This review aims to assess and recommend approaches for targeted and agnostic High Throughput Sequencing of RNA viruses in a variety of sample matrices. HTS also referred to as deep sequencing, next generation sequencing and third generation sequencing; has much to offer to the field of environmental virology as its increased sequencing depth circumvents issues with cloning environmental isolates for Sanger sequencing. That said however, it is important to consider the challenges and biases that method choice can impart to sequencing results. Here, methodology choices from RNA extraction, reverse transcription to library preparation are compared based on their impact on the detection or characterization of RNA viruses.

Norovirus contamination of oysters is the lead cause of non-bacterial gastroenteritis and a significant food safety concern for the oyster industry. Here, norovirus reduction from Pacific oysters (Crassostrea gigas), contaminated in the marine environment, was studied in laboratory depuration trials and in two commercial settings. Norovirus concentrations were measured in oyster digestive tissue before, during and post-depuration using the ISO 15216-1 quantitative real-time RT-PCR method. Results of the laboratory-based studies demonstrate that statistically significant reductions of up to 74% of the initial norovirus GII concentration was achieved after 3 days at 17–21 °C and after 4 days at 11–15 °C, compared to 44% reduction at 7–9 °C. In many trials norovirus GII concentrations were reduced to levels below 100 genome copies per gram (gcg−1; limit of quantitation; LOQ). Virus reduction was also assessed in commercial depuration systems, routinely used by two Irish oyster producers. Up to 68% reduction was recorded for norovirus GI and up to 90% for norovirus GII reducing the geometric mean virus concentration close to or below the LOQ. In both commercial settings there was a significant difference between the levels of reduction of norovirus GI compared to GII (p < 0.05). Additionally, the ability to reduce the norovirus concentration in oysters to < LOQ differed when contaminated with concentrations below and above 1000 gcg−1. These results indicate that depuration, carried out at elevated (> 11 °C) water temperatures for at least 3 days, can reduce the concentration of norovirus in oysters and therefore consumer exposure providing a practical risk management tool for the shellfish industry.

While foodborne outbreaks account for approximately 14% of norovirus cases (L. Verhoef, J.

A complexity of factors, from health and technology innovations to policy redesign to achieve consumer-directed care, are impacting traditional roles for Australian allied health practitioners (AHPs). This pilot study considers roles for AHPs in relation to assistive technology (AT) interventions. Articulating ‘who does what’ may serve a number of purposes including de-professionalization of the discourse; better utilization of support networks and workforces; and alignment with contemporary policy. Yet, a suitable framework to assist with collaborative AT implementation between relevant stakeholders was not identified within the existing literature. This research aimed to develop and pilot an AT collaboration tool which enables AHPs, consumers, their support networks and the support workforce, to navigate policy redesign toward ethical consumer-directed implementation of AT interventions. An AT collaboration tool was developed based upon practice-based knowledge, relevant regulatory and practice evidence and identifies relevant stakeholders, AT service steps and roles, and quality indicators to support competent practice. The tool was piloted in four separate and diverse practice analyses of AT interventions (custom prosthetics, home enteral nutrition, communication devices, and vehicle modifications) considering four allied health professions (prosthetics and orthotics, dietetics, speech pathology, occupational therapy). Pilot testing of the tool supports the feasibility of re-framing AT provision using competency-based and risk-informed approaches and enabling more inclusive roles for consumers and the support workforce. Further testing of the tool is indicated, followed by strategic actions for uptake by individuals, professions and policymakers. The AT collaboration tool has potential to enable AHPs to fulfil ethical obligations for consumer-centered practice, and to facilitate consumer choice, both in Australia and internationally.

In benchmarking bioinformatic pipelines for analyzing high-throughput sequencing (HTS) data sets, we provide method standardization for bioinformatics broadly and specifically for norovirus in situations for which no officially endorsed methods exist at present. This study provides recommendations for the appropriate analysis and classification of norovirus amplicon HTS data and will be widely applicable during outbreak investigations.

A significant decrease in norovirus prevalence and concentration was observed in oyster production areas in Ireland during winter 2020/21.  Oyster production areas impacted by human wastewater discharges that were under-going norovirus surveillance since 2018 were investigated. Samples collected in the winter seasons of 2018/19 and 2019/20, prior to when the COVID-19 pandemic interventions were applied, showed a prevalence of 94.3% and 96.6% respectively and geometric mean concentrations of 533 and 323 genome copies per gram (gcg -1 ) respectively. These values decreased significantly during the winter of 2020/21 (prevalence of 63.2% and geometric concentration of &lt;LOQ) coinciding with the control measures to mitigate the transmission of SARS-CoV-2. Divergence between norovirus GI and GII prevalence and concentrations was observed over the three year monitoring period. Norovirus GII was the dominant genogroup detected in winter 2020/21 with over half of samples positive although concentrations detected were significantly lower than pre-pandemic winters with a geometric mean concentration of &lt;LOQ.

Purpose: Dysphagia (swallowing difficulty) impacts physical health, quality of life, and mealtime enjoyment. Staff who provide mealtime assistance to people with dysphagia require adequate training to help ensure that the mealtimes are safe and enjoyable. This systematic review examined literature relating to training in dysphagia (e.g., recognizing signs and symptoms) and mealtime assistance, its components, and benefits for people with dysphagia. Method: In July 2020, five scientific databases were searched for papers meeting the inclusion criteria relating to mealtime assistance training. The quality of the studies was evaluated using the Quality Assessment Tool for Studies of Diverse Design, with scores ranging from 38.1% to 83.3%. We completed a qualitative synthesis using the data extracted from the included studies. Results: Twenty-four studies met the inclusion criteria. Participants in these studies benefited from both group training and one-on-one training. Training programs had many formats including computer-based, face-to-face, individual training, and group training. Each included study demonstrated some level of positive impact to the learners, such as improved knowledge and skills in mealtime management for people with dysphagia. No studies reported negative outcomes. Training duration ranged from 30 min to 5 days. Conclusions: The benefits of different components of mealtime training (e.g., group training, or face-to-face training) for mealtime assistance for people with dysphagia were reviewed. Further research is needed to compare the effectiveness of different training formats, involving not only the assistant but also people with dysphagia as both trainers and trainees, and determine the health outcomes of training programs for people with dysphagia.

Norovirus is a highly diverse RNA virus often implicated in food-borne outbreaks, particularly shellfish. Shellfish are filter feeders, and when harvested in bays exposed to wastewater overflow or storm overflows, they can harbour various pathogens, including human pathogenic viruses. The application of Sanger or amplicon-based High Throughput Sequencing (HTS) technologies to identify human pathogens in shellfish faces two main challenges i) distinguishing multiple genotypes/variants in a single sample and ii) low concentrations of norovirus RNA. Here we have assessed the performance of a novel norovirus capsid amplicon HTS method. We generated a panel of spiked oysters containing various norovirus concentrations with different genotypic compositions. Several DNA polymerase and Reverse Transcriptase (RT) enzymes were compared, and performance was evaluated based on i) the number of reads passing quality filters per sample, ii) the number of correct genotypes identified, and iii) the sequence identity of outputs compared to Sanger-derived sequences. A combination of the reverse transcriptase LunaScript and the DNA polymerase AmpliTaq Gold provided the best results. The method was then employed, and compared with Sanger sequencing, to characterise norovirus populations in naturally contaminated oysters.