Large-scale evolutionary surveillance of the 2009 H1N1 influenza A virus using resequencing arrays

In April 2009, a new influenza A (H1N1 2009) virus emerged that rapidly spread around the world. While current variants of this virus have caused widespread disease, particularly in vulnerable groups, there remains the possibility that future variants may cause increased virulence, drug resistance or vaccine escape. Early detection of these virus variants may offer the chance for increased containment and potentially prevention of the virus spread. We have developed and field-tested a resequencing kit that is capable of interrogating all eight segments of the 2009 influenza A(H1N1) virus genome and its variants, with added focus on critical regions such as drug-binding sites, structural components and mutation hotspots. The accompanying base-calling software (EvolSTAR) introduces novel methods that utilize neighbourhood hybridization intensity profiles and substitution bias of probes on the microarray for mutation confirmation and recovery of ambiguous base queries. Our results demonstrate that EvolSTAR is highly accurate and has a much improved call rate. The high throughput and short turn-around time from sample to sequence and analysis results (30 h for 24 samples) makes this kit an efficient large-scale evolutionary biosurveillance tool

Cybersecurity, our digital anchor: A European perspective

The Report ‘Cybersecurity – Our Digital Anchor’ brings together research from different disciplinary fields of the Joint Research Centre (JRC), the European Commission's science and knowledge service. It provides multidimensional insights into the growth of cybersecurity over the last 40 years, identifying weaknesses in the current digital evolution and their impacts on European citizens and industry. The report also sets out the elements that potentially could be used to shape a brighter and more secure future for Europe’s digital society, taking into account the new cybersecurity challenges triggered by the COVID-19 crisis. According to some projections, cybercrime will cost the world EUR 5.5 trillion by the end of 2020, up from EUR 2.7 trillion in 2015, due in part to the exploitation of the COVID-19 pandemic by cyber criminals. This figure represents the largest transfer of economic wealth in history, more profitable than the global trade in all major illegal drugs combined, putting at risk incentives for innovation and investment. Furthermore, cyber threats have moved beyond cybercrime and have become a matter of national security. The report addresses relevant issues, including: - Critical infrastructures: today, digital technologies are at the heart of all our critical infrastructures. Hence, their cybersecurity is already – and will become increasingly – a matter of critical infrastructure protection (see the cases of Estonia and Ukraine). - Magnitude of impact: the number of citizens, organisations and businesses impacted simultaneously by a single attack can be huge. - Complexity and duration of attacks: attacks are becoming more and more complex, demonstrating attackers’ enhanced planning capabilities. Moreover, attacks are often only detected post-mortem . - Computational power: the spread of malware also able to infect mobile and Internet of Things (IoT) devices (as in the case of Mirai botnet), hugely increases the distributed computational power of the attacks (especially in the case of denial of services (DoS)). The same phenomenon makes the eradication of an attack much more difficult. - Societal aspects: cyber threats can have a potentially massive impact on society, up to the point of undermining the trust citizens have in digital services. As such services are intertwined with our daily life, any successful cybersecurity strategy must take into consideration the human and, more generally, societal aspects. This report shows how the evolution of cybersecurity has always been determined by a type of cause-and-effect trend: the rise in new digital technologies followed by the discovery of new vulnerabilities, for which new cybersecurity measures must be identified. However, the magnitude and impacts of today's cyber attacks are now so critical that the digital society must prepare itself before attacks happen. Cybersecurity resilience along with measures to deter attacks and new ways to avoid software vulnerabilities should be enhanced, developed and supported. The ‘leitmotiv’ of this report is the need for a paradigm shift in the way cybersecurity is designed and deployed, to make it more proactive and better linked to societal needs. Given that data flows and information are the lifeblood of today’s digital society, cybersecurity is essential for ensuring that digital services work safely and securely while simultaneously guaranteeing citizens’ privacy and data protection. Thus, cybersecurity is evolving from a technological ‘option’ to a societal must. From big data to hyperconnectivity, from edge computing to the IoT, to artificial intelligence (AI), quantum computing and blockchain technologies, the ‘nitty-gritty’ details of cybersecurity implementation will always remain field-specific due to specific sectoral constraints. This brings with it inherent risks of a digital society with heterogeneous and inconsistent levels of security. To counteract this, we argue for a coherent, cross-sectoral and cross-societal cybersecurity strategy which can be implemented across all layers of European society. This strategy should cover not only the technological aspects but also the societal dimensions of ‘behaving in a cyber-secure way’. Consequently, the report concludes by presenting a series of possible actions instrumental to building a European digital society secure by design.JRC.E.3-Cyber and Digital Citizens' Securit

Pathogen chip for respiratory tract infections.

Determining the viral etiology of respiratory tract infections (RTI) has been limited for the most part to specific primer PCR-based methods due to their increased sensitivity and specificity compared to other methods, such as tissue culture. However, specific primer approaches have limited the ability to fully understand the diversity of infecting pathogens. A pathogen chip system (PathChip), developed at the Genome Institute of Singapore (GIS), using a random-tagged PCR coupled to a chip with over 170,000 probes, has the potential to recognize all known human viral pathogens. We tested 290 nasal wash specimens from Filipino children <2 years of age with respiratory tract infections using culture and 3 PCR methods-EraGen, Luminex, and the GIS PathChip. The PathChip had good diagnostic accuracy, ranging from 85.9% (95% confidence interval [CI], 81.3 to 89.7%) for rhinovirus/enteroviruses to 98.6% (95% CI, 96.5 to 99.6%) for PIV 2, compared to the other methods and additionally identified a number of viruses not detected by these methods