Publications
11 results found
Drake K, Boyd O, Franceschi V, et al., 2024, Phylogenomic early warning signals for SARS-CoV-2 epidemic waves, EBioMedicine, Vol: 100, ISSN: 2352-3964
Background:Epidemic waves of coronavirus disease 2019 (COVID-19) infections have often been associated with the emergence of novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants. Rapid detection of growing genomic variants can therefore serve as a predictor of future waves, enabling timely implementation of countermeasures such as non-pharmaceutical interventions (social distancing), additional vaccination (booster campaigns), or healthcare capacity adjustments. The large amount of SARS-CoV-2 genomic sequence data produced during the pandemic has provided a unique opportunity to explore the utility of these data for generating early warning signals (EWS).Methods:We developed an analytical pipeline (Transmission Fitness Polymorphism Scanner – designated in an R package mrc-ide/tfpscanner) for systematically exploring all clades within a SARS-CoV-2 virus phylogeny to detect variants showing unusually high growth rates. We investigated the use of these cluster growth rates as the basis for a variety of statistical time series to use as leading indicators for the epidemic waves in the UK during the pandemic between August 2020 and March 2022. We also compared the performance of these phylogeny-derived leading indicators with a range of non-phylogeny-derived leading indicators. Our experiments simulated data generation and real-time analysis.Findings:Using phylogenomic analysis, we identified leading indicators that would have generated EWS ahead of significant increases in COVID-19 hospitalisations in the UK between August 2020 and March 2022. Our results also show that EWS lead time is sensitive to the threshold set for the number of false positive (FP) EWS. It is often possible to generate longer EWS lead times if more FP EWS are tolerated. On the basis of maximising lead time and minimising the number of FP EWS, the best performing leading indicators that we identified, amongst a set of 1.4 million, were the maximum logistic growth rate (
FitzGerald V, Pickup DM, Drake KO, et al., 2007, A high energy X-ray diffraction study of sol-gel derived (Ta<sub>2</sub>O<sub>5</sub>)<sub><i>x</i></sub>(SiO<sub>2</sub>)<sub>1-<i>x</i></sub> glasses (<i>x</i>=0.05, 0.11 and 0.25) -: elucidating the role of tantalum in silica, JOURNAL OF SOL-GEL SCIENCE AND TECHNOLOGY, Vol: 44, Pages: 153-159, ISSN: 0928-0707
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- Citations: 1
FitzGerald V, Drake KO, Jones JR, et al., 2007, <i>In situ</i> high-energy X-ray diffraction study of a bioactive calcium silicate foam immersed in simulated body fluid, JOURNAL OF SYNCHROTRON RADIATION, Vol: 14, Pages: 492-499, ISSN: 1600-5775
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- Citations: 10
Pickup DM, Sowrey FE, Skipper LJ, et al., 2005, The structure of TiO<sub>2</sub>-SiO<sub>2</sub> and CaO-SiO<sub>2</sub> sol-gel glasses from neutron diffraction and solid state NMR using isotopic enrichment of titanium, calcium and oxygen, 9th International Conference on the Structure of Non-Crystalline Materials (NCM9), Publisher: SOC GLASS TECHNOLOGY, Pages: 433-438, ISSN: 0031-9090
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- Citations: 3
Drake KO, Carta D, Skipper L, et al., 2005, A multinuclear solid state NMR study of the sol-gel formation of amorphous Nb<sub>2</sub>O<sub>5</sub>-SiO<sub>2</sub> materials, SOLID STATE NUCLEAR MAGNETIC RESONANCE, Vol: 27, Pages: 28-36, ISSN: 0926-2040
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- Citations: 28
Skipper LJ, Sowrey FE, Pickup DM, et al., 2005, The structure of a bioactive calcia-silica sol-gel glass, JOURNAL OF MATERIALS CHEMISTRY, Vol: 15, Pages: 2369-2374, ISSN: 0959-9428
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- Citations: 56
Skipper LJ, Sowrey FE, Pickup DM, et al., 2005, The atomic-scale interaction of bioactive glasses with simulated body fluid, Zurich-Uetikon, 1st international meeting on applied physics, Badajoz, Spain, 13 - 18 October 2003, Publisher: Trans Tech Publications Ltd, Pages: 21-25
Pickup DM, Sowrey FE, Newport RJ, et al., 2004, The structure of TiO<sub>2</sub>-SiO<sub>2</sub> sol-gel glasses from neutron diffraction with isotopic substitution of titanium and <SUP>17</SUP>O and <SUP>49</SUP>Ti solid-state NMR with isotopic enrichment, JOURNAL OF PHYSICAL CHEMISTRY B, Vol: 108, Pages: 10872-10880, ISSN: 1520-6106
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- Citations: 21
Pickup DM, Sowrey FE, Drake KO, et al., 2004, New insights into medium-range order around titanium sol-gel derived silica through isotope in difference neutron diffraction and reverse Monte Carlo modelling, CHEMICAL PHYSICS LETTERS, Vol: 392, Pages: 503-507, ISSN: 0009-2614
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- Citations: 6
Skipper LJ, Sowrey FE, Pickup DM, et al., 2004, Structural studies of bioactivity in sol-gel-derived glasses by X-ray spectroscopy, Journal of Biomedical Materials Research Part A, Vol: 70, Pages: 354-360, ISSN: 0021-9304
Sowrey FE, Skipper LJ, Pickup DM, et al., 2004, Systematic empirical analysis of calcium-oxygen coordination environment by calcium K-edge XANES, PHYSICAL CHEMISTRY CHEMICAL PHYSICS, Vol: 6, Pages: 188-192, ISSN: 1463-9076
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- Citations: 89
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