Spatial growth rate of emerging SARS-CoV-2 lineages in England, September 2020-December 2021
| Title: | Spatial growth rate of emerging SARS-CoV-2 lineages in England, September 2020-December 2021 |
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| Authors: | Smallman-Raynor, MR; Cliff, AD; Robson, SC; Connor, TR; Loman, NJ; Golubchik, T; Martinez Nunez, RT; Bonsall, D; Rambaut, A; Snell, LB; Livett, R; Ludden, C; Corden, S; Nastouli, E; Nebbia, G; Johnston, I; Lythgoe, K; Torok, ME; Goodfellow, IG; Prieto, JA; Saeed, K; Jackson, DK; Houlihan, C; Frampton, D; Hamilton, WL; Witney, AA; Bucca, G; Pope, CF; Moore, C; Thomson, EC; Harrison, EM; Smith, CP; Rogan, F; Beckwith, SM; Murray, A; Singleton, D; Eastick, K; Sheridan, LA; Randell, PA; Jackson, LM; Ariani, CV; Gonçalves, S; Fairley, DJ; Loose, MW; Watkins, J; Moses, S; Nicholls, S; Bull, M; Amato, R; Smith, DL; Aanensen, DM; Barrett, JC; Aggarwal, D; Shepherd, JG; Curran, MD; Parmar, S; Parker, MD; Williams, C; Glaysher, S; Underwood, AP; Bashton, M; Pacchiarini, N; Loveson, KF; Byott, M; Carabelli, AM; Templeton, KE; de Silva, TI; Wang, D; Langford, CF; Sillitoe, J; Gunson, RN; Cottrell, S; O'Grady, J; Kwiatkowski, D; Lillie, PJ; Cortes, N; Moore, N; Thomas, C; Burns, PJ; Mahungu, TW; Liggett, S; Beckett, AH; Holden, MTG; Levett, LJ; Osman, H; Hassan-Ibrahim, MO; Simpson, DA; Chand, M; Gupta, RK; Darby, AC; Paterson, S; Pybus, OG; Volz, EM; de Angelis, D; Robertson, DL; Page, AJ; Martincorena, I; Aigrain, L; Bassett, AR; Wong, N; Taha, Y; Erkiert, MJ; Spencer Chapman, MH; Dewar, R; McHugh, MP; Mookerjee, S; Aplin, S; Harvey, M; Sass, T; Umpleby, H; Wheeler, H; McKenna, JP; Warne, B; Taylor, JF; Chaudhry, Y; Izuagbe, R; Jahun, AS; Young, GR; McMurray, CL; McCann, CM; Nelson, A; Elliott, S; Lowe, H; Price, A; Crown, MR; Rey, S; Roy, S; Temperton, B; Shaaban, S; Hesketh, AR; Laing, KG; Monahan, IM; Heaney, J; Pelosi, E; Silviera, S; Wilson-Davies, E; Fryer, H; Adams, H; du Plessis, L; Johnson, R; Harvey, WT; Hughes, J; Orton, RJ; Spurgin, LG; Bourgeois, Y; Ruis, C; O'Toole, Á; Gourtovaia, M; Sanderson, T; Fraser, C; Edgeworth, J; Breuer, J; Michell, SL; Todd, JA; John, M; Buck, D; Gajee, K; Kay, GL; Peacock, SJ; Heyburn, D; Kitchman, K; McNally, A; Pritchard, DT; Dervisevic, S; Muir, P; Robinson, E; Vipond, BB; Ramadan, NA; Jeanes, C; Weldon, D; Catalan, J; Jones, N; da Silva Filipe, A; Fuchs, M; Miskelly, J; Jeffries, AR; Oliver, K; Park, NR; Ash, A; Koshy, C; Barrow, M; Buchan, SL; Mantzouratou, A; Clark, G; Holmes, CW; Campbell, S; Davis, T; Tan, NK; Brown, JR; Harris, KA; Kidd, SP; Grant, PR; Xu-McCrae, L; Cox, A; Madona, P; Pond, M; Withell, KT; Graham, C; Denton-Smith, R; Swindells, E; Turnbull, R; Sloan, TJ; Bosworth, A; Hutchings, S; Pymont, HM; Casey, A; Ratcliffe, L; Jones, CR; Knight, BA; Haque, T; Hart, J; Irish-Tavares, D; Witele, E; Mower, C; Watson, LK; Collins, J; Eltringham, G; Crudgington, D; Macklin, B; Iturriza-Gomara, M; Lucaci, AO; McClure, PC; Carlile, M; Holmes, N; Storey, N; Rooke, S; Yebra, G; Craine, N; Perry, M; Alikhan, N - F; Bridgett, S; Cook, KF; Fearn, C; Goudarzi, S; Lyons, RA; Williams, T; Haldenby, ST; Durham, J; Leonard, S; Davies, RM; Batra, R; Blane, B; Spyer, MJ; Smith, P; Yavus, M; Williams, RJ; Mahanama, AIK; Samaraweera, B; Girgis, ST; Hansford, SE; Green, A; Beaver, C; Bellis, KL; Dorman, MJ; Kay, S; Prestwood, L; Rajatileka, S; Quick, J; Poplawski, R; Reynolds, N; Mack, A; Morriss, A; Whalley, T; Patel, B; Georgana, I; Hosmillo, M; Pinckert, ML; Stockton, J; Henderson, JH; Hollis, A; Stanley, W; Yew, WC; Myers, R; Thornton, A; Adams, A; Annett, T; Asad, H; Birchley, A; Coombes, J; Evans, JM; Fina, L; Gatica-Wilcox, B; Gilbert, L; Graham, L; Hey, J; Hilvers, E; Jones, S; Jones, H; Kumziene-Summerhayes, S; McKerr, C; Powell, J; Pugh, G; Taylor, S; Trotter, AJ; Williams, CA; Kermack, LM; Foulkes, BH; Gallis, M; Hornsby, HR; Louka, SF; Pohare, M; Wolverson, P; Zhang, P; MacIntyre-Cockett, G; Trebes, A; Moll, RJ; Ferguson, L; Goldstein, EJ; Maclean, A; Tomb, R; Starinskij, I; Thomson, L; Southgate, J; Kraemer, MUG; Raghwani, J; Zarebski, AE; Boyd, O; Geidelberg, L; Illingworth, CJ; Jackson, C; Pascall, D; Vattipally, S; Freeman, TM; Hsu, SN; Lindsey, BB; James, K; Lewis, K; Tonkin-Hill, G; Tovar-Corona, JM; Cox, M; Abudahab, K; Menegazzo, M; Taylor, BEW; Yeats, CA; Mukaddas, A; Wright, DW; de Oliveira Martins, L; Colquhoun, R; Hill, V; Jackson, B; McCrone, JT; Medd, N; Scher, E; Keatley, J - P; Curran, T; Morgan, S; Maxwell, P; Smith, K; Eldirdiri, S; Kenyon, A; Holmes, AH; Price, JR; Wyatt, T; Mather, AE; Skvortsov, T; Hartley, JA; Guest, M; Kitchen, C; Merrick, I; Munn, R; Bertolusso, B; Lynch, J; Vernet, G; Kirk, S; Wastnedge, E; Stanley, R; Idle, G; Bradley, DT; Poyner, J; Mori, M; Jones, O; Wright, V; Brooks, E; Churcher, CM; Fragakis, M; Galai, K; Jermy, A; Judges, S; McManus, GM; Smith, KS; Westwick, E; Attwood, SW; Bolt, F; Davies, A; De Lacy, E; Downing, F; Edwards, S; Meadows, L; Jeremiah, S; Smith, N; Foulser, L; Charalampous, T; Patel, A; Berry, L; Boswell, T; Fleming, VM; Howson-Wells, HC; Joseph, A; Khakh, M; Lister, MM; Bird, PW; Fallon, K; Helmer, T; Odedra, M; Shaw, J; Tang, JW; Willford, NJ; Blakey, V; Raviprakash, V; Sheriff, N; Williams, L - A; Feltwell, T; Bedford, L; Cargill, JS; Hughes, W; Moore, J; Stonehouse, S; Atkinson, L; Lee, JCD; Shah, D; Alcolea-Medina, A; Ohemeng-Kumi, N; Ramble, J; Sehmi, J; Williams, R; Chatterton, W; Pusok, M; Everson, W; Castigador, A; Macnaughton, E; El Bouzidi, K; Lampejo, T; Sudhanva, M; Breen, C; Sluga, G; Ahmad, SSY; George, RP; Machin, NW; Binns, D; James, V; Blacow, R; Coupland, L; Smith, L; Barton, E; Padgett, D; Scott, G; Cross, A; Mirfenderesky, M; Greenaway, J; Cole, K; Clarke, P; Duckworth, N; Walsh, S; Bicknell, K; Impey, R; Wyllie, S; Hopes, R; Bishop, C; Chalker, V; Harrison, I; Gifford, L; Molnar, Z; Auckland, C; Evans, C; Johnson, K; Partridge, DG; Raza, M; Baker, P; Bonner, S; Essex, S; Murray, LJ; Lawton, AI; Burton-Fanning, S; Payne, BAI; Waugh, S; Gomes, AN; Kimuli, M; Murray, DR; Ashfield, P; Dobie, D; Ashford, F; Best, A; Crawford, L; Cumley, N; Mayhew, M; Megram, O; Mirza, J; Moles-Garcia, E; Percival, B; Driscoll, M; Ensell, L; Lowe, HL; Maftei, L; Mondani, M; Chaloner, NJ; Cogger, BJ; Easton, LJ; Huckson, H; Lewis, J; Lowdon, S; Malone, CS; Munemo, F; Mutingwende, M; Nicodemi, R; Podplomyk, O; Somassa, T; Beggs, A; Richter, A; Cormie, C; Dias, J; Forrest, S; Higginson, EE; Maes, M; Young, J; Davidson, RK; Jackson, KA; Turtle, L; Keeley, AJ; Ball, J; Byaruhanga, T; Chappell, JG; Dey, J; Hill, JD; Park, EJ; Fanaie, A; Hilson, RA; Yaze, G; Lo, S; Afifi, S; Beer, R; Maksimovic, J; McCluggage, K; Spellman, K; Bresner, C; Fuller, W; Marchbank, A; Workman, T; Shelest, E; Debebe, J; Sang, F; Zamudio, ME; Francois, S; Gutierrez, B; Vasylyeva, TI; Flaviani, F; Ragonnet-Cronin, M; Smollett, KL; Broos, A; Mair, D; Nichols, J; Nomikou, K; Tong, L; Tsatsani, I; O'Brien, S; Rushton, S; Sanderson, R; Perkins, J; Cotton, S; Gallagher, A; Allara, E; Pearson, C; Bibby, D; Dabrera, G; Ellaby, N; Gallagher, E; Hubb, J; Lackenby, A; Lee, D; Manesis, N; Mbisa, T; Platt, S; Twohig, KA; Morgan, M; Aydin, A; Baker, DJ; Foster-Nyarko, E; Prosolek, SJ; Rudder, S; Baxter, C; Carvalho, SF; Lavin, D; Mariappan, A; Radulescu, C; Singh, A; Tang, M; Morcrette, H; Bayzid, N; Cotic, M; Balcazar, CE; Gallagher, MD; Maloney, D; Stanton, TD; Williamson, KA; Manley, R; Michelsen, ML; Sambles, CM; Studholme, DJ; Warwick-Dugdale, J; Eccles, R; Gemmell, M; Gregory, R; Hughes, M; Nelson, C; Rainbow, L; Vamos, EE; Webster, HJ; Whitehead, M; Wierzbicki, C; Angyal, A; Green, LR; Whiteley, M; Betteridge, E; Bronner, IF; Farr, BW; Goodwin, S; Lensing, SV; McCarthy, SA; Quail, MA; Rajan, D; Redshaw, NM; Scott, C; Shirley, L; Thurston, SAJ; Rowe, W; Gaskin, A; Le-Viet, T; Bonfield, J; Liddle, J; Whitwham, A |
| Publication Year: | 2022 |
| Collection: | Bournemouth University Research Online (BURO) |
| Description: | This paper uses a robust method of spatial epidemiological analysis to assess the spatial growth rate of multiple lineages of SARS-CoV-2 in the local authority areas of England, September 2020–December 2021. Using the genomic surveillance records of the COVID-19 Genomics UK (COG-UK) Consortium, the analysis identifies a substantial (7.6-fold) difference in the average rate of spatial growth of 37 sample lineages, from the slowest (Delta AY.4.3) to the fastest (Omicron BA.1). Spatial growth of the Omicron (B.1.1.529 and BA) variant was found to be 2.81× faster than the Delta (B.1.617.2 and AY) variant and 3.76× faster than the Alpha (B.1.1.7 and Q) variant. In addition to AY.4.2 (a designated variant under investigation, VUI-21OCT-01), three Delta sublineages (AY.43, AY.98 and AY.120) were found to display a statistically faster rate of spatial growth than the parent lineage and would seem to merit further investigation. We suggest that the monitoring of spatial growth rates is a potentially valuable adjunct to outbreak response procedures for emerging SARS-CoV-2 variants in a defined population. |
| Document Type: | article in journal/newspaper |
| File Description: | application/pdf |
| Language: | English |
| Relation: | https://eprints.bournemouth.ac.uk/39820/1/spatial-growth-rate-of-emerging-sars-cov-2-lineages-in-england-september-2020-december-2021.pdf; Smallman-Raynor, M., Cliff, A., Robson, S., Connor, T., Loman, N., Golubchik, T, Martinez Nunez, R., Bonsall, D, Rambaut, A, Snell, L., Livett, R, Ludden, C, Corden, S, Nastouli, E, Nebbia, G, Johnston, I, Lythgoe, K, Torok, M., Goodfellow, I., Prieto, J., Saeed, K, Jackson, D., Houlihan, C, Frampton, D, Hamilton, W., Witney, A., Bucca, G, Pope, C., Moore, C, Thomson, E., Harrison, E., Smith, C., Rogan, F, Beckwith, S., Murray, A, Singleton, D, Eastick, K, Sheridan, L., Randell, P., Jackson, L., Ariani, C., Gonçalves, S, Fairley, D., Loose, M., Watkins, J, Moses, S, Nicholls, S, Bull, M, Amato, R, Smith, D., Aanensen, D., Barrett, J., Aggarwal, D, Shepherd, J., Curran, M., Parmar, S, Parker, M., Williams, C, Glaysher, S, Underwood, A., Bashton, M, Pacchiarini, N, Loveson, K., Byott, M, Carabelli, A., Templeton, K., de Silva, T., Wang, D, Langford, C., Sillitoe, J, Gunson, R., Cottrell, S, O'Grady, J, Kwiatkowski, D, Lillie, P., Cortes, N, Moore, N, Thomas, C, Burns, P., Mahungu, T., Liggett, S, Beckett, A., Holden, M., Levett, L., Osman, H, Hassan-Ibrahim, M., Simpson, D., Chand, M, Gupta, R., Darby, A., Paterson, S, Pybus, O., Volz, E., de Angelis, D, Robertson, D., Page, A., Martincorena, I, Aigrain, L, Bassett, A., Wong, N, Taha, Y, Erkiert, M., Spencer Chapman, M., Dewar, R, McHugh, M., Mookerjee, S, Aplin, S, Harvey, M, Sass, T, Umpleby, H, Wheeler, H, McKenna, J., Warne, B, Taylor, J., Chaudhry, Y, Izuagbe, R, Jahun, A., Young, G., McMurray, C., McCann, C., Nelson, A, Elliott, S, Lowe, H, Price, A, Crown, M., Rey, S, Roy, S, Temperton, B, Shaaban, S, Hesketh, A., Laing, K., Monahan, I., Heaney, J, Pelosi, E, Silviera, S, Wilson-Davies, E, Fryer, H, Adams, H, du Plessis, L, Johnson, R, Harvey, W., Hughes, J, Orton, R., Spurgin, L., Bourgeois, Y, Ruis, C, O'Toole, Á, Gourtovaia, M, Sanderson, T, Fraser, C, Edgeworth, J, Breuer, J, Michell, S., Todd, J., John, M, Buck, D, Gajee, K, Kay, G., Peacock, S., Heyburn, D, Kitchman, K, McNally, A, Pritchard, D., Dervisevic, S, Muir, P, Robinson, E, Vipond, B., Ramadan, N., Jeanes, C, Weldon, D, Catalan, J, Jones, N, da Silva Filipe, A, Williams, C, Fuchs, M, Miskelly, J, Jeffries, A., Oliver, K, Park, N., Ash, A, Koshy, C, Barrow, M, Buchan, S., Mantzouratou, A, Clark, G, Holmes, C., Campbell, S, Davis, T, Tan, N., Brown, J., Harris, K., Kidd, S., Grant, P., Xu-McCrae, L, Cox, A, Madona, P, Pond, M, Withell, K., Williams, C, Graham, C, Denton-Smith, R, Swindells, E, Turnbull, R, Sloan, T., Bosworth, A, Hutchings, S, Pymont, H., Casey, A, Ratcliffe, L, Jones, C., Knight, B., Haque, T, Hart, J, Irish-Tavares, D, Witele, E, Mower, C, Watson, L., Collins, J, Eltringham, G, Crudgington, D, Macklin, B, Iturriza-Gomara, M, Lucaci, A., McClure, P., Carlile, M, Holmes, N, Moore, C, Storey, N, Rooke, S, Yebra, G, Craine, N, Perry, M, Alikhan, N - F, Bridgett, S, Cook, K., Fearn, C, Goudarzi, S, Lyons, R., Williams, T, Haldenby, S., Durham, J, Leonard, S, Davies, R., Batra, R, Blane, B, Spyer, M., Smith, P, Yavus, M, Williams, R., Mahanama, A., Samaraweera, B, Girgis, S., Hansford, S., Green, A, Beaver, C, Bellis, K., Dorman, M., Kay, S, Prestwood, L, Rajatileka, S, Quick, J, Poplawski, R, Reynolds, N, Mack, A, Morriss, A, Whalley, T, Patel, B, Georgana, I, Hosmillo, M, Pinckert, M., Stockton, J, Henderson, J., Hollis, A, Stanley, W, Yew, W., Myers, R, Thornton, A, Adams, A, Annett, T, Asad, H, Birchley, A, Coombes, J, Evans, J., Fina, L, Gatica-Wilcox, B, Gilbert, L, Graham, L, Hey, J, Hilvers, E, Jones, S, Jones, H, Kumziene-Summerhayes, S, McKerr, C, Powell, J, Pugh, G, Taylor, S, Trotter, A., Williams, C., Kermack, L., Foulkes, B., Gallis, M, Hornsby, H., Louka, S., Pohare, M, Wolverson, P, Zhang, P, MacIntyre-Cockett, G, Trebes, A, Moll, R., Ferguson, L, Goldstein, E., Maclean, A, Tomb, R, Starinskij, I, Thomson, L, Southgate, J, Kraemer, M., Raghwani, J, Zarebski, A., Boyd, O, Geidelberg, L, Illingworth, C., Jackson, C, Pascall, D, Vattipally, S, Freeman, T., Hsu, S., Lindsey, B., James, K, Lewis, K, Tonkin-Hill, G, Tovar-Corona, J., Cox, M, Abudahab, K, Menegazzo, M, Taylor, B., Yeats, C., Mukaddas, A, Wright, D., de Oliveira Martins, L, Colquhoun, R, Hill, V, Jackson, B, McCrone, J., Medd, N, Scher, E, Keatley, J - P, Curran, T, Morgan, S, Maxwell, P, Smith, K, Eldirdiri, S, Kenyon, A, Holmes, A., Price, J., Wyatt, T, Mather, A., Skvortsov, T, Hartley, J., Guest, M, Kitchen, C, Merrick, I, Munn, R, Bertolusso, B, Lynch, J, Vernet, G, Kirk, S, Wastnedge, E, Stanley, R, Idle, G, Bradley, D., Poyner, J, Mori, M, Jones, O, Wright, V, Brooks, E, Churcher, C., Fragakis, M, Galai, K, Jermy, A, Judges, S, McManus, G., Smith, K., Westwick, E, Attwood, S., Bolt, F, Davies, A, De Lacy, E, Downing, F, Edwards, S, Meadows, L, Jeremiah, S, Smith, N, Foulser, L, Charalampous, T, Patel, A, Berry, L, Boswell, T, Fleming, V., Howson-Wells, H., Joseph, A, Khakh, M, Lister, M., Bird, P., Fallon, K, Helmer, T, Odedra, M, Shaw, J, Tang, J., Willford, N., Blakey, V, Raviprakash, V, Sheriff, N, Williams, L - A, Feltwell, T, Bedford, L, Cargill, J., Hughes, W, Moore, J, Stonehouse, S, Atkinson, L, Lee, J., Shah, D, Alcolea-Medina, A, Ohemeng-Kumi, N, Ramble, J, Sehmi, J, Williams, R, Chatterton, W, Pusok, M, Everson, W, Castigador, A, Macnaughton, E, El Bouzidi, K, Lampejo, T, Sudhanva, M, Breen, C, Sluga, G, Ahmad, S., George, R., Machin, N., Binns, D, James, V, Blacow, R, Coupland, L, Smith, L, Barton, E, Padgett, D, Scott, G, Cross, A, Mirfenderesky, M, Greenaway, J, Cole, K, Clarke, P, Duckworth, N, Walsh, S, Bicknell, K, Impey, R, Wyllie, S, Hopes, R, Bishop, C, Chalker, V, Harrison, I, Gifford, L, Molnar, Z, Auckland, C, Evans, C, Johnson, K, Partridge, D., Raza, M, Baker, P, Bonner, S, Essex, S, Murray, L., Lawton, A., Burton-Fanning, S, Payne, B., Waugh, S, Gomes, A., Kimuli, M, Murray, D., Ashfield, P, Dobie, D, Ashford, F, Best, A, Crawford, L, Cumley, N, Mayhew, M, Megram, O, Mirza, J, Moles-Garcia, E, Percival, B, Driscoll, M, Ensell, L, Lowe, H., Maftei, L, Mondani, M, Chaloner, N., Cogger, B., Easton, L., Huckson, H, Lewis, J, Lowdon, S, Malone, C., Munemo, F, Mutingwende, M, Nicodemi, R, Podplomyk, O, Somassa, T, Beggs, A, Richter, A, Cormie, C, Dias, J, Forrest, S, Higginson, E., Maes, M, Young, J, Davidson, R., Jackson, K., Turtle, L, Keeley, A., Ball, J, Byaruhanga, T, Chappell, J., Dey, J, Hill, J., Park, E., Fanaie, A, Hilson, R., Yaze, G, Lo, S, Afifi, S, Beer, R, Maksimovic, J, McCluggage, K, Spellman, K, Bresner, C, Fuller, W, Marchbank, A, Workman, T, Shelest, E, Debebe, J, Sang, F, Zamudio, M., Francois, S, Gutierrez, B, Vasylyeva, T., Flaviani, F, Ragonnet-Cronin, M, Smollett, K., Broos, A, Mair, D, Nichols, J, Nomikou, K, Tong, L, Tsatsani, I, O'Brien, S, Rushton, S, Sanderson, R, Perkins, J, Cotton, S, Gallagher, A, Allara, E, Pearson, C, Bibby, D, Dabrera, G, Ellaby, N, Gallagher, E, Hubb, J, Lackenby, A, Lee, D, Manesis, N, Mbisa, T, Platt, S, Twohig, K., Morgan, M, Aydin, A, Baker, D., Foster-Nyarko, E, Prosolek, S., Rudder, S, Baxter, C, Carvalho, S., Lavin, D, Mariappan, A, Radulescu, C, Singh, A, Tang, M, Morcrette, H, Bayzid, N, Cotic, M, Balcazar, C., Gallagher, M., Maloney, D, Stanton, T., Williamson, K., Manley, R, Michelsen, M., Sambles, C., Studholme, D., Warwick-Dugdale, J, Eccles, R, Gemmell, M, Gregory, R, Hughes, M, Nelson, C, Rainbow, L, Vamos, E., Webster, H., Whitehead, M, Wierzbicki, C, Angyal, A, Green, L., Whiteley, M, Betteridge, E, Bronner, I., Farr, B., Goodwin, S, Lensing, S., McCarthy, S., Quail, M., Rajan, D, Redshaw, N., Scott, C, Shirley, L, Thurston, S., Rowe, W, Gaskin, A, Le-Viet, T, Bonfield, J, Liddle, J and Whitwham, A, 2022. Spatial growth rate of emerging SARS-CoV-2 lineages in England, September 2020-December 2021. Epidemiology and Infection, 150, e145. |
| Availability: | https://eprints.bournemouth.ac.uk/39820/ |
| Rights: | cc_by_4 |
| Accession Number: | edsbas.6FBC144A |
| Database: | BASE |