COVFlow: phylodynamics analyses of viruses from selected SARS-CoV-2 genome sequences

10.24072/pcjournal.333 - Peer Community Journal, Volume 3 (2023), article no. e101.

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Phylodynamic analyses can generate important and timely data to optimise public health response to SARS-CoV-2 outbreaks and epidemics. However, their implementation is hampered by the massive amount of sequence data and the difficulty to parameterise dedicated software packages. We introduce the COVFlow pipeline, accessible at, which allows a user to select sequences from the Global Initiative on Sharing Avian Influenza Data (GISAID) database according to user-specified criteria, to perform basic phylogenetic analyses, and to produce an XML file to be run in the Beast2 software package. We illustrate the potential of this tool by studying two sets of sequences from the Delta variant in two French regions. This pipeline can facilitate the use of virus sequence data at the local level, for instance, to track the dynamics of a particular lineage or variant in a region of interest.  

Published online:
DOI: 10.24072/pcjournal.333
Keywords: COVID-19, molecular epidemiology, sequence database, phylogenetics, public health
Danesh, Gonché 1; Boennec, Corentin 1; Verdurme, Laura 2; Roussel, Mathilde 2; Trombert-Paolantoni, Sabine 2; Visseaux, Benoit 2; Haim-Boukobza, Stéphanie 2; Alizon, Samuel 1, 3

1 MIVEGEC, CNRS, IRD, Université de Montpellier, France
2 Laboratoire CERBA, Saint Ouen L’Aumône, France
3 Center for Interdisciplinary Research in Biology (CIRB), College de France, CNRS, INSERM, Université PSL, Paris, France
License: CC-BY 4.0
Copyrights: The authors retain unrestricted copyrights and publishing rights
     author = {Danesh, Gonch\'e and Boennec, Corentin and Verdurme, Laura and Roussel, Mathilde and Trombert-Paolantoni, Sabine and Visseaux, Benoit and Haim-Boukobza, St\'ephanie and Alizon, Samuel},
     title = {COVFlow: phylodynamics analyses of viruses from selected {SARS-CoV-2} genome sequences},
     journal = {Peer Community Journal},
     eid = {e101},
     publisher = {Peer Community In},
     volume = {3},
     year = {2023},
     doi = {10.24072/pcjournal.333},
     language = {en},
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%A Roussel, Mathilde
%A Trombert-Paolantoni, Sabine
%A Visseaux, Benoit
%A Haim-Boukobza, Stéphanie
%A Alizon, Samuel
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Danesh, Gonché; Boennec, Corentin; Verdurme, Laura; Roussel, Mathilde; Trombert-Paolantoni, Sabine; Visseaux, Benoit; Haim-Boukobza, Stéphanie; Alizon, Samuel. COVFlow: phylodynamics analyses of viruses from selected SARS-CoV-2 genome sequences. Peer Community Journal, Volume 3 (2023), article  no. e101. doi : 10.24072/pcjournal.333.

Peer reviewed and recommended by PCI : 10.24072/pci.genomics.100239

Conflict of interest of the recommender and peer reviewers:
The recommender in charge of the evaluation of the article and the reviewers declared that they have no conflict of interest (as defined in the code of conduct of PCI) with the authors or with the content of the article.

[1] Aksamentov, I.; Roemer, C.; Hodcroft, E. B.; Neher, R. A. Nextclade: clade assignment, mutation calling and quality control for viral genomes, Journal of Open Source Software, Volume 6 (2021) no. 67, p. 3773 | DOI

[2] Alizon, S. Superspreading genomes, Science, Volume 371 (2021) no. 6529, pp. 574-575 | DOI

[3] Alizon, S.; Haim-Boukobza, S.; Foulongne, V.; Verdurme, L.; Trombert-Paolantoni, S.; Lecorche, E.; Roquebert, B.; Sofonea, M. T. Rapid spread of the SARS-CoV-2 Delta variant in some French regions, June 2021, Eurosurveillance, Volume 26 (2021) no. 28, p. 2100573 | DOI

[4] Bouckaert, R.; Heled, J.; Kühnert, D.; Vaughan, T.; Wu, C.-H.; Xie, D.; Suchard, M. A.; Rambaut, A.; Drummond, A. J. BEAST 2: A Software Platform for Bayesian Evolutionary Analysis, PLoS Computational Biology, Volume 10 (2014) no. 4 | DOI

[5] Chen, C.; Nadeau, S.; Yared, M.; Voinov, P.; Xie, N.; Roemer, C.; Stadler, T. CoV-Spectrum: analysis of globally shared SARS-CoV-2 data to identify and characterize new variants, Bioinformatics, Volume 38 (2022) no. 6, pp. 1735-1737 | DOI

[6] Coppée, R.; Blanquart, F.; Jary, A.; Leducq, V.; Ferré, V. M.; Franco Yusti, A. M.; Daniel, L.; Charpentier, C.; Lebourgeois, S.; Zafilaza, K.; Calvez, V.; Descamps, D.; Marcelin, A.-G.; Visseaux, B.; Bridier-Nahmias, A. Phylodynamics of SARS-CoV-2 in France, Europe, and the world in 2020, eLife, Volume 12 (2023) | DOI

[7] Cori, A.; Ferguson, N. M.; Fraser, C.; Cauchemez, S. A New Framework and Software to Estimate Time-Varying Reproduction Numbers During Epidemics, Am J Epidemiol, Volume 178 (2013) no. 9, pp. 1505-1512 | DOI

[8] Danesh, G.; Boennec, C.; Verdurme, L.; Roussel, M.; Trombert-Paolantoni, S.; Visseaux, B.; Haim-Boukobza, S.; Alizon, S. COVFlow: performing virus phylodynamics analyses from selected SARS-CoV-2 genome sequences, Zenodo, 2023 | DOI

[9] Danesh, G.; Boennec, C.; Verdurme, L.; Roussel, M.; Trombert-Paolantoni, S.; Visseaux, B.; Haim-Boukobza, S.; Alizon, S. COVFlow: viral phylodynamics pipeline, Zenodo, 2023 | DOI

[10] Danesh, G.; Elie, B.; Michalakis, Y.; Sofonea, M. T.; Bal, A.; Behillil, S.; Destras, G.; Boutolleau, D.; Burrel, S.; Marcelin, A.-G.; Plantier, J.-C.; Thibault, V.; Simon-Loriere, E.; van der Werf, S.; Lina, B.; Josset, L.; Enouf, V.; Alizon, S. Early phylodynamics analysis of the COVID-19 epidemic in France, Peer Community Journal, Volume 1 (2021), p. e45 | DOI

[11] Elbe, S.; Buckland-Merrett, G. Data, disease and diplomacy: GISAID's innovative contribution to global health, Global Challenges, Volume 1 (2017) no. 1, pp. 33-46 | DOI

[12] Gambaro, F.; Baidaliuk, A.; Behillil, S.; Donati, F.; Albert, M.; Alexandru, A.; Vanpeene, M.; Bizard, M.; Brisebarre, A.; Barbet, M.; Derrar, F.; Werf, S. v. d.; Enouf, V.; Simon-Loriere, E. Introductions and early spread of SARS-CoV-2 in France, Eurosurveillance, Volume 25 (2020) no. 26, p. 2001200 | DOI

[13] Gangavarapu, K.; Latif, A. A.; Mullen, J. L.; Alkuzweny, M.; Hufbauer, E.; Tsueng, G.; Haag, E.; Zeller, M.; Aceves, C. M.; Zaiets, K.; Cano, M.; Zhou, X.; Qian, Z.; Sattler, R.; Matteson, N. L.; Levy, J. I.; Lee, R. T. C.; Freitas, L.; Maurer-Stroh, S.; Suchard, M. A.; Wu, C.; Su, A. I.; Andersen, K. G.; Hughes, L. D. genomic reports: scalable and dynamic surveillance of SARS-CoV-2 variants and mutations, Nature Methods, Volume 20 (2023) no. 4, pp. 512-522 | DOI

[14] Grenfell, B. T.; Pybus, O. G.; Gog, J. R.; Wood, J. L.; Daly, J. M.; Mumford, J. A.; Holmes, E. C. Unifying the epidemiological and evolutionary dynamics of pathogens, Science, Volume 303 (2004) no. 5656, p. 327-32 | DOI

[15] Grüning, B.; Dale, R.; Sjödin, A.; Chapman, B. A.; Rowe, J.; Tomkins-Tinch, C. H.; Valieris, R.; Köster, J. Bioconda: sustainable and comprehensive software distribution for the life sciences, Nature Methods, Volume 15 (2018) no. 7, pp. 475-476 | DOI

[16] Guindon, S.; De Maio, N. Accounting for spatial sampling patterns in Bayesian phylogeography, Proceedings of the National Academy of Sciences, Volume 118 (2021) no. 52, p. e2105273118 | DOI

[17] Hadfield, J.; Megill, C.; Bell, S. M.; Huddleston, J.; Potter, B.; Callender, C.; Sagulenko, P.; Bedford, T.; Neher, R. A. Nextstrain: real-time tracking of pathogen evolution, Bioinformatics, Volume 34 (2018) no. 23, pp. 4121-4123 | DOI

[18] Hall, M. D.; Woolhouse, M. E. J.; Rambaut, A. The effects of sampling strategy on the quality of reconstruction of viral population dynamics using Bayesian skyline family coalescent methods: A simulation study, Virus Evolution, Volume 2 (2016) no. 1, p. vew003 | DOI

[19] Huddleston, J.; Hadfield, J.; Sibley, T. R.; Lee, J.; Fay, K.; Ilcisin, M.; Harkins, E.; Bedford, T.; Neher, R. A.; Hodcroft, E. B. Augur: a bioinformatics toolkit for phylogenetic analyses of human pathogens, Journal of Open Source Software, Volume 6 (2021) no. 57, p. 2906 | DOI

[20] Karcher, M. D.; Carvalho, L. M.; Suchard, M. A.; Dudas, G.; Minin, V. N. Estimating effective population size changes from preferentially sampled genetic sequences, PLOS Computational Biology, Volume 16 (2020) no. 10, p. e1007774 | DOI

[21] Katoh, K.; Standley, D. M. MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability, Molecular Biology and Evolution, Volume 30 (2013) no. 4, pp. 772-780 | DOI

[22] Khare, S.; Gurry, C.; Freitas, L.; Schultz, M. B.; Bach, G.; Diallo, A.; Akite, N.; Ho, J.; Lee, R. T.; Yeo, W.; Team, G. C. C.; Maurer-Stroh, S. GISAID’s Role in Pandemic Response, China CDC Weekly, Volume 3 (2021) no. 49, pp. 1049-1051 | DOI

[23] Köster, J.; Rahmann, S. "Snakemake—a scalable bioinformatics workflow engine", Bioinformatics, Volume 28 (2012) no. 19, pp. 2520-2522

[24] Lerat, E. A pipeline to select SARS-CoV-2 sequences for reliable phylodynamic analyses, Peer Community In Genomics (2023), p. 100239 | DOI

[25] Louca, S.; McLaughlin, A.; MacPherson, A.; Joy, J. B.; Pennell, M. W. Fundamental Identifiability Limits in Molecular Epidemiology, Molecular Biology and Evolution, Volume 38 (2021) no. 9, pp. 4010-4024 | DOI

[26] Louis du Plessis; John T. McCrone; Alexander E. Zarebski; Verity Hill; Christopher Ruis; Bernardo Gutierrez; Jayna Raghwani; Jordan Ashworth; Rachel Colquhoun; Thomas R. Connor; Nuno R. Faria; Ben Jackson; Nicholas J. Loman; Áine O’Toole; Samuel M. Nicholls; Kris V. Parag; Emily Scher; Tetyana I. Vasylyeva; Erik M. Volz; Alexander Watts; Isaac I. Bogoch; Kamran Khan; COVID-19 Genomics UK (COG-UK) Consortium†; David M. Aanensen; Moritz U. G. Kraemer; Andrew Rambaut; Oliver G. Pybus Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK, Science, Volume 371 (2021) no. 6530, pp. 708-712 | DOI

[27] Martin, M. A.; VanInsberghe, D.; Koelle, K. Insights from SARS-CoV-2 sequences, Science, Volume 371 (2021) no. 6528, pp. 466-467 | DOI

[28] Minh, B. Q.; Schmidt, H. A.; Chernomor, O.; Schrempf, D.; Woodhams, M. D.; von Haeseler, A.; Lanfear, R. IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era, Molecular Biology and Evolution, Volume 37 (2020) no. 5, pp. 1530-1534 | DOI

[29] 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. "Assignment of epidemiological lineages in an emerging pandemic using the pangolin tool", Virus Evolution, Volume 7 (2021) no. 2 (veab064) | DOI

[30] Rambaut, A. Phylodynamic Analysis 176 genomes 6 Mar 2020,, 2020 (Library Catalog:

[31] Rambaut, A.; Drummond, A. J.; Xie, D.; Baele, G.; Suchard, M. A. "Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7", Systematic Biology, Volume 67 (2018) no. 5, pp. 901-904 | DOI

[32] Sagulenko, P.; Puller, V.; Neher, R. A. TreeTime: Maximum-likelihood phylodynamic analysis, Virus Evolution, Volume 4 (2018) no. 1 | DOI

[33] Sofonea, M. T.; Roquebert, B.; Foulongne, V.; Morquin, D.; Verdurme, L.; Trombert-Paolantoni, S.; Roussel, M.; Bonetti, J.-C.; Zerah, J.; Haim-Boukobza, S.; Alizon, S. Analyzing and Modeling the Spread of SARS-CoV-2 Omicron Lineages BA.1 and BA.2, France, September 2021–February 2022, Emerging Infectious Diseases, Volume 28 (2022) no. 7, pp. 1355-1365 | DOI

[34] Stadler, T.; Kühnert, D.; Bonhoeffer, S.; Drummond, A. J. Birth-death skyline plot reveals temporal changes of epidemic spread in HIV and hepatitis C virus (HCV), Proc Natl Acad Sci USA, Volume 110 (2013) no. 1, p. 228-33 | DOI

[35] Suchard, M. A.; Lemey, P.; Baele, G.; Ayres, D. L.; Drummond, A. J.; Rambaut, A. Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10, Virus Evolution, Volume 4 (2018) no. 1 | DOI

[36] Thompson, R. N.; Stockwin, J. E.; van Gaalen, R. D.; Polonsky, J. A.; Kamvar, Z. N.; Demarsh, P. A.; Dahlqwist, E.; Li, S.; Miguel, E.; Jombart, T.; Lessler, J.; Cauchemez, S.; Cori, A. Improved inference of time-varying reproduction numbers during infectious disease outbreaks, Epidemics, Volume 29 (2019), p. 100356 | DOI

[37] 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.; Jarrett, R.; Pacchiarini, 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.; Koshy, C.; Wise, E.; Cortes, N.; Lynch, J.; Kidd, S.; Mori, M.; Fairley, D. J.; Curran, T.; McKenna, J. P.; Adams, H.; Fraser, C.; Golubchik, T.; Bonsall, D.; Moore, C.; Caddy, S. L.; Khokhar, F. A.; Wantoch, M.; Reynolds, N.; Warne, B.; Maksimovic, J.; Spellman, K.; McCluggage, K.; John, M.; Beer, R.; Afifi, S.; Morgan, S.; Marchbank, A.; Price, A.; Kitchen, C.; Gulliver, H.; Merrick, I.; Southgate, J.; Guest, M.; Munn, R.; Workman, T.; Connor, T. R.; Fuller, W.; Bresner, C.; Snell, L. B.; Charalampous, T.; Nebbia, G.; Batra, R.; Edgeworth, J.; Robson, S. C.; Beckett, A.; Loveson, K. F.; Aanensen, D. M.; Underwood, A. P.; Yeats, C. A.; Abudahab, K.; Taylor, B. E.; Menegazzo, M.; Clark, G.; Smith, W.; Khakh, M.; Fleming, V. M.; Lister, M. M.; Howson-Wells, H. C.; Berry, L.; Boswell, T.; Joseph, A.; Willingham, I.; Bird, P.; Helmer, T.; Fallon, K.; Holmes, C.; Tang, J.; Raviprakash, V.; Campbell, S.; Sheriff, N.; Loose, M. W.; Holmes, N.; Moore, C.; Carlile, M.; Wright, V.; Sang, F.; Debebe, J.; Coll, F.; Signell, A. W.; Betancor, G.; Wilson, H. D.; Feltwell, T.; Houldcroft, C. J.; Eldirdiri, S.; Kenyon, A.; Davis, T.; Pybus, O.; du Plessis, L.; Zarebski, A.; Raghwani, J.; Kraemer, M.; Francois, S.; Attwood, S.; Vasylyeva, T.; Torok, M. E.; Hamilton, W. L.; Goodfellow, I. G.; Hall, G.; Jahun, A. S.; Chaudhry, Y.; Hosmillo, M.; Pinckert, M. L.; Georgana, I.; Yakovleva, A.; Meredith, L. W.; Moses, S.; Lowe, H.; Ryan, F.; Fisher, C. L.; Awan, A. R.; Boyes, J.; Breuer, J.; Harris, K. A.; Brown, J. R.; Shah, D.; Atkinson, L.; Lee, J. C.; Alcolea-Medina, A.; Moore, N.; Cortes, N.; Williams, R.; Chapman, M. R.; Levett, L. J.; Heaney, J.; Smith, D. L.; Bashton, M.; Young, G. R.; Allan, J.; Loh, J.; Randell, P. A.; Cox, A.; Madona, P.; Holmes, A.; Bolt, F.; Price, J.; Mookerjee, S.; Rowan, A.; Taylor, G. P.; Ragonnet-Cronin, M.; Nascimento, F. F.; Jorgensen, D.; Siveroni, I.; Johnson, R.; Boyd, O.; Geidelberg, L.; Volz, E. M.; Brunker, K.; Smollett, K. L.; Loman, N. J.; Quick, J.; McMurray, C.; Stockton, J.; Nicholls, S.; Rowe, W.; Poplawski, R.; Martinez-Nunez, R. T.; Mason, J.; Robinson, T. I.; O'Toole, E.; Watts, J.; Breen, C.; Cowell, A.; Ludden, C.; Sluga, G.; Machin, N. W.; Ahmad, S. S.; George, R. P.; Halstead, F.; Sivaprakasam, V.; Thomson, E. C.; Shepherd, J. G.; Asamaphan, P.; Niebel, M. O.; Li, K. K.; Shah, R. N.; Jesudason, N. G.; Parr, Y. A.; Tong, L.; Broos, A.; Mair, D.; Nichols, J.; Carmichael, S. N.; Nomikou, K.; Aranday-Cortes, E.; Johnson, N.; Starinskij, I.; da Silva Filipe, A.; Robertson, D. L.; Orton, R. J.; Hughes, J.; Vattipally, S.; Singer, J. B.; Hale, A. D.; Macfarlane-Smith, L. R.; Harper, K. L.; Taha, Y.; Payne, B. A.; Burton-Fanning, S.; Waugh, S.; Collins, J.; Eltringham, G.; Templeton, K. E.; McHugh, M. P.; Dewar, R.; Wastenge, E.; Dervisevic, S.; Stanley, R.; Prakash, R.; Stuart, C.; Elumogo, N.; Sethi, D. K.; Meader, E. J.; Coupland, L. J.; Potter, W.; Graham, C.; Barton, E.; Padgett, D.; Scott, G.; Swindells, E.; Greenaway, J.; Nelson, A.; Yew, W. C.; Resende Silva, P. C.; Andersson, M.; Shaw, R.; Peto, T.; Justice, A.; Eyre, D.; Crooke, D.; Hoosdally, S.; Sloan, T. J.; Duckworth, N.; Walsh, S.; Chauhan, A. J.; Glaysher, S.; Bicknell, K.; Wyllie, S.; Butcher, E.; Elliott, S.; Lloyd, A.; Impey, R.; Levene, N.; Monaghan, L.; Bradley, D. T.; Allara, E.; Pearson, C.; Muir, P.; Vipond, I. B.; Hopes, R.; Pymont, H. M.; Hutchings, S.; Curran, M. D.; Parmar, S.; Lackenby, A.; Mbisa, T.; Platt, S.; Miah, S.; Bibby, D.; Manso, C.; Hubb, J.; Chand, M.; Dabrera, G.; Ramsay, M.; Bradshaw, D.; Thornton, A.; Myers, R.; Schaefer, U.; Groves, N.; Gallagher, E.; Lee, D.; Williams, D.; Ellaby, N.; Harrison, I.; Hartman, H.; Manesis, N.; Patel, V.; Bishop, C.; Chalker, V.; Osman, H.; Bosworth, A.; Robinson, E.; Holden, M. T.; Shaaban, S.; Birchley, A.; Adams, A.; Davies, A.; Gaskin, A.; Plimmer, A.; Gatica-Wilcox, B.; McKerr, C.; Moore, C.; Williams, C.; Heyburn, D.; De Lacy, E.; Hilvers, E.; Downing, F.; Shankar, G.; Jones, H.; Asad, H.; Coombes, J.; Watkins, J.; Evans, J. M.; Fina, L.; Gifford, L.; Gilbert, L.; Graham, L.; Perry, M.; Morgan, M.; Bull, M.; Cronin, M.; Pacchiarini, N.; Craine, N.; Jones, R.; Howe, R.; Corden, S.; Rey, S.; Kumziene-Summerhayes, S.; Taylor, S.; Cottrell, S.; Jones, S.; Edwards, S.; O’Grady, J.; Page, A. J.; Wain, J.; Webber, M. A.; Mather, A. E.; Baker, D. J.; Rudder, S.; Yasir, M.; Thomson, N. M.; Aydin, A.; Tedim, A. P.; Kay, G. L.; Trotter, A. J.; Gilroy, R. A.; Alikhan, N.-F.; de Oliveira Martins, L.; Le-Viet, T.; Meadows, L.; Kolyva, A.; Diaz, M.; Bell, A.; Gutierrez, A. V.; Charles, I. G.; Adriaenssens, E. M.; Kingsley, R. A.; Casey, A.; Simpson, D. A.; Molnar, Z.; Thompson, T.; Acheson, E.; Masoli, J. A.; Knight, B. A.; Hattersley, A.; Ellard, S.; Auckland, C.; Mahungu, T. W.; Irish-Tavares, D.; Haque, T.; Bourgeois, Y.; Scarlett, G. P.; Partridge, D. G.; Raza, M.; Evans, C.; Johnson, K.; Liggett, S.; Baker, P.; Essex, S.; Lyons, R. A.; Caller, L. G.; Castellano, S.; Williams, R. J.; Kristiansen, M.; Roy, S.; Williams, C. A.; Dyal, P. L.; Tutill, H. J.; Panchbhaya, Y. N.; Forrest, L. M.; Niola, P.; Findlay, J.; Brooks, T. T.; Gavriil, A.; Mestek-Boukhibar, L.; Weeks, S.; Pandey, S.; Berry, L.; Jones, K.; Richter, A.; Beggs, A.; Smith, C. P.; Bucca, G.; Hesketh, A. R.; Harrison, E. M.; Peacock, S. J.; Palmer, S.; Churcher, C. M.; Bellis, K. L.; Girgis, S. T.; Naydenova, P.; Blane, B.; Sridhar, S.; Ruis, C.; Forrest, S.; Cormie, C.; Gill, H. K.; Dias, J.; Higginson, E. E.; Maes, M.; Young, J.; Kermack, L. M.; Hadjirin, N. F.; Aggarwal, D.; Griffith, L.; Swingler, T.; Davidson, R. K.; Rambaut, A.; Williams, T.; Balcazar, C. E.; Gallagher, M. D.; O'Toole, Á.; Rooke, S.; Jackson, B.; Colquhoun, R.; Ashworth, J.; Hill, V.; McCrone, J.; Scher, E.; Yu, X.; Williamson, K. A.; Stanton, T. D.; Michell, S. L.; Bewshea, C. M.; Temperton, B.; Michelsen, M. L.; Warwick-Dugdale, J.; Manley, R.; Farbos, A.; Harrison, J. W.; Sambles, C. M.; Studholme, D. J.; Jeffries, A. R.; Darby, A. C.; Hiscox, J. A.; Paterson, S.; Iturriza-Gomara, M.; Jackson, K. A.; Lucaci, A. O.; Vamos, E. E.; Hughes, M.; Rainbow, L.; Eccles, R.; Nelson, C.; Whitehead, M.; Turtle, L.; Haldenby, S. T.; Gregory, R.; Gemmell, M.; Kwiatkowski, D.; de Silva, T. I.; Smith, N.; Angyal, A.; Lindsey, B. B.; Groves, D. C.; Green, L. R.; Wang, D.; Freeman, T. M.; Parker, M. D.; Keeley, A. J.; Parsons, P. J.; Tucker, R. M.; Brown, R.; Wyles, M.; Constantinidou, C.; Unnikrishnan, M.; Ott, S.; Cheng, J. K.; Bridgewater, H. E.; Frost, L. R.; Taylor-Joyce, G.; Stark, R.; Baxter, L.; Alam, M. T.; Brown, P. E.; McClure, P. C.; Chappell, J. G.; Tsoleridis, T.; Ball, J.; Grammatopoulos, D.; Buck, D.; Todd, J. A.; Green, A.; Trebes, A.; MacIntyre-Cockett, G.; de Cesare, M.; Langford, C.; Alderton, A.; Amato, R.; Goncalves, S.; Jackson, D. K.; Johnston, I.; Sillitoe, J.; Palmer, S.; Lawniczak, M.; Berriman, M.; Danesh, J.; Livett, R.; Shirley, L.; Farr, B.; Quail, M.; Thurston, S.; Park, N.; Betteridge, E.; Weldon, D.; Goodwin, S.; Nelson, R.; Beaver, C.; Letchford, L.; Jackson, D. A.; Foulser, L.; McMinn, L.; Prestwood, L.; Kay, S.; Kane, L.; Dorman, M. J.; Martincorena, I.; Puethe, C.; Keatley, J.-P.; Tonkin-Hill, G.; Smith, C.; Jamrozy, D.; Beale, M. A.; Patel, M.; Ariani, C.; Spencer-Chapman, M.; Drury, E.; Lo, S.; Rajatileka, S.; Scott, C.; James, K.; Buddenborg, S. K.; Berger, D. J.; Patel, G.; Garcia-Casado, M. V.; Dibling, T.; McGuigan, S.; Rogers, H. A.; Hunter, A. D.; Souster, E.; Neaverson, A. S. Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity, Cell, Volume 184 (2021) no. 1 | DOI

[38] Wilkinson, E.; Giovanetti, M.; Tegally, H.; San, J. E.; Lessells, R.; et al. A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa, Science, Volume 374 (2021) no. 6566, pp. 423-431 | DOI

[39] Zhou, F.; Yu, T.; Du, R.; Fan, G.; Liu, Y.; Liu, Z.; Xiang, J.; Wang, Y.; Song, B.; Gu, X.; Guan, L.; Wei, Y.; Li, H.; Wu, X.; Xu, J.; Tu, S.; Zhang, Y.; Chen, H.; Cao, B. Clinical course and risk factors for mortality of adult inpatients with COVID-19 in Wuhan, China: a retrospective cohort study, The Lancet, Volume 395 (2020) no. 10229, pp. 1054-1062 | DOI

[40] 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.; Bogoch, I. I.; Khan, K.; Aanensen, D. M.; Kraemer, M. U. G.; Rambaut, A.; Pybus, O. G. Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK, Science, Volume 371 (2021) no. 6530, pp. 708-712 | DOI

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