Latest Publications
Symptom prevalence and Secondary Attack Rate of SARS-CoV-2 in Rural Kenyan Households: a prospective cohort study
Katherine E. Gallagher & Joyce Nyiro, Charles N. Agoti, Eric Maitha, James Nyagwange, Angela Karani, Christian Bottomley, Nickson Murunga, George Githinji, Martin Mutunga, Lynette Isabella Ochola-Oyier, Ivy Kombe, Amek Nyaguara, E. Wangeci Kagucia, George Warimwe, Ambrose Agweyu, Benjamin Tsofa, Philip Bejon, J. Anthony G. Scott, David James Nokes
We estimated the secondary attack rate of SARS-CoV-2 among household contacts of PCR-confirmed cases of COVID-19 in rural Kenya and analysed risk factors for transmission. We enrolled incident PCR-confirmed cases and their household members. At baseline, a questionnaire, a blood sample, and naso-oropharyngeal swabs were collected. Household members were followed 4, 7, 10, 14, 21 and 28 days after the date of the first PCR-positive in the household; naso-oropharyngeal swabs were collected at each visit and used to define secondary cases. Blood samples were collected every 1–2 weeks. Symptoms were collected in a daily symptom diary. We used binomial regression to estimate secondary attack rates and survival analysis to analyse risk factors for transmission. Households in our setting experienced a lower 7-day attack rate than a recent meta-analysis indicated as the global average (23%–43% depending on variant), and infection is mostly asymptomatic in our setting.
Incorporating heterogeneity in farmer disease control behaviour into a livestock disease transmission model
Hill, Edward M, Prosser, Naomi S, Brown, Paul E, Ferguson, Eamonn, Green, Martin J, Kaler, Jasmeet, Keeling, Matt J and Tildesley, Michael J
Human behaviour is critical to effective responses to livestock disease outbreaks, especially with respect to vaccination uptake. Traditionally, mathematical models used to inform this behaviour have not taken heterogeneity in farmer behaviour into account. We address this by exploring how heterogeneity in farmers vaccination behaviour can be incorporated to inform mathematical models. We developed and used a graphical user interface to elicit farmers (n = 60) vaccination decisions to an unfolding fast-spreading epidemic and linked this to their psychosocial and behavioural profiles. We identified, via cluster analysis, robust patterns of heterogeneity in vaccination behaviour. By incorporating these vaccination behavioural groupings into a mathematical model for a fast-spreading livestock infection, using computational simulation we explored how the inclusion of heterogeneity in farmer disease control behaviour may impact epidemiological and economic focused outcomes.
Intrinsic disorder and conformational co-existence in auxin co-receptors
Sigurd Ramans-Harborough, Arnout P. Kalverda, Iain W. Manfield, Gary S. Thompson, Martin Kieffer, Veselina Uzunova, Mussa Quareshy, Justyna M. Prusinska, Suruchi Roychoudhry, Ken-ichiro Hayashi, Richard Napier, Charo del Genio, Stefan Kepinski
AUXIN/INDOLE 3-ACETIC ACID (Aux/IAA) transcriptional repressor proteins and the TRANSPORT INHIBITOR RESISTANT 1/AUXIN SIGNALING F-BOX (TIR1/AFB) proteins to which they bind act as auxin coreceptors. While the structure of TIR1 has been solved, structural characterization of the regions of the Aux/IAA protein responsible for auxin perception has been complicated by their predicted disorder. Here, we use NMR, CD and molecular dynamics simulation to investigate the N-terminal domains of the Aux/IAA protein IAA17/AXR3. Our results and approach provide a platform for exploring the functional significance of variation in the Aux/IAA coreceptor family and for understanding the role of intrinsic disorder in auxin signal transduction and other signaling systems.
Modelling African horse sickness emergence and transmission in the South African control area using a deterministic metapopulation approach
Joanna N de Klerk, Erin E Gorsich, John D Grewar, Benjamin D Atkins, Warren S D Tennant, Karien Labuschagne, Michael J Tildesley
African horse sickness is an equine orbivirus transmitted by Culicoides Latreille biting midges. The disease is endemic in South Africa; however, a unique control area has been set up in the Western Cape where increased surveillance and control measures have been put in place. A deterministic metapopulation model was developed to explore if an outbreak might occur, and how it might develop, if a latently infected horse was to be imported into the control area, by varying the geographical location and months of import. A sensitivity analysis indicated that control measures such as vaccination and vector control are potentially effective to manage the spread of an outbreak, and shortening the vaccination window to July to September may reduce the risk of vaccine-associated outbreaks.
Genetic and physiological responses to light quality in a deep ocean ecotype of Ostreococcus, an ecologically important photosynthetic picoeukaryote
Elizabeth Sands, Sian Davies, Richard John Puxty, Valerie Vergé, François-Yves Bouget, David John Scanlan, Isabelle Alice Carre
Phytoplankton are exposed to dramatic variations in light quality when cells are carried by upwelling or downwelling currents or encounter sediment. We investigated the potential impact of light quality changes in Ostreococcus, a key marine photosynthetic picoeukaryote, by analysing changes in its transcriptome, pigment content and photophysiology after acclimation to monochromatic red, green or blue lightThe results demonstrate that light quality can have a major influence on the physiology of eukaryotic phytoplankton and suggest that different light quality environments can drive selection for diverse patterns of responsiveness and environmental niche partitioning.
Analysis of Escherichia coli O157 strains in cattle and humans between Scotland and England & Wales: implications for human health
Margo Chase-Topping, Timothy J. Dallman, Lesley Allison , Nadejda Lupolova, Louise Matthews, Sonia Mitchell, Christopher J. Banks, Jamie Prentice, Helen Brown, Sue Tongue, Madeleine Henry, Judith Evans, George Gunn, Deborah Hoyle, Tom N. McNeilly, Stephen Fitzgerald, Alison Smith-Palmer, Sharif Shaaban, Anne Holmes, Mary Hanson, Mark Woolhouse, Xavier Didelot, Claire Jenkins and David L. Gall
For the last two decades, the human infection frequency of Escherichia coli O157 (O157) in Scotland has been 2.5-fold higher than in England and Wales. Results from national cattle surveys conducted in Scotland and England and Wales in 2014/2015 were combined with data on reported human clinical cases from the same time frame to determine if strain differences in national populations of O157 in cattle could be associated with higher human infection rates in Scotland. There was evidence of limited cattle strain migration between nations and clinical isolates from one nation were more similar to cattle isolates from the same nation, with sub-lineage Ic (mainly PT21/28) exhibiting clear national association and evidence of local transmission in Scotland. While we propose the higher rate of O157 clinical cases in Scotland is a consequence of the nationally higher level of Stx2a+O157 strains in Scottish cattle, we discuss the multiple additional factors that may also contribute to the different infection rates between these nations.