Nanopore ReCappable Sequencing maps SARS-CoV-2 5' capping sites and provides new insights into the structure of sgRNAs (preprint)

The SARS-CoV-2 virus has a complex transcriptome characterised by multiple, nested sub genomic RNAs used to express structural and accessory proteins. Long-read sequencing technologies such as nanopore direct RNA sequencing can recover full-length transcripts, greatly simplifying the assembly of structurally complex RNAs. However, these techniques do not detect the 5' cap, thus preventing reliable identification and quantification of full-length, coding transcript models. Here we used Nanopore ReCappable Sequencing (NRCeq), a new technique that can identify capped full-length RNAs, to assemble a complete annotation of SARS-CoV-2 sgRNAs and annotate the location of capping sites across the viral genome. We obtained robust estimates of sgRNA expression across cell lines and viral isolates and identified novel canonical and non-canonical sgRNAs, including one that uses a previously un-annotated leader-to-body junction site. The data generated in this work constitute a useful resource for the scientific community and provide important insights into the mechanisms that regulate the transcription of SARS-CoV-2 sgRNAs.

Using Genomic Concordance to Estimate COVID-19 Transmission Risk Across Different Community Settings in England 2020/21 (preprint)

Background: Identifying areas that pose the greatest risk for community transmission of COVID-19 is essential to direct public health action and allow safe re-opening of society. Spread of B.1.1.7 (alpha) lineage provided a unique opportunity to quantify COVID-19 transmission risk associated with community settings in England 2020/21. Methods: All cases of COVID-19 occurring between 11/2020 and 01/2021 reported through the English national contact tracing system included. Recruitment occurred when B.1.1.7 regional prevalence was between 20-80%. Case groups were defined as: >2 cases reporting the same, location and attendance date 7-3 days before onset. Genetic concordance, presence/absence of S-gene target failure (SGTF) in grouped cases, was determined. Odds ratios for concordance and 95% confidence intervals were calculated. Sensitivity analysis compared concordance in single to 2-3 day case groups. Findings: There were 41,325 case groups with SGTF data containing 115,410 exposure events. Odds ratios ranged from 1.87 (95% CI:1.76-1.98) for shops, 29.9 (95% CI:23.1-38.7), nursery/preschool and 35.6 (95% CI:19.7-64.2) for visiting friends/relatives. Odds ratios of concordance increased with larger cluster sizes in educational settings. Concordance estimates were reduced when case grouping time period was increased from 1 to 2-3 days. Interpretation: Transmission risk varies across community settings, likely due to different behavioural or environmental factors. Risk does not capture number of users which also affects impact of settings on transmission. Limited data for certain settings due to non-pharmaceutical interventions in place. We recommend data are used to guide policy and prioritise action when assessing and managing COVID-19 community case clusters. Funding: EB funded by EMBL. No additional funding.Declaration of Interest: None to declare

Genomic reconstruction of the SARS-CoV-2 epidemic across England from September 2020 to May 2021 (preprint)

Despite regional successes in controlling the SARS-CoV-2 pandemic, global cases have reached an all time high in April 2021 in part due to the evolution of more transmissible variants. Here we use the dense genomic surveillance generated by the COVID-19 Genomics UK Consortium to reconstruct the dynamics of 62 different lineages in each of 315 English local authorities between September 2020 and April 2021. This analysis reveals a series of sub-epidemics that peaked in the early autumn of 2020, followed by a singular jump in transmissibility of the B.1.1.7 lineage. B.1.1.7 grew when other lineages declined during the second national lockdown and regionally tiered restrictions between November and December 2020. A third more stringent national lockdown eventually suppressed B.1.1.7 and eliminated nearly all other lineages in early 2021. However, a series of variants (mostly containing the spike E484K mutation) defied these trends and persisted at moderately increasing proportions. Accounting for sustained introductions, however, indicates that their transmissibility is unlikely to exceed that of B.1.1.7. Finally, B.1.617.2 was repeatedly introduced to England and grew rapidly in April 2021, constituting approximately 40% of sampled COVID-19 genomes on May 15.