TY - JOUR
T1 - Altered subgenomic RNA abundance provides unique insight into SARS-CoV-2 B.1.1.7/Alpha variant infections
AU - COVID-19 Genomics UK COG-UK Consor
AU - Parker, Matthew D.
AU - Stewart, Hazel
AU - Shehata, Ola M.
AU - Lindsey, Benjamin B.
AU - Shah, Dhruv R.
AU - Hsu, Sharon
AU - Keeley, Alexander J.
AU - Partridge, David G.
AU - Leary, Shay
AU - Cope, Alison
AU - State, Amy
AU - Johnson, Katie
AU - Ali, Nasar
AU - Raghei, Rasha
AU - Heffer, Joe
AU - Smith, Nikki
AU - Zhang, Peijun
AU - Gallis, Marta
AU - Louka, Stavroula F.
AU - Hornsby, Hailey R.
AU - Alamri, Hatoon
AU - Whiteley, Max
AU - Foulkes, Benjamin H.
AU - Christou, Stella
AU - Wolverson, Paige
AU - Pohare, Manoj
AU - Hansford, Samantha E.
AU - Green, Luke R.
AU - Evans, Cariad
AU - Raza, Mohammad
AU - Wang, Dennis
AU - Firth, Andrew E.
AU - Edgar, James R.
AU - Gaudieri, Silvana
AU - Mallal, Simon
AU - Collins, Mark O.
AU - Peden, Andrew A.
AU - de Silva, Thushan
PY - 2022/7/5
Y1 - 2022/7/5
N2 - Matthew Parker et al. use the ARTIC network tiled amplicon PCR and Oxford Nanopore sequencing of thousands of SARS-CoV-2 samples to detect subgenomic RNA changes in the B.1.1.7 lineage endemic in the UK in late 2020/early 2021. They discovered higher subgenomic RNA in B.1.1.7 compared to previous lineages, and find a noncanonical subgenomic RNA that could encode ORF9b.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.
AB - Matthew Parker et al. use the ARTIC network tiled amplicon PCR and Oxford Nanopore sequencing of thousands of SARS-CoV-2 samples to detect subgenomic RNA changes in the B.1.1.7 lineage endemic in the UK in late 2020/early 2021. They discovered higher subgenomic RNA in B.1.1.7 compared to previous lineages, and find a noncanonical subgenomic RNA that could encode ORF9b.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.
UR - http://www.scopus.com/inward/record.url?scp=85137123628&partnerID=8YFLogxK
U2 - 10.1038/s42003-022-03565-9
DO - 10.1038/s42003-022-03565-9
M3 - Article
C2 - 35790808
SN - 2399-3642
VL - 5
JO - Communications Biology
JF - Communications Biology
IS - 1
M1 - 666
ER -