1. Altered subgenomic RNA abundance provides unique insight into SARS-CoV-2 B.1.1.7/Alpha variant infections
- Author
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Parker, M.D., Stewart, H., Shehata, O.M., Lindsey, B.B., Shah, D.R., Hsu, S., Keeley, A.J., Partridge, D.G., Leary, S., Cope, A., State, A., Johnson, K., Ali, N., Raghei, R., Heffer, J., Smith, N., Zhang, P., Gallis, M., Louka, S.F., Hornsby, H.R., Alamri, H., Whiteley, M., Foulkes, B.H., Christou, S., Wolverson, P., Pohare, M., Hansford, S.E., Green, L.R., Evans, C., Raza, M., Wang, D., Firth, A.E., Edgar, J.R., Gaudieri, S., Mallal, S., Collins, M.O., Peden, A.A., de Silva, T.I., Parker, M.D., Stewart, H., Shehata, O.M., Lindsey, B.B., Shah, D.R., Hsu, S., Keeley, A.J., Partridge, D.G., Leary, S., Cope, A., State, A., Johnson, K., Ali, N., Raghei, R., Heffer, J., Smith, N., Zhang, P., Gallis, M., Louka, S.F., Hornsby, H.R., Alamri, H., Whiteley, M., Foulkes, B.H., Christou, S., Wolverson, P., Pohare, M., Hansford, S.E., Green, L.R., Evans, C., Raza, M., Wang, D., Firth, A.E., Edgar, J.R., Gaudieri, S., Mallal, S., Collins, M.O., Peden, A.A., and de Silva, T.I.
- Abstract
B.1.1.7 lineage SARS-CoV-2 is more transmissible, leads to greater clinical severity, and results in modest reductions in antibody neutralization. Subgenomic RNA (sgRNA) is produced by discontinuous transcription of the SARS-CoV-2 genome. Applying our tool (periscope) to ARTIC Network Oxford Nanopore Technologies genomic sequencing data from 4400 SARS-CoV-2 positive clinical samples, we show that normalised sgRNA is significantly increased in B.1.1.7 (alpha) infections (n = 879). This increase is seen over the previous dominant lineage in the UK, B.1.177 (n = 943), which is independent of genomic reads, E cycle threshold and days since symptom onset at sampling. A noncanonical sgRNA which could represent ORF9b is found in 98.4% of B.1.1.7 SARS-CoV-2 infections compared with only 13.8% of other lineages, with a 16-fold increase in median sgRNA abundance. We demonstrate that ORF9b protein levels are increased 6-fold in B.1.1.7 compared to a B lineage virus in vitro. We hypothesise that increased ORF9b in B.1.1.7 is a direct consequence of a triple nucleotide mutation in nucleocapsid (28280:GAT > CAT, D3L) creating a transcription regulatory-like sequence complementary to a region 3’ of the genomic leader. These findings provide a unique insight into the biology of B.1.1.7 and support monitoring of sgRNA profiles to evaluate emerging potential variants of concern.
- Published
- 2022