Subgenomic RNA identification in SARS-CoV-2 genomic sequencing data.

We have developed periscope, a tool for the detection and quantification of subgenomic RNA (sgRNA) in SARS-CoV-2 genomic sequence data. The translation of the SARS-CoV-2 RNA genome for most open reading frames (ORFs) occurs via RNA intermediates termed "subgenomic RNAs." sgRNAs are produced through discontinuous transcription, which relies on homology between transcription regulatory sequences (TRS-B) upstream of the ORF start codons and that of the TRS-L, which is located in the 5' UTR. TRS-L is immediately preceded by a leader sequence. This leader sequence is therefore found at the 5' end of all sgRNA. We applied periscope to 1155 SARS-CoV-2 genomes from Sheffield, United Kingdom, and validated our findings using orthogonal data sets and in vitro cell systems. By using a simple local alignment to detect reads that contain the leader sequence, we were able to identify and quantify reads arising from canonical and noncanonical sgRNA. We were able to detect all canonical sgRNAs at the expected abundances, with the exception of ORF10. A number of recurrent noncanonical sgRNAs are detected. We show that the results are reproducible using technical replicates and determine the optimum number of reads for sgRNA analysis. In VeroE6 ACE2+/- cell lines, periscope can detect the changes in the kinetics of sgRNA in orthogonal sequencing data sets. Finally, variants found in genomic RNA are transmitted to sgRNAs with high fidelity in most cases. This tool can be applied to all sequenced COVID-19 samples worldwide to provide comprehensive analysis of SARS-CoV-2 sgRNA.

A cohort analysis of patients receiving neoadjuvant androgen deprivation therapy prior to robot-assisted laparoscopic prostatectomy during the Covid-19 pandemic.

Objectives: The purpose of this study was to investigate localised prostate cancer treated with or without neoadjuvant androgen deprivation therapy prior to robot-assisted laparoscopic prostatectomy, and the impact of Covid-19 treatment disruption, on clinico-pathologic outcomes. Patients and methods: Data was retrospectively collected from 124 consecutive patients treated with robot-assisted laparoscopic prostatectomy between November 2019-September 2020. Sixty-two patients were treated before 13 March 2020 (historic cohort) and 62 afterwards (covid cohort). Thirty-seven patients in the covid cohort additionally received neoadjuvant androgen deprivation therapy (mean duration of 3 months) consisting of bicalutamide 150 mg once a day for 4 weeks, with leuprolide 3.75 mg monthly injections commencing after week 1, up until the date of surgery. Results: Statistical analysis found no difference in peri-operative measures and length of stay for patients treated with or without neoadjuvant androgen deprivation therapy. Patients with delayed surgical treatment offered neoadjuvant androgen deprivation therapy showed a trend towards a reduction in positive surgical margins (p=0.134), N1 disease (p=0.424) and pathological down-staging (50% patients with pT2 disease). Patients within the covid cohort experienced significantly increased detectable prostate-specific antigen levels (p<0.007). Conclusion: Our study demonstrated that a three-month duration of neoadjuvant androgen deprivation therapy prior to robot-assisted laparoscopic prostatectomy may improve pathological outcomes but this time-frame is inadequate to influence detectable prostate-specific antigen levels. Covid-19-related treatment delays led to significantly increased detectable prostate-specific antigen levels. Level of evidence: 2b.