Rowland Raymond Kao

The University of Edinburgh | UoE · Royal (Dick) School of Veterinary Studies

For a disease such as COVID-19, it is important to identify individuals in a population at heightened risk of infection, as well as broader patterns of infection spread. This is both to estimate burden on healthcare systems (given substantial variation in disease severity from person to person), and to better control the spread of infection. In Sco...

Background : Mobility restrictions prevent the spread of infections to disease-free areas, and early in the coronavirus disease 2019 (COVID-19) pandemic, most countries imposed severe restrictions on mobility as soon as it was clear that containment of local outbreaks was insufficient to control spread. These restrictions have adverse impacts on th...

Wastewater based epidemiology (WBE) has become an important tool during the COVID-19 pandemic, however the relationship between SARS-CoV-2 RNA in wastewater treatment plant influent (WWTP) and cases in the community is not well-defined. We report here the development of a national WBE program across 28 WWTPs serving 50% of the population of Scotlan...

Understanding how emergent pathogens successfully establish themselves and persist in previously unaffected populations is a crucial problem in disease ecology, with important implications for disease management. In multi‐host pathogen systems this problem is particularly difficult, as the importance of each host species to transmission is often po...

Streptococcus agalactiae, also known as group B Streptococcus (GBS), is a pathogen of humans and animals. It is an important cause of mastitis in dairy cattle, causing decreased milk quality and quantity. Denmark is the only country to have implemented a national surveillance and control campaign for GBS in dairy cattle. After a significant decline...

Background In the context of an outbreak the natural boundaries of islands can allow for control of movements between populations. We estimate the risk of introduction of COVID-19 to each of the Hebridean islands situated off the west coast of mainland Scotland due to individual movements, and explore control strategies to mitigate this risk. Metho...

Multi-host pathogens are particularly difficult to control, especially when at least one of the hosts acts as a hidden reservoir. Deep sequencing of densely sampled pathogens has the potential to transform this understanding, but requires analytical approaches that jointly consider epidemiological and genetic data to best address this problem. Whil...

The genetic diversity and frequent emergence of novel genetic variants of porcine reproductive and respiratory syndrome virus type-2 (PRRSV) hinders control efforts, yet drivers of macro-evolutionary patterns of PRRSV remain poorly documented. Utilizing a comprehensive database of >20,000 orf5 sequences, our objective was to classify variants accor...

Background COVID-19 patients shed SARS-CoV-2 RNA in their faeces. We hypothesised that detection of SARS-CoV-2 RNA in wastewater treatment plant (WWTP) influent could be a valuable tool to assist in public health decision making. We aimed to rapidly develop and validate a scalable methodology for the detection of SARS-CoV-2 RNA in wastewater that c...

Multi-host pathogens are particularly difficult to control, especially when at least one of the hosts acts as a hidden reservoir. Deep sequencing of densely sampled pathogens has the potential to transform this understanding, but requires analytical approaches that jointly consider epidemiological and genetic data to best address this problem. Whil...

Background Bovine tuberculosis (bTB) is a costly epidemiologically complex, multi-host, endemic disease. Lack of understanding of transmission dynamics may undermine eradication efforts. Pathogen whole genome sequencing improves epidemiological inferences, providing a means to determine the relative importance of inter- and intra- species host tran...

Introduction The objective of this study is to show the importance of interspecies links and temporal network dynamics of a multi-species livestock movement network. Although both cattle and sheep networks have been previously studied, cattle-sheep multi-species networks have not generally been studied in-depth. The central question of this study i...

The number of positive diagnostic tests for SARS-CoV-2 is a critical metric that is commonly used to assess epidemic severity and the efficacy of current levels of control. However, a proportion of individuals infected with SARS-CoV-2 may never receive a diagnostic test, while many of those who are tested may receive a false negative result. Conseq...

The second SARS virus, SARS-CoV-2, emerged in December 2019, and within a month was globally distributed. It was first introduced into Scotland in February 2020 associated with returning travellers and visitors. By March it was circulating in communities across the UK, and to control COVID-19 cases, and prevent overwhelming of the National Health S...

Established methods for whole-genome-sequencing (WGS) technology allow for the detection of single-nucleotide polymorphisms (SNPs) in the pathogen genomes sourced from host samples. The information obtained can be used to track the pathogen’s evolution in time and potentially identify ‘who-infected-whom’ with unprecedented accuracy. Successful meth...

Controlling the regional re-emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) after its initial spread in ever-changing personal contact networks and disease landscapes is a challenging task. In a landscape context, contact opportunities within and between populations are changing rapidly as lockdown measures are relaxed and...

Restrictions on mobility are a key component of infectious disease controls, preventing the spread of infections to as yet unexposed areas, or to regions which have previously eliminated outbreaks. However, even under the most severe restrictions, some travel must inevitably continue, at the very minimum to retain essential services. For COVID-19,...

Understanding how an emergent pathogen successfully establishes itself and persists in a previously unaffected population is a crucial problem in disease ecology. In multi-host pathogen systems this problem is particularly difficult, as the importance of each host species to transmission is often poorly characterised, and the epidemiology of the di...

We introduce a game inspired by the challenges of disease management in livestock farming and the transmission of endemic disease through a trade network. Success in this game comes from balancing the cost of buying new stock with the risk that it will be carrying some disease. When players follow a simple memory-based strategy we observe a spontan...

Controlling the regional re-emergence of SARS-CoV-2 after its initial spread in ever-changing personal contact networks and disease landscapes is a challenging task. In a landscape context, contact opportunities within and between populations are changing rapidly as lockdown measures are relaxed and a number of social activities re-activated. Using...

Control of bovine tuberculosis (bTB), caused by Mycobacterium bovis , in the Republic of Ireland costs €84 million each year. Badgers are recognized as being a wildlife source for M. bovis infection of cattle. Deer are thought to act as spillover hosts for infection; however, population density is recognized as an important driver in shifting their...

Established methods for whole-genome-sequencing (WGS) technology allow for the detection of single-nucleotide polymorphisms (SNPs) in the pathogen genomes sourced from host samples. The information obtained can be used to track the pathogen’s evolution in time and potentially identify ‘who-infected-whom’ with unprecedented accuracy. Successful meth...

We introduce a game inspired by the challenges of disease management in livestock farming and the transmission of endemic disease through a trade network. Success in this game comes from balancing the cost of buying new stock with the risk that it will be carrying some disease. When players follow a simple memory-based strategy we observe a spontan...

Recombination is an important feature of HIV evolution, occurring both within and between the major branches of diversity (subtypes). The Ugandan epidemic is primarily composed of two subtypes, A1 and D, that have been co-circulating for 50 years, frequently recombining in dually infected patients. Here, we investigate the frequency of recombinants...

Quantifying pathogen transmission in multi-host systems is difficult, as exemplified in bovine tuberculosis (bTB) systems, but is crucial for control. The agent of bTB, Mycobacterium bovis, persists in cattle populations worldwide, often where potential wildlife reservoirs exist. However, the relative contribution of different host species to bTB p...

Livestock movements are an important mechanism of infectious disease transmission. Where these are well recorded, network analysis tools have been used to successfully identify system properties, highlight vulnerabilities to transmission, and inform targeted surveillance and control. Here we highlight the main uses of network properties in understa...

The role of wildlife in the persistence and spread of livestock diseases is difficult to quantify and control. These difficulties are exacerbated when several wildlife species are potentially involved. Bovine tuberculosis (bTB), caused by Mycobacterium bovis, has experienced an ecological shift in Michigan, with spillover from cattle leading to an...

The complex transmission ecologies of vector-borne and zoonotic diseases pose challenges to their control, especially in changing landscapes. Human incidence of zoonotic malaria (Plasmodium knowlesi) is associated with deforestation although mechanisms are unknown. Here, a novel application of a method for predicting disease occurrence that combine...

The ability to DNA fingerprint Mycobacterium bovis isolates helped to define the role of wildlife in the persistence of bovine tuberculosis in New Zealand. DNA fingerprinting results currently help to guide wildlife control measures and also aid in tracing the source of infections that result from movement of livestock. During the last 5 years we h...

Isolate metadata, coverage statistics, in silico Spoligotype data and metadata explanations.

Comparison of RaxML and BioNJ phylogenies. (a) NZ M. bovis tree. The four clades identified in Figure 1 with differently colored branches are boxed in the same color in this Figure. (b) Mt. Cargill outbreak investigation- all isolates shown in the Phylogram in Figure 3a are compared. Outbreak isolates are boxed in red. (c-d) South Westland investig...

Global distribution of NZ spoligotypes. Coloring in these plots reflects the relative abundance of this type in the indicated region.

Square ML Phylogram illustrating the relationship of West Coast types considered for the South Westland investigations. Breakdown isolate metadata is colored red, livestock metadata is colored blue and wildlife metadata is colored black.

SNPs excluded from the analysis. Numbers indicate regions or individual positions in UK reference version NC_002945.3 for which SNPs were excluded from all isolates.

Distance Matrices. Closely related isolates are colored green, more distant isolates yellow, then orange with the most distinct isolates colored red. Color bars indicate the corresponding cluster in Figures 3, 4 and 6.

The movements of livestock between premises and markets can be characterised as a dynamic network where the structure of the network itself can critically impact the transmission dynamics of many infectious diseases. As evidenced by the 2001 foot-and-mouth disease (FMD) epidemic in the UK, this can involve transmission over large geographical dista...

In many populations, the patterns of potentially infectious contacts are transients that can be described as a network with dynamic links. The relative timescales of link and contagion dynamics and the characteristics that drive their tempos can lead to important differences to the static case. Here, we propose some essential nomenclature for their...

Bovine tuberculosis (bTB) is a chronic zoonosis with major health and economic impact on the cattle industry. Despite extensive control measures in cattle and culling trials in wildlife, the reasons behind the expansion of areas with high incidence of bTB breakdowns in Great Britain remain unexplained. By balancing the importance of cattle movement...

Process models that focus on explicitly representing biological mechanisms are increasingly important in disease ecology and animal health research. However, the large number of process modelling approaches makes it difficult to decide which is most appropriate for a given disease system and research question. Here, we discuss different motivations...

Background The patterns of relative species abundance are commonly studied in ecology and epidemiology to provide insights into underlying dynamical processes. Molecular types (MVLA-types) of Mycobacterium bovis, the causal agent of bovine tuberculosis, are now routinely recorded in culture-confirmed bovine tuberculosis cases in Northern Ireland. I...

Disease surveillance can be made more effective by either improving disease detection, providing cost savings, or doing both. Currently, cattle herds in low-risk areas (LRAs) for bovine tuberculosis (bTB) in England are tested once every 4 years. In Scotland, the default herd testing frequency is also 4 years, but a risk-based system exempts some h...

The role of host movement in the spread of vector-borne diseases of livestock has been little studied. Here we develop a mathematical framework that allows us to disentangle and quantify the roles of vector dispersal and livestock movement in transmission between farms. We apply this framework to outbreaks of bluetongue virus (BTV) and Schmallenber...

Model for t ransmission via movement of infected livestock. (DOCX)

Implementation of the approximate Bayesian computation sequential Monte Carlo scheme. (DOCX)

Observed and predicted spread of bluetongue virus serotype 8 in Great Britain in 2007 for the model in which vector dispersal is described by an exponential kernel. Panels A-F are the same as for Fig 1 in the main paper and results are based on 1000 replicates of the model with parameters sampled from the joint posterior distribution. (TIF)

Observed and predicted spread of bluetongue virus serotype 8 in Great Britain in 2007 for the model in which vector dispersal is described by a fat-tailed kernel. Panels A-F are the same as for Fig 1 in the main paper and results are based on 1000 replicates of the model with parameters sampled from the joint posterior distribution. (TIF)

Marginal posterior distributions for the parameters in the model for the transmission of bluetongue virus within a farm. In each plot the posterior density for the parameter is shown for the diffusion model (black), exponential kernel (red), Gaussian kernel (green), fat-tailed kernel (blue) and stepped kernel (magenta); the prior distribution is sh...

Quantifying the importance of transmission routes for bluetongue virus between farms for different times of incursion assuming 2007 temperatures. Panels are the same as in S7 Fig. (TIF)

Observed and predicted spread of bluetongue virus serotype 8 in Great Britain in 2007 for the model in which vector dispersal is described by a Gaussian kernel. Panels A-F are the same as for Fig 1 in the main paper and results are based on 1000 replicates of the model with parameters sampled from the joint posterior distribution. (TIF)