Summary SARS-CoV-2 Spike protein is critical for virus infection via engagement of ACE2 1 , and is a major antibody target. Here we report chronic SARS-CoV-2 with reduced sensitivity to neutralising antibodies in an immune suppressed individual treated with convalescent plasma, generating whole genome ultradeep sequences over 23 time points spanning 101 days. Little change was observed in the overall viral population structure following two courses of remdesivir over the first 57 days. However, following convalescent plasma therapy we observed large, dynamic virus population shifts, with the emergence of a dominant viral strain bearing D796H in S2 and ΔH69/ΔV70 in the S1 N-terminal domain NTD of the Spike protein. As passively transferred serum antibodies diminished, viruses with the escape genotype diminished in frequency, before returning during a final, unsuccessful course of convalescent plasma. In vitro , the Spike escape double mutant bearing ΔH69/ΔV70 and D796H conferred modestly decreased sensitivity to convalescent plasma, whilst maintaining infectivity similar to wild type. D796H appeared to be the main contributor to decreased susceptibility but incurred an infectivity defect. The ΔH69/ΔV70 single mutant had two-fold higher infectivity compared to wild type, possibly compensating for the reduced infectivity of D796H. These data reveal strong selection on SARS-CoV-2 during convalescent plasma therapy associated with emergence of viral variants with evidence of reduced susceptibility to neutralising antibodies.

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BackgroundTransporting over two billion passengers per year, global airline travel has the potential to spread emerging infectious diseases, both via transportation of infectious cases and through in-flight transmission. Current World Health Organization (WHO) guidance recommends contact tracing of passengers seated within two rows of a case of influenza during air travel.ObjectivesThe objectives of this study were to describe flight-related transmission of influenza A(H1N1)pdm09 during a commercial flight carrying the first cases reported in the United Kingdom and to test the specific hypothesis that passengers seated within two rows of an infectious case are at greater risk of infection.MethodsAn historical cohort study, supplemented by contact tracing, enhanced surveillance data and laboratory testing, was used to establish a case status for passengers on board the flight.ResultsData were available for 239 of 278 (86·0%) of passengers on the flight, of whom six were considered infectious in-flight and one immune. The attack rate (AR) was 10 of 232 (4·3%; 95% CI 1·7–6·9%). There was no evidence that the AR for those seated within two rows of an infectious case was different from those who were not (relative risk 0·9; 95% CI 0·2–3·1; P = 1·00). Laboratory testing using PCR and/or serology, available for 118 of 239 (49·4%) of the passengers, was largely consistent with clinically defined case status.ConclusionsThis study of A(H1N1)pdm09 does not support current WHO guidance regarding the contact tracing of passengers seated within two rows of an infectious case of influenza during air travel.

Mitigation of SARS-CoV-2 transmission from international travel is a priority. We evaluated the effectiveness of travellers being required to quarantine for 14-days on return to England in Summer 2020. We identified 4,207 travel-related SARS-CoV-2 cases and their contacts, and identified 827 associated SARS-CoV-2 genomes. Overall, quarantine was associated with a lower rate of contacts, and the impact of quarantine was greatest in the 16–20 age-group. 186 SARS-CoV-2 genomes were sufficiently unique to identify travel-related clusters. Fewer genomically-linked cases were observed for index cases who returned from countries with quarantine requirement compared to countries with no quarantine requirement. This difference was explained by fewer importation events per identified genome for these cases, as opposed to fewer onward contacts per case. Overall, our study demonstrates that a 14-day quarantine period reduces, but does not completely eliminate, the onward transmission of imported cases, mainly by dissuading travel to countries with a quarantine requirement.

Geospatial technologies are emerging as one of the most promising environments for development of emergency management framework. Geospatial technologies such as Remote Sensing, Geographic Information Systems and Global Positioning Systems integrated with valuable near/real-time field information can provide a comprehensive platform for emergency management. Satellite imagery, vector database, Location Based Services and ancillary data having the relevant attribute information with access and query tools helps the disaster manager to analyse the required information for relief operations. However, the conceptual design of the database, integration procedures, development of decision support functions and dissemination of information integrating real-time information from the field are very important issues in development framework for emergency management. There are some technological challenges in the emergency response for deriving the required outputs such as damage assessment, evacuation planning, situation monitoring, information dissemination, and coordination of resource and logistic planning. This article provides a framework for the integration of various multi-disciplinary technologies for addressing emergency management.