Deployment of whole genome next-generation sequencing of SARS-CoV-2 in a military maritime setting.

BACKGROUND: SARS-CoV-2 can spread rapidly on maritime platforms. Several outbreaks of SARS-CoV-2 have been reported on warships at sea, where transmission is facilitated by living and working in close quarters. Core components of infection control measures such as social distancing, patient isolation and quarantine of exposed persons are extremely difficult to implement. Whole genome sequencing (WGS) of SARS-CoV-2 has facilitated epidemiological investigations of outbreaks, impacting on outbreak management in real time by identifying transmission patterns, clusters of infection and guiding control measures. We suggest such a capability could mitigate against the impact of SARS-CoV-2 in maritime settings. METHODS: We set out to establish SARS-CoV-2 WGS using miniaturised nanopore sequencing technology aboard the Royal Fleet Auxiliary ARGUS while at sea. Objectives included designing a simplified protocol requiring minimal reagents and processing steps, the use of miniaturised equipment compatible for use in limited space, and a streamlined and standalone data analysis capability to allow rapid in situ data acquisition and interpretation. RESULTS: Eleven clinical samples with blinded SARS-CoV-2 status were tested at sea. Following viral RNA extraction and ARTIC sequencing library preparation, reverse transcription and ARTIC PCR-tiling were performed. Samples were subsequently barcoded and sequenced using the Oxford Nanopore MinION Mk1B. An offline version of the MinKNOW software was used followed by CLC Genomics Workbench for downstream analysis for variant identification and phylogenetic tree construction. All samples were correctly classified, and relatedness identified. CONCLUSIONS: It is feasible to establish a small footprint sequencing capability to conduct SARS-CoV-2 WGS in a military maritime environment at sea with limited access to reach-back support. This proof-of-concept study has highlighted the potential of deploying such technology in the future to military environments, both maritime and land-based, to provide meaningful clinical data to aid outbreak investigations.

Attitudes to fertility issues among adults with cystic fibrosis in Scotland. The Collaborative Group of Scottish Adult CF Centres.

BACKGROUND: With increasing life expectancy, issues of fertility and pregnancy are pertinent to patients with cystic fibrosis. For this reason, the four Scottish Cystic Fibrosis centres asked men and women with cystic fibrosis about their attitudes to fertility and to information given to them by health professionals. METHODS: A postal questionnaire was sent to 116 men and 79 women aged 16 years and over attending four Scottish Cystic Fibrosis clinics. RESULTS: There was a 70% response rate (82 men, 54 women). All but two men knew that they were likely to be infertile. 37% of respondents lived with a partner; 14 women (26%) and five men (6%) had children. For 85% of men and 72% of women having children was important now or would be in the next 10 years. 43% of men and 26% of women had never had any discussion on fertility issues with cystic fibrosis health professionals. 56% of men thought that first discussion with a health professional about infertility should be before the age of 16 years; 12% remembered having a first discussion at that age. Learning of their infertility was associated with strong negative emotions for most men. Women were more likely than men to have initiated first discussion (17 (32%) versus eight (10%); p<0.01). Twenty five men (31%) and 32 women (59%) were currently using contraception. Ten men (12%) and 15 women (28%) had discussed contraception at the Cystic Fibrosis clinic (p = 0.01). CONCLUSIONS: Parenting and fertility issues are important for men and women with cystic fibrosis but many patients do not find out what they want to know from discussion with health professionals. Patients want discussion to begin in early adolescence. Men in particular are likely to be reluctant to introduce these issues; health professionals should be aware of the need actively to initiate discussion.

Relationship between p53 mutation incidence in oral cavity squamous cell carcinomas and patient tobacco use.

It is well-established that a high incidence of p53 mutations exist in oral cavity squamous cell carcinomas (OCSCCs). To determine whether p53 mutations are etiologically associated with OCSCC development or are associated with exposure to specific carcinogens, we have analyzed the conserved regions of the p53 gene (exons 5-9) in 48 OCSCCs obtained from patients with varied tobacco and alcohol use histories by polymerase chain reaction/single strand conformational polymorphism (PCR/SSCP) and DNA sequencing analysis. Thirty-eight percent (18/48) of the OCSCCs exhibited a mutation in exons 5-9 of the p53 gene. There was a significantly higher incidence of p53 mutations in OCSCCs from tobacco users (predominantly cigarette smokers) compared to those who had never used tobacco. No increase in the incidence of p53 mutation was observed in tobacco users who drank alcohol. G to A transitions and deletions were the predominant mutations observed in OCSCCs from tobacco users. No specific pattern of mutation was observed in OCSCCs from those subjects who had never used tobacco. These data suggest that a history of tobacco use was associated with a high incidence of p53 mutations in patients with OCSCC and that tobacco carcinogens include a specific pattern of mutations in oral cavity tissue in vivo.

A low incidence of p53 mutations in pre-malignant lesions of the oral cavity from non-tobacco users.

To determine the incidence of p53 mutations in pre-malignant lesions of the oral cavity from individuals without prior history of tobacco use, we have analyzed the conserved regions of the p53 gene (exons 5-9) in archival oral cavity lesion specimens obtained from patients with varied tobacco use histories, by polymerase chain reaction/single strand conformational polymorphism (PCR/SSCP) and DNA sequencing analysis. Twenty-six lesions were analyzed from 14 patients, with multiple lesions obtained from 8 patients. Six of these patients used tobacco, (3 being cigarette smokers, 1 ex-cigarette smoker, 1 moderate cigar smoker and 1 snuff chewer). The remaining 8 patients had no prior history of tobacco use. Thirteen of the pre-malignant lesions exhibited severe dysplasia, 9 exhibited moderate dysplasia and 4 exhibited mild dysplasia. Four of the 26 lesions exhibited p53 mutations, each being from a tobacco user. None of the 13 lesions from never-tobacco users exhibited p53 mutations. There was a significantly higher p53 mutation incidence in pre-malignant lesions from tobacco users (including ex-smokers) than in non-tobacco users as well as in cigarette smokers plus snuff chewers than in non-tobacco users. Two of the mutations were observed in lesions exhibiting severe dysplasia: 1 in a lesion exhibiting moderate dysplasia and 1 in a lesion exhibiting mild dysplasia. These data suggest that p53 mutation may be a very early event in oral cavity tumor progression and demonstrate that pre-malignant lesions obtained from non-tobacco users do not exhibit p53 mutations.

Oxidized low density lipoprotein increases U937 cell 5-lipoxygenase activity: induction of 5-lipoxygenase activating protein.

This study examines the effects of oxidized low density lipoprotein (ox-LDL) on mononuclear cell arachidonic acid (AA) metabolism. U937 and HL60 cells, employed as models for mononuclear cells and promyelocytic cells, respectively, were exposed to ox-LDL (20 micrograms protein/ml) for 24 hours. HPLC analysis of 1-14C-AA metabolites indicates that ox-LDL increases U937 and HL60 cell production of 15-hydroxyeicosatetraenoic acid (15-HETE) and 5-hydroxyeicosatetraenoic acid (5-HETE). Northern analysis indicates that ox-LDL increases U937 cell FLAP transcript levels 10-times control levels but did not appear to alter 5-lipoxygenase (5-LO) mRNA levels. In contrast, ox-LDL increases HL60 cell transcript levels for FLAP and 5-LO 1.5 times and 10 times control levels, respectively. Thus, we propose that ox-LDL plays an important role in the up-regulation of the 5-LO pathway in mononuclear cells. Such activation may explain, in part, the mechanisms by which ox-LDL promotes atherogenesis.

Associations between patient religiosity and alcohol attitudes and knowledge in an alcohol treatment program.

Studies, carried out in generalized populations, have shown inverse relationships between degree of religiosity and attitudes towards drinking, knowledge about alcohol, amount of alcohol consumed, and physical complications of alcohol abuse. Within a population of chronic male alcoholics, we found that the more religious patients had a more anti-alcohol attitude; however, none of the other correlations was statistically significant. Within this population, the least religious patients were more likely to change their attitude toward alcohol and to increase their knowledge of the deleterious effects of alcohol after 4 weeks of treatment on an inpatient rehabilitation unit.