2024 (Accepted for publication)
Lambisia, AW., Mutunga, M., Katama, EN., Agoti, CN. and Houldcroft, CJ., 2024 (Accepted for publication). Multi-species co-circulation of adenoviruses identified by next generation sequencing during an acute gastroenteritis outbreak in coastal Kenya in 2023 Open Forum Infectious Diseases,
Doi: http://doi.org/10.1093/ofid/ofae505
2023 (Accepted for publication)
Houldcroft, C., Lambisia, A. and Agoti, C., 2023 (Accepted for publication). Genomic epidemiology of Human Adenovirus F40 and F41 in Coastal Kenya: A retrospective hospital-based surveillance study (2013-2022) Virus Evolution,
Houldcroft, C. and Scheib, C., 2023 (Accepted for publication). An adagio for viruses, played out on ancient DNA Genome Biology and Evolution,
Houldcroft, C. and Underdown, S., 2023 (Accepted for publication). Infectious Disease in the Pleistocene: Old Friends or Old Foes? American Journal of Biological Anthropology,
2023
Houldcroft, CJ. and Underdown, S., 2023. Infectious disease in the Pleistocene: Old friends or old foes? American Journal of Biological Anthropology, v. 182
Doi: 10.1002/ajpa.24737
2022 (Accepted for publication)
Scheib, C., Houldcroft, C., Robb, J., Cessford, C., Dittmar, J., Inskip, S., Rose, A. and Hui, R., 2022 (Accepted for publication). Ancient herpes simplex 1 genomes reveal recent viral structure in Eurasia Science Advances,
Doi: http://doi.org/10.1126/sciadv.abo4435
Houldcroft, C. and Reyne, M., 2022 (Accepted for publication). Detection of human adenovirus F41 in wastewater and its relationship to clinical cases of acute hepatitis of unknown aetiology Science of the Total Environment,
Maes, M., Goodfellow, I., Kovalenko, G., Khokhar, F., Baker, S., Skittrall, J. and Houldcroft, C., 2022 (Accepted for publication). Multiplex MinION sequencing suggests enteric adenovirus F41 genetic diversity comparable to pre-COVID-19 era Microbial Genomics,
Davies, E., Noor, M., Lim, YE., Houldcroft, C., Okecha, G., Atkinson, C., Reeves, M., Jackson, S. and Wills, M., 2022 (Accepted for publication). HCMV Carriage in the Elderly diminishes Anti-viral Functionality of the Adaptive Immune Response resulting in Virus Replication at Peripheral Sites Frontiers in Immunology,
2022
Illingworth, CJR., Hamilton, WL., Jackson, C., Warne, B., Popay, A., Meredith, L., Hosmillo, M., Jahun, A., Fieldman, T., Routledge, M., Houldcroft, CJ., Caller, L., Caddy, S., Yakovleva, A., Hall, G., Khokhar, FA., Feltwell, T., Pinckert, ML., Georgana, I., Chaudhry, Y., Curran, M., Parmar, S., Sparkes, D., Rivett, L., Jones, NK., Sridhar, S., Forrest, S., Dymond, T., Grainger, K., Workman, C., Gkrania-Klotsas, E., Brown, NM., Weekes, MP., Baker, S., Peacock, SJ., Gouliouris, T., Goodfellow, I., Angelis, DD. and Török, ME., 2022. A2B-COVID: A Tool for Rapidly Evaluating Potential SARS-CoV-2 Transmission Events. Mol Biol Evol, v. 39
Doi: http://doi.org/10.1093/molbev/msac025
Tierney, AL., Alali, WM., Scott, T., Rees-Unwin, KS., CITIID-NIHR BioResource COVID-19 Collaboration, , Clark, SJ. and Unwin, RD., 2022. Levels of soluble complement regulators predict severity of COVID-19 symptoms. Front Immunol, v. 13
Doi: http://doi.org/10.3389/fimmu.2022.1032331
Needham, EJ., Ren, AL., Digby, RJ., Norton, EJ., Ebrahimi, S., Outtrim, JG., Chatfield, DA., Manktelow, AE., Leibowitz, MM., Newcombe, VFJ., Doffinger, R., Barcenas-Morales, G., Fonseca, C., Taussig, MJ., Burnstein, RM., Samanta, RJ., Dunai, C., Sithole, N., Ashton, NJ., Zetterberg, H., Gisslén, M., Edén, A., Marklund, E., Openshaw, PJM., Dunning, J., Griffiths, MJ., Cavanagh, J., Breen, G., Irani, SR., Elmer, A., Kingston, N., Summers, C., Bradley, JR., Taams, LS., Michael, BD., Bullmore, ET., Smith, KGC., Lyons, PA., Coles, AJ., Menon, DK., Cambridge NeuroCOVID Group, , CITIID-NIHR COVID-19 BioResource Collaboration, and Cambridge NIHR Clinical Research Facility, , 2022. Brain injury in COVID-19 is associated with dysregulated innate and adaptive immune responses. Brain, v. 145
Doi: http://doi.org/10.1093/brain/awac321
2021 (Accepted for publication)
Snell, LB., Fisher, CL., Taj, U., Stirrup, O., Merrick, B., Alcolea-Medina, A., Charalampous, T., Signell, AW., Wilson, HD., Betancor, G., Kia Ik, MT., Cunningham, E., Cliff, PR., Pickering, S., Galao, RP., Batra, R., Neil, SJD., Malim, MH., Doores, KJ., Douthwaite, ST., Nebbia, G., COVID-19 Genomics UK (COG-UK) consortium, , Edgeworth, JD. and Awan, AR., 2021 (Accepted for publication). Combined epidemiological and genomic analysis of nosocomial SARS-CoV-2 infection early in the pandemic and the role of unidentified cases in transmission Clinical Microbiology and Infection,
Doi: http://doi.org/10.1016/j.cmi.2021.07.040
Peacock, S., Illingworth, C., Torok, ME. and Goodfellow, I., 2021 (Accepted for publication). Superspreaders drive the largest outbreaks of hospital onset COVID-19 infections eLife, v. 10
Doi: http://doi.org/10.7554/eLife.67308
Peacock, S., Hamilton, W., Torok, ME., COG-UK Consortium, , Goodfellow, I. and Dougan, G., 2021 (Accepted for publication). Genomic epidemiology of COVID-19 in 1 care homes in the
2 East of England eLife,
Doi: http://doi.org/10.7554/eLife.64618
Jackson, S., Chen, K., Groves, IJ., Sedikides, GX., Gandhi, A., Houldcroft, CJ., Poole, E., Montanuy, I., Mason, GM., Okecha, G., Reeves, MB., Sinclair, JH. and Wills, MR., 2021 (Accepted for publication). Latent cytomegalovirus-driven recruitment of activated CD4+ T cells promotes virus reactivation Frontiers in Immunology,
Doi: http://doi.org/10.3389/fimmu.2021.657945
Myers, C., Houldcroft, C., Rolfe, K. and Breuer, J., 2021 (Accepted for publication). Using Whole Genome Sequences to Investigate Adenovirus Outbreaks in a Haematopoietic Stem Cell Transplant Unit Frontiers in Microbiology,
Doi: http://doi.org/10.3389/fmicb.2021.667790
Houldcroft, C., van dorp, L., Balloux, F. and richard, D., 2021 (Accepted for publication). COVID-19, the first pandemic in the post-genomic era Current Opinion in Virology,
Tonkin-Hill, G., Martincorena, I., Amato, R., Lawson, AR., Gerstung, M., Johnston, I., Jackson, DK., Park, N., Lensing, SV., Quail, MA., Gonçalves, S., Ariani, C., Spencer Chapman, M., Hamilton, WL., Meredith, LW., Hall, G., Jahun, AS., Chaudhry, Y., Hosmillo, M., Pinckert, ML., Georgana, I., Yakovleva, A., Caller, LG., Caddy, SL., Feltwell, T., Khokhar, FA., Houldcroft, CJ., Curran, MD., Parmar, S., COVID-19 Genomics UK (COG-UK) Consortium, , Alderton, A., Nelson, R., Harrison, EM., Sillitoe, J., Bentley, SD., Barrett, JC., Torok, ME., Goodfellow, IG., Langford, C., Kwiatkowski, D. and Wellcome Sanger Institute COVID-19 Surveillance Team, , 2021 (Accepted for publication). Patterns of within-host genetic diversity in SARS-CoV-2 eLife, v. 10
Doi: http://doi.org/10.7554/eLife.66857
2021
Volz, E., Hill, V., McCrone, JT., Price, A., Jorgensen, D., O'Toole, Á., Southgate, J., Johnson, R., Jackson, B., Nascimento, FF., Rey, SM., Nicholls, SM., Colquhoun, RM., da Silva Filipe, A., Shepherd, J., Pascall, DJ., Shah, R., Jesudason, N., Li, K., Jarrett, R., Pacchiarini, N., Bull, M., Geidelberg, L., Siveroni, I., COG-UK Consortium, , Goodfellow, I., Loman, NJ., Pybus, OG., Robertson, DL., Thomson, EC., Rambaut, A. and Connor, TR., 2021. Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity Cell, v. 184
Doi: http://doi.org/10.1016/j.cell.2020.11.020
Venturini, C., Houldcroft, CJ., Lazareva, A., Wegner, F., Morfopoulou, S., Amrolia, PJ., Golwala, Z., Rao, A., Marks, SD., Simmonds, J., Yoshikawa, T., Farrell, PJ., Cohen, JI., Worth, AJ. and Breuer, J., 2021. Epstein-Barr virus (EBV) deletions as biomarkers of response to treatment of chronic active EBV. Br J Haematol, v. 195
Doi: http://doi.org/10.1111/bjh.17790
2020 (Accepted for publication)
Weekes, M., rivett, L., Sridhar, S., sparkes, D., routledge, M., jones, N., forrest, S., young, J., Pereira-Dias, J., hamilton, W., torok, E., Meredith, L., curran, M., fuller, S., Samworth, R., Bradley, J., Dougan, G., Smith, K., Lehner, P., Matheson, N., Goodfellow, I. and Baker, S., 2020 (Accepted for publication). Screening of healthcare workers for SARS-CoV-2 highlights the role of asymptomatic carriage in COVID-19 transmission eLife,
Weekes, M., 2020 (Accepted for publication). Effective control of SARS-CoV-2 transmission between healthcare workers during a period of diminished community prevalence of COVID-19 eLife,
Doi: http://doi.org/10.7554/eLife.59391
2020
Houldcroft, C., Jackson, S., Lim, Y., Davies, E., Okecha, G. and Wills, M., 2020. Assessing anti-HCMV cell mediated immune responses in transplant recipients and healthy controls using a novel functional assay Frontiers in Cellular and Infection Microbiology,
Doi: http://doi.org/10.3389/fcimb.2020.00275
Myers, C., Houldcroft, C., Roy, S., Margetts, B., Best, T., Venturini, C., Guerra-Assunção, J., Williams, C., Williams, R., Dunn, H., Hartley, J., Rolfe, K. and Breuer, J., 2020. Using Whole Genome Sequences to Investigate Adenovirus Outbreaks, Including Five Deaths in a Haematopoietic Stem Cell Transplant Unit
Doi: http://doi.org/10.1101/2020.11.26.20239111
Venturini, C., Houldcroft, C., Lazareva, A., Wegner, F., Morfopoulou, S., Amrolia, P., Golwala, Z., Rao, A., Marks, S., Simmonds, J., Yoshikawa, T., Farrell, P., Cohen, J., Worth, A. and Breuer, J., 2020. EBV deletions as biomarkers of response to treatment of Chronic Active Epstein Barr Virus
Doi: http://doi.org/10.1101/2020.12.18.20248315
Peacock, S., Meredith, L., Dougan, G., Torok, ME., Baker, S., Brwon, N. and Gouliouris, T., 2020. Rapid implementation of SARS-CoV-2 sequencing to
investigate cases of health-care associated COVID-19:
a prospective genomic surveillance study Lancet Infectious Diseases,
Doi: http://doi.org/10.1016/S1473-3099(20)30562-4
Tonkin-Hill, G., Martincorena, I., Amato, R., Lawson, A., Gerstung, M., Johnston, I., Jackson, D., Park, N., Lensing, S., Quail, M., Gonçalves, S., Ariani, C., Chapman, MS., Hamilton, W., Meredith, L., Hall, G., Jahun, A., Chaudhry, Y., Hosmillo, M., Pinckert, M., Georgana, I., Yakovleva, A., Caller, L., Caddy, S., Feltwell, T., Khokhar, F., Houldcroft, C., Curran, M., Parmar, S., The COVID-19 Genomics UK (COG-UK) Consortium, , Alderton, A., Nelson, R., Harrison, E., Sillitoe, J., Bentley, S., Barrett, J., Torok, E., Goodfellow, I., Langford, C., Kwiatkowski, D. and Wellcome Sanger Institute COVID-19 Surveillance Team, , 2020. Patterns of within-host genetic diversity in SARS-CoV-2
Doi: 10.1101/2020.12.23.424229
Mavian, C., Houldcroft, C., Villabona-Arenas, J. and Salemi, M., 2020. Sampling bias and incorrect rooting make phylogenetic network tracing of SARS-COV-2 infections unreliable Proceedings of the National Academy of Sciences of USA,
2019 (Accepted for publication)
Cudini, J., Roy, S., Houldcroft, C., Bryant, J., Depledge, D., Veys, P., Goldstein, R. and Breuer, J., 2019 (Accepted for publication). Human cytomegalovirus haplotype reconstruction reveals high diversity due to superinfection and evidence of within-host recombination Proceedings of the National Academy of Sciences of the United States of America,
Doi: http://doi.org/10.1073/pnas.1818130116
Houldcroft, C. and Cudini, J., 2019 (Accepted for publication). Reply to Jensen and Kowalik: Consideration of mixed infections is central to understanding HCMV intrahost diversity. Proceedings of the National Academy of Sciences of USA,
2019
Houldcroft, C., Ham, E. and underdown, S., 2019. The relative roles of maternal survival and inter-personal violence as selection pressures on the persistence of Neanderthal hypercoagulability alleles in modern Europeans Annals of Human Biology,
2018 (Accepted for publication)
Houldcroft, CJ., Breuer, J., Cudini, J., Roy, S., Morfopoulou, S., Margetts, B., Depledge, D., Shah, D., Brown, J., Hartley, J. and Rao, K., 2018 (Accepted for publication). Use of whole-genome sequencing of adenovirus in immunocompromised paediatric patients to identify nosocomial transmission and mixed-genotype infection Journal of Infectious Diseases,
Doi: http://doi.org/10.1093/infdis/jiy323
Houldcroft, CJ., Underdown, S., Pimenoff, V. and Rifkin, R., 2018 (Accepted for publication). The Role of aDNA in Understanding the Co-Evolutionary Patterns of Human Sexually Transmitted Infections Genes,
Depledge, D., Houldcroft, CJ., Cudini, J. and Breuer, J., 2018 (Accepted for publication). High Viral Diversity and Mixed Infections in Cerebral Spinal Fluid From Cases of Varicella Zoster Virus Encephalitis Journal of Infectious Diseases,
Doi: http://doi.org/10.1093/infdis/jiy358
2018
Underdown, SJ., Soundararajan, K. and Houldcroft, C., 2018. Network analysis of the hominin origin of Herpes Simplex virus 2 from fossil data Virus Evolution, v. 3
Doi: http://doi.org/10.1093/ve/vex026
Underdown, S., Kumar, K. and Houldcroft, C., 2018. Network analysis of the hominin origin of Herpes Simplex virus 2 from fossil data Virus Evolution,
Doi: http://doi.org/10.1101/105007
Houldcroft, CJ., Beale, MA., Sayeed, MA., Qadri, F., Dougan, G. and Mutreja, A., 2018. Identification of novel adenovirus genotype 90 in children from Bangladesh. Microb Genom, v. 4
Doi: http://doi.org/10.1099/mgen.0.000221
2017 (Accepted for publication)
Underdown, S., Kumar, K. and Houldcroft, CJ., 2017 (Accepted for publication). Network analysis of the hominin origin of Herpes Simplex virus 2 from fossil data Virus Evolution, v. 3
Doi: http://doi.org/10.1093/ve/vex026
Houldcroft, CJ., Ramond, J-B., Rifkin, RF. and Underdown, SJ., 2017 (Accepted for publication). Migrating microbes: what pathogens can tell us about population movements and human evolution Annals of Human Biology,
Doi: http://doi.org/10.1080/03014460.2017.1325515
2017
2016
Munro, AC. and Houldcroft, C., 2016. Human cancers and mammalian retroviruses: Should we worry about bovine leukemia virus? Future Virology, v. 11
Doi: http://doi.org/10.2217/fvl.16.5
Houldcroft, CJ., Bryant, JM., Depledge, DP., Margetts, BK., Simmonds, J., Nicolaou, S., Tutill, HJ., Williams, R., Worth, AJJ., Marks, SD., Veys, P., Whittaker, E. and Breuer, J., 2016. Detection of Low Frequency Multi-Drug Resistance and Novel Putative Maribavir Resistance in Immunocompromised Pediatric Patients with Cytomegalovirus. Front Microbiol, v. 7
Doi: http://doi.org/10.3389/fmicb.2016.01317
Worth, AJJ., Houldcroft, CJ. and Booth, C., 2016. Severe Epstein-Barr virus infection in primary immunodeficiency and the normal host. Br J Haematol, v. 175
Doi: http://doi.org/10.1111/bjh.14339
Houldcroft, CJ. and Underdown, SJ., 2016. Neanderthal genomics suggests a pleistocene time frame for the first epidemiologic transition. American Journal of Physical Anthropology, v. 160
Doi: http://doi.org/10.1002/ajpa.22985
2015
Houldcroft, CJ. and Kellam, P., 2015. Host genetics of Epstein-Barr virus infection, latency and disease. Rev Med Virol, v. 25
Doi: http://doi.org/10.1002/rmv.1816
Houldcroft, C., 2015. Sequencing drug-resistant cytomegalovirus in pediatric patients: Toward personalized medicine Future Virology, v. 10
Doi: http://doi.org/10.2217/fvl.15.58
Houldcroft, CJ. and Breuer, J., 2015. Tales from the crypt and coral reef: the successes and challenges of identifying new herpesviruses using metagenomics. Front Microbiol, v. 6
Doi: http://doi.org/10.3389/fmicb.2015.00188
2014
Houldcroft, CJ., Petrova, V., Liu, JZ., Frampton, D., Anderson, CA., Gall, A. and Kellam, P., 2014. Host genetic variants and gene expression patterns associated with Epstein-Barr virus copy number in lymphoblastoid cell lines. PLoS One, v. 9
Doi: http://doi.org/10.1371/journal.pone.0108384
2010
Hué, S., Gray, ER., Gall, A., Katzourakis, A., Tan, CP., Houldcroft, CJ., McLaren, S., Pillay, D., Futreal, A., Garson, JA., Pybus, OG., Kellam, P. and Towers, GJ., 2010. Disease-associated XMRV sequences are consistent with laboratory contamination. Retrovirology, v. 7
Doi: http://doi.org/10.1186/1742-4690-7-111
