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medrxiv; 2021.
Preprint in English | medRxiv | ID: ppzbmed-10.1101.2021.07.15.21260006


Objectives To define risk factors for SARS-CoV-2 infection in University of Cambridge students during a period of increased incidence in October and November 2020. Study design Survey Methods Routine public health surveillance identified a marked increase in the numbers of University of Cambridge students with respiratory illness and SARS-CoV-2 positivity in the 10 days after a national lockdown was announced in the UK on 5 November 2020. Cases were identified both through symptom-triggered testing and a universal asymptomatic testing program. An online questionnaire was sent to all University of Cambridge students on 25 November to investigate risk factors for testing positive in the period after 30 October 2020. This asked about symptoms, SARS-CoV-2 test results, in-person teaching settings, other aspects of University life, and attendance at social events in the period just prior to lockdown, from 30th October and 4th November 2020. Univariate and multivariable analyses were undertaken evaluating potential risk factors for SARS-CoV-2 positivity. Results Among 3,980 students responding to the questionnaire, 99 (2.5%) reported testing SARS-CoV-2 positive in the period studied; 28 (28%) were asymptomatic. We found strong independent associations with SARS-CoV-2 positivity were attendance at two social settings in the City of Cambridge (adjusted odds ratio favouring disease 13.0 (95% CI 6.2,26.9) and 14.2 (95% CI 2.9,70)), with weaker evidence of association with three further social settings. By contrast, we did not observe strong independent associations between disease risk and type of accommodation or attendance at, or participation in, a range of activities associated with the University curriculum. Conclusions Attendance at social settings can facilitate widespread SARS-CoV-2 transmission in University students. Constraint of transmission in higher education settings needs to emphasise risks outside University premises, as well as a COVID-safe environment within University premises.

COVID-19 , Respiratory Insufficiency
medrxiv; 2020.
Preprint in English | medRxiv | ID: ppzbmed-10.1101.2020.05.08.20095687


Background The burden and impact of healthcare-associated COVID-19 infections is unknown. We aimed to examine the utility of rapid sequencing of SARS-CoV-2 combined with detailed epidemiological analysis to investigate healthcare-associated COVID-19 infections and to inform infection control measures. Methods We set up rapid viral sequencing of SARS-CoV-2 from PCR-positive diagnostic samples using nanopore sequencing, enabling sample-to-sequence in less than 24 hours. We established a rapid review and reporting system with integration of genomic and epidemiological data to investigate suspected cases of healthcare-associated COVID-19. Results Between 13 March and 24 April 2020 we collected clinical data and samples from 5191 COVID-19 patients in the East of England. We sequenced 1000 samples, producing 747 complete viral genomes. We conducted combined epidemiological and genomic analysis of 299 patients at our hospital and identified 26 genomic clusters involving 114 patients. 66 cases (57.9%) had a strong epidemiological link and 15 cases (13.2%) had a plausible epidemiological link. These results were fed back clinical, infection control and hospital management teams, resulting in infection control interventions and informing patient safety reporting. Conclusions We established real-time genomic surveillance of SARS-CoV-2 in a UK hospital and demonstrated the benefit of combined genomic and epidemiological analysis for the investigation of healthcare-associated COVID-19 infections. This approach enabled us to detect cryptic transmission events and identify opportunities to target infection control interventions to reduce further healthcare-associated infections.