COVID-19 Outputs

CVR COVID-19 related publications and software

CVR COVID-19 related publications

1. Genomic epidemiology of SARS-CoV-2 spread in Scotland highlights the role of European travel in COVID-19 emergence. Ana Da Silva Filipe, James Shepherd et al.Nature Microbiology, 2021 Jan;6(1):112-122. 


2. SARS-CoV-2 serosurveillance reveals the impact of caretype and demography on virus 2 exposure and antibody-mediated immunity.Ellen Hughes, Julien Amat et al. Journal of Infectious Disease, 2020 Dec; jiaa788. 


3. Evaluating the effects of SARS-CoV-2 Spike mutation D614G on transmissibility and pathogenicity. Erik Volz and Verity Hill et al. Cell, 2021 Jan; 184: 64-75.


4. Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic. Maciej Boni and PhilippeLemey et al. Nature Microbiology, 2020 Jul; 5: 1408-1417. 


5. Risk stratification of patients admitted to hospital with covid-19 using the ISARIC WHO Clinical Characterisation Protocol: development and validation of the 4C Mortality Score. Stephen Knight and Antonia Ho et al. BMJ, 2020 Sept; 370:m3339


6. Circulating SARS-CoV-2 spike N439K variant maintains fitness while evading antibody-mediated immunity. Emma Thomson, Laura Rosen et al. Cell, 2021 Mar; 184(5): p1171-1187.


7. SARS-CoV-2 suppresses mRNA splicing, translation, and protein trafficking in a multipronged mechanism to evade host defenses.Abkih Banerjee, Mario Blanco et al. Cell, 2020 Nov; 183(5): 1325-1339. 


8. Viral zoonotic risk is homogenous among taxonomic orders of mammalian and avian reservoir hosts. NardusMollentze, Daniel Streiker et al. Proceedings of the National Academy of Sciences USA, 2020 Apr; 117(17): 9423-9430. 


9. Epidemiology of seasonal coronaviruses: Establishing the context for COVID-19 emergence. SemaNickbakhsh, Antonia Ho et al. The Journal of Infectious Diseases, 2020 Jul; 222(1): 17-25. 


9. SARS-CoV-2, SARS-CoV-1 and MERS-CoV viral load dynamics, duration of viral shedding and infectiousness: a living systematic review and meta-analysis. MugeCevik, Matthew Tate et al. Lancet Microbe, 2021 Jan; 2: e13-22. 


10. No evidence for distinct types in the evolution of SARS-CoV-2. Oscar MacLean, Matthew Tate et al. Virus Evolution, 2020 Jan; 6(1): veaa034.


11. Novel coronavirus 2019-nCoV (COVID-19): early estimation of epidemiological parameters and epidemic size estimates.Jonathan Read, Jessica Bridgen et al. Phil Trans B, 2021 May; 376(1829): 20200265 


12. Development and validation of the 4C Deterioration model for adults hospitalised with COVID-19.Rishi Gupta, Ewen Harrison et al. Lancet Respiratory Medicine, 2021 Jan; 9(4): 349-359  


13. COVID-19 Pandemic: a focused review for clinicians.Muge Cevik, Connor Bamford et al. Clinical Microbiology and Infection, 2020 Jul; 26(7):842-847.


14. COVID-19 and the cardiovascular system: implications for risk assessment, diagnosis, and treatment options.Tomasz Guzik, Saidi Mohiddin et al. Cardiovascular Research, 2020 Aug; 116(10): 1666-1687. 


15. Features of 20,133 hospitalised UK patients with COVID-19 using the ISARIC WHO Clinical Characterisation Protocol.Annemarie Docherty, Ewen Harrison et al. BMJ, 2020 May; 369: m1985.


16. Insights into SARS-CoV-2, the Coronavirus Underlying COVID-19: Recent Genomic Data and the Development of Reverse Genetics Systems. Severino Jefferson Ribeiro da Silva, Renata PessoaGermano Mendes et al. Journal of General Virology, 2020 Jun; 101(10): 1021-1024. 


17. Main Routes of Entry and Genomic Diversity of SARS-CoV-2, Uganda. DanielBugembe, John Kayiwa et al. Emerging Infectious Diseases, 2020 Oct; 26(10): 2411-2415.


18. Comparative Host-Coronavirus Protein Interaction Networks Reveal Pan-Viral Disease Mechanisms. Daniel Gordon, Joseph Hiatt et al. Science, 2020 Dec; 370(6521): eabe9403.


19. Genetic mechanisms of critical illness in Covid-19. ErolaPairo-Castineira, Sara Clohisey et al. Nature, 2020 Dec; 591(7848): p92-98. 


20. The Chief Scientist Office Cardiovascular and Pulmonary Imaging in SARS Coronavirus disease-19 (CISCO-19) study. KennethMangion, Andrew Morrow et al. Cardiovascular Research, 2020 Dec; 116(14): 2185-2196. 


21. Clinical and Laboratory Diagnosis of SARS-CoV-2, the Virus Causing COVID-19. Severino Jefferson Ribeiro da Silva, Caroline Silva et al. ACS Infectious Diseases, 2020 Aug; 6(9): 2319-2336.  


22. Viral CpG deficiency provides no evidence that dogs were intermediate hosts for SARS-CoV-2. David Pollock, Todd Castoeet al. Molecular Biology and Evolution, 2020 Sep; 37(9): 2706-2710. 


23. Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research. FranziskaHufsky, Kevin Lamkiewicz et al. Briefings in Bioinformatics, 2020 Nov; bbaa32.


24. A Plasmid DNA-Launched SARS-CoV-2 Reverse Genetics System and Coronavirus Toolkit for COVID-19 Research. Suzannah Rihn, Andres Meritset al. PLoS Biology, 2021 Feb; 19(2): e3001091 


25. Field Evaluation of the Performance of a SARS-CoV-2 Antigen Rapid Diagnostic Test in Uganda using Nasopharyngeal Samples. Aminah Nalumansi, Tom Lutaloet al. International Journal of Infectious Diseases, 2021 Mar; 104: p282-286. 


26. Stapled ACE2 peptidomimetics designed to target the SARS-CoV-2 spike protein do not prevent virus internalisation. Danielle Morgan, Caroline Morriset al. Peptide Science, 2021 Jan; e24217. 


27. Hypoxic and Pharmacological Activation of HIF Inhibits SARS-CoV-2 Infection of Lung Epithelial Cells. Peter Wing, Thomas Keeleyet al. Cell Reports, 2021 Apr; 35(3): 109020. 


28. Efficacy and safety of COVID-19 vaccines in older people. RoySoiza, Chiara Scicluna and Emma Thomson. Age and Ageing, 2020 Dec; afaa274. 


29. SARS-CoV-2 and cats. Margaret Hosie, Katrin Hartmannet al. European Advisory Board on Cat Diseases, 2020 Dec. 


30. The case for adopting a combined comparative medicine and One Health approach to tackle emerging diseases. Margaret Hosie and Seema Jasim. Veterinary Record, 2020 Jul; 187(1): 24-26. 


31. Safety and efficacy of the ChAdOx1 nCoV-19 vaccine (AZD1222) against SARS-CoV-2: an interim analysis of four randomised controlled trials in Brazil, South Africa, and the UK. Merryn Voysey, Sue Ann Costa Clemenset al. The Lancet, 2021 Jan; 397: 99-111.


32. Possibility for reverse zoonotic transmission of SARS-CoV-2 to free-ranging wildlife: A case study of bats. KevinOlival, Paul Cryan et al. PLOS Pathogens, 2020 Sep; 16(9): e1008758. 


33. Natural selection in the evolution of SARS-CoV-2 in bats, not humans, created a highly capable human pathogen. Oscar MacLean, Spyros Lytraset al. PLoS Biology, 2021 Mar; 19(3): e3001115.


34. Ethnicity and Outcomes from COVID-19: The ISARIC CCP-UK Prospective Observational Cohort Study of Hospitalised Patients. Ewen Harrison, Annemarie Docherty et al. Pre-print. 


35. Improvements to the ARTIC multiplex PCR method for SARS-CoV-2 genome sequencing using nanopore. John Tyson, Phillip Jameset al. Pre-print.


36. Respiratory disease in cats associated with human-to-cat transmission of SARS-CoV-2 in the UK. Margaret Hosie, Ilaria Epifanoet al. Pre-print. 


37. Alternate primers for whole-genome SARS-CoV-2 sequencing. Matthew Cotton, Dan LuleBugembe et al. Virus Evolution, 2021 Jan; 7(1): veab006. 


38. CoV-GLUE: a web application for tracking SARS-CoV-2 genomic variation. Joshua Singer, Robert Giffordet al. Pre-print. 


39. Periscope: sub-genomic RNA identification in SARS-CoV-2 Genomic Sequencing Data. Matthew Parker, Benjamin Lindseyet al. Genome Res, 2021 Mar; 31(4): p645-658. 


40. Global analysis of protein-RNA interactions in SARS-CoV-2 infected cells reveals key regulators of infection. Wael Kamel, Marko Noerenberget al. Molecular Cell, 2021 Jul; 81(13): p2851-2867.  


41. Elevated temperature inhibits SARS-CoV-2 replication in respiratory epithelium independently of the induction of IFN-mediated innate immune defences. Vanessa Herder, Kieran Deeet al. Pre-print.


42. Human rhinovirus infection inhibits SARS-CoV-2 replication in the respiratory epithelium. Kieran Dee, Daniel Goldfarbet al. The Journal of Infectious Diseases. 2021 Jul; 224(1).  


43. Meta-analysis of virus-induced host gene expression reveals unique signatures of immune dysregulation induced by SARS-CoV-2. SrikeerthanaKuchi, Quan Gu et al. Pre-print.


44. What is the recovery rate and risk of long-term consequences following a diagnosis of COVID-19? - A harmonised, global longitudinal observational study. Louise Sigfrid, MugeCevik et al. BMJ Open, 2021 Mar; 11(3): e043887.  


45. Glasgow Early Treatment Arm Favirpiravir (GETAFIX) for adults with early stage COVID-19: A structured summary of a study protocol for a randomised controlled trial. Catherine Hanna, Kevin Blythet al. Trials, 2020 Nov; 21: 935.


46. Identifying and prioritising potential human-infecting viruses from their genome sequences. NardusMollentze, Simon Babayan and Daniel Streicker. Pre-print. 


47. Long Covid in adults discharged from UK hospitals after Covid-19: A prospective, multicentre cohort study using the ISARIC WHO Clinical Characterisation ProtocolJanet Scott, Louise Sigfrid et al. Lancet Regional Health Europe. In press.


48. Genetic epidemiology of SARS-CoV-2 transmission in renal dialysis units – A high risk community-hospital interface. Kathy K. Li, Y. Mun Woo et al. Journal of Infection, 2021 Jul; 83(1): 96-103. 


49. Co-infections, secondary infections, and antimicrobial use in patients hospitalised with COVID-19 during the first pandemic wave from the ISARIC WHO CCP-UK study: a multicentre, prospective cohort study. Clark D Russell, Cameron J Fairfield et al. Lancet Microbe, 2021 Jun; 2(8): e354-365.


50. Characterisation of in-hospital complications associated with COVID-19 using the ISARIC WHO Clinical Characterisation Protocol UK: a prospective, multicentre cohort study. Thomas M Drake, Aya M Riad et al. Lancet, 2021 Jul; 398(10296): p223-237. 


51. Changes in in-hospital mortality in the first wave of COVID-19: a multicentre prospective observational cohort study using the WHO Clinical Characterisation Protocol UK.Annemarie B Docherty, Rachel H Mullholland et al. Lancet Respir Med, 2021 May; 9(7): p773-785. 

CVR COVID-19 Software


SARS-CoV-2 will naturally accumulate nucleotide mutations (changes) in its RNA genome as the pandemic progresses. Many of the observed changes will have little or no impact on virus biology but some genetic variants may change or alter the virus phenotype. Tracking the emergence of these mutations will help us understand the evolution and spread of the virus at a global level. CoV-GLUE contains a database of replacements, insertions and deletions which have been observed in sequences sampled from the pandemic.

  • CoV-GLUE - is developed and maintained by the CVR

Viral Host Predictor

Viral Host Predictor uses machine-learning algorithms developed in our study by Babayan et al. (2018) to predict the reservoir hosts, arthropod vectors and arthropod-borne transmission status of RNA viruses.  

  • Viral Host Predictor - provides a fast and simple way to predict the animal origins of RNA viruses

COG-UK / Mutation Explorer (COG-UK/ME)

COG-UK/ME provides information and structural context on mutations and associated variants in the genes encoding SARS-COV-2 proteins that have been identified from sequence data generated by the COVID-19 Genomics (COG-UK) Consortium.