Correction: Development of a non-infectious control for viral hemorrhagic fever PCR assays.

[This corrects the article DOI: 10.1371/journal.pntd.

Developing digital learning to help reduce laboratory inequalities: a viral haemorrhagic fever case study.

Countries with the highest potential exposure to viral haemorrhagic fever viruses are also those with low expenditure on health services, limiting the capacity for surveillance and detection of these viruses, and effective treatment and outbreak containment. The COVID-19 pandemic further limited travel and in-person collaborative training opportunities for researchers, laboratory and public health professionals. Digital learning offers the prospect of addressing some of the shortfall in training needs.

First Detection and Genetic Characterization of Felis catus Papillomavirus Type 11, the First Type to Infect Domestic Cats.

Domestic cats are currently recognized to be infected by 10 different Felis catus papillomavirus (FcaPV) types that are classified into three genera. Examination of a skin sample from a cat with presumptive allergic dermatitis revealed clusters of large amphophilic intracytoplasmic bodies within epidermal cells. A 312 bp section of DNA from a novel PV type was amplified from the sample, while the entire 7569 bp genome was amplified and sequenced from a skin swab.

Metabarcoding captures genetic diversity and links cases in outbreaks of cryptosporidiosis in New Zealand.

Cryptosporidiosis is a disease caused by the parasite Cryptosporidium. Globally, it is a leading cause of diarrhoea and a notifiable disease in New Zealand. Molecular analyses of Cryptosporidium isolated from notified cases do not always provide support for epidemiological links between individuals.

Quantifying Replication Slippage Error in Cryptosporidium Metabarcoding Studies.

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 synthesized 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.

Canis Familiaris Papillomavirus Type 26: A Novel Papillomavirus of Dogs and the First Canine Papillomavirus within the Genus.

Domestic dogs are currently recognized as being infected by 25 different canine papillomavirus (CPV) types classified into three genera. A short sequence from a novel CPV type was amplified, along with CPV1, from a papilloma (wart) from the mouth of a dog. The entire 7499 bp genome was amplified, and CPV26 contained putative coding regions that were predicted to produce four early proteins and two late ones.

Development of a non-infectious control for viral hemorrhagic fever PCR assays.

Assay validation is an essential component of disease surveillance testing, but can be problematic in settings where access to positive control material is limited and a safety risk for handlers. Here we describe a single non-infectious synthetic control that can help develop and validate the PCR based detection of the viral causes of Crimean-Congo hemorrhagic fever, Ebola virus disease, Lassa fever, Marburg virus disease and Rift Valley fever. We designed non-infectious synthetic DNA oligonucleotide sequences incorporating primer binding sites suitable for five assays, and a T7 promotor site which was used to transcribe the sequence.

Genomic Characterization of Canis Familiaris Papillomavirus Type 25, a Novel Papillomavirus Associated with a Viral Plaque from the Pinna of a Dog.

A 14-year-old West Highland White terrier dog developed multiple raised plaques that were confined to the concave surface of the right pinna. Histology allowed a diagnosis of viral plaque, although the lesions contained some unusual microscopic features. A papillomaviral (PV) DNA sequence was amplified from the plaque using consensus PCR primers.

Genetic characterisation of Felis catus papillomavirus type 7, a rare infection of cats that may be associated with skin cancer.

Six Felis catus papillomavirus (FcaPV) types have been fully sequenceed from domestic cats including some that have been associated with the development of neoplasia. A sequence from a novel FcaPV type was amplified from a basal cell carcinoma that contained unusual histological evidence of PV infection and intense p16 protein (p16) immunostaining. The entire 7467 bp genome was amplified using 'outward facing' primers.

A novel, stain-free, natural auto-fluorescent signal, Sig M, identified from cytometric and transcriptomic analysis of infectivity of and .

Cryptosporidiosis is a worldwide diarrheal disease caused by the protozoan . The primary symptom is diarrhea, but patients may exhibit different symptoms based on the species of the parasite they are infected with. Furthermore, some genotypes within species are more transmissible and apparently virulent than others.

Abundant dsRNA picobirnaviruses show little geographic or host association in terrestrial systems.

Picobirnaviruses are double-stranded RNA viruses known from a wide range of host species and locations but with unknown pathogenicity and host relationships. Here, we examined the diversity of picobirnaviruses from cattle and gorillas within and around Bwindi Impenetrable Forest National Park (BIFNP), Uganda, where wild and domesticated animals and humans live in relatively close contact. We use metagenomic sequencing with bioinformatic analyses to examine genetic diversity.

Diagnosis of protozoa diarrhoea in Campylobacter patients increases markedly with molecular techniques.

Cryptosporidium and Giardia are major causes of diarrhoea globally, and two of the most notified infectious diseases in New Zealand. Diagnosis requires laboratory confirmation carried out mostly via antigen or microscopy-based techniques. However, these methods are increasingly being superseded by molecular techniques.

Molecular Evidence of Leptospira spp. in Isolated Fijian Bats.

Bats host several zoonotic pathogens. Island biogeography and epidemiologic theory predict small remote islands have lower infection diversity. Molecular studies of urine and feces from three species at 10 sites from three islands suggest multiple pathogenic Leptospira, but not coronavirus, paramyxovirus, or Histoplasma, circulate in isolated Pacific Fijian bat populations.

Genomic Characterisation of Canis Familiaris Papillomavirus Type 24, a Novel Papillomavirus Associated with Extensive Pigmented Plaque Formation in a Pug Dog.

Numerous large dark plaques developed over the ventrum, legs and head of a 9-year-old pug dog over a 4-year-period. Histology confirmed a diagnosis of viral pigmented plaque and a short section of a novel papillomavirus (PV) type was amplified using consensus PCR primers. Taking advantage of the circular nature of PV DNA, 'outward facing' PCR primers allowed amplification of the full sequence.

Uncovering the genetic diversity of Giardia intestinalis in isolates from outbreaks in New Zealand.

Background: Giardia intestinalis is one of the most common causes of diarrhoea worldwide. Molecular techniques have greatly improved our understanding of the taxonomy and epidemiology of this parasite. Co-infection with mixed (sub-) assemblages has been reported, however, Sanger sequencing is sometimes unable to identify shared subtypes between samples involved in the same epidemiologically linked event, due to samples showing multiple dominant subtypes within the same outbreak.

Community health and human-animal contacts on the edges of Bwindi Impenetrable National Park, Uganda.

Cross-species transmission of pathogens is intimately linked to human and environmental health. With limited healthcare and challenging living conditions, people living in poverty may be particularly susceptible to endemic and emerging diseases. Similarly, wildlife is impacted by human influences, including pathogen sharing, especially for species in close contact with people and domesticated animals.

Estimating the age of the subfamily Orthocoronavirinae using host divergence times as calibration ages at two internal nodes.

Viruses of the subfamily Orthocoronavirinae can cause mild to severe disease in people, including COVID-19, MERS and SARS. Their most common natural hosts are bat and bird species, which are mostly split across four virus genera. Molecular clock analyses of orthocoronaviruses suggested the most recent common ancestor of these viruses might have emerged either around 10,000 years ago or, using models accounting for selection, many millions of years.

First report of novel assemblages and mixed infections of Giardia duodenalis in human isolates from New Zealand.

Giardia duodenalis (syn. G. intestinalis and G.

High-Yield Purification of Giardia intestinalis Cysts from Fecal Samples.

Giardia is an enteric protozoan parasite that causes gastroenteritis in all classes of vertebrates. It is ranked among the leading causes of death in children under 5 years of age. Giardiasis affects approximately 280 million people worldwide annually, a situation exacerbated by the low availability of effective treatments and the lack of a vaccine.

Investigating the Meat Pathway as a Source of Human Nontyphoidal Salmonella Bloodstream Infections and Diarrhea in East Africa.

Background: Salmonella Enteritidis and Salmonella Typhimurium are major causes of bloodstream infection and diarrheal disease in East Africa. Sources of human infection, including the role of the meat pathway, are poorly understood.

Methods: We collected cattle, goat, and poultry meat pathway samples from December 2015 through August 2017 in Tanzania and isolated Salmonella using standard methods.

The Challenges of Analysing Highly Diverse Picobirnavirus Sequence Data.

The reliable identification and classification of infectious diseases is critical for understanding their biology and controlling their impact. Recent advances in sequencing technology have allowed insight into the remarkable diversity of the virosphere, of which a large component remains undiscovered. For these emerging or undescribed viruses, the process of classifying unknown sequences is heavily reliant on existing nucleotide sequence information in public databases.

Historical translocations by Māori may explain the distribution and genetic structure of a threatened surf clam in Aotearoa (New Zealand).

The population genetic structure of toheroa (Paphies ventricosa), an Aotearoa (New Zealand) endemic surf clam, was assessed to determine levels of inter-population connectivity and test hypotheses regarding life history, habitat distribution and connectivity in coastal vs. estuarine taxa. Ninety-eight toheroa from populations across the length of New Zealand were sequenced for the mitochondrial cytochrome c oxidase I gene with analyses suggesting a population genetic structure unique among New Zealand marine invertebrates.

Decoupled responses of soil bacteria and their invertebrate consumer to warming, but not freeze-thaw cycles, in the Antarctic Dry Valleys.

Altered temperature profiles resulting in increased warming and freeze-thaw cycle (FTC) frequency pose great ecological challenges to organisms in alpine and polar ecosystems. We performed a laboratory microcosm experiment to investigate how temperature variability affects soil bacterial cell numbers, and abundance and traits of soil microfauna (the microbivorous nematode Scottnema lindsayae) from McMurdo Dry Valleys, Antarctica. FTCs and constant freezing shifted nematode body size distribution towards large individuals, driven by higher mortality among smaller individuals.

Ecological biogeography of the terrestrial nematodes of victoria land, antarctica.

The terrestrial ecosystems of Victoria Land, Antarctica are characteristically simple in terms of biological diversity and ecological functioning. Nematodes are the most commonly encountered and abundant metazoans of Victoria Land soils, yet little is known of their diversity and distribution. Herein we present a summary of the geographic distribution, habitats and ecology of the terrestrial nematodes of Victoria Land from published and unpublished sources.