected benefit from a specific proposed study to get better information about the parameter. The methods are applicable both to situations where the model is used to make a decision between alternative policies, and situations where the model is simply used to estimate a quantity (such as expected gains in survival under a scenario). This paper explains how to calculate and interpret the expected value of information in the context of a simple model describing the health impacts of air pollution from motorised transport. We provide a general-purpose R package and full code to reproduce the example analyses.

Journal article

Volz E, Mishra S, Chand M, Barrett JC, Johnson R, Geidelberg L, Hinsley WR, Laydon DJ, Dabrera G, O'Toole Á, Amato R, Ragonnet-Cronin M, Harrison I, Jackson B, Ariani CV, Boyd O, Loman NJ, McCrone JT, Gonçalves S, Jorgensen D, Myers R, Hill V, Jackson DK, Gaythorpe K, Groves N, Sillitoe J, Kwiatkowski DP, COVID-19 Genomics UK COG-UK consortium, Flaxman S, Ratmann O, Bhatt S, Hopkins S, Gandy A, Rambaut A, Ferguson NM, Volz E, Mishra S, Chand M, Barrett JC, Johnson R, Geidelberg L, Hinsley WR, Laydon DJ, Dabrera G, OToole Á, Amato R, Ragonnet-Cronin M, Harrison I, Jackson B, Ariani CV, Boyd O, Loman N, McCrone JT, Gonc calves S, Jorgensen D, Myers R, Hill V, Jackson DK, Gaythorpe K, Groves N, Sillitoe J, Kwiatkowski DP, Flaxman S, Ratman O, Bhatt S, Hopkins S, Gandy A, Rambaut A, Ferguson NMet al., 2021, Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England, Nature, Vol: 593, Pages: 266-269, ISSN: 0028-0836

The SARS-CoV-2 lineage B.1.1.7, designated a Variant of Concern 202012/01 (VOC) by Public Health England1, originated in the UK in late Summer to early Autumn 20202. Whole genome SARS-CoV-2 sequence data collected from community-based diagnostic testing shows an unprecedentedly rapid expansion of the B.1.1.7 lineage during Autumn 2020, suggesting a selective advantage. We find that changes in VOC frequency inferred from genetic data correspond closely to changes inferred by S-gene target failures (SGTF) in community-based diagnostic PCR testing. Analysis of trends in SGTF and non-SGTF case numbers in local areas across England shows that the VOC has higher transmissibility than non-VOC lineages, even if the VOC has a different latent period or generation time. The SGTF data indicate a transient shift in the age composition of reported cases, with a larger share of under 20 year olds among reported VOC than non-VOC cases. Time-varying reproduction numbers for the VOC and cocirculating lineages were estimated using SGTF and genomic data. The best supported models did not indicate a substantial difference in VOC transmissibility among different age groups. There is a consensus among all analyses that the VOC has a substantial transmission advantage with a 50% to 100% higher reproduction number.

Journal article

Ragonnet-Cronin M, Boyd O, Geidelberg L, Jorgensen D, Nascimento F, Siveroni I, Johnson R, Baguelin M, Cucunuba Z, Jauneikaite E, Mishra S, Watson O, Ferguson N, Cori A, Donnelly C, Volz Eet al., 2021, Genetic evidence for the association between COVID-19 epidemic severity and timing of non-pharmaceutical interventions, Nature Communications, Vol: 12, Pages: 1-7, ISSN: 2041-1723

Unprecedented public health interventions including travel restrictions and national lockdowns have been implemented to stem the COVID-19 epidemic, but the effectiveness of non- pharmaceutical interventions is still debated. We carried out a phylogenetic analysis of more than 29,000 publicly available whole genome SARS-CoV-2 sequences from 57 locations to estimate the time that the epidemic originated in different places. These estimates were examined in relation to the dates of the most stringent interventions in each location as well as to the number of cumulative COVID-19 deaths and phylodynamic estimates of epidemic size. Here we report that the time elapsed between epidemic origin and maximum intervention is associated with different measures of epidemic severity and explains 11% of the variance in reported deaths one month after the most stringent intervention. Locations where strong non-pharmaceutical interventions were implemented earlier experienced 30 much less severe COVID-19 morbidity and mortality during the period of study.

Journal article

Geidelberg L, Boyd O, Jorgensen D, Siveroni I, Nascimento FF, Johnson R, Ragonnet-Cronin M, Fu H, Wang H, Xi X, Chen W, Liu D, Chen Y, Tian M, Tan W, Zai J, Sun W, Li J, Li J, Volz E, Li X, Nie Qet al., 2021, Genomic epidemiology of a densely sampled COVID-19 outbreak in China, Virus Evolution, Vol: 7, Pages: 1-7, ISSN: 2057-1577

Analysis of genetic sequence data from the SARS-CoV-2 pandemic can provide insights into epidemic origins, worldwide dispersal, and epidemiological history. With few exceptions, genomic epidemiological analysis has focused on geographically distributed data sets with few isolates in any given location. Here we report an analysis of 20 whole SARS- CoV-2 genomes from a single relatively small and geographically constrained outbreak in Weifang, People’s Republic of China. Using Bayesian model-based phylodynamic methods, we estimate a mean basic reproduction number (R0) of 3.4 (95% highest posterior density interval: 2.1-5.2) in Weifang, and a mean effective reproduction number (Rt ) that falls below 1 on February 4th. We further estimate the number of infections through time and compare these estimates to confirmed diagnoses by the Weifang Centers for Disease Control. We find that these estimates are consistent with reported cases and there is unlikely to be a large undiagnosed burden of infection over the period we studied.

Journal article

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