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Dr Arthur Morris
Teams and roles for Arthur Morris
HCRW Advanced Research Fellow
School of Biosciences
Overview
Health and Care Research Wales Advanced Reseach Fellow.
My research focuses on developing and applying computational methods to analyse pathogen genomes. By working closely with partners in UK Public Health and Defence agencies, I aim to implement these tools and methodologies into operational biosurveillance and defence services.
My research interests include:
- Pathogen Genomics: Employing population genomics to deepen our understanding of pathogens which represent key threats to public health worldwide.
- Novel Computational Methodologies: Creating novel software for efficient pathogen genome analysis, designed for implementation by public health agencies.
- Wastewater Surveillance: Analyzing DNA from waste-water to monitor pathogen prevalence within the local population.
- SARS-CoV-2 Epidemiology: Investigating the epidemiology of SARS-CoV-2 in the UK throughout the pandemic.
Publication
2025
- Morris, A. V. et al. 2025. Investigating within-host population diversity of Cryptosporidium parvum using BlooMine. BMC Genomics 26 (1) 1067. (10.1186/s12864-025-12206-4)
- Morris, A. V. et al. 2025. Parapipe: a pipeline for parasite next-generation sequencing data analysis applied to Cryptosporidium. Access Microbiology 7 (8)(10.1099/acmi.0.000993.v3)
2023
- Cotton, S. et al., 2023. Investigation of hospital discharge cases and SARS-CoV-2 introduction into Lothian care homes. Journal of Hospital Infection 135 , pp.28-36. (10.1016/j.jhin.2023.02.010)
- Morris, A. V. , Price, A. and Connor, T. 2023. Afanc: a metagenomics tool for variant level disambiguation of NGS datasets. [Online].bioRXiv. (10.1101/2023.10.05.560444)Available at: https://doi.org/10.1101/2023.10.05.560444.
2022
- Eales, O. et al., 2022. SARS-CoV-2 lineage dynamics in England from September to November 2021: high diversity of Delta sub-lineages and increased transmissibility of AY.4.2. BMC Infectious Diseases 22 (1) 647. (10.1186/s12879-022-07628-4)
- Kläser, K. et al., 2022. COVID-19 due to the B.1.617.2 (Delta) variant compared to B.1.1.7 (Alpha) variant of SARS-CoV-2: a prospective observational cohort study. Scientific Reports 12 (1) 10904. (10.1038/s41598-022-14016-0)
- Nickbakhsh, S. et al., 2022. Genomic epidemiology of SARS-CoV-2 in a university outbreak setting and implications for public health planning. Scientific Reports 12 (1) 11735. (10.1038/s41598-022-15661-1)
- Willett, B. J. et al., 2022. SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway. Nature Microbiology 7 , pp.1161-1179. (10.1038/s41564-022-01143-7)
2021
- Vöhringer, H. S. et al., 2021. Genomic reconstruction of the SARS-CoV-2 epidemic in England. Nature 600 (7889), pp.506-511. (10.1038/s41586-021-04069-y)
2020
- Morris, A. et al. 2020. Generating reliable genome assemblies of intestinal protozoans from clinical samples for the purpose of biomarker discovery. Presented at: Biomedical Engineering Systems and Technologies BIOSTEC 2019 Prague, Czech Republic 22-24 February 2019. Published in: Roque, A. et al., Communications in Computer and Information Science. Vol. 1211.Springer, Cham. , pp.216-241. (10.1007/978-3-030-46970-2_11)
2019
- Morris, A. et al. 2019. Direct sequencing of Cryptosporidium in stool samples for public health. Frontiers in Public Health 7 (10.3389/fpubh.2019.00360)
- Swain, M. et al., 2019. Identifying and resolving genome misassembly issues important for biomarker discovery in the protozoan parasite, cryptosporidium. Presented at: 12th International Joint Conference on Biomedical Engineering Systems and Technologies Prague, Czech Republic 22–24 February 2019. Proceedings of the 12th International Joint Conference on Biomedical Engineering Systems and Technologies. Vol. 3., pp.90-100. (10.5220/0007397200900100)
2017
- Castro, P. D. J. and Morris, A. V. 2017. Burrowing mites in companion animals. UK-VET Companion animal 22 (8), pp.446-452. (10.12968/coan.2017.22.8.446)
2016
- Castro, P. D. J. and Morris, A. V. 2016. Feline lungworm: biology, epidemiology, diagnosis and treatment. The Veterinary Nurse 7 (9), pp.508-513. (10.12968/vetn.2016.7.9.508)
Articles
- Castro, P. D. J. and Morris, A. V. 2017. Burrowing mites in companion animals. UK-VET Companion animal 22 (8), pp.446-452. (10.12968/coan.2017.22.8.446)
- Castro, P. D. J. and Morris, A. V. 2016. Feline lungworm: biology, epidemiology, diagnosis and treatment. The Veterinary Nurse 7 (9), pp.508-513. (10.12968/vetn.2016.7.9.508)
- Cotton, S. et al., 2023. Investigation of hospital discharge cases and SARS-CoV-2 introduction into Lothian care homes. Journal of Hospital Infection 135 , pp.28-36. (10.1016/j.jhin.2023.02.010)
- Eales, O. et al., 2022. SARS-CoV-2 lineage dynamics in England from September to November 2021: high diversity of Delta sub-lineages and increased transmissibility of AY.4.2. BMC Infectious Diseases 22 (1) 647. (10.1186/s12879-022-07628-4)
- Kläser, K. et al., 2022. COVID-19 due to the B.1.617.2 (Delta) variant compared to B.1.1.7 (Alpha) variant of SARS-CoV-2: a prospective observational cohort study. Scientific Reports 12 (1) 10904. (10.1038/s41598-022-14016-0)
- Morris, A. et al. 2019. Direct sequencing of Cryptosporidium in stool samples for public health. Frontiers in Public Health 7 (10.3389/fpubh.2019.00360)
- Morris, A. V. et al. 2025. Investigating within-host population diversity of Cryptosporidium parvum using BlooMine. BMC Genomics 26 (1) 1067. (10.1186/s12864-025-12206-4)
- Morris, A. V. et al. 2025. Parapipe: a pipeline for parasite next-generation sequencing data analysis applied to Cryptosporidium. Access Microbiology 7 (8)(10.1099/acmi.0.000993.v3)
- Nickbakhsh, S. et al., 2022. Genomic epidemiology of SARS-CoV-2 in a university outbreak setting and implications for public health planning. Scientific Reports 12 (1) 11735. (10.1038/s41598-022-15661-1)
- Vöhringer, H. S. et al., 2021. Genomic reconstruction of the SARS-CoV-2 epidemic in England. Nature 600 (7889), pp.506-511. (10.1038/s41586-021-04069-y)
- Willett, B. J. et al., 2022. SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway. Nature Microbiology 7 , pp.1161-1179. (10.1038/s41564-022-01143-7)
Conferences
- Morris, A. et al. 2020. Generating reliable genome assemblies of intestinal protozoans from clinical samples for the purpose of biomarker discovery. Presented at: Biomedical Engineering Systems and Technologies BIOSTEC 2019 Prague, Czech Republic 22-24 February 2019. Published in: Roque, A. et al., Communications in Computer and Information Science. Vol. 1211.Springer, Cham. , pp.216-241. (10.1007/978-3-030-46970-2_11)
- Swain, M. et al., 2019. Identifying and resolving genome misassembly issues important for biomarker discovery in the protozoan parasite, cryptosporidium. Presented at: 12th International Joint Conference on Biomedical Engineering Systems and Technologies Prague, Czech Republic 22–24 February 2019. Proceedings of the 12th International Joint Conference on Biomedical Engineering Systems and Technologies. Vol. 3., pp.90-100. (10.5220/0007397200900100)
Websites
- Morris, A. V. , Price, A. and Connor, T. 2023. Afanc: a metagenomics tool for variant level disambiguation of NGS datasets. [Online].bioRXiv. (10.1101/2023.10.05.560444)Available at: https://doi.org/10.1101/2023.10.05.560444.
Research
I am currently principle investigator on two research projects.
Unleashing modern genomics for precision Public Health surveillance of Cryptosporidium - funded by Health and Care research Wales.
I collaberation with the UK Cryptosporidium Reference Unit, we intend to establish the lab and computational methodologies for the first national Cryptosporidium genomic surveillance service.
Chasing GHOSTs: context aware genomic anomaly detection with Afanc-detect - funded by the Defence Sciencec and Technology Laboratory as part of the UK Defence and Security Accelerator.
This project aims to determine whether an incident involving a biological hazard is natural or nefarious in origin. We aim to leverage the power of genomics and statistical modelling techniques to develop methodologies which provide more information than the identification of a biological organism.
Contact Details
Research themes
Specialisms
- Bioinformatics and computational biology
- Pathogen Genomics
- Biostatistics