SARS-CoV-2 sequencing: A comparison of highthroughput methods

Background/Objectives: The COVID-19 pandemic continues to threaten public health and burden healthcare systems worldwide. Whole SARS-CoV-2 genome sequencing has become essential for epidemiological monitoring and identification of new variants, which could represent a risk of increased transmissibility, virulence, or resistance to vaccines or treatment. In this study, we assess the performance of various target enrichment methods for whole SARS-CoV-2 sequencing. Method(s): We applied three target enrichment methods - two multiplex amplification methods and one hybridization capture - to the same set of nasopharyngeal patient samples (N = 93) in high-throughput mode. SARS-CoV-2 genome was obtained using short-read next-generation sequencing. Result(s): All three methods provided excellent breadth of coverage of SARS-CoV-2 genome (above 99%), albeit with vastly different sequencing depth (5-fold difference) and uniformity of coverage (20% difference in coefficient of variation). Poor local coverage has negative impact on variant calling in the concerned region, leading to an occasional allele drop-out (1.2% SNPs affected for one method). Conclusion(s): We discuss the performance of each target enrichment method and their potential for scaling up, in order to promote prospective programs of large-scale genomic surveillance of SARS-CoV-2 worldwide. Genomic surveillance will be crucial to overcoming the ongoing pandemic of COVID-19, despite its successive waves and continually emerging variants.

Real-time genotyping-based breast cancer risk assessment in MyPeBS, an international randomized trial in the general population comparing risk-stratified to standard breast cancer screening (BCS)

Background: Risk-stratified BCS, integrating personal, familial variables and a polygenic risk score (PRS) is a promising strategy that may improve current BCS outcomes. Real-time risk assessment and field implementation are some of the main challenges for such an approach. Methods: MyPeBS is an ongoing EU-funded international randomized trial running in 6 countries. Eligible women (wn) aged 40-70 are randomized 1:1 between continuing standard organized BCS as recommended in their participating country/region and switching to risk-stratified BCS, in which BCS schedule and modalities are adapted to the individual predicted 5-year risk of invasive BC (IBC). Primary endpoint is 4-year incidence of stage 2 and higher BC. Secondary endpoints include PROs. 5-year IBC risk is estimated using the Mammorisk® BCSC-derived or the Tyrer Cuzick risk score and the centrally-determined PRS313 obtained from a saliva sample and calibrated for national BC incidence and age. We aim to describe 1) the feasibility of real-time assessment of BC risk and 2) the characteristics and risk profiles of the participants. Results: As of Sept. 7, 2021, 16,550 wn had been randomized. 29% were aged <50 (median age 54 (range 40-70), 13% had a previous benign breast biopsy, 40% a mammographic breast density C or D, 19% a 1st degree family history of breast or ovarian cancer;72% had tertiary education. 36% were estimated at low risk (<1% risk of IBC at 5 years), 29% at average risk, and 35% at high (34%) or very high risk (1%) (>1.67% and >6% risk, respectively). Only 2.5% of DNA extractions were not usable for genotyping, due to DNA concentration or quality;and 98.8% of the eligible DNA samples were successfully genotyped. Median turnover time from saliva sampling to risk result available was 11 weeks despite the COVID pandemic (currently 7 weeks). Conclusions: Real-time BC risk assessment based on a large set of polymorphisms, family, screening and hormonal history, and breast density is feasible within organized screening programmes. Participants are so far representative of different categories with some over-representation of highly educated participants. Clinical trial identification: NCT03672331. Legal entity responsible for the study: Unicancer. Funding: European Commission and French National Cancer Institute. Disclosure: S. Delaloge: Financial Interests, Institutional, Advisory Board: AstraZeneca;Financial Interests, Institutional, Invited Speaker: Exact Sciences;Financial Interests, Institutional, Advisory Board: Novartis;Financial Interests, Institutional, Advisory Board: Pierre fabre;Financial Interests, Institutional, Advisory Board: Orion;Financial Interests, Institutional, Advisory Board: Sanofi;Financial Interests, Institutional, Advisory Board: Rappta;Financial Interests, Institutional, Advisory Board: Cellectis;Financial Interests, Institutional, Advisory Board: Isis/servier;Financial Interests, Institutional, Invited Speaker: Pfizer;Financial Interests, Institutional, Invited Speaker: Seagen;Financial Interests, Institutional, Invited Speaker: Lilly;Financial Interests, Institutional, Invited Speaker: AstraZeneca;Financial Interests, Institutional, Invited Speaker: MSD;Financial Interests, Institutional, Advisory Board, ad board: Besins Healthcare;Financial Interests, Institutional, Invited Speaker: Roche Genentech;Financial Interests, Institutional, Invited Speaker: BMS;Financial Interests, Institutional, Invited Speaker: Puma;Financial Interests, Institutional, Invited Speaker: AstraZeneca;Financial Interests, Institutional, Invited Speaker: Orion;Financial Interests, Institutional, Invited Speaker: Sanofi;Financial Interests, Institutional, Funding: GE;Financial Interests, Institutional, Invited Speaker: Pfizer;Financial Interests, Institutional, Invited Speaker, clinical research funding to my institution: Taiho;Non-Financial Interests, Invited Speaker, Société Française de Sénologie et Pathologie Mammaire: SFSPM. D. Keatley: Financial Interests, Personal, Advisory Board: Public Advisory Board of Heealth Data UK. E. Gauthier: Financial Interests, Personal, Stocks/Shares: Predilife;Financial Interests, Personal, Full or part-time Employment: Predilife. S. Michiels: Financial Interests, Personal, Advisory Role: IDDI;Financial Interests, Personal, Advisory Role: Amaris;Financial Interests, Personal, Advisory Role: Roche;Financial Interests, Personal, Advisory Role: Sensorion;Financial Interests, Personal, Advisory Role: Biophytis;Financial Interests, Personal, Advisory Role: Servier;Financial Interests, Personal, Advisory Role: Yuhan. All other authors have declared no conflicts of interest.

Assessing the multi-disciplinary team response to NIV withdrawal guidelines in patients with COVID-19

IntroductionWithdrawal of NIV in COVID-19 patients at end of life presents several challenges. Patients are often more alert and have a higher symptom burden than in other end of life situations where NIV is withdrawn. The NIV withdrawal guideline, created by the centre, was updated to reflect the requirement for higher doses of anticipatory medications required for some patients in this cohort after learning from the first wave of COVID-19. The aim of this study was to review staff response to the guideline and its efficacy. MethodA questionnaire was sent to physician associates, nursing staff and doctors of all grades who have worked on the Respiratory Support Unit during the COVID-19 pandemic. This collected several types of data on staff perception of NIV withdrawal in COVID-19 patients.ResultsThe questionnaire generated 39 responses from the multidisciplinary team (MDT).97% of respondents found the withdrawal of NIV in COVID-19 challenging, and 74% felt this was more difficult in patients with COVID-19 than with other pathologies. 87% were aware of the Trust guideline regarding NIV withdrawal and 82% used it in their practice. All respondents felt the guideline was useful. While the majority of healthcare workers felt that adequate symptom control was achieved, 20% of respondents did not. This unease was further evidenced as 64% of respondents had issues or concerns regarding the use of anticipatory medications. The predominant concerns were that medication doses were started too low (35%) or too late (46%). 71% of respondents found discussions with families regarding commencing palliation challenging. All members of the multidisciplinary team found an MDT approach, including the involvement of Palliative Care colleagues, a useful source of support. The team was united in finding debriefs useful.ConclusionsOverall, this study identified that timing and dosage of anticipatory medications are a particular challenge in withdrawal of NIV in patients with COVID-19. There is scope for additional learning regarding symptom management during withdrawal of NIV. Maintaining a close relationship with the Palliative Care team provides benefit to patients, their families and staff. Further work will also focus on supporting staff in difficult conversations.