COVID-19: from rapid genome sequencing to fast decisions
Authors: Ole Behrmann, Martin Spiegel
Journal: The Lancet Infectious Diseases (2020)

Nucleic acid amplification tests are invaluable tools for rapid and accurate detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections,1D'Cruz RJ Currier AW Sampson VB Laboratory testing methods for novel severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2).Front Cell Dev Biol. 2020; 8: 468Crossref PubMed Scopus (103) Google Scholar, 2Shi J Han D Zhang R Li J Zhang R Molecular and serological assays for SARS-CoV-2: insights from genome and clinical characteristics.Clin Chem. 2020; (published online May 21.)https://doi:10.1093/clinchem/hvaa122Crossref Scopus (27) Google Scholar but they are of limited use when identifying transmission events and infection clusters.3Bi Q Wu Y Mei S et al.Epidemiology and transmission of COVID-19 in 391 cases and 1286 of their close contacts in Shenzhen, China: a retrospective cohort study.Lancet Infect Dis. 2020; (published online April 27.)https://doi.org/10.1016/S1473-3099(20)30287-5Summary Full Text Full Text PDF PubMed Scopus (1082) Google Scholar In The Lancet Infectious Diseases, Luke Meredith and colleagues present an innovative combination of rapid full-genome sequencing of SARS-CoV-2 with epidemiological data to track health-care associated SARS-CoV-2 infections in their hospital and in health-care associated community settings.4Meredith 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 surveillance study.Lancet Infect Dis. 2020; (published online July 14.)https://doi.org/10.1016/S1473-3099(20)30562-4Summary Full Text Full Text PDF PubMed Scopus (262) Google Scholar Within 6 weeks, the authors were able to obtain 747 full SARS-CoV-2 genomes from 1009 PCR-positive patient samples. To obtain rapid results, sequencing was done by direct (nanopore) sequencing of amplicon libraries, which were generated with use of a multiplex PCR approach.5Quick J nCoV-2019 sequencing protocol v2 v1.https://www.protocols.io/view/ncov-2019-sequencing-protocol-v2-bdp7i5rnDate accessed: June 30, 2020Google Scholar, 6Freed N Silander O nCoV-2019 sequencing protocol (RAPID barcoding, 1200bp amplicon) v3.https://www.protocols.io/view/ncov-2019-sequencing-protocol-rapid-barcoding-1200-bgggjttwDate accessed: June 30, 2020Google Scholar On a weekly basis the sequenced samples underwent bioinformatic analysis and were combined with epidemiological data. Although the genetic diversity of SARS-CoV-2 is currently low, the combination of genetic, clinical, and epidemiological data was highly effective. With this approach, the authors could identify two infection clusters in their hospital, one in an outpatient dialysis unit and another one in a care home, which would not have been detected without full-genome sequencing. The results were reported back to infection control and management teams and were used to improve patient isolation, ward cleaning procedures, use of personal protection equipment, and staff physical distancing behaviour. Therefore, the combination of rapid genomic and epidemiological analyses in near real time allows the rapid optimisation of countermeasures in ongoing ward and community outbreaks of COVID-19. The study by Meredith and colleagues convincingly shows the power of direct sequencing as a tool to track SARS-CoV-2 transmission in a very short timeframe and could be a blueprint for tracing of other viral pathogens. We believe that the presented study provides a first glimpse into the point-of-care sequencing revolution provided by novel third-generation technology based on nanopores. Although current protocols are done in a central laboratory, further technological advances in both sequencing and sample preparation technology will enable highly decentralised workflows directly at the bedside or ward level. By contrast with sequencing-by-synthesis approaches, nanopore technology can directly sequence DNA and RNA molecules in the kilobase range, making it potentially suitable for the direct detection of viral genomes without the need for a time consuming PCR step. An additional benefit of this approach is the possibility to theoretically detect any viral pathogen. However, further increases in sensitivity are needed for this approach to be suitable for real clinical samples.7Taiaroa G Rawlinson D Featherstone L et al.Direct RNA sequencing and early evolution of SARS-CoV-2.bioRxiv. 2020; (published online April 3.) (preprint)https://doi.org/10.1101/2020.03.05.976167Google Scholar, 8Davidson AD Williamson MK Lewis S et al.Characterisation of the transcriptome and proteome of SARS-CoV-2 using direct RNA sequencing and tandem mass spectrometry reveals evidence for a cell passage induced in-frame deletion in the spike glycoprotein that removes the furin-like cleavage site.bioRxiv. 2020; (published online March 24.) (preprint)https://doi.org/10.1101/2020.03.22.002204Google Scholar Before true viral pathogen detection by amplification-free direct sequencing will be possible, it is probable that small integrated library preparation devices will be developed. These devices are likely to be based on microfluidic technology and will enable the clinical end user to do third-generation sequencing directly from samples such as nasopharyngeal swabs without specialised training. In addition, software tools will be needed to automate what has been done manually in the present study—integrate sequencing and epidemiological data to derive action plans for outbreak control. We declare no competing interests. Rapid implementation of SARS-CoV-2 sequencing to investigate cases of health-care associated COVID-19: a prospective genomic surveillance studyWe established real-time genomic surveillance of SARS-CoV-2 in a UK hospital and showed the benefit of combined genomic and epidemiological analysis for the investigation of health-care associated COVID-19. This approach enabled us to detect cryptic transmission events and identify opportunities to target infection-control interventions to further reduce health-care associated infections. Our findings have important implications for national public health policy as they enable rapid tracking and investigation of infections in hospital and community settings. Full-Text PDF Open Access