Retrieval of the Complete Coding Sequence of the UK-Endemic Tatenale Orthohantavirus Reveals Extensive Strain Variation and Supports Its Classification as a Novel Species

©2020 by the authors. Licensee MDPI, Basel, Switzerland. Orthohantaviruses are globally distributed viruses, associated with rodents and other small mammals. However, data on the circulation of orthohantaviruses within the UK, particularly the UK-endemic Tatenale virus, is sparse. In this study, 531 animals from five rodent species were collected from two locations in northern and central England and screened using a degenerate, pan- orthohantavirus RT-PCR assay. Tatenale virus was detected in a single field vole (Microtus agrestis) from central England and twelve field voles from northern England. Unbiased high-throughput sequencing of the central English strain resulted in the recovery of the complete coding sequence of a novel strain of Tatenale virus, whilst PCR-primer walking of the northern English strain recovered almost complete coding sequence of a previously identified strain. These findings represented the detection of a third lineage of Tatenale virus in the United Kingdom and extended the known geographic distribution of these viruses from northern to central England. Furthermore, the recovery of the complete coding sequence revealed that Tatenale virus was sufficiently related to the recently identified Traemersee virus, to meet the accepted criteria for classification as a single species of orthohantavirus

Patterns and causes of spatial and temporal variability of dust presence in the central and western Sahara

Dust is a critical component of the Earth System. The central and western Sahara (CWS) is the dustiest place on Earth during the northern hemisphere summer. Understanding patterns and causes of spatial and temporal variability of dust presence here is essential for its reliable simulation in numerical models of weather and climate. Four papers in this thesis contribute to that objective, utilising a combination of high temporal resolution satellite data and global atmospheric reanalyses for June – August 2004 – 2010 inclusive. The first paper develops an objective dust detection scheme for the CWS using data from the Spinning Enhanced Visible and Infrared Imager (SEVIRI), which are available every 15 minutes around the clock. These data have shed valuable insight on CWS dust processes, but their subjective application has to date limited their range of applications. The SEVIRI dust flag (SDF) developed here is evaluated against other widely used surface and satellite derived indicators of dustiness and it is found to reliably detect the presence of moderate-heavy dust loadings. The distribution of dust each summer is presented, revealing a high degree of interannual variability in overall dust coverage. The second paper utilises SDF to create an objective, high spatial resolution dust source map, based on the automated tracking of individual dust plumes. The most active sources are associated predominantly with palaeo-lakes and outwash plains, typically around the Saharan mountains. There is a clear intraseasonal progression of active source areas, controlled by regional climatology. The tracking scheme describes the transport trajectory of dust events following their initiation and the spatial association with deep convection at this time, revealing a clear regional divide in the relative importance of known meteorological mechanisms that drive dust emission from the dominant sources. The third paper uses an unsupervised clustering algorithm to classify maps of daily dust presence frequency and identify patterns of intraseasonal variability in CWS dust coverage. The resulting idealised dust states vary according to frequency of dust occurrence and its location, demonstrating a clear progression in preferred dust location from June – August and preferred state transitions from one day to the next. High daily dust occurrence frequency corresponds to an advanced West African Monsoon flow and low daily dust occurrence frequency corresponds to a Harmattan-dominated CWS. The overall location of the dust is linked to the location of the Sahara Heat Low, which changes as the summer progresses. The final paper addresses interannual variability in summertime dust presence frequency by comparing the 2 years with highest (2005) and lowest (2008) dust presence. The key difference is the occurrence of 3 multi-day periods in 2005 characterised by anomalously high dust presence. Case study comparison with the 3 periods of highest dust presence in 2008 identifies the anticyclonic circulation of the midtroposphere as a key control on dust duration over the CWS, dictating whether emitted dust is efficiently transported away from the CWS or whether it remains in suspension over the region for prolonged periods of time, up to several days in the anomalously dusty periods of 2005.</p

Patterns and causes of spatial and temporal variability of dust presence in the central and western Sahara

Dust is a critical component of the Earth System. The central and western Sahara (CWS) is the dustiest place on Earth during the northern hemisphere summer. Understanding patterns and causes of spatial and temporal variability of dust presence here is essential for its reliable simulation in numerical models of weather and climate. Four papers in this thesis contribute to that objective, utilising a combination of high temporal resolution satellite data and global atmospheric reanalyses for June – August 2004 – 2010 inclusive. The first paper develops an objective dust detection scheme for the CWS using data from the Spinning Enhanced Visible and Infrared Imager (SEVIRI), which are available every 15 minutes around the clock. These data have shed valuable insight on CWS dust processes, but their subjective application has to date limited their range of applications. The SEVIRI dust flag (SDF) developed here is evaluated against other widely used surface and satellite derived indicators of dustiness and it is found to reliably detect the presence of moderate-heavy dust loadings. The distribution of dust each summer is presented, revealing a high degree of interannual variability in overall dust coverage. The second paper utilises SDF to create an objective, high spatial resolution dust source map, based on the automated tracking of individual dust plumes. The most active sources are associated predominantly with palaeo-lakes and outwash plains, typically around the Saharan mountains. There is a clear intraseasonal progression of active source areas, controlled by regional climatology. The tracking scheme describes the transport trajectory of dust events following their initiation and the spatial association with deep convection at this time, revealing a clear regional divide in the relative importance of known meteorological mechanisms that drive dust emission from the dominant sources. The third paper uses an unsupervised clustering algorithm to classify maps of daily dust presence frequency and identify patterns of intraseasonal variability in CWS dust coverage. The resulting idealised dust states vary according to frequency of dust occurrence and its location, demonstrating a clear progression in preferred dust location from June – August and preferred state transitions from one day to the next. High daily dust occurrence frequency corresponds to an advanced West African Monsoon flow and low daily dust occurrence frequency corresponds to a Harmattan-dominated CWS. The overall location of the dust is linked to the location of the Sahara Heat Low, which changes as the summer progresses. The final paper addresses interannual variability in summertime dust presence frequency by comparing the 2 years with highest (2005) and lowest (2008) dust presence. The key difference is the occurrence of 3 multi-day periods in 2005 characterised by anomalously high dust presence. Case study comparison with the 3 periods of highest dust presence in 2008 identifies the anticyclonic circulation of the midtroposphere as a key control on dust duration over the CWS, dictating whether emitted dust is efficiently transported away from the CWS or whether it remains in suspension over the region for prolonged periods of time, up to several days in the anomalously dusty periods of 2005

Patterns and causes of spatial and temporal variability of dust presence in the central and western Sahara

Dust is a critical component of the Earth System. The central and western Sahara (CWS) is the dustiest place on Earth during the northern hemisphere summer. Understanding patterns and causes of spatial and temporal variability of dust presence here is essential for its reliable simulation in numerical models of weather and climate. Four papers in this thesis contribute to that objective, utilising a combination of high temporal resolution satellite data and global atmospheric reanalyses for June – August 2004 – 2010 inclusive. The first paper develops an objective dust detection scheme for the CWS using data from the Spinning Enhanced Visible and Infrared Imager (SEVIRI), which are available every 15 minutes around the clock. These data have shed valuable insight on CWS dust processes, but their subjective application has to date limited their range of applications. The SEVIRI dust flag (SDF) developed here is evaluated against other widely used surface and satellite derived indicators of dustiness and it is found to reliably detect the presence of moderate-heavy dust loadings. The distribution of dust each summer is presented, revealing a high degree of interannual variability in overall dust coverage. The second paper utilises SDF to create an objective, high spatial resolution dust source map, based on the automated tracking of individual dust plumes. The most active sources are associated predominantly with palaeo-lakes and outwash plains, typically around the Saharan mountains. There is a clear intraseasonal progression of active source areas, controlled by regional climatology. The tracking scheme describes the transport trajectory of dust events following their initiation and the spatial association with deep convection at this time, revealing a clear regional divide in the relative importance of known meteorological mechanisms that drive dust emission from the dominant sources. The third paper uses an unsupervised clustering algorithm to classify maps of daily dust presence frequency and identify patterns of intraseasonal variability in CWS dust coverage. The resulting idealised dust states vary according to frequency of dust occurrence and its location, demonstrating a clear progression in preferred dust location from June – August and preferred state transitions from one day to the next. High daily dust occurrence frequency corresponds to an advanced West African Monsoon flow and low daily dust occurrence frequency corresponds to a Harmattan-dominated CWS. The overall location of the dust is linked to the location of the Sahara Heat Low, which changes as the summer progresses. The final paper addresses interannual variability in summertime dust presence frequency by comparing the 2 years with highest (2005) and lowest (2008) dust presence. The key difference is the occurrence of 3 multi-day periods in 2005 characterised by anomalously high dust presence. Case study comparison with the 3 periods of highest dust presence in 2008 identifies the anticyclonic circulation of the midtroposphere as a key control on dust duration over the CWS, dictating whether emitted dust is efficiently transported away from the CWS or whether it remains in suspension over the region for prolonged periods of time, up to several days in the anomalously dusty periods of 2005.This thesis is not currently available in ORA

Wetland inundation dynamics in a model of land-surface climate: Evaluation in the Niger Inland Delta region

Observed river gauging data show significant evaporative losses from the land and water surface in the Niger Inland delta. These losses indicate an important potential feedback between the land-surface and atmosphere. Moreover, the reduction in river flow downstream of the wetland has clear implications for water management in the region and beyond. Here we have modelled the evaporative losses that occur over the Niger Inland Delta by adding an over-bank flow parameterization to the Joint UK Land-Environment Simulator (JULES) land-surface model. The hydrological component of this model comprises a probability-distributed model of soil moisture and runoff production (PDM) coupled with a discrete approximation to the 1D kinematic wave equation to route river water down-slope (G2G). We use sub-grid-resolution topographic data to derive a two-parameter frequency distribution of inundated areas for each grid-box which we then employ to represent over-bank inundation in the model. The model was driven using data from the ALMIP experiment (ALMIP stands for AMMA Land-surface Model Inter-comparison Project, wherein AMMA stands for African Monsoon Multidisciplinary Analyses). The model reproduces the salient features of the observed river flow and inundation patterns; these include significant evaporative losses from the inundated region accounting for doubling of the total land-atmosphere water flux during periods of greatest flooding. Our predictions of inundated area are in good agreement with observed estimates of the extent of inundation obtained using satellite infra-red and microwave remote sensin

Estimates of Flood Inundation and Evaporation in the Niger Inland Delta Region using the JULES land-surface model

Observed river gauging data indicate significant evaporative losses from the land and water surface in the Niger Inland delta. These losses indicate an important potential feedback between the land-surface and atmosphere. Moreover, the reduction of flow downstream of the wetland has clear implications for water management in the region and beyond. Here we have modelled the land-atmosphere coupling in the Niger Inland Delta by adding an overbank flow parameterization to the Joint UK Land-Environment Simulator (JULES) land-surface model (Blyth et al., 2002). Our hydrological model comprises a probability-distributed model of soil moisture and runoff production (PDM; Moore, 2007) coupled with a discrete approximation to the 1D kinematic wave equation to route river water downslope (G2G; Bell et al., 2007). The model was driven using data from the ALMIP experiment (Boone et al., 2006). The model simulates the broad features of the observed river flow pattern, including a downstream attenuation of the flood-wave through the wetland region. The model results illustrate significant evaporative losses from the inundated region leading to a ~10 percent reduction in river flow. The greatest relative decreases in river flow occur during spring and summer low flows. Moisture flux from the inundated region is greatly increased, accounting for up to 50 percent of the total land-atmosphere water flux during periods of maximum flooding. Moreover, a surface temperature anomaly of up to -8 K was observed in the inundated region Further work is planned to use sub-grid-resolution topographic data to improve the representation of overbank flow in the model; to compare the extents of modelled and observed inundated areas using satellite microwave remote sensing; and to include wetland evaporation process in online climate simulations to investigate land-atmosphere feedbacks

Cowpox in zoo and wild animals in the United Kingdom

Cowpox virus is considered to be a re-emerging zoonotic pathogen and a public health threat due to increasing numbers of cases in humans and animals in Europe over the past decade, including within the United Kingdom (UK). We present epidemiological data and diagnostic features of 27 recent, naturally occurring cowpox cases in zoo and wild animals across the UK, including the first reports of cowpox in two snow leopards (Panthera uncia), a Bengal tiger (Panthera tigris tigris), three Chilean pudus (Pudu puda), a Malayan tapir (Tapirus indicus) and a Eurasian otter (Lutra lutra), and the first reports of Orthopoxvirus infection in a lar gibbon (Hylobates lar), a Southern tamandua (Tamandua tetradactyla) and an aardvark (Orycteropus afer). This study provides a detailed overview of cowpox infections in a wide range of non-domestic animal species, presents a range of methods for diagnosis and demonstrates the value of retrospective analysis of pathology surveillance in revealing epidemiological links