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Sanderson T, Hisner R, Donovan-Banfield I, Hartman H, Løchen A, Peacock TP, Ruis C. A molnupiravir-associated mutational signature in global SARS-CoV-2 genomes. Nature 2023; 623:594-600. [PMID: 37748513 PMCID: PMC10651478 DOI: 10.1038/s41586-023-06649-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 09/15/2023] [Indexed: 09/27/2023]
Abstract
Molnupiravir, an antiviral medication widely used against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), acts by inducing mutations in the virus genome during replication. Most random mutations are likely to be deleterious to the virus and many will be lethal; thus, molnupiravir-induced elevated mutation rates reduce viral load1,2. However, if some patients treated with molnupiravir do not fully clear the SARS-CoV-2 infections, there could be the potential for onward transmission of molnupiravir-mutated viruses. Here we show that SARS-CoV-2 sequencing databases contain extensive evidence of molnupiravir mutagenesis. Using a systematic approach, we find that a specific class of long phylogenetic branches, distinguished by a high proportion of G-to-A and C-to-T mutations, are found almost exclusively in sequences from 2022, after the introduction of molnupiravir treatment, and in countries and age groups with widespread use of the drug. We identify a mutational spectrum, with preferred nucleotide contexts, from viruses in patients known to have been treated with molnupiravir and show that its signature matches that seen in these long branches, in some cases with onward transmission of molnupiravir-derived lineages. Finally, we analyse treatment records to confirm a direct association between these high G-to-A branches and the use of molnupiravir.
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Affiliation(s)
| | - Ryan Hisner
- Department of Bioinformatics, University of Cape Town, Cape Town, South Africa
| | - I'ah Donovan-Banfield
- Department of Infection Biology and Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Health Protection Research Unit in Emerging and Zoonotic Infections, National Institute for Health and Care Research, Liverpool, UK
| | | | | | - Thomas P Peacock
- Department of Infectious Disease, Imperial College London, London, UK
- The Pirbright Institute, Pirbright, UK
| | - Christopher Ruis
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Medical Research Council-Laboratory of Molecular Biology, Cambridge, UK.
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK.
- Cambridge Centre for AI in Medicine, University of Cambridge, Cambridge, UK.
- Victor Phillip Dahdaleh Heart & Lung Research Institute, University of Cambridge, Cambridge, UK.
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2
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Khoo SH, FitzGerald R, Saunders G, Middleton C, Ahmad S, Edwards CJ, Hadjiyiannakis D, Walker L, Lyon R, Shaw V, Mozgunov P, Periselneris J, Woods C, Bullock K, Hale C, Reynolds H, Downs N, Ewings S, Buadi A, Cameron D, Edwards T, Knox E, Donovan-Banfield I, Greenhalf W, Chiong J, Lavelle-Langham L, Jacobs M, Northey J, Painter W, Holman W, Lalloo DG, Tetlow M, Hiscox JA, Jaki T, Fletcher T, Griffiths G, Hayden F, Darbyshire J, Lucas A, Lorch U, Freedman A, Knight R, Julious S, Byrne R, Cubas Atienzar A, Jones J, Williams C, Song A, Dixon J, Alexandersson A, Hatchard P, Tilt E, Titman A, Doce Carracedo A, Chandran Gorner V, Davies A, Woodhouse L, Carlucci N, Okenyi E, Bula M, Dodd K, Gibney J, Dry L, Rashid Gardner Z, Sammour A, Cole C, Rowland T, Tsakiroglu M, Yip V, Osanlou R, Stewart A, Parker B, Turgut T, Ahmed A, Starkey K, Subin S, Stockdale J, Herring L, Baker J, Oliver A, Pacurar M, Owens D, Munro A, Babbage G, Faust S, Harvey M, Pratt D, Nagra D, Vyas A. Molnupiravir versus placebo in unvaccinated and vaccinated patients with early SARS-CoV-2 infection in the UK (AGILE CST-2): a randomised, placebo-controlled, double-blind, phase 2 trial. Lancet Infect Dis 2023; 23:183-195. [PMID: 36272432 PMCID: PMC9662684 DOI: 10.1016/s1473-3099(22)00644-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 09/06/2022] [Accepted: 09/12/2022] [Indexed: 11/06/2022]
Abstract
BACKGROUND The antiviral drug molnupiravir was licensed for treating at-risk patients with COVID-19 on the basis of data from unvaccinated adults. We aimed to evaluate the safety and virological efficacy of molnupiravir in vaccinated and unvaccinated individuals with COVID-19. METHODS This randomised, placebo-controlled, double-blind, phase 2 trial (AGILE CST-2) was done at five National Institute for Health and Care Research sites in the UK. Eligible participants were adult (aged ≥18 years) outpatients with PCR-confirmed, mild-to-moderate SARS-CoV-2 infection who were within 5 days of symptom onset. Using permuted blocks (block size 2 or 4) and stratifying by site, participants were randomly assigned (1:1) to receive either molnupiravir (orally; 800 mg twice daily for 5 days) plus standard of care or matching placebo plus standard of care. The primary outcome was the time from randomisation to SARS-CoV-2 PCR negativity on nasopharyngeal swabs and was analysed by use of a Bayesian Cox proportional hazards model for estimating the probability of a superior virological response (hazard ratio [HR]>1) for molnupiravir versus placebo. Our primary model used a two-point prior based on equal prior probabilities (50%) that the HR was 1·0 or 1·5. We defined a priori that if the probability of a HR of more than 1 was more than 80% molnupiravir would be recommended for further testing. The primary outcome was analysed in the intention-to-treat population and safety was analysed in the safety population, comprising participants who had received at least one dose of allocated treatment. This trial is registered in ClinicalTrials.gov, NCT04746183, and the ISRCTN registry, ISRCTN27106947, and is ongoing. FINDINGS Between Nov 18, 2020, and March 16, 2022, 1723 patients were assessed for eligibility, of whom 180 were randomly assigned to receive either molnupiravir (n=90) or placebo (n=90) and were included in the intention-to-treat analysis. 103 (57%) of 180 participants were female and 77 (43%) were male and 90 (50%) participants had received at least one dose of a COVID-19 vaccine. SARS-CoV-2 infections with the delta (B.1.617.2; 72 [40%] of 180), alpha (B.1.1.7; 37 [21%]), omicron (B.1.1.529; 38 [21%]), and EU1 (B.1.177; 28 [16%]) variants were represented. All 180 participants received at least one dose of treatment and four participants discontinued the study (one in the molnupiravir group and three in the placebo group). Participants in the molnupiravir group had a faster median time from randomisation to negative PCR (8 days [95% CI 8-9]) than participants in the placebo group (11 days [10-11]; HR 1·30, 95% credible interval 0·92-1·71; log-rank p=0·074). The probability of molnupiravir being superior to placebo (HR>1) was 75·4%, which was less than our threshold of 80%. 73 (81%) of 90 participants in the molnupiravir group and 68 (76%) of 90 participants in the placebo group had at least one adverse event by day 29. One participant in the molnupiravir group and three participants in the placebo group had an adverse event of a Common Terminology Criteria for Adverse Events grade 3 or higher severity. No participants died (due to any cause) during the trial. INTERPRETATION We found molnupiravir to be well tolerated and, although our predefined threshold was not reached, we observed some evidence that molnupiravir has antiviral activity in vaccinated and unvaccinated individuals infected with a broad range of SARS-CoV-2 variants, although this evidence is not conclusive. FUNDING Ridgeback Biotherapeutics, the UK National Institute for Health and Care Research, the Medical Research Council, and the Wellcome Trust.
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Affiliation(s)
- Saye H Khoo
- Pharmacology and Therapeutics, University of Liverpool, Liverpool, UK; Tropical and Infectious Disease Unit, Liverpool University Hospital NHS Foundation Trust, Liverpool, UK.
| | - Richard FitzGerald
- Pharmacology and Therapeutics, University of Liverpool, Liverpool, UK,NIHR Royal Liverpool and Broadgreen Clinical Research Facility, Liverpool University Hospital NHS Foundation Trust, Liverpool, UK
| | - Geoffrey Saunders
- Southampton Clinical Trials Unit, University of Southampton, Southampton, UK
| | - Calley Middleton
- Southampton Clinical Trials Unit, University of Southampton, Southampton, UK
| | - Shazaad Ahmad
- NIHR Manchester Clinical Research Facility, Manchester University NHS Foundation Trust, Manchester, UK
| | - Christopher J Edwards
- Human Development and Health School, University of Southampton, Southampton, UK,NIHR Southampton Clinical Research Facility, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Dennis Hadjiyiannakis
- NIHR Lancashire Clinical Research Facility, Lancashire Teaching Hospitals NHS Foundation Trust, Preston, UK
| | - Lauren Walker
- Pharmacology and Therapeutics, University of Liverpool, Liverpool, UK,NIHR Royal Liverpool and Broadgreen Clinical Research Facility, Liverpool University Hospital NHS Foundation Trust, Liverpool, UK
| | - Rebecca Lyon
- NIHR Royal Liverpool and Broadgreen Clinical Research Facility, Liverpool University Hospital NHS Foundation Trust, Liverpool, UK
| | - Victoria Shaw
- Clinical Directorate, University of Liverpool, Liverpool, UK
| | - Pavel Mozgunov
- MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
| | - Jimstan Periselneris
- NIHR Kings Clinical Research Facility, King's College Hospital NHS Foundation Trust, London, UK
| | - Christie Woods
- NIHR Royal Liverpool and Broadgreen Clinical Research Facility, Liverpool University Hospital NHS Foundation Trust, Liverpool, UK
| | - Katie Bullock
- Molecular & Clinical Cancer Medicine, University of Liverpool, Liverpool, UK
| | - Colin Hale
- NIHR Royal Liverpool and Broadgreen Clinical Research Facility, Liverpool University Hospital NHS Foundation Trust, Liverpool, UK
| | - Helen Reynolds
- Pharmacology and Therapeutics, University of Liverpool, Liverpool, UK
| | - Nichola Downs
- Southampton Clinical Trials Unit, University of Southampton, Southampton, UK
| | - Sean Ewings
- Southampton Clinical Trials Unit, University of Southampton, Southampton, UK
| | - Amanda Buadi
- NIHR Southampton Clinical Research Facility, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - David Cameron
- NIHR Lancashire Clinical Research Facility, Lancashire Teaching Hospitals NHS Foundation Trust, Preston, UK
| | | | - Emma Knox
- Southampton Clinical Trials Unit, University of Southampton, Southampton, UK
| | - I'ah Donovan-Banfield
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK,National Institute of Health Research Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, UK
| | - William Greenhalf
- Molecular & Clinical Cancer Medicine, University of Liverpool, Liverpool, UK
| | - Justin Chiong
- Pharmacology and Therapeutics, University of Liverpool, Liverpool, UK
| | | | - Michael Jacobs
- Infectious Diseases, Royal Free London NHS Foundation Trust, London, UK
| | - Josh Northey
- Southampton Clinical Trials Unit, University of Southampton, Southampton, UK
| | | | | | | | - Michelle Tetlow
- Pharmacology and Therapeutics, University of Liverpool, Liverpool, UK
| | - Julian A Hiscox
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK,National Institute of Health Research Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, UK
| | - Thomas Jaki
- MRC Biostatistics Unit, University of Cambridge, Cambridge, UK,Computational Statistics, University of Regensburg, Regensburg, Germany
| | - Thomas Fletcher
- Tropical and Infectious Disease Unit, Liverpool University Hospital NHS Foundation Trust, Liverpool, UK,Clinical Sciences, Liverpool, UK
| | - Gareth Griffiths
- Southampton Clinical Trials Unit, University of Southampton, Southampton, UK
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Dong X, Penrice-Randal R, Goldswain H, Prince T, Randle N, Donovan-Banfield I, Salguero FJ, Tree J, Vamos E, Nelson C, Clark J, Ryan Y, Stewart JP, Semple MG, Baillie JK, Openshaw PJM, Turtle L, Matthews DA, Carroll MW, Darby AC, Hiscox JA. Analysis of SARS-CoV-2 known and novel subgenomic mRNAs in cell culture, animal model, and clinical samples using LeTRS, a bioinformatic tool to identify unique sequence identifiers. Gigascience 2022; 11:6593429. [PMID: 35639883 PMCID: PMC9154083 DOI: 10.1093/gigascience/giac045] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 12/08/2021] [Accepted: 04/07/2022] [Indexed: 12/30/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has a complex strategy for the transcription of viral subgenomic mRNAs (sgmRNAs), which are targets for nucleic acid diagnostics. Each of these sgmRNAs has a unique 5' sequence, the leader-transcriptional regulatory sequence gene junction (leader-TRS junction), that can be identified using sequencing. High-resolution sequencing has been used to investigate the biology of SARS-CoV-2 and the host response in cell culture and animal models and from clinical samples. LeTRS, a bioinformatics tool, was developed to identify leader-TRS junctions and can be used as a proxy to quantify sgmRNAs for understanding virus biology. LeTRS is readily adaptable for other coronaviruses such as Middle East respiratory syndrome coronavirus or a future newly discovered coronavirus. LeTRS was tested on published data sets and novel clinical samples from patients and longitudinal samples from animal models with coronavirus disease 2019. LeTRS identified known leader-TRS junctions and identified putative novel sgmRNAs that were common across different mammalian species. This may be indicative of an evolutionary mechanism where plasticity in transcription generates novel open reading frames, which can then subject to selection pressure. The data indicated multiphasic abundance of sgmRNAs in two different animal models. This recapitulates the relative sgmRNA abundance observed in cells at early points in infection but not at late points. This pattern is reflected in some human nasopharyngeal samples and therefore has implications for transmission models and nucleic acid-based diagnostics. LeTRS provides a quantitative measure of sgmRNA abundance from sequencing data. This can be used to assess the biology of SARS-CoV-2 (or other coronaviruses) in clinical and nonclinical samples, especially to evaluate different variants and medical countermeasures that may influence viral RNA synthesis.
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Affiliation(s)
- Xiaofeng Dong
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L3 5RF, UK
| | - Rebekah Penrice-Randal
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L3 5RF, UK
| | - Hannah Goldswain
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L3 5RF, UK
| | - Tessa Prince
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L3 5RF, UK
| | - Nadine Randle
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L3 5RF, UK
| | - I'ah Donovan-Banfield
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L3 5RF, UK
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, Liverpool, L69 7BE, UK
| | | | - Julia Tree
- UK-Health Security Agency, Salisbury, SP4 0JG, UK
| | - Ecaterina Vamos
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L3 5RF, UK
| | - Charlotte Nelson
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L3 5RF, UK
| | - Jordan Clark
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L3 5RF, UK
| | - Yan Ryan
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L3 5RF, UK
| | - James P Stewart
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L3 5RF, UK
| | - Malcolm G Semple
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L3 5RF, UK
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, Liverpool, L69 7BE, UK
| | - J Kenneth Baillie
- The Roslin Institute, University of Edinburgh, Edinburgh, EH25 9RG, UK
| | - Peter J M Openshaw
- National Heart and Lung Institute, Imperial College London, London, SW3 6LY, UK
| | - Lance Turtle
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L3 5RF, UK
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, Liverpool, L69 7BE, UK
| | | | - Miles W Carroll
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, Liverpool, L69 7BE, UK
- UK-Health Security Agency, Salisbury, SP4 0JG, UK
| | - Alistair C Darby
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L3 5RF, UK
| | - Julian A Hiscox
- Correspondence address.Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, ic2 Building, Liverpool, L3 5RF, UK. E-mail:
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4
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Zhou J, Peacock TP, Brown JC, Goldhill DH, Elrefaey AME, Penrice-Randal R, Cowton VM, De Lorenzo G, Furnon W, Harvey WT, Kugathasan R, Frise R, Baillon L, Lassaunière R, Thakur N, Gallo G, Goldswain H, Donovan-Banfield I, Dong X, Randle NP, Sweeney F, Glynn MC, Quantrill JL, McKay PF, Patel AH, Palmarini M, Hiscox JA, Bailey D, Barclay WS. Mutations that adapt SARS-CoV-2 to mink or ferret do not increase fitness in the human airway. Cell Rep 2022; 38:110344. [PMID: 35093235 PMCID: PMC8768428 DOI: 10.1016/j.celrep.2022.110344] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 11/11/2021] [Accepted: 01/14/2022] [Indexed: 12/18/2022] Open
Abstract
SARS-CoV-2 has a broad mammalian species tropism infecting humans, cats, dogs, and farmed mink. Since the start of the 2019 pandemic, several reverse zoonotic outbreaks of SARS-CoV-2 have occurred in mink, one of which reinfected humans and caused a cluster of infections in Denmark. Here we investigate the molecular basis of mink and ferret adaptation and demonstrate the spike mutations Y453F, F486L, and N501T all specifically adapt SARS-CoV-2 to use mustelid ACE2. Furthermore, we risk assess these mutations and conclude mink-adapted viruses are unlikely to pose an increased threat to humans, as Y453F attenuates the virus replication in human cells and all three mink adaptations have minimal antigenic impact. Finally, we show that certain SARS-CoV-2 variants emerging from circulation in humans may naturally have a greater propensity to infect mustelid hosts and therefore these species should continue to be surveyed for reverse zoonotic infections.
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Affiliation(s)
- Jie Zhou
- Department of Infectious Disease, Imperial College London, London, UK
| | - Thomas P Peacock
- Department of Infectious Disease, Imperial College London, London, UK
| | - Jonathan C Brown
- Department of Infectious Disease, Imperial College London, London, UK
| | - Daniel H Goldhill
- Department of Infectious Disease, Imperial College London, London, UK
| | | | - Rebekah Penrice-Randal
- Institute of Infection, Veterinary and Ecology Sciences, University of Liverpool, Liverpool, UK
| | - Vanessa M Cowton
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | | | - Wilhelm Furnon
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - William T Harvey
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | | | - Rebecca Frise
- Department of Infectious Disease, Imperial College London, London, UK
| | - Laury Baillon
- Department of Infectious Disease, Imperial College London, London, UK
| | - Ria Lassaunière
- Virus & Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Nazia Thakur
- The Pirbright Institute, Woking, Surrey, UK; The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Hannah Goldswain
- Institute of Infection, Veterinary and Ecology Sciences, University of Liverpool, Liverpool, UK
| | - I'ah Donovan-Banfield
- Institute of Infection, Veterinary and Ecology Sciences, University of Liverpool, Liverpool, UK
| | - Xiaofeng Dong
- Institute of Infection, Veterinary and Ecology Sciences, University of Liverpool, Liverpool, UK
| | - Nadine P Randle
- Institute of Infection, Veterinary and Ecology Sciences, University of Liverpool, Liverpool, UK
| | - Fiachra Sweeney
- Department of Infectious Disease, Imperial College London, London, UK
| | - Martha C Glynn
- Department of Infectious Disease, Imperial College London, London, UK
| | | | - Paul F McKay
- Department of Infectious Disease, Imperial College London, London, UK
| | - Arvind H Patel
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | | | - Julian A Hiscox
- Institute of Infection, Veterinary and Ecology Sciences, University of Liverpool, Liverpool, UK; Infectious Diseases Horizontal Technology Centre (ID HTC), A(∗)STAR, Singapore, Singapore
| | | | - Wendy S Barclay
- Department of Infectious Disease, Imperial College London, London, UK.
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5
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Donovan-Banfield I, Turnell AS, Hiscox JA, Leppard KN, Matthews DA. Deep splicing plasticity of the human adenovirus type 5 transcriptome drives virus evolution. Commun Biol 2020; 3:124. [PMID: 32170151 PMCID: PMC7070027 DOI: 10.1038/s42003-020-0849-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 02/12/2020] [Indexed: 02/06/2023] Open
Abstract
Viral genomes have high gene densities and complex transcription strategies rendering transcriptome analysis through short-read RNA-seq approaches problematic. Adenovirus transcription and splicing is especially complex. We used long-read direct RNA sequencing to study adenovirus transcription and splicing during infection. This revealed a previously unappreciated complexity of alternative splicing and potential for secondary initiating codon usage. Moreover, we find that most viral transcripts tend to shorten polyadenylation lengths as infection progresses. Development of an open reading frame centric bioinformatics analysis pipeline provided a deeper quantitative and qualitative understanding of adenovirus's genetic potential. Across the viral genome adenovirus makes multiple distinctly spliced transcripts that code for the same protein. Over 11,000 different splicing patterns were recorded across the viral genome, most occurring at low levels. This low-level use of alternative splicing patterns potentially enables the virus to maximise its coding potential over evolutionary timescales.
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Affiliation(s)
- I'ah Donovan-Banfield
- Department of Cellular and Molecular Medicine, School of Medical Sciences University Walk, University of Bristol, Bristol, BS8 1TD, UK
| | - Andrew S Turnell
- Institute of Cancer and Genomic Sciences College of Medical and Dental Sciences University of Birmingham Edgbaston, Birmingham, B15 2TT, UK
| | - Julian A Hiscox
- Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, ic2 Building, Liverpool, L3 5RF, UK
| | - Keith N Leppard
- Life Sciences University of Warwick Coventry, Coventry, CV4 7AL, UK
| | - David A Matthews
- Department of Cellular and Molecular Medicine, School of Medical Sciences University Walk, University of Bristol, Bristol, BS8 1TD, UK.
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