Verity Hill

• Chrispin Chaguza
• Kien Pham
• Nathan Grubaugh
• Scott Roberts
• Wade Schulz

Arboviruses; Dengue Virus; Disease Outbreaks; Encephalitis Virus, Eastern Equine; Epidemiology; Biological Evolution; Phylogeny; RNA Viruses; West Nile virus; Molecular Epidemiology; Genomics; Ebolavirus

Emerging Infectious Diseases; Epidemiology Methods; Evolution; Global Health; Viruses; Neglected Tropical Diseases; Mosquito-borne Diseases; COVID-19

• Accelerated SARS-CoV-2 intrahost evolution leading to distinct genotypes during chronic infection.Chaguza C, Hahn AM, Petrone ME, Zhou S, Ferguson D, Breban MI, Pham K, Peña-Hernández MA, Castaldi C, Hill V, Schulz W, Swanstrom RI, Roberts SC, Grubaugh ND. Accelerated SARS-CoV-2 intrahost evolution leading to distinct genotypes during chronic infection. MedRxiv : The Preprint Server For Health Sciences 2022 PMID: 35794895, PMCID: PMC9258298, DOI: 10.1101/2022.06.29.22276868.
• Making genomic surveillance deliver: A lineage classification and nomenclature system to inform rabies elimination.Campbell K, Gifford RJ, Singer J, Hill V, O'Toole A, Rambaut A, Hampson K, Brunker K. Making genomic surveillance deliver: A lineage classification and nomenclature system to inform rabies elimination. PLoS Pathogens 2022, 18: e1010023. PMID: 35500026, DOI: 10.1371/journal.ppat.1010023.
• Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa.Viana R, Moyo S, Amoako DG, Tegally H, Scheepers C, Althaus CL, Anyaneji UJ, Bester PA, Boni MF, Chand M, Choga WT, Colquhoun R, Davids M, Deforche K, Doolabh D, du Plessis L, Engelbrecht S, Everatt J, Giandhari J, Giovanetti M, Hardie D, Hill V, Hsiao NY, Iranzadeh A, Ismail A, Joseph C, Joseph R, Koopile L, Kosakovsky Pond SL, Kraemer MUG, Kuate-Lere L, Laguda-Akingba O, Lesetedi-Mafoko O, Lessells RJ, Lockman S, Lucaci AG, Maharaj A, Mahlangu B, Maponga T, Mahlakwane K, Makatini Z, Marais G, Maruapula D, Masupu K, Matshaba M, Mayaphi S, Mbhele N, Mbulawa MB, Mendes A, Mlisana K, Mnguni A, Mohale T, Moir M, Moruisi K, Mosepele M, Motsatsi G, Motswaledi MS, Mphoyakgosi T, Msomi N, Mwangi PN, Naidoo Y, Ntuli N, Nyaga M, Olubayo L, Pillay S, Radibe B, Ramphal Y, Ramphal U, San JE, 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 CK, Wilkinson E, Wolter N, Zarebski AE, Zuze B, Goedhals D, Preiser W, Treurnicht F, Venter M, Williamson C, Pybus OG, Bhiman J, Glass A, Martin DP, Rambaut A, Gaseitsiwe S, von Gottberg A, de Oliveira T. Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa. Nature 2022, 603: 679-686. PMID: 35042229, PMCID: PMC8942855, DOI: 10.1038/s41586-022-04411-y.
• Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission.Aggarwal D, Warne B, Jahun AS, Hamilton WL, Fieldman T, du Plessis L, Hill V, Blane B, Watkins E, Wright E, Hall G, Ludden C, Myers R, Hosmillo M, Chaudhry Y, Pinckert ML, Georgana I, Izuagbe R, Leek D, Nsonwu O, Hughes GJ, Packer S, Page AJ, Metaxaki M, Fuller S, Weale G, Holgate J, Brown CA, Howes R, McFarlane D, Dougan G, Pybus OG, Angelis D, Maxwell PH, Peacock SJ, Weekes MP, Illingworth C, Harrison EM, Matheson NJ, Goodfellow IG. Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission. Nature Communications 2022, 13: 751. PMID: 35136068, PMCID: PMC8826310, DOI: 10.1038/s41467-021-27942-w.
• Progress and challenges in virus genomic epidemiology.Hill V, Ruis C, Bajaj S, Pybus OG, Kraemer MUG. Progress and challenges in virus genomic epidemiology. Trends In Parasitology 2021, 37: 1038-1049. PMID: 34620561, DOI: 10.1016/j.pt.2021.08.007.
• Generation and transmission of interlineage recombinants in the SARS-CoV-2 pandemic.Jackson B, Boni MF, Bull MJ, Colleran A, Colquhoun RM, Darby AC, Haldenby S, Hill V, Lucaci A, McCrone JT, Nicholls SM, O'Toole Á, Pacchiarini N, Poplawski R, Scher E, Todd F, Webster HJ, Whitehead M, Wierzbicki C, Loman NJ, Connor TR, Robertson DL, Pybus OG, Rambaut A. Generation and transmission of interlineage recombinants in the SARS-CoV-2 pandemic. Cell 2021, 184: 5179-5188.e8. PMID: 34499854, PMCID: PMC8367733, DOI: 10.1016/j.cell.2021.08.014.
• Genomic sequencing of SARS-CoV-2 in Rwanda reveals the importance of incoming travelers on lineage diversity.Butera Y, Mukantwari E, Artesi M, Umuringa JD, O'Toole ÁN, Hill V, Rooke S, Hong SL, Dellicour S, Majyambere O, Bontems S, Boujemla B, Quick J, Resende PC, Loman N, Umumararungu E, Kabanda A, Murindahabi MM, Tuyisenge P, Gashegu M, Rwabihama JP, 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. Genomic sequencing of SARS-CoV-2 in Rwanda reveals the importance of incoming travelers on lineage diversity. Nature Communications 2021, 12: 5705. PMID: 34588460, PMCID: PMC8481346, DOI: 10.1038/s41467-021-25985-7.
• Spatiotemporal invasion dynamics of SARS-CoV-2 lineage B.1.1.7 emergence.Kraemer MUG, Hill V, Ruis C, Dellicour S, Bajaj S, McCrone JT, Baele G, Parag KV, Battle AL, Gutierrez B, Jackson B, Colquhoun R, O'Toole Á, Klein B, Vespignani A, Volz E, Faria NR, Aanensen DM, Loman NJ, du Plessis L, Cauchemez S, Rambaut A, Scarpino SV, Pybus OG. Spatiotemporal invasion dynamics of SARS-CoV-2 lineage B.1.1.7 emergence. Science (New York, N.Y.) 2021, 373: 889-895. PMID: 34301854, DOI: 10.1126/science.abj0113.
• CLIMB-COVID: continuous integration supporting decentralised sequencing for SARS-CoV-2 genomic surveillance.Nicholls SM, Poplawski R, Bull MJ, Underwood A, Chapman M, Abu-Dahab K, Taylor B, Colquhoun RM, Rowe WPM, Jackson B, Hill V, O'Toole Á, Rey S, Southgate J, Amato R, Livett R, Gonçalves S, Harrison EM, Peacock SJ, Aanensen DM, Rambaut A, Connor TR, Loman NJ. CLIMB-COVID: continuous integration supporting decentralised sequencing for SARS-CoV-2 genomic surveillance. Genome Biology 2021, 22: 196. PMID: 34210356, PMCID: PMC8247108, DOI: 10.1186/s13059-021-02395-y.
• Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK.du Plessis L, McCrone JT, Zarebski AE, Hill V, Ruis C, Gutierrez B, Raghwani J, Ashworth J, Colquhoun R, Connor TR, Faria NR, Jackson B, Loman NJ, O'Toole Á, Nicholls SM, Parag KV, Scher E, Vasylyeva TI, Volz EM, Watts A, Bogoch II, Khan K, Aanensen DM, Kraemer MUG, Rambaut A, Pybus OG. Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK. Science (New York, N.Y.) 2021, 371: 708-712. PMID: 33419936, PMCID: PMC7877493, DOI: 10.1126/science.abf2946.
• Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity.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, Goodfellow I, Loman NJ, Pybus OG, Robertson DL, Thomson EC, Rambaut A, Connor TR. Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity. Cell 2021, 184: 64-75.e11. PMID: 33275900, PMCID: PMC7674007, DOI: 10.1016/j.cell.2020.11.020.
• Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2 with grinch.O'Toole Á, Hill V, Pybus OG, Watts A, Bogoch II, Khan K, Messina JP, Tegally H, Lessells RR, Giandhari J, Pillay S, Tumedi KA, Nyepetsi G, Kebabonye M, Matsheka M, Mine M, Tokajian S, Hassan H, Salloum T, Merhi G, Koweyes J, Geoghegan JL, de Ligt J, Ren X, Storey M, Freed NE, Pattabiraman C, Prasad P, Desai AS, Vasanthapuram R, Schulz TF, Steinbrück L, Stadler T, Parisi A, Bianco A, García de Viedma D, Buenestado-Serrano S, Borges V, Isidro J, Duarte S, Gomes JP, Zuckerman NS, Mandelboim M, Mor O, Seemann T, Arnott A, Draper J, Gall M, Rawlinson W, Deveson I, Schlebusch S, McMahon J, Leong L, Lim CK, Chironna M, Loconsole D, Bal A, Josset L, Holmes E, St George K, Lasek-Nesselquist E, Sikkema RS, 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 MUG. Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2 with grinch. Wellcome Open Research 2021, 6: 121. PMID: 34095513, PMCID: PMC8176267.2, DOI: 10.12688/wellcomeopenres.16661.2.
• Assignment of epidemiological lineages in an emerging pandemic using the pangolin tool.O'Toole Á, Scher E, Underwood A, Jackson B, Hill V, McCrone JT, Colquhoun R, Ruis C, Abu-Dahab K, Taylor B, Yeats C, du Plessis L, Maloney D, Medd N, Attwood SW, Aanensen DM, Holmes EC, Pybus OG, Rambaut A. Assignment of epidemiological lineages in an emerging pandemic using the pangolin tool. Virus Evolution 2021, 7: veab064. PMID: 34527285, PMCID: PMC8344591, DOI: 10.1093/ve/veab064.
• A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology.Rambaut A, Holmes EC, O'Toole Á, Hill V, McCrone JT, Ruis C, du Plessis L, Pybus OG. A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nature Microbiology 2020, 5: 1403-1407. PMID: 32669681, PMCID: PMC7610519, DOI: 10.1038/s41564-020-0770-5.
• Early Insights from Statistical and Mathematical Modeling of Key Epidemiologic Parameters of COVID-19.Biggerstaff M, Cowling BJ, Cucunubá ZM, Dinh L, Ferguson NM, Gao H, Hill V, Imai N, Johansson MA, Kada S, Morgan O, Pastore Y Piontti A, Polonsky JA, Prasad PV, Quandelacy TM, Rambaut A, Tappero JW, Vandemaele KA, Vespignani A, Warmbrod KL, Wong JY. Early Insights from Statistical and Mathematical Modeling of Key Epidemiologic Parameters of COVID-19. Emerging Infectious Diseases 2020, 26: e1-e14. PMID: 32917290, PMCID: PMC7588530, DOI: 10.3201/eid2611.201074.
• The emergence of SARS-CoV-2 in Europe and North America.Worobey M, Pekar J, Larsen BB, Nelson MI, Hill V, Joy JB, Rambaut A, Suchard MA, Wertheim JO, Lemey P. The emergence of SARS-CoV-2 in Europe and North America. Science (New York, N.Y.) 2020, 370: 564-570. PMID: 32912998, PMCID: PMC7810038, DOI: 10.1126/science.abc8169.
• Accommodating individual travel history and unsampled diversity in Bayesian phylogeographic inference of SARS-CoV-2.Lemey P, Hong SL, Hill V, Baele G, Poletto C, Colizza V, O'Toole Á, McCrone JT, Andersen KG, Worobey M, Nelson MI, Rambaut A, Suchard MA. Accommodating individual travel history and unsampled diversity in Bayesian phylogeographic inference of SARS-CoV-2. Nature Communications 2020, 11: 5110. PMID: 33037213, PMCID: PMC7547076, DOI: 10.1038/s41467-020-18877-9.
• Genomic Epidemiology of SARS-CoV-2 in Guangdong Province, China.Lu J, du Plessis L, Liu Z, Hill V, Kang M, Lin H, Sun J, François S, Kraemer MUG, Faria NR, McCrone JT, Peng J, Xiong Q, Yuan R, Zeng L, Zhou P, Liang C, Yi L, Liu J, Xiao J, Hu J, Liu T, Ma W, Li W, Su J, Zheng H, Peng B, Fang S, Su W, Li K, Sun R, Bai R, Tang X, Liang M, Quick J, Song T, Rambaut A, Loman N, Raghwani J, Pybus OG, Ke C. Genomic Epidemiology of SARS-CoV-2 in Guangdong Province, China. Cell 2020, 181: 997-1003.e9. PMID: 32359424, PMCID: PMC7192124, DOI: 10.1016/j.cell.2020.04.023.
• Bayesian estimation of past population dynamics in BEAST 1.10 using the Skygrid coalescent model.Hill V, Baele G. Bayesian estimation of past population dynamics in BEAST 1.10 using the Skygrid coalescent model. Molecular Biology And Evolution 2019 PMID: 31364710, PMCID: PMC6805224, DOI: 10.1093/molbev/msz172.