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Article ; Online: Lineage frequency time series reveal elevated levels of genetic drift in SARS-CoV-2 transmission in England.

Yu, QinQin / Ascensao, Joao A / Okada, Takashi / Boyd, Olivia / Volz, Erik / Hallatschek, Oskar

2024 Volume 20, Issue 4, Page(s) e1012090

Abstract: Genetic drift in infectious disease transmission results from randomness of transmission and host recovery or death. The strength of genetic drift for SARS-CoV-2 transmission is expected to be high due to high levels of superspreading, and this is ... ...

Abstract	Genetic drift in infectious disease transmission results from randomness of transmission and host recovery or death. The strength of genetic drift for SARS-CoV-2 transmission is expected to be high due to high levels of superspreading, and this is expected to substantially impact disease epidemiology and evolution. However, we don't yet have an understanding of how genetic drift changes over time or across locations. Furthermore, noise that results from data collection can potentially confound estimates of genetic drift. To address this challenge, we develop and validate a method to jointly infer genetic drift and measurement noise from time-series lineage frequency data. Our method is highly scalable to increasingly large genomic datasets, which overcomes a limitation in commonly used phylogenetic methods. We apply this method to over 490,000 SARS-CoV-2 genomic sequences from England collected between March 2020 and December 2021 by the COVID-19 Genomics UK (COG-UK) consortium and separately infer the strength of genetic drift for pre-B.1.177, B.1.177, Alpha, and Delta. We find that even after correcting for measurement noise, the strength of genetic drift is consistently, throughout time, higher than that expected from the observed number of COVID-19 positive individuals in England by 1 to 3 orders of magnitude, which cannot be explained by literature values of superspreading. Our estimates of genetic drift suggest low and time-varying establishment probabilities for new mutations, inform the parametrization of SARS-CoV-2 evolutionary models, and motivate future studies of the potential mechanisms for increased stochasticity in this system.
MeSH term(s)	COVID-19/transmission ; COVID-19/epidemiology ; COVID-19/virology ; COVID-19/genetics ; Humans ; SARS-CoV-2/genetics ; Genetic Drift ; England/epidemiology ; Phylogeny ; Genome, Viral
Language	English
Publishing date	2024-04-15
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2205412-1
ISSN	1553-7374 ; 1553-7374
ISSN (online)	1553-7374
ISSN	1553-7374
DOI	10.1371/journal.ppat.1012090
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Phylogenomic early warning signals for SARS-CoV-2 epidemic waves.

Drake, Kieran O / Boyd, Olivia / Franceschi, Vinicius B / Colquhoun, Rachel M / Ellaby, Nicholas A F / Volz, Erik M

EBioMedicine

2024 Volume 100, Page(s) 104939

Abstract: 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 ... ...

Abstract	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 (LGR) amongst clusters of the dominant Pango lineage and the mean simple LGR across a broader set of clusters. In the case of the former, the time between the EWS and wave inflection points (a conservative measure of wave start dates) for the seven waves ranged between a 20-day lead time and a 7-day lag, with a mean lead time of 5.4 days. The maximum number of FP EWS generated prior to a true positive (TP) EWS was two and this only occurred for two of the seven waves in the period. The mean simple LGR amongst a broader set of clusters also performed well in terms of lead time but with slightly more FP EWS. Interpretation: As a result of the significant surveillance effort during the pandemic, early detection of SARS-CoV-2 variants of concern Alpha, Delta, and Omicron provided some of the first examples where timely detection and characterisation of pathogen variants has been used to tailor public health response. The success of our method in generating early warning signals based on phylogenomic analysis for SARS-CoV-2 in the UK may make it a worthwhile addition to existing surveillance strategies. In addition, the method may be translatable to other countries and/or regions, and to other pathogens with large-scale and rapid genomic surveillance. Funding: This research was funded in whole, or in part, by the Wellcome Trust (220885_Z_20_Z). For the purpose of open access, the author has applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission. KOD, OB, VBF and EMV acknowledge funding from the MRC Centre for Global Infectious Disease Analysis (reference MR/X020258/1), jointly funded by the UK Medical Research Council (MRC) and the UK Foreign, Commonwealth & Development Office (FCDO), under the MRC/FCDO Concordat agreement and is also part of the EDCTP2 programme supported by the European Union. RMC acknowledges funding from the Wellcome Trust Collaborators Award (206298/Z/17/Z).
MeSH term(s)	Humans ; SARS-CoV-2/genetics ; COVID-19/diagnosis ; COVID-19/epidemiology ; COVID-19/prevention & control ; Phylogeny ; Pandemics/prevention & control
Language	English
Publishing date	2024-01-08
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2851331-9
ISSN	2352-3964
ISSN (online)	2352-3964
DOI	10.1016/j.ebiom.2023.104939
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Article: Taxonomic review of New World Tachyina (Coleoptera, Carabidae): descriptions of new genera, subgenera, and species, with an updated key to the subtribe in the Americas.

Boyd, Olivia F / Erwin, Terry L

ZooKeys

2016 , Issue 626, Page(s) 87–123

Abstract: The classification of the carabid subtribe Tachyina (Trechitae: Bembidiini) is reviewed in light of newly discovered diversity from Central and South America. Described herein are three new genera ( ...

Abstract	The classification of the carabid subtribe Tachyina (Trechitae: Bembidiini) is reviewed in light of newly discovered diversity from Central and South America. Described herein are three new genera (
Language	English
Publishing date	2016-10-20
Publishing country	Bulgaria
Document type	Review ; Journal Article
ZDB-ID	2445640-8
ISSN	1313-2970 ; 1313-2989
ISSN (online)	1313-2970
ISSN	1313-2989
DOI	10.3897/zookeys.626.10033
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Article: Geographically structured genetic diversity in the cave beetle Darlingtoneakentuckensis Valentine, 1952 (Coleoptera, Carabidae, Trechini, Trechini)

Boyd, Olivia F / Philips, T. Keith / Johnson, Jarrett R / Nixon, Jedidiah J

Subterranean biology. 2020 Mar. 10, v. 34

2020

Abstract: Cave beetles of the eastern USA are one of many poorly studied groups of insects and nearly all previous work delimiting species is based solely on morphology. This study assesses genetic diversity in the monotypic cave carabid beetle genus ... ...

Abstract	Cave beetles of the eastern USA are one of many poorly studied groups of insects and nearly all previous work delimiting species is based solely on morphology. This study assesses genetic diversity in the monotypic cave carabid beetle genus DarlingtoneaValentine 1952, to test the relationship between putative geographical barriers to subterranean dispersal and the boundaries of genetically distinct groups. Approximately 400bp of the mitochondrial cytochrome oxidase I (COI) gene was sequenced from up to four individuals from each of 27 populations, sampled from caves along the escarpments of the Mississippian and Cumberland plateaus in eastern Kentucky, USA. The 81 individuals sequenced yielded 28 unique haplotypes. Hierarchical analyses of molecular variance (AMOVA) within and among geographically defined groups tested two a priori hypotheses of structure based on major and minor river drainages, as well as genetic distance clusters defined a posteriori from an unrooted analysis. High genetic differentiation (FST) between populations was found across analyses. The influence of isolation by distance could potentially account for much but not all of the variation found among geographically defined groups at both levels. High variability among the three northernmost genetic clusters (FCT), low variability among populations within clusters (FSC), and low within-cluster Mantel correlations indicate the importance of unidentified likely intra-karst barriers to gene flow separating closely grouped cave populations. Overall phylogeographic patterns are consistent with previous evidence of population isolation among cave systems in the region, revealing geographically structured cryptic diversity in Darlingtonea over its distribution. The landscape features considered a priori in this study were not predictive of the genetic breaks among the three northern clusters, which are genetically distinct despite their close geographic proximity.
Keywords	Carabidae ; Mississippian period ; cytochrome-c oxidase ; gene flow ; genes ; genetic distance ; genetic variation ; haplotypes ; landscapes ; mitochondria ; phylogeography ; rivers ; variance ; Kentucky
Language	English
Dates of publication	2020-0310
Size	p. 1-23.
Publishing place	Pensoft Publishers
Document type	Article
Note	NAL-light
ZDB-ID	2633922-5
ISSN	1314-2615 ; 1768-1448
ISSN (online)	1314-2615
ISSN	1768-1448
DOI	10.3897/subtbiol.34.46348
Database	NAL-Catalogue (AGRICOLA)

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Article: Rhodacyclopentanones as Linchpins for the Atom Economical Assembly of Diverse Polyheterocycles

Wang, Gang-Wei / Boyd, Olivia / Young, Tom A / Bertrand, Sophie M / Bower, John F

Journal of the American Chemical Society. 2020 Jan. 21, v. 142, no. 4

2020

Abstract: We outline a conceptual blueprint that provides direct and atom economical access to a wide range of complex polyheterocycles. Our method capitalizes on the ambiphilic reactivity of rhodacyclopentanones that arise upon exposure of cyclopropanes to Rh(I) ... ...

Abstract	We outline a conceptual blueprint that provides direct and atom economical access to a wide range of complex polyheterocycles. Our method capitalizes on the ambiphilic reactivity of rhodacyclopentanones that arise upon exposure of cyclopropanes to Rh(I) catalysts and CO. Using this approach, a wide array of polycyclizations are achieved, including variants that involve powerful dearomatizations and medium ring formations.
Keywords	carbon monoxide ; catalysts ; rhodium
Language	English
Dates of publication	2020-0121
Size	p. 1740-1745.
Publishing place	American Chemical Society
Document type	Article
ZDB-ID	3155-0
ISSN	1520-5126 ; 0002-7863
ISSN (online)	1520-5126
ISSN	0002-7863
DOI	10.1021/jacs.9b12421
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Rhodacyclopentanones as Linchpins for the Atom Economical Assembly of Diverse Polyheterocycles.

Wang, Gang-Wei / Boyd, Olivia / Young, Tom A / Bertrand, Sophie M / Bower, John F

Journal of the American Chemical Society

2020 Volume 142, Issue 4, Page(s) 1740–1745

Abstract	We outline a conceptual blueprint that provides direct and atom economical access to a wide range of complex polyheterocycles. Our method capitalizes on the ambiphilic reactivity of rhodacyclopentanones that arise upon exposure of cyclopropanes to Rh(I) catalysts and CO. Using this approach, a wide array of polycyclizations are achieved, including variants that involve powerful dearomatizations and medium ring formations.
Language	English
Publishing date	2020-01-21
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	3155-0
ISSN	1520-5126 ; 0002-7863
ISSN (online)	1520-5126
ISSN	0002-7863
DOI	10.1021/jacs.9b12421
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Thesis ; Online: China’s energy reform and climate policy

Boyd, Olivia T.

The ideas motivating change

2012

Abstract: China has embarked on an ambitious and unprecedented programme of energy reform and climate change mitigation. Yet the motivations for this important shift remain unclear. This paper surveys key central government documents and articles by China’s ... ...

Abstract	China has embarked on an ambitious and unprecedented programme of energy reform and climate change mitigation. Yet the motivations for this important shift remain unclear. This paper surveys key central government documents and articles by China’s leading energy academics to investigate the ideas influencing China’s new energy and climate policies. Three key ideas in particular are supportive of greater climate mitigation than in the past. First, domestic energy security concerns have risen on the central government agenda as a result of electricity shortages and rapidly rising energy consumption. Such concerns have deeply influenced China’s ambitious and largely successful energy efficiency policies. Second, growing awareness of the environmental constraints on economic growth in general, and the potential damages of dangerous climate change in particular, has prompted stronger official rhetoric in favour of green development. The appearance of targets and policies that specifically target carbon emissions reductions in the 12th FYP for the first time suggests that climate change mitigation is becoming a motivation for policy action in its own right, rather than simply a co-benefit of policies enacted for other purposes. Third, a conviction that the world is moving towards low-carbon energy forms has given rise to the belief that China must become a technological and economic leader in this transition. Large levels of public financing to support the development of China’s wind power and solar PV sectors suggests that the Chinese government has strong vested interests in seeing China successfully compete and lead in global low-carbon energy markets. In order to understand the shift in China’s approach to climate change since the 11th FYP, it is important to understand how new ideas such as these have reframed and reshaped the Chinese government’s interests and objectives.
Keywords	China ; climate change ; mitigation ; energy policy ; environment ; renewable energy ; energy efficiency ; carbon market ; pollution ; reform ; Environmental Economics and Policy ; Resource /Energy Economics and Policy ; Q54 ; Q48 ; Q58 ; P28
Subject code	950
Language	English
Publishing country	us
Document type	Thesis ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Taxonomic review of New World Tachyina (Coleoptera, Carabidae): descriptions of new genera, subgenera, and species, with an updated key to the subtribe in the Americas

Boyd, Olivia F / Erwin, Terry L

ZooKeys. 2016 Oct. 20, v. 626

2016

Abstract	The classification of the carabid subtribe Tachyina (Trechitae: Bembidiini) is reviewed in light of newly discovered diversity from Central and South America. Described herein are three new genera (Tachyxysta gen. n., Stigmatachys gen. n., Nothoderis gen. n.), two new subgenera of Meotachys (Scolistichus subgen. n., Hylotachys subgen. n.), and two new subgenera of Elaphropus (Ammotachys subgen. n., Idiotachys subgen. n.). Two names previously synonymized under Polyderis (Polyderidius Jeannel, 1962) and Elaphropus (Nototachys Alluaud, 1930) are elevated to generic and subgeneric status, respectively. Eight new species are recognized: Tachyxysta howdenorum (type locality: México: Chiapas: El Aguacero, 680m); Elaphropus marchantarius (type locality: Brazil, Amazonas, Rio Solimões, Ilha de Marchantaria), Elaphropus acutifrons (type locality: Brazil: Pará, Santarém) and Elaphropus occidentalis (type locality: Perú: Loreto, Pithecia, 74°45'W 05°28'S); Stigmatachys uvea (type locality: Perú: Loreto: Campamento San Jacinto, 2°18.75'S, 75°51.77'W, 175–215m); and Meotachys riparius (type locality: Colombia: Amazonas: Leticia, 700 ft), Meotachys ballorum (type locality: Brazil: Amazonas, Rio Negro Cucui), and Meotachys rubrum (type locality: Perú: Madre de Dios: Rio Manu, Pakitza, 11°56°47'S 071°17°00'W, 356m). An updated key to the genera and subgenera of Tachyina occurring in the New World is provided, with accompanying illustrations.
Keywords	Carabidae ; new species ; taxonomic keys ; Brazil ; Colombia ; Mexico
Language	English
Dates of publication	2016-1020
Size	p. 87-123.
Publishing place	Pensoft Publishers
Document type	Article
Note	NAL-light
ZDB-ID	2445640-8
ISSN	1313-2970 ; 1313-2989
ISSN (online)	1313-2970
ISSN	1313-2989
DOI	10.3897/zookeys.626.10033
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Design, Synthesis, and Evaluation of Inhibitors of Hedgehog Acyltransferase.

Ritzefeld, Markus / Zhang, Leran / Xiao, Zhangping / Andrei, Sebastian A / Boyd, Olivia / Masumoto, Naoko / Rodgers, Ursula R / Artelsmair, Markus / Sefer, Lea / Hayes, Angela / Gavriil, Efthymios-Spyridon / Raynaud, Florence I / Burke, Rosemary / Blagg, Julian / Rzepa, Henry S / Siebold, Christian / Magee, Anthony I / Lanyon-Hogg, Thomas / Tate, Edward W

Journal of medicinal chemistry

2024 Volume 67, Issue 2, Page(s) 1061–1078

Abstract: Hedgehog signaling is involved in embryonic development and cancer growth. Functional activity of secreted Hedgehog signaling proteins is dependent ... ...

Abstract	Hedgehog signaling is involved in embryonic development and cancer growth. Functional activity of secreted Hedgehog signaling proteins is dependent on
MeSH term(s)	Hedgehog Proteins/metabolism ; Pyridines/chemistry ; Pyridines/pharmacology
Chemical Substances	Hedgehog Proteins ; Pyridines
Language	English
Publishing date	2024-01-10
Publishing country	United States
Document type	Journal Article
ZDB-ID	218133-2
ISSN	1520-4804 ; 0022-2623
ISSN (online)	1520-4804
ISSN	0022-2623
DOI	10.1021/acs.jmedchem.3c01363
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Article: (with research data) MonotomidGen - A matrix-based interactive key to the New World genera of Monotomidae (Coleoptera, Cucujoidea).

McElrath, Thomas C / Boyd, Olivia F / McHugh, Joseph V

ZooKeys

2016 , Issue 634, Page(s) 47–55

Abstract: A matrix-based ... ...

Abstract	A matrix-based Lucid
Language	English
Publishing date	2016-11-21
Publishing country	Bulgaria
Document type	Journal Article
ZDB-ID	2445640-8
ISSN	1313-2970 ; 1313-2989
ISSN (online)	1313-2970
ISSN	1313-2989
DOI	10.3897/zookeys.634.9857
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