Dr Katherine Smollett
- Research Scientist (Virology)
telephone:
0141 330 8214
email:
Katherine.Smollett@glasgow.ac.uk
https://orcid.org/0000-0001-7961-7377Biography
I joined CVR Genomics as a Research Associate in 2017 and have gained extensive experience in viral genomics. Previously I worked s a post-doctoral researcher investigating gene regulation of Mycobacterium tuberculosis at the MRC-National Institute for Medical Research, and then in examining mechanisms of transcriptional control in Archaea at University College London. I have a doctorate in molecular microbiology from Imperial College London.
Research interests
CVR Genomics is the sequencing facility at the MRC-University of Glasgow Centre for virus research headed by Dr Ana Filipe. Our aim is to provide the CVR community and its collaborators with expertise in high-throughput sequencing to contribute to the understanding of viruses.
My current research focuses on developing and implementing sequencing workflows for the discovery and characterisation of emerging viral pathogens. For which I have expertise in a range of specialist techniques and technologies, including metagenomics, bulk transcriptomics, and targeted enrichment with sequencing on Illumina and Oxford Nanopore instruments.
Publications
2024
Ranum, J. N. et al. (2024) Cryptic proteins translated from deletion-containing viral genomes dramatically expand the influenza virus proteome. Nucleic Acids Research, 52(6), pp. 3199-3212. (doi: 10.1093/nar/gkae133) (PMID:38407436) (PMCID:PMC11014358)
2023
Jones, S. et al. (2023) SARS-CoV-2 in domestic UK cats from Alpha to Omicron: Swab surveillance and case reports. Viruses, 15(8), 1769. (doi: 10.3390/v15081769) (PMID:37632111) (PMCID:PMC10459977)
Pascall, D. J. et al. (2023) Directions of change in intrinsic case severity across successive SARS-CoV-2 variant waves have been inconsistent. Journal of Infection, 87(2), pp. 128-135. (doi: 10.1016/j.jinf.2023.05.019) (PMID:37270070) (PMCID:PMC10234362)
Ho, A. et al. (2023) Adeno-associated virus 2 infection in children with non-A-E hepatitis. Nature, 617(7961), pp. 555-563. (doi: 10.1038/s41586-023-05948-2) (PMID:36996873)
Pascall, D. J. et al. (2023) The SARS-CoV-2 Alpha variant was associated with increased clinical severity of COVID-19 in Scotland: a genomics-based retrospective cohort analysis. PLoS ONE, 18(4), e0284187. (doi: 10.1371/journal.pone.0284187) (PMID:37053201) (PMCID:PMC10101505)
Tong, L., Smollett, K. , Kwok, K. , Nomikou, K. , Galarion, M. J., Mair, D. , Filipe, A. and Nichols, J. (2023) Discovery of RNA and DNA viruses using next-generation sequencing: Metagenomics V.1. [Protocols]
Tong, L., Smollett, K. , Kwok, K. , Nomikou, K. , Galarion, M. J., Mair, D. , Filipe, A. and Nichols, J. (2023) Discovery of RNA and DNA viruses using next-generation sequencing: Targeted enrichment. [Protocols]
2022
Smollett, K. (2022) Library pooling and quality control for Illumina sequencing. [Protocols]
Smollett, K. , Tong, L., Nomikou, K. , Nichols, J. , Kwok, K. , Galarion, M. J., Mair, D. and Filipe, A. (2022) Library clean up and quality control for Illumina sequencing. [Protocols]
Willett, B. J. et al. (2022) Publisher Correction: SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway. Nature Microbiology, 7, 1709. (doi: 10.1038/s41564-022-01241-6) (PMID:36114232) (PMCID:PMC9483304)
Willett, B. J. et al. (2022) SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway. Nature Microbiology, 7(8), pp. 1161-1179. (doi: 10.1038/s41564-022-01143-7) (PMID:35798890) (PMCID:PMC9352574)
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, 11735. (doi: 10.1038/s41598-022-15661-1) (PMID:35853960) (PMCID:PMC9296497)
Aggarwal, D. et al. (2022) Genomic assessment of quarantine measures to prevent SARS-CoV-2 importation and transmission. Nature Communications, 13, 1012. (doi: 10.1038/s41467-022-28371-z) (PMID:35197443) (PMCID:PMC8866425)
Aggarwal, D. et al. (2022) Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission. Nature Communications, 13, 751. (doi: 10.1038/s41467-021-27942-w) (PMID:35136068) (PMCID:PMC8826310)
2021
Vöhringer, H. S. et al. (2021) Genomic reconstruction of the SARS-CoV-2 epidemic in England. Nature, 600(7889), pp. 506-511. (doi: 10.1038/s41586-021-04069-y) (PMID:34649268) (PMCID:PMC8674138)
Shaw, A. E. et al. (2021) The antiviral state has shaped the CpG composition of the vertebrate interferome to avoid self-targeting. PLoS Biology, 19(9), e3001352. (doi: 10.1371/journal.pbio.3001352) (PMID:34491982) (PMCID:PMC8423302)
Li, K. K. et al. (2021) Genetic epidemiology of SARS-CoV-2 transmission in renal dialysis units - a high risk community-hospital interface. Journal of Infection, 83(1), pp. 96-103. (doi: 10.1016/j.jinf.2021.04.020) (PMID:33895226) (PMCID:PMC8061788)
Davis, C. A. et al. (2021) Hepatitis E virus: whole genome sequencing as a new tool for understanding HEV epidemiology and phenotypes. Journal of Clinical Virology, 139, 104738. (doi: 10.1016/j.jcv.2021.104738) (PMID:33933822)
Volz, E. et al. (2021) Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England. Nature, 593(7858), pp. 266-269. (doi: 10.1038/s41586-021-03470-x) (PMID:33767447)
Thomson, E. C. et al. (2021) Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. Cell, 184(5), 1171-1187.e20. (doi: 10.1016/j.cell.2021.01.037) (PMID:33621484) (PMCID:PMC7843029)
Rihn, S. J. et al. (2021) A plasmid DNA-launched SARS-CoV-2 reverse genetics system and coronavirus toolkit for COVID-19 research. PLoS Biology, 19(2), e3001091. (doi: 10.1371/journal.pbio.3001091) (PMID:33630831) (PMCID:PMC7906417)
Da Silva Filipe, A. et al. (2021) Genomic epidemiology reveals multiple introductions of SARS-CoV-2 from mainland Europe into Scotland. Nature Microbiology, 6(1), pp. 112-122. (doi: 10.1038/s41564-020-00838-z) (PMID:33349681)
2019
Ankcorn, M. et al. (2019) Convalescent plasma therapy for persistent hepatitis E virus infection. Journal of Hepatology, 71(2), pp. 434-438. (doi: 10.1016/j.jhep.2019.04.008) (PMID:31075322)
McFarlane, S. et al. (2019) The histone chaperone HIRA promotes the induction of host innate immune defences in response to HSV-1 infection. PLoS Pathogens, 15(3), e1007667. (doi: 10.1371/journal.ppat.1007667) (PMID:30901352) (PMCID:PMC6472835)
2017
Smollett, K. , Blombach, F., Reichelt, R., Thomm, M. and Werner, F. (2017) A global analysis of transcription reveals two modes of Spt4/5 recruitment to archaeal RNA polymerase. Nature Microbiology, 2, p. 17021. (doi: 10.1038/nmicrobiol.2017.21) (PMID:28248297)
Smollett, K. , Blombach, F., Fouqueau, T. and Werner, F. (2017) A global characterisation of the archaeal transcription machinery. In: Clouet-d'Orval, B. (ed.) RNA Metabolism and Gene Expression in Archaea. Series: Nucleic acids and molecular biology, 32 (32). Springer International Publishing, pp. 1-26. ISBN 9783319657943 (doi: 10.1007/978-3-319-65795-0_1)
2016
Sheppard, C. et al. (2016) Repression of RNA polymerase by the archaeo-viral regulator ORF145/RIP. Nature Communications, 7, 13595. (doi: 10.1038/ncomms13595) (PMID:27882920) (PMCID:PMC5123050)
Blombach, F., Smollett, K. L. , Grohmann, D. and Werner, F. (2016) Molecular mechanisms of transcription initiation—structure, function, and evolution of TFE/TFIIE-like factors and open complex formation. Journal of Molecular Biology, 428(12), pp. 2592-2606. (doi: 10.1016/j.jmb.2016.04.016) (PMID:27107643)
Schulz, S., Gietl, A., Smollett, K. , Tinnefeld, P., Werner, F. and Grohmann, D. (2016) TFE and Spt4/5 open and close the RNA polymerase clamp during the transcription cycle. Proceedings of the National Academy of Sciences of the United States of America, 113(13), E1816-E1825. (doi: 10.1073/pnas.1515817113) (PMID:26979960) (PMCID:PMC4822635)
Articles
Ranum, J. N. et al. (2024) Cryptic proteins translated from deletion-containing viral genomes dramatically expand the influenza virus proteome. Nucleic Acids Research, 52(6), pp. 3199-3212. (doi: 10.1093/nar/gkae133) (PMID:38407436) (PMCID:PMC11014358)
Jones, S. et al. (2023) SARS-CoV-2 in domestic UK cats from Alpha to Omicron: Swab surveillance and case reports. Viruses, 15(8), 1769. (doi: 10.3390/v15081769) (PMID:37632111) (PMCID:PMC10459977)
Pascall, D. J. et al. (2023) Directions of change in intrinsic case severity across successive SARS-CoV-2 variant waves have been inconsistent. Journal of Infection, 87(2), pp. 128-135. (doi: 10.1016/j.jinf.2023.05.019) (PMID:37270070) (PMCID:PMC10234362)
Ho, A. et al. (2023) Adeno-associated virus 2 infection in children with non-A-E hepatitis. Nature, 617(7961), pp. 555-563. (doi: 10.1038/s41586-023-05948-2) (PMID:36996873)
Pascall, D. J. et al. (2023) The SARS-CoV-2 Alpha variant was associated with increased clinical severity of COVID-19 in Scotland: a genomics-based retrospective cohort analysis. PLoS ONE, 18(4), e0284187. (doi: 10.1371/journal.pone.0284187) (PMID:37053201) (PMCID:PMC10101505)
Willett, B. J. et al. (2022) Publisher Correction: SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway. Nature Microbiology, 7, 1709. (doi: 10.1038/s41564-022-01241-6) (PMID:36114232) (PMCID:PMC9483304)
Willett, B. J. et al. (2022) SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway. Nature Microbiology, 7(8), pp. 1161-1179. (doi: 10.1038/s41564-022-01143-7) (PMID:35798890) (PMCID:PMC9352574)
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, 11735. (doi: 10.1038/s41598-022-15661-1) (PMID:35853960) (PMCID:PMC9296497)
Aggarwal, D. et al. (2022) Genomic assessment of quarantine measures to prevent SARS-CoV-2 importation and transmission. Nature Communications, 13, 1012. (doi: 10.1038/s41467-022-28371-z) (PMID:35197443) (PMCID:PMC8866425)
Aggarwal, D. et al. (2022) Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission. Nature Communications, 13, 751. (doi: 10.1038/s41467-021-27942-w) (PMID:35136068) (PMCID:PMC8826310)
Vöhringer, H. S. et al. (2021) Genomic reconstruction of the SARS-CoV-2 epidemic in England. Nature, 600(7889), pp. 506-511. (doi: 10.1038/s41586-021-04069-y) (PMID:34649268) (PMCID:PMC8674138)
Shaw, A. E. et al. (2021) The antiviral state has shaped the CpG composition of the vertebrate interferome to avoid self-targeting. PLoS Biology, 19(9), e3001352. (doi: 10.1371/journal.pbio.3001352) (PMID:34491982) (PMCID:PMC8423302)
Li, K. K. et al. (2021) Genetic epidemiology of SARS-CoV-2 transmission in renal dialysis units - a high risk community-hospital interface. Journal of Infection, 83(1), pp. 96-103. (doi: 10.1016/j.jinf.2021.04.020) (PMID:33895226) (PMCID:PMC8061788)
Davis, C. A. et al. (2021) Hepatitis E virus: whole genome sequencing as a new tool for understanding HEV epidemiology and phenotypes. Journal of Clinical Virology, 139, 104738. (doi: 10.1016/j.jcv.2021.104738) (PMID:33933822)
Volz, E. et al. (2021) Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England. Nature, 593(7858), pp. 266-269. (doi: 10.1038/s41586-021-03470-x) (PMID:33767447)
Thomson, E. C. et al. (2021) Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. Cell, 184(5), 1171-1187.e20. (doi: 10.1016/j.cell.2021.01.037) (PMID:33621484) (PMCID:PMC7843029)
Rihn, S. J. et al. (2021) A plasmid DNA-launched SARS-CoV-2 reverse genetics system and coronavirus toolkit for COVID-19 research. PLoS Biology, 19(2), e3001091. (doi: 10.1371/journal.pbio.3001091) (PMID:33630831) (PMCID:PMC7906417)
Da Silva Filipe, A. et al. (2021) Genomic epidemiology reveals multiple introductions of SARS-CoV-2 from mainland Europe into Scotland. Nature Microbiology, 6(1), pp. 112-122. (doi: 10.1038/s41564-020-00838-z) (PMID:33349681)
Ankcorn, M. et al. (2019) Convalescent plasma therapy for persistent hepatitis E virus infection. Journal of Hepatology, 71(2), pp. 434-438. (doi: 10.1016/j.jhep.2019.04.008) (PMID:31075322)
McFarlane, S. et al. (2019) The histone chaperone HIRA promotes the induction of host innate immune defences in response to HSV-1 infection. PLoS Pathogens, 15(3), e1007667. (doi: 10.1371/journal.ppat.1007667) (PMID:30901352) (PMCID:PMC6472835)
Smollett, K. , Blombach, F., Reichelt, R., Thomm, M. and Werner, F. (2017) A global analysis of transcription reveals two modes of Spt4/5 recruitment to archaeal RNA polymerase. Nature Microbiology, 2, p. 17021. (doi: 10.1038/nmicrobiol.2017.21) (PMID:28248297)
Sheppard, C. et al. (2016) Repression of RNA polymerase by the archaeo-viral regulator ORF145/RIP. Nature Communications, 7, 13595. (doi: 10.1038/ncomms13595) (PMID:27882920) (PMCID:PMC5123050)
Blombach, F., Smollett, K. L. , Grohmann, D. and Werner, F. (2016) Molecular mechanisms of transcription initiation—structure, function, and evolution of TFE/TFIIE-like factors and open complex formation. Journal of Molecular Biology, 428(12), pp. 2592-2606. (doi: 10.1016/j.jmb.2016.04.016) (PMID:27107643)
Schulz, S., Gietl, A., Smollett, K. , Tinnefeld, P., Werner, F. and Grohmann, D. (2016) TFE and Spt4/5 open and close the RNA polymerase clamp during the transcription cycle. Proceedings of the National Academy of Sciences of the United States of America, 113(13), E1816-E1825. (doi: 10.1073/pnas.1515817113) (PMID:26979960) (PMCID:PMC4822635)
Book Sections
Smollett, K. , Blombach, F., Fouqueau, T. and Werner, F. (2017) A global characterisation of the archaeal transcription machinery. In: Clouet-d'Orval, B. (ed.) RNA Metabolism and Gene Expression in Archaea. Series: Nucleic acids and molecular biology, 32 (32). Springer International Publishing, pp. 1-26. ISBN 9783319657943 (doi: 10.1007/978-3-319-65795-0_1)
Protocols
Tong, L., Smollett, K. , Kwok, K. , Nomikou, K. , Galarion, M. J., Mair, D. , Filipe, A. and Nichols, J. (2023) Discovery of RNA and DNA viruses using next-generation sequencing: Metagenomics V.1. [Protocols]
Tong, L., Smollett, K. , Kwok, K. , Nomikou, K. , Galarion, M. J., Mair, D. , Filipe, A. and Nichols, J. (2023) Discovery of RNA and DNA viruses using next-generation sequencing: Targeted enrichment. [Protocols]
Smollett, K. (2022) Library pooling and quality control for Illumina sequencing. [Protocols]
Smollett, K. , Tong, L., Nomikou, K. , Nichols, J. , Kwok, K. , Galarion, M. J., Mair, D. and Filipe, A. (2022) Library clean up and quality control for Illumina sequencing. [Protocols]
Research datasets
2024
Furnon, W. , Cowton, V. M., De Lorenzo, G. , Orton, R. , Herder, V. , Cantoni, D. , Ilia, G., Correa Mendonca, D. , Kerr, K., Allan, J., Upfold, N. , Meehan, G. R. , Bakshi, S., Das, U. R., Molina Arias, S., McElwee, M., Little, S., Logan, N., Kwok, K. , Smollett, K. , Willett, B. , Da Silva Filipe, A. , Robertson, D. L. , Grove, J. , Patel, A. H. and Palmarini, M. (2024) Phenotypic evolution of SARS-CoV-2 spike throughout the COVID-19 pandemic. [Data Collection]
2021
Shaw, A., Rihn, S. , Mollentze, N. , Wickenhagen, A., Stewart, D., Orton, R. , Kuchi, S., Bakshi, S., Collados Rodriguez, M. , Turnbull, M. , Busby, J., Gu, Q. , Smollett, K., Bamford, C., Sugrue, E. , Johnson, P. , Da Silva Filipe, A. , Castello, A. , Streicker, D. , Robertson, D. , Palmarini, M. and Wilson, S. (2021) The 'antiviral state' has shaped the CpG composition of the vertebrate interferome to avoid self-targeting. [Data Collection] (Unpublished)
