Prevalence and risk factors for long COVID among adults in Scotland using electronic health records: a national, retrospective, observational cohort study

Background

Long COVID is a debilitating multisystem condition. The objective of this study was to estimate the prevalence of long COVID in the adult population of Scotland, and to identify risk factors associated with its development.

Methods

In this national, retrospective, observational cohort study, we analysed electronic health records (EHRs) for all adults (≥18 years) registered with a general medical practice and resident in Scotland between March 1, 2020, and October 26, 2022 (98-99% of the population). We linked data from primary care, secondary care, laboratory testing and prescribing. Four outcome measures were used to identify long COVID: clinical codes, free text in primary care records, free text on sick notes, and a novel operational definition. The operational definition was developed using Poisson regression to identify clinical encounters indicative of long COVID from a sample of negative and positive COVID-19 cases matched on time-varying propensity to test positive for SARS-CoV-2. Possible risk factors for long COVID were identified by stratifying descriptive statistics by long COVID status.

Findings

Of 4,676,390 participants, 81,219 (1.7%) were identified as having long COVID. Clinical codes identified the fewest cases (n = 1,092, 0.02%), followed by free text (n = 8,368, 0.2%), sick notes (n = 14,469, 0.3%), and the operational definition (n = 64,193, 1.4%). There was limited overlap in cases identified by the measures; however, temporal trends and patient characteristics were consistent across measures. Compared with the general population, a higher proportion of people with long COVID were female (65.1% versus 50.4%), aged 38-67 (63.7% versus 48.9%), overweight or obese (45.7% versus 29.4%), had one or more comorbidities (52.7% versus 36.0%), were immunosuppressed (6.9% versus 3.2%), shielding (7.9% versus 3.4%), or hospitalised within 28 days of testing positive (8.8% versus 3.3%%), and had tested positive before Omicron became the dominant variant (44.9% versus 35.9%). The operational definition identified long COVID cases with combinations of clinical encounters (from four symptoms, six investigation types, and seven management strategies) recorded in EHRs within 4-26 weeks of a positive SARS-CoV-2 test. These combinations were significantly (p < 0.0001) more prevalent in positive COVID-19 patients than in matched negative controls. In a case-crossover analysis, 16.4% of those identified by the operational definition had similar healthcare patterns recorded before testing positive.

Interpretation

The prevalence of long COVID presenting in general practice was estimated to be 0.02-1.7%, depending on the measure used. Due to challenges in diagnosing long COVID and inconsistent recording of information in EHRs, the true prevalence of long COVID is likely to be higher. The operational definition provided a novel approach but relied on a restricted set of symptoms and may misclassify individuals with pre-existing health conditions. Further research is needed to refine and validate this approach.

Funding

Chief Scientist Office (Scotland), Medical Research Council, and BREATHE.

Quality of ethnicity data within Scottish health records and implications of misclassification for ethnic inequalities in severe COVID-19: a national linked data study

BACKGROUND

We compared the quality of ethnicity coding within the Public Health Scotland Ethnicity Look-up (PHS-EL) dataset, and other National Health Service datasets, with the 2011 Scottish Census.

METHODS

Measures of quality included the level of missingness and misclassification. We examined the impact of misclassification using Cox proportional hazards to compare the risk of severe coronavirus disease (COVID-19) (hospitalization & death) by ethnic group.

RESULTS

Misclassification within PHS-EL was higher for all minority ethnic groups [12.5 to 69.1%] compared with the White Scottish majority [5.1%] and highest in the White Gypsy/Traveller group [69.1%]. Missingness in PHS-EL was highest among the White Other British group [39%] and lowest among the Pakistani group [17%]. PHS-EL data often underestimated severe COVID-19 risk compared with Census data. e.g. in the White Gypsy/Traveller group the Hazard Ratio (HR) was 1.68 [95% Confidence Intervals (CI): 1.03, 2.74] compared with the White Scottish majority using Census ethnicity data and 0.73 [95% CI: 0.10, 5.15] using PHS-EL data; and HR was 2.03 [95% CI: 1.20, 3.44] in the Census for the Bangladeshi group versus 1.45 [95% CI: 0.75, 2.78] in PHS-EL.

CONCLUSIONS

Poor quality ethnicity coding in health records can bias estimates, thereby threatening monitoring and understanding ethnic inequalities in health.

Risk of winter hospitalisation and death from acute respiratory infections in Scotland: national retrospective cohort study

OBJECTIVES

We undertook a national analysis to characterise and identify risk factors for acute respiratory infections (ARIs) resulting in hospitalisation during the winter period in Scotland.

DESIGN

A population-based retrospective cohort analysis.

SETTING

Scotland.

PARTICIPANTS

The study involved 5.4 million residents in Scotland.

MAIN OUTCOME MEASURES

Cox proportional hazard models were used to estimate adjusted hazard ratios (aHRs) and 95% confidence intervals (CIs) for the association between risk factors and ARI hospitalisation.

RESULTS

Between 1 September 2022 and 31 January 2023, there were 22,284 (10.9% of 203,549 with any emergency hospitalisation) ARI hospitalisations (1759 in children and 20,525 in adults) in Scotland. Compared with the reference group of children aged 6-17 years, the risk of ARI hospitalisation was higher in children aged 3-5 years (aHR = 4.55; 95% CI: 4.11-5.04). Compared with those aged 25-29 years, the risk of ARI hospitalisation was highest among the oldest adults aged ≥80 years (aHR = 7.86; 95% CI: 7.06-8.76). Adults from more deprived areas (most deprived vs. least deprived, aHR = 1.64; 95% CI: 1.57-1.72), with existing health conditions (≥5 vs. 0 health conditions, aHR = 4.84; 95% CI: 4.53-5.18) or with history of all-cause emergency admissions (≥6 vs. 0 previous emergency admissions, aHR = 7.53; 95% CI: 5.48-10.35) were at a higher risk of ARI hospitalisations. The risk increased by the number of existing health conditions and previous emergency admission. Similar associations were seen in children.

CONCLUSIONS

Younger children, older adults, those from more deprived backgrounds and individuals with greater numbers of pre-existing conditions and previous emergency admission were at increased risk for winter hospitalisations for ARI.

Risk of severe COVID-19 outcomes after autumn 2022 COVID-19 booster vaccinations: a pooled analysis of national prospective cohort studies involving 7.4 million adults in England, Northern Ireland, Scotland and Wales

Background

UK COVID-19 vaccination policy has evolved to offering COVID-19 booster doses to individuals at increased risk of severe Illness from COVID-19. Building on our analyses of vaccine effectiveness of first, second and initial booster doses, we aimed to identify individuals at increased risk of severe outcomes (i.e., COVID-19 related hospitalisation or death) post the autumn 2022 booster dose.

Methods

We undertook a national population-based cohort analysis across all four UK nations through linked primary care, vaccination, hospitalisation and mortality data. We included individuals who received autumn 2022 booster doses of BNT162b2 (Comirnaty) or mRNA-1273 (Spikevax) during the period September 1, 2022 to December 31, 2022 to investigate the risk of severe COVID-19 outcomes. Cox proportional hazard models were used to estimate adjusted hazard ratios (aHR) and 95% confidence intervals (CIs) for the association between demographic and clinical factors and severe COVID-19 outcomes after the autumn booster dose. Analyses were adjusted for age, sex, body mass index (BMI), deprivation, urban/rural areas and comorbidities. Stratified analyses were conducted by vaccine type. We then conducted a fixed-effect meta-analysis to combine results across the four UK nations.

Findings

Between September 1, 2022 and December 31, 2022, 7,451,890 individuals ≥18 years received an autumn booster dose. 3500 had severe COVID-19 outcomes (2.9 events per 1000 person-years). Being male (male vs female, aHR 1.41 (1.32-1.51)), older adults (≥80 years vs 18-49 years; 10.43 (8.06-13.50)), underweight (BMI <18.5 vs BMI 25.0-29.9; 2.94 (2.51-3.44)), those with comorbidities (≥5 comorbidities vs none; 9.45 (8.15-10.96)) had a higher risk of COVID-19 hospitalisation or death after the autumn booster dose. Those with a larger household size (≥11 people within household vs 2 people; 1.56 (1.23-1.98)) and from more deprived areas (most deprived vs least deprived quintile; 1.35 (1.21-1.51)) had modestly higher risks. We also observed at least a two-fold increase in risk for those with various chronic neurological conditions, including Down's syndrome, immunodeficiency, chronic kidney disease, cancer, chronic respiratory disease, or cardiovascular disease.

Interpretation

Males, older individuals, underweight individuals, those with an increasing number of comorbidities, from a larger household or more deprived areas, and those with specific underlying health conditions remained at increased risk of COVID-19 hospitalisation and death after the autumn 2022 vaccine booster dose. There is now a need to focus on these risk groups for investigating immunogenicity and efficacy of further booster doses or therapeutics.

Funding

National Core Studies-Immunity, UK Research and Innovation (Medical Research Council and Economic and Social Research Council), Health Data Research UK, the Scottish Government, and the University of Edinburgh.

BNT162b2 COVID-19 vaccination uptake, safety, effectiveness and waning in children and young people aged 12-17 years in Scotland

Background

The two-dose BNT162b2 (Pfizer-BioNTech) vaccine has demonstrated high efficacy against COVID-19 disease in clinical trials of children and young people (CYP). Consequently, we investigated the uptake, safety, effectiveness and waning of the protective effect of the BNT162b2 against symptomatic COVID-19 in CYP aged 12-17 years in Scotland.

Methods

The analysis of the vaccine uptake was based on information from the Turas Vaccination Management Tool, inclusive of Mar 1, 2022. Vaccine safety was evaluated using national data on hospital admissions and General Practice (GP) consultations, through a self-controlled case series (SCCS) design, investigating 17 health outcomes of interest. Vaccine effectiveness (VE) against symptomatic COVID-19 disease for Delta and Omicron variants was estimated using a test-negative design (TND) and S-gene status in a prospective cohort study using the Scotland-wide Early Pandemic Evaluation and Enhanced Surveillance of COVID-19 (EAVE II) surveillance platform. The waning of the VE following each dose of BNT162b2 was assessed using a matching process followed by conditional logistic regression.

Findings

Between Aug 6, 2021 and Mar 1, 2022, 75.9% of the 112,609 CYP aged 16-17 years received the first and 49.0% the second COVID-19 vaccine dose. Among 237,681 CYP aged 12-15 years, the uptake was 64.5% and 37.2%, respectively. For 12-17-year-olds, BNT162b2 showed an excellent safety record, with no increase in hospital stays following vaccination for any of the 17 investigated health outcomes. In the 16-17-year-old group, VE against symptomatic COVID-19 during the Delta period was 64.2% (95% confidence interval [CI] 59.2-68.5) at 2-5 weeks after the first dose and 95.6% (77.0-99.1) at 2-5 weeks after the second dose. The respective VEs against symptomatic COVID-19 in the Omicron period were 22.8% (95% CI -6.4-44.0) and 65.5% (95% CI 56.0-73.0). In children aged 12-15 years, VE against symptomatic COVID-19 during the Delta period was 65.4% (95% CI 61.5-68.8) at 2-5 weeks after the first dose, with no observed cases at 2-5 weeks after the second dose. The corresponding VE against symptomatic COVID-19 during the Omicron period were 30.2% (95% CI 18.4-40.3) and 81.2% (95% CI 77.7-84.2). The waning of the protective effect against the symptomatic disease began after five weeks post-first and post-second dose.

Interpretation

During the study period, uptake of BNT162b2 in Scotland has covered more than two-thirds of CYP aged 12-17 years with the first dose and about 40% with the second dose. We found no increased likelihood of admission to hospital with a range of health outcomes in the period after vaccination. Vaccination with both doses was associated with a substantial reduction in the risk of COVID-19 symptomatic disease during both the Delta and Omicron periods, but this protection began to wane after five weeks.

Funding

UK Research and Innovation (Medical Research Council); Research and Innovation Industrial Strategy Challenge Fund; Chief Scientist's Office of the Scottish Government; Health Data Research UK; National Core Studies - Data and Connectivity.

Uptake, effectiveness and safety of COVID-19 vaccines in children and young people in Scotland: Protocol for early pandemic evaluation and enhanced surveillance of COVID-19 (EAVE II)

BACKGROUND

The dynamics of acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission and severity of disease among children and young people (CYP) across different settings are of considerable clinical, public health and societal interest. Severe COVID-19 cases, requiring hospitalisations, and deaths have been reported in some CYP suggesting a need to extend vaccinations to these age groups. As part of the ongoing Early Pandemic Evaluation and Enhanced Surveillance of COVID-19 (EAVE II) study, we aim to investigate the uptake, effectiveness and safety of COVID-19 vaccines in children and young people (CYP) aged 0 to 17 years in Scotland. Specifically, we will estimate: (i) uptake of vaccines against COVID-19, (ii) vaccine effectiveness (VE) against the outcomes of symptomatic SARS-CoV-2 infection, hospitalisation, intensive care unit (ICU) admissions, and death; (iii) VE for first/second dose timing among different age groups and risk groups; and (iv) the safety of vaccines.

METHODS AND ANALYSIS

We will conduct an open prospective cohort study classifying exposure as time-varying. We will compare outcomes amongst first dose vaccinated and second dose vaccinated CYP to those not yet vaccinated. A Test Negative Design (TND) case control study will be nested within this national cohort to investigate VE against symptomatic infection. The primary outcomes will be (i) uptake of vaccines against COVID-19, (ii) time to COVID-19 infection, hospitalisation, ICU admissions or death, and (iii) adverse events related to vaccines. Vaccination status (unvaccinated, one dose and two doses) will be defined as a time-varying exposure. Data from multiple sources will be linked using a unique identifier. We will conduct descriptive analyses to explore trends in vaccine uptake, and association between different exposure variables and vaccine uptake will be determined using multivariable logistic regression models. VE will be assessed from time-dependent Cox models or Poisson regression models, adjusted for relevant confounders, including age, sex, socioeconomic status, and comorbidities. We will employ self-controlled study designs to determine the risk of adverse events following COVID-19 vaccination.

ETHICS AND DISSEMINATION

Ethics approval was obtained from the National Research Ethics Committee, South East Scotland 02. We will present findings of this study at international conferences, in peer-reviewed journals and to policy-makers.

Transcriptomic and genomic variants between koala populations reveals underlying genetic components to disorders in a bottlenecked population

Historical hunting pressures on koalas in the southern part of their range in Australia have led to a marked genetic bottleneck when compared with their northern counterparts. There are a range of suspected genetic disorders such as testicular abnormalities, oxalate nephrosis and microcephaly reported at higher prevalence in these genetically restricted southern animals. This paper reports analysis of differential expression of genes from RNAseq of lymph nodes, SNPs present in genes and the fixation index (population differentiation due to genetic structure) of these SNPs from two populations, one in south east Queensland, representative of the northern genotype and one in the Mount Lofty Ranges South Australia, representative of the southern genotype. SNPs that differ between these two populations were significantly enriched in genes associated with brain diseases. Genes which were differentially expressed between the two populations included many associated with brain development or disease, and in addition a number associated with testicular development, including the androgen receptor. Finally, one of the 8 genes both differentially expressed and with a statistical difference in SNP frequency between populations was SLC26A6 (solute carrier family 26 member 6), an anion transporter that was upregulated in SA koalas and is associated with oxalate transport and calcium oxalate uroliths in humans. Together the differences in SNPs and gene expression described in this paper suggest an underlying genetic basis for several disorders commonly seen in southern Australian koalas, supporting the need for further research into the genetic basis of these conditions, and highlighting that genetic selection in managed populations may need to be considered in the future.

Hypertrophic osteopathy in South Australian koalas (Phascolarctos cinereus) with concurrent pulmonary actinomycosis

Pulmonary actinomycosis is described in 17 South Australian koalas necropsied between 2016 and 2019. From these cases, four koalas had secondary hypertrophic osteopathy. Plain radiographical and computed tomography images demonstrated periosteal reaction on multiple appendicular skeletal bones in all cases, including scapula, humerus, ulna, radius, ilium, femur, tibia, fibula, metacarpus, metatarsus and phalanx. Grossly, periosteal surfaces of the metaphyses and diaphyses of long bones were thickened and roughened; microscopically, this was characterised by bi-layered proliferation of well-differentiated trabecular bony spicules oriented perpendicular to the cortex (pseudocortices) and separated by vascular connective tissue, typical for hypertrophic osteopathy. Well characterised in domestic species and rarely reported in marsupials, this is the first radiographical and pathological characterisation of hypertrophic osteopathy in koalas, associated with pulmonary actinomycosis in all cases.

Symmetric dimethylarginine values in koalas (Phascolarctos cinereus) based on oxalate nephrosis status

Oxalate nephrosis is a prevalent renal disease in koalas (Phascolarctos cinereus) of the Mount Lofty Ranges population in South Australia. The symmetric dimethylarginine (SDMA) assay is widely used in companion animals to diagnose renal disease, particularly in the early stages. This study aimed to determine: (1) reference intervals for SDMA in koalas and (2) SDMA values of koalas with oxalate nephrosis. Blood samples were collected from 41 Mount Lofty Ranges koalas euthanased on welfare grounds. Koalas were necropsied and, based on renal histopathology, were classified as unaffected (n = 22) or affected (n = 19) by oxalate nephrosis. Serum or plasma samples were analysed for creatinine, urea and SDMA and urine samples for urine specific gravity (USG). The reference interval for SDMA in unaffected koalas was 2.4-22.9 μg/dL. In koalas with oxalate nephrosis, SDMA was elevated in 74% of cases above the upper limit of the confidence interval. SDMA was elevated in three affected koalas with normal creatinine values. A positive correlation was found between SDMA and creatinine (R = 0.775, P < 0.001) and SDMA and urea (R = 0.580, P < 0.001) and a negative correlation between SDMA and USG (R = -0.495, P = 0.027). In conclusion, SDMA correlates well with other commonly used tests of renal function in koalas and should be included as part of the standard diagnostic process to increase the accuracy of oxalate nephrosis diagnosis in koalas.

Pathological Findings in Koala Retrovirus-positive Koalas (Phascolarctos cinereus) from Northern and Southern Australia

Koala retrovirus (KoRV) infection shows differences in prevalence and load between northern and southern Australian koala populations; however, the effect of this on diseases such as lymphoma and chlamydial disease is unclear. This study compared clinicopathological findings, haematology and splenic lymphoid area of KoRV-positive koalas from northern (Queensland [Qld], n = 67) and southern (South Australia [SA], n = 92) populations in order to provide further insight into KoRV pathogenesis. Blood was collected for routine haematology and for measurement of KoRV proviral load by quantitative polymerase chain reaction (qPCR). Plasma samples were assessed for KoRV viral load by reverse transcriptase qPCR and conjunctival and cloacal swabs were collected for measurement of the load of Chlamydia pecorum (qPCR). During necropsy examination, spleen was collected for lymphoid area analysis. Lymphoma was morphologically similar between the populations and occurred in koalas with the highest KoRV proviral and viral loads. Severe ocular chlamydial disease was observed in both populations, but urinary tract disease was more severe in Qld, despite similar C. pecorum loads. No associations between KoRV and chlamydial disease severity or load were observed, except in SA where viral load correlated positively with chlamydial disease severity. In both populations, proviral and viral loads correlated positively with lymphocyte and metarubricyte counts and correlated negatively with erythrocyte and neutrophil counts. Splenic lymphoid area was correlated positively with viral load. This study has shown further evidence for KoRV-induced oncogenesis and highlighted that lymphocytes and splenic lymphoid tissue may be key sites for KoRV replication. However, KoRV infection appears to be highly complex and continued investigation is required to fully understand its pathogenesis.

Haematological reference intervals of wild southern Australian koalas (Phascolarctos cinereus)

OBJECTIVE

Current haematology reference intervals (RIs) for koalas were developed in northern Australian koalas, using low numbers and/or individuals of unknown Chlamydia pecorum and koala retrovirus (KoRV) status. This study developed haematological RIs for wild, clinically healthy southern Australian koalas of known C. pecorum and KoRV infection status and investigated the effects of population, age and sex.

METHODS

Haematological RIs were determined for 138 clinically healthy South Australian koalas (Mount Lofty Ranges [MLR], n = 68; Kangaroo Island, n = 70) examined in April 2016 and February 2017, respectively. C. pecorum and KoRV status were determined by PCR.

RESULTS

RIs for southern koala haematological parameters were established for all koalas based on the finding that there were limited differences in haematological values in koalas with subclinical C. pecorum or KoRV infections (P > 0.05), except KoRV-infected koalas had a lower haematocrit than noninfected koalas. MLR koalas had significantly lower erythrocyte mass and leucocyte counts than Kangaroo Island koalas. Young koalas had significantly lower haemoglobin, haematocrit and higher mean cellular haemoglobin concentration and lymphocyte counts than adult koalas. MLR male koalas had elevated erythrocyte, leucocyte and neutrophil counts compared with MLR females.

CONCLUSION

The haematological RIs developed in this study are based on a large number of clinically healthy koalas, where subclinical C. pecorum and KoRV infections had no effect on haematological values and will be a valuable tool during clinical examination and disease investigation by veterinarians and researchers Australia-wide.

Necropsy findings of koalas from the Mount Lofty Ranges population in South Australia

OBJECTIVE

This study reports necropsy findings of koalas from the Mount Lofty Ranges region in order to identify health threats to this mainland South Australian population.

METHODS

Koalas from the Mount Lofty Ranges region (n = 85) that had died or been euthanased on welfare grounds were examined at necropsy during 2012-13 at the School of Animal and Veterinary Sciences, University of Adelaide. Disease findings, approximate age, sex and body condition of koalas were recorded. Histopathological examination was undertaken on gross lesions and in suspect cases, skin scrapings taken for microscopy and PCR performed for Chlamydia pecorum detection.

RESULTS

Traumatic injury was the most common necropsy finding (48/85; 57%), caused by motor vehicle accidents (35/48; 73%), canine attacks (11/48; 23%) or bushfire burns (2/48; 4%). Oxalate nephrosis (27/85; 32%) was also more common than other conditions. Infectious diseases included chlamydiosis (10/85; 12%) and sarcoptic mange (7/85; 8%). Marked testis asymmetry was evident in 11% (6/56) of males, with histopathology suggestive of atrophic change in four animals. Other pathological conditions included gastrointestinal disease (7/85; 8%) and respiratory disease (3/85; 4%). Almost half of the koalas (38/85; 45%) were found to have two or more abnormalities at necropsy.

CONCLUSION

This study found trauma, mainly from motor vehicle accidents, and oxalate nephrosis to be the predominant causes of death and/or disease in koalas from the Mount Lofty Ranges region. Recent emergence of both clinical chlamydiosis and sarcoptic mange has also occurred, providing insight into the health status and causes of disease or injury in this South Australian mainland koala population.

Towards automated cancer screening: Label-free classification of fixed cell samples using wavelength modulated Raman spectroscopy

The ability to provide quantitative, objective and automated pathological analysis would provide enormous benefits for national cancer screening programmes, in terms of both resource reduction and improved patient wellbeing. The move towards molecular pathology through spectroscopic methods shows great promise, but has been restricted by spectral quality, acquisition times and lack of direct clinical application. In this paper, we present the application of wavelength modulated Raman spectroscopy for the automated label- and fluorescence-free classification of fixed squamous epithelial cells in suspension, such as those produced during a cervical smear test. Direct comparison with standard Raman spectroscopy shows marked improvement of sensitivity and specificity when considering both human papillomavirus (sensitivity +12.0%, specificity +5.3%) and transformation status (sensitivity +10.3%, specificity +11.1%). Studies on the impact of intracellular sampling location and storage effects suggest that wavelength modulated Raman spectroscopy is sufficiently robust to be used in fixed cell classification, but requires further investigations of potential sources of molecular variation in order to improve current clinical tools.

Identification of stable reference genes for quantitative PCR in koalas

To better understand host and immune response to diseases, gene expression studies require identification of reference genes with stable expression for accurate normalisation. This study describes the identification and testing of reference genes with stable expression profiles in koala lymph node tissues across two genetically distinct koala populations. From the 25 most stable genes identified in transcriptome analysis, 11 genes were selected for verification using reverse transcription quantitative PCR, in addition to the commonly used ACTB and GAPDH genes. The expression data were analysed using stable genes statistical software - geNorm, BestKeeper, NormFinder, the comparative ΔCt method and RefFinder. All 13 genes showed relative stability in expression in koala lymph node tissues, however Tmem97 and Hmg20a were identified as the most stable genes across the two koala populations.

Morbillivirus-associated unusual mortality event in South Australian bottlenose dolphins is largest reported for the Southern Hemisphere

Cases of morbillivirus have been recorded in the Southern Hemisphere but have not been linked to significant marine mammal mortality. Post-mortems were conducted on 58 carcasses (44 Indo-Pacific bottlenose dolphins, two common bottlenose dolphins, 12 short-beaked common dolphins) from South Australia during 2005-2013, including an unusual mortality event (UME) in St Vincent Gulf Bioregion (SVG) during 2013. Diagnostic pathology, circumstance of death, body condition, age and stomach contents were documented for Indo-Pacific bottlenose dolphins. At least 50 dolphins died during the UME, 41 were Indo-Pacific bottlenose dolphins and most were young. The UME lasted about seven months and had two peaks, the first being the largest. Effect on the population is unknown. Diagnostic testing for morbillivirus was conducted on 57 carcasses, with evidence for infection in all species during 2011-2013. All tested UME bottlenose dolphins were positive for cetacean morbillivirus (CeMV), and the pathology included interstitial pneumonia, lymphoid depletion and syncytia. Concurrent pathologies, including lung parasite and fungal infections, and severe cutaneous bruising were observed in many dolphins. The event coincided with elevated water temperatures, a diatom bloom and significant fish die-offs. We conclude that the cause for the UME was multifactorial and that CeMV was a major contributor.

Pathological findings in wild harvested dugongs Dugong dugon of central Torres Strait, Australia

The dugong Dugong dugon is classified as Vulnerable to extinction but may be endangered in some regions. Cause of death in stranded dugongs has not been determined in a large proportion of animals examined, with investigations hindered by limited information on dugong health and diseases, and paucity of knowledge of common or endemic pathological findings. Here we describe pathological findings in harvested dugongs from the relatively pristine area of central Torres Strait, and we characterise lesions attributable to drowning. Other recorded lesions were mild and predominated by host reaction to the presence of trematodes within the gastrointestinal tracts, liver and pancreas. Ascarid worm burdens were low in comparison to dugongs from developed coastlines. Hepatocellular lipofuscin and ferritin pigmentation were commonly observed, more pronounced in livers of older animals and concurrent with periportal and bridging fibrosis. Lesions attributable to drowning included incomplete collapse of lungs, dorsal or diffuse pulmonary congestion, mild intra-alveolar haemorrhage and oedema, mild interstitial oedema and rupture of peripheral alveolar septae with acute myofibre fragmentation and degeneration. No accumulation of foam or aspiration of water or particulate matter was observed, suggesting that dugongs 'dry drown'. Morphometric features of normal spleen are also presented. Characterisation of common pathological findings and those attributable to drowning in this species will aid in the interpretation of post mortem findings for the significant number of dugongs found deceased along urbanised coastlines.

Age-dependent changes in gross and histological morphology of the thyroid gland in South Australian koalas (Phascolarctos cinereus)

Studies characterising the thyroid gland structure of koalas are limited and have not previously been undertaken in South Australian populations. Hence, this study aimed to describe the thyroid gland morphology of koalas from the Mount Lofty region, South Australia. Results showed that thyroid gland morphology was highly variable between individual koalas (n = 36), ranging from that considered typical for healthy mammals, in which small colloid-filled follicles were lined by cuboidal epithelium, to that consistent with colloidal goitre, in which macrofollicles distended with colloid were lined by flattened epithelium. Juvenile koalas more frequently showed typical thyroid gland morphology than adults, with significantly higher thyroid follicle density (P < 0.05) and a higher proportion of follicles lined by cuboidal epithelium compared with flattened epithelium (P < 0.05). Thyroid glands of most adult koalas were characterised by colloidal macrofollicles (P < 0.01), and classified as colloidal goitre. There were no significant differences in thyroid gland morphology based on health status or sex of koalas. These findings suggest that an age-dependent colloidal goitre occurs in adult koalas, which is unlikely to have ill effects and may be associated with the low metabolic rate of this species, or exposure to a dietary goitrogen.

Pathological Features of Oxalate Nephrosis in a Population of Koalas (Phascolarctos cinereus) in South Australia

The wild and captive koala population of the Mt Lofty Ranges in South Australia has a high level of renal dysfunction in which crystals consistent with calcium oxalate have been observed in the kidneys. This study aimed to describe the pathological features of the renal disease in this population, confirm the composition of renal crystals as calcium oxalate, and determine whether any age or sex predispositions exist for this disease. A total of 51 koalas (28 wild rescues, 23 captive) were examined at necropsy, of which 28 (55%) were found to have gross and/or histological evidence of oxalate nephrosis. Histopathological features included intratubular and interstitial inflammation, tubule dilation, glomerular atrophy, tubule loss, and cortical fibrosis. Calcium oxalate crystals were demonstrated using a combination of polarization microscopy, alizarin red S staining, infrared spectroscopy, and energy-dispersive X-ray analysis with scanning electron microscopy. Uric acid and phosphate deposits were also shown to be present but were associated with minimal histopathological changes. No significant differences were found between the numbers of affected captive and wild rescued koalas; also, there were no sex or age predispositions identified, but it was found that oxalate nephrosis may affect koalas <2 years of age. The findings of this study suggest that oxalate nephrosis is a leading disease in this koala population. Possible causes of this disease are currently under investigation.

Ventricular and Extraventricular Ependymal Tumors in 18 Cats

Ependymal tumors are reported rarely in domestic animals. The aims of this study were to examine the clinical and pathologic features of ventricular and extraventricular ependymomas and subependymomas in 18 domestic cats examined between 1978 and 2011. Parameters examined included age, sex, breed, clinical signs, and macroscopic and histopathologic features. The mean age of affected cats was 9 years, 4 months; median age, 8.5 years. There were 8 female and 4 male cats, and 6 cats for which sex was not recorded. Breeds included 10 domestic shorthaired, 2 domestic longhaired, 1 Persian, and 1 Siamese. Clinical signs included altered mentation or behavior, seizures, circling, propulsive gait, generalized discomfort, and loss of condition. The tumors often formed intraventricular masses and usually arose from the lining of the lateral or third ventricles, followed by the fourth ventricle, mesencephalic aqueduct, and spinal cord central canal. Three tumors were extraventricular, forming masses within the cerebrum and adjacent subarachnoid space. Histologically, 15 tumors were classified as variants of ependymomas (classic, papillary, tanycytic, or clear cell) and 3 as subependymomas. Tumors were generally well demarcated; however, 6 ependymomas focally or extensively infiltrated the adjacent neural parenchyma. Characteristic perivascular pseudorosettes were observed in all ependymomas; true rosettes were less common. Some tumors had areas of necrosis, mineralization, cholesterol clefts, and/or hemorrhage. This cohort study of feline ependymal tumors includes subependymoma and primary extraventricular ependymoma, variants not previously described in the veterinary literature but well recognized in humans.

Fatal aortic oesophageal fistula following oesophageal foreign body removal in a dog

An eight-month-old male Pomeranian was presented with hypovolaemic shock 7 days after successful oesophageal foreign body removal. On presentation the dog was anaemic and no coagulation abnormalities were detected. A fluid-filled oesophagus was visible on thoracic radiography and frank blood was aspirated from the oesophagus following oro-oesophageal intubation. Fluid resuscitation and blood transfusions were administered but attempts at stabilisation were unsuccessful and the dog died. At post-mortem examination, a 2-mm aortic oesophageal fistula was identified on the ventral aspect of the aorta at the level of heart base that communicated with the overlying oesophagus. Aortic oesophageal fistula has been reported in human medicine and occurs secondary to a number of conditions including oesophageal foreign bodies. These prove fatal without rapid stabilisation and surgery.

Pleuropulmonary blastoma in an equine fetus

Pleuropulmonary blastoma (PPB) is a rare biphasic tumor of children formed by mixed epithelial-and-mesenchymal elements. In this article, the authors report a pulmonary mass in an equine fetus with characteristics of PPB. A soft multicystic broad-based pleural mass was identified in the right caudal lung lobe. The mass comprised solid areas of loose mesenchyme, fenestrated by small ducts or large cystic areas lined by cuboidal epithelium. Mesenchymal elements had moderate anisocytosis, anisokaryosis, and cellular pleomorphism and were immunoreactive for vimentin. Epithelial cells lining ducts and cystic lumina were nonciliated and cuboidal with central round nuclei, minimal cellular pleomorphism, and strong immunoreactivity for cytokeratin. Pertinent characteristics in common with human PPB were the pleural-based location, the dual solid or delicate multiloculated cystic structure, the primitive mesenchymatous stroma fenestrated by well-differentiated cuboidal epithelial-lined lumina, and the occurrence during gestation.

Cutaneous papillomatosis and carcinomatosis in the Western barred bandicoot (Perameles bougainville)

A progressive wart-like syndrome in both captive and wild populations of the Western barred bandicoot (WBB) is hindering conservation efforts to prevent the extinction of this endangered marsupial. In this study, 42 WBBs exhibiting the papillomatosis and carcinomatosis syndrome were examined. The disease was characterized by multicentric proliferative lesions involving cutaneous and mucosal surfaces, which were seen clinically to increase in size with time. Grossly and histologically the smaller skin lesions resembled papillomas, whereas the larger lesions were most commonly observed to be squamous cell carcinomas. Large amphophilic intranuclear inclusion bodies were observed in hyperplastic conjunctival lesions of 8 WBBs under light microscopy. Conjunctival lesions from 2 WBBs examined using transmission electron microscopy contained a crystalline array of spherical electron-dense particles of 45-nm diameter, within the nucleus of conjunctival epithelial cells, consistent with a papillomavirus or polyomavirus. Conjunctival samples from 3 bandicoots that contained intranuclear inclusion bodies also demonstrated a positive immunohistochemical reaction after indirect immunohistochemistry for papillomavirus structural antigens. Ultrastructural and/or immunohistochemical evidence of an etiologic agent was not identified in the nonconjunctival lesions examined. Here we describe the gross, histopathologic, ultrastructural, and immunohistochemical findings of a papillomatosis and carcinomatosis syndrome recently identified in the WBB.

Klossiella quimrensis (Apicomplexa: Klossiellidae) causes renal coccidiosis in western barred bandicoots Perameles bougainville (Marsupialia: Peramelidae) in Western Australia

Previous studies have described a range of Klossiella species parasitic in marsupial hosts. Klossiella quimrensis is the etiologic agent of renal coccidiosis in the peramelid marsupial hosts Isoodon obesulus and Perameles gunnii in Eastern Australia, but there is no previous report of klossiellosis in Western Australian peramelids. This study describes klossiellosis diagnosed by histology of renal tissue sections collected during necropsy of 20 Perameles bougainville between 2000 and 2005. Sporonts, sporoblasts, and macrogametes were identified within parasitophorous vacuoles of epithelial cells located near the renal corticomedullary junction. The prevalence of renal coccidiosis in P. bougainville diagnosed by renal histology is estimated at 30%. Only a single unsporulated sporocyst was detected by examination of cystocentesis-collected urine, indicating that microscopic evaluation of urine samples is an insensitive diagnostic test for detection of K. quimrensis in P. bougainville. This infection in P. bougainville is indirectly associated with mild multifocal interstitial lymphohistiocytic nephritis and is likely to be only minimally pathogenic in otherwise healthy individuals. Our study also extends the host and geographic range of K. quimrensis to include P. bougainville and Western Australia.

A new eimeria species parasitic in western barred bandicoots, Perameles bougainville (Marsupialia: Peramelidae), in western Australia

Feces from western barred bandicoots, Perameles bougainville, examined during routine monitoring of captive breeding colonies and wild populations were frequently found to contain oocysts. Fecal oocysts from 1 individual housed at Kanyana Wildlife Rehabilitation Centre were allowed to sporulate in 2% potassium dichromate (K2Cr2O7) at room temperature. Sporulated oocysts are subspheroidal 18.8 X 17.9 (16.9-21.0 x 16.0-19.9) microm, with length/width (L/W) ratio of 1.05 (1.00-1.15), lack a micropyle and oocyst residuum, but they usually have a polar granule within a smooth trilaminate oocyst wall 1.0 (0.7-1.3) microm thick. Sporocysts are ovoid, 9.1 x 7.0 (8.1-10.8 x 6.1-8.6) microm, with L/W ratio of 1.32 (1.04-1.51), have a Stieda body, sporocyst residuum, and 2 comma-shaped sporozoites, each containing 2 spheroidal refractile bodies. Sporulation takes 2-5 days at room temperature. This is the first formal description of an Eimeria species parasitic in the order Peramelemorphia.