Characterising proteolysis during SARS-CoV-2 infection identifies viral cleavage sites and cellular targets with therapeutic potential.

SARS-CoV-2 is the causative agent behind the COVID-19 pandemic, responsible for over 170 million infections, and over 3.7 million deaths worldwide. Efforts to test, treat and vaccinate against this pathogen all benefit from an improved understanding of the basic biology of SARS-CoV-2. Both viral and cellular proteases play a crucial role in SARS-CoV-2 replication. Here, we study proteolytic cleavage of viral and cellular proteins in two cell line models of SARS-CoV-2 replication using mass spectrometry to identify protein neo-N-termini generated through protease activity. We identify previously unknown cleavage sites in multiple viral proteins, including major antigens S and N: the main targets for vaccine and antibody testing efforts. We discover significant increases in cellular cleavage events consistent with cleavage by SARS-CoV-2 main protease, and identify 14 potential high-confidence substrates of the main and papain-like proteases. We show that siRNA depletion of these cellular proteins inhibits SARS-CoV-2 replication, and that drugs targeting two of these proteins: the tyrosine kinase SRC and Ser/Thr kinase MYLK, show a dose-dependent reduction in SARS-CoV-2 titres. Overall, our study provides a powerful resource to understand proteolysis in the context of viral infection, and to inform the development of targeted strategies to inhibit SARS-CoV-2 and treat COVID-19.

Stock market reactions to favorable and unfavorable information security events: A systematic literature review

The rapid digital transformations across every industry sector, accelerated partly due to the COVID-19 pandemic, have increased organizations’ use of information systems for operational and strategic purposes. These organizational responses have led to a confluence of digital, biological, and physical technologies that are revolutionizing business practices and workflows. But accompanying the pervasive use of digital technologies and the evolutionary nature of digital assets, is a shifting world of cyberattacks and information security (ISec) cybercrimes. Dynamic cybercrimes make it increasingly difficult for managers and researchers to anticipate the types, magnitude, and severity of future information security (ISec) breaches. Thus, we perform a systematic literature review (SLR) that explores, gathers, and categorizes event studies to examine the influence of favorable and unfavorable ISec events on stock markets. We extend the research conducted by Spanos and Angelis (2016) and provide a comprehensive understanding of the market's efficiency to process public information released about ISec events, ISec contingency factors, and the influence of ISec events on stock prices and factors other than price. Our systematic search reveals 58 relevant papers that include 80 studies. We find that in 75% of the studies ISec events can significantly affect a company's stock market performance, and that such effects are primarily exhibited within two days before and after the event day. Further, the magnitude of abnormal returns is higher in studies examining unfavorable ISec events, such as ISec breaches, compared to abnormal returns from favorable events, such as ISec investments and ISec certifications. In the end, our SLR serves as a foundation for ISec and management communities to build upon to keep industry and academia apprised of continually developing trends, new attack vectors and types of data breaches, protective ISec behaviors and programs, and their subsequent influences on stock market values and returns. © 2021 Elsevier Ltd

Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England.

The SARS-CoV-2 lineage B.1.1.7, designated variant of concern (VOC) 202012/01 by Public Health England1, was first identified in the UK in late summer to early autumn 20202. Whole-genome SARS-CoV-2 sequence data collected from community-based diagnostic testing for COVID-19 show an extremely rapid expansion of the B.1.1.7 lineage during autumn 2020, suggesting that it has a selective advantage. Here we show that changes in VOC frequency inferred from genetic data correspond closely to changes inferred by S gene target failures (SGTF) in community-based diagnostic PCR testing. Analysis of trends in SGTF and non-SGTF case numbers in local areas across England shows that B.1.1.7 has higher transmissibility than non-VOC lineages, even if it has a different latent period or generation time. The SGTF data indicate a transient shift in the age composition of reported cases, with cases of B.1.1.7 including a larger share of under 20-year-olds than non-VOC cases. We estimated time-varying reproduction numbers for B.1.1.7 and co-circulating lineages using SGTF and genomic data. The best-supported models did not indicate a substantial difference in VOC transmissibility among different age groups, but all analyses agreed that B.1.1.7 has a substantial transmission advantage over other lineages, with a 50% to 100% higher reproduction number.

Genomic epidemiology of COVID-19 in care homes in the east of England.

COVID-19 poses a major challenge to care homes, as SARS-CoV-2 is readily transmitted and causes disproportionately severe disease in older people. Here, 1167 residents from 337 care homes were identified from a dataset of 6600 COVID-19 cases from the East of England. Older age and being a care home resident were associated with increased mortality. SARS-CoV-2 genomes were available for 700 residents from 292 care homes. By integrating genomic and temporal data, 409 viral clusters within the 292 homes were identified, indicating two different patterns - outbreaks among care home residents and independent introductions with limited onward transmission. Approximately 70% of residents in the genomic analysis were admitted to hospital during the study, providing extensive opportunities for transmission between care homes and hospitals. Limiting viral transmission within care homes should be a key target for infection control to reduce COVID-19 mortality in this population.

Transmission of SARS-CoV-2 Lineage B.1.1.7 in England: Insights from linking epidemiological and genetic data (preprint)

The SARS-CoV-2 lineage B.1.1.7, now designated Variant of Concern 202012/01 (VOC) by Public Health England, originated in the UK in late Summer to early Autumn 2020. We examine epidemiological evidence for this VOC having a transmission advantage from several perspectives. First, whole genome sequence data collected from community-based diagnostic testing provides an indication of changing prevalence of different genetic variants through time. Phylodynamic modelling additionally indicates that genetic diversity of this lineage has changed in a manner consistent with exponential growth. Second, we find that changes in VOC frequency inferred from genetic data correspond closely to changes inferred by S-gene target failures (SGTF) in community-based diagnostic PCR testing. Third, we examine growth trends in SGTF and non-SGTF case numbers at local area level across England, and show that the VOC has higher transmissibility than non-VOC lineages, even if the VOC has a different latent period or generation time. Available SGTF data indicate a shift in the age composition of reported cases, with a larger share of under 20 year olds among reported VOC than non-VOC cases. Fourth, we assess the association of VOC frequency with independent estimates of the overall SARS-CoV-2 reproduction number through time. Finally, we fit a semi-mechanistic model directly to local VOC and non-VOC case incidence to estimate the reproduction numbers over time for each. There is a consensus among all analyses that the VOC has a substantial transmission advantage, with the estimated difference in reproduction numbers between VOC and non-VOC ranging between 0.4 and 0.7, and the ratio of reproduction numbers varying between 1.4 and 1.8. We note that these estimates of transmission advantage apply to a period where high levels of social distancing were in place in England; extrapolation to other transmission contexts therefore requires caution.

A Proposed Framework for Identifying the Role of Data Science in Handling Future Pandemics for Malaysian SMEs through Technology Acceptance Model

The year 2020 will be written in the history as the year that has caused catastrophic impact on health, human lives, and most importantly the economy that has been rumbled in some countries to the levels of World War I and II. This pandemic also exposed the loopholes in the systems for few 'Developed Nations', 'Established Public Health Systems', and 'Billion Dollar Forex Reserves' that most of the countries relied upon in general. All these were challenged to the core once the COVID-19 pandemic started growing exponentially from March 2020 forcing the countries to go under lockdown which has curved down their economic charts. Malaysia too has suffered with a months-long lockdown, growing unemployment and shrinking economy. The SMEs in Malaysia are among the worst affected. In May 2020, almost 50% of the SMEs reached a position where their very existence was at stake. A potential second or third wave of COVID-19 or some other pandemic in future is not any surprise for Malaysia. But, how far the country and its SMEs are prepared to face such situation again is the question. A quick and accurate data analytics on historical pandemics, hospital data, infection rates, tracking, testing and treatments offered may help in predicting the primary signs that can protect from disasters to a great extent. This study applies 'technology acceptance model' to Malaysian SMEs to explore the possibility of Data Science in launching accurate forecasts that could keep them in a better position rather than getting caught in surprise lockdowns. Since the acceleration in the spread of infectious diseases lately around the globe is due to the growth in the human population and globalisation, Data Analytics can be used to predict where the potential outbreaks may unfold next and thereby to flag the early alert. © 2020 IEEE.

Characterisation of protease activity during SARS-CoV-2 infection identifies novel viral cleavage sites and cellular targets for drug repurposing (preprint)

SARS-CoV-2 is the causative agent behind the COVID-19 pandemic, and responsible for tens of millions of infections, and hundreds of thousands of deaths worldwide. Efforts to test, treat and vaccinate against this pathogen all benefit from an improved understanding of the basic biology of SARS-CoV-2. Both viral and cellular proteases play a crucial role in SARS-CoV-2 replication, and inhibitors targeting proteases have already shown success at inhibiting SARS-CoV-2 in cell culture models. Here, we study proteolytic cleavage of viral and cellular proteins in two cell line models of SARS-CoV-2 replication using mass spectrometry to identify protein neo-N-termini generated through protease activity. We identify multiple previously unknown cleavage sites in multiple viral proteins, including major antigenic proteins S and N, which are the main targets for vaccine and antibody testing efforts. We discovered significant increases in cellular cleavage events consistent with cleavage by SARS-CoV-2 main protease, and identify 14 potential high-confidence substrates of the main and papain-like proteases. We showed that siRNA depletion of these cellular proteins inhibits SARS-CoV-2 replication, and that drugs targeting two of these proteins: the tyrosine kinase SRC and the Ser/Thr kinase MYLK/MLCK, showed a dose-dependent reduction in SARS-CoV-2 titres. Overall, our study provides a powerful resource to understand proteolysis in the context of viral infection, and to inform the development of targeted strategies to inhibit SARS-CoV-2 and treat COVID-19 disease.

COVID-19 and Thrombotic or Thromboembolic Disease: Implications for Prevention, Antithrombotic Therapy, and Follow-Up: JACC State-of-the-Art Review.

Coronavirus disease-2019 (COVID-19), a viral respiratory illness caused by the severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2), may predispose patients to thrombotic disease, both in the venous and arterial circulations, because of excessive inflammation, platelet activation, endothelial dysfunction, and stasis. In addition, many patients receiving antithrombotic therapy for thrombotic disease may develop COVID-19, which can have implications for choice, dosing, and laboratory monitoring of antithrombotic therapy. Moreover, during a time with much focus on COVID-19, it is critical to consider how to optimize the available technology to care for patients without COVID-19 who have thrombotic disease. Herein, the authors review the current understanding of the pathogenesis, epidemiology, management, and outcomes of patients with COVID-19 who develop venous or arterial thrombosis, of those with pre-existing thrombotic disease who develop COVID-19, or those who need prevention or care for their thrombotic disease during the COVID-19 pandemic.

Pharmacological Agents Targeting Thromboinflammation in COVID-19: Review and Implications for Future Research.

Coronavirus disease 2019 (COVID-19), currently a worldwide pandemic, is a viral illness caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The suspected contribution of thrombotic events to morbidity and mortality in COVID-19 patients has prompted a search for novel potential options for preventing COVID-19-associated thrombotic disease. In this article by the Global COVID-19 Thrombosis Collaborative Group, we describe novel dosing approaches for commonly used antithrombotic agents (especially heparin-based regimens) and the potential use of less widely used antithrombotic drugs in the absence of confirmed thrombosis. Although these therapies may have direct antithrombotic effects, other mechanisms of action, including anti-inflammatory or antiviral effects, have been postulated. Based on survey results from this group of authors, we suggest research priorities for specific agents and subgroups of patients with COVID-19. Further, we review other agents, including immunomodulators, that may have antithrombotic properties. It is our hope that the present document will encourage and stimulate future prospective studies and randomized trials to study the safety, efficacy, and optimal use of these agents for prevention or management of thrombosis in COVID-19.

Preparedness and Best Practice in Radiology Department for COVID-19 and Other Future Pandemics of Severe Acute Respiratory Infection.

The COVID-19 global pandemic has emerged as an unprecedented health care crisis. To reduce risks of severe acute respiratory syndrome coronavirus 2 transmission in the Radiology Department, this article describes measures to increase the preparedness of Radiology Department, such as careful screening of staff and patients, thorough disinfection of equipments and rooms, appropriate use of personal protection equipment, and early isolation of patients with incidentally detected computed tomography findings suspicious for COVID-19. The familiarity of radiologists with clinical and imaging manifestations of COVID-19 pneumonia and their prognostic implications is essential to provide optimal care to patients.