Rapid genome sequencing in hospitals to identify potential vaccine-escape SARS-CoV-2 variants
Authors: Luke B Snell, Penelope R Cliff, Themoula Charalampous, Adela Alcolea-Medina, Saidat A R T Ebie, Jasveen K Sehmi, Flavia Flaviani, Rahul Batra, Sam T Douthwaite, Jonathan D Edgeworth, Gaia Nebbia
Journal: The Lancet Infectious Diseases (2021)

SARS-CoV-2 genome sequencing is embedded in academic and public health laboratories, but whether there are benefits to rapid sequencing in front-line hospital laboratories is unclear. We did rapid genome sequencing of SARS-CoV-2-positive nose and throat swabs from patients admitted to our hospital since July 7, 2021, to identify potential SARS-CoV-2 vaccine-escape variants for infection control and public health purposes. In addition, we did PCR-based genotyping of all new SARS-CoV-2 cases for three south London hospitals (Guy's and St Thomas', King's College, and Princess Royal University) using the AusDiagnostics SARS-CoV-2 Typing Panel (16-well) on the AusDiagnostics HighPlex, sequencing any non-typeable results. We identified two cases of a potential vaccine-escape variant from the B.1.621 lineage. This variant of interest,1European Centre for Disease Prevention and ControlSARS-CoV-2 variants of concern as of 15 July 2021.https://www.ecdc.europa.eu/en/covid-19/variants-concernDate accessed: July 17, 2021Google Scholar first identified in Colombia, has lineage-associated spike mutations R346K, E484K, and P681H, which have been reported to show reduced neutralisation by antibodies.2Jangra S Ye C Rathnasinghe R et al.SARS-CoV-2 spike E484K mutation reduces antibody neutralisation.Lancet Microbe. 2021; 2: e283-e284Summary Full Text Full Text PDF PubMed Scopus (255) Google Scholar, 3Greaney AJ Starr TN Barnes CO et al.Mapping mutations to the SARS-CoV-2 RBD that escape binding by different classes of antibodies.Nat Commun. 2021; 12: 1-14Crossref PubMed Scopus (224) Google Scholar, 4Hu J Peng P Wang K et al.Emerging SARS-CoV-2 variants reduce neutralization sensitivity to convalescent sera and monoclonal antibodies.Cell Mol Immunol. 2021; 18: 1061-1063Crossref PubMed Scopus (74) Google Scholar In addition, the variant we detected harbours a K417N spike mutation, which is associated with vaccine escape in the beta variant first identified in South Africa.5Madhi SA Baillie V Cutland CL et al.Efficacy of the ChAdOx1 nCoV-19 COVID-19 vaccine against the B.1.351 variant.N Engl J Med. 2021; 384: 1885-1898Crossref PubMed Scopus (871) Google Scholar, 6Cele S Gazy I Jackson L et al.Escape of SARS-CoV-2 501Y.V2 from neutralization by convalescent plasma.Nature. 2021; 593: 142-146Crossref PubMed Scopus (393) Google Scholar We first identified this variant on July 12, 2021, and since then more cases have been reported by public health authorities.7Public Health EnglandSARS-CoV-2 variants of concern under investigation in England. Technical briefing 19.https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/1005517/Technical_Briefing_19.pdfDate: 23 July 2021Date accessed: August 6, 2021Google Scholar The presence of mutations associated with vaccine escape might warrant reclassification of this variant to a variant of concern and deployment of additional public health resources to contain spread. These two community cases with identical genomes (GISAID accession numbers EPI_ISL_2993635 and EPI_ISL_2993634) presented to different hospitals; both individuals were unvaccinated, lived 5 miles apart, and had no known epidemiological contact or recent travel. This finding indicates ongoing community transmission of this variant even in a setting where, as of writing, the delta variant accounts for 99% of cases, further suggesting that this variant has a fitness advantage, perhaps through the potential to escape vaccination. Our sequencing workflow uses Oxford Nanopore technology with rapid barcoding kits (SQK-RBK004) and the ARTIC Network SARS-CoV-2 bioinformatic pipeline with Pango nomenclature and type-variant tools. Previous studies have shown the ability of this technology to provide sequencing data in 24 h.8Meredith LW Hamilton WL Warne B et al.Rapid implementation of SARS-CoV-2 sequencing to investigate cases of health-care associated COVID-19: a prospective genomic surveillance study.Lancet Infect Dis. 2020; 20: 1263-1271Summary Full Text Full Text PDF PubMed Scopus (264) Google Scholar This workflow can complete in 8 h, allowing whole-genome sequencing and variant reporting to be completed on the same day as sample positivity. By contrast, the average turnaround time from our offsite reference sequencing laboratory is around 10 working days. For both cases, the variant was reported to Public Health England within 72 h of sampling. Our experience suggests that using rapid workflows in hospitals, close to where samples are tested, could improve public health surveillance efforts and expedite identification of new variants. This is particularly important as physical-distancing measures are lifted in the context of ongoing high rates of community transmission in a partially vaccinated population. This will undoubtedly lead to the emergence of vaccine-escape variants, however, the frequency at which they will arise and their capacity for sustained transmission are unknown. Further work is ongoing to characterise this variant and assess escape from neutralisation by antibodies generated from past infection and vaccination. We declare no competing interests. This work was funded by the National Institute for Health Research Biomedical Research Centre programme of infection and immunity (RJ112/N027) based at Guy's and St Thomas' National Health Service (NHS) Foundation Trust and King's College London, Guy's and St Thomas' NHS Foundation Trust, and The Guy's and St Thomas' Charity.