Publications

Selected Publications from 2023

• Astuti, Y., Raymant, M., Quaranta, V., Clarke, K., Abudula, M., Smith, O., Bellomo, G., Chandran-Gorner, V., Nourse, C., Halloran, C. and Ghaneh, P., 2024. Efferocytosis reprograms the tumor microenvironment to promote pancreatic cancer liver metastasis. Nature cancer, pp.1-17.
• Iannucci, S., Harvey, W.T., Hughes, J., Robertson, D.L., Poyade, M. and Hutchinson, E., 2023. The SARS-CoV-2 Spike Protein Mutation Explorer: using an interactive application to improve the public understanding of SARS-CoV-2 variants of concern. Journal of Visual Communication in Medicine, 46(3), pp.122-132.
• Pascall, D.J., Vink, E., Blacow, R., Bulteel, N., Campbell, A., Campbell, R., Clifford, S., Davis, C., da Silva Filipe, A., El Sakka, N. and Fjodorova, L., 2023. Directions of change in intrinsic case severity across successive SARS-CoV-2 variant waves have been inconsistent. Journal of Infection.
• Panovska-Griffiths, J., Swallow, B., Hinch, R., Cohen, J., Rosenfeld, K., Stuart, R.M., Ferretti, L., Di Lauro, F., Wymant, C., Izzo, A. and Waites, W., 2022. Statistical and agent-based modelling of the transmissibility of different SARS-CoV-2 variants in England and impact of different interventions. Philosophical Transactions of the Royal Society A, 380(2233), p.20210315.
• O’Toole, Á., Hill, V., Jackson, B., Dewar, R., Sahadeo, N., Colquhoun, R., Rooke, S., McCrone, J.T., Duggan, K., McHugh, M.P. and Nicholls, S.M., 2022. Genomics-informed outbreak investigations of SARS-CoV-2 using civet. PLOS global public health, 2(12), p.e0000704.
• McCrone, J.T., Hill, V., Bajaj, S., Pena, R.E., Lambert, B.C., Inward, R., Bhatt, S., Volz, E., Ruis, C., Dellicour, S. and Baele, G., 2022. Context-specific emergence and growth of the SARS-CoV-2 Delta variant. Nature, 610(7930), pp.154-160.
• Pascall, D.J., Vink, E., Blacow, R., Bulteel, N., Campbell, A., Campbell, R., Clifford, S., Davis, C., da Silva Filipe, A., El Sakka, N. and Fjodorova, L., 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), p.e0284187.
• Cook, K.F., Beckett, A.H., Glaysher, S., Goudarzi, S., Fearn, C., Loveson, K.F., Elliott, S., Wyllie, S., Lloyd, A., Bicknell, K. and Lumley, S., 2023. Multiple pathways of SARS-CoV-2 nosocomial transmission uncovered by integrated genomic and epidemiological analyses during the second wave of the COVID-19 pandemic in the UK. Frontiers in cellular and infection microbiology, 12, p.1968.
• Burnside, G., Cheyne, C.P., Leeming, G., Humann, M., Darby, A., Green, M.A., Crozier, A., Maskell, S., O’Halloran, K., Musi, E. and Carmi, E., 2023. COVID-19 risk mitigation in reopening mass cultural events: population-based observational study for the UK Events Research Programme in Liverpool City Region. Journal of the Royal Society of Medicine, p.01410768231182389.
• Foxley-Marrable, M., D’Cruz, L., Meredith, P., Glaysher, S., Beckett, A.H., Goudarzi, S., Fearn, C., Cook, K.F., Loveson, K.F., Dent, H. and Paul, H., 2023. Combining viral genomics and clinical data to assess risk factors for severe COVID-19 (mortality, ICU admission, or intubation) amongst hospital patients in a large acute UK NHS hospital Trust. Plos one, 18(3), p.e0283447.
• Dolton, G., Rius, C., Hasan, M.S., Wall, A., Szomolay, B., Behiry, E., Whalley, T., Southgate, J., Fuller, A., Morin, T. and Topley, K., 2022. Emergence of immune escape at dominant SARS-CoV-2 killer T cell epitope. Cell, 185(16), pp.2936-2951.
• Cox, M., Peacock, T.P., Harvey, W.T., Hughes, J., Wright, D.W., Willett, B.J., Thomson, E., Gupta, R.K., Peacock, S.J., Robertson, D.L. and Carabelli, A.M., 2023. SARS-CoV-2 variant evasion of monoclonal antibodies based on in vitro studies. Nature Reviews Microbiology, 21(2), pp.112-124.
• Marjanovic, S., Romanelli, R.J., Ali, G.C., Leach, B., Bonsu, M., Rodriguez-Rincon, D. and Ling, T., 2022. COVID-19 Genomics UK (COG-UK) Consortium. Rand Health Quarterly, 9(4).
• Stirrup, O., Blackstone, J., Mapp, F., MacNeil, A., Panca, M., Holmes, A., Machin, N., Shin, G.Y., Mahungu, T., Saeed, K. and Saluja, T., 2022. Effectiveness of rapid SARS-CoV-2 genome sequencing in supporting infection control for hospital-onset COVID-19 infection: Multicentre, prospective study. Elife, 11, p.e78427.
• Colton, H., Parker, M.D., Stirrup, O., Blackstone, J., Loose, M., McClure, C.P., Roy, S., Williams, C., McLeod, J., Smith, D. and Taha, Y., 2023. Factors affecting turnaround time of SARS-CoV-2 sequencing for inpatient infection prevention and control decision making: analysis of data from the COG-UK HOCI study. Journal of Hospital Infection, 131, pp.34-42.
• Cotton, S., McHugh, M.P., Dewar, R., Haas, J.G., Templeton, K., Robson, S.C., Connor, T.R., Loman, N.J., Golubchik, T., Nunez, R.T.M. and Bonsall, D., 2023. Investigation of hospital discharge cases and SARS-CoV-2 introduction into Lothian care homes. Journal of Hospital Infection, 135, pp.28-36.
• Bailey, C., Sanderson, T., Townsley, H., Goldman, J., Black, J.R., Young, G., Goldstone, R., Fowler, A.S., Ward, S., Jackson, D.J. and Cubitt, L., 2023. Independent SARS-CoV-2 staff testing protected academic and health-care institutions in northwest London. The Lancet.
• Parker, M.D., Stewart, H., Shehata, O.M., Lindsey, B.B., Shah, D.R., Hsu, S., Keeley, A.J., Partridge, D.G., Leary, S., Cope, A. and State, A., 2022. Altered subgenomic RNA abundance provides unique insight into SARS-CoV-2 B. 1.1. 7/Alpha variant infections. Communications biology, 5(1), p.666.
• Eales, O., Page, A.J., de Oliveira Martins, L., Wang, H., Bodinier, B., Haw, D., Jonnerby, J., Atchison, C., Ashby, D. and Barclay, W., 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), p.647.
• Hinch, R., Panovska-Griffiths, J., Probert, W.J., Ferretti, L., Wymant, C., Di Lauro, F., Baya, N., Ghafari, M., Abeler-Dörner, L., COVID-19 Genomics UK (COG-UK) Consortium and Fraser, C., 2022. Estimating SARS-CoV-2 variant fitness and the impact of interventions in England using statistical and geo-spatial agent-based models. Philosophical Transactions of the Royal Society A, 380(2233), p.20210304.
• Hettle, D., Hutchings, S., Muir, P., Moran, E. and COVID, T., 2022. Persistent SARS-CoV-2 infection in immunocompromised patients facilitates rapid viral evolution: Retrospective cohort study and literature review. Clinical Infection in Practice, p.100210.
• Worsley, S.F., Davies, C.S., Mannarelli, M.E., Komdeur, J., Dugdale, H.L. and Richardson, D.S., 2022. Assessing the causes and consequences of gut mycobiome variation in a wild population of the Seychelles warbler. Microbiome, 10(1), p.242.
• Hillary, L.S., Adriaenssens, E.M., Jones, D.L. and McDonald, J.E., 2022. RNA-viromics reveals diverse communities of soil RNA viruses with the potential to affect grassland ecosystems across multiple trophic levels. ISME communications, 2(1), p.34.
• Veltsos, P., Porcelli, D., Fang, Y., Cossins, A.R., Ritchie, M.G. and Snook, R.R., 2022. Experimental sexual selection reveals rapid evolutionary divergence in sex‐specific transcriptomes and their interactions following mating. Molecular Ecology, 31(12), pp.3374-3388.
• Montejo-Kovacevich, G., Meier, J.I., Bacquet, C.N., Warren, I.A., Chan, Y.F., Kucka, M., Salazar, C., Rueda-M, N., Montgomery, S.H., McMillan, W.O. and Kozak, K.M., 2022. Repeated genetic adaptation to altitude in two tropical butterflies. Nature Communications, 13(1), p.4676.
• Marsh, K.J., Raulo, A.M., Brouard, M., Troitsky, T., English, H.M., Allen, B., Raval, R., Venkatesan, S., Pedersen, A.B., Webster, J.P. and Knowles, S.C., 2022. Synchronous seasonality in the gut microbiota of wild mouse populations. Frontiers in Microbiology, 13, p.809735.
• Barão-Nóbrega, J.A.L., González-Jaurégui, M. and Jehle, R., 2022. N-mixture models provide informative crocodile (Crocodylus moreletii) abundance estimates in dynamic environments. PeerJ, 10, p.e12906.
• Jones, S., Bell, T., Coleman, C.M., Harris, D., Woodward, G., Worledge, L., Roberts, H., McElhinney, L., Aegerter, J., Ransome, E. and Savolainen, V., 2022. Testing bats in rehabilitation for SARS‐CoV‐2 before release into the wild. Conservation Science and Practice, 4(7), p.e12707.
• Jackson, H.A., Percival‐Alwyn, L., Ryan, C., Albeshr, M.F., Venturi, L., Morales, H.E., Mathers, T.C., Cocker, J., Speak, S.A., Accinelli, G.G. and Barker, T., 2022. Genomic erosion in a demographically recovered bird species during conservation rescue. Conservation Biology, 36(4), p.e13918.
• Dunn, J.C., Thomas, R.C., Hipperson, H., Sheehan, D.J., Orsman, C., Mallord, J. and Goodman, S.J., 2023. Evidence for strain-specific virulence of Trichomonas gallinae in African columbiformes. Parasitology, 150(2), pp.206-211.
• Dulias, K., Foody, M.G.B., Justeau, P., Silva, M., Martiniano, R., Oteo-García, G., Fichera, A., Rodrigues, S., Gandini, F., Meynert, A. and Donnelly, K., 2022. Ancient DNA at the edge of the world: Continental immigration and the persistence of Neolithic male lineages in Bronze Age Orkney. Proceedings of the National Academy of Sciences, 119(8), p.e2108001119.
• Dimitriu, T., Kurilovich, E., Łapińska, U., Severinov, K., Pagliara, S., Szczelkun, M.D. and Westra, E.R., 2022. Bacteriostatic antibiotics promote CRISPR-Cas adaptive immunity by enabling increased spacer acquisition. Cell host & microbe, 30(1), pp.31-40.
• Davies, C.S., Worsley, S.F., Maher, K.H., Komdeur, J., Burke, T., Dugdale, H.L. and Richardson, D.S., 2022. Immunogenetic variation shapes the gut microbiome in a natural vertebrate population. Microbiome, 10(1), p.41.
• Brunner, F.S., Brown, M.R., Bassano, I., Denise, H., Khalifa, M.S., Wade, M.J., van Aerle, R., Kevill, J.L., Jones, D.L., Farkas, K. and Jeffries, A.R., 2022. City-wide wastewater genomic surveillance through the successive emergence of SARS-CoV-2 Alpha and Delta variants. Water research, 226, p.119306.
• Braga, L.P., Orland, C., Emilson, E.J., Fitch, A.A., Osterholz, H., Dittmar, T., Basiliko, N., Mykytczuk, N.C. and Tanentzap, A.J., 2022. Viruses direct carbon cycling in lake sediments under global change. Proceedings of the National Academy of Sciences, 119(41), p.e2202261119.
• Ransome, E., Hobbs, F., Jones, S., Coleman, C.M., Harris, N.D., Woodward, G., Bell, T., Trew, J., Kolarević, S., Kračun-Kolarević, M. and Savolainen, V., 2023. Evaluating the transmission risk of SARS-CoV-2 from sewage pollution. Science of The Total Environment, 858, p.159161.
• Barnes, K., Levy, J., Andersen, K., Gauld, J., Rigby, J., Kanjerwa, O., Uzzell, C., Chilupsya, C., Anscombe, C., Tomkins-Tinch, C. and Mbeti, O., 2023. Utilizing river and wastewater as a SARS-CoV-2 surveillance tool to predict trends and identify variants of concern in settings with limited formal sewage systems. Research Square.
• Gómez, P., Hall, A.R., Paterson, S. and Buckling, A., 2022. Rapid decline of adaptation of Pseudomonas fluorescens to soil biotic environment. Biology Letters, 18(3), p.20210593.
• Harney, E., Paterson, S., Collin, H., Chan, B.H., Bennett, D. and Plaistow, S.J., 2022. Pollution induces epigenetic effects that are stably transmitted across multiple generations. Evolution letters, 6(2), pp.118-135.
• Choo, S.W., Chong, J.L., Gaubert, P., Hughes, A.C., O'Brien, S., Chaber, A.L., Antunes, A., Platto, S., Sun, N.C.M., Yu, L. and Koepfli, K.P., 2022. A collective statement in support of saving pangolins. Science of the Total Environment, 824, p.153666.
• Kevill, J.L., Pellett, C., Brown, M.R., Bassano, I., Denise, H., McDonald, J.E., Malham, S.K., Porter, J., Warren, J., Evens, N.P. and Paterson, S., 2022. A comparison of precipitation and filtration-based SARS-CoV-2 recovery methods and the influence of temperature, turbidity, and surfactant load in urban wastewater. Science of the Total Environment, 808, p.151916.
• Winder, L.A., Parsons, P., Horsburgh, G., Maher, K., Hipperson, H., Wierzbicki, C., Jeffries, A.R., Brown, M.R., Fairbrother-Browne, A., Denise, H. and Khalifa, M.S., 2022. Comparison of multiple whole-genome and Spike-only sequencing protocols for estimating variant frequencies via wastewater-based epidemiology. medRxiv, pp.2022-12.
• Luján, A.M., Paterson, S., Hesse, E., Sommer, L.M., Marvig, R.L., Sharma, M.D., Alseth, E.O., Ciofu, O., Smania, A.M., Molin, S. and Johansen, H.K., 2022. Polymicrobial infections can select against Pseudomonas aeruginosa mutators because of quorum-sensing trade-offs. Nature ecology & evolution, 6(7), pp.979-988.
• Laine, V.N., Sävilammi, T., Wahlberg, N., Meramo, K., Ossa, G., Johnson, J.S., Blomberg, A.S., Yeszhanov, A.B., Yung, V., Paterson, S. and Lilley, T.M., 2023. Whole-genome analysis reveals contrasting relationships among nuclear and mitochondrial genomes between three sympatric bat species. Genome biology and evolution, 15(1), p.evac175.
• Wanelik, K.M., Begon, M., Bradley, J.E., Friberg, I.M., Jackson, J.A., Taylor, C.H. and Paterson, S., 2023. Effects of an IgE receptor polymorphism acting on immunity, susceptibility to infection, and reproduction in a wild rodent. Elife, 12, p.e77666.
• Brunner, F., Payne, A., Cairns, E., Airey, G., Gregory, R., Pickwell, N., Holmes, N., Wilson, M., Carlile, M., Hill, V. and Child, H., 2023. Wastewater genomic surveillance tracks the spread of the SARS-CoV-2 Omicron variant across England. medRxiv, pp.2023-02.
• Taylor, C.H., Friberg, I.M., Jackson, J.A., Arriero, E., Begon, M., Wanelik, K.M., Paterson, S. and Bradley, J.E., 2023. Living with chronic infection: Persistent immunomodulation during avirulent haemoparasitic infection in a wild rodent. Molecular ecology, 32(5), pp.1197-1210.
• Fenn, J., Taylor, C., Goertz, S., Wanelik, K.M., Paterson, S., Begon, M., Jackson, J. and Bradley, J., 2023. Discrete patterns of microbiome variability across timescales in a wild rodent population. BMC microbiology, 23(1), p.87.
• Maestri, A., Pursey, E., Chong, C., Pons, B.J., Gandon, S., Custodio, R., Chisnall, M., Grasso, A., Paterson, S., Baker, K.S. and van Houte, S., 2023. Bacterial defences interact synergistically by disrupting phage cooperation. bioRxiv, pp.2023-03.
• Child, H.T., O’Neill, P.A., Moore, K., Rowe, W., Denise, H., Bass, D., Wade, M.J., Loose, M., Paterson, S., van Aerle, R. and Jeffries, A.R., 2023. Optimised protocol for monitoring SARS-CoV-2 in wastewater using reverse complement PCR-based whole-genome sequencing. PLoS One, 18(4), p.e0284211.
• Bassano, I., Ramachandran, V.K., Khalifa, M.S., Lilley, C.J., Brown, M.R., van Aerle, R., Denise, H., Rowe, W., George, A., Cairns, E. and Wierzbicki, C., 2023. Evaluation of variant calling algorithms for wastewater-based epidemiology using mixed populations of SARS-CoV-2 variants in synthetic and wastewater samples. Microbial Genomics, 9(4).
• Keshaviah, A., Diamond, M.B., Wade, M.J., Scarpino, S.V., Ahmed, W., Amman, F., Aruna, O., Badilla-Aguilar, A., Bar-Or, I., Bergthaler, A. and Bines, J.E., 2023. Wastewater monitoring can anchor global disease surveillance systems. The Lancet Global Health, 11(6), pp.e976-e981.
• Wanelik, K.M., Begon, M., Bradley, J.E., Friberg, I.M., Taylor, C.H., Jackson, J.A. and Paterson, S., 2023. Early life immune expression profiles predict later life health and fitness in a wild rodent. Molecular ecology.
• Kharaz, Y.A., Fang, Y., Welting, T., Peffers, M. and Comerford, E.J., 2020. Small RNA signatures of the anterior cruciate ligament from patients with knee joint osteoarthritis. MedRxiv, pp.2020-05.
• Nyangiri, O.A., Mulindwa, J., Namulondo, J., Kitibwa, A., Nassuuna, J., Elliott, A., Kimuda, M.P., Boobo, A., Nerima, B., Adriko, M. and Dunton, N.J., 2023. Variants of IL6, IL10, FCN2, RNASE3, IL12B and IL17B loci are associated with Schistosoma mansoni worm burden in the Albert Nile region of Uganda. PLOS Neglected Tropical Diseases, 17(11), p.e0011796.
• Nambala, P., Mulindwa, J., Noyes, H., Alibu, V.P., Nerima, B., Namulondo, J., Nyangiri, O., Matovu, E., MacLeod, A., Musaya, J. and TrypanoGEN+ Research Group as Members of the H3Africa Consortium, 2023. Differences in gene expression profiles in early and late stage rhodesiense HAT individuals in Malawi. PLOS Neglected Tropical Diseases, 17(12), p.e0011803.
• Namulondo, J., Nyangiri, O.A., Kimuda, M.P., Nambala, P., Nassuuna, J., Egesa, M., Nerima, B., Biryomumaisho, S., Mugasa, C.M., Nabukenya, I. and Kato, D., 2023. Transcriptome analysis of peripheral blood of Schistosoma mansoni infected children from the Albert Nile region in Uganda reveals genes implicated in fibrosis pathology. bioRxiv, pp.2023-06.
• Zamboulis, D.E., Marr, N., Lenzi, L., Birch, H.L., Screen, H.R., Clegg, P.D. and Thorpe, C.T., 2023. The interfascicular matrix of energy storing tendons houses heterogenous cell populations disproportionately affected by ageing. bioRxiv, pp.2023-01.
• Panca, M., Blackstone, J., Stirrup, O., Cutino-Moguel, M.T., Thomson, E., Peters, C., Snell, L.B., Nebbia, G., Holmes, A., Chawla, A. and Machin, N., 2023. Evaluating the cost implications of integrating SARS-CoV-2 genome sequencing for infection prevention and control investigation of nosocomial transmission within hospitals. Journal of Hospital Infection.
• Fisher, A.M., Airey, G., Liu, Y., Gemmell, M., Thomas, J., Bentley, E.G., Whitehead, M.A., Paxton, W.A., Pollakis, G., Paterson, S. and Viney, M., 2023. The ecology of viruses in urban rodents with a focus on SARS-CoV-2. Emerging microbes & infections, (just-accepted), p.2217940.
• Olsson-Brown, A., Yip, V., Ogiji, E.D., Jolly, C., Ressel, L., Sharma, A., Bergfeld, W., Liu, X., Khirwadkar, N., Bellon, T. and Dickinson, A., 2023. TNF-α‒Mediated keratinocyte expression and release of matrix metalloproteinase 9: Putative mechanism of pathogenesis in stevens‒johnson syndrome/toxic epidermal necrolysis. Journal of Investigative Dermatology, 143(6), pp.1023-1030.
• Quinn, L.M., Haldenby, S., Antzcak, P., Fowler, A., Bullock, K., Kenny, J., Gilbert, T., Andrews, T., Diaz-Nieto, R., Fenwick, S. and Jones, R., 2023. Genomic profiling of idiopathic peri-hilar cholangiocarcinoma reveals new targets and mutational pathways. Scientific Reports, 13(1), p.6681.
• Sollazzo, G., Gouvi, G., Nikolouli, K., Aumann, R.A., Djambazian, H., Whitehead, M.A., Berube, P., Chen, S.H., Tsiamis, G., Darby, A.C. and Ragoussis, J., 2023. Genomic and cytogenetic analysis of the Ceratitis capitata temperature-sensitive lethal region. G3: Genes, Genomes, Genetics, p.jkad074.
• Charras, A., Haldenby, S., Smith, E.M., Egbivwie, N., Olohan, L., Kenny, J.G., Schwarz, K., Roberts, C., Al-Abadi, E., Armon, K. and Bailey, K., 2023. Panel sequencing links rare, likely damaging gene variants with distinct clinical phenotypes and outcomes in juvenile-onset SLE. Rheumatology, 62(SI2), pp.SI210-SI225.
• Pérez-Hernández, T., Hernández, J.N., Machín, C., McNeilly, T.N., Nisbet, A.J., Matthews, J.B., Burgess, S.T. and González, J.F., 2023. Exploring the transcriptomic changes underlying recombinant vaccine efficacy against Teladorsagia circumcincta in 3-month-old lambs. Veterinary Parasitology, p.109960.
• Dimitriu, T., Souissi, W., Morwool, P., Darby, A., Crickmore, N. and Raymond, B., 2023. Selecting for infectivity across metapopulations can increase virulence in the social microbe Bacillus thuringiensis. Evolutionary Applications, 16(3), pp.705-720.
• Mewamba, E.M., Noyes, H., Tiofack, A.A.Z., Kamga, R.M.N., Kamdem, C.N., Mengoue, L.E.T., Ofon, E., Ngassam, R.I.K., Nyangiri, O., Bucheton, B. and Njiokou, F., 2023. Association between polymorphisms of IL4, IL13, IL10, STAT6 and IFNG genes, cytokines and immunoglobulin E levels with high burden of Schistosoma mansoni in children from schistosomiasis endemic areas of Cameroon. Infection, Genetics and Evolution, 111, p.105416.
• Beesley, N.J., Cwiklinski, K., Allen, K., Hoyle, R.C., Spithill, T.W., La Course, E.J., Williams, D.J., Paterson, S. and Hodgkinson, J.E., 2023. A major locus confers triclabendazole resistance in Fasciola hepatica and shows dominant inheritance. PLoS Pathogens, 19(1), p.e1011081.

Publications from previous years can be found by following the links below:

• Selected publications 2022
• Selected publications 2021
• Selected publications 2020
• Selected publications 2019
• Selected publications 2018

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