Genomics-informed outbreak investigations of SARS-CoV-2 using civet

The scale of data produced during the SARS-CoV-2 pandemic has been unprecedented, with more than 13 million sequences shared publicly at the time of writing. This wealth of sequence data provides important context for interpreting local outbreaks. However, placing sequences of interest into national and international context is difficult given the size of the global dataset. Often outbreak investigations and genomic surveillance efforts require running similar analyses again and again on the latest dataset and producing reports. We developed civet (cluster investigation and virus epidemiology tool) to aid these routine analyses and facilitate virus outbreak investigation and surveillance. Civet can place sequences of interest in the local context of background diversity, resolving the query into different 'catchments' and presenting the phylogenetic results alongside metadata in an interactive, distributable report. Civet can be used on a fine scale for clinical outbreak investigation, for local surveillance and cluster discovery, and to routinely summarise the virus diversity circulating on a national level. Civet reports have helped researchers and public health bodies feedback genomic information in the appropriate context within a timeframe that is useful for public health.

Genomics-informed outbreak investigations of SARS-CoV-2 using civet.

The scale of data produced during the SARS-CoV-2 pandemic has been unprecedented, with more than 13 million sequences shared publicly at the time of writing. This wealth of sequence data provides important context for interpreting local outbreaks. However, placing sequences of interest into national and international context is difficult given the size of the global dataset. Often outbreak investigations and genomic surveillance efforts require running similar analyses again and again on the latest dataset and producing reports. We developed civet (cluster investigation and virus epidemiology tool) to aid these routine analyses and facilitate virus outbreak investigation and surveillance. Civet can place sequences of interest in the local context of background diversity, resolving the query into different 'catchments' and presenting the phylogenetic results alongside metadata in an interactive, distributable report. Civet can be used on a fine scale for clinical outbreak investigation, for local surveillance and cluster discovery, and to routinely summarise the virus diversity circulating on a national level. Civet reports have helped researchers and public health bodies feedback genomic information in the appropriate context within a timeframe that is useful for public health.

Preventing facial pressure injuries among health care staff working in diverse COVID-19 care environments.

The aim of this study was to determine the impact of a specially designed care bundle on the development of facial pressure injuries among frontline health care workers wearing personal protective equipment (PPE) during the COVID-19 pandemic. This was a mixed methods study. First, a pre-posttest observational design was employed to evaluate the impact of the pre-piloted intervention, a care bundle including skin cleansing and hydration, protective material use, facemask selection and skin inspection, developed in line with international best practice guidelines. Data were collected using survey methodology. Frontline COVID-19 staff working in acute, community and ambulance services were invited to participate. Then, judgemental and volunteer sampling was used to select participants to undertake semi-structured interviews to elicit feedback on their perceptions of the care bundle. The sample included 120 acute hospital staff, 60 Ambulance staff, 24 Community Hub staff and 20 COVID-19 testing centre staff. A survey response rate of 61% was realised (n = 135/224). Of the participants, 32% (n = 43) had a facial pressure ulcer (FPI) pre-intervention and 13% (n = 18) developed an FPI while using the care bundle. The odds ratio (OR) was 0.33 (95% CI: 0.18 to 0.61; P = .0004), indicating a 77% reduction in the odds of FPI development with use of the care bundle. Analysis of the qualitative data from 22 interviews identified three key themes, the context for the care bundle, the ease of use of the care bundle and the care bundle as a solution to FPI development. The care bundle reduced the incidence of FPI among the participants and was found to be easy to use. Implementation of skin protection for frontline staff continues to be important given the persistently high incidence of COVID-19 and the ongoing need to wear PPE for protracted durations.

The effect of prone positioning on pressure injury incidence in adult intensive care unit patients: A meta-review of systematic reviews.

OBJECTIVE: Numerous systematic reviews have examined the impact of prone positioning on outcomes, including pressure injury (PI). The objective of this meta-review was to synthesise the evidence on the effect of prone positioning on the incidence and location of PIs in adult intensive care unit patients. REVIEW METHOD: This is a meta-review of published systematic reviews. Five databases were searched; data were extracted by three authors and adjudicated by a fourth. The AMSTAR-2 tool was used to quality appraise the selected articles, which was completed by three authors with a fourth adjudicating. RESULTS: Ten systematic reviews were synthesised. The cumulative incidence of PI in 15,979 adult patients ranged from 25.7% to 48.5%. One study did not report adult numbers. Only one review reported the secondary outcome of PI location. PIs were identified in 13 locations such as the face, chest, iliac crest, and knees. Using the AMSTAR-2, three reviews were assessed as high quality, six as moderate quality, and one as low quality. CONCLUSION: The high incidence of PI in the prone position highlights the need for targeted preventative strategies. Care bundles may be one approach, given their beneficial effects for the prevention of PI in other populations. This review highlights the need for proactive approaches to limit unintended consequences of the use of the prone position, especially notable in the current COVID-19 pandemic.

The role of viral genomics in understanding COVID-19 outbreaks in long-term care facilities.

We reviewed all genomic epidemiology studies on COVID-19 in long-term care facilities (LTCFs) that had been published to date. We found that staff and residents were usually infected with identical, or near identical, SARS-CoV-2 genomes. Outbreaks usually involved one predominant cluster, and the same lineages persisted in LTCFs despite infection control measures. Outbreaks were most commonly due to single or few introductions followed by a spread rather than a series of seeding events from the community into LTCFs. The sequencing of samples taken consecutively from the same individuals at the same facilities showed the persistence of the same genome sequence, indicating that the sequencing technique was robust over time. When combined with local epidemiology, genomics allowed probable transmission sources to be better characterised. The transmission between LTCFs was detected in multiple studies. The mortality rate among residents was high in all facilities, regardless of the lineage. Bioinformatics methods were inadequate in a third of the studies reviewed, and reproducing the analyses was difficult because sequencing data were not available in many facilities.

Facial pressure injuries and the COVID-19 pandemic: skin protection care to enhance staff safety in an acute hospital setting.

OBJECTIVES: The aim of this study was to determine the impact of a specially designed care bundle on the development of facial pressure injuries (PI) among frontline healthcare workers wearing personal protective equipment (PPE) during the COVID-19 pandemic. The primary outcome of interest was the incidence of facial PIs. The secondary outcomes of interest were facial pain while wearing PPE and ease of use of the care bundle. METHODS: This study used a voluntary survey by questionnaire, supplemented by a qualitative analysis of interviews from a small purposive sample that took place in one large Irish hospital over a two-month period in 2020. The hospital was a city-based public university teaching hospital with 800 inpatient beds. The intervention was a care bundle consisting of skin protection, face mask selection, material use, skin inspection, cleansing and hydration developed in line with international best practice guidelines. All staff working in COVID-19 wards, intensive care units and the emergency department in the hospital were given a kitbag containing the elements of the care bundle plus an information pamphlet. Data were collected via a survey and interviews. RESULTS: A total of 114 staff provided feedback on the use of the care bundle. Before using the care bundle 29% (n=33) of the respondents reported developing a facial PI, whereas after using the care bundle only 8% (n=9) of the respondents reported developing a facial PI. The odds ratio (OR) of skin injury development was 4.75 (95% confidence interval (CI): 2.15-10.49; p=0.0001), suggesting that after the care bundle was issued, those who responded to the survey were almost five times less likely to develop a skin injury. Interviews with 14 staff determined that the bundle was easy to use and safe. CONCLUSION: Among those who responded to the survey, the use of the bundle was associated with a reduction in the incidence of skin injury from 29% to 8%, and respondents found the bundle easy to use, safe and effective. As with evidence from the international literature, this study has identified that when skincare is prioritised, and a systematic preventative care bundle approach is adopted, there are clear benefits for the individuals involved.

eHealth for neonatal nurse education despite Covid-19.

AIM: The aim of this contemporary issue paper is to challenge the premise that the term "eHealth" is relatable to patient or service users only. It will be critically explored if the term can be broadened to include neonatal nurse education interventions. DESIGN: A review of current literature will form the basis for the critical discussion of the term eHealth, and why it can be associated with neonatal nurse education. METHODS: The critical discussion will identify and review past and current literature relating to eHealth and its origins. It will portray the viability of the term eHealth as more than just a patient associated intervention, and why it should also be encompassed as a neonatal nurse education option. CONCLUSION: eHealth is traditionally identifiable as a service user intervention or source of information. The term should be broadened to encompass neonatal nurse education and used as a resource that is easily accessible and user friendly. This will in turn encourage the personal and professional development of neonatal nurses and should ultimately contribute to evidence based best practices in the clinical environment, despite the current global pandemic.

Differences Between Autistic and Non-autistic Adults in the Recognition of Anger From Dynamic Expressions Remain After Controlling for Alexithymia. (preprint)

A burgeoning literature suggests that alexithymia, and not autism, is responsible for the difficulties with static emotion recognition that are documented in the autistic population. Here we investigate whether alexithymia can also account for difficulties with dynamic facial expressions. Autistic and control adults (N=60) matched on age, gender, non-verbal reasoning ability and alexithymia, completed an emotion recognition task, which employed dynamic point light displays of emotional facial expressions that varied in speed and spatial exaggeration. The ASD group exhibited significantly lower recognition accuracy for angry, but not happy or sad, expressions with normal speed and spatial exaggeration. The level of autistic, and not alexithymic, traits was a significant predictor of accuracy for angry expressions with normal speed and spatial exaggeration.

Prevention of pressure ulcers among individuals cared for in the prone position: lessons for the COVID-19 emergency.

OBJECTIVE: Pressure ulcers (PUs) involve the destruction of skin and underlying tissue due to prolonged pressure and shear forces. These ulcers are painful and significantly reduce a person's quality of life. PUs are also expensive to manage and impact negatively on the achievement of cost-effective, efficient care delivery. METHOD: Prone positioning is a postural therapy that aims to enhance respiratory function through increasing oxygenation levels. In contemporary clinical practice, ventilation in the prone position is indicated for patients with severe acute respiratory distress syndrome. However, despite its advantages in terms of respiratory function, several studies have examined complications of prone position ventilation and have identified PUs (facial PUs as well as PUs on other weight-bearing areas of the body) as a frequent complication in patients who are already in a precarious medical situation. International data suggest that up to 57% of patients nursed in the prone position develop a PU. The aim of this clinical review is to identify and review evidence-based recommendations developed to facilitate the selection and application of preventive interventions aimed at reducing PU development in patients ventilated in the prone position. Given the current COVID-19 crisis, this review is timely as intensive care unit (ICU) patients with COVID-19 require ventilation in the prone position at a level that is disproportionate to the general intensive care population. Up to 28% of patients admitted to the ICU with confirmed infection due to severe COVID-19 are cared for in the prone position. The scope of this review is limited to adult individuals only. RESULTS: The skin assessment should be undertaken before proning and following positioning the patient back into the supine position. Although it is essential to keep the skin clean and moisturised, using pH-balanced cleansers, there is inconsistency in terms of the evidence to support the type of moisturiser. Use of positioning devices in addition to repositioning is recommended to offload pressure points on the face and body. Further, using dressings such as hydrocolloids, transparent film and silicone may be of benefit in decreasing facial skin breakdown. CONCLUSION: Given the importance of PU prevention in this cohort of patients, adopting a focused prevention strategy, including skin assessment and care, offloading and pressure redistribution, and dressings for prevention may contribute to a reduction in the incidence and prevalence of these largely preventable wounds.