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- Martin, DP, et al.
(author)
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Selection analysis identifies unusual clustered mutational changes in Omicron lineage BA.1 that likely impact Spike function
- 2022
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In: bioRxiv : the preprint server for biology. - : Cold Spring Harbor Laboratory.
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Journal article (other academic/artistic)abstract
- Among the 30 non-synonymous nucleotide substitutions in the Omicron S-gene are 13 that have only rarely been seen in other SARS-CoV-2 sequences. These mutations cluster within three functionally important regions of the S-gene at sites that will likely impact (i) interactions between subunits of the Spike trimer and the predisposition of subunits to shift from down to up configurations, (ii) interactions of Spike with ACE2 receptors, and (iii) the priming of Spike for membrane fusion. We show here that, based on both the rarity of these 13 mutations in intrapatient sequencing reads and patterns of selection at the codon sites where the mutations occur in SARS-CoV-2 and related sarbecoviruses, prior to the emergence of Omicron the mutations would have been predicted to decrease the fitness of any genomes within which they occurred. We further propose that the mutations in each of the three clusters therefore cooperatively interact to both mitigate their individual fitness costs, and adaptively alter the function of Spike. Given the evident epidemic growth advantages of Omicron over all previously known SARS-CoV-2 lineages, it is crucial to determine both how such complex and highly adaptive mutation constellations were assembled within the Omicron S-gene, and why, despite unprecedented global genomic surveillance efforts, the early stages of this assembly process went completely undetected.
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- Duarte-Salles, T, et al.
(author)
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COMPARATIVE RISK OF CANCER ASSOCIATED WITH FIRST-LINE DMARDS USE IN RHEUMATOID ARTHRITIS: REAL WORLD EVIDENCE FROM THE OHDSI NETWORK
- 2020
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In: ANNALS OF THE RHEUMATIC DISEASES. - : BMJ. - 0003-4967 .- 1468-2060. ; 79, s. 1000-1000
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Conference paper (other academic/artistic)abstract
- Conventional synthetic disease-modifying antirheumatic drugs (csDMARDs) are recommended as first line treatment for rheumatoid arthritis (RA) patients, but limited information exists on the comparative risk of cancer associated with their use.Objectives:To compare the risk of incident overall (excluding non-melanoma skin) and site-specific cancers (colorectal, lung, lymphoma, leukaemia) associated with first-line use of csDMARDs in patients with RA.Methods:We conducted a multinational cohort study informed by data from 7 healthcare databases including claims and electronic medical records from 4 countries (SIDIAP-Spain, MDCR-US Optum-US, CCAE-US, IQVIA AMBEMR-US, IQVIA-Germany, THIN-UK) part of the Observational Health Data Sciences and Informatics (OHDSI) network. All patients aged ≥18 years who initiated methotrexate (MTX), hydroxychloroquine (HCQ), sulphasalazine (SSZ), or leflunomide (LEF) as first-line monotherapy after a diagnosis of RA between 2005 to 2018 were eligible. Individuals with a prior diagnosis of another inflammatory arthropathy or cancer, or <1 year of follow-up were excluded. Patients were followed from 1-year after treatment initiation to the earliest of incident cancer, loss to follow-up, or 5-years. Cox proportional-hazard models for MTX against each other csDMARD were performed after propensity score stratification. A large set of negative control outcomes were analysed to calibrate hazard ratios (cHRs). Estimates were pooled where homogeneity across sources was adequate (I2<0.4).Results:Across the databases, 127,547 RA patients initiating csDMARD therapy were included in the analyses (MTX: 73,996, HCL: 36,381 SSZ: 9,383 LEF: 7,787). The pooled incidence rate of overall cancer for MTX was 22.8 per 1,000 person years. The pooled summary and source-specific estimated cHRs for overall cancer are shown below in Figure 1. While little difference was seen for HCQ and SSZ compared to MTX, LEF was consistently associated with a reduced cancer risk: pooled cHR (95% CI) 0.67 (0.59 to 0.76) and cHRs ranged from 0.53 (0.36 to 0.80) in CCAE-US to 0.84 (0.58 to 1.22) in SIDIAP-Spain. There were insufficient cases to look site-specific cancers within data sources, although pooled results suggest little risk difference in leukemia, lymphoma, colorectal, or lung cancers.Figure 1.Calibrated hazard ratios (cHRs) of overall cancer risk with their respective confidence intervals (95%CI) by study database. Database estimates not reported where adequate covariate balance not attained. Meta-analysis results not reported where I2>0.4.Conclusion:Compared to MTX users, patients treated with LEF had a lower risk of overall cancer. Risk of four specific cancers did not differ by first line csDMARD exposure.Disclosure of Interests: :Talita Duarte-Salles: None declared, Martina Recalde: None declared, James Weaver Shareholder of: J&J Shares, Grant/research support from: Full-time employment salary from Janssen, Consultant of: Janssen employee, Employee of: Janssen, Paid instructor for: Janssen employee, have instructed at conferences, Speakers bureau: Janssen employee, have spoken at conferences, Edward Burn: None declared, Karine Marinier Employee of: Servier, Yesika Díaz: None declared, Ben Illingens: None declared, David Vizcaya Employee of: Bayer, Katerina Chatzidionysiou Consultant of: AbbVie, Pfizer, Lilly., Patrick Ryan: None declared, Daniel Prieto-Alhambra Grant/research support from: Professor Prieto-Alhambra has received research Grants from AMGEN, UCB Biopharma and Les Laboratoires Servier, Consultant of: DPA’s department has received fees for consultancy services from UCB Biopharma, Speakers bureau: DPA’s department has received fees for speaker and advisory board membership services from Amgen
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- Martin, DP, et al.
(author)
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The emergence and ongoing convergent evolution of the N501Y lineages coincides with a major global shift in the SARS-CoV-2 selective landscape
- 2021
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In: medRxiv : the preprint server for health sciences. - : Cold Spring Harbor Laboratory.
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Journal article (other academic/artistic)abstract
- The emergence and rapid rise in prevalence of three independent SARS-CoV-2 “501Y lineages’’, B.1.1.7, B.1.351 and P.1, in the last three months of 2020 prompted renewed concerns about the evolutionary capacity of SARS-CoV-2 to adapt to both rising population immunity, and public health interventions such as vaccines and social distancing. Viruses giving rise to the different 501Y lineages have, presumably under intense natural selection following a shift in host environment, independently acquired multiple unique and convergent mutations. As a consequence, all have gained epidemiological and immunological properties that will likely complicate the control of COVID-19. Here, by examining patterns of mutations that arose in SARS-CoV-2 genomes during the pandemic we find evidence of a major change in the selective forces acting on various SARS-CoV-2 genes and gene segments (such as S, nsp2 and nsp6), that likely coincided with the emergence of the 501Y lineages. In addition to involving continuing sequence diversification, we find evidence that a significant portion of the ongoing adaptive evolution of the 501Y lineages also involves further convergence between the lineages. Our findings highlight the importance of monitoring how members of these known 501Y lineages, and others still undiscovered, are convergently evolving similar strategies to ensure their persistence in the face of mounting infection and vaccine induced host immune recognition.
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