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Cambridge Public Health

 

Host-pathogen interactions, particularly the herpesviruses and their co-evolution with the human immune system

Publications from Elements

Journal articles

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

  • Pimenoff, VN. and Houldcroft, CJ., 2021. How infectious diseases arrived in the colonial Americas. Elife, v. 10
    Doi: http://doi.org/10.7554/eLife.72791
  • 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
  • The COVID-19 Genomics UK (COG-UK) consortium, , 2020. An integrated national scale SARS-CoV-2 genomic surveillance network The Lancet Microbe, v. 1
    Doi: http://doi.org/10.1016/S2666-5247(20)30054-9
  • 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., Alderton, A., Nelson, R., Harrison, E., Sillitoe, J., Bentley, S., Barrett, J., Torok, E., Goodfellow, I., Langford, C., Kwiatkowski, D., The COVID-19 Genomics UK (COG-UK) Consortium, and Wellcome Sanger Institute COVID-19 Surveillance Team, , 2020. Patterns of within-host genetic diversity in SARS-CoV-2
    Doi: http://doi.org/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,
  • Houldcroft, C., Underdown, S. and Rifkin, R., 2019. Human biology and ancient DNA: exploring disease, domestication and movement Annals of Human Biology,
    Doi: http://doi.org/10.1080/03014460.2019.1629536
  • Houldcroft, C., 2019. Human Herpesvirus Sequencing in the Genomic Era: The Growing Ranks of the Herpetic Legion Pathogens, v. 8
    Doi: http://doi.org/10.3390/pathogens8040186
  • 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

  • Houldcroft, CJ., Beale, MA. and Breuer, J., 2017. Clinical and biological insights from viral genome sequencing Nature Reviews Microbiology, v. 15
    Doi: http://doi.org/10.1038/nrmicro.2016.182
  • 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

  • Archer, E. and Houldcroft, CJ., 2014. Genome watch: rabid about whole lyssa genomes. Nat Rev Microbiol, v. 12
    Doi: http://doi.org/10.1038/nrmicro3263
  • 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
  • Book chapters

    2023 (Accepted for publication)

  • Houldcroft, C., 2023 (Accepted for publication). Pathogens as tracers of past human demography and migrations
  • Internet publications

    2021

  • Illingworth, C., Hamilton, W., Warne, B., Routledge, M., Popay, A., jackson, C., Fieldman, T., Meredith, LW., Houldcroft, CJ., Hosmillo, M., Jahun, AS., Caller, LG., Caddy, SL., Yakovleva, A., Hall, G., Khokhar, FA., Feltwell, T., Pinckert, ML., Georgana, I., Chaudhry, Y., Curran, MD., Parmar, S., Sparkes, D., Rivett, L., Jones, NK., Sridhar, S., Forrest, S., Dymond, T., Grainger, K., Workman, C., Gkrania-Klotsas, E., Brown, NM., Baker, S., Weekes, MP., Peacock, SJ., Goodfellow, I., Gouliouris, T., de Angelis, D. and Török, E., 2021. Superspreaders drive the largest outbreaks of hospital onset COVID-19 infection
    Doi: 10.31219/osf.io/wmkn3
  • 2020

  • Meredith, L., Hamilton, W., Warne, B., Houldcroft, C., Hosmillo, M., Jahun, A., Curran, M., Parmar, S., Caller, L., Caddy, S., Khokhar, F., Yakovleva, A., Hall, G., Feltwell, T., Forrest, S., Sridhar, S., Weekes, M., Baker, S., Brown, N., Moore, E., Popay, A., Roddick, I., Reacher, M., Gouliouris, T., Peacock, S., Dougan, G., Török, E. and Goodfellow, I., 2020. Rapid implementation of real-time SARS-CoV-2 sequencing to investigate healthcare-associated COVID-19 infections
    Doi: http://doi.org/10.1101/2020.05.08.20095687
  • Hamilton, W., Tonkin-Hill, G., Smith, E., Aggarwal, D., Houldcroft, C., Warne, B., Brown, C., Meredith, L., Hosmillo, M., Jahun, A., Curran, M., Parmar, S., Caller, L., Caddy, S., Khokhar, F., Yakovleva, A., Hall, G., Feltwell, T., Pinckert, M., Georgana, I., Chaudhry, Y., Brown, N., Gonçalves, S., Amato, R., Harrison, E., Beale, M., Chapman, MS., Jackson, D., Johnston, I., Alderton, A., Sillitoe, J., Langford, C., Dougan, G., Peacock, S., Kwiatkowski, D., Goodfellow, I., Török, E. and COVID-19 Genomics Consortium UK, , 2020. Genomic epidemiology of COVID-19 in care homes in the East of England
    Doi: http://doi.org/10.1101/2020.08.26.20182279
  • 2015

  • Houldcroft, CJ. and Underdown, S., 2015. Neanderthal Genomics Suggests a Pleistocene Time Frame for the First Epidemiologic Transition
    Doi: 10.1101/017343
  • Conference proceedings

    2016

  • Houldcroft, CJ., Depledge, DP., Williams, R., Cloutman-Green, E., Standing, JF. and Breuer, J., 2016. Whole-genome sequencing of adenovirus in immunocompromised paediatric patients directly from clinical samples elucidates molecular epidemiology of suspected outbreaks JOURNAL OF CLINICAL VIROLOGY, v. 82
    Doi: http://doi.org/10.1016/j.jcv.2016.08.026