Select Publications

For a full list of publications see Google Scholar or NCBI Bibliography

2024

  1. Paredes, M. I., Ahmed, N., Figgins, M., Colizza, V., Lemey, P., McCrone, J. T., Müller, N., Tran-Kiem, C., & Bedford, T. (2024). Underdetected dispersal and extensive local transmission drove the 2022 mpox epidemic. Cell, 187(6), 1374–1386.
  2. Kelly, S. P., McEwen, L. M., Isaksson, M., Murphy, S., White, S., Levy, M. E., McCrone, J. T., Levan, G., Santhanam, S., Baniecki, M. L., & others. (2024). Viral SARS-CoV-2 Rebound Rates in Linked Commercial Pharmacy-Based Testing and Health Care Claims. Open Forum Infectious Diseases, 11(6).
  3. Carnegie, L., McCrone, J., Du Plessis, L., Hasan, M., Ali, M. Z., Begum, R., Hassan, M. Z., Islam, S., Rahman, M. H., Uddin, A. S. M., & others. (2024). Genomic epidemiology of early SARS-CoV-2 transmission dynamics in Bangladesh. MedRxiv, 2024–2005.

2023

  1. Sahadeo, N. S. D., Nicholls, S., Moreira, F. R. R., O’Toole, Á., Ramkissoon, V., Whittaker, C., Hill, V., McCrone, J. T., Mohammed, N., Ramjag, A., & others. (2023). Implementation of genomic surveillance of SARS-CoV-2 in the Caribbean: Lessons learned for sustainability in resource-limited settings. PLOS Global Public Health, 3(2), e0001455.
  2. Tsui, J. L.-H., McCrone*, J. T., Lambert*, B., Bajaj*, S., Inward*, R. P. D., Bosetti*, P., Pena*, R. E., Tegally, H., Hill, V., Zarebski, A. E., Peacock, T. P., Liu, L., Wu, N., Davis, M., Bogoch, I. I., Khan, K., Kall, M., Aziz, N. I. B. A., Colquhoun, R., … Kraemer, M. U. G. (2023). Genomic assessment of invasion dynamics of SARS-CoV-2 Omicron BA.1. Science, 381(6655), 336–343. https://doi.org/10.1126/science.adg6605

2022

  1. McCrone*, J. T., Hill*, V., Bajaj*, S., Pena*, R. E., Lambert, B. C., Inward, R., Bhatt, S., Volz, E., Ruis, C., Dellicour, S., Baele, G., Zarebski, A. E., Sadilek, A., Wu, N., Schneider, A., Ji, X., Raghwani, J., Jackson, B., Colquhoun, R., … Consortium, T. C. O. V. I. D.-19 G. U. K. (C. O. G.-U. K. (2022). Context-specific emergence and growth of the SARS-CoV-2 Delta variant. Nature, 610(7930), 154–160. https://doi.org/10.1038/s41586-022-05200-3
  2. Raghwani, J., Plessis, L. D., McCrone, J. T., Hill, S. C., Parag, K. V., Thézé, J., Kumar, D., Puvar, A., Pandit, R., Pybus, O. G., Fournié, G., Joshi, M., & Joshi, C. G. (2022). Genomic epidemiology of early SARS-CoV-2 transmission dynamics in Gujarat, India. Emerging Infectious Disease.
  3. Bolze, A., Basler, T., White, S., Dei Rossi, A., Wyman, D., Dai, H., Roychoudhury, P., Greninger, A. L., Hayashibara, K., Beatty, M., Shah, S., Stous, S., McCrone, J. T., Kil, E., Cassens, T., Tsan, K., Nguyen, J., Ramirez, J., Carter, S., … Luo, S. (2022). Evidence for SARS-CoV-2 Delta and Omicron co-infections and recombination. Med, 3(12), 848–859.e4. https://doi.org/https://doi.org/10.1016/j.medj.2022.10.002
  4. O’Toole, Á., Hill, V., Jackson, B., Dewar, R., Sahadeo, N., Colquhoun, R., Rooke, S., McCrone, J. T., Duggan, K., McHugh, M. P., & others. (2022). Genomics-informed outbreak investigations of SARS-CoV-2 using civet. PLOS Global Public Health, 2(12), e0000704.
  5. Hill, V., Du Plessis, L., Peacock, T. P., Aggarwal, D., Colquhoun, R., Carabelli, A. M., Ellaby, N., Gallagher, E., Groves, N., Jackson, B., McCrone, J. T., O’Toole, Á., Price, A., Sanderson, T., Scher, E., Southgate, J., Volz, E., Barclay, W. S., Barrett, J. C., … Rambaut, T. C. O. V. I. D.-19 G. U. K. (C. O. G.-U. K. C., Andrew. (2022). The origins and molecular evolution of SARS-CoV-2 lineage B.1.1.7 in the UK. Virus Evolution, 8(2). https://doi.org/10.1093/ve/veac080

2021

  1. Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil. (2021). Science, 372(6544), 815–821.
  2. Genomic Epidemiology of SARS-CoV-2 Transmission Lineages in Ecuador. (2021). Virus Evolution. https://doi.org/10.1093/ve/veab051
  3. Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England. (2021). Nature, 593(7858), 266–269.
  4. da Silva Filipe, A., Shepherd, J. G., Williams, T., Hughes, J., Aranday-Cortes, E., Asamaphan, P., Ashraf, S., ..., McCrone, J. T., ..., Robertson, D. L., Templeton, K., & Thomson (52 authors ), E. C. (2021). Genomic epidemiology reveals multiple introductions of SARS-CoV-2 from mainland Europe into Scotland. Nat Microbiol, 6(1), 112–122.
  5. du Plessis*, L., McCrone*, J. T., Zarebski*, A. E., Hill*, V., Ruis, C., Gutierrez, B., Raghwani, J., Ashworth, J., Colquhoun, R., Connor, T. R., Faria, N. R., Jackson, B., Loman, N. J., O’Toole, Á., Nicholls, S. M., Parag, K. V., Scher, E., Vasylyeva, T. I., Volz, E. M., … Pybus, O. G. (2021). Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK. Science, 371(6530), 708–712.
  6. Volz, E., Hill, V., McCrone, J. T., Price, A., Jorgensen, D., O’Toole, Á., Southgate, J., Johnson, R., Jackson, B., Nascimento, F. F., Rey, S. M., Nicholls, S. M., Colquhoun, R. M., da Silva Filipe, A., Shepherd, J., Pascall, D. J., Shah, R., Jesudason, N., Li, K., … Neaverson, A. S. (2021). Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity. Cell, 184(1), 64–75.
  7. Jackson, B., Boni, M., Bull, M., Colleran, A., Colquhoun, R., Derby, A., Haldenby, S., Hill, V., Lucaci, A., McCrone, J. T., Nicholls, S., O’Toole, Á., Pacchiarini, N., Poplawski, R., Scher, E., Todd, F., Webster, H., Whitehead, M., Wierzbicki, C., … Rambaut, A. (2021). Generation and transmission of inter-lineage recombinants in the SARS-CoV-2 pandemic. Cell. https://doi.org/https://doi.org/10.1016/j.cell.2021.08.014
  8. O’Toole, Á. N., Scher, E., Underwood, A., Jackson, B., Hill, V., McCrone, J., Colquhoun, R., Ruis, C., Abu-Dahab, K., Taylor, B., Yeats, C., du Plessis, L., Maloney, D., Medd, N., Attwood, S., Aanensen, D., Holmes, E., Pybus, O., & Rambaut, A. (2021). Assignment of epidemiological lineages in an emerging pandemic using the pangolin tool. Virus Evolution. https://doi.org/10.1093/ve/veab064
  9. Kraemer, M. U. G., Hill, V., Ruis, C., Simon Dellicour, S. B., McCrone, J. T., Baele, G., Parag, K. V., Battle, A. L., Gutierrez, B., Jackson, B., Colquhoun, R., O’Toole, Á., Klein, B., Vespignani, A., consortium, T. C. O. V. I. D. G. U. K. (C. G.-U. K., Volz, E., Faria, N. R., Aanensen, D., Loman, N. J., … Pybus, O. G. (2021). Spatio-temporal invasion dynamics of SARS-CoV-2 lineage B.1.1.7 emergence. Science, 373(6557), 889–895.
  10. Resurgence of Ebola virus in 2021 in Guinea suggests a new paradigm for outbreaks. (2021). Nature, 597(7877), 539–543 .

2020

  1. Lemey, P., Hong, S. L., Hill, V., Baele, G., Poletto, C., Colizza, V., O’Toole, Á., McCrone, J. T., Andersen, K. G., Worobey, M., Nelson, M. I., Rambaut, A., & Suchard, M. A. (2020). Accommodating individual travel history and unsampled diversity in Bayesian phylogeographic inference of SARS-CoV-2. Nat Commun, 11(1), 5110.
  2. Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020. (2020). Euro Surveill, 25(32).
  3. Rambaut, A., Holmes, E. C., O’Toole, Á., Hill, V., McCrone, J. T., Ruis, C., du Plessis, L., & Pybus, O. G. (2020). A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nat Microbiol, 5(11), 1403–1407.
  4. Lu, J., du Plessis, L., Liu, Z., Hill, V., Kang, M., Lin, H., Sun, J., François, S., Kraemer, M. U. G., Faria, N. R., McCrone, J. T., Peng, J., Xiong, Q., Yuan, R., Zeng, L., Zhou, P., Liang, C., Yi, L., Liu, J., … Ke, C. (2020). Genomic Epidemiology of SARS-CoV-2 in Guangdong Province, China. Cell, 181(5), 997–1003.
  5. Valesano, A. L., Fitzsimmons, W. J., McCrone, J. T., Petrie, J. G., Monto, A. S., Martin, E. T., & Lauring, A. S. (2020). Influenza B Viruses Exhibit Lower Within-Host Diversity than Influenza A Viruses in Human Hosts. J Virol, 94(5).
  6. McCrone, J. T., Woods, R. J., Monto, A. S., Martin, E. T., & Lauring, A. S. (2020). The effective population size and mutation rate of influenza A virus in acutely infected individuals. BioRxiv. https://doi.org/10.1101/2020.10.24.353748

2018

  1. Fitzsimmons, W. J., Woods, R. J., McCrone, J. T., Woodman, A., Arnold, J. J., Yennawar, M., Evans, R., Cameron, C. E., & Lauring, A. S. (2018). A speed-fidelity trade-off determines the mutation rate and virulence of an RNA virus. PLoS Biol, 16(6), e2006459.
  2. McCrone, J. T., Woods, R. J., Martin, E. T., Malosh, R. E., Monto, A. S., & Lauring, A. S. (2018). Stochastic processes constrain the within and between host evolution of influenza virus. Elife, 7.
  3. McCrone, J. T., & Lauring, A. S. (2018). Genetic bottlenecks in intraspecies virus transmission. Curr Opin Virol, 28, 20–25.

2017

  1. Debbink*, K., McCrone*, J. T., Petrie, J. G., Truscon, R., Johnson, E., Mantlo, E. K., Monto, A. S., & Lauring, A. S. (2017). Vaccination has minimal impact on the intrahost diversity of H3N2 influenza viruses. PLoS Pathog, 13(1), e1006194.

2016

  1. Visher, E., Whitefield, S. E., McCrone, J. T., Fitzsimmons, W., & Lauring, A. S. (2016). The Mutational Robustness of Influenza A Virus. PLoS Pathog, 12(8), e1005856.
  2. McCrone, J. T., & Lauring, A. S. (2016). Measurements of Intrahost Viral Diversity Are Extremely Sensitive to Systematic Errors in Variant Calling. J Virol, 90(15), 6884–6895.
  3. Marino, S., Gideon, H. P., Gong, C., Mankad, S., McCrone, J. T., Lin, P. L., Linderman, J. J., Flynn, J. L., & Kirschner, D. E. (2016). Computational and Empirical Studies Predict Mycobacterium tuberculosis-Specific T Cells as a Biomarker for Infection Outcome. PLoS Comput Biol, 12(4), e1004804.

2010

  1. Butchbach, M. E., Rose, F. F., Rhoades, S., Marston, J., McCrone, J. T., Sinnott, R., & Lorson, C. L. (2010). Effect of diet on the survival and phenotype of a mouse model for spinal muscular atrophy. Biochem Biophys Res Commun, 391(1), 835–840.