Modelling the impact of non-pharmaceutical interventions on workplace transmission of SARS-CoV-2 in the home-delivery sector.

OBJECTIVE: We aimed to use mathematical models of SARS-COV-2 to assess the potential efficacy of non-pharmaceutical interventions on transmission in the parcel delivery and logistics sector. METHODS: We devloped a network-based model of workplace contacts based on data and consultations from companies in the parcel delivery and logistics sectors. We used these in stochastic simulations of disease transmission to predict the probability of workplace outbreaks in this settings. Individuals in the model have different viral load trajectories based on SARS-CoV-2 in-host dynamics, which couple to their infectiousness and test positive probability over time, in order to determine the impact of testing and isolation measures. RESULTS: The baseline model (without any interventions) showed different workplace infection rates for staff in different job roles. Based on our assumptions of contact patterns in the parcel delivery work setting we found that when a delivery driver was the index case, on average they infect only 0.14 other employees, while for warehouse and office workers this went up to 0.65 and 2.24 respectively. In the LIDD setting this was predicted to be 1.40, 0.98, and 1.34 respectively. Nonetheless, the vast majority of simulations resulted in 0 secondary cases among customers (even without contact-free delivery). Our results showed that a combination of social distancing, office staff working from home, and fixed driver pairings (all interventions carried out by the companies we consulted) reduce the risk of workplace outbreaks by 3-4 times. CONCLUSION: This work suggests that, without interventions, significant transmission could have occured in these workplaces, but that these posed minimal risk to customers. We found that identifying and isolating regular close-contacts of infectious individuals (i.e. house-share, carpools, or delivery pairs) is an efficient measure for stopping workplace outbreaks. Regular testing can make these isolation measures even more effective but also increases the number of staff isolating at one time. It is therefore more efficient to use these isolation measures in addition to social distancing and contact reduction interventions, rather than instead of, as these reduce both transmission and the number of people needing to isolate at one time.

Pre-COVID-19 cognitive social capital and peri-COVID-19 depression: A prospective cohort study on the contextual moderating effect of the COVID-19 pandemic in China, 2016–2020

Social capital could protect mental health. We examined whether the COVID-19 context and province-level COVID-19 situation altered the longitudinal association between cognitive social capital (generalized trust, trust in neighbors, trust in local government officials, and reciprocity) and depression. Results from multilevel mixed-effects linear regression models showed that trust in neighbors, trust in local government officials, and reciprocity were more crucial in longitudinally reducing depression in 2020 than in 2018. Also, as compared with provinces where the COVID-19 situation was less poor, trust in local government officials in provinces with a worse COVID-19 situation in 2018 was more crucial in reducing depression in 2020. Therefore, cognitive social capital should be taken into account for pandemic preparedness and mental health resilience.

The unreversible reduced but persistent activated NK and CD8+ T cells in severe/critical COVID-19 during omicron pandemic in China.

As a hallmark of COVID-19 progression, lymphopenia alongside its subtle immune disturbance has been widely reported, but yet to be thoroughly elucidated. Aiming at exploring clinical immune biomarkers with accessibility in the current and acute omicron epidemic abrupted in China post-control era, we design a real-world prospective observation cohort in Peking Union Medical College Hospital to describe immunological, haematological profiles inducing lymphocyte subsets related to SARS-CoV-2 infection. In this COVID-19 cohort, we enrolled 17 mild/moderate (M/M), 24 severe (S) and 25 critical (C) patients. The dynamics of lymphocytes of COVID-19 demonstrated that the sharp decline of NK, CD8+, and CD4+ T cell counts was the main contributor to lymphopenia in the S/C group, compared to the M/M group. Expressions of activation marker CD38 and proliferation marker Ki-67 both in CD8+ T and NK cells were significantly higher in all COVID-19 patients than that in healthy donors, independent of disease severity. The subsequent analysis showed in contrast to the M/M group, NK and CD8+ T cell counts remained low-level after therapy in the S/C group. CD38 and Ki-67 expressions in NK and CD8+ T cells still stay at a high level, despite active treatment. Targeting relatively elderly patients with SARS-CoV-2 infection, severe COVID-19 features the unreversible reduction of NK and CD8+ T cells with persistent activation and proliferation, which assist clinicians in early recognizing and saving severe or critical COVID-19 patients. Given that immunophenotype, the new immunotherapy improving NK and CD8+ T lymphocyte antiviral efficiency should be considered.

Contact patterns of UK home delivery drivers and their use of protective measures during the COVID-19 pandemic: a cross-sectional study.

OBJECTIVES: To quantify contact patterns of UK home delivery drivers and identify protective measures adopted during the pandemic. METHODS: We conducted a cross-sectional online survey to measure the interactions of 170 UK delivery drivers during a working shift between 7 December 2020 and 31 March 2021. RESULTS: Delivery drivers had a mean number of 71.6 (95% CI 61.0 to 84.1) customer contacts per shift and 15.0 (95% CI 11.2 to 19.2) depot contacts per shift. Maintaining physical distancing with customers was more common than at delivery depots. Prolonged contact (more than 5 min) with customers was reported by 5.4% of drivers on their last shift. We found 3.0% of drivers had tested positive for SARS-CoV-2 since the start of the pandemic and 16.8% of drivers had self-isolated due to a suspected or confirmed case of COVID-19. In addition, 5.3% (95% CI 2.3% to 10.2%) of participants reported having worked while ill with COVID-19 symptoms, or with a member of their household having a suspected or confirmed case of COVID-19. CONCLUSION: Delivery drivers had a large number of face-to-face customer and depot contacts per shift compared with other working adults during this time. However, transmission risk may be curtailed as contact with customers was of short duration. Most drivers were unable to maintain physical distance with customers and at depots at all times. Usage of protective items such as face masks and hand sanitiser was widespread.

SARS-CoV-2 Variants Increase Kinetic Stability of Open Spike Conformations as an Evolutionary Strategy.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) harbor mutations in the spike (S) glycoprotein that confer more efficient transmission and dampen the efficacy of COVID-19 vaccines and antibody therapies. S mediates virus entry and is the primary target for antibody responses, with structural studies of soluble S variants revealing an increased propensity toward conformations accessible to the human angiotensin-converting enzyme 2 (hACE2) receptor. However, real-time observations of conformational dynamics that govern the structural equilibriums of the S variants have been lacking. Here, we report single-molecule Förster resonance energy transfer (smFRET) studies of critical mutations observed in VOCs, including D614G and E484K, in the context of virus particles. Investigated variants predominately occupied more open hACE2-accessible conformations, agreeing with previous structures of soluble trimers. Additionally, these S variants exhibited slower transitions in hACE2-accessible/bound states. Our finding of increased S kinetic stability in the open conformation provides a new perspective on SARS-CoV-2 adaptation to the human population. IMPORTANCE SARS-CoV-2 surface S glycoprotein-the target of antibodies and vaccines-is responsible for binding to the cellular receptor hACE2. The interactions between S and hACE2 trigger structural rearrangements of S from closed to open conformations prerequisite for virus entry. Under the selection pressure imposed by adaptation to the human host and increasing vaccinations and convalescent patients, SARS-CoV-2 is evolving and has adopted numerous mutations on S variants. These promote virus spreading and immune evasion, partially by increasing the propensity of S to adopt receptor-binding competent open conformations. Here, we determined a time dimension, using smFRET to delineate the temporal prevalence of distinct structures of S in the context of virus particles. We present the first experimental evidence of decelerated transition dynamics from the open state, revealing increased stability of S open conformations to be part of the SARS-CoV-2 adaption strategies.

The impact of the COVID-19 pandemic on China's economic structure: An input-output approach.

Recognizing the impact of COVID-19 on economic structure is an urgently required task for the post-pandemic era. However, studies have been hampered in undertaking this task by a lack of current data and the use of inappropriate methods. This paper fills the gap in the literature by applying a network analysis method using the newly released input-output tables of China and evaluating the structural impacts on the economy, including the changes in the sectoral closeness, betweenness, risk condition, and network backbone. The modelling results demonstrate that the pandemic has accelerated the structural transformation process of the Chinese economy: the traditional growth engines, such as the petroleum and finance industries, have lagged, whereas new growth engine sectors, including the digital services and scientific research industries, have expanded rapidly. Accordingly, we propose that the government formulate policies to stabilize old growth engine industries and foster new drivers to promote a sustainable economic recovery in China.

Analysis on a nosocomial infection event in a designated COVID-19 hospital in Shandong from the perspective of disease control

Objective: To analyze a nosocomial infection event in a designated hospital of coronavirus disease 2019 (COVID-19) in Shandong province retrospectively from the perspective of disease control and provide evidence to prevent the incidence of similar event.

Agility and Sustainability: A Qualitative Evaluation of COVID-19 Non-pharmaceutical Interventions in the UK Logistics Sector.

Background: The emergence of SARS-CoV-2 triggered a chain of public health responses that radically changed our way of living and working. Non-healthcare sectors, such as the logistics sector, play a key role in such responses. This research aims to qualitatively evaluate the non-pharmaceutical interventions (NPIs) implemented in the UK logistics sector during the COVID-19 pandemic. Methods: We conducted nine semi-structured interviews in July-August 2020 and May-June 2021. In total 11 interviewees represented six companies occupying a range of positions in the UK's logistics sector, including takeaway food delivery, large and small goods delivery and home appliance installation, and logistics technology providers. Thematic analysis was completed using NVivo12. Codes relevant to NPIs were grouped into themes and mapped deductively onto an adapted Hierarchy of Control (HoC) framework, focusing on delivery workers. Codes relevant to the implementation process of NPIs were grouped into themes/subthemes to identify key characteristics of rapid responses, and barriers and facilitators. Results: HoC analysis suggests the sector has implemented a wide range of risk mitigation measures, with each company developing their own portfolio of measures. Contact-free delivery was the most commonly implemented measure and perceived effective. The other implemented measures included social distancing, internal contact tracing, communication and collaboration with other key stakeholders of the sector. Process evaluation identified facilitators of rapid responses including capacity to develop interventions internally, localized government support, strong external mandates, effective communication, leadership support and financial support for self-isolation, while barriers included unclear government guidance, shortage of testing capacity and supply, high costs and diversified language and cultural backgrounds. Main sustainability issues included compliance fatigue, and the possible mental health impacts of a prolonged rapid response. Conclusions: This research identified drivers and obstacles of rapid implementation of NPIs in response to a respiratory infection pandemic. Existing implementation process models do not consider speed to respond and the absence or lack of guidance in emergency situations such as the COVID-19. We recommend the development of a rapid response model to inform the design of effective and sustainable infection prevention and control policies and to focus future research priorities.

Structural Plasticity and Immune Evasion of SARS-CoV-2 Spike Variants.

The global pandemic of COVID-19 caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has significantly affected every human life and overloaded the health care system worldwide. Limited therapeutic options combined with the consecutive waves of the infection and emergence of novel SARS-CoV-2 variants, especially variants of concern (VOCs), have prolonged the COVID-19 pandemic and challenged its control. The Spike (S) protein on the surface of SARS-CoV-2 is the primary target exposed to the host and essential for virus entry into cells. The parental (Wuhan-Hu-1 or USA/WA1 strain) S protein is the virus-specific component of currently implemented vaccines. However, S is most prone to mutations, potentially shifting the dynamics of virus-host interactions by affecting S conformational/structural profiles. Scientists have rapidly resolved atomic structures of S VOCs and elucidated molecular details of these mutations, which can inform the design of S-directed novel therapeutics and broadly protective vaccines. Here, we discuss recent findings on S-associated virus transmissibility and immune evasion of SARS-CoV-2 VOCs and experimental approaches used to profile these properties. We summarize the structural studies that document the structural flexibility/plasticity of S VOCs and the potential roles of accumulated mutations on S structures and functions. We focus on the molecular interpretation of structures of the S variants and its insights into the molecular mechanism underlying antibody evasion and host cell-receptor binding.

Fast and sensitive detection of SARS-CoV-2 RNA using suboptimal protospacer adjacent motifs for Cas12a.

CRISPR-based assays for the detection of nucleic acids are highly specific, yet they are not fast, sensitive or easy to use. Here we report a one-step fluorescence assay for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in nasopharyngeal samples, with a sample-to-answer time of less than 20 minutes and a sensitivity comparable to that of quantitative real-time PCR with reverse transcription (RT-qPCR). The assay uses suboptimal protospacer adjacent motifs, allowing for flexibility in the design of CRISPR RNAs and slowing down the kinetics of Cas12a-mediated collateral cleavage of fluorescent DNA reporters and cis cleavage of substrates, which leads to stronger fluorescence owing to the accumulation of amplicons generated by isothermal recombinase polymerase amplification. In a set of 204 nasopharyngeal samples with RT-qPCR cycle thresholds ranging from 18.1 to 35.8, the assay detected SARS-CoV-2 with a sensitivity of 94.2% and a specificity of 100%, without the need for RNA extraction. Rapid and sensitive assays for nucleic acid testing in one pot that allow for flexibility in assay design may aid the development of reliable point-of-care nucleic acid testing.

A Limited Spreading Event of COVID-19 Caused by Delta Variant in a Cosmetic Hospital - Yantai City, Shandong Province, China, 2021.

What is already known about this topic?: Coronavirus disease 2019 (COVID-19) outbreaks in the past were mostly caused by overseas transmission, but if control measures are not appropriately applied, domestic transmission could also cause large-scale local epidemics. What is added by this report?: This report covers all information of epidemic investigation processes, epidemiological characteristics and exposure history, transmission chains, sequencing results as well as public health measures taken for the COVID-19 cluster epidemic caused by the Delta variant in a cosmetic hospital in Yantai City in August 2021. What are the implications for public health practice?: The information provided in this report, including active case finding, community management, and mass testing, may assist public health professionals in dealing with local COVID-19 epidemics caused by domestic transmission.