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More than 80 % of world trade is delivered via sea, making the maritime supply chain a very important backbone for the economy (UNCTAD 2020). Containerized trade regularly outperforms other types of transport in terms of growth, coinciding with consistent increases of average container vessel sizes (UNCTAD 2020). Container terminal operations are heavily affected by this development, since less but larger port calls create unwanted peaks and stress on the terminals and the hinterland. Not all container terminals are affected equally by the described situation. Economic cycles and events such as the global COVID-19 pandemic or the Russian war in Ukraine change the global supply chains, trade characteristics and transport demands between ports in the world. In 2004, Hartmann proposed an approach to create scenarios for simulation and optimization in the sense of container terminal planning and logistics. Due to the significant changes in maritime trade over the years, a new approach for generating synthetic container flow data became practical. In 2021, we introduced a rethought and reworked approach on this topic.The proposed tool, named ConFlowGen, aims to assist planners, scientists, and other maritime experts with providing comprehensive container flow scenarios based on minimal inputs and assumptions of the user. In this paper, we introduce ConFlowGen's general principle of operation in an exemplary use case in the context of container terminal planning.

Abstract Background On December 8th 2020, NHS England administered the first COVID-19 vaccination as part of an ambitious vaccination programme during a global health emergency. Aims To develop a framework for detailed near-real-time monitoring of COVID-19 vaccine roll-out; to describe trends and variation in coverage by geographic area, and between key clinical and demographic patient groups. Methods Working on behalf of NHS England we used routine clinical data from 23.4 million patients to conduct a retrospective cohort study of comprehensive electronic health record data in NHS England, using the OpenSAFELY-TPP platform which covers approximately 40% of the general population in England with weekly data updates. We developed algorithms to identify key demographic and clinical sub-groups within this population and generated descriptive statistics on proportion of eligible patients receiving the vaccine among key Joint Committee on Vaccination and Immunisation (JCVI) target groups. Results Between December 8th and January 13th 961,580 people out of 23.4m in our dataset received a COVID-19 vaccine. Of 1,160,062 patients aged 80 or over and not living in a care home (currently targeted by JCVI) 476,375 had been vaccinated in total (41.1%). We observed a substantial divergence in vaccination by ethnicity within this group (White 42.5% vaccinated, Black 20.5%) and across rankings of deprivation (least deprived 44.7%, most deprived 37.9%). Patients with pre-existing medical conditions were equally likely, or more likely, to have received a vaccine across most co-morbidity groups with two exceptions: severe mental illness (30.3% vaccinated) and learning disability (28.1%). We identify substantial variation in vaccination among the over-80s between Sustainability and Transformation Partnerships (STPs; Range 12%-74%); lower vaccination rates among ethnic minority and deprived groups was observed in most but not all STPs. In the 70-79 age cohort 74,108 people (3.6%) had been vaccinated. 378,921 vaccine recipients under 70 and not identifiably resident in a care home were presumed to be health or social care workers; 32,174 recipients were identified as older aged care home residents (33.2% coverage). Of all those vaccinated, 169,472 had received a second dose (17.6%). Conclusions The NHS in England has rapidly delivered mass vaccination. We were able to deploy a data monitoring framework across small clinical subgroups using linked patient-level NHS data on 23.4 million people with very short delays from vaccine administration to completed analysis. Targeted activity may be needed to address lower vaccination rates observed among certain key groups: ethnic minorities, people living in areas of higher deprivation, and those with severe mental illness or learning disabilities. However we note that this data is only from the first preliminary weeks of the vaccination programme. Variation in vaccination coverage between groups and regions will have many complex drivers, the figures presented in this manuscript require thoughtful interpretation to support a rapidly evolving NHS vaccination campaign; we are sharing local level data with national and regional NHS teams on request.

AbstractProlonged infections of immunocompromised individuals have been proposed as a crucial source of new variants of SARS-CoV-2 during the COVID-19 pandemic. In principle, sustained within-host antigenic evolution in immunocompromised hosts could allow novel immune escape variants to emerge more rapidly, but little is known about how and when immunocompromised hosts play a critical role in pathogen evolution. Here, we use a simple mathematical model to understand the effects of immunocompromised hosts on the emergence of immune escape variants in the presence and absence of epistasis. We show that when the pathogen does not have to cross a fitness valley for immune escape to occur (no epistasis), immunocompromised individuals have no qualitative effect on antigenic evolution (although they may accelerate immune escape if within-host evolutionary dynamics are faster in immunocompromised individuals). But if a fitness valley exists between immune escape variants at the between-host level (epistasis), then persistent infections of immunocompromised individuals allow mutations to accumulate, therefore facilitating rather than simply speeding up antigenic evolution. Our results suggest that better genomic surveillance of infected immunocompromised individuals and better global health equality, including improving access to vaccines and treatments for individuals who are immunocompromised (especially in lower- and middle-income countries), may be crucial to preventing the emergence of future immune escape variants of SARS-CoV-2.Lay SummaryWe study the role that immunocompromised individuals may play in the evolution of novel variants of the coronavirus responsible for the COVID-19 pandemic. We show that immunocompromised hosts can be crucial for the evolution of immune escape variants. Targeted treatment and surveillance may therefore prevent the emergence of new variants.

AO_SCPLOWBSTRACTC_SCPLOWNon-pharmaceutical interventions (NPIs), such as social distancing and contact tracing, have been widely implemented during the COVID-19 pandemic. In addition to playing an important role in suppressing transmission, NPIs influence pathogen evolution by mediating mutation supply and altering the strength of selection for novel variants. However, it is unclear how NPIs might affect the emergence of novel variants of concern that are able to escape pre-existing immunity (partially or fully), are more transmissible, or cause greater mortality. Here, we analyse a stochastic two-strain epidemiological model to determine how the strength of NPIs affects the emergence of variants with similar or contrasting life-history characteristics to the wildtype. We show that, while stronger and timelier NPIs generally reduce the likelihood of variant emergence, it is possible for more transmissible variants with high cross immunity to have a greater probability of emerging at intermediate levels of NPIs. However, since one cannot predict the characteristics of a variant, the best strategy to prevent emergence is likely to be implementation of strong, timely NPIs. AO_SCPLOWUTHORC_SCPLOWO_SCPCAP C_SCPCAPO_SCPLOWSUMMARYC_SCPLOWDuring the COVID-19 pandemic, a wide range of non-pharmaceutical interventions, including mask wearing, quarantine, isolation, and lockdowns, have been used by governments around the world to suppress virus transmission. Although considerable efforts have been made to understand how such interventions affect transmission, much less attention has been paid to their effects on pathogen evolution. While vaccines are well-known to affect virus evolution, non-pharmaceutical interventions also influence mutation supply and the strength of selection, and hence play a key role in the emergence of novel variants. Here, we use a relatively simple mathematical model to explore how non-pharmaceutical interventions during an epidemic affect the emergence of a novel variant of a pathogen. We show that in general, it is important to implement effective transmission-reducing public health measures in a timely manner to prevent the emergence of novel variants, which may be more transmissible, more deadly, or able to escape immunity.

AbstractSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) surface spike glycoprotein - a major antibody target - is critical for virus entry via engagement of human angiotensin-converting enzyme 2 (ACE2) receptor. Despite successes with existing vaccines and therapies that primarily target the receptor binding domain (RBD) of the spike protein, the susceptibility of RBD to mutations provides escape routes for the SARS-CoV-2 from neutralizing antibodies. On the other hand, structural conservation in the spike protein can be targeted to reduce escape mutations and achieve broad protection. Here, we designed candidate stable immunogens that mimic surface features of selected conserved regions of spike protein through ‘epitope grafting,’ in which we present the target epitope topology on diverse heterologous scaffolds that can structurally accommodate the spike epitopes. Structural characterization of the epitope-scaffolds showed stark agreement with our computational models and target epitopes. The sera from mice immunized with engineered designs display epitope-scaffolds and spike binding activity. We also demonstrated the utility of the designed epitope-scaffolds in diagnostic applications. Taken all together, our study provides important methodology for targeting the conserved, non-RBD structural motifs of spike protein for SARS-CoV-2 epitope vaccine design and demonstrates the potential utility of ‘epitope grafting’ in rational vaccine design.

Background: The COVID-19 pandemic has resulted in profound and far-reaching impacts on maternal and newborn care and outcomes. As part of the ASPIRE COVID-19 project, we describe processes and outcome measures relating to safe and personalised maternity care in England which we map against a pre-developed ASPIRE framework to establish the potential impact of the COVID-19 pandemic for two UK trusts. Methods: We undertook a mixed-methods system-wide case study using quantitative routinely collected data and qualitative data from two Trusts and their service users from 2019 to 2021 (start and completion dates varied by available data). We mapped findings to our prior ASPIRE conceptual framework that explains pathways for the impact of COVID-19 on safe and personalised care. Results: The ASPIRE framework enabled us to develop a comprehensive, systems-level understanding of the impact of the pandemic on service delivery, user experience and staff wellbeing, and place it within the context of pre-existing challenges. Maternity services experienced some impacts on core service coverage, though not on Trust level clinical health outcomes (with the possible exception of readmissions in one Trust). Both users and staff found some pandemic-driven changes challenging such as remote or reduced antenatal and community postnatal contacts, and restrictions on companionship. Other key changes included an increased need for mental health support, changes in the availability and uptake of home birth services and changes in induction procedures. Many emergency adaptations persisted at the end of data collection. Differences between the trusts indicate complex change pathways. Staff reported some removal of bureaucracy, which allowed greater flexibility. During the first wave of COVID-19 staffing numbers increased, resolving some pre-pandemic shortages: however, by October 2021 they declined markedly. Trying to maintain the quality and availability of services had marked negative consequences for personnel. Timely routine clinical and staffing data were not always available and personalised care and user and staff experiences were poorly captured. Conclusions: The COVID-19 crisis magnified pre-pandemic problems and in particular, poor staffing levels. Maintaining services took a significant toll on staff wellbeing. There is some evidence that these pressures are continuing. There was marked variation in Trust responses. Lack of accessible and timely data at Trust and national levels hampered rapid insights. The ASPIRE COVID-19 framework could be useful for modelling the impact of future crises on routine care.

Abstract Background Between 2019 and 2021, the first Irish health system performance assessment (HSPA) framework was developed. As routinely collected health data are necessary to continuously populate indicators of an HSPA framework, a purpose-driven assessment of the health information system (HIS) in Ireland and its fitness to support the implementation of an HSPA framework was conducted. This study reports on the status of the Irish HIS through a multimethod assessment based on continuous broad stakeholder involvement. Methods Between May and November 2020, over 50 informants were engaged in individual and group interviews and stakeholder consultation workshops as part of the HIS assessment process. Descriptive themes and high-level data availability heatmaps were derived from interview and workshop data using thematic analysis. Indicator “passports” for the HSPA framework were populated during stakeholder consultation workshops and analysed using univariate descriptive statistics. Results The HIS in Ireland was able to provide administrative, survey and registry-based data for public sector acute care services, focusing on structure, process and output metrics. Significant data availability gaps, most notably from primary care, private hospitals and community care, were reported, with little availability of electronic health record and people-reported data. Data on outcome metrics were mostly missing, as were linkage possibilities across datasets for care pathway monitoring. The COVID-19 pandemic highlighted the national HIS’s shortcomings but also the capacity for rapid development and improvement. Conclusions A tailor-made assessment of the HIS in Ireland, involving a broad set of relevant stakeholders, revealed strengths, weaknesses and areas for improvement in the Irish health data landscape. It also contributed to the development of a national HSPA framework and momentum to further strengthen data infrastructure and governance, while working towards a more data-driven and person-centred healthcare system. This work demonstrates the utility of an inclusive HIS assessment process and is applicable beyond Ireland, where this case study was conducted.