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Article ; Online: Genomic analysis of canine pneumoviruses and canine respiratory coronavirus from New Zealand.

Dunowska, M / More, G D / Biggs, P J / Cave, N J

2024 , Page(s) 1–10

Abstract: Aims: To isolate canine respiratory coronavirus (CRCoV) and canine pneumovirus (CnPnV) in cell culture and to compare partial genomic sequences of CRCoV and CnPnV from New Zealand with those from other countries.: Methods: Oropharyngeal swab samples ... ...

Abstract	Aims: To isolate canine respiratory coronavirus (CRCoV) and canine pneumovirus (CnPnV) in cell culture and to compare partial genomic sequences of CRCoV and CnPnV from New Zealand with those from other countries. Methods: Oropharyngeal swab samples from dogs affected by canine infectious respiratory disease syndrome that were positive for CnPnV (n = 15) or CRCoV (n = 1) by virus-specific reverse transcriptase quantitative PCR (RT-qPCR) in a previous study comprised the starting material. Virus isolation was performed in HRT-18 cells for CRCoV and RAW 264.7 and Vero cells for CnPnV. The entire sequence of CnPnV G protein (1,266 nucleotides) and most (8,063/9,707 nucleotides) of the 3' region of CRCoV that codes for 10 structural and accessory proteins were amplified and sequenced. The sequences were analysed and compared with other sequences available in GenBank using standard molecular tools including phylogenetic analysis. Results: Virus isolation was unsuccessful for both CRCoV and CnPnV. Pneumovirus G protein was amplified from 3/15 (20%) samples that were positive for CnPnV RNA by RT-qPCR. Two of these (NZ-048 and NZ-049) were 100% identical to each other, and 90.9% identical to the third one (NZ-007). Based on phylogenetic analysis of the G protein gene, CnPnV NZ-048 and NZ-049 clustered with sequences from the USA, Thailand and Italy in group A, and CnPnV NZ-007 clustered with sequences from the USA in group B. The characteristics of the predicted genes (length, position) and their putative protein products (size, predicted structure, presence of N- and O-glycosylation sites) of the New Zealand CRCoV sequence were consistent with those reported previously, except for the region located between open reading frame (ORF)3 (coding for S protein) and ORF6 (coding for E protein). The New Zealand virus was predicted to encode 5.9 kDa, 27 kDa and 12.7 kDa proteins, which differed from the putative coding capacity of this region reported for CRCoV from other countries. Conclusions: This report represents the first characterisation of partial genomic sequences of CRCoV and CnPnV from New Zealand. Our results suggest that the population of CnPnV circulating in New Zealand is not homogeneous, and that the viruses from two clades described overseas are also present here. Limited conclusions can be made based on only one CRCoV sequence, but the putative differences in the coding capacity of New Zealand CRCoV support the previously reported variability of this region. The reasons for such variability and its biological implications need to be further elucidated.
Language	English
Publishing date	2024-04-22
Publishing country	England
Document type	Journal Article
ZDB-ID	415642-0
ISSN	1176-0710 ; 0048-0169
ISSN (online)	1176-0710
ISSN	0048-0169
DOI	10.1080/00480169.2024.2339845
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Article ; Online: Quantifying replication slippage error in Cryptosporidium metabarcoding studies.

Knox, M A / Biggs, P J / Garcia-R, J C / Hayman, D T S

The Journal of infectious diseases

2024

Abstract: Genetic variation in Cryptosporidium, a common protozoan gut parasite in humans, is often based on marker genes containing trinucleotide repeats, which differentiate subtypes and track outbreaks. However, repeat regions have high replication slippage ... ...

Abstract	Genetic variation in Cryptosporidium, a common protozoan gut parasite in humans, is often based on marker genes containing trinucleotide repeats, which differentiate subtypes and track outbreaks. However, repeat regions have high replication slippage rates, making it difficult to discern biological diversity from error. Here, we synthesised Cryptosporidium DNA in clonal plasmid vectors, amplified them in different mock community ratios and sequenced them using next generation sequencing to determine the rate of replication slippage with dada2. Our results indicate that slippage rates increase with the length of the repeat region and can contribute to error rates of up to 20%.
Language	English
Publishing date	2024-02-08
Publishing country	United States
Document type	Journal Article
ZDB-ID	3019-3
ISSN	1537-6613 ; 0022-1899
ISSN (online)	1537-6613
ISSN	0022-1899
DOI	10.1093/infdis/jiae065
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Article: Acalculous cholecystitis presentation in a young patient.

Biggs, Megan / Abutalib, Jabeen / Roach, Paul

Journal of family medicine and primary care

2022 Volume 11, Issue 7, Page(s) 4033–4035

Abstract: Acute acalculous cholecystitis accounts for only 5-10% of cholecystitis cases and is often associated with severe trauma, critical illness, or chronic disease. Our case describes an otherwise healthy 25-year-old female presenting with acute abdominal ... ...

Abstract	Acute acalculous cholecystitis accounts for only 5-10% of cholecystitis cases and is often associated with severe trauma, critical illness, or chronic disease. Our case describes an otherwise healthy 25-year-old female presenting with acute abdominal pain. After undergoing a magnetic resonance cholangiopancreatography and cholescintigraphy she was diagnosed with acute acalculous cholecystitis. Her symptoms resolved following laparoscopic cholecystectomy which highlights the importance of prompt diagnosis and treatment of acalculous cholecystitis even in the absence of trauma or critical illness.
Language	English
Publishing date	2022-07-22
Publishing country	India
Document type	Case Reports
ZDB-ID	2735275-4
ISSN	2278-7135 ; 2249-4863
ISSN (online)	2278-7135
ISSN	2249-4863
DOI	10.4103/jfmpc.jfmpc_1950_21
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Article: Inborn errors of immunity in adulthood.

Wang, Joanne J F / Dhir, Arün / Hildebrand, Kyla J / Turvey, Stuart E / Schellenberg, Robert / Chen, Luke Y C / Pourshahnazari, Persia / Biggs, Catherine M

Allergy, asthma, and clinical immunology : official journal of the Canadian Society of Allergy and Clinical Immunology

2024 Volume 20, Issue 1, Page(s) 6

Abstract: Inborn errors of immunity (IEIs) are a group of conditions whereby parts of the immune system are missing or dysfunctional. Once thought to primarily be a pediatric disorder, it is now estimated that more than 50% of worldwide incident IEI cases are ... ...

Abstract	Inborn errors of immunity (IEIs) are a group of conditions whereby parts of the immune system are missing or dysfunctional. Once thought to primarily be a pediatric disorder, it is now estimated that more than 50% of worldwide incident IEI cases are accounted for by adults. Delayed diagnosis, late symptom onset, and IEI phenocopies can all lead to adult-onset recognition of IEIs. Lack of awareness regarding the diversity of IEI manifestations in adults contributes to diagnostic and treatment delays. Prompt referral to immunology is critical so that patients can receive a precise molecular diagnosis and targeted therapy when available. This article serves as a primer on IEIs in adulthood, highlighting the pathophysiology, epidemiology and clinical features. We present clinical vignettes of three key IEIs to assist clinicians in building illness scripts on their presentations. We provide a framework for the laboratory evaluation of IEIs and their initial treatment, with the aim of improving recognition and management of these conditions.
Language	English
Publishing date	2024-01-17
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	2434973-2
ISSN	1710-1492 ; 1710-1484
ISSN (online)	1710-1492
ISSN	1710-1484
DOI	10.1186/s13223-023-00862-8
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Article ; Online: High-resolution genomic analysis to investigate the impact of the invasive brushtail possum (Trichosurus vulpecula) and other wildlife on microbial water quality assessments.

Moinet, Marie / Rogers, Lynn / Biggs, Patrick / Marshall, Jonathan / Muirhead, Richard / Devane, Megan / Stott, Rebecca / Cookson, Adrian

PloS one

2024 Volume 19, Issue 1, Page(s) e0295529

Abstract: Escherichia coli are routine indicators of fecal contamination in water quality assessments. Contrary to livestock and human activities, brushtail possums (Trichosurus vulpecula), common invasive marsupials in Aotearoa/New Zealand, have not been ... ...

Abstract	Escherichia coli are routine indicators of fecal contamination in water quality assessments. Contrary to livestock and human activities, brushtail possums (Trichosurus vulpecula), common invasive marsupials in Aotearoa/New Zealand, have not been thoroughly studied as a source of fecal contamination in freshwater. To investigate their potential role, Escherichia spp. isolates (n = 420) were recovered from possum gut contents and feces and were compared to those from water, soil, sediment, and periphyton samples, and from birds and other introduced mammals collected within the Mākirikiri Reserve, Dannevirke. Isolates were characterized using E. coli-specific real-time PCR targeting the uidA gene, Sanger sequencing of a partial gnd PCR product to generate a gnd sequence type (gST), and for 101 isolates, whole genome sequencing. Escherichia populations from 106 animal and environmental sample enrichments were analyzed using gnd metabarcoding. The alpha diversity of Escherichia gSTs was significantly lower in possums and animals compared with aquatic environmental samples, and some gSTs were shared between sample types, e.g., gST535 (in 85% of samples) and gST258 (71%). Forty percent of isolates gnd-typed and 75% of reads obtained by metabarcoding had gSTs shared between possums, other animals, and the environment. Core-genome single nucleotide polymorphism (SNP) analysis showed limited variation between several animal and environmental isolates (<10 SNPs). Our data show at an unprecedented scale that Escherichia clones are shared between possums, other wildlife, water, and the wider environment. These findings support the potential role of possums as contributors to fecal contamination in Aotearoa/New Zealand freshwater. Our study deepens the current knowledge of Escherichia populations in under-sampled wildlife. It presents a successful application of high-resolution genomic methods for fecal source tracking, thereby broadening the analytical toolbox available to water quality managers. Phylogenetic analysis of isolates and profiling of Escherichia populations provided useful information on the source(s) of fecal contamination and suggest that comprehensive invasive species management strategies may assist in restoring not only ecosystem health but also water health where microbial water quality is compromised.
MeSH term(s)	Animals ; Humans ; Animals, Wild ; Trichosurus/genetics ; Water Quality ; Ecosystem ; Phylogeny ; Escherichia coli/genetics ; Genomics ; New Zealand
Language	English
Publishing date	2024-01-18
Publishing country	United States
Document type	Journal Article
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0295529
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Article ; Online: A survey of case studies on the use of forensic three-dimensional printing in England and Wales.

Errickson, D / Carew, R M / Collings, A J / Biggs, M J P / Haig, P / O'Hora, H / Marsh, N / Roberts, J

International journal of legal medicine

2022 Volume 136, Issue 6, Page(s) 1605–1619

Abstract: 3D printing has rapidly developed and been applied in forensic science due to its use in creating demonstrations for courts of law. Much of the literature on this specific topic has focused on the use of 3D printed models in academia, the potential ... ...

Abstract	3D printing has rapidly developed and been applied in forensic science due to its use in creating demonstrations for courts of law. Much of the literature on this specific topic has focused on the use of 3D printed models in academia, the potential influence on a jury, and its use as a long-term documentation process, but with few actual forensic case examples. This paper offers an insight into the development of 3D printing in forensic practice and how 3D printing is currently being used in the criminal justice system in England and Wales.A series of case reports were gathered from multiple police forces and forensic practitioners in the UK to identify how 3D printing was being used. These discussions established who was requesting 3D printed exhibits, what type of technologies were being utilised, what type of exhibits were being printed, and resulting feedback for the use of 3D printed material within a criminal case. As a result, this research demonstrates the current use of 3D printing in England and Wales, discussing the associated cases that have been known to incorporate 3D prints. Likewise, this work explores the limitations that have been encountered by forensic practitioners and identifies a series of research questions that should be considered in future investigations.
MeSH term(s)	England ; Forensic Medicine ; Humans ; Police ; Printing, Three-Dimensional ; Wales
Language	English
Publishing date	2022-08-08
Publishing country	Germany
Document type	Journal Article
ZDB-ID	1055109-8
ISSN	1437-1596 ; 0937-9827
ISSN (online)	1437-1596
ISSN	0937-9827
DOI	10.1007/s00414-022-02872-4
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Article ; Online: The potential for refining nitrogen fertiliser management through accounting for climate impacts: An exploratory study for the Tully region.

Biggs, J S / Everingham, Y / Skocaj, D M / Schroeder, B L / Sexton, J / Thorburn, P J

Marine pollution bulletin

2021 Volume 170, Page(s) 112664

Abstract: Increasing the precision of nitrogen (N) fertiliser management in cropping systems is integral to increasing the environmental and economic sustainability of cropping. In a simulation study, we found that natural variability in year-to-year climate had a ...

Abstract	Increasing the precision of nitrogen (N) fertiliser management in cropping systems is integral to increasing the environmental and economic sustainability of cropping. In a simulation study, we found that natural variability in year-to-year climate had a major effect on optimum N fertiliser rates for sugarcane in the Tully region of north-eastern Australia, where N discharges pose high risks to Great Barrier Reef ecosystems. There were interactions between climate and other factors affecting crop growth that made optimum N rates field-specific. The regional average optimum N fertiliser rate was substantially lower than current industry guidelines. Likewise, simulated N losses to the environment at optimum N fertiliser rates were substantially lower than the simulated losses at current industry fertiliser guidelines. Dissolved N discharged from rivers is related to fertiliser applications. If the reductions in N applications identified in the study occurred in the Tully region, the reduction in dissolved N discharges from rivers in the region would almost meet current water quality improvement targets. Whilst there were many assumptions made in this exploratory study, and there are many steps between the study and a practically implemented dynamic N fertiliser recommendation system, the potential environmental benefits justify field validation and further development of the concepts identified in the study.
MeSH term(s)	Agriculture ; Climate ; Ecosystem ; Fertilizers/analysis ; Nitrogen
Chemical Substances	Fertilizers ; Nitrogen (N762921K75)
Language	English
Publishing date	2021-06-30
Publishing country	England
Document type	Journal Article
ZDB-ID	2001296-2
ISSN	1879-3363 ; 0025-326X
ISSN (online)	1879-3363
ISSN	0025-326X
DOI	10.1016/j.marpolbul.2021.112664
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Article: Opportunities, approaches and challenges to the engagement of citizens in filling small water body data gaps.

Kelly-Quinn, M / Biggs, J N / Brooks, S / Fortuño, P / Hegarty, S / Jones, J I / Regan, F

Hydrobiologia

2022 , Page(s) 1–21

Abstract: Monitoring the condition (water quality, biodiversity, hydromorphology) of small water bodies presents a challenge for the relevant authorities in terms of time and resources (labour and financial) due to the extensive length of the stream network or the ...

Abstract	Monitoring the condition (water quality, biodiversity, hydromorphology) of small water bodies presents a challenge for the relevant authorities in terms of time and resources (labour and financial) due to the extensive length of the stream network or the sheer number of small standing water bodies. Citizen science can help address information gaps, but the effort required should not be underestimated if such projects are to generate reliable and sustained data collection. The overall aim of this paper is to propose a framework for operationalisation of citizen science targeting collection of data from small water bodies. We first consider the data gaps and the elements (water chemistry, ecology, hydromorphology) to be addressed, in order to define where citizen science could best make an impact. We review examples of tools and methods that are appropriate for small water bodies, based on experience from a selection of freshwater citizen science projects, and the support that is needed for effective and sustained small water body projects across Europe.
Language	English
Publishing date	2022-08-31
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	214428-1
ISSN	1573-5117 ; 0018-8158
ISSN (online)	1573-5117
ISSN	0018-8158
DOI	10.1007/s10750-022-04973-y
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Article ; Online: A molecular survey of canine respiratory viruses in New Zealand.

More, G D / Cave, N J / Biggs, P J / Acke, E / Dunowska, M

New Zealand veterinary journal

2021 Volume 69, Issue 4, Page(s) 224–233

Abstract: ... dogs and in 23/60 (38%) samples from healthy dogs (p = 0.84). CIRDS-affected dogs were most commonly ... than diseased dogs (RR 0.38; 95% CI = 0.15-0.99; p = 0.045).: Conclusions: The frequency of detection of viruses ...

Abstract	Aims: The aim of this study was to identify viruses associated with canine infectious respiratory disease syndrome (CIRDS) among a population of New Zealand dogs. Methods: Convenience samples of oropharyngeal swabs were collected from 116 dogs, including 56 CIRDS-affected and 60 healthy dogs from various locations in New Zealand between March 2014 and February 2016. Pooled samples from CIRDS-affected (n = 50) and from healthy (n = 50) dogs were tested for the presence of canine respiratory viruses using next generation sequencing (NGS). Individual samples (n = 116) were then tested by quantitative PCR (qPCR) and reverse transcriptase qPCR (RT-qPCR) for specific viruses. Groups were compared using Fisher's exact or χ Results: Canine pneumovirus (CnPnV), canine respiratory coronavirus (CRCoV), canine herpesvirus-1 (CHV-1), canine picornavirus and influenza C virus sequences were identified by NGS in the pooled sample from CIRDS-affected but not healthy dogs. At least one virus was detected by qPCR/RT-qPCR in 20/56 (36%) samples from CIRDS dogs and in 23/60 (38%) samples from healthy dogs (p = 0.84). CIRDS-affected dogs were most commonly positive for CnPnV (14/56, 25%) followed by canine adenovirus-2 (CAdV-2, 5/56, 9%), canine parainfluenza virus (CpiV) and CHV-1 (2/56, 4% each), and CRCoV (1/56, 2%). Only CnPnV (17/60, 28%) and CAdV-2 (14/60, 23%) were identified in samples from healthy dogs, and CAdV-2 was more likely to be detected healthy than diseased dogs (RR 0.38; 95% CI = 0.15-0.99; p = 0.045). Conclusions: The frequency of detection of viruses traditionally linked to CIRDS (CAdV-2 and CPiV) among diseased dogs was low. This suggests that other pathogens are likely to have contributed to development of CIRDS among sampled dogs. Our data represent the first detection of CnPnV in New Zealand, but the role of this virus in CIRDS remains unclear. On-going monitoring of canine respiratory pathogens by NGS would be beneficial, as it allows rapid detection of novel viruses that may be introduced to the New Zealand canine population in the future. Such monitoring could be done using pooled samples to minimise costs. Clinical relevance: Testing for novel respiratory viruses such as CnPnV and CRCoV should be considered in all routine laboratory investigations of CIRDS cases, particularly in dogs vaccinated with currently available kennel cough vaccines.
MeSH term(s)	Animals ; Dog Diseases/epidemiology ; Dog Diseases/virology ; Dogs ; Female ; High-Throughput Nucleotide Sequencing ; Male ; Molecular Epidemiology ; New Zealand/epidemiology ; Polymerase Chain Reaction ; Respiratory Tract Infections/epidemiology ; Respiratory Tract Infections/veterinary ; Respiratory Tract Infections/virology ; Reverse Transcriptase Polymerase Chain Reaction ; Virus Diseases/epidemiology ; Virus Diseases/veterinary
Language	English
Publishing date	2021-04-12
Publishing country	England
Document type	Journal Article
ZDB-ID	415642-0
ISSN	1176-0710 ; 0048-0169
ISSN (online)	1176-0710
ISSN	0048-0169
DOI	10.1080/00480169.2021.1915211
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Article: Hearing loss in inner ear and systemic autoimmune disease: A systematic review of post-cochlear implantation outcomes.

Lee, Jonathan / Biggs, Kirsty / Muzaffar, Jameel / Bance, Manohar / Monksfield, Peter

Laryngoscope investigative otolaryngology

2021 Volume 6, Issue 3, Page(s) 469–487

Abstract: Objectives: To assess outcomes following cochlear implantation (CI) in patients with hearing loss secondary to primary or secondary autoimmune inner ear disease (AIED).: Methods: A systematic review and narrative synthesis was completed according to ... ...

Abstract	Objectives: To assess outcomes following cochlear implantation (CI) in patients with hearing loss secondary to primary or secondary autoimmune inner ear disease (AIED). Methods: A systematic review and narrative synthesis was completed according to PRISMA guidelines. Databases searched included MEDLINE, PubMed, EMBASE, Web of Science, Cochrane Collection, and ClinicalTrials.gov. No limits were placed on year of publication or language. Results: A total of 551 studies were identified, of which 29 were included after removal of duplicates, and screening the title, abstract, and full text. All except one study were OCEBM grade IV. 114 of 115 patients displayed improvement in hearing following cochlear implantation. With implant use, roughly a third of these patients had hearing that improved over time, a third improved and plateaued, and a third remained stable. There was no additional risk of perioperative complications found in AIED patients compared what is generally accepted in general cochlear implantation, although two episodes of device failure after 6 months were noted, and four patients with secondary AIED displayed poor initial audiological outcomes. Conclusion: CI in both primary and secondary AIED provides marked improvement in hearing. Early CI may be a valid management option, provide long-lasting hearing in patients and reduce the side effects of long-term systemic immunosuppressants. However, patients should be counseled residual hearing may be lost if there is cochlear ossification or fibrosis which may make implant insertion more traumatic. Level of evidence: NA.
Language	English
Publishing date	2021-05-04
Publishing country	United States
Document type	Journal Article ; Review
ISSN	2378-8038
ISSN	2378-8038
DOI	10.1002/lio2.563
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