Eurosurveillance - Volume 25, Issue 6, 13 February 2020

Timely detection of novel coronavirus (2019-nCoV) infection cases is crucial to interrupt the spread of this virus. We assessed the required expertise and capacity for molecular detection of 2019-nCoV in specialised laboratories in 30 European Union/European Economic Area (EU/EEA) countries. Thirty-eight laboratories in 24 EU/EEA countries had diagnostic tests available by 29 January 2020. A coverage of all EU/EEA countries was expected by mid-February. Availability of primers/probes, positive controls and personnel were main implementation barriers.

In Tuscany, Italy, New Delhi metallo-beta-lactamase-producing carbapenem-resistant Enterobacterales (NDM-CRE) have increased since November 2018. Between November 2018 and October 2019, 1,645 samples were NDM-CRE-positive: 1,270 (77.2%) cases of intestinal carriage, 129 (7.8%) bloodstream infections and 246 (14.9%) infections/colonisations at other sites. Klebsiella pneumoniae were prevalent (1,495; 90.9%), with ST147/NDM-1 the dominant clone. Delayed outbreak identification and response resulted in sustained NDM-CRE transmission in the North-West area of Tuscany, but successfully contained spread within the region.

A novel coronavirus (severe acute respiratory syndrome coronavirus 2, SARS-CoV-2) causing a cluster of respiratory infections (coronavirus disease 2019, COVID-19) in Wuhan, China, was identified on 7 January 2020. The epidemic quickly disseminated from Wuhan and as at 12 February 2020, 45,179 cases have been confirmed in 25 countries, including 1,116 deaths. Strengthened surveillance was implemented in France on 10 January 2020 in order to identify imported cases early and prevent secondary transmission. Three categories of risk exposure and follow-up procedure were defined for contacts. Three cases of COVID-19 were confirmed on 24 January, the first cases in Europe. Contact tracing was immediately initiated. Five contacts were evaluated as at low risk of exposure and 18 at moderate/high risk. As at 12 February 2020, two cases have been discharged and the third one remains symptomatic with a persistent cough, and no secondary transmission has been identified. Effective collaboration between all parties involved in the surveillance and response to emerging threats is required to detect imported cases early and to implement adequate control measures.

Next generation sequencing (NGS) is becoming the new gold standard in public health microbiology. Like any disruptive technology, its growing popularity inevitably attracts cyber security actors, for whom the health sector is attractive because it combines mission-critical infrastructure and high-value data with cybersecurity vulnerabilities. In this Perspective, we explore cyber security aspects of microbial NGS. We discuss the motivations and objectives for such attack, its feasibility and implications, and highlight policy considerations aimed at threat mitigation. Particular focus is placed on the attack vectors, where the entire process of NGS, from sample to result, could be vulnerable, and a risk assessment based on probability and impact for representative attack vectors is presented. Cyber attacks on microbial NGS could result in loss of confidentiality (leakage of personal or institutional data), integrity (misdetection of pathogens) and availability (denial of sequencing services). NGS platforms are also at risk of being used as propagation vectors, compromising an entire system or network. Owing to the rapid evolution of microbial NGS and its applications, and in light of the dynamics of the cyber security domain, frequent risk assessments should be carried out in order to identify new threats and underpin constantly updated public health policies.