Andrew Rambaut

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  • 2023

    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.

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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.

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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.

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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.

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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.

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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.

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  • 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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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  • 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.

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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

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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.

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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.

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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.

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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.

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  • 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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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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  • 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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  • Ebola virus transmission initiated by systemic ebola virus disease relapse

    Mbala-Kingebeni, P., Pratt, C., Ruffin, M. M., Pauthner, M. G., Bile, F., Rambaut, A., Nkuba Ndaye, A., Black, A., Kinganda Lusamaki, E., Faye, M., Aziza, A., Diagne, M. M., Mukadi, D., White, B., Hadfield, J., Gangavarapu, K., Bisento, N., Kazadi, D., Nsunda, B., Akonga, M., & 31 othersTshiani, O., Misasi, J., Ploquin, A., Epaso, V., Sana Paka, E., N’kasar, Y. T. T., Mambu, F., Edidi, F., Matondo, M., Bula Bula, J., Diallo, B., Keita, M., Darnycka Belizaire, M. R., Fall, I. S., Yam, A., Sabue, M., Rimion, A. W., Salfati, E. L., Torkamani, A., Suchard, M. A., Crozier, I., Hensley, LE., Rambaut, A., Faye, O., Sall, A. A., Sullivan, N. J., Bedford, T., Andersen, K. G., Wiley, M. R., Ahuka-Mundeke, S. & Muyembe-Tamfum, J-J., 1 Apr 2021, (E-pub ahead of print) In: New England Journal of Medicine. 384, p. 1240-1247 8 p.

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  • Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England

    Volz, E. M., Mishra, S., Chand, M., Barrett, J., Johnson, R., Geidelberg, L., Hinsley, W. R., Laydon, D. J., Dabrera, G., O'Toole, Á., Amato, R., Ragonnet-Cronin, M., Harrison, I., Jackson, B., Ariani, C. V., Boyd, O., Loman, N. J., McCrone, J. T., Gonçalves, S., Jorgensen, D., & 14 othersMyers, R., Hill, V., Jackson, D. K., Gaythorpe, K., Groves, N., Sillitoe, J., Kwiatkowski, D. P., Flaxman, S., Ratmann, O., Bhatt, S., Hopkins, S., Gandy, A., Rambaut, A. & Ferguson, N. M., 25 Mar 2021, In: Nature. 593, p. 266-269 4 p.

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  • Establishment & lineage dynamics of the SARS-CoV-2 epidemic in the UK

    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., Watts, A., & 6 othersBogoch, I. I., Khan, K., Aanensen, D. M., Kraemer, M. U. G., Rambaut, A. & Pybus, O. G., 12 Feb 2021, In: Science. 371, 6530, p. 708-712 5 p.

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  • Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity

    ISARIC4C Investigators, 28 Jan 2021, (E-pub ahead of print) In: Cell.

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  • 2020

    Genomic epidemiology reveals multiple introductions of SARS-CoV-2 from mainland Europe into Scotland

    da Silva Filipe, A., Shepherd, J. G., Williams, T., Hughes, J., Aranday-Cortes, E., Asamaphan, P., Ashraf, S., Balcazar, C., Brunker, K., Campbell, A., Carmichael, S., Davis, C., Dewar, R., Gallagher, M. D., Gunson, R., Hill, V., Ho, A., Jackson, B., James, E., Jesudason, N., & 30 othersJohnson, N., McWilliam Leitch, E. C., Li, K., MacLean, A., Mair, D., McAllister, D. A., McCrone, J. T., McDonald, S. E., McHugh, M. P., Morris, A. K., Nichols, J., Niebel, M., Nomikou, K., Orton, R. J., O'Toole, Á., Palmarini, M., Parcell, B. J., Parr, Y. A., Rambaut, A., Rooke, S., Shaaban, S., Shah, R., Singer, J. B., Smollett, K., Starinskij, I., Tong, L., Wastnedge, E., Holden, M. T. G., Robertson, D. L. & Templeton, K., 21 Dec 2020, In: Nature Microbiology. 6, 1, p. 112-122 11 p.

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  • Determinants of dengue virus dispersal in the Americas

    Allicock, O. M., Sahadeo, N., Lemey, P., Auguste, A. J., Suchard, M. A., Rambaut, A. & Carrington, C. V. F., 2 Dec 2020, In: Virus Evolution. 6, 2, 13 p., veaa074.

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  • Evaluating the effects of SARS-CoV-2 spike mutation D614G on transmissibility and pathogenicity

    Volz, E. M., 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., Filipe, A. D. S., Shepherd, J., Pascall, D. J., Shah, R., Jesudason, N., Li, K., Jarrett, R. F., & 11 othersPacchiarini, N., Bull, M., Geidelberg, L., Siveroni, I., Goodfellow, I., Loman, N. J., Pybus, O. G., Robertson, D. L., Thomson, E. C., Rambaut, A. & Connor, T. R., 19 Nov 2020, In: Cell. 184, 1, p. 64-75.E11 24 p.

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  • A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology

    Rambaut, A., Holmes, E. C., O'Toole, Á., Hill, V., McCrone, JT., Ruis, C., du Plessis, L. & Pybus, O. G., 1 Nov 2020, In: Nature Microbiology. 5, p. 1403-1407 5 p.

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  • COVID-19 in health-care workers in three hospitals in the south of the Netherlands: A cross-sectional study

    Sikkema, R. S., Pas, S. D., Nieuwenhuijse, D. F., O'Toole, Á., Verweij, J. J., van der Linden, A., Chestakova, I., Schapendonk, C., Pronk, M., Lexmond, P., Bestebroer, T., Overmars, R. J., van Nieuwkoop, S., van den Bijllaardt, W., Bentvelsen, R. G., van Rijen, M. M. L., Buiting, A. G. M., van Oudheusden, A. J. G., Diederen, B. M., Bergmans, A. M. C., & 8 othersvan der Eijk, A., Molenkamp, R., Rambaut, A., Timen, A., Kluytmans, J. A. J. W., Oude Munnink, B. B., Kluytmans van den Bergh, M. F. Q. & Koopmans, M. P. G., 1 Nov 2020, In: The Lancet Infectious Diseases. 20, 11, p. 1273-1280 8 p.

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  • Early insights from statistical and mathematical modeling of key epidemiologic parameters of COVID-19

    Biggerstaff, M., Cowling, B. J., Cucunubá, Z. M., Dinh, L., Ferguson, N. M., Gao, H., Hill, V., Imai, N., Johansson, M. A., Kada, S., Morgan, O., Pastore y Piontti, A., Polonsky, J. A., Venkata Prasad, P., Quandelacy, T. M., Rambaut, A., Tappero, J. W., Vandemaele, K. A., Vespignani, A., Warmbrod, K. L., & 1 othersWong, J. Y., 1 Nov 2020, In: Emerging Infectious Diseases. 26, 11

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  • Accommodating individual travel history and unsampled diversity in Bayesian phylogeographic inference of SARS-CoV-2

    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., 9 Oct 2020, In: Nature Communications. 11, 5110.

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  • Gradients do grow on trees: A linear-time O(N)-dimensional gradient for statistical phylogenetics

    Ji, X., Zhang, Z., Holbrook, A., Nishimura, A., Baele, G., Rambaut, A., Lemey, P. & Suchard, M. A., 1 Oct 2020, In: Molecular Biology and Evolution. 37, 10, p. 3047-3060 14 p.

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  • The emergence of SARS-CoV-2 in Europe and North America

    Worobey, M., Pekar, J., Larsen, B. B., Nelson, M. I., Hill, V., Joy, J. B., Rambaut, A., Suchard, M. A., Wertheim, J. O. & Lemey, P., 10 Sept 2020, In: Science. 370, 6516, p. 564-570 7 p.

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  • Identification of common deletions in the spike protein of severe acute respiratory syndrome coronavirus 2

    Liu, Z., Zheng, H., Lin, H., Li, M., Yuan, R., Peng, J., Xiong, Q., Sun, J., Li, B., Wu, J., Yi, L., Peng, X., Zhang, H., Zhang, W., Hulswit, R. J. G., Loman, N., Rambaut, A., Ke, C., Bowden, T. A., Pybus, O. G., & 1 othersLu, J., 1 Sept 2020, In: Journal of Virology. 94, 17, 28 p., e00790-20.

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  • Rapid and sensitive direct detection and identification of poliovirus from stool and environmental surveillance samples using nanopore sequencing

    Shaw, A. G., Majumdar, M., Troman, C., O'toole, Á., Benny, B., Abraham, D., Praharaj, I., Kang, G., Sharif, S., Alam, M. M., Shaukat, S., Angez, M., Khurshid, A., Mahmood, N., Arshad, Y., Rehman, L., Mujtaba, G., Akthar, R., Salman, M., Klapsa, D., & 6 othersHajarha, Y., Asghar, H., Bandyopadhyay, A., Rambaut, A., Martin, J. & Grassly, N., 24 Aug 2020, In: Journal of Clinical Microbiology. 58, 9, 13 p., e00920-20.

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  • Temporal signal and the phylodynamic threshold of SARS-CoV-2

    Duchene, S., Featherstone, L., Haritopoulou-Sinanidou, M., Rambaut, A., Lemey, P. & Baele, G., 19 Aug 2020, In: Virus Evolution. 6, 2, 8 p., veaa061.

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