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.

Development and operation of the defence COVID-19 lab as a SARS-CoV-2 diagnostic screening capability for UK military personnel

BACKGROUND

In the face of the COVID-19 pandemic, the Defence Science and Technology Laboratory (Dstl) and Defence Pathology combined to form the Defence Clinical Lab (DCL), an accredited (ISO/IEC 17025:2017) high-throughput SARS-CoV-2 PCR screening capability for military personnel.

LABORATORY STRUCTURE AND RESOURCE

The DCL was modular in organisation, with laboratory modules and supporting functions combining to provide the accredited SARS-CoV-2 (envelope (E)-gene) PCR assay. The DCL was resourced by Dstl scientists and military clinicians and biomedical scientists.

LABORATORY RESULTS

Over 12 months of operation, the DCL was open on 289 days and tested over 72 000 samples. Six hundred military SARS-CoV-2-positive results were reported with a median E-gene quantitation cycle (Cq) value of 30.44. The lowest Cq value for a positive result observed was 11.20. Only 64 samples (0.09%) were voided due to assay inhibition after processing started.

CONCLUSIONS

Through a sustained effort and despite various operational issues, the collaboration between Dstl scientific expertise and Defence Pathology clinical expertise provided the UK military with an accredited high-throughput SARS-CoV-2 PCR test capability at the height of the COVID-19 pandemic. The DCL helped facilitate military training and operational deployments contributing to the maintenance of UK military capability. In offering a bespoke capability, including features such as testing samples in unit batches and oversight by military consultant microbiologists, the DCL provided additional benefits to the UK Ministry of Defence that were potentially not available from other SARS-CoV-2 PCR laboratories. The links between Dstl and Defence Pathology have also been strengthened, benefitting future research activities and operational responses.

Microbiological Assay-Trienzyme Procedure for Total Folates in Cereals and Cereal Foods: Collaborative Study

In 1996, U.S. Food and Drug Administration regulations mandated the fortification of enriched cereal-grain products with folic acid, thereby emphasizing the need for validated methods for total folates in foods, particularly cereal products. The AOAC Official Methods (944.12, 960.46) currently used for the analysis of folate in foods for compliance purposes are microbiological methods. When the fortification regulations were finalized, no Official AOAC or Approved AACC methods for folate in cereal-grain products were in place. The AOAC Official Method (992.05) for folic acid in infant formula does not incorporate important improvements in the extraction procedure and was not considered suitable for the analysis of folates in foods in general. Amicrobiological assay protocol using a trienzyme extraction procedure was prepared and submitted for comments to 40 laboratories with recognized experience in folate analysis. On the basis of comments, the method was revised to have the conjugase (gamma-glutamyl-carboxy-peptidase) treatment follow a protease treatment, to include the use of cryoprotected inoculum, and to include the spectroscopic standardization of the standard and optional use of microtiter plates. Thirteen laboratories participated in a collaborative study of 10 required and 10 optional cereal-grain products, including flour, bread, cookies, baking mixes, and ready-to-eat breakfast cereals. The majority of the participating laboratories performed the assay by the standard test tube method; others used the microtiter plate modification for endpoint quantitation with equal success. For the required products, the relative standard deviation between laboratories (RSDR) ranged from 7.4 to 21.6% for 8 fortified (or enriched) products compared with expected (Horwitz equation-based) values of 11–20%. RSDR values were higher (22.7–52.9%) for 2 unfortified cereal-grain products. For the optional products, the RSDR ranged from 1.8 to 11.2% for 8 fortified products. RSDR values were higher (27.9–28.7%) for 2 unfortified cereal-grain products. Based on the results of the collaborative study, the microbiological assay with trienzyme extraction is recommended for adoption as Official First Action.

A Medium for the Presumptive Detection of Enterobacter sakazakii in Infant Formula: Interlaboratory Study

A standard method for the detection of Enterobacteriaceae was modified for the presumptive detection of Enterobacter sakazakii, and the modified method was validated in an interlaboratory trial with 16 laboratories from 8 European countries. The modification included a differential-elective medium for the isolation of E. sakazakii, consisting of nutrient agar (NA) supplemented with 4-methyl-umbelliferyl α-D-glucoside (α-MUG). A 25 g sample was added to 225 mL buffered peptone water. After incubation at 35° or 37°C for 16 or 20 h, 10 mL nonselective enrichment was transferred into 90 mL selective enrichment. The selective enrichment was streaked on violet-red bile glucose agar (VRBGA) and incubated at 37°C for 24 h. It was streaked in parallel on NA plates supplemented with α-MUG at 50 mg/L and incubated at 25°C for 16 h, and afterwards for an additional 24 h at room temperature in the dark. E. sakazakii appeared as vivid yellow colonies under normal light and showed blue/violet fluorescence under UV light on NA + α-MUG plates. Validation samples represented powdered infant formula without E. sakazakii (blanks) and with low (1–10 colony-forming units [CFU]/25 g) and medium (1–10 CFU/g) contamination levels. All samples contained Pseudomonas aeruginosa and Lactobacillus spp. as background flora. The specificity for blank samples was 100%. The sensitivity of the low contamination level was similar for VRBGA and NA + α-MUG, i.e., 66.7% (66.7% accordance, 53.9% concordance). For the medium level the sensitivities were 96.7% (93.3% accordance, 93.5% concordance) for VRBGA and 98.3% (96.9% accordance, 96.9% concordance) for NA + α-MUG.

Evaluating a pilot mental health awareness for managers' training course

BACKGROUND

Despite the substantial personal and economic consequences of mental ill-health, and the relationship between mental ill-health and poor management provision, further work is needed to provide a robust evaluation of employment interventions to address mental ill-health in the workplace.

AIMS

To provide a pilot service evaluation of a UK organization's mental health awareness for managers' training provision.

METHODS

Participants were 93 employees at a UK-based organization who attended one of the three different types of, independently facilitated, half-day training courses designed to raise managers' awareness and understanding of mental health. All participants were asked to complete three questionnaires (one prior to the training session, one immediately following the training session and one 3 months after the training session). Each questionnaire contained six questions concerning participants' awareness of mental ill-health, and their confidence in dealing with mental ill-health among employees.

RESULTS

Participants reported feeling more aware of mental ill-health at work and more confident in their ability to address mental ill-health among their employees after attending mental health awareness for managers' training.

CONCLUSIONS

Although further work is needed to explore the efficacy of different types of training, the results of our pilot evaluation alongside the extant literature suggest that workplace interventions can have positive implications for good mental health.

A survey of international antisepsis procedures for neuraxial catheterisation in labour

BACKGROUND

Neuraxial analgesia during labour is a mainstay of anaesthetic practice globally. Despite the potential for significant neurological and infectious complications, international antisepsis practices for neuraxial anaesthesia vary widely.

AIMS

The primary aim of this study was to clarify international antisepsis practices prior to neuraxial analgesia in labour. The secondary aim was to determine an approximate international incidence of neuraxial infections and neurological complications secondary to neuraxial analgesia techniques in labour.

MATERIALS AND METHODS

Heads of Departments of Anaesthesiology were invited to complete an online questionnaire exploring antisepsis practices and complications of neuraxial catheterisation. Data from 151 institutions in 13 countries were collected over 11months.

RESULTS

Data were collected for an estimated 6008540 deliveries and 3770800 neuraxial catheterisations. The average annual birth rate per institution was 3979 births, with an average of 2497 neuraxial catheterizations (representing 62.8% of deliveries). Forty-nine percent of responders reported always wearing sterile gowns for the procedure, whereas 47.7% never wear gowns. Chlorhexidine was used by 88.1% of those surveyed, and 96.7% always wore facemasks. Thirty-four percent of institutions reported infectious complications over a 10-year period. Ninety neuraxial infections were estimated, giving an approximate incidence of 1:41898 catheterisations (2.39 infections per 100000 catheterisations). A total of 202 neurological complications were reported, with an approximate incidence of 1:18667 catheterisations (5.36 neurological complications per 100000 catheterisations).

CONCLUSION

The survey demonstrated marked variation in aseptic practice between both responding centres and countries. The incidence of infectious and neurological complications secondary to neuraxial catherisation in labour has been approximated.

The challenge of teaching undergraduates evidence-based veterinary medicine

The Royal College of Veterinary Surgeons now lists 'How to evaluate evidence' as a day one competence for newly qualified vets. In this article, representatives from each of the veterinary schools in the UK discuss how the challenge of delivering and assessing the concepts of evidence-based veterinary medicine in a crowded undergraduate curriculum can be met.

Astaxanthin attenuates neurotoxicity in a mouse model of Parkinson’s disease

Background: Astaxanthin (AXT) is a natural carotenoid with diverse biological activities. Although it is best known as a potent antioxidant, recent work suggests additional mechanisms of action that have the potential to oppose the ongoing pathophysiology of Parkinson’s disease (PD). For example, AXT has a putative role in modulating microglial activity and preserving mitochondrial function, thereby implicating this compound as a neuroprotective agent. Both oxidative stress and inflammation are involved in the progression of many neurodegenerative diseases. Therefore, we examined the efficacy for AXT to reduced neurotoxicity in a toxic model of PD in mice. Methods: In this study, we used a 4-week dietary supplementation of algae derived AXT to reduce 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) induced dopaminergic cell death.Results: AXT treated mice were protected against the loss of tyrosine hydroxylase (TH) staining in the substantia nigra (SN) after MPTP exposure compared to the control diet. This effect of preserved TH immunoreactivity was also observed in the striatum. Furthermore, AXT administration was able to interrupt the neuroinflammatory process known to contribute to neurodegeneration in this model.Conclusions: We demonstrate that AXT neuroprotection was associated with attenuated microglial activation as indicated by reduced immunohistochemical detection of IBA-1 in the SN and striatum of AXT treated mice. Altogether, these studies suggest that AXT has neuroprotective property in the central nervous system against MPTP neurodegeneration.Keywords: Astaxanthin, Neuroprotection, Neurodegeneration, Neuroinflammation, Parkinson’s disease

Aqueous humor endothelin-1 and total retinal blood flow in patients with non-proliferative diabetic retinopathy

PurposeThe purpose of this study was to determine the association between aqueous ET-1 levels and total retinal blood flow (TRBF) in patients with non-insulin-dependent type 2 diabetes mellitus (T2DM) and early non-proliferative diabetic retinopathy (NPDR).Patients and methodsA total of 15 age-matched controls and 15 T2DM patients with NPDR were recruited into the study. Aqueous humor (~80-120 μl) was collected before cataract surgery to measure the levels of ET-1 using suspension multiplex array technology. Four weeks post surgery, six images were acquired to assess TRBF using the prototype RTVue Doppler FD-OCT (Optovue, Inc., Fremont, CA, USA) with a double circular scan protocol. At the same visit, forearm blood was collected to determine plasma glycosylated hemoglobin (A1c) levels.ResultsAqueous ET-1 was significantly elevated in the NPDR group compared with the control group (3.5±1.8 vs 2.2±0.8, P=0.02). TRBF was found to be significantly reduced in the NPDR group compared with the control group (34.5±9.1 vs 44.1±4.6 μl/min, P=0.002). TRBF and aqueous ET-1 were not correlated within the NPDR group (r=-0.24, P=0.22). In a multivariate analysis, high A1c was associated with reduced TRBF and aqueous ET-1 levels across control and NPDR groups (P<0.01).ConclusionAqueous ET-1 levels were increased while TRBF was reduced in patients with NPDR compared with the control group. Although not directly associated, the vasoconstrictory effects of ET-1 are consistent with a reduced TRBF observed in early DR. ET-1 dysregulation may contribute to a reduction in retinal blood flow during early DR.

Differences in musculoskeletal health due to gender in a rural multiethnic cohort: a Project FRONTIER study

Background

Very few studies have investigated differences in musculoskeletal health due to gender in a large rural population. The aim of this study is to investigate factors affecting musculoskeletal health in terms of hand grip strength, musculoskeletal discomfort, and gait disturbance in a rural-dwelling, multi-ethnic cohort.

Methods

Data for 1117 participants (40 years and older, 70 % female) of an ongoing rural healthcare study, Project FRONTIER, were analyzed. Subjects with a history of neurological disease, stroke and movement disorder were excluded. Dominant hand grip strength was assessed by dynamometry. Gait disturbance including stiff, spastic, narrow-based, wide-based, unstable or shuffling gait was rated. Musculoskeletal discomfort was assessed by self-reported survey. Data were analyzed by linear, logistic regression and negative binomial regressions as appropriate. Demographic and socioeconomic factors were adjusted in the multiple variable analyses.

Results

In both genders, advanced age was a risk factor for weaker hand grip strength; arthritis was positively associated with musculoskeletal discomfort, and fair or poor health was significantly associated with increased risk of gait disturbance. Greater waist circumference was associated with greater musculoskeletal discomfort in males only. In females, advanced age is the risk factor for musculoskeletal discomfort as well as gait disturbance. Females with fair or poor health had weaker hand grip strength. Higher C-reactive protein and HbA1c levels were also positively associated with gait disturbance in females, but not in males.

Conclusion

This cross-sectional study demonstrates how gender affects hand grip strength, musculoskeletal discomfort, and gait in a rural-dwelling multi-ethnic cohort. Our results suggest that musculoskeletal health may need to be assessed differently between males and females.

Coccidia (Apicomplexa: Eimeriidae) of Three-toed Box Turtles, Terrapene carolina triunguis (Reptilia: Testudines), from Arkansas and Oklahoma

We collected 50 three-toed box turtles (Terrapene carolina triunguis) from 9 counties of Arkansas and 4 counties of Oklahoma, and examined their feces for coccidial parasites. Nine of 24 (38%) turtles from Arkansas and 8 of 26 (31%) from Oklahoma were found to be passing oocysts of Eimeria ornata. This represents two new geographic distributional records for this coccidian. Measurements of individual isolates of E. ornata as well as morphological characteristics are provided with comparison to its original description and to another Terrapene coccidian, Eimeria carri. In addition, we noted an adelid pseudoparasite being passed by a single T. c. triunguis from Oklahoma that likely represents a parasite of arthropods.

PET and SPECT imaging of a radiolabeled minigastrin analogue conjugated with DOTA, NOTA, and NODAGA and labeled with (64)Cu, (68)Ga, and (111)In

Cholecystokinin-2 (CCK-2) receptors, overexpressed in cancer types such as small cell lung cancers (SCLC) and medullary thyroid carcinomas (MTC), may serve as targets for peptide receptor radionuclide imaging. A variety of CCK and gastrin analogues has been developed, but a major drawback is metabolic instability or high kidney uptake. The minigastrin analogue PP-F11 has previously been shown to be a promising peptide for imaging of CCK-2 receptor positive tumors and was therefore further evaluated. The peptide was conjugated with one of the macrocyclic chelators DOTA, NOTA, or NODAGA. The peptide conjugates were then radiolabeled with either (68)Ga, (64)Cu, or (111)In. All (radio)labeled compounds were evaluated in vitro (IC50) and in vivo (biodistribution and PET/CT and SPECT/CT imaging). IC50 values were in the low nanomolar range for all compounds (0.79-1.51 nM). In the biodistribution studies, (68)Ga- and (111)In-labeled peptides showed higher tumor-to-background ratios than the (64)Cu-labeled compounds. All tested radiolabeled compounds clearly visualized the CCK2 receptor positive tumor in PET or SPECT imaging. The chelator did not seem to affect in vivo behavior of the peptide for (111)In- and (68)Ga-labeled peptides. In contrast, the biodistribution of the (64)Cu-labeled peptides showed high uptake in the liver and in other organs, most likely caused by high blood levels, probably due to dissociation of (64)Cu from the chelator and subsequent transchelation to proteins. Based on the present study, (68)Ga-DOTA-PP-F11 might be a promising radiopharmaceutical for PET/CT imaging of CCK2 receptor expressing tumors such as MTC and SCLC. Clinical studies are warranted to investigate the potential of this tracer.

The effect of hypercapnia on the sensitivity to flicker defined stimuli

BACKGROUND/AIMS

To investigate the effect of increased CO2 levels on flicker defined stimuli.

METHODS

The sensitivity of two flicker defined tasks was measured in nine healthy, trained observers using the Flicker Defined Form (FDF) stimulus of the Heidelberg Edge Perimeter (HEP; Heidelberg Engineering) and Frequency Doubling Technology (FDT) stimulus of the Matrix perimeter (Carl Zeiss Meditec) during normoxia and 15% hypercapnia (end-tidal CO2 increased by 15% relative to baseline). HEP-FDF and Matrix-FDT sensitivities were analysed for the global field, superior and inferior hemifields and at specific matched eccentricities, using repeated measures analysis of variance. The main effect of hypercapnia on flicker sensitivity was analysed using regression models.

RESULTS

Higher flicker sensitivity outcomes with increasing CO2 values were found for HEP-FDF and Matrix-FDT with a statistically significant main effect for HEP-FDF global, superior and inferior hemifields (p<0.01 for all) as well as 6°, 18°, 12° and 24° eccentricities (p=0.03, 0.04, 0.01, 0.05, respectively). When comparing mean sensitivity values between normocapnia and hypercapnia conditions, no statistically significantly different results were found for HEP-FDF and Matrix-FDT (p>0.05).

CONCLUSIONS

As CO2 levels were increased in healthy young individuals, there was an associated increase in visual sensitivity that was only significant for HEP-FDF stimuli, highlighting the different mechanisms involved in processing each of HEP-FDF and Matrix-FDT stimuli. Mean visual sensitivity outcomes were found to be similar for normocapnia and hypercapnia suggesting that a capability to compensate for a mild and stable increase in systemic CO2 levels may exist.

Serum placental-type alkaline-phosphatase levels in patients with epithelial ovarian-carcinoma

Serum placental alkaline phosphatase (PLAP)-type immunoreactivity was measured in 190 women with epithelial ovarian malignancy, 27 women with borderline ovarian cancer and 334 control subjects with non-neoplastic or benign gynaecological disease. Smoking, ABO blood group and menopausal status affect serum concentrations of PLAP and results were corrected for these. Circulating levels were elevated in patients with cancer and increased with stage. Levels were unaltered in borderline ovarian disease. Two-year stage corrected survival analysis demonstrated a significant worsening of prognosis in patients with serum PLAP-type levels greater than the 100th centile for controls.

Plasma levels of potassium and magnessium after modified ultrafiltration in pediatric cardiac surgery with cardiopulmonary bypass

Objective: Modified ultrafiltration (MUF) reduces some of the complications associated with cardiopulmonary bypass (CPB) in pediatric cardiac surgery. However, we have observed hypokalemia and hypomagnesemia in children when MUF is used. Such alterations may elicit severe arrhythmias in the postoperative period. To date, no studies have focused on the effects MUF may have in plasma levels of potassium (K) and magnesium (Mg). The objective of our study was to determine if there is any variation in plasma levels of K (plK) and Mg (plMg) after MUF in children undergoing cardiac surgery with CPB.

Patients: Sixteen children scheduled for cardiac surgery with CBP and MUF were prospectively studied. Anesthetic, CPB and MUF management were standardized for all patients, the latter lasting for 10 minutes.

Results: Plasma K average levels before and after MUF were 4.16 mmol/L and 3.58 mmol/L, respectively. The average plasma Mg levels before and after MUF were 4.82 mmol/L and 4.81 mmol/L, respectively.

Conclusions: The plasma level of K is reduced by 13.7% after MUF (p<0.0001). The reduction in Mg at the same period of time was not statistically significant (p<0.970).

Iridovirus infections among Missouri River sturgeon: initial characterization, transmission, and evidence for establishment of a carrier state

Iridovirus infections of the integument were associated with disease and mortality among hatchery-reared populations of juvenile pallid sturgeon Scaphirhynchus albus and shovelnose sturgeon S. platorynchus from the Missouri River. Virus-infected cells in the integument of fins and body were greatly enlarged, possessed pleomorphic and eccentric nuclei, and exhibited an amphophilic to eosinophilic staining of the cytoplasm in hematoxylin-and-eosin-stained sections. Virus particles found in the host cell cytoplasm were composed of an outer hexagonal capsid measuring 254 nm in diameter and surrounding a dense nucleoid. Despite numerous attempts, the virus could not be propagated on routine cell lines used in fish viral diagnostics or from established cell lines from white sturgeon Acipenser transmontanus, pallid sturgeon, or shovelnose sturgeon. Bath exposures of healthy juvenile pallid sturgeon to a crude extract or a 0.45-microm-filtered extract from the fins of infected fish resulted in transmission of the virus and mortality. At water temperatures of 15 degrees C, the first deaths occurred at approximately 1 month; mortality peaked between 50 and 60 d postexposure, after which surviving fish recovered. Presence of the virus was confirmed among dead and moribund pallid sturgeon by both histology and detection of viral DNA by polymerase chain reaction methods. Feeding of infected tissues and cohabitation with virus-infected shovelnose sturgeon also resulted in successful virus transmission to juvenile pallid sturgeon. Virus infections among experimentally exposed pallid sturgeon that recovered from clinical episodes persisted for at least 8.5 months, and these apparently healthy fish transmitted the virus and disease to juvenile pallid sturgeon by cohabitation. The newly described Missouri River sturgeon iridovirus (MRSIV) as found in pallid sturgeon and shovelnose sturgeon shares many properties with a group of iridoviruses associated with serious skin and gill infections in several species of sturgeon.

Stresses in UHV Planar Magnetron Sputtered Films

A method has been developed to measure the stress in films which have been sputtered using a planar magnetron in a small-scale UHV chamber. The stress has been measured for diffent materials as a function of the sputtering gas pressure P and the substrate-target distance d. It is found that the stress in films of the same material deposited at different values of d is dependent only on the pressure-distance product (Pd), except at short (less than about 30mm) distances. The value of Pd required to produce a stress-free film is found to increase with the more extreme ratios between the atomic masses of the film material and the sputtering gas for the case of metals. However, the required Pd product is higher for the case of amorphous semiconductors. The stress in alloy films is also investigated.