ABSTRACT
BACKGROUND: SARS-CoV-2 can spread rapidly on maritime platforms. Several outbreaks of SARS-CoV-2 have been reported on warships at sea, where transmission is facilitated by living and working in close quarters. Core components of infection control measures such as social distancing, patient isolation and quarantine of exposed persons are extremely difficult to implement. Whole genome sequencing (WGS) of SARS-CoV-2 has facilitated epidemiological investigations of outbreaks, impacting on outbreak management in real time by identifying transmission patterns, clusters of infection and guiding control measures. We suggest such a capability could mitigate against the impact of SARS-CoV-2 in maritime settings. METHODS: We set out to establish SARS-CoV-2 WGS using miniaturised nanopore sequencing technology aboard the Royal Fleet Auxiliary ARGUS while at sea. Objectives included designing a simplified protocol requiring minimal reagents and processing steps, the use of miniaturised equipment compatible for use in limited space, and a streamlined and standalone data analysis capability to allow rapid in situ data acquisition and interpretation. RESULTS: Eleven clinical samples with blinded SARS-CoV-2 status were tested at sea. Following viral RNA extraction and ARTIC sequencing library preparation, reverse transcription and ARTIC PCR-tiling were performed. Samples were subsequently barcoded and sequenced using the Oxford Nanopore MinION Mk1B. An offline version of the MinKNOW software was used followed by CLC Genomics Workbench for downstream analysis for variant identification and phylogenetic tree construction. All samples were correctly classified, and relatedness identified. CONCLUSIONS: It is feasible to establish a small footprint sequencing capability to conduct SARS-CoV-2 WGS in a military maritime environment at sea with limited access to reach-back support. This proof-of-concept study has highlighted the potential of deploying such technology in the future to military environments, both maritime and land-based, to provide meaningful clinical data to aid outbreak investigations.
ABSTRACT
Background: Patients requiring haemodialysis (HD) have disproportionately poorer outcomes from SARS-CoV-2 infection and vaccines afford an opportunity to improve this. However, the efficacy of booster doses on infection with emerging variants remains unclear in this population. Method(s): We report the real-world impact of SARS-CoV-2 booster vaccinations in an ethnically diverse urban cohort of 1172 patients receiving in-centre HD who were routinely screened for SARS-CoV-2 infection by weekly nasopharyngeal PCR between 1st December 2021 and 31st March 2022, during dominant UK prevalence of B.1.1.529 variant ("Omicron"). Where possible, genomic sequencing was performed as standard of care. Result(s): At the start of the observation period, 896 (76.5%) had received 3 doses of SARS-CoV-2 vaccine and only 87 (7.4%) were unvaccinated. By end of study 664 (59.5%) had received 4 vaccine doses. 305 patients had PCR positive SARS-CoV-2 infection, with Omicron variant confirmed in all but one of samples successfully tested. Clinical course of infection was mild: around half of patients asymptomatic, only 1 in 20 hospitalised, case fatality 3%. Three or more vaccine doses significantly associated with reduced risk of SARS-CoV-2 PCR positivity compared to unvaccinated status, together with White ethnicity and lower deprivation index (Cox regression p<0.03). However, 2 booster doses further reduced the risk of infection by around a third compared to 1 boost, independent of age, gender and comorbidity. Conclusion(s): A second SARS-CoV-2 booster vaccine further reduces the risk of Omicron infection in haemodialysis patients. As such, a double-boost policy could significantly reduce the burden and associated spread of SARS-CoV-2 infection in this vulnerable population.