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Andrew Rambaut

PROF

 https://orcid.org/0000-0003-4337-3707

Accepting PhD Students

Search results

  • 2024

    A phylogenetics and variant calling pipeline to support SARS-CoV-2 genomic epidemiology in the UK

    Colquhoun, R., O’Toole, Á., Hill, V., McCrone, J. T., Yu, X., Nicholls, S. M., Poplawski, R., Whalley, T., Groves, N., Ellaby, N., Loman, N., Connor, T. & Rambaut, A., 17 Oct 2024, (E-pub ahead of print) In: Virus Evolution. 10, 1, 6 p., veae083.

    Research output: Contribution to journal › Article › peer-review

    Open Access
    File

  • Co-circulation of monkeypox virus subcladesIa and Ib in Kinshasa Province, Democratic Republic of the Congo, July to August 2024

    Wawina-Bokalanga, T., Akil-Bandali, P., Kinganda-Lusamaki, E., Lokilo, E., Jansen, D., Amuri-Aziza, A., Makangara-Cigolo, J-C., Pukuta-Simbu, E., Ola-Mpumbe, R., Muyembe, M., Kacita, C., Paku-Tshambu, P., Dantas, P. H. L. F., Tshiani-Mbaya, O., Luakanda, G., Nkuba-Ndaye, A., Matondo, M., Vakaniaki, E. H., Tessema, S., Ndembi, N., & 18 othersO’Toole, Á., De Block, T., Ngandu, C., Hoff, N. A., Low, N., Subissi, L., Merritt, S., Muyembe-Tamfum, J-J., Liesenborghs, L., Peeters, M., Delaporte, E., Kindrachuk, J., Rimoin, A. W., Ahuka-Mundeke, S., Rambaut, A., Mwamba, D., Vercauteren, K. & Mbala-Kingebeni, P., 19 Sept 2024, In: Eurosurveillance. 29, 38, 6 p.

    Research output: Contribution to journal › Letter › peer-review

    Open Access
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  • Genetic tracing of market wildlife and viruses at the epicenter of the COVID-19 pandemic

    Crits-Christoph, A., Levy, J. I., Pekar, J. E., Goldstein, S. A., Singh, R., Hensel, Z., Gangavarapu, K., Rogers, M. B., Moshiri, N., Garry, R. F., Holmes, E. C., Koopmans, M. P. G., Lemey, P., Peacock, T. P., Popescu, S., Rambaut, A., Robertson, D. L., Suchard, M. A., Wertheim, J. O., Rasmussen, A. L., & 3 othersAndersen, K. G., Worobey, M. & Débarre, F., 19 Sept 2024, In: Cell. 187, 19, 27 p., 5468-5482.e11.

    Research output: Contribution to journal › Article › peer-review

  • Clockor2: Inferring global and local strict molecular clocks using root-to-tip regression

    Featherstone, L. A., Rambaut, A., Duchene, S. & Wirth, W., May 2024, In: Systematic biology. 73, 3, p. 623-628 6 p., syae003.

    Research output: Contribution to journal › Article › peer-review

    Open Access
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  • Integrating dynamical modeling and phylogeographic inference to characterize global influenza circulation

    Parino, F., Gustani-Buss, E., Bedford, T., Suchard, M. A., Trovão, N. S., Rambaut, A., Colizza, V., Poletto, C. & Lemey, P., 15 Mar 2024, (Unpublished) medRxiv, 22 p.

    Research output: Working paper › Preprint

    File

  • Automated detection and classification of polioviruses from nanopore sequencing reads using piranha

    O'Toole, Á., Colquhoun, R., Ansley, C., Troman, C., Maloney, D., Vance, Z., Akello, J., Bujaki, E., Majumdar, M., Khurshid, A., Arshad, Y., Alam, M. M., Martin, J., Shaw, A. G., Grassly, N. C. & Rambaut, A., Mar 2024, In: Virus Evolution. 10, 1, p. veae023 12 p.

    Research output: Contribution to journal › Article › peer-review

    Open Access
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  • A framework for automated scalable designation of viral pathogen lineages from genomic data

    McBroome, J., de Bernardi Schneider, A., Roemer, C., Wolfinger, M. T., Hinrichs, A. S., O'Toole, A. N., Ruis, C., Turakhia, Y., Rambaut, A. & Corbett-Detig, R., Feb 2024, In: Nature Microbiology. 9, 2, p. 550-560 11 p.

    Research output: Contribution to journal › Article › peer-review

    Open Access
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  • 2023

    APOBEC3 deaminase editing in mpox virus as evidence for sustained human transmission since at least 2016

    O'Toole, Á., Neher, R. A., Ndodo, N., Borges, V., Gannon, B., Gomes, J. P., Groves, N., King, D. J., Maloney, D., Lemey, P., Lewandowski, K., Loman, N., Myers, R., Omah, I. F., Suchard, M. A., Worobey, M., Chand, M., Ihekweazu, C., Ulaeto, D., Adetifa, I., & 1 othersRambaut, A., 3 Nov 2023, In: Science (New York, N.Y.). 382, 6670, p. 595-600 6 p.

    Research output: Contribution to journal › Article › peer-review

    Open Access
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  • SARS-CoV-2 evolution in the Omicron era

    Roemer, C., Sheward, D. J., Hisner, R., Gueli, F., Sakaguchi, H., Frohberg, N., Schoenmakers, J., Sato, K., O'Toole, Á., Rambaut, A., Pybus, O. G., Ruis, C., Murrell, B. & Peacock, T. P., Nov 2023, In: Nature Microbiology. 8, 11, p. 1952-1959 8 p.

    Research output: Contribution to journal › Comment/debate › peer-review

  • SCORPIO: a utility for defining and classifying mutation constellations of virus genomes

    Colquhoun, R., Jackson, B., O'Toole, Á. & Rambaut, A., 1 Oct 2023, In: Bioinformatics. 39, 10, 4 p., btad575.

    Research output: Contribution to journal › Article › peer-review

    Open Access
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  • Distinct monkeypox virus lineages co-circulating in humans before 2022

    Ndodo, N., Ashcroft, J., Lewandowski, K., Yinka-Ogunleye, A., Chukwu, C., Ahmad, A., King, D., Akinpelu, A., Maluquer de Motes, C., Ribeca, P., Sumner, R. P., Rambaut, A., Chester, M., Maishman, T., Bamidele, O., Mba, N., Babatunde, O., Aruna, O., Pullan, S. T., Gannon, B., & 4 othersBrown, C. S., Ihekweazu, C., Adetifa, I. & Ulaeto, D. O., 14 Sept 2023, In: Nature Medicine. 29, 9, p. 2317-2324 10 p.

    Research output: Contribution to journal › Article › peer-review

    Open Access
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  • Sensitive poliovirus detection using nested PCR and nanopore sequencing: a prospective validation study

    Shaw, A. G., Mampuela, T. K., Lofiko, E. L., Pratt, C., Troman, C., Bujaki, E., O'Toole, Á., Akello, J. O., Aziza, A. A., Lusamaki, E. K., Makangara, J. C., Akonga, M., Lay, Y., Nsunda, B., White, B., Jorgensen, D., Pukuta, E., Riziki, Y., Rankin, K. E., Rambaut, A., & 5 othersAhuka-Mundeke, S., Muyembe, J-J., Martin, J., Grassly, N. C. & Mbala-Kingebeni, P., 1 Sept 2023, In: Nature Microbiology. 8, p. 1634-1640 7 p.

    Research output: Contribution to journal › Article › peer-review

    Open Access
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  • Genomic assessment of invasion dynamics of SARS-CoV-2 Omicron BA.1

    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., Abdul Aziz, N. I. B., Colquhoun, R., O'Toole, Á., & 20 othersJackson, B., Dasgupta, A., Wilkinson, E., de Oliveira, T., Connor, T. R., Loman, N. J., Colizza, V., Fraser, C., Volz, E., Ji, X., Gutierrez, B., Chand, M., Dellicour, S., Cauchemez, S., Raghwani, J., Suchard, M. A., Lemey, P., Rambaut, A., Pybus, O. G. & Kraemer, M. U. G., 21 Jul 2023, In: Science (New York, N.Y.). 381, 6655, p. 336-343 8 p.

    Research output: Contribution to journal › Article › peer-review

    Open Access
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  • Comparison of eleven RNA extraction methods for poliovirus direct molecular detection in stool samples

    Akello, J. O., Bujaki, E., Shaw, A. G., Khurshid, A., Arshad, Y., Troman, C., Majumdar, M., O'Toole, Á., Rambaut, A., Alam, M. M., Martin, J. & Grassly, N. C., 20 Mar 2023, In: Microbiology Spectrum. 11, 2, e0425222.

    Research output: Contribution to journal › Article › peer-review

    Open Access
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  • Quantifying the value of viral genomics when inferring who infected whom in the 2014–16 Ebola virus outbreak in Guinea

    Robert, A., Tsui lok hei, J., Watson, C. H., Gsell, P., Hall, Y., Rambaut, A., Longini, I. M., Sakoba, K., Kucharski, A. J., Touré, A., Danmadji nadlaou, S., Saidou barry, M., Fofana, T. O., Lansana kaba, I., Sylla, L., Diaby, M. L., Soumah, O., Diallo, A., Niare, A., Diallo, A., & 5 othersEggo, R. M., Caroll, M. W., Henao-Restrepo, A. M., Edmunds, W. J. & Hué, S., 7 Mar 2023, In: Virus Evolution. 9, 1, vead007.

    Research output: Contribution to journal › Article › peer-review

    Open Access
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  • New nomenclature for mpox (monkeypox) and monkeypox virus clades

    Ulaeto, D., Agafonov, A., Burchfield, J., Carter, L., Happi, C., Jakob, R., Krpelanova, E., Kuppalli, K., Lefkowitz, E. J., Mauldin, M. R., De oliveira, T., Onoja, B., Otieno, J., Rambaut, A., Subissi, L., Yinka-Ogunleye, A. & Lewis, R. F., 6 Feb 2023, In: The Lancet Infectious Diseases. 23, 3, p. 273-275 3 p.

    Research output: Contribution to journal › Comment/debate › peer-review

  • 2022

    Genomics-informed outbreak investigations of SARS-CoV-2 using civet

    O'Toole, Á., Hill, V., Jackson, B., Dewar, R., Sahadeo, N., Colquhoun, R., Rooke, S., McCrone, J. T., Duggan, K., McHugh, M. P., Nicholls, S. M., Poplawski, R., Aanensen, D., Holden, M., Connor, T., Loman, N., Goodfellow, I., Carrington, C. V. F., Templeton, K. & Rambaut, A., 9 Dec 2022, In: PLOS Global Public Health . 2, 12, 15 p., e0000704.

    Research output: Contribution to journal › Article › peer-review

    Open Access
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  • Context-specific emergence and growth of the SARS-CoV-2 Delta variant

    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., O'Toole, Á., & 20 othersPeacock, T. P., Twohig, K., Thelwall, S., Dabrera, G., Myers, R., Faria, N. R., Huber, C., Bogoch, I. I., Khan, K., du Plessis, L., Barrett, J. C., Aanensen, D. M., Barclay, W. S., Chand, M., Connor, T., Loman, N. J., Suchard, M. A., Pybus, O. G., Rambaut, A. & Kraemer, M. U. G., 6 Oct 2022, In: Nature. 610, 7930, p. 154-160 6 p.

    Research output: Contribution to journal › Article › peer-review

    Open Access
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  • SPREAD 4: Online visualisation of pathogen phylogeographic reconstructions

    Nahata, K. D., Bielejec, F., Monetta, J., Dellicour, S., Rambaut, A., Suchard, M. A., Baele, G. & Lemey, P., 26 Sept 2022, In: Virus Evolution. 8, 2, p. veac088 5 p., veac088.

    Research output: Contribution to journal › Article › peer-review

    Open Access
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  • The origins and molecular evolution of SARS-CoV-2 lineage B.1.1.7 in the UK

    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., Chand, M., & 9 othersConnor, T., Goodfellow, I., Gupta, R. K., Harrison, E. M., Loman, N., Myers, R., Robertson, D. L., Pybus, O. G. & Rambaut, A., 21 Sept 2022, In: Virus Evolution. 8, 2, 13 p., veac080.

    Research output: Contribution to journal › Article › peer-review

    Open Access
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  • Emergence of SARS-CoV-2 Omicron lineages BA.4 and BA.5 in South Africa

    Tegally, H., Moir, M., Everatt, J., Giovanetti, M., Scheepers, C., Wilkinson, E., Subramoney, K., Makatini, Z., Moyo, S., Amoako, D. G., Baxter, C., Althaus, C. L., Anyaneji, U. J., Kekana, D., Viana, R., Giandhari, J., Lessells, R. J., Maponga, T., Maruapula, D., Choga, W., & 36 othersMatshaba, M., Mbulawa, M. B., Msomi, N., Naidoo, Y., Pillay, S., Sanko, T. J., San, J. E., Scott, L., Singh, L., Magini, N. A., Smith-Lawrence, P., Stevens, W., Dor, G., Tshiabuila, D., Wolter, N., Preiser, W., Treurnicht, F. K., Venter, M., Chiloane, G., Mcintyre, C., O’toole, A., Ruis, C., Peacock, T. P., Roemer, C., Pond, S. L. K., Williamson, C., Pybus, O. G., Bhiman, J. N., Glass, A., Martin, D. P., Jackson, B., Rambaut, A., Laguda-Akingba, O., Gaseitsiwe, S., Von Gottberg, A. & De Oliveira, T., 1 Sept 2022, In: Nature Medicine. 28, 9, p. 1785-1790 18 p.

    Research output: Contribution to journal › Article › peer-review

    Open Access
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  • The Huanan seafood wholesale market in Wuhan was the early epicenter of the COVID-19 pandemic

    Worobey, M., Levy, J. I., Malpica Serrano, L., Crits-Christoph, A., Pekar, J. E., Goldstein, S. A., Rasmussen, A. L., Kraemer, M. U. G., Newman, C., Koopmans, M. P. G., Suchard, M. A., Wertheim, J. O., Lemey, P., Robertson, D. L., Garry, R. F., Holmes, E. C., Rambaut, A. & Andersen, K. G., 26 Aug 2022, In: Science. 377, 6609, p. 951-959 9 p.

    Research output: Contribution to journal › Article › peer-review

    Open Access
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  • The molecular epidemiology of multiple zoonotic origins of SARS-CoV-2

    Pekar, J. E., Magee, A., Parker, E., Moshiri, N., Izhikevich, K., Havens, J. L., Gangavarapu, K., Malpica Serrano, L. M., Crits-Christoph, A., Matteson, N. L., Zeller, M., Levy, J. I., Wang, J. C., Hughes, S., Lee, J., Park, H., Park, M. S., Ching Zi Yan, K., Lin, R. T. P., Mat Isa, M. N., & 9 othersNoor, Y. M., Vasylyeva, T. I., Garry, R. F., Holmes, E. C., Rambaut, A., Suchard, M. A., Andersen, K. G., Worobey, M. & Wertheim, J. O., 26 Aug 2022, In: Science (New York, N.Y.). 377, 6609, p. 960-966 7 p.

    Research output: Contribution to journal › Article › peer-review

    Open Access
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  • Urgent need for a non-discriminatory and non-stigmatizing nomenclature for monkeypox virus

    Happi, C., Adetifa, I., Mbala, P., Njouom, R., Nakoune, E., Happi, A., Ndodo, N., Ayansola, O., Mboowa, G., Bedford, T., Neher, R. A., Roemer, C., Hodcroft, E., Tegally, H., O’toole, Á., Rambaut, A., Pybus, O., Kraemer, M. U. G., Wilkinson, E., Isidro, J., & 13 othersBorges, V., Pinto, M., Gomes, J. P., Freitas, L., Resende, P. C., Lee, R. T. C., Maurer-Stroh, S., Baxter, C., Lessells, R., Ogwell, A. E., Kebede, Y., Tessema, S. K. & De Oliveira, T., 23 Aug 2022, In: PLoS Biology. 20, 8, 6 p., e3001769.

    Research output: Contribution to journal › Article › peer-review

    Open Access
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  • Emergence and widespread circulation of a recombinant SARS-CoV-2 lineage in North America

    Gutierrez, B., Castelán Sánchez, H. G., Candido, D. D. S., Jackson, B., Fleishon, S., Houzet, R., Ruis, C., Delaye, L., Faria, N. R., Rambaut, A., Pybus, O. G. & Escalera-Zamudio, M., 10 Aug 2022, In: Cell Host & Microbe. 30, 8, p. 1-12 12 p.

    Research output: Contribution to journal › Article › peer-review

    Open Access
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  • Shotgun metagenomic sequencing of the first case of monkeypox virus in Brazil, 2022

    Claro, I. M., Romano, C. M., Candido, D. D. S., Lima, E. L. D., Lindoso, J. A. L., Ramundo, M. S., Moreira, F. R. R., Barra, L. A. C., Borges, L. M. S., Medeiros, L. A., Tomishige, M. Y. S., Moutinho, T., Silva, A. J. D. D., Rodrigues, C. C. M., Azevedo, L. C. F. D., Villas-Boas, L. S., Silva, C. A. M. D., Coletti, T. M., Manuli, E. R., O'Toole, A., & 6 othersQuick, J., Loman, N., Rambaut, A., Faria, N. R., Figueiredo-Mello, C. & Sabino, E. C., 24 Jun 2022, In: Revista do Instituto de Medicina Tropical de Sao Paulo. 64, 4 p.

    Research output: Contribution to journal › Article › peer-review

    Open Access
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  • An early warning system for emerging SARS-CoV-2 variants

    Subissi, L., von Gottberg, A., Thukral, L., Worp, N., Oude Munnink, B. B., Rathore, S., Abu-Raddad, L. J., Aguilera, X., Alm, E., Archer, B. N., Attar Cohen, H., Barakat, A., Barclay, W. S., Bhiman, J. N., Caly, L., Chand, M., Chen, M., Cullinane, A., de Oliveira, T., Drosten, C., & 41 othersDruce, J., Effler, P., El Masry, I., Faye, A., Gaseitsiwe, S., Ghedin, E., Grant, R., Haagmans, B. L., Herring, B. L., Iyer, S. S., Kassamali, Z., Kakkar, M., Kondor, R. J., Leite, J. A., Leo, Y-S., Leung, G. M., Marklewitz, M., Moyo, S., Mendez-Rico, J., Melhem, N. M., Munster, V., Nahapetyan, K., Oh, D-Y., Pavlin, B. I., Peacock, T. P., Peiris, M., Peng, Z., Poon, L. L. M., Rambaut, A., Sacks, J., Shen, Y., Siqueira, M. M., Tessema, S. K., Volz, E. M., Thiel, V., van der Werf, S., Briand, S., Perkins, M. D., Van Kerkhove, M. D., Koopmans, M. P. G. & Agrawal, A., 30 May 2022, In: Nature Medicine. 28, 6, p. 1110-1115 6 p.

    Research output: Contribution to journal › Comment/debate › peer-review

  • Making genomic surveillance deliver: A lineage classification and nomenclature system to inform rabies elimination

    Campbell, K., Gifford, R. J., Singer, J., Hill, V., O’toole, A., Rambaut, A., Hampson, K. & Brunker, K., 2 May 2022, In: PLoS Pathogens. 18, 5, e1010023.

    Research output: Contribution to journal › Article › peer-review

    Open Access
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  • Procalcitonin Is Not a Reliable Biomarker of Bacterial Coinfection in People With Coronavirus Disease 2019 Undergoing Microbiological Investigation at the Time of Hospital Admission

    ISARIC4C Investigators, Relph, K. A., Russell, C. D., Fairfield, C. J., Turtle, L., De Silva, T., Siggins, M. K., Drake, T. M., Thwaites, R. S., Abrams, S., Moore, S. C., Hardwick, H. E., Oosthuyzen, W., Harrison, E. M., Docherty, A. B., Openshaw, P. J. M., Baillie, J. K., Semple, M. G. & Ho, A., 1 May 2022, In: Open forum infectious diseases. 9, 5

    Research output: Contribution to journal › Article › peer-review

    Open Access
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  • Tracking SARS-CoV-2 mutations and variants through the COG-UK-Mutation Explorer

    Wright, D. W., Harvey, W. T., Hughes, J., Cox, M., Peacock, T. P., Colquhoun, R., Jackson, B., Orton, R., Nielsen, M., Hsu, N. S., Harrison, E. M., de Silva, T. I., Rambaut, A., Peacock, S. J., Robertson, D. L. & Carabelli, A. M., 18 Mar 2022, In: Virus Evolution. 8, 1, p. 1-14 14 p., veac023.

    Research output: Contribution to journal › Article › peer-review

    Open Access
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  • Pango lineage designation and assignment using SARS-CoV-2 spike gene nucleotide sequences

    O’Toole, Á., Pybus, O. G., Abram, M. E., Kelly, E. J. & Rambaut, A., 11 Feb 2022, In: BMC Genomics. 23, 1, 13 p., 121.

    Research output: Contribution to journal › Article › peer-review

    Open Access
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  • Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa

    Viana, R., Moyo, S., Amoako, D. G., Tegally, H., Scheepers, C., Althaus, C. L., Anyaneji, U. J., Bester, P. A., Boni, M. F., Chand, M., Choga, W. T., Colquhoun, R., Davids, M., Deforche, K., Doolabh, D., du Plessis, L., Engelbrecht, S., Everatt, J., Giandhari, J., Giovanetti, M., & 79 othersHardie, D., Hill, V., Hsiao, N. Y., Iranzadeh, A., Ismail, A., Joseph, C., Joseph, R., Koopile, L., Kosakovsky Pond, S. L., Kraemer, M. U. G., Kuate-Lere, L., Laguda-Akingba, O., Lesetedi-Mafoko, O., Lessells, R. J., Lockman, S., Lucaci, A. G., Maharaj, A., Mahlangu, B., Maponga, T., Mahlakwane, K., Makatini, Z., Marais, G., Maruapula, D., Masupu, K., Matshaba, M., Mayaphi, S., Mbhele, N., Mbulawa, M. B., Mendes, A., Mlisana, K., Mnguni, A., Mohale, T., Moir, M., Moruisi, K., Mosepele, M., Motsatsi, G., Motswaledi, M. S., Mphoyakgosi, T., Msomi, N., Mwangi, P. N., Naidoo, Y., Ntuli, N., Nyaga, M., Olubayo, L., Pillay, S., Radibe, B., Ramphal, Y., Ramphal, U., San, J. E., Scott, L., Shapiro, R., Singh, L., Smith-Lawrence, P., Stevens, W., Strydom, A., Subramoney, K., Tebeila, N., Tshiabuila, D., Tsui, J., van Wyk, S., Weaver, S., Wibmer, C. K., Wilkinson, E., Wolter, N., Zarebski, A. E., Zuze, B., Goedhals, D., Preiser, W., Treurnicht, F., Venter, M., Williamson, C., Pybus, O. G., Bhiman, J., Glass, A., Martin, D. P., Rambaut, A., Gaseitsiwe, S., von Gottberg, A. & de Oliveira, T., 7 Jan 2022, In: Nature. 603, p. 679-686 8 p.

    Research output: Contribution to journal › Article › peer-review

    Open Access
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  • 2021

    The impact of viral mutations on recognition by SARS-CoV-2 specific T cells

    COVID-19 Genomics UK (COG-UK) Consortium, ISARIC4C Investigators, de Silva, T. I., Liu, G., Lindsey, B. B., Dong, D., Moore, S. C., Hsu, N. S., Shah, D., Wellington, D., Mentzer, A. J., Angyal, A., Brown, R., Parker, M. D., Ying, Z., Yao, X., Turtle, L., Dunachie, S., Maini, M. K., Ogg, G., & 4 othersKnight, J. C., Peng, Y., Rowland-Jones, S. L. & Dong, T., 19 Nov 2021, In: iScience. 24, 11, 103353.

    Research output: Contribution to journal › Article › peer-review

    Open Access
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  • Monitoring key epidemiological parameters of SARS-CoV-2 transmission

    Kraemer, M. U. G., Pybus, O. G., Fraser, C., Cauchemez, S., Rambaut, A. & Cowling, B. J., 8 Nov 2021, In: Nature Medicine. 27, 11, p. 1854-1855 2 p.

    Research output: Contribution to journal › Letter › peer-review

  • Genomic sequencing of SARS-CoV-2 in Rwanda reveals the importance of incoming travelers on lineage diversity

    Butera, Y., Mukantwari, E., Artesi, M., Umuringa, J. D., O’Toole, Á. N., Hill, V., Rooke, S., Hong, S. L., Dellicour, S., Majyambere, O., Bontems, S., Boujemla, B., Quick, J., Resende, P. C., Loman, N., Umumararungu, E., Kabanda, A., Murindahabi, M. M., Tuyisenge, P., Gashegu, M., & 16 othersRwabihama, J. P., Sindayiheba, R., Gikic, D., Souopgui, J., Ndifon, W., Rutayisire, R., Gatare, S., Mpunga, T., Ngamije, D., Bours, V., Rambaut, A., Nsanzimana, S., Baele, G., Durkin, K., Mutesa, L. & Rujeni, N., 29 Sept 2021, In: Nature Communications. 12, 1, 5705.

    Research output: Contribution to journal › Article › peer-review

    Open Access
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  • A prenylated dsRNA sensor protects against severe COVID-19

    ISARIC4C Investigators, 28 Sept 2021, (E-pub ahead of print) In: Science (New York, N.Y.). eabj3624.

    Research output: Contribution to journal › Article › peer-review

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  • The origins of SARS-CoV-2: A critical review

    Holmes, E. C., Goldstein, S. A., Rasmussen, A. L., Robertson, D. L., Crits-Christoph, A., Wertheim, J. O., Anthony, S. J., Barclay, W. S., Boni, M. F., Doherty, P. C., Farrar, J., Geoghegan, J. L., Jiang, X., Leibowitz, J. L., Neil, S. J. D., Skern, T., Weiss, S. R., Worobey, M., Andersen, K. G., Garry, R. F., & 1 othersRambaut, A., 16 Sept 2021, In: Cell. 184, 19, p. 4848-4856 9 p.

    Research output: Contribution to journal › Review article › peer-review

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  • Resurgence of Ebola virus in 2021 in Guinea suggests a new paradigm for outbreaks

    Keita, A. K., Koundouno, F. R., Faye, M., Düx, A., Hinzmann, J., Diallo, H., Ayouba, A., Le Marcis, F., Soropogui, B., Ifono, K., Diagne, M. M., Sow, M. S., Bore, J. A., Calvignac-Spencer, S., Vidal, N., Camara, J., Keita, M. B., Renevey, A., Diallo, A., Soumah, A. K., & 51 othersMillimono, S. L., Mari-Saez, A., Diop, M., Doré, A., Soumah, F. Y., Kourouma, K., Vielle, N. J., Loucoubar, C., Camara, I., Kourouma, K., Annibaldis, G., Bah, A., Thielebein, A., Pahlmann, M., Pullan, S. T., Carroll, M. W., Quick, J., Formenty, P., Legand, A., Pietro, K., Wiley, M. R., Tordo, N., Peyrefitte, C., McCrone, J. T., Rambaut, A., Sidibé, Y., Barry, M. D., Kourouma, M., Saouromou, C. D., Condé, M., Baldé, M., Povogui, M., Keita, S., Diakite, M., Bah, M. S., Sidibe, A., Diakite, D., Sako, F. B., Traore, F. A., Ki-Zerbo, G. A., Lemey, P., Günther, S., Kafetzopoulou, L. E., Sall, A. A., Delaporte, E., Duraffour, S., Faye, O., Leendertz, F. H., Peeters, M., Toure, A. & Magassouba, N. F., 15 Sept 2021, In: Nature. 597, 7877, p. 539-543 5 p.

    Research output: Contribution to journal › Article › peer-review

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  • Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2

    O'Toole, Á., Hill, V., Pybus, O. G., Watts, A., Bogoch, I. I., Khan, K., Messina, J. P., Tegally, H., Lessells, R. R., Giandhari, J., Pillay, S., Tumedi, K. A., Nyepetsi, G., Kebabonye, M., Matsheka, M., Mine, M., Tokajian, S., Hassan, H., Salloum, T., Merhi, G., & 69 othersKoweyes, J., Geoghegan, J. L., De Ligt, J., Ren, X., Storey, M., Freed, N. E., Pattabiraman, C., Prasad, P., Desai, A. S., Vasanthapuram, R., Schulz, T. F., Steinbrück, L., Stadler, T., Parisi, A., Bianco, A., García De Viedma, D., Buenestado-Serrano, S., Borges, V., Isidro, J., Duarte, S., Gomes, J. P., Zuckerman, N. S., Mandelboim, M., Mor, O., Seemann, T., Arnott, A., Draper, J., Gall, M., Rawlinson, W., Deveson, I., Schlebusch, S., McMahon, J., Leong, L., Lim, C. K., Chironna, M., Loconsole, D., Bal, A., Josset, L., Holmes, E., St. George, K., Lasek-nesselquist, E., Sikkema, R. S., Oude Munnink, B., Koopmans, M., Brytting, M., Sudha Rani, V., Pavani, S., Smura, T., Heim, A., Kurkela, S., Umair, M., Salman, M., Bartolini, B., Rueca, M., Drosten, C., Wolff, T., Silander, O., Eggink, D., Reusken, C., Vennema, H., Park, A., Carrington, C., Sahadeo, N., Carr, M., Gonzalez, G., De Oliveira, T., Faria, N., Rambaut, A. & Kraemer, M. U. G., 15 Sept 2021, In: Wellcome Open Research. 6, 121 p.

    Research output: Contribution to journal › Article › peer-review

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  • Spatiotemporal invasion dynamics of SARS-CoV-2 lineage B.1.1.7 emergence

    Kraemer, M. U. G., Hill, V., Ruis, C., Dellicour, S., Bajaj, S., McCrone, J. T., Baele, G., Parag, K. V., Battle, A. L., Gutierrez, B., Jackson, B., Colquhoun, R., O’Toole, Á., Klein, B., Vespignani, A., Volz, E., Faria, N. R., Aanensen, D. M., Loman, N. J., Du Plessis, L., & 4 othersCauchemez, S., Rambaut, A., Scarpino, S. V. & Pybus, O. G., 20 Aug 2021, In: Science. 373, 6557, p. 889-895 7 p.

    Research output: Contribution to journal › Article › peer-review

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  • Generation and transmission of interlineage recombinants in the SARS-CoV-2 pandemic

    Jackson, B., Boni, M. F., Bull, M. J., Colleran, A., Colquhoun, R. M., Darby, A. C., Haldenby, S., Hill, V., Lucaci, A., McCrone, J. T., Nicholls, S. M., O'Toole, Á., Pacchiarini, N., Poplawski, R., Scher, E., Todd, F., Webster, H. J., Whitehead, M., Wierzbicki, C., Loman, N. J., & 4 othersConnor, T. R., Robertson, D. L., Pybus, O. G. & Rambaut, A., 17 Aug 2021, In: Cell. 184, 20, p. 5179-5188.e8 10 p.

    Research output: Contribution to journal › Article › peer-review

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  • Relax, keep walking - A practical guide to continuous phylogeographic Inference with BEAST

    Dellicour, S., Gill, M. S., Faria, N. R., Rambaut, A., Pybus, O. G., Suchard, M. A. & Lemey, P., 1 Aug 2021, In: Molecular Biology and Evolution. 38, 8, p. 3486-3493 8 p.

    Research output: Contribution to journal › Article › peer-review

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  • Assignment of epidemiological lineages in an emerging pandemic using the pangolin tool

    O’Toole, Á., Scher, E., Underwood, A., Jackson, B., Hill, V., McCrone, J. T., Colquhoun, R., Ruis, C., Abu-Dahab, K., Taylor, B., Yeats, C., Du Plessis, L., Maloney, D., Medd, N., Attwood, S. W., Aanensen, D. M., Holmes, E. C., Pybus, O. G. & Rambaut, A., 30 Jul 2021, In: Virus Evolution. 9 p., veab064.

    Research output: Contribution to journal › Article › peer-review

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  • Mapping the human genetic architecture of COVID-19

    COVID-19 Host Genetics Initiative, Baillie, J. K., Wilson, J. F., Bulteel, N., Hayward, C., Klaric, L., Porteous, D. J., Russell, C. D., Tenesa, A., Norman, L., Scott-Brown, J. & Swann, O., 8 Jul 2021, (E-pub ahead of print) In: Nature.

    Research output: Contribution to journal › Article › peer-review

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  • CLIMB-COVID: Continuous integration supporting decentralised sequencing for SARS-CoV-2 genomic surveillance

    Nicholls, S. M., Poplawski, R., Bull, M. J., Underwood, A., Chapman, M., Abu-Dahab, K., Taylor, B., Colquhoun, R. M., Rowe, W. P. M., Jackson, B., Hill, V., O’Toole, Á., Rey, S., Southgate, J., Amato, R., Livett, R., Gonçalves, S., Harrison, E. M., Peacock, S. J., Aanensen, D. M., & 3 othersRambaut, A., Connor, T. R. & Loman, N. J., 1 Jul 2021, In: Genome Biology. 22, 196, 21 p.

    Research output: Contribution to journal › Editorial › peer-review

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  • SARS-CoV-2 variants, spike mutations and immune escape

    Harvey, W. T., Carabelli, A. M., Jackson, B., Gupta, R. K., Thomson, E. C., Harrison, E. M., Ludden, C., Reeve, R., Rambaut, A., Peacock, S. J. & Robertson, D., 1 Jul 2021, In: Nature Reviews Microbiology. 19, 7, p. 409-424 15 p.

    Research output: Contribution to journal › Review article › peer-review

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  • Emergence and spread of a SARS-CoV-2 lineage A variant (A.23.1) with altered spike protein in Uganda

    Bugembe, D. L., Phan, M. V. T., Ssewanyana, I., Semanda, P., Nansumba, H., Dhaala, B., Nabadda, S., O’Toole, Á. N., Rambaut, A., Kaleebu, P. & Cotten, M., 23 Jun 2021, In: Nature Microbiology. 6, p. 1094-1101 7 p.

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  • SARS-CoV-2 Variants of Interest and Concern naming scheme conducive for global discourse

    Konings, F., Perkins, M. D., Kuhn, J. H., Pallen, M. J., Alm, E. J., Archer, B. N., Barakat, A., Bedford, T., Bhiman, J. N., Caly, L., Carter, L. L., Cullinane, A., De Oliveira, T., Druce, J., El Masry, I., Evans, R., Gao, G. F., Gorbalenya, A. E., Hamblion, E., Herring, B. L., & 27 othersHodcroft, E., Holmes, E. C., Kakkar, M., Khare, S., Koopmans, M. P. G., Korber, B., Leite, J., MacCannell, D., Marklewitz, M., Maurer-Stroh, S., Rico, J. A. M., Munster, V. J., Neher, R., Munnink, B. O., Pavlin, B. I., Peiris, M., Poon, L., Pybus, O., Rambaut, A., Resende, P., Subissi, L., Thiel, V., Tong, S., Van Der Werf, S., Von Gottberg, A., Ziebuhr, J. & Van Kerkhove, M. D., 9 Jun 2021, In: Nature Microbiology. 6, p. 821-823 3 p.

    Research output: Contribution to journal › Comment/debate › peer-review

  • Changes in in-hospital mortality in the first wave of COVID-19: a multicentre prospective observational cohort study using the WHO Clinical Characterisation Protocol UK

    ISARIC investigators, 1 May 2021, In: The Lancet Respiratory Medicine.

    Research output: Contribution to journal › Article › peer-review

    Open Access
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  • Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil

    Faria, N. R., Mellan, T. A., Whittaker, C., Claro, I. M., Candido, D. D. S., Mishra, S., Crispim, M. A. E., Sales, F. C. S., Hawryluk, I., McCrone, J. T., Hulswit, R. J. G., Franco, L. A. M., Ramundo, M. S., de Jesus, J. G., Andrade, P. S., Coletti, T. M., Ferreira, G. M., Silva, C. A. M., Manuli, E. R., Pereira, R. H. M., & 52 othersPeixoto, P. S., Kraemer, M. U. G., Gaburo, N., Camilo, C. D. C., Hoeltgebaum, H., Souza, W. M., Rocha, E. C., de Souza, L. M., de Pinho, M. C., Araujo, L. J. T., Malta, F. S. V., de Lima, A. B., Silva, J. D. P., Zauli, D. A. G., Ferreira, A. C. D. S., Schnekenberg, R. P., Laydon, D. J., Walker, P. G. T., Schlüter, H. M., Dos Santos, A. L. P., Vidal, M. S., Del Caro, V. S., Filho, R. M. F., Dos Santos, H. M., Aguiar, R. S., Proença-Modena, J. L., Nelson, B., Hay, J. A., Monod, M., Miscouridou, X., Coupland, H., Sonabend, R., Vollmer, M., Gandy, A., Prete, C. A., Nascimento, V. H., Suchard, M. A., Bowden, T. A., Pond, S. L. K., Wu, C-H., Ratmann, O., Ferguson, N. M., Dye, C., Loman, N. J., Lemey, P., Rambaut, A., Fraiji, N. A., Carvalho, M. D. P. S. S., Pybus, O. G., Flaxman, S., Bhatt, S. & Sabino, E. C., 14 Apr 2021, In: Science. 14 p., eabh2644.

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