A framework for real-time monitoring, analysis and adaptive sampling of viral amplicon nanopore sequencing.

The ongoing SARS-CoV-2 pandemic demonstrates the utility of real-time sequence analysis in monitoring and surveillance of pathogens. However, cost-effective sequencing requires that samples be PCR amplified and multiplexed via barcoding onto a single flow cell, resulting in challenges with maximising and balancing coverage for each sample. To address this, we developed a real-time analysis pipeline to maximise flow cell performance and optimise sequencing time and costs for any amplicon based sequencing. We extended our nanopore analysis platform MinoTour to incorporate ARTIC network bioinformatics analysis pipelines. MinoTour predicts which samples will reach sufficient coverage for downstream analysis and runs the ARTIC networks Medaka pipeline once sufficient coverage has been reached. We show that stopping a viral sequencing run earlier, at the point that sufficient data has become available, has no negative effect on subsequent down-stream analysis. A separate tool, SwordFish, is used to automate adaptive sampling on Nanopore sequencers during the sequencing run. This enables normalisation of coverage both within (amplicons) and between samples (barcodes) on barcoded sequencing runs. We show that this process enriches under-represented samples and amplicons in a library as well as reducing the time taken to obtain complete genomes without affecting the consensus sequence.

A scoping review on the impact of the COVID-19 pandemic on physical activity and sedentary behavior in Saudi Arabia.

BACKGROUND: In Saudi Arabia, stay-at-home orders to address the coronavirus disease 2019 (COVID-19) pandemic between March 15 and 23, 2020 and eased on May 28, 2020. We conducted a scoping review to systematically describe physical activity and sedentary behavior in Saudi Arabia associated with the timing of the lockdown. METHODS: We searched six databases on December 13, 2021 for articles published in English or Arabic from 2018 to the search date. Studies must have reported data from Saudi Arabia for any age and measured physical activity or sedentary behavior. RESULTS: Overall, 286 records were found; after excluding duplicates, 209 records were screened, and 19 studies were included in the review. Overall, 15 studies were cross-sectional, and 4 studies were prospective cohorts. Three studies included children and adolescents (age: 2-18 years), and 16 studies included adults (age: 15-99 years). Data collection periods were < = 5 months, with 17 studies collecting data in 2020 only, one study in 2020-2021, and one study in 2021. The median analytic sample size was 363 (interquartile range 262-640). Three studies of children/adolescents collected behaviors online at one time using parental reporting, with one also allowing self-reporting. All three studies found that physical activity was lower during and/or following the lockdown than before the lockdown. Two studies found screen time, television watching, and playing video games were higher during or following the lockdown than before the lockdown. Sixteen adult studies assessed physical activity, with 15 utilizing self-reporting and one using accelerometry. Physical activity, exercise, walking, and park visits were all lower during or following the lockdown than before the lockdown. Six adult studies assessed sedentary behavior using self-report. Sitting time (4 studies) and screen time (2 studies) were higher during or following the lockdown than before the lockdown. CONCLUSIONS: Among children, adolescents, and adults, studies consistently indicated that in the short-term, physical activity decreased and sedentary behavior increased in conjunction with the movement restrictions. Given the widespread impact of the pandemic on other health behaviors, it would be important to continue tracking behaviors post-lockdown and identify subpopulations that may not have returned to their physical activity and sedentary behavior to pre-pandemic levels to focus on intervention efforts.

Emergency Department Point-Of-Care Echocardiography and Lung Ultrasound in Predicting COVID-19 Severity.

OBJECTIVES: We sought to determine if point-of-care ultrasound (POCUS) performed on patients with COVID-19 in the emergency department (ED) can help predict disease course, severity, or identify complications. METHODS: This was a retrospective cohort study of adult ED patients who tested positive for COVID-19 at hospital admission or within 2 weeks of presentation and received heart or lung POCUS. Clips were reviewed for presence of decreased left ventricular ejection fraction (LVEF), right ventricular dilation, presence of B-lines, and pleural line abnormalities. Patients with worsening hypoxemic respiratory failure or shock requiring higher level of care and patients who expired were considered to have developed severe COVID-19. Regression analysis was performed to determine if there was a correlation between ED POCUS findings and development of severe COVID-19. RESULTS: A total of 155 patients met study criteria; 148 patients had documented cardiac views and 116 patients had documented lung views (113 with both). Mean age was 66.5 years old (±18.6) and 53% of subjects were female. Subjects with decreased LVEF that was not previously documented had increased odds of having severe COVID during their hospitalization compared to those with old or no dysfunction (OR 5.66, 95% CI: 1.55-19.95, P = .08). The presence of pleural line abnormalities was also predictive for development of severe COVID (OR 2.68, 95% CI: 1.04-6.92, P = .04). CONCLUSION: POCUS findings of previously unidentified decreased LVEF and pleural line abnormalities in patients with COVID-19 evaluated in the ED were correlated to a more severe clinical course and worse prognosis.

Clinical outcomes and immune responses to SARS-CoV-2 vaccination in severe aplastic anaemia.

Patients with severe aplastic anaemia (SAA) are often not vaccinated against viruses due to concerns of ineffective protective antibody response and potential for pathogenic global immune system activation, leading to relapse. We evaluated the impact of COVID-19 vaccination on haematological indices and disease status and characterized the humoural and cellular responses to vaccination in 50 SAA patients, who were previously treated with immunosuppressive therapy (IST). There was no significant difference in haemoglobin (p = 0.52), platelet count (p = 0.67), absolute lymphocyte (p = 0.42) and neutrophil (p = 0.98) counts prior to and after completion of vaccination series. Relapse after vaccination, defined as a progressive decline in counts requiring treatment, occurred in three patients (6%). Humoural response was detectable in 90% (28/31) of cases by reduction in an in-vitro Angiotensin II Converting Enzyme (ACE2) binding and neutralization assay, even in patients receiving ciclosporin (10/11, 90.1%). Comparison of spike-specific T-cell responses in 27 SAA patients and 10 control subjects revealed qualitatively similar CD4+ Th1-dominant responses to vaccination. There was no difference in CD4+ (p = 0.77) or CD8+ (p = 0.74) T-cell responses between patients on or off ciclosporin therapy at the time of vaccination. Our data highlight appropriate humoural and cellular responses in SAA previously treated with IST and true relapse after vaccination is rare.

Overt and Occult Hypoxemia in Patients Hospitalized With COVID-19.

Progressive hypoxemia is the predominant mode of deterioration in COVID-19. Among hypoxemia measures, the ratio of the Pao2 to the Fio2 (P/F ratio) has optimal construct validity but poor availability because it requires arterial blood sampling. Pulse oximetry reports oxygenation continuously (ratio of the Spo2 to the Fio2 [S/F ratio]), but it is affected by skin color and occult hypoxemia can occur in Black patients. Oxygen dissociation curves allow noninvasive estimation of P/F ratios (ePFRs) but remain unproven. OBJECTIVES: Measure overt and occult hypoxemia using ePFR. DESIGN SETTING AND PARTICIPANTS: We retrospectively studied COVID-19 hospital encounters (n = 5,319) at two academic centers (University of Virginia [UVA] and Emory University). MAIN OUTCOMES AND MEASURES: We measured primary outcomes (death or ICU transfer within 24 hr), ePFR, conventional hypoxemia measures, baseline predictors (age, sex, race, comorbidity), and acute predictors (National Early Warning Score [NEWS] and Sequential Organ Failure Assessment [SOFA]). We updated predictors every 15 minutes. We assessed predictive validity using adjusted odds ratios (AORs) and area under the receiver operating characteristic curves (AUROCs). We quantified disparities (Black vs non-Black) in empirical cumulative distributions using the Kolmogorov-Smirnov (K-S) two-sample test. RESULTS: Overt hypoxemia (low ePFR) predicted bad outcomes (AOR for a 100-point ePFR drop: 2.7 [UVA]; 1.7 [Emory]; p < 0.01) with better discrimination (AUROC: 0.76 [UVA]; 0.71 [Emory]) than NEWS (0.70 [both sites]) or SOFA (0.68 [UVA]; 0.65 [Emory]) and similar to S/F ratio (0.76 [UVA]; 0.70 [Emory]). We found racial differences consistent with occult hypoxemia. Black patients had better apparent oxygenation (K-S distance: 0.17 [both sites]; p < 0.01) but, for comparable ePFRs, worse outcomes than other patients (AOR: 2.2 [UVA]; 1.2 [Emory]; p < 0.01). CONCLUSIONS AND RELEVANCE: The ePFR was a valid measure of overt hypoxemia. In COVID-19, it may outperform multi-organ dysfunction models. By accounting for biased oximetry as well as clinicians' real-time responses to it (supplemental oxygen adjustment), ePFRs may reveal racial disparities attributable to occult hypoxemia.

Overt and Occult Hypoxemia in Patients Hospitalized With COVID-19

IMPORTANCE: Progressive hypoxemia is the predominant mode of deterioration in COVID-19. Among hypoxemia measures, the ratio of the Pao2 to the Fio2 (P/F ratio) has optimal construct validity but poor availability because it requires arterial blood sampling. Pulse oximetry reports oxygenation continuously (ratio of the Spo2 to the Fio2 [S/F ratio]), but it is affected by skin color and occult hypoxemia can occur in Black patients. Oxygen dissociation curves allow noninvasive estimation of P/F ratios (ePFRs) but remain unproven. OBJECTIVES: Measure overt and occult hypoxemia using ePFR. DESIGN, SETTING, AND PARTICIPANTS: We retrospectively studied COVID-19 hospital encounters (n = 5,319) at two academic centers (University of Virginia [UVA] and Emory University). MAIN OUTCOMES AND MEASURES: We measured primary outcomes (death or ICU transfer within 24 hr), ePFR, conventional hypoxemia measures, baseline predictors (age, sex, race, comorbidity), and acute predictors (National Early Warning Score [NEWS] and Sequential Organ Failure Assessment [SOFA]). We updated predictors every 15 minutes. We assessed predictive validity using adjusted odds ratios (AORs) and area under the receiver operating characteristic curves (AUROCs). We quantified disparities (Black vs non-Black) in empirical cumulative distributions using the Kolmogorov-Smirnov (K-S) two-sample test. RESULTS: Overt hypoxemia (low ePFR) predicted bad outcomes (AOR for a 100-point ePFR drop: 2.7 [UVA];1.7 [Emory];p < 0.01) with better discrimination (AUROC: 0.76 [UVA];0.71 [Emory]) than NEWS (0.70 [both sites]) or SOFA (0.68 [UVA];0.65 [Emory]) and similar to S/F ratio (0.76 [UVA];0.70 [Emory]). We found racial differences consistent with occult hypoxemia. Black patients had better apparent oxygenation (K-S distance: 0.17 [both sites];p < 0.01) but, for comparable ePFRs, worse outcomes than other patients (AOR: 2.2 [UVA];1.2 [Emory];p < 0.01). CONCLUSIONS AND RELEVANCE: The ePFR was a valid measure of overt hypoxemia. In COVID-19, it may outperform multi-organ dysfunction models. By accounting for biased oximetry as well as clinicians' real-time responses to it (supplemental oxygen adjustment), ePFRs may reveal racial disparities attributable to occult hypoxemia.

Immune correlates analysis of the ENSEMBLE single Ad26.COV2.S dose vaccine efficacy clinical trial.

Measuring immune correlates of disease acquisition and protection in the context of a clinical trial is a prerequisite for improved vaccine design. We analysed binding and neutralizing antibody measurements 4 weeks post vaccination as correlates of risk of moderate to severe-critical COVID-19 through 83 d post vaccination in the phase 3, double-blind placebo-controlled phase of ENSEMBLE, an international randomized efficacy trial of a single dose of Ad26.COV2.S. We also evaluated correlates of protection in the trial cohort. Of the three antibody immune markers we measured, we found most support for 50% inhibitory dilution (ID50) neutralizing antibody titre as a correlate of risk and of protection. The outcome hazard ratio was 0.49 (95% confidence interval 0.29, 0.81; P = 0.006) per 10-fold increase in ID50; vaccine efficacy was 60% (43%, 72%) at non-quantifiable ID50 (<2.7 IU50 ml-1) and increased to 89% (78%, 96%) at ID50 = 96.3 IU50 ml-1. Comparison of the vaccine efficacy by ID50 titre curves for ENSEMBLE-US, the COVE trial of the mRNA-1273 vaccine and the COV002-UK trial of the AZD1222 vaccine supported the ID50 titre as a correlate of protection across trials and vaccine types.

Implementation of a mailed faecal immunochemical test programme for colorectal cancer screening among Veterans.

BACKGROUND: Screening for colorectal cancer (CRC) with faecal immunochemical test (FIT) is effective at reducing CRC mortality. Unfortunately, the COVID-19 pandemic has been associated with deferred care, especially screening for CRC. AIM: We sought to develop a mailed FIT programme (MFP) to increase CRC screening and make recommendations for adoption across the Veterans Health Administration (VHA) and for other large healthcare systems. SETTING: 2 regional VA medical centres in California and Washington state. PARTICIPANTS: 5667 average risk veterans aged 50-75 overdue or due within 90 days for CRC screening. PROGRAMME DESCRIPTION: A multidisciplinary implementation team collaborated to mail an FIT kit to eligible veterans. Both sites mailed a primer postcard, and one site added an automated reminder call. PROGRAMME EVALUATION: We monitored FIT return and positivity rate, as well as impact of the programme on clinical staff. 34% of FIT kits were returned within 90 days and 7.8% were abnormal. DISCUSSION: We successfully implemented a population-based MFP at multiple regional VA sites and recommend that these efforts be spread across VA. Our model of regional leadership, facility champions and using centralised resources can be adaptable to other large healthcare systems. MFPs support catch-up from disrupted care by addressing access to CRC screening, unburden primary care visits and conserve limited procedural resources.

mRNA-1273 or mRNA-Omicron boost in vaccinated macaques elicits similar B cell expansion, neutralizing responses, and protection from Omicron.

SARS-CoV-2 Omicron is highly transmissible and has substantial resistance to neutralization following immunization with ancestral spike-matched vaccines. It is unclear whether boosting with Omicron-matched vaccines would enhance protection. Here, nonhuman primates that received mRNA-1273 at weeks 0 and 4 were boosted at week 41 with mRNA-1273 or mRNA-Omicron. Neutralizing titers against D614G were 4,760 and 270 reciprocal ID50 at week 6 (peak) and week 41 (preboost), respectively, and 320 and 110 for Omicron. 2 weeks after the boost, titers against D614G and Omicron increased to 5,360 and 2,980 for mRNA-1273 boost and 2,670 and 1,930 for mRNA-Omicron, respectively. Similar increases against BA.2 were observed. Following either boost, 70%-80% of spike-specific B cells were cross-reactive against WA1 and Omicron. Equivalent control of virus replication in lower airways was observed following Omicron challenge 1 month after either boost. These data show that mRNA-1273 and mRNA-Omicron elicit comparable immunity and protection shortly after the boost.

Luxury fashion retailers' localised marketing strategies in practice – evidence from China

Purpose>From an international retailing perspective, this empirical study aims to examine luxury fashion retailers' changing marketing strategies in China.Design/methodology/approach>Using case studies of 14 luxury fashion retailers, qualitative data were collected via 31 semi-structured executive interviews.Findings>Both standardised global and localised multinational marketing strategies were found to have initially been employed by luxury fashion retailers entering into China. Subsequently, localised multinational strategies became increasingly important for their post-entry operations and business development, particularly in terms of their product strategies. More specifically, as well as the introduction of Chinese brand names, product design has been adapted according to Chinese market conditions, and product portfolios have been adapted to satisfy regional differences. However, localised product sourcing in China is far less common.Research limitations/implications>As the findings are generated from China, they may not explain luxury fashion retailers' marketing strategies in other markets. Despite the relatively small sample size, the 14 luxury fashion retailer case studies originate from across a wide range of countries, retail formats and ownership structures and are therefore considered to be varied enough to represent the market.Practical implications>The study offers practitioners insights into the success that can be generated by the manipulation of marketing strategies, particularly product strategies, within the world's second biggest luxury market.Originality/value>This paper extends the current international retailing literature by examining and comparing the motives and practices of luxury fashion retailers and the increasing localisation of their marketing strategies in China as they move from initial market entry into their post-entry operations.

Availability of the core components of the World Health Organization infection prevention and control strategies in health facilities in Southwestern Uganda: Implications for control of COVID-19.

BACKGROUND: Infection prevention and control (IPC) practices are required to prevent nosocomial infection by severe acute respiratory syndrome coronavirus 2. In low- and middle-income countries, where resources are often limited, IPC practices are infrequently assessed. AIM: To assess the availability of the core components of World Health Organization (WHO) IPC practices at health facilities in Southwestern Uganda. METHODS: We assessed the availability of WHO IPC core components using a modified WHO IPC Assessment tool. We determined differences between government versus private ownership and by type of health facility. FINDINGS: We assessed 111 of 224 (50%) health facilities in four districts. The most frequently achieved core component of IPC strategies was environmental cleanliness with 75 of 111 (68%) facilities scoring >85%. The most infrequently achieved core component of IPC strategies was personal protective equipment (PPE) with only one of seven (14%) hospitals and no other facilities scoring >85%. Of the 20 hospital or health center IV facilities, five (25%) received an overall score of >85% compared to only one of 91 (1%) health center II or III facilities (odds ratio [OR] 30.0 [95% CI: 3.27-274.99], p=0.003). Of the 73 government facilities, two (3%) received an overall score of >85% compared to five of 38 (13%) private facilities (OR 0.24 [95% CI: 0.04-1.37], p=0.11). CONCLUSION: Few facilities in four districts in Southwestern Uganda achieved >85% availability of WHO IPC core components. Provision of PPE in these facilities should be prioritized.

The Impact of Real-Time Whole-Genome Sequencing in Controlling Healthcare-Associated SARS-CoV-2 Outbreaks.

Nosocomial severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections have severely affected bed capacity and patient flow. We utilized whole-genome sequencing (WGS) to identify outbreaks and focus infection control resources and intervention during the United Kingdom's second pandemic wave in late 2020. Phylogenetic analysis of WGS and epidemiological data pinpointed an initial transmission event to an admission ward, with immediate prior community infection linkage documented. High incidence of asymptomatic staff infection with genetically identical viral sequences was also observed, which may have contributed to the propagation of the outbreak. WGS allowed timely nosocomial transmission intervention measures, including admissions ward point-of-care testing and introduction of portable HEPA14 filters. Conversely, WGS excluded nosocomial transmission in 2 instances with temporospatial linkage, conserving time and resources. In summary, WGS significantly enhanced understanding of SARS-CoV-2 clusters in a hospital setting, both identifying high-risk areas and conversely validating existing control measures in other units, maintaining clinical service overall.

Engaging Community Health Workers and Social Care Staff as Social First Responders during the COVID-19 Crisis.

In this public health practice vignette, we describe an ongoing community and system intervention to identify and address social determinants of health and related needs experienced by ChristianaCare patients and the greater community during the Coronavirus pandemic. This intervention, being conducted by the ChristianaCare Office of Health Equity, in partnership with ChristianaCare's embedded research institute, the Value Institute, and the Community Outreach and Education division of the Helen F. Graham Cancer Center and Research Institute, engages more than 25 community health workers, health Guides, Latinx health promoters and other social care staff as social first responders during the COVID-19 crisis. These experienced front-line social care staff screen patients and community members for social needs; make referrals to agencies and organizations for needed assistance (e.g., food, housing, financial assistance); assess people's understanding of COVID-19 and preventive measures; provide education about COVID-19; and, connect patients and community members to COVID-19 testing and any relevant clinical services. While this ongoing intervention is under evaluation, we share here some preliminary lessons-learned and discuss the critical role that social first responders can play in reducing the growing adverse social and health impacts of COVID-19 across the state of Delaware.

Retrospective screening of routine respiratory samples revealed undetected community transmission and missed intervention opportunities for SARS-CoV-2 in the United Kingdom.

In the early phases of the SARS coronavirus type 2 (SARS-CoV-2) pandemic, testing focused on individuals fitting a strict case definition involving a limited set of symptoms together with an identified epidemiological risk, such as contact with an infected individual or travel to a high-risk area. To assess whether this impaired our ability to detect and control early introductions of the virus into the UK, we PCR-tested archival specimens collected on admission to a large UK teaching hospital who retrospectively were identified as having a clinical presentation compatible with COVID-19. In addition, we screened available archival specimens submitted for respiratory virus diagnosis, and dating back to early January 2020, for the presence of SARS-CoV-2 RNA. Our data provides evidence for widespread community circulation of SARS-CoV-2 in early February 2020 and into March that was undetected at the time due to restrictive case definitions informing testing policy. Genome sequence data showed that many of these early cases were infected with a distinct lineage of the virus. Sequences obtained from the first officially recorded case in Nottinghamshire - a traveller returning from Daegu, South Korea - also clustered with these early UK sequences suggesting acquisition of the virus occurred in the UK and not Daegu. Analysis of a larger sample of sequences obtained in the Nottinghamshire area revealed multiple viral introductions, mainly in late February and through March. These data highlight the importance of timely and extensive community testing to prevent future widespread transmission of the virus.

Late onset of Guillain-Barré syndrome following SARS-CoV-2 infection: part of 'long COVID-19 syndrome'?

We describe a case of delayed onset, acute demyelinating neuropathy secondary to novel SARS-CoV-2 infection. A previously healthy 46-year-old man presented with bilateral leg pain and loss of sensation in his feet 53 days after having COVID-19 pneumonitis. He developed painful sensory symptoms followed by a rapidly progressive lower motor neuron weakness involving all limbs, face and respiratory muscles, needing ventilatory support. In keeping with a diagnosis of Guillain-Barré syndrome, cerebrospinal fluid examination showed albuminocytologic dissociation and nerve conduction studies supported the diagnosis of an acute inflammatory demyelinating polyradiculoneuropathy. The delayed neurological dysfunction seen in our patient following SARS-CoV-2 infection may indicate a novel mechanism of disease that is part of the emerging 'long COVID-19 syndrome'.