The replication-competent HIV reservoir is a genetically restricted, younger subset of the overall pool of HIV proviruses persisting during therapy, which is highly genetically stable over time

Within-host HIV populations continually diversify during untreated infection, and this diversity persists within infected cell reservoirs during antiretroviral therapy (ART). Achieving a better understanding of on-ART proviral evolutionary dynamics, and a better appreciation of how the overall persisting pool of (largely genetically defective) proviruses differs from the much smaller replication-competent HIV reservoir, is critical to HIV cure efforts. We reconstructed within-host HIV evolutionary histories in blood from seven participants of the Women's Interagency HIV Study who experienced HIV seroconversion, and used these data to characterize the diversity, lineage origins, and ages of proviral env-gp120 sequences sampled longitudinally up to 12 years on ART. We also studied HIV sequences emerging from the reservoir in two participants. We observed that proviral clonality generally increased over time on ART, with clones frequently persisting long term. While on-ART proviral integration dates generally spanned the duration of untreated infection, HIV emerging in plasma was exclusively younger (i.e., dated to the years immediately pre-ART). The genetic and age distributions of distinct proviral sequences remained stable during ART in all but one participant, in whom there was evidence that younger proviruses had been preferentially eliminated after 12 years on ART. Analysis of the gag region in three participants corroborated our env-gp120-based observations, indicating that our observations are not influenced by the HIV region studied. Our results underscore the remarkable genetic stability of the distinct proviral sequences that persist in blood during ART. Our results also suggest that the replication-competent HIV reservoir is a genetically restricted, younger subset of this overall proviral pool.IMPORTANCECharacterizing the genetically diverse HIV sequences that persist in the reservoir despite antiretroviral therapy (ART) is critical to cure efforts. Our observations confirm that proviruses persisting in blood on ART, which are largely genetically defective, broadly reflect the extent of within-host HIV evolution pre-ART. Moreover, on-ART clonal expansion is not appreciably accompanied by the loss of distinct proviral lineages. In fact, on-ART proviral genetic composition remained stable in all but one participant, in whom, after 12 years on ART, proviruses dating to around near ART initiation had been preferentially eliminated. We also identified recombinant proviruses between parental sequence fragments of different ages. Though rare, such sequences suggest that reservoir cells can be superinfected with HIV from another infection era. Overall, our finding that the replication-competent reservoir in blood is a genetically restricted, younger subset of all persisting proviruses suggests that HIV cure strategies will need to eliminate a reservoir that differs in key respects from the overall proviral pool.

"Community 101 for researchers": an online training program to build capacity for ethical community-engaged research with Native Hawaiians and Pacific Islanders

To address the history of unethical research and community distrust in research among Native Hawaiian and Pacific Islander communities, we developed the "Community 101 for Researchers" training program, which was launched in 2014 to enhance the capacity of researchers to engage in ethical community-engaged research. The purpose of this paper is to describe the development of this training program as well as its reach and feedback from participants. The Community 101 training program is a self-paced, 2-h online training program featuring community-engaged researchers from the University of Hawai'i and their longstanding community partners. Throughout the five modules, we highlight the historical context of Native Hawaiians and Pacific Islander populations in Hawai'i related to research ethics and use examples from the community as well as our own research projects that integrate community ethics, relevance, benefits, and input. To determine reach and gather participant feedback on the training, we extracted data from the user accounts. The training has been completed by 697 users to-date since its launch. Despite very little advertisement, an average of nearly 70 users have completed the Community 101 Program each year. The majority of the participants were located in Hawai'i though participants were also from other states and territories in the US, and international locations. The majority of participants were from universities in Hawai'i in 51 different departments demonstrating multidisciplinary relevance of the program's training. The general feedback from the 96 participants who completed an optional anonymous evaluation survey given at the end of the training was positive. The "Community 101 for Researchers" Training program is an accessible and relevant tool that can be used to advance ethical community engaged research, specifically with Native Hawaiian and Pacific Islander communities.

HIV reservoirs are dominated by genetically younger and clonally enriched proviruses

IMPORTANCE

Characterizing the human immunodeficiency virus (HIV) reservoir that endures despite antiretroviral therapy (ART) is critical to cure efforts. We observed that the oldest proviruses persisting during ART were exclusively defective, while intact proviruses (and rebound HIV) dated to nearer ART initiation. This helps explain why studies that sampled sub-genomic proviruses on-ART (which are largely defective) routinely found sequences dating to early infection, whereas those that sampled replication-competent HIV found almost none. Together with our findings that intact proviruses were more likely to be clonal, and that on-ART low-level/isolated viremia originated from proviruses of varying ages (including possibly defective ones), our observations indicate that (i) on-ART and rebound viremia can have distinct within-host origins, (ii) intact proviruses have shorter lifespans than grossly defective ones and thus depend more heavily on clonal expansion for persistence, and (iii) an HIV reservoir predominantly "dating" to near ART initiation will be substantially adapted to within-host pressures, complicating immune-based cure strategies.

The replication-competent HIV reservoir is a genetically restricted, younger subset of the overall pool of HIV proviruses persisting during therapy, which is highly genetically stable over time

Within-host HIV populations continually diversify during untreated infection, and members of these diverse forms persist within infected cell reservoirs, even during antiretroviral therapy (ART). Characterizing the diverse viral sequences that persist during ART is critical to HIV cure efforts, but our knowledge of on-ART proviral evolutionary dynamics remains incomplete, as does our understanding of the differences between the overall pool of persisting proviral DNA (which is largely genetically defective) and the subset of intact HIV sequences capable of reactivating. Here, we reconstructed within-host HIV evolutionary histories in blood from seven participants of the Women's Interagency HIV Study (WIHS) who experienced HIV seroconversion. We measured diversity, lineage origins and ages of proviral sequences (env-gp120) sampled up to four times, up to 12 years on ART. We used the same techniques to study HIV sequences emerging from the reservoir in two participants. Proviral clonality generally increased over time on ART, with clones frequently persisting across multiple time points. The integration dates of proviruses persisting on ART generally spanned the duration of untreated infection (though were often skewed towards years immediately pre-ART), while in contrast, reservoir-origin viremia emerging in plasma was exclusively "younger" (i.e., dated to the years immediately pre-ART). The genetic and age distributions of distinct proviral sequences remained highly stable during ART in all but one participant in whom, after 12 years, there was evidence that "younger" proviruses had been preferentially eliminated. Analysis of within-host recombinant proviral sequences also suggested that HIV reservoirs can be superinfected with virus reactivated from an older era, yielding infectious viral progeny with mosaic genomes of sequences with different ages. Overall, results underscore the remarkable genetic stability of distinct proviral sequences that persist on ART, yet suggest that replication-competent HIV reservoir represents a genetically-restricted and overall "younger" subset of the overall persisting proviral pool in blood.

Inferring Human Immunodeficiency Virus 1 Proviral Integration Dates With Bayesian Inference

Human immunodeficiency virus 1 (HIV) proviruses archived in the persistent reservoir currently pose the greatest obstacle to HIV cure due to their evasion of combined antiretroviral therapy and ability to reseed HIV infection. Understanding the dynamics of the HIV persistent reservoir is imperative for discovering a durable HIV cure. Here, we explore Bayesian methods using the software BEAST2 to estimate HIV proviral integration dates. We started with within-host longitudinal HIV sequences collected prior to therapy, along with sequences collected from the persistent reservoir during suppressive therapy. We built a BEAST2 model to estimate integration dates of proviral sequences collected during suppressive therapy, implementing a tip date random walker to adjust the sequence tip dates and a latency-specific prior to inform the dates. To validate our method, we implemented it on both simulated and empirical data sets. Consistent with previous studies, we found that proviral integration dates were spread throughout active infection. Path sampling to select an alternative prior for date estimation in place of the latency-specific prior produced unrealistic results in one empirical data set, whereas on another data set, the latency-specific prior was selected as best fitting. Our Bayesian method outperforms current date estimation techniques with a root mean squared error of 0.89 years on simulated data relative to 1.23-1.89 years with previously developed methods. Bayesian methods offer an adaptable framework for inferring proviral integration dates.

HIV reservoirs are dominated by genetically younger and clonally enriched proviruses

In order to cure HIV, we need to better understand the within-host evolutionary origins of the small reservoir of genome-intact proviruses that persists within infected cells during antiretroviral therapy (ART). Most prior studies on reservoir evolutionary dynamics however did not discriminate genome-intact proviruses from the vast background of defective ones. We reconstructed within-host pre-ART HIV evolutionary histories in six individuals and leveraged this information to infer the ages of intact and defective proviruses sampled after an average >9 years on ART, along with the ages of rebound and low-level/isolated viremia occurring during this time. We observed that the longest-lived proviruses persisting on ART were exclusively defective, usually due to large deletions. In contrast, intact proviruses and rebound HIV exclusively dated to the years immediately preceding ART. These observations are consistent with genome-intact proviruses having shorter lifespans, likely due to the cumulative risk of elimination following viral reactivation and protein production. Consistent with this, intact proviruses (and those with packaging signal defects) were three times more likely to be genetically identical compared to other proviral types, highlighting clonal expansion as particularly important in ensuring their survival. By contrast, low-level/isolated viremia sequences were genetically heterogeneous and sometimes ancestral, where viremia may have originated from defective proviruses. Results reveal that the HIV reservoir is dominated by clonally-enriched and genetically younger sequences that date to the untreated infection period when viral populations had been under within-host selection pressures for the longest duration. Knowledge of these qualities may help focus strategies for reservoir elimination.

Proviral Turnover During Untreated HIV Infection Is Dynamic and Variable Between Hosts, Impacting Reservoir Composition on ART

Human immunodeficiency virus (HIV) can persist as an integrated provirus, in a transcriptionally repressed state, within infected cells. This small yet enduring pool of cellular reservoirs that harbor replication-competent HIV is the main barrier to cure. Entry of viral sequences into cellular reservoirs begins shortly after infection, and cells containing integrated proviral DNA are extremely stable once suppressive antiretroviral therapy (ART) is initiated. During untreated HIV infection however, reservoir turnover is likely to be more dynamic. Understanding these dynamics is important because the longevity of the persisting proviral pool during untreated infection dictates reservoir composition at ART initiation. If the persisting proviral pool turns over slowly pre-ART, then HIV sequences seeded into it during early infection would have a high likelihood of persisting for long periods. However, if pre-ART turnover was rapid, the persisting proviral pool would rapidly shift toward recently circulating HIV sequences. One-way to estimate this turnover rate is from the age distributions of proviruses sampled shortly after therapy initiation: this is because, at the time of sampling, the majority of proviral turnover would have already occurred prior to ART. Recently, methods to estimate a provirus’ age from its sequence have made this possible. Using data from 12 individuals with HIV subtype C for whom proviral ages had been determined phylogenetically, we estimated that the average proviral half-life during untreated infection was 0.78 (range 0.45–2.38) years, which is >15 times faster than that of proviral DNA during suppressive ART. We further show that proviral turnover during untreated infection correlates with both viral setpoint and rate of CD4+ T-cell decline during this period. Overall, our results support dynamic proviral turnover pre-ART in most individuals, which helps explain why many individuals’ reservoirs are skewed toward younger HIV sequences. Broadly, our findings are consistent with the notion that active viral replication creates an environment less favorable to proviral persistence, while viral suppression creates conditions more favorable to persistence, where ART stabilizes the proviral pool by dramatically slowing its rate of decay. Strategies to inhibit this stabilizing effect and/or to enhance reservoir turnover during ART could represent additional strategies to reduce the HIV reservoir.

Animal medical genetics: a historical perspective on more than 50 years of research into genetic disorders of animals at Massey University

Over the last 50 years, there have been major advances in knowledge and technology regarding genetic diseases, and the subsequent ability to control them in a cost-effective manner. This review traces these advances through research into genetic diseases of animals at Massey University (Palmerston North, NZ), and briefly discusses the disorders investigated during that time, with additional detail for disorders of major importance such as bovine α-mannosidosis, ovine ceroid-lipofuscinosis, canine mucopolysaccharidosis IIIA and feline hyperchylomicronaemia. The overall research has made a significant contribution to veterinary medicine, has provided new biological knowledge and advanced our understanding of similar disorders in human patients, including testing various specific therapies prior to human clinical trials.

Simulating within host human immunodeficiency virus 1 genome evolution in the persistent reservoir

The complexities of viral evolution can be difficult to elucidate. Software simulating viral evolution provides powerful tools for exploring hypotheses of viral systems, especially in situations where thorough empirical data are difficult to obtain or parameters of interest are difficult to measure. Human immunodeficiency virus 1 (HIV-1) infection has no durable cure; this is primarily due to the virus’ ability to integrate into the genome of host cells, where it can remain in a transcriptionally latent state. An effective cure strategy must eliminate every copy of HIV-1 in this ‘persistent reservoir’ because proviruses can reactivate, even decades later, to resume an active infection. However, many features of the persistent reservoir remain unclear, including the temporal dynamics of HIV-1 integration frequency and the longevity of the resulting reservoir. Thus, sophisticated analyses are required to measure these features and determine their temporal dynamics. Here, we present software that is an extension of SANTA-SIM to include multiple compartments of viral populations. We used the resulting software to create a model of HIV-1 within host evolution that incorporates the persistent HIV-1 reservoir. This model is composed of two compartments, an active compartment and a latent compartment. With this model, we compared five different date estimation methods (Closest Sequence, Clade, Linear Regression, Least Squares, and Maximum Likelihood) to recover the integration dates of genomes in our model’s HIV-1 reservoir. We found that the Least Squares method performed the best with the highest concordance (0.80) between real and estimated dates and the lowest absolute error (all pairwise t tests: P < 0.01). Our software is a useful tool for validating bioinformatics software and understanding the dynamics of the persistent HIV-1 reservoir.

Treeio: An R Package for Phylogenetic Tree Input and Output with Richly Annotated and Associated Data

Phylogenetic trees and data are often stored in incompatible and inconsistent formats. The outputs of software tools that contain trees with analysis findings are often not compatible with each other, making it hard to integrate the results of different analyses in a comparative study. The treeio package is designed to connect phylogenetic tree input and output. It supports extracting phylogenetic trees as well as the outputs of commonly used analytical software. It can link external data to phylogenies and merge tree data obtained from different sources, enabling analyses of phylogeny-associated data from different disciplines in an evolutionary context. Treeio also supports export of a phylogenetic tree with heterogeneous-associated data to a single tree file, including BEAST compatible NEXUS and jtree formats; these facilitate data sharing as well as file format conversion for downstream analysis. The treeio package is designed to work with the tidytree and ggtree packages. Tree data can be processed using the tidy interface with tidytree and visualized by ggtree. The treeio package is released within the Bioconductor and rOpenSci projects. It is available at https://www.bioconductor.org/packages/treeio/.

HIV-1 variants are archived throughout infection and persist in the reservoir

The HIV-1 reservoir consists of latently infected cells that persist despite antiretroviral therapy (ART). Elucidating the proviral genetic composition of the reservoir, particularly in the context of pre-therapy viral diversity, is therefore important to understanding reservoir formation and the persistence of latently infected cells. Here we investigate reservoir proviral variants from 13 Zambian acutely-infected individuals with additional pre-therapy sampling for a unique comparison to the ART-naïve quasispecies. We identified complete transmitted/founder (TF) viruses from seroconversion plasma samples, and additionally amplified and sequenced HIV-1 from plasma obtained one year post-infection and just prior to ART initiation. While the majority of proviral variants in the reservoir were most closely related to viral variants from the latest pre-therapy time point, we also identified reservoir proviral variants dating to or near the time of infection, and to intermediate time points between infection and treatment initiation. Reservoir proviral variants differing by five or fewer nucleotide changes from the TF virus persisted during treatment in five individuals, including proviral variants that exactly matched the TF in two individuals, one of whom had remained ART-naïve for more than six years. Proviral variants during treatment were significantly less divergent from the TF virus than plasma variants present at the last ART-naïve time point. These findings indicate that reservoir proviral variants are archived throughout infection, recapitulating much of the viral diversity that arises throughout untreated HIV-1 infection, and strategies to target and reduce the reservoir must therefore permit for the clearance of proviruses encompassing this extensive diversity.

Despite reducing viremia to levels below the limit of detection in standard assays, effective antiretroviral therapy (ART) does not eradicate cells latently infected with HIV-1. These cells serve as a reservoir for viral rebound if therapy is interrupted; thus, understanding the composition of the reservoir may yield further targets for HIV-1 cure strategies. We have taken a genetic approach to elucidating the reservoir in 13 Zambian subtype C seroconvertors who were followed longitudinally through ART initiation and virologic suppression. In five of the 13 individuals, provirus sequences identical to or differing by five or fewer nucleotides from the transmitted/founder virus were detected, indicating archiving and persistence of early infection variants for more than six years following infection. While the majority of proviral variants in latently infected cells were most closely related to plasma virus circulating immediately prior to treatment initiation, additional variants dating to intermediate time points in the infection were also observed. These findings demonstrate that virus is archived during all stages of ART-naïve infection, and these variants persist throughout ART. HIV-1 cure strategies to eliminate the reservoir must address the broad genetic diversity of a within-host proviral quasispecies including variants archived from acute through chronic infection.

First case of a dog infected with Aspergillus (Phialosimplex) caninus in Australasia

Case history: A 2-year-old Rottweiler dog from Perth (WA, Australia) was referred for assessment of a chronic productive cough and weight loss.Clinical findings: Severely enlarged bilateral superficial cervical lymph nodes and severely enlarged abdominal organs were present. The body condition score was poor and there was moderate muscle wasting. Thoracic and abdominal computed tomography images revealed severe diffuse enlargement of thoracic and abdominal lymph nodes, hepatomegaly and diffuse splenomegaly. A diffuse bronchial pattern with severe multifocal saccular bronchiectasis was identified in the lungs.Diagnostic findings: Fungal organisms were seen within macrophages on cytological preparations and on histopathological sections of biopsies of the superficial cervical lymph node. Macrophages contained intracytoplasmic, non-filamentous round-to-ovoid organisms, which varied in size from 5-30 µm in diameter with variable morphology. Budding was not observed, and no hyphae were present. Fungal culture of lymph node tissue resulted in growth of Aspergillus (Phialosimplex) caninus which was confirmed by amplification and sequencing of a segment of the 16S-23S rRNA internal transcribed spacer. Concurrent bacterial bronchitis was diagnosed on culture of broncho-alveolar fluid.Diagnosis: Disseminated aspergillosis caused by Aspergillus caninus.Clinical relevance: This is believed to be the first report of infection caused by A. caninus in a dog in Australasia. The dog was treated with itraconazole for 7 months and was still alive 7 months after the start of treatment.

Longitudinal within-host evolution of HIV Nef-mediated CD4, HLA and SERINC5 downregulation activity: a case study

The HIV accessory protein Nef downregulates the viral entry receptor CD4, the Human Leukocyte Antigen (HLA)-A and -B molecules, the Serine incorporator 5 (SERINC5) protein and other molecules from the infected cell surface, thereby promoting viral infectivity, replication and immune evasion. The nef locus also represents one of the most genetically variable regions in the HIV genome, and nef sequences undergo substantial evolution within a single individual over the course of infection. Few studies however have simultaneously characterized the impact of within-host nef sequence evolution on Nef protein function over prolonged timescales. Here, we isolated 50 unique Nef clones by single-genome amplification over an 11-year period from the plasma of an individual who was largely naïve to antiretroviral treatment during this time. Together, these clones harbored nonsynonymous substitutions at 13% of nef’s codons. We assessed their ability to downregulate cell-surface CD4, HLA and SERINC5 and observed that all three Nef functions declined modestly over time, where the reductions in CD4 and HLA downregulation (an average of 0.6% and 2.0% per year, respectively) achieved statistical significance. The results from this case study support all three Nef activities as being important to maintain throughout untreated HIV infection, but nevertheless suggest that, despite nef’s mutational plasticity, within-host viral evolution can compromise Nef function, albeit modestly, over prolonged periods.

Tree shape-based approaches for the comparative study of cophylogeny

Cophylogeny is the congruence of phylogenetic relationships between two different groups of organisms due to their long-term interaction. We investigated the use of tree shape distance measures to quantify the degree of cophylogeny. We implemented a reverse-time simulation model of pathogen phylogenies within a fixed host tree, given cospeciation probability, host switching, and pathogen speciation rates. We used this model to evaluate 18 distance measures between host and pathogen trees including two kernel distances that we developed for labeled and unlabeled trees, which use branch lengths and accommodate different size trees. Finally, we used these measures to revisit published cophylogenetic studies, where authors described the observed associations as representing a high or low degree of cophylogeny. Our simulations demonstrated that some measures are more informative than others with respect to specific coevolution parameters especially when these did not assume extreme values. For real datasets, trees' associations projection revealed clustering of high concordance studies suggesting that investigators are describing it in a consistent way. Our results support the hypothesis that measures can be useful for quantifying cophylogeny. This motivates their usage in the field of coevolution and supports the development of simulation-based methods, i.e., approximate Bayesian computation, to estimate the underlying coevolutionary parameters.

The global origins of resistance-associated variants in the non-structural proteins 5A and 5B of the hepatitis C virus

New, costly, fast acting, therapies targeting the non-structural proteins 5A and 5B (NS5A and NS5B) regions of the hepatitis C virus (HCV) genome are curative in the majority of cases. Variants with certain mutations in the NS5A and NS5B regions of HCV have been shown to reduce susceptibility to direct-acting NS5A and NS5B therapy and are found in treatment naïve patients. Despite this, the ease with which these variants evolve is poorly known, as are their evolutionary and geographic origins. To address this crucial gap we inferred the evolutionary and geographic origins of resistance-associated variants (RAVs) in the HCV NS5A and NS5B regions of subtypes 1a, 1b, and 3a sequences available from global databases. We found that RAVs in the NS5A region of HCV, when prevalent, were widely dispersed throughout the phylogenetic tree of HCV with multiple independent origins and that these variants are globally distributed. In contrast, most of the NS5B C316N variants came from one of two clades in the phylogenetic tree of HCV subtype 1b. The presence of serine (S) at codon 218 of HCV NS5B appears to facilitate the evolution of the C316N RAV. Other NS5B RAVs did not arise very frequently in our data set, except for S556G in subtype 1b and with respect to geography NS5B RAVs were also globally distributed. The inferred distribution of RAVs in the NS5A region and frequency of their origin suggest a low fitness barrier without the need for co-evolution of compensatory mutations. A low fitness barrier may allow rapid selection of de novo resistance to NS5A inhibitors during therapy.

node.dating: dating ancestors in phylogenetic trees in R

Summary

Phylogenetic trees encode the evolutionary distances between species or populations. With sufficient information, these evolutionary distances can be rescaled over time to provide estimates of the dates of the most recent ancestors of the species. Here we present the R program node.dating, divergence-time analysis software, which uses a maximum-likelihood method to estimate the dates of the internal nodes of a phylogenetic tree.

Availability and Implementation

node.dating is available as a part of the R v3.30 package ape v4.0 (cran.r-project.org). node.dating is also available in the GitHub repository: https://github.com/brj1/node.dating , along with supplementary software and tests.

Contact

brj1@sfu.ca.

Supplementary information

Supplementary data are available at Bioinformatics online.

Regional variations in percutaneous absorption of methimazole: an in vitro study on cat skin

The use of transdermal gel medications in cats has become popular in veterinary medicine due to the ease of administration compared to oral medication. The research to support systemic absorption of drugs after transdermal gel administration and the preferred skin region to apply these drugs in cats is limited. The aim of this study was to characterize the effect of different skin regions on the percutaneous absorption pharmacokinetics of a commercially available transdermal methimazole after a finite dose was applied to feline skin in vitro. A commercial formulation of methimazole (10 mg) was applied to four skin regions (the inner stratum corneum of the ear, groin, neck, and thorax regions) from six cats. The receptor medium was sampled up to 36 h postapplication, and methimazole concentrations were measured using high-performance liquid chromatography. Methimazole was absorbed more completely across the pinnal skin, compared to the groin, neck, and thorax (P < 0.001), which justifies application to the pinna to maximize efficacy and also to minimize the effects of grooming.

Percutaneous absorption of methimazole: an in vitro study of the absorption pharmacokinetics for two different vehicles

The use of transdermal medications in cats has become popular in veterinary medicine due to the ease of administration compared to oral medication. However, the research to support systemic absorption of drugs applied to the pinna after transdermal administration in cats is limited. The aim of this study was to characterize the percutaneous absorption pharmacokinetics of methimazole in a lipophilic vehicle compared to methimazole in Pluronic(®) lecithin organogel (PLO) using a finite dose applied to feline ear skin in an in vitro Franz cell model. The two formulations of methimazole (10 mg) were applied to the inner stratum corneum of six pairs of feline ears. The receptor medium was sampled up to 30 h post-administration, and methimazole concentrations were measured using high-performance liquid chromatography (HPLC). Histological examination of all ears was undertaken as small differences in the thickness of ear skin may have contributed to inter-individual differences in methimazole absorption between six cats. Methimazole was absorbed more completely across the pinnal skin when administered in the lipophilic vehicle compared to administration in the PLO gel (P < 0.001).

Choanal atresia in a cat

CASE HISTORY

A 5-month-old domestic shorthair kitten with a history of chronic left unilateral nasal discharge was examined.

CLINICAL FINDINGS

Endoscopy and computed tomography (CT) demonstrated a complete membranous obstruction of the left nasal choana, confirming congenital unilateral choanal atresia. In addition, congenital hydrocephalus was detected on CT. Nasopharyngoscopy was performed for confirmation and treatment of choanal atresia.

DIAGNOSIS

Unilateral membranous choanal atresia associated with congenital hydrocephalus.

CLINICAL RELEVANCE

This report describes a rare congenital condition and for the first time, CT imaging provided an accurate diagnosis and allowed planning for the successful treatment of unilateral membranous choanal atresia. In addition, concurrent congenital hydrocephalus was diagnosed.

A serological survey of leptospiral antibodies in dogs in New Zealand

AIM

To investigate the prevalence of titres to four endemic leptospiral serovars in dog sera from the lower half of the North Island, and the South Island of New Zealand submitted to diagnostic laboratories, and to explore the association between the prevalence of seropositive samples to leptospirosis and breed group, age group and sex.

METHODS

Serum samples from 655 dogs residing in the central and lower North Island and from the South Island of New Zealand were sourced from the Massey University Veterinary Teaching Hospital and from submissions to New Zealand Veterinary Pathology in 2005. They were screened by the Microscopic Agglutination Test (MAT) against Leptospira interrogans serovars Copenhageni and Pomona and L. borgpetersenii serovars Hardjo and Ballum. Titres greater or equal to 96 were considered positive. Variables investigated for their association with the prevalence of seropositive samples to leptospirosis included serovar, breed, North vs. South Island, age and sex.

RESULTS

Positive MAT titres to Leptospira interrogans serovar Copenhageni were found in 10.3 % of dogs (95% CI=8.1-12.9), and were more common than positive titres to other leptospiral serovars. Small breeds did not have a lower prevalence of Copenhageni titres than other breeds. Positive titres to Leptospira borgpetersenii serovar Hardjo were associated with breeds of dogs used as farm working dogs. There was no significant difference in the prevalence of positive leptospiral titres between dogs from the North or South Islands. Dogs greater than 12 years of age were less likely to have positive titres to Leptospira than younger dogs. No association was found between positive titres and sex.

CONCLUSIONS

Breeds of dogs used as farm working were at greater risk of exposure to Leptospira borgpetersenii serovar Hardjo. Small breeds did not have a lower risk of seropositivity to Copenhageni than farm working breeds. Further study should be undertaken to confirm the prevalence of positive titres to leptospirosis in farm dogs and dogs resident in the South Island.

CLINICAL RELEVANCE

The risk of dogs being exposed to Leptospira interrogans serovar Copenhageni, and requirement for vaccination against serovar Copenhageni, cannot be determined by geographical location or breed group. Vaccination against Leptospira borgpetersenii serovar Hardjo is likely to be beneficial in working dogs.

Permanent monoparesis in a dog after intramedullary injection of iohexol into the lumbar spinal cord

Abstract

CASE HISTORY

An 8-year-old, spayed, Doberman Pinscher bitch presented for assessment of acute hindlimb paresis.

CLINICAL FINDINGS

During a lumbar myelographic contrast study a small volume of iohexol contrast agent was inadvertently injected into the cord parenchyma. After surgical hemilaminectomy for an intervertebral disc extrusion at L1-2 the dog recovered use of one hindlimb, but had ongoing extensor weakness of the left hindlimb. Left femoral nerve function had not returned after 14 months.

DIAGNOSIS

EMG findings 14 months after the incident indicated persistent femoral neuropathy consistent with the intramedullary contrast injection at L3-4.

CLINICAL RELEVANCE

Inadvertent deposition of iohexol into spinal cord parenchyma may be rare, but if it occurs it can have long-lasting consequences.

A retrospective study of gastric dilatation and gastric dilatation and volvulus in working farm dogs in New Zealand

AIMS

To present findings from a case series of gastric dilatation (GD) or gastric dilatation and volvulus (GDV) in working farm dogs in New Zealand that were examined at veterinary clinics, and to identify possible risk factors for GD or GDV in working farm dogs in New Zealand using a case-control study.

METHODS

This retrospective study included a case-series and a case-control study. The case series analysed information from 62 case records of GD or GDV in working farm dogs seen between August 2004 and September 2009 at 13 veterinary clinics throughout New Zealand. Cases were classified as GD or GDV if the diagnosis was confirmed by radiography, surgery or post-mortem examination. Details of history and treatment, as well as outcomes, were obtained for each case. For the case-control study, records of 41 working farm dogs with GD or GDV (cases) seen between April 2008 and April 2009, and 82 working farm dogs examined because of trauma over the same period and in the same 13 clinics (controls), were used to model the risk factors for GD or GDV.

RESULTS

From the case-series study, 40/62 (65%) cases of GD or GDV that were examined and treated at the veterinary clinics returned to work. Of the 41 dogs where the gastric contents were recorded, 25 (61%) had predominantly food or bones in the stomach, and 26/27 dogs had a history of having eaten meat, bones or scavenged a carcass. The case-control study showed that the significant risk factors for GD or GDV, compared with control dogs presenting with trauma, were breed, age and season. The odds that a case of GD or GDV was a Huntaway, after adjusting for age and season, was 19 times higher than the odds a control was a Huntaway. Gender and bodyweight were not identified as risk factors.

CONCLUSIONS AND CLINICAL RELEVANCE

A high proportion of farm working dogs with GD or GDV were successfully treated by veterinarians. The risk of a case of GD or GDV being a Huntaway was significantly higher than for a dog presenting as a trauma case. However the influences of the season of the year, climatic factors and nutritional factors on the pathogenesis need to be identified before adequate preventative measures can be recommended.

Congenital hypothyroidism of dogs and cats: a review

Congenital hypothyroidism is a rare and underdiagnosed congenital endocrine disorder in dogs and cats and the true incidence is unknown. The disorder may cause a range of clinical signs depending on the primary defect, which affect production of thyroid hormones; some cases present when adult. Hallmark clinical signs of congenital hypothyroidism are mental impairment and skeletal developmental abnormalities, resulting in disproportionate dwarfism; goitre may or may not be present. Documented causes of congenital hypothyroidism in dogs include deficiency of, or unresponsiveness to, thyrotropin-releasing hormone (TRH) or thyroid-stimulating hormone (TSH), thyroid dysgenesis, dyshormonogenesis and iodine deficiency. In cats, TSH unresponsiveness, thyroid dysgenesis, dyshormonogenesis and iodine deficiency have been confirmed. Adequate replacement therapy results in a successful outcome in the majority of cases, especially when started early in life, as permanent developmental abnormalities can be prevented. This review describes reported cases in dogs and cats, diagnostic investigation, and recommendations for treatment.

A longitudinal serological survey of parvovirus infection in dogs

Serum samples collected from dogs routinely presented at a clinic between June 1974 and October 1980 were tested for the presence of haemagglutination inhibition (HI) titres to canine parvovirus. The first positive titre (>1:320) was demonstrated in serum collected in October 1979. The first confirmed clinical case of canine parvovirus enteritis was diagnosed by the authors in July 1979. In addition, between 1st December 1980 and 1st March 1981, serum samples were collected from 106 healthy dogs which were presented for canine parvovirus vaccination for the first time. Twenty-four dogs (approx. 23%) showed HI titres >1:320 indicating probable previous canine parvovirus infection. Therefore approx. 80% of dogs in the clinic area were at risk at that time and vaccination should have protected them from infection.

Intestinal lymphangiectasia in a dog

An eight-month-old female crossbred terrier was presented with a short history of diarrhoea, dyspnoea and abdominal distension. Clinical examination revealed thoracic effusion, ascites, and subcutaneous oedema. Hypoalbuminaemia, hypoglobulinaemia and lymphopaenia were all present. Histological examination of a jejunal biopsy confirmed a diagnosis of intestinal Iymphangiectasia. Full clinical recovery followed treatment by dietary management.

Granulomatous meningoencephalomyelitis of dogs in New Zealand

A progressive neurological disease affecting twenty-two young adult dogs of smaller breeds is reported. The disease was most often acute in onset and the neurological signs included cervical pain, seizures, behavioural changes, ataxia, head tilt, muscle tremor and paresis. The lesions were those of a disseminated granulomatous meningoencephalomyelitis in which perivascular cuffs of macrophages and lymphoid cells were the predominant finding. Severe lesions were most often seen in the cerebral white matter although the brain stem, mid-brain and spinal cord were also commonly affected.

Primary idiopathic hypoparathyroidism in St. Bernard dogs

Primary hypoparathyroidism was diagnosed in three St. Bernard bitches. Anorexia, behavioural changes, muscle tremors, seizures, panting respiration, and cataracts were the clinical signs observed. The serum concentration of calcium was low, the phosphorus concentration elevated, and the immunoreactive parathyroid hormone level low in all dogs. The aetiology of the hypoparathyroidism was not determined in any of the dogs. Treatment with synthetic vitamin D (1,25-dihydroxycholecalciferol) and an oral calcium supplement was successful in restoring and then maintaining a normal concentration of serum calcium in two of the dogs.

An unusual myopathy in a dog

A nine-month-old Cavalier King Charles Spaniel was examined because it could not withdraw its tongue into its mouth and had difficulty eating and drinking. These clinical signs were first observed when the dog was two months of age. On percussion of the tongue a dimple could be produced and there was electromyographic evidence of myotonia. Histological examination showed replacement of muscle fibres by adipose tissue, focal areas of myonecrosis, neutrophil infiltration and proliferation of sub-sarcolemmal nuclei. These changes were considered to be consistent with a primary myopathy similar to paramyotonia in man. No related dogs were found to be affected.

Protozoa1 encephalomyelitis of dogs involvingNeosporum caninumandToxoplasma gondiiin New Zealand

In a retrospective study of 15 cases of encephalomyelitis in dogs, three cases of Neospora caninum and two cases of Toxoplasma gondii infection were identified using immunohistochemical staining of central nervous system sections. All cases of neosporosis showed ataxia and progressive hind limb paralysis due to multifocal non-suppurative meningoencephalomyelitis which was most severe in the spinal cord and base of the brain stem. Neospora tissue cysts could not be distinguished morphologically from those of T. gondii using light microscopy, but electron microscopy confirmed their characteristic features. Although Neospora abortion in cattle has only recently been recognised in New Zealand, this study has shown that neosporosis has been present in dogs since at least 1972.

The experimental induction of leukoencephalomyelopathy in cats

Leukoencephalomyelopathy of undetermined etiology has been described in specific pathogen-free cats. A study was established to assess if the long-term feeding of a gamma-irradiated diet could induce this disease. Cats fed exclusively on diet irradiated at 25.7-38.1 kGy ("typical" dose) and 38.1-53.6 kGy (high-end dose), respectively, developed typical lesions with attendant, progressively severe ataxia between study days 140 and 174. The onset of ataxia at day 140 and the number of animals affected at this time were similar in animals fed each ration. A maximum ataxia "score" was first reached by an animal on the high-end dose diet on day 167 and by 2 cats fed the "typical-end" dose diet 21 days later. Ataxic cats and 1 animal euthanized on day 93 prior to the onset of ataxia exhibited varying degrees of Wallerian degeneration in the spinal cord and brain, similar to the spontaneous disease. The elevated total antioxidant status of spinal cord segments and hepatic superoxide dismutase concentration of cats fed typical and high-end treated diets suggested free-radical involvement in the pathogenesis. The significantly elevated peroxide concentrations of the irradiated diets (1,040% and 6,440% of untreated values) may have resulted in increased oxidative insult, a factor possibly exacerbated by the treated diets' reduced vitamin A content. This study has reproduced leukoencephalomyelopathy in cats similar to spontaneous outbreaks by feeding a gamma-irradiated dry diet with elevated peroxide and reduced vitamin A concentrations.

A comparison of different culture methods for the recovery of Campylobacter species from pets

Five culture methods for the recovery of Campylobacter species (spp.) were evaluated on 361 rectal swabs collected from cats and dogs in Ireland. Speciation using PCR methods was performed on all isolates to assess the sensitivity of each culture method for isolation of Campylobacter spp., and to establish the prevalence of Campylobacter jejuni, C. coli, C. upsaliensis, C. lari and C. helveticus. Overall 163 of 361 (45.2%) samples were confirmed Campylobacter spp. positive. Direct plating onto modified charcoal cefoperazone deoxycholate agar (mCCDA) with cefoperazone, amphotericin and teicoplanin (CAT) selective supplement yielded a significantly higher prevalence of Campylobacter spp. (33.0%) than each of the other four methods (P < or = 0.05). This method was also the most sensitive method for isolation of C. upsaliensis compared with any of the other four methods used in the current study (P < or = 0.05). A direct plating method onto mCCDA agar with CCDA selective supplement and a filtration method onto blood agar after pre-enrichment in CAT supplemented broth yielded lower Campylobacter spp. prevalences of 19.7% and 17.5% respectively. A filtration method onto CAT agar and pre-enrichment in Preston broth before plating onto mCCDA agar were less sensitive for the isolation of Campylobacter spp. Speciation results of Campylobacter isolates revealed the majority of Campylobacter isolates were C. upsaliensis (50.0%) and C. jejuni (41.9%). A small number of isolates were C. coli (2.6%), C. lari (1.5%) and C. helveticus (1.1%). The overall detection of Campylobacter spp. in the 361 pets sampled was significantly increased by using a combination of isolation methods (P < or = 0.05), producing a more accurate determination of the prevalence of Campylobacter spp. in pets in Ireland and of the actual Campylobacter species. As the majority of Campylobacter spp. were recovered by direct plating onto mCCDA agar with CAT supplement, this method is the method of choice if only a single method is selected for isolation of the most common Campylobacter spp. detected in pets and humans.

Leukoencephalomyelopathy in specific pathogen-free cats

Investigations were carried out on 8 specific pathogen-free cats (5 male and 3 female) from a colony experiencing "outbreaks" of progressive hind limb ataxia in 190 of 540 at-risk animals ranging from 3 months to 3 years old. These studies identified moderate to severe bilateral axonal degeneration within white matter regions of the cervical, thoracic, and lumbar spinal cord and in the white matter of the cerebral internal capsule and peduncle, in the roof of the fourth ventricle and inferior cerebellar peduncle, and in the external arcuate and pyramidal fibres of the medulla. There were varying degrees of accompanying microgliosis, astrocytosis, and capillary hyperplasia. Such a clinicopathologic syndrome, termed feline leukoencephalomyelopathy, has previously been described in cat colonies in Britain and New Zealand, although its etiology has not been determined. The degenerative nature of the lesions and their bilateral distribution suggest possible nutritional, metabolic, or toxic causes. Although these findings provide circumstantial evidence that the exclusive feeding of a gamma-irradiated diet of reduced vitamin A content is associated with the development of the neuronal lesions, further tissue micronutrient and antioxidant analysis will be required to support this hypothesis.

Characterization of certain inflammatory variables in the peripheral blood of clinically healthy dogs

Many laboratory techniques have been developed to study and quantify the inflammatory response, including the release of acid hydrolase enzymes, leukotriene B(4) (LTB(4)) production, reactive oxygen species (ROS) production and complement conversion studies. Although extensively studied in human health and disease, the relevance of such tests in the dog is largely unknown. After isolation of the peripheral blood mononuclear cell (PBMC) and polymorphonuclear cell (PMN) fractions from the peripheral blood of 38 clinically healthy dogs, values for ROS production were similar for both cell fractions when measured by luminol-enhanced chemiluminescence (17,853+/-9,695 U/10(6) cells versus 19,138+/-14,569 U/10(6) cells for the PBMC (n=38) and PMN (n=18) fractions, respectively). However, the mean time taken to reach maximum chemiluminescence was noticeably shorter in the PBMC fraction (5.1+/-3.3 versus 10.7+/-2.5 min for PBMCs (n=36) and PMNs (n=18), respectively). Intracellular concentrations of beta-glucuronidase, beta-galactosidase and N-acetyl-beta-glucosaminidase were assayed by spectrofluorometry. Mean values for all three enzymes were higher in PBMCs (n=31-35) than in PMNs (n=10-14). Both cell fractions released 20% of the intracellular enzyme concentration when stimulated with opsonized zymosan. Following incubation with A23187 (1 microM), mean LTB(4) production was higher in PBMCs (4.45+/-2.92 ng/10(6) cells; n=27) than in PMNs (0.96+/-2.22 ng/10(6) cells; n=13) using a validated high performance liquid chromatography (HPLC) assay. Immunoprecipitation studies revealed that the mean percentage conversion of C3 to C3b following stimulation with opsonized zymosan was 57.3+/-13.4% (n=36). The results provide normal values for clinically healthy dogs that may subsequently be used in future studies investigating dogs with various inflammatory disorders.

Prevalence of thermophilic Campylobacter species in cats and dogs in two animal shelters in Ireland

Rectal swabs or faecal samples for the isolation of Campylobacter species were taken from 120 dogs and cats in an animal shelter in which only one kitten showed signs of gastrointestinal disease, and rectal swabs were taken from 46 dogs, 22 of which showed signs of gastrointestinal disease, in another shelter. At the first shelter, the swabs from 24 of 47 dogs (51.1 per cent) and 36 of 48 cats (75 per cent) yielded a Campylobacter species. The rate of isolation was significantly higher from dogs and cats less than six months old, and significantly higher from cats than from dogs (P< or =0.05). At the second shelter Campylobacter species were isolated from 40 of 46 dogs (87 per cent), but there was no significant difference between the age groups. Campylobacter species were isolated from 19 (86.4 per cent) of the 22 dogs with signs of gastrointestinal disease and from 21 (87.5 per cent) of the 24 unaffected dogs. Several culture methods were applied to the samples collected from both shelters, and the combination significantly increased the recovery of Campylobacter species.

Increased leukotriene B4 production, complement C3 conversion and acid hydrolase enzyme concentrations in different leucocyte sub-populations of dogs with atopic dermatitis

Various markers of the inflammatory response were measured in peripheral blood mononuclear cells (PBMCs) and polymorphonuclear neutrophils (PMNs) from 31 dogs with atopic dermatitis (AD). The variables assayed included chemiluminescence, acid hydrolase enzyme concentrations, leukotriene B(4) (LTB(4)) production and complement C3 conversion. The results were compared to those derived from a population of clinically healthy dogs. Dogs with AD exhibited a significant increase in median LTB(4) production in PMNs compared to controls (0.94 versus 0.00 ng/10(6) cells; P<0.01). Significant increases in the median concentrations of intracellular beta-galactosidase (PBMC fraction - 0.42 versus 0.25 mU/10(6) cells; P<0.05) (PMN fraction - 0.47 versus 0.12 mU/10(6) cells; P<0.01) and beta-glucuronidase (PBMC fraction - 0.52 versus 0.27 mU/10(6) cells; P<0.05) were also evident in the AD group. Although median maximum chemiluminescence values for both leucocyte sub-populations were higher in controls, the differences recorded were not significant (P>0.05). However, the median time taken to reach maximum chemiluminescence was significantly shorter in the PMN fraction of dogs with AD (7.00 versus 10.00 min; P<0.01). Atopic dogs had a significant increase in the median percentage conversion of complement C3 to C3b (66.0 versus 57.3%; P<0.01). The results of this study indicate a priming of the inflammatory response in dogs with AD. The role of LTB(4) in the pathogenesis of canine AD and the potential efficacy of leukotriene antagonists in the treatment of this disorder warrant further investigation.

The amended insulin to glucose ratio and diagnosis of insulinoma in dogs

Amended insulin to glucose ratios were calculated from the concentrations of serum insulin and blood glucose measured concurrently during either a glucagon tolerance test or after feeding in healthy dogs. Values greater than 30 microU/mg which are supportive of a diagnosis of insulinoma were obtained at certain times during the test period. Amended insulin to glucose ratios calculated from serum insulin and blood glucose concentrations obtained during a glucagon tolerance test and an oral glucose tolerance test on a dog with an insulinoma were less than 30 microU/mg, or equivocal, at different times during the test period. This indicates that under some circumstances healthy dogs may have elevated amended insulin to glucose ratios, and dogs with insulinoma may have a normal amended insulin to glucose ratio. Care is essential for interpretation of amended insulin to glucose ratios, and a diagnosis of insulinoma using the ratio must be made in conjunction with appropriate clinical signs of hypoglycaemia.

Local current field radio frequency hyperthermia for the treatment of superficial skin tumours in cats

Local current field radiofrequency (LCF-RF) hyperthermia was used to treat 38 superficial skin tumours (predominantly squamous cell carcinomas) of the nose, face and ears in 35 cats. LCF-RF hyperthermia was applied at 50 degrees C for 60 seconds at single or multiple sites depending on the tumour size. Each cat was observed over a four-month period after treatment and 14 out of 35 cases were also available for re-evaluation eight months after treatment. Tumours which had not resolved completely within one month after the initial treatment were re-treated. LCF-RF hyperthermia is most suited for the treatment of superficial skin tumours (<5 mm diameter). Ninety-two per cent (12/13) of tumours of this dimension showed some regression and 69% (9/13) completely resolved. Larger tumours >5mm diameter) were also successfully treated. 54% (8/14) regressed but only 14% (2/14) completely resolved. LCF-RF hyperthermia is not recommended for the treatment of tumours of the pinnae as 5 of the 6 tumours at this site failed to respond.

The prevalence of feline immunodeficiency virus infection in hyperthyroid cats

One hundred and thirty-four male and female hyperthyroid cats (mean age 11.9 years) were tested for the presence of feline immunodeficiency virus antibodies. Thirty-two (23.9%) were positive. The prevalence of feline immunodeficiency virus antibodies was greater in male cats (30.5%) than in female cats (17.2%). The prevalence of feline immunodeficiency virus infection in hyperthyroid cats is similar to the prevalence of feline immunodeficiency virus in the sick cat population and less than that of sick aged cats at the Massey University Clinic and Hospital. The findings of this survey do not support involvement of feline immunodeficiency virus in the pathogenesis of hyperthyroidism in the cat.

A survey of anaesthetic equipment in veterinary practices in New Zealand

Sixty-four anaesthetic machines and 89 breathing circuits were surveyed in New Zealand veterinary practices. Each machine and circuit was tested for correct function. Sixty-six percent of machines checked were 10 years or older and vaporiser out-of-circuit machines totalled 72% of machines surveyed. Twenty-five percent of the temperature compensated vaporisers had been serviced within the previous 1 year, 33% serviced between 1 and 10 years ago, while the remaining 42% had no service record or had not been serviced for over 10 years. Sixty-six percent of machines had some type of scavenging device. Nineteen percent of machines had a leak in the high pressure system. Thirty percent of the anaesthetic machine low pressure systems leaked and 76% of the patient breathing circuits leaked. Overall, 91% of all anaesthetic machines and breathing circuits showed malfunctions which could increase practice operating costs, increase the exposure of practice personnel to anaesthetic agents, and increase patient morbidity.