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Genomic reconstruction of the SARS-CoV-2 epidemic in England
Nature, Volume: 600, Issue: 7889, Pages: 506 - 511
Swansea University Author:
Ronan Lyons
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DOI (Published version): 10.1038/s41586-021-04069-y
Abstract
The evolution of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus leads to new variants that warrant timely epidemiological characterization. Here we use the dense genomic surveillance data generated by the COVID-19 Genomics UK Consortium to reconstruct the dynamics of 71 diffe...
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ISSN: | 0028-0836 1476-4687 |
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Springer Science and Business Media LLC
2021
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URI: | https://cronfa.swan.ac.uk/Record/cronfa66422 |
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<?xml version="1.0" encoding="utf-8"?><rfc1807 xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:xsd="http://www.w3.org/2001/XMLSchema"><bib-version>v2</bib-version><id>66422</id><entry>2024-05-15</entry><title>Genomic reconstruction of the SARS-CoV-2 epidemic in England</title><swanseaauthors><author><sid>83efcf2a9dfcf8b55586999d3d152ac6</sid><ORCID>0000-0001-5225-000X</ORCID><firstname>Ronan</firstname><surname>Lyons</surname><name>Ronan Lyons</name><active>true</active><ethesisStudent>false</ethesisStudent></author></swanseaauthors><date>2024-05-15</date><deptcode>MEDS</deptcode><abstract>The evolution of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus leads to new variants that warrant timely epidemiological characterization. Here we use the dense genomic surveillance data generated by the COVID-19 Genomics UK Consortium to reconstruct the dynamics of 71 different lineages in each of 315 English local authorities between September 2020 and June 2021. This analysis reveals a series of subepidemics that peaked in early autumn 2020, followed by a jump in transmissibility of the B.1.1.7/Alpha lineage. The Alpha variant grew when other lineages declined during the second national lockdown and regionally tiered restrictions between November and December 2020. A third more stringent national lockdown suppressed the Alpha variant and eliminated nearly all other lineages in early 2021. Yet a series of variants (most of which contained the spike E484K mutation) defied these trends and persisted at moderately increasing proportions. However, by accounting for sustained introductions, we found that the transmissibility of these variants is unlikely to have exceeded the transmissibility of the Alpha variant. Finally, B.1.617.2/Delta was repeatedly introduced in England and grew rapidly in early summer 2021, constituting approximately 98% of sampled SARS-CoV-2 genomes on 26 June 2021.</abstract><type>Journal Article</type><journal>Nature</journal><volume>600</volume><journalNumber>7889</journalNumber><paginationStart>506</paginationStart><paginationEnd>511</paginationEnd><publisher>Springer Science and Business Media LLC</publisher><placeOfPublication/><isbnPrint/><isbnElectronic/><issnPrint>0028-0836</issnPrint><issnElectronic>1476-4687</issnElectronic><keywords/><publishedDay>16</publishedDay><publishedMonth>12</publishedMonth><publishedYear>2021</publishedYear><publishedDate>2021-12-16</publishedDate><doi>10.1038/s41586-021-04069-y</doi><url/><notes>Publisher Correction: Genomic reconstruction of the SARS CoV-2 epidemic in England available at https://doi.org/10.1038/s41586-022-04887-8</notes><college>COLLEGE NANME</college><department>Medical School</department><CollegeCode>COLLEGE CODE</CollegeCode><DepartmentCode>MEDS</DepartmentCode><institution>Swansea University</institution><apcterm/><funders>Open access funding provided by Deutsches Krebsforschungszentrum (DKFZ).</funders><projectreference/><lastEdited>2024-06-24T12:29:31.9625493</lastEdited><Created>2024-05-15T08:23:25.2739890</Created><path><level id="1">Faculty of Medicine, Health and Life Sciences</level><level id="2">Swansea University Medical School - Health Data Science</level></path><authors><author><firstname>Harald S.</firstname><surname>Vöhringer</surname><order>1</order></author><author><firstname>Theo</firstname><surname>Sanderson</surname><order>2</order></author><author><firstname>Matthew</firstname><surname>Sinnott</surname><orcid>0000-0002-3054-7846</orcid><order>3</order></author><author><firstname>Nicola De</firstname><surname>Maio</surname><order>4</order></author><author><firstname>Thuy</firstname><surname>Nguyen</surname><order>5</order></author><author><firstname>Richard</firstname><surname>Goater</surname><orcid>0000-0001-9954-841x</orcid><order>6</order></author><author><firstname>Frank</firstname><surname>Schwach</surname><order>7</order></author><author><firstname>Ian</firstname><surname>Harrison</surname><orcid>0000-0003-4117-961x</orcid><order>8</order></author><author><firstname>Joel</firstname><surname>Hellewell</surname><orcid>0000-0003-2683-0849</orcid><order>9</order></author><author><firstname>Cristina V.</firstname><surname>Ariani</surname><order>10</order></author><author><firstname>Sonia</firstname><surname>Gonçalves</surname><order>11</order></author><author><firstname>David K.</firstname><surname>Jackson</surname><orcid>0000-0002-8090-9462</orcid><order>12</order></author><author><firstname>Ian</firstname><surname>Johnston</surname><order>13</order></author><author><firstname>Alexander W.</firstname><surname>Jung</surname><order>14</order></author><author><firstname>Callum</firstname><surname>Saint</surname><orcid>0000-0001-8720-9736</orcid><order>15</order></author><author><firstname>John</firstname><surname>Sillitoe</surname><order>16</order></author><author><firstname>Maria</firstname><surname>Suciu</surname><order>17</order></author><author><firstname>Nick</firstname><surname>Goldman</surname><orcid>0000-0001-8486-2211</orcid><order>18</order></author><author><firstname>Jasmina</firstname><surname>Panovska-Griffiths</surname><orcid>0000-0002-7720-1121</orcid><order>19</order></author><author><firstname>Irina</firstname><surname>Abnizova</surname><order>20</order></author><author><firstname>Louise</firstname><surname>Aigrain</surname><order>21</order></author><author><firstname>Alex</firstname><surname>Alderton</surname><order>22</order></author><author><firstname>Mozam</firstname><surname>Ali</surname><order>23</order></author><author><firstname>Laura</firstname><surname>Allen</surname><order>24</order></author><author><firstname>Roberto</firstname><surname>Amato</surname><order>25</order></author><author><firstname>Ralph</firstname><surname>Anderson</surname><order>26</order></author><author><firstname>Cristina</firstname><surname>Ariani</surname><order>27</order></author><author><firstname>Siobhan</firstname><surname>Austin-Guest</surname><order>28</order></author><author><firstname>Sendu</firstname><surname>Bala</surname><order>29</order></author><author><firstname>Jeffrey</firstname><surname>Barrett</surname><order>30</order></author><author><firstname>Andrew</firstname><surname>Bassett</surname><order>31</order></author><author><firstname>Kristina</firstname><surname>Battleday</surname><order>32</order></author><author><firstname>James</firstname><surname>Beal</surname><order>33</order></author><author><firstname>Mathew</firstname><surname>Beale</surname><order>34</order></author><author><firstname>Charlotte</firstname><surname>Beaver</surname><order>35</order></author><author><firstname>Sam</firstname><surname>Bellany</surname><order>36</order></author><author><firstname>Tristram</firstname><surname>Bellerby</surname><order>37</order></author><author><firstname>Katie</firstname><surname>Bellis</surname><order>38</order></author><author><firstname>Duncan</firstname><surname>Berger</surname><order>39</order></author><author><firstname>Matt</firstname><surname>Berriman</surname><order>40</order></author><author><firstname>Emma</firstname><surname>Betteridge</surname><order>41</order></author><author><firstname>Paul</firstname><surname>Bevan</surname><order>42</order></author><author><firstname>Simon</firstname><surname>Binley</surname><order>43</order></author><author><firstname>Jason</firstname><surname>Bishop</surname><order>44</order></author><author><firstname>Kirsty</firstname><surname>Blackburn</surname><order>45</order></author><author><firstname>James</firstname><surname>Bonfield</surname><order>46</order></author><author><firstname>Nick</firstname><surname>Boughton</surname><order>47</order></author><author><firstname>Sam</firstname><surname>Bowker</surname><order>48</order></author><author><firstname>Timothy</firstname><surname>Brendler-Spaeth</surname><order>49</order></author><author><firstname>Iraad</firstname><surname>Bronner</surname><order>50</order></author><author><firstname>Tanya</firstname><surname>Brooklyn</surname><order>51</order></author><author><firstname>Sarah Kay</firstname><surname>Buddenborg</surname><order>52</order></author><author><firstname>Robert</firstname><surname>Bush</surname><order>53</order></author><author><firstname>Catarina</firstname><surname>Caetano</surname><order>54</order></author><author><firstname>Alex</firstname><surname>Cagan</surname><order>55</order></author><author><firstname>Nicola</firstname><surname>Carter</surname><order>56</order></author><author><firstname>Joanna</firstname><surname>Cartwright</surname><order>57</order></author><author><firstname>Tiago 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e><surname>Neaverson</surname><order>201</order></author><author><firstname>Rachel</firstname><surname>Nelson</surname><order>202</order></author><author><firstname>Ed</firstname><surname>Nerou</surname><order>203</order></author><author><firstname>Jon</firstname><surname>Nicholson</surname><order>204</order></author><author><firstname>Tabea</firstname><surname>Nimz</surname><order>205</order></author><author><firstname>Guillaume G.</firstname><surname>Noell</surname><order>206</order></author><author><firstname>Sarah</firstname><surname>O’Meara</surname><order>207</order></author><author><firstname>Valeriu</firstname><surname>Ohan</surname><order>208</order></author><author><firstname>Karen</firstname><surname>Oliver</surname><order>209</order></author><author><firstname>Charles</firstname><surname>Olney</surname><order>210</order></author><author><firstname>Doug</firstname><surname>Ormond</surname><order>211</order></author><author><firstname>Agnes</firstname><surname>Oszlanczi</surname><order>212</order></author><author><firstname>Steve</firstname><surname>Palmer</surname><order>213</order></author><author><firstname>Yoke Fei</firstname><surname>Pang</surname><order>214</order></author><author><firstname>Barbora</firstname><surname>Pardubska</surname><order>215</order></author><author><firstname>Naomi</firstname><surname>Park</surname><order>216</order></author><author><firstname>Aaron</firstname><surname>Parmar</surname><order>217</order></author><author><firstname>Gaurang</firstname><surname>Patel</surname><order>218</order></author><author><firstname>Minal</firstname><surname>Patel</surname><order>219</order></author><author><firstname>Maggie</firstname><surname>Payne</surname><order>220</order></author><author><firstname>Sharon</firstname><surname>Peacock</surname><order>221</order></author><author><firstname>Arabella</firstname><surname>Petersen</surname><order>222</order></author><author><firstname>Deborah</firstname><surname>Plowman</surname><order>223</order></author><author><firstname>Tom</firstname><surname>Preston</surname><order>224</order></author><author><firstname>Liam</firstname><surname>Prestwood</surname><order>225</order></author><author><firstname>Christoph</firstname><surname>Puethe</surname><order>226</order></author><author><firstname>Michael</firstname><surname>Quail</surname><order>227</order></author><author><firstname>Diana</firstname><surname>Rajan</surname><order>228</order></author><author><firstname>Shavanthi</firstname><surname>Rajatileka</surname><order>229</order></author><author><firstname>Richard</firstname><surname>Rance</surname><order>230</order></author><author><firstname>Suzannah</firstname><surname>Rawlings</surname><order>231</order></author><author><firstname>Nicholas</firstname><surname>Redshaw</surname><order>232</order></author><author><firstname>Joe</firstname><surname>Reynolds</surname><order>233</order></author><author><firstname>Mark</firstname><surname>Reynolds</surname><order>234</order></author><author><firstname>Simon</firstname><surname>Rice</surname><order>235</order></author><author><firstname>Matt</firstname><surname>Richardson</surname><order>236</order></author><author><firstname>Connor</firstname><surname>Roberts</surname><order>237</order></author><author><firstname>Katrina</firstname><surname>Robinson</surname><order>238</order></author><author><firstname>Melanie</firstname><surname>Robinson</surname><order>239</order></author><author><firstname>David</firstname><surname>Robinson</surname><order>240</order></author><author><firstname>Hazel</firstname><surname>Rogers</surname><order>241</order></author><author><firstname>Eduardo Martin</firstname><surname>Rojo</surname><order>242</order></author><author><firstname>Daljit</firstname><surname>Roopra</surname><order>243</order></author><author><firstname>Mark</firstname><surname>Rose</surname><order>244</order></author><author><firstname>Luke</firstname><surname>Rudd</surname><order>245</order></author><author><firstname>Ramin</firstname><surname>Sadri</surname><order>246</order></author><author><firstname>Nicholas</firstname><surname>Salmon</surname><order>247</order></author><author><firstname>David</firstname><surname>Saul</surname><order>248</order></author><author><firstname>Frank</firstname><surname>Schwach</surname><order>249</order></author><author><firstname>Carol</firstname><surname>Scott</surname><order>250</order></author><author><firstname>Phil</firstname><surname>Seekings</surname><order>251</order></author><author><firstname>Lesley</firstname><surname>Shirley</surname><order>252</order></author><author><firstname>Alison</firstname><surname>Simms</surname><order>253</order></author><author><firstname>Matthew</firstname><surname>Sinnott</surname><order>254</order></author><author><firstname>Shanthi</firstname><surname>Sivadasan</surname><order>255</order></author><author><firstname>Bart</firstname><surname>Siwek</surname><order>256</order></author><author><firstname>Dale</firstname><surname>Sizer</surname><order>257</order></author><author><firstname>Kenneth</firstname><surname>Skeldon</surname><order>258</order></author><author><firstname>Jason</firstname><surname>Skelton</surname><order>259</order></author><author><firstname>Joanna</firstname><surname>Slater-Tunstill</surname><order>260</order></author><author><firstname>Lisa</firstname><surname>Sloper</surname><order>261</order></author><author><firstname>Nathalie</firstname><surname>Smerdon</surname><order>262</order></author><author><firstname>Chris</firstname><surname>Smith</surname><order>263</order></author><author><firstname>Christen</firstname><surname>Smith</surname><order>264</order></author><author><firstname>James</firstname><surname>Smith</surname><order>265</order></author><author><firstname>Katie</firstname><surname>Smith</surname><order>266</order></author><author><firstname>Michelle</firstname><surname>Smith</surname><order>267</order></author><author><firstname>Sean</firstname><surname>Smith</surname><order>268</order></author><author><firstname>Tina</firstname><surname>Smith</surname><order>269</order></author><author><firstname>Leighton</firstname><surname>Sneade</surname><order>270</order></author><author><firstname>Carmen Diaz</firstname><surname>Soria</surname><order>271</order></author><author><firstname>Catarina</firstname><surname>Sousa</surname><order>272</order></author><author><firstname>Emily</firstname><surname>Souster</surname><order>273</order></author><author><firstname>Andrew</firstname><surname>Sparkes</surname><order>274</order></author><author><firstname>Michael</firstname><surname>Spencer-Chapman</surname><order>275</order></author><author><firstname>Janet</firstname><surname>Squares</surname><order>276</order></author><author><firstname>Robert</firstname><surname>Stanley</surname><order>277</order></author><author><firstname>Claire</firstname><surname>Steed</surname><order>278</order></author><author><firstname>Tim</firstname><surname>Stickland</surname><order>279</order></author><author><firstname>Ian</firstname><surname>Still</surname><order>280</order></author><author><firstname>Michael R.</firstname><surname>Stratton</surname><order>281</order></author><author><firstname>Michelle</firstname><surname>Strickland</surname><order>282</order></author><author><firstname>Allen</firstname><surname>Swann</surname><order>283</order></author><author><firstname>Agnieszka</firstname><surname>Swiatkowska</surname><order>284</order></author><author><firstname>Neil</firstname><surname>Sycamore</surname><order>285</order></author><author><firstname>Emma</firstname><surname>Swift</surname><order>286</order></author><author><firstname>Edward</firstname><surname>Symons</surname><order>287</order></author><author><firstname>Suzanne</firstname><surname>Szluha</surname><order>288</order></author><author><firstname>Emma</firstname><surname>Taluy</surname><order>289</order></author><author><firstname>Nunu</firstname><surname>Tao</surname><order>290</order></author><author><firstname>Katy</firstname><surname>Taylor</surname><order>291</order></author><author><firstname>Sam</firstname><surname>Taylor</surname><order>292</order></author><author><firstname>Stacey</firstname><surname>Thompson</surname><order>293</order></author><author><firstname>Mark</firstname><surname>Thompson</surname><order>294</order></author><author><firstname>Mark</firstname><surname>Thomson</surname><order>295</order></author><author><firstname>Nicholas</firstname><surname>Thomson</surname><order>296</order></author><author><firstname>Scott</firstname><surname>Thurston</surname><order>297</order></author><author><firstname>Gerry</firstname><surname>Tonkin-Hill</surname><order>298</order></author><author><firstname>Dee</firstname><surname>Toombs</surname><order>299</order></author><author><firstname>Benjamin</firstname><surname>Topping</surname><order>300</order></author><author><firstname>Jaime</firstname><surname>Tovar-Corona</surname><order>301</order></author><author><firstname>Daniel</firstname><surname>Ungureanu</surname><order>302</order></author><author><firstname>James</firstname><surname>Uphill</surname><order>303</order></author><author><firstname>Jana</firstname><surname>Urbanova</surname><order>304</order></author><author><firstname>Philip Jansen Van</firstname><surname>Vuuren</surname><order>305</order></author><author><firstname>Valerie</firstname><surname>Vancollie</surname><order>306</order></author><author><firstname>Paul</firstname><surname>Voak</surname><order>307</order></author><author><firstname>Danielle</firstname><surname>Walker</surname><order>308</order></author><author><firstname>Matthew</firstname><surname>Walker</surname><order>309</order></author><author><firstname>Matt</firstname><surname>Waller</surname><order>310</order></author><author><firstname>Gary</firstname><surname>Ward</surname><order>311</order></author><author><firstname>Charlie</firstname><surname>Weatherhogg</surname><order>312</order></author><author><firstname>Niki</firstname><surname>Webb</surname><order>313</order></author><author><firstname>Danni</firstname><surname>Weldon</surname><order>314</order></author><author><firstname>Alan</firstname><surname>Wells</surname><order>315</order></author><author><firstname>Eloise</firstname><surname>Wells</surname><order>316</order></author><author><firstname>Luke</firstname><surname>Westwood</surname><order>317</order></author><author><firstname>Theo</firstname><surname>Whipp</surname><order>318</order></author><author><firstname>Thomas</firstname><surname>Whiteley</surname><order>319</order></author><author><firstname>Georgia</firstname><surname>Whitton</surname><order>320</order></author><author><firstname>Andrew</firstname><surname>Whitwham</surname><order>321</order></author><author><firstname>Sara</firstname><surname>Widaa</surname><order>322</order></author><author><firstname>Mia</firstname><surname>Williams</surname><order>323</order></author><author><firstname>Mark</firstname><surname>Wilson</surname><order>324</order></author><author><firstname>Sean</firstname><surname>Wright</surname><order>325</order></author><author><firstname>Samuel C.</firstname><surname>Robson</surname><order>326</order></author><author><firstname>Thomas R.</firstname><surname>Connor</surname><order>327</order></author><author><firstname>Nicholas J.</firstname><surname>Loman</surname><order>328</order></author><author><firstname>Tanya</firstname><surname>Golubchik</surname><order>329</order></author><author><firstname>Rocio T. Martinez</firstname><surname>Nunez</surname><order>330</order></author><author><firstname>David</firstname><surname>Bonsall</surname><order>331</order></author><author><firstname>Andrew</firstname><surname>Rambaut</surname><order>332</order></author><author><firstname>Luke B.</firstname><surname>Snell</surname><order>333</order></author><author><firstname>Catherine</firstname><surname>Ludden</surname><order>334</order></author><author><firstname>Sally</firstname><surname>Corden</surname><order>335</order></author><author><firstname>Eleni</firstname><surname>Nastouli</surname><order>336</order></author><author><firstname>Gaia</firstname><surname>Nebbia</surname><order>337</order></author><author><firstname>Katrina</firstname><surname>Lythgoe</surname><order>338</order></author><author><firstname>M. Estee</firstname><surname>Torok</surname><order>339</order></author><author><firstname>Ian G.</firstname><surname>Goodfellow</surname><order>340</order></author><author><firstname>Jacqui A.</firstname><surname>Prieto</surname><order>341</order></author><author><firstname>Kordo</firstname><surname>Saeed</surname><order>342</order></author><author><firstname>Catherine</firstname><surname>Houlihan</surname><order>343</order></author><author><firstname>Dan</firstname><surname>Frampton</surname><order>344</order></author><author><firstname>William L.</firstname><surname>Hamilton</surname><order>345</order></author><author><firstname>Adam A.</firstname><surname>Witney</surname><order>346</order></author><author><firstname>Giselda</firstname><surname>Bucca</surname><order>347</order></author><author><firstname>Cassie F.</firstname><surname>Pope</surname><order>348</order></author><author><firstname>Catherine</firstname><surname>Moore</surname><order>349</order></author><author><firstname>Emma C.</firstname><surname>Thomson</surname><order>350</order></author><author><firstname>Ewan M.</firstname><surname>Harrison</surname><order>351</order></author><author><firstname>Colin P.</firstname><surname>Smith</surname><order>352</order></author><author><firstname>Fiona</firstname><surname>Rogan</surname><order>353</order></author><author><firstname>Shaun M.</firstname><surname>Beckwith</surname><order>354</order></author><author><firstname>Abigail</firstname><surname>Murray</surname><order>355</order></author><author><firstname>Dawn</firstname><surname>Singleton</surname><order>356</order></author><author><firstname>Kirstine</firstname><surname>Eastick</surname><order>357</order></author><author><firstname>Liz A.</firstname><surname>Sheridan</surname><order>358</order></author><author><firstname>Paul</firstname><surname>Randell</surname><order>359</order></author><author><firstname>Leigh M.</firstname><surname>Jackson</surname><order>360</order></author><author><firstname>Sónia</firstname><surname>Gonçalves</surname><order>361</order></author><author><firstname>Derek J.</firstname><surname>Fairley</surname><order>362</order></author><author><firstname>Matthew W.</firstname><surname>Loose</surname><order>363</order></author><author><firstname>Joanne</firstname><surname>Watkins</surname><order>364</order></author><author><firstname>Samuel</firstname><surname>Moses</surname><order>365</order></author><author><firstname>Sam</firstname><surname>Nicholls</surname><order>366</order></author><author><firstname>Matthew</firstname><surname>Bull</surname><order>367</order></author><author><firstname>Darren L.</firstname><surname>Smith</surname><order>368</order></author><author><firstname>David M.</firstname><surname>Aanensen</surname><order>369</order></author><author><firstname>Dinesh</firstname><surname>Aggarwal</surname><order>370</order></author><author><firstname>James 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F.</firstname><surname>Loveson</surname><order>380</order></author><author><firstname>Matthew</firstname><surname>Byott</surname><order>381</order></author><author><firstname>Alessandro M.</firstname><surname>Carabelli</surname><order>382</order></author><author><firstname>Kate E.</firstname><surname>Templeton</surname><order>383</order></author><author><firstname>Thushan I. de</firstname><surname>Silva</surname><order>384</order></author><author><firstname>Dennis</firstname><surname>Wang</surname><order>385</order></author><author><firstname>Cordelia F.</firstname><surname>Langford</surname><order>386</order></author><author><firstname>Rory 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v2 66422 2024-05-15 Genomic reconstruction of the SARS-CoV-2 epidemic in England 83efcf2a9dfcf8b55586999d3d152ac6 0000-0001-5225-000X Ronan Lyons Ronan Lyons true false 2024-05-15 MEDS The evolution of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus leads to new variants that warrant timely epidemiological characterization. Here we use the dense genomic surveillance data generated by the COVID-19 Genomics UK Consortium to reconstruct the dynamics of 71 different lineages in each of 315 English local authorities between September 2020 and June 2021. This analysis reveals a series of subepidemics that peaked in early autumn 2020, followed by a jump in transmissibility of the B.1.1.7/Alpha lineage. The Alpha variant grew when other lineages declined during the second national lockdown and regionally tiered restrictions between November and December 2020. A third more stringent national lockdown suppressed the Alpha variant and eliminated nearly all other lineages in early 2021. Yet a series of variants (most of which contained the spike E484K mutation) defied these trends and persisted at moderately increasing proportions. However, by accounting for sustained introductions, we found that the transmissibility of these variants is unlikely to have exceeded the transmissibility of the Alpha variant. Finally, B.1.617.2/Delta was repeatedly introduced in England and grew rapidly in early summer 2021, constituting approximately 98% of sampled SARS-CoV-2 genomes on 26 June 2021. Journal Article Nature 600 7889 506 511 Springer Science and Business Media LLC 0028-0836 1476-4687 16 12 2021 2021-12-16 10.1038/s41586-021-04069-y Publisher Correction: Genomic reconstruction of the SARS CoV-2 epidemic in England available at https://doi.org/10.1038/s41586-022-04887-8 COLLEGE NANME Medical School COLLEGE CODE MEDS Swansea University Open access funding provided by Deutsches Krebsforschungszentrum (DKFZ). 2024-06-24T12:29:31.9625493 2024-05-15T08:23:25.2739890 Faculty of Medicine, Health and Life Sciences Swansea University Medical School - Health Data Science Harald S. Vöhringer 1 Theo Sanderson 2 Matthew Sinnott 0000-0002-3054-7846 3 Nicola De Maio 4 Thuy Nguyen 5 Richard Goater 0000-0001-9954-841x 6 Frank Schwach 7 Ian Harrison 0000-0003-4117-961x 8 Joel Hellewell 0000-0003-2683-0849 9 Cristina V. Ariani 10 Sonia Gonçalves 11 David K. Jackson 0000-0002-8090-9462 12 Ian Johnston 13 Alexander W. Jung 14 Callum Saint 0000-0001-8720-9736 15 John Sillitoe 16 Maria Suciu 17 Nick Goldman 0000-0001-8486-2211 18 Jasmina Panovska-Griffiths 0000-0002-7720-1121 19 Irina Abnizova 20 Louise Aigrain 21 Alex Alderton 22 Mozam Ali 23 Laura Allen 24 Roberto Amato 25 Ralph Anderson 26 Cristina Ariani 27 Siobhan Austin-Guest 28 Sendu Bala 29 Jeffrey Barrett 30 Andrew Bassett 31 Kristina Battleday 32 James Beal 33 Mathew Beale 34 Charlotte Beaver 35 Sam Bellany 36 Tristram Bellerby 37 Katie Bellis 38 Duncan Berger 39 Matt Berriman 40 Emma Betteridge 41 Paul Bevan 42 Simon Binley 43 Jason Bishop 44 Kirsty Blackburn 45 James Bonfield 46 Nick Boughton 47 Sam Bowker 48 Timothy Brendler-Spaeth 49 Iraad Bronner 50 Tanya Brooklyn 51 Sarah Kay Buddenborg 52 Robert Bush 53 Catarina Caetano 54 Alex Cagan 55 Nicola Carter 56 Joanna Cartwright 57 Tiago Carvalho Monteiro 58 Liz Chapman 59 Tracey-Jane Chillingworth 60 Peter Clapham 61 Richard Clark 62 Adrian Clarke 63 Catriona Clarke 64 Daryl Cole 65 Elizabeth Cook 66 Maria Coppola 67 Linda Cornell 68 Clare Cornwell 69 Craig Corton 70 Abby Crackett 71 Alison Cranage 72 Harriet Craven 73 Sarah Craw 74 Mark Crawford 75 Tim Cutts 76 Monika Dabrowska 77 Matt Davies 78 Robert Davies 79 Joseph Dawson 80 Callum Day 81 Aiden Densem 82 Thomas Dibling 83 Cat Dockree 84 David Dodd 85 Sunil Dogga 86 Matthew Dorman 87 Gordon Dougan 88 Martin Dougherty 89 Alexander Dove 90 Lucy Drummond 91 Eleanor Drury 92 Monika Dudek 93 Jillian Durham 94 Laura Durrant 95 Elizabeth Easthope 96 Sabine Eckert 97 Pete Ellis 98 Ben Farr 99 Michael Fenton 100 Marcella Ferrero 101 Neil Flack 102 Howerd Fordham 103 Grace Forsythe 104 Luke Foulser 105 Matt Francis 106 Audrey Fraser 107 Adam Freeman 108 Anastasia Galvin 109 Maria Garcia-Casado 110 Alex Gedny 111 Sophia Girgis 112 James Glover 113 Sonia Goncalves 114 Scott Goodwin 115 Oliver Gould 116 Marina Gourtovaia 117 Andy Gray 118 Emma Gray 119 Coline Griffiths 120 Yong Gu 121 Florence Guerin 122 Will Hamilton 123 Hannah Hanks 124 Ewan Harrison 125 Alexandria Harrott 126 Edward Harry 127 Julia Harvison 128 Paul Heath 129 Anastasia Hernandez-Koutoucheva 130 Rhiannon Hobbs 131 Dave Holland 132 Sarah Holmes 133 Gary Hornett 134 Nicholas Hough 135 Liz Huckle 136 Lena Hughes-Hallet 137 Adam Hunter 138 Stephen Inglis 139 Sameena Iqbal 140 Adam Jackson 141 David Jackson 142 Keith James 143 Dorota Jamrozy 144 Carlos Jimenez Verdejo 145 Matthew Jones 146 Kalyan Kallepally 147 Leanne Kane 148 Keely Kay 149 Sally Kay 150 Jon Keatley 151 Alan Keith 152 Alison King 153 Lucy Kitchin 154 Matt Kleanthous 155 Martina Klimekova 156 Petra Korlevic 157 Ksenia Krasheninnkova 158 Greg Lane 159 Cordelia Langford 160 Adam Laverack 161 Katharine Law 162 Mara Lawniczak 163 Stefanie Lensing 164 Steven Leonard 165 Laura Letchford 166 Kevin Lewis 167 Amanah Lewis-Wade 168 Jennifer Liddle 169 Quan Lin 170 Sarah Lindsay 171 Sally Linsdell 172 Rich Livett 173 Stephanie Lo 174 Rhona Long 175 Jamie Lovell 176 Jon Lovell 177 Catherine Ludden 178 James Mack 179 Mark Maddison 180 Aleksei Makunin 181 Irfan Mamun 182 Jenny Mansfield 183 Neil Marriott 184 Matt Martin 185 Matthew Mayho 186 Shane McCarthy 187 Jo McClintock 188 Samantha McGuigan 189 Sandra McHugh 190 Liz McMinn 191 Carl Meadows 192 Emily Mobley 193 Robin Moll 194 Maria Morra 195 Leanne Morrow 196 Kathryn Murie 197 Sian Nash 198 Claire Nathwani 199 Plamena Naydenova 200 Alexandra Neaverson 201 Rachel Nelson 202 Ed Nerou 203 Jon Nicholson 204 Tabea Nimz 205 Guillaume G. Noell 206 Sarah O’Meara 207 Valeriu Ohan 208 Karen Oliver 209 Charles Olney 210 Doug Ormond 211 Agnes Oszlanczi 212 Steve Palmer 213 Yoke Fei Pang 214 Barbora Pardubska 215 Naomi Park 216 Aaron Parmar 217 Gaurang Patel 218 Minal Patel 219 Maggie Payne 220 Sharon Peacock 221 Arabella Petersen 222 Deborah Plowman 223 Tom Preston 224 Liam Prestwood 225 Christoph Puethe 226 Michael Quail 227 Diana Rajan 228 Shavanthi Rajatileka 229 Richard Rance 230 Suzannah Rawlings 231 Nicholas Redshaw 232 Joe Reynolds 233 Mark Reynolds 234 Simon Rice 235 Matt Richardson 236 Connor Roberts 237 Katrina Robinson 238 Melanie Robinson 239 David Robinson 240 Hazel Rogers 241 Eduardo Martin Rojo 242 Daljit Roopra 243 Mark Rose 244 Luke Rudd 245 Ramin Sadri 246 Nicholas Salmon 247 David Saul 248 Frank Schwach 249 Carol Scott 250 Phil Seekings 251 Lesley Shirley 252 Alison Simms 253 Matthew Sinnott 254 Shanthi Sivadasan 255 Bart Siwek 256 Dale Sizer 257 Kenneth Skeldon 258 Jason Skelton 259 Joanna Slater-Tunstill 260 Lisa Sloper 261 Nathalie Smerdon 262 Chris Smith 263 Christen Smith 264 James Smith 265 Katie Smith 266 Michelle Smith 267 Sean Smith 268 Tina Smith 269 Leighton Sneade 270 Carmen Diaz Soria 271 Catarina Sousa 272 Emily Souster 273 Andrew Sparkes 274 Michael Spencer-Chapman 275 Janet Squares 276 Robert Stanley 277 Claire Steed 278 Tim Stickland 279 Ian Still 280 Michael R. Stratton 281 Michelle Strickland 282 Allen Swann 283 Agnieszka Swiatkowska 284 Neil Sycamore 285 Emma Swift 286 Edward Symons 287 Suzanne Szluha 288 Emma Taluy 289 Nunu Tao 290 Katy Taylor 291 Sam Taylor 292 Stacey Thompson 293 Mark Thompson 294 Mark Thomson 295 Nicholas Thomson 296 Scott Thurston 297 Gerry Tonkin-Hill 298 Dee Toombs 299 Benjamin Topping 300 Jaime Tovar-Corona 301 Daniel Ungureanu 302 James Uphill 303 Jana Urbanova 304 Philip Jansen Van Vuuren 305 Valerie Vancollie 306 Paul Voak 307 Danielle Walker 308 Matthew Walker 309 Matt Waller 310 Gary Ward 311 Charlie Weatherhogg 312 Niki Webb 313 Danni Weldon 314 Alan Wells 315 Eloise Wells 316 Luke Westwood 317 Theo Whipp 318 Thomas Whiteley 319 Georgia Whitton 320 Andrew Whitwham 321 Sara Widaa 322 Mia Williams 323 Mark Wilson 324 Sean Wright 325 Samuel C. Robson 326 Thomas R. Connor 327 Nicholas J. Loman 328 Tanya Golubchik 329 Rocio T. Martinez Nunez 330 David Bonsall 331 Andrew Rambaut 332 Luke B. Snell 333 Catherine Ludden 334 Sally Corden 335 Eleni Nastouli 336 Gaia Nebbia 337 Katrina Lythgoe 338 M. Estee Torok 339 Ian G. Goodfellow 340 Jacqui A. Prieto 341 Kordo Saeed 342 Catherine Houlihan 343 Dan Frampton 344 William L. Hamilton 345 Adam A. Witney 346 Giselda Bucca 347 Cassie F. Pope 348 Catherine Moore 349 Emma C. Thomson 350 Ewan M. Harrison 351 Colin P. Smith 352 Fiona Rogan 353 Shaun M. Beckwith 354 Abigail Murray 355 Dawn Singleton 356 Kirstine Eastick 357 Liz A. Sheridan 358 Paul Randell 359 Leigh M. Jackson 360 Sónia Gonçalves 361 Derek J. Fairley 362 Matthew W. Loose 363 Joanne Watkins 364 Samuel Moses 365 Sam Nicholls 366 Matthew Bull 367 Darren L. Smith 368 David M. Aanensen 369 Dinesh Aggarwal 370 James G. Shepherd 371 Martin D. Curran 372 Surendra Parmar 373 Matthew D. Parker 374 Catryn Williams 375 Sharon Glaysher 376 Anthony P. Underwood 377 Matthew Bashton 378 Nicole Pacchiarini 379 Katie F. Loveson 380 Matthew Byott 381 Alessandro M. Carabelli 382 Kate E. Templeton 383 Thushan I. de Silva 384 Dennis Wang 385 Cordelia F. Langford 386 Rory N. Gunson 387 Simon Cottrell 388 Justin O’Grady 389 Dominic Kwiatkowski 390 Patrick J. Lillie 391 Nicholas Cortes 392 Nathan Moore 393 Claire Thomas 394 Phillipa J. Burns 395 Tabitha W. Mahungu 396 Steven Liggett 397 Angela H. Beckett 398 Matthew T. G. Holden 399 Lisa J. Levett 400 Husam Osman 401 Mohammed O. Hassan-Ibrahim 402 David A. Simpson 403 Meera Chand 404 Ravi K. Gupta 405 Alistair C. Darby 406 Steve Paterson 407 Oliver G. Pybus 408 Erik Volz 409 Daniela de Angelis 410 David L. Robertson 411 Andrew J. Page 412 Andrew R. Bassett 413 Nick Wong 414 Yusri Taha 415 Michelle J. Erkiert 416 Michael H. Spencer Chapman 417 Rebecca Dewar 418 Martin P. McHugh 419 Siddharth Mookerjee 420 Stephen Aplin 421 Matthew Harvey 422 Thea Sass 423 Helen Umpleby 424 Helen Wheeler 425 James P. McKenna 426 Ben Warne 427 Joshua F. Taylor 428 Yasmin Chaudhry 429 Rhys Izuagbe 430 Aminu S. Jahun 431 Gregory R. Young 432 Claire McMurray 433 Clare M. McCann 434 Andrew Nelson 435 Scott Elliott 436 Hannah Lowe 437 Anna Price 438 Matthew R. Crown 439 Sara Rey 440 Sunando Roy 441 Ben Temperton 442 Sharif Shaaban 443 Andrew R. Hesketh 444 Kenneth G. Laing 445 Irene M. Monahan 446 Judith Heaney 447 Emanuela Pelosi 448 Siona Silviera 449 Eleri Wilson-Davies 450 Helen Fryer 451 Helen Adams 452 Louis du Plessis 453 Rob Johnson 454 William T. Harvey 455 Joseph Hughes 456 Richard J. Orton 457 Lewis G. Spurgin 458 Yann Bourgeois 459 Chris Ruis 460 Áine O’Toole 461 Theo Sanderson 462 Christophe Fraser 463 Jonathan Edgeworth 464 Judith Breuer 465 Stephen L. Michell 466 John A. Todd 467 Michaela John 468 David Buck 469 Kavitha Gajee 470 Gemma L. Kay 471 Sharon J. Peacock 472 David Heyburn 473 Katie Kitchman 474 Alan McNally 475 David T. Pritchard 476 Samir Dervisevic 477 Peter Muir 478 Esther Robinson 479 Barry B. Vipond 480 Newara A. Ramadan 481 Christopher Jeanes 482 Jana Catalan 483 Neil Jones 484 Ana da Silva Filipe 485 Chris Williams 486 Marc Fuchs 487 Julia Miskelly 488 Aaron R. Jeffries 489 Naomi R. Park 490 Amy Ash 491 Cherian Koshy 492 Magdalena Barrow 493 Sarah L. Buchan 494 Anna Mantzouratou 495 Gemma Clark 496 Christopher W. Holmes 497 Sharon Campbell 498 Thomas Davis 499 Ngee Keong Tan 500 Julianne R. Brown 501 Kathryn A. Harris 502 Stephen P. Kidd 503 Paul R. Grant 504 Li Xu-McCrae 505 Alison Cox 506 Pinglawathee Madona 507 Marcus Pond 508 Paul A. Randell 509 Karen T. Withell 510 Cheryl Williams 511 Clive Graham 512 Rebecca Denton-Smith 513 Emma Swindells 514 Robyn Turnbull 515 Tim J. Sloan 516 Andrew Bosworth 517 Stephanie Hutchings 518 Hannah M. Pymont 519 Anna Casey 520 Liz Ratcliffe 521 Christopher R. Jones 522 Bridget A. Knight 523 Tanzina Haque 524 Jennifer Hart 525 Dianne Irish-Tavares 526 Eric Witele 527 Craig Mower 528 Louisa K. Watson 529 Jennifer Collins 530 Gary Eltringham 531 Dorian Crudgington 532 Ben Macklin 533 Miren Iturriza-Gomara 534 Anita O. Lucaci 535 Patrick C. McClure 536 Matthew Carlile 537 Nadine Holmes 538 Christopher Moore 539 Nathaniel Storey 540 Stefan Rooke 541 Gonzalo Yebra 542 Noel Craine 543 Malorie Perry 544 Nabil-Fareed Alikhan 545 Stephen Bridgett 546 Kate F. Cook 547 Christopher Fearn 548 Salman Goudarzi 549 Ronan A. Lyons 550 Thomas Williams 551 Sam T. Haldenby 552 Robert M. Davies 553 Rahul Batra 554 Beth Blane 555 Moira J. Spyer 556 Perminder Smith 557 Mehmet Yavus 558 Rachel J. Williams 559 Adhyana I. K. Mahanama 560 Buddhini Samaraweera 561 Sophia T. Girgis 562 Samantha E. Hansford 563 Angie Green 564 Katherine L. Bellis 565 Matthew J. Dorman 566 Joshua Quick 567 Radoslaw Poplawski 568 Nicola Reynolds 569 Andrew Mack 570 Arthur Morriss 571 Thomas Whalley 572 Bindi Patel 573 Iliana Georgana 574 Myra Hosmillo 575 Malte L. Pinckert 576 Joanne Stockton 577 John H. Henderson 578 Amy Hollis 579 William Stanley 580 Wen C. Yew 581 Richard Myers 582 Alicia Thornton 583 Alexander Adams 584 Tara Annett 585 Hibo Asad 586 Alec Birchley 587 Jason Coombes 588 Johnathan M. Evans 589 Laia Fina 590 Bree Gatica-Wilcox 591 Lauren Gilbert 592 Lee Graham 593 Jessica Hey 594 Ember Hilvers 595 Sophie Jones 596 Hannah Jones 597 Sara Kumziene-Summerhayes 598 Caoimhe McKerr 599 Jessica Powell 600 Georgia Pugh 601 Sarah Taylor 602 Alexander J. Trotter 603 Charlotte A. Williams 604 Leanne M. Kermack 605 Benjamin H. Foulkes 606 Marta Gallis 607 Hailey R. Hornsby 608 Stavroula F. Louka 609 Manoj Pohare 610 Paige Wolverson 611 Peijun Zhang 612 George MacIntyre-Cockett 613 Amy Trebes 614 Robin J. Moll 615 Lynne Ferguson 616 Emily J. Goldstein 617 Alasdair Maclean 618 Rachael Tomb 619 Igor Starinskij 620 Laura Thomson 621 Joel Southgate 622 Moritz U. G. Kraemer 623 Jayna Raghwani 624 Alex E. Zarebski 625 Olivia Boyd 626 Lily Geidelberg 627 Chris J. Illingworth 628 Chris Jackson 629 David Pascall 630 Sreenu Vattipally 631 Timothy M. Freeman 632 Sharon N. Hsu 633 Benjamin B. Lindsey 634 Jaime M. Tovar-Corona 635 MacGregor Cox 636 Khalil Abudahab 637 Mirko Menegazzo 638 Ben E. W. Taylor 639 Corin A. Yeats 640 Afrida Mukaddas 641 Derek W. Wright 642 Leonardo de Oliveira Martins 643 Rachel Colquhoun 644 Verity Hill 645 Ben Jackson 646 J. T. McCrone 647 Nathan Medd 648 Emily Scher 649 Jon-Paul Keatley 650 Tanya Curran 651 Sian Morgan 652 Patrick Maxwell 653 Ken Smith 654 Sahar Eldirdiri 655 Anita Kenyon 656 Alison H. Holmes 657 James R. Price 658 Tim Wyatt 659 Alison E. Mather 660 Timofey Skvortsov 661 John A. Hartley 662 Martyn Guest 663 Christine Kitchen 664 Ian Merrick 665 Robert Munn 666 Beatrice Bertolusso 667 Jessica Lynch 668 Gabrielle Vernet 669 Stuart Kirk 670 Elizabeth Wastnedge 671 Rachael Stanley 672 Giles Idle 673 Declan T. Bradley 674 Jennifer Poyner 675 Matilde Mori 676 Owen Jones 677 Victoria Wright 678 Ellena Brooks 679 Carol M. Churcher 680 Mireille Fragakis 681 Katerina Galai 682 Andrew Jermy 683 Sarah Judges 684 Georgina M. McManus 685 Kim S. Smith 686 Elaine Westwick 687 Stephen W. Attwood 688 Frances Bolt 689 Alisha Davies 690 Elen De Lacy 691 Fatima Downing 692 Sue Edwards 693 Lizzie Meadows 694 Sarah Jeremiah 695 Nikki Smith 696 Themoula Charalampous 697 Amita Patel 698 Louise Berry 699 Tim Boswell 700 Vicki M. Fleming 701 Hannah C. Howson-Wells 702 Amelia Joseph 703 Manjinder Khakh 704 Michelle M. Lister 705 Paul W. Bird 706 Karlie Fallon 707 Thomas Helmer 708 Claire L. McMurray 709 Mina Odedra 710 Jessica Shaw 711 Julian W. Tang 712 Nicholas J. Willford 713 Victoria Blakey 714 Veena Raviprakash 715 Nicola Sheriff 716 Lesley-Anne Williams 717 Theresa Feltwell 718 Luke Bedford 719 James S. Cargill 720 Warwick Hughes 721 Jonathan Moore 722 Susanne Stonehouse 723 Laura Atkinson 724 Jack C. D. Lee 725 Divya Shah 726 Adela Alcolea 727 Natasha Ohemeng-Kumi 728 John Ramble 729 Jasveen Sehmi 730 Rebecca Williams 731 Wendy Chatterton 732 Monika Pusok 733 William Everson 734 Anibolina Castigador 735 Emily Macnaughton 736 Kate El Bouzidi 737 Temi Lampejo 738 Malur Sudhanva 739 Cassie Breen 740 Graciela Sluga 741 Shazaad S. Y. Ahmad 742 Ryan P. George 743 Nicholas W. Machin 744 Debbie Binns 745 Victoria James 746 Rachel Blacow 747 Lindsay Coupland 748 Louise Smith 749 Edward Barton 750 Debra Padgett 751 Garren Scott 752 Aidan Cross 753 Mariyam Mirfenderesky 754 Jane Greenaway 755 Kevin Cole 756 Phillip Clarke 757 Nichola Duckworth 758 Sarah Walsh 759 Kelly Bicknell 760 Robert Impey 761 Sarah Wyllie 762 Richard Hopes 763 Chloe Bishop 764 Vicki Chalker 765 Laura Gifford 766 Zoltan Molnar 767 Cressida Auckland 768 Cariad Evans 769 Kate Johnson 770 David G. Partridge 771 Mohammad Raza 772 Paul Baker 773 Stephen Bonner 774 Sarah Essex 775 Leanne J. Murray 776 Andrew I. Lawton 777 Shirelle Burton-Fanning 778 Brendan A. I. Payne 779 Sheila Waugh 780 Andrea N. Gomes 781 Maimuna Kimuli 782 Darren R. Murray 783 Paula Ashfield 784 Donald Dobie 785 Fiona Ashford 786 Angus Best 787 Liam Crawford 788 Nicola Cumley 789 Megan Mayhew 790 Oliver Megram 791 Jeremy Mirza 792 Emma Moles-Garcia 793 Benita Percival 794 Leah Ensell 795 Helen L. Lowe 796 Laurentiu Maftei 797 Matteo Mondani 798 Nicola J. Chaloner 799 Benjamin J. Cogger 800 Lisa J. Easton 801 Hannah Huckson 802 Jonathan Lewis 803 Sarah Lowdon 804 Cassandra S. Malone 805 Florence Munemo 806 Manasa Mutingwende 807 Roberto Nicodemi 808 Olga Podplomyk 809 Thomas Somassa 810 Andrew Beggs 811 Alex Richter 812 Claire Cormie 813 Joana Dias 814 Sally Forrest 815 Ellen E. Higginson 816 Mailis Maes 817 Jamie Young 818 Rose K. Davidson 819 Kathryn A. Jackson 820 Lance Turtle 821 Alexander J. Keeley 822 Jonathan Ball 823 Timothy Byaruhanga 824 Joseph G. Chappell 825 Jayasree Dey 826 Jack D. Hill 827 Emily J. Park 828 Arezou Fanaie 829 Rachel A. Hilson 830 Geraldine Yaze 831 Safiah Afifi 832 Robert Beer 833 Joshua Maksimovic 834 Kathryn McCluggage Masters 835 Karla Spellman 836 Catherine Bresner 837 William Fuller 838 Angela Marchbank 839 Trudy Workman 840 Ekaterina Shelest 841 Johnny Debebe 842 Fei Sang 843 Marina Escalera Zamudio 844 Sarah Francois 845 Bernardo Gutierrez 846 Tetyana I. Vasylyeva 847 Flavia Flaviani 848 Manon Ragonnet-Cronin 849 Katherine L. Smollett 850 Alice Broos 851 Daniel Mair 852 Jenna Nichols 853 Kyriaki Nomikou 854 Lily Tong 855 Ioulia Tsatsani 856 Sarah O’Brien 857 Steven Rushton 858 Roy Sanderson 859 Jon Perkins 860 Seb Cotton 861 Abbie Gallagher 862 Elias Allara 863 Clare Pearson 864 David Bibby 865 Gavin Dabrera 866 Nicholas Ellaby 867 Eileen Gallagher 868 Jonathan Hubb 869 Angie Lackenby 870 David Lee 871 Nikos Manesis 872 Tamyo Mbisa 873 Steven Platt 874 Katherine A. Twohig 875 Mari Morgan 876 Alp Aydin 877 David J. Baker 878 Ebenezer Foster-Nyarko 879 Sophie J. Prosolek 880 Steven Rudder 881 Chris Baxter 882 Sílvia F. Carvalho 883 Deborah Lavin 884 Arun Mariappan 885 Clara Radulescu 886 Aditi Singh 887 Miao Tang 888 Helen Morcrette 889 Nadua Bayzid 890 Marius Cotic 891 Carlos E. Balcazar 892 Michael D. Gallagher 893 Daniel Maloney 894 Thomas D. Stanton 895 Kathleen A. Williamson 896 Robin Manley 897 Michelle L. Michelsen 898 Christine M. Sambles 899 David J. Studholme 900 Joanna Warwick-Dugdale 901 Richard Eccles 902 Matthew Gemmell 903 Richard Gregory 904 Margaret Hughes 905 Charlotte Nelson 906 Lucille Rainbow 907 Edith E. Vamos 908 Hermione J. Webster 909 Mark Whitehead 910 Claudia Wierzbicki 911 Adrienn Angyal 912 Luke R. Green 913 Max Whiteley 914 Iraad F. Bronner 915 Ben W. Farr 916 Stefanie V. Lensing 917 Shane A. McCarthy 918 Michael A. Quail 919 Nicholas M. Redshaw 920 Scott A. J. Thurston 921 Will Rowe 922 Amy Gaskin 923 Thanh Le-Viet 924 Jennifier Liddle 925 Ewan Birney 0000-0001-8314-8497 926 Erik Volz 0000-0001-6268-8937 927 Sebastian Funk 0000-0002-2842-3406 928 Dominic Kwiatkowski 0000-0002-5023-0176 929 Meera Chand 930 Inigo Martincorena 0000-0003-1122-4416 931 Jeffrey C. Barrett 0000-0002-1152-370x 932 Moritz Gerstung 0000-0001-6709-963x 933 (The Wellcome Sanger Institute COVID-19 Surveillance Team) 934 (The COVID-19 Genomics UK (COG-UK) Consortium*) 935 (Funding acquisition, leadership and supervision, metadata curation, project administration, samples and logistics, sequencing and analysis, software and analysis tools, and visualization) 936 (Funding acquisition, leadership and supervision, metadata curation, project administration, samples and logistics, sequencing and analysis, and software and analysis tools) 937 (Leadership and supervision, metadata curation, project administration, samples and logistics, sequencing and analysis, software and analysis tools, and visualization) 938 (Funding acquisition, leadership and supervision, metadata curation, samples and logistics, sequencing and analysis, and visualization) 939 (Funding acquisition, leadership and supervision, project administration, samples and logistics, sequencing and analysis, and 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curation, and sequencing and analysis) 1004 (Metadata curation, and software and analysis tools) 1005 (Project administration, and samples and logistics) 1006 (Project administration, and sequencing and analysis) 1007 (Project administration, and software and analysis tools) 1008 (Samples and logistics, and sequencing and analysis) 1009 (Samples and logistics, and software and analysis tools) 1010 (Sequencing and analysis, and software and analysis tools) 1011 (Sequencing and analysis, and visualization) 1012 (Software and analysis tools, and visualization) 1013 (Leadership and supervision) 1014 (Metadata curation) 1015 (Project administration) 1016 (Samples and logistics) 1017 (Sequencing and analysis) 1018 (Software and analysis tools) 1019 Ronan Lyons 0000-0001-5225-000X 1020 66422__30370__957b95ce96544597a61d9d846848ae6d.pdf 66422.pdf 2024-05-15T08:28:06.6267312 Output 13299713 application/pdf Version of Record true This article is licensed under a Creative Commons Attribution 4.0 International License. true eng https://creativecommons.org/licenses/by/4.0/ |
title |
Genomic reconstruction of the SARS-CoV-2 epidemic in England |
spellingShingle |
Genomic reconstruction of the SARS-CoV-2 epidemic in England Ronan Lyons |
title_short |
Genomic reconstruction of the SARS-CoV-2 epidemic in England |
title_full |
Genomic reconstruction of the SARS-CoV-2 epidemic in England |
title_fullStr |
Genomic reconstruction of the SARS-CoV-2 epidemic in England |
title_full_unstemmed |
Genomic reconstruction of the SARS-CoV-2 epidemic in England |
title_sort |
Genomic reconstruction of the SARS-CoV-2 epidemic in England |
author_id_str_mv |
83efcf2a9dfcf8b55586999d3d152ac6 |
author_id_fullname_str_mv |
83efcf2a9dfcf8b55586999d3d152ac6_***_Ronan Lyons |
author |
Ronan Lyons |
author2 |
Harald S. Vöhringer Theo Sanderson Matthew Sinnott Nicola De Maio Thuy Nguyen Richard Goater Frank Schwach Ian Harrison Joel Hellewell Cristina V. Ariani Sonia Gonçalves David K. Jackson Ian Johnston Alexander W. Jung Callum Saint John Sillitoe Maria Suciu Nick Goldman Jasmina Panovska-Griffiths Irina Abnizova Louise Aigrain Alex Alderton Mozam Ali Laura Allen Roberto Amato Ralph Anderson Cristina Ariani Siobhan Austin-Guest Sendu Bala Jeffrey Barrett Andrew Bassett Kristina Battleday James Beal Mathew Beale Charlotte Beaver Sam Bellany Tristram Bellerby Katie Bellis Duncan Berger Matt Berriman Emma Betteridge Paul Bevan Simon Binley Jason Bishop Kirsty Blackburn James Bonfield Nick Boughton Sam Bowker Timothy Brendler-Spaeth Iraad Bronner Tanya Brooklyn Sarah Kay Buddenborg Robert Bush Catarina Caetano Alex Cagan Nicola Carter Joanna Cartwright Tiago Carvalho Monteiro Liz Chapman Tracey-Jane Chillingworth Peter Clapham Richard Clark Adrian Clarke Catriona Clarke Daryl Cole Elizabeth Cook Maria Coppola Linda Cornell Clare Cornwell Craig Corton Abby Crackett Alison Cranage Harriet Craven Sarah Craw Mark Crawford Tim Cutts Monika Dabrowska Matt Davies Robert Davies Joseph Dawson Callum Day Aiden Densem Thomas Dibling Cat Dockree David Dodd Sunil Dogga Matthew Dorman Gordon Dougan Martin Dougherty Alexander Dove Lucy Drummond Eleanor Drury Monika Dudek Jillian Durham Laura Durrant Elizabeth Easthope Sabine Eckert Pete Ellis Ben Farr Michael Fenton Marcella Ferrero Neil Flack Howerd Fordham Grace Forsythe Luke Foulser Matt Francis Audrey Fraser Adam Freeman Anastasia Galvin Maria Garcia-Casado Alex Gedny Sophia Girgis James Glover Sonia Goncalves Scott Goodwin Oliver Gould Marina Gourtovaia Andy Gray Emma Gray Coline Griffiths Yong Gu Florence Guerin Will Hamilton Hannah Hanks Ewan Harrison Alexandria Harrott Edward Harry Julia Harvison Paul Heath Anastasia Hernandez-Koutoucheva Rhiannon Hobbs Dave Holland Sarah Holmes Gary Hornett Nicholas Hough Liz Huckle Lena Hughes-Hallet Adam Hunter Stephen Inglis Sameena Iqbal Adam Jackson David Jackson Keith James Dorota Jamrozy Carlos Jimenez Verdejo Matthew Jones Kalyan Kallepally Leanne Kane Keely Kay Sally Kay Jon Keatley Alan Keith Alison King Lucy Kitchin Matt Kleanthous Martina Klimekova Petra Korlevic Ksenia Krasheninnkova Greg Lane Cordelia Langford Adam Laverack Katharine Law Mara Lawniczak Stefanie Lensing Steven Leonard Laura Letchford Kevin Lewis Amanah Lewis-Wade Jennifer Liddle Quan Lin Sarah Lindsay Sally Linsdell Rich Livett Stephanie Lo Rhona Long Jamie Lovell Jon Lovell Catherine Ludden James Mack Mark Maddison Aleksei Makunin Irfan Mamun Jenny Mansfield Neil Marriott Matt Martin Matthew Mayho Shane McCarthy Jo McClintock Samantha McGuigan Sandra McHugh Liz McMinn Carl Meadows Emily Mobley Robin Moll Maria Morra Leanne Morrow Kathryn Murie Sian Nash Claire Nathwani Plamena Naydenova Alexandra Neaverson Rachel Nelson Ed Nerou Jon Nicholson Tabea Nimz Guillaume G. Noell Sarah O’Meara Valeriu Ohan Karen Oliver Charles Olney Doug Ormond Agnes Oszlanczi Steve Palmer Yoke Fei Pang Barbora Pardubska Naomi Park Aaron Parmar Gaurang Patel Minal Patel Maggie Payne Sharon Peacock Arabella Petersen Deborah Plowman Tom Preston Liam Prestwood Christoph Puethe Michael Quail Diana Rajan Shavanthi Rajatileka Richard Rance Suzannah Rawlings Nicholas Redshaw Joe Reynolds Mark Reynolds Simon Rice Matt Richardson Connor Roberts Katrina Robinson Melanie Robinson David Robinson Hazel Rogers Eduardo Martin Rojo Daljit Roopra Mark Rose Luke Rudd Ramin Sadri Nicholas Salmon David Saul Frank Schwach Carol Scott Phil Seekings Lesley Shirley Alison Simms Matthew Sinnott Shanthi Sivadasan Bart Siwek Dale Sizer Kenneth Skeldon Jason Skelton Joanna Slater-Tunstill Lisa Sloper Nathalie Smerdon Chris Smith Christen Smith James Smith Katie Smith Michelle Smith Sean Smith Tina Smith Leighton Sneade Carmen Diaz Soria Catarina Sousa Emily Souster Andrew Sparkes Michael Spencer-Chapman Janet Squares Robert Stanley Claire Steed Tim Stickland Ian Still Michael R. Stratton Michelle Strickland Allen Swann Agnieszka Swiatkowska Neil Sycamore Emma Swift Edward Symons Suzanne Szluha Emma Taluy Nunu Tao Katy Taylor Sam Taylor Stacey Thompson Mark Thompson Mark Thomson Nicholas Thomson Scott Thurston Gerry Tonkin-Hill Dee Toombs Benjamin Topping Jaime Tovar-Corona Daniel Ungureanu James Uphill Jana Urbanova Philip Jansen Van Vuuren Valerie Vancollie Paul Voak Danielle Walker Matthew Walker Matt Waller Gary Ward Charlie Weatherhogg Niki Webb Danni Weldon Alan Wells Eloise Wells Luke Westwood Theo Whipp Thomas Whiteley Georgia Whitton Andrew Whitwham Sara Widaa Mia Williams Mark Wilson Sean Wright Samuel C. Robson Thomas R. Connor Nicholas J. Loman Tanya Golubchik Rocio T. Martinez Nunez David Bonsall Andrew Rambaut Luke B. Snell Catherine Ludden Sally Corden Eleni Nastouli Gaia Nebbia Katrina Lythgoe M. Estee Torok Ian G. Goodfellow Jacqui A. Prieto Kordo Saeed Catherine Houlihan Dan Frampton William L. Hamilton Adam A. Witney Giselda Bucca Cassie F. Pope Catherine Moore Emma C. Thomson Ewan M. Harrison Colin P. Smith Fiona Rogan Shaun M. Beckwith Abigail Murray Dawn Singleton Kirstine Eastick Liz A. Sheridan Paul Randell Leigh M. Jackson Sónia Gonçalves Derek J. Fairley Matthew W. Loose Joanne Watkins Samuel Moses Sam Nicholls Matthew Bull Darren L. Smith David M. Aanensen Dinesh Aggarwal James G. Shepherd Martin D. Curran Surendra Parmar Matthew D. Parker Catryn Williams Sharon Glaysher Anthony P. Underwood Matthew Bashton Nicole Pacchiarini Katie F. Loveson Matthew Byott Alessandro M. Carabelli Kate E. Templeton Thushan I. de Silva Dennis Wang Cordelia F. Langford Rory N. Gunson Simon Cottrell Justin O’Grady Dominic Kwiatkowski Patrick J. Lillie Nicholas Cortes Nathan Moore Claire Thomas Phillipa J. Burns Tabitha W. Mahungu Steven Liggett Angela H. Beckett Matthew T. G. Holden Lisa J. Levett Husam Osman Mohammed O. Hassan-Ibrahim David A. Simpson Meera Chand Ravi K. Gupta Alistair C. Darby Steve Paterson Oliver G. Pybus Erik Volz Daniela de Angelis David L. Robertson Andrew J. Page Andrew R. Bassett Nick Wong Yusri Taha Michelle J. Erkiert Michael H. Spencer Chapman Rebecca Dewar Martin P. McHugh Siddharth Mookerjee Stephen Aplin Matthew Harvey Thea Sass Helen Umpleby Helen Wheeler James P. McKenna Ben Warne Joshua F. Taylor Yasmin Chaudhry Rhys Izuagbe Aminu S. Jahun Gregory R. Young Claire McMurray Clare M. McCann Andrew Nelson Scott Elliott Hannah Lowe Anna Price Matthew R. Crown Sara Rey Sunando Roy Ben Temperton Sharif Shaaban Andrew R. Hesketh Kenneth G. Laing Irene M. Monahan Judith Heaney Emanuela Pelosi Siona Silviera Eleri Wilson-Davies Helen Fryer Helen Adams Louis du Plessis Rob Johnson William T. Harvey Joseph Hughes Richard J. Orton Lewis G. Spurgin Yann Bourgeois Chris Ruis Áine O’Toole Theo Sanderson Christophe Fraser Jonathan Edgeworth Judith Breuer Stephen L. Michell John A. Todd Michaela John David Buck Kavitha Gajee Gemma L. Kay Sharon J. Peacock David Heyburn Katie Kitchman Alan McNally David T. Pritchard Samir Dervisevic Peter Muir Esther Robinson Barry B. Vipond Newara A. Ramadan Christopher Jeanes Jana Catalan Neil Jones Ana da Silva Filipe Chris Williams Marc Fuchs Julia Miskelly Aaron R. Jeffries Naomi R. Park Amy Ash Cherian Koshy Magdalena Barrow Sarah L. Buchan Anna Mantzouratou Gemma Clark Christopher W. Holmes Sharon Campbell Thomas Davis Ngee Keong Tan Julianne R. Brown Kathryn A. Harris Stephen P. Kidd Paul R. Grant Li Xu-McCrae Alison Cox Pinglawathee Madona Marcus Pond Paul A. Randell Karen T. Withell Cheryl Williams Clive Graham Rebecca Denton-Smith Emma Swindells Robyn Turnbull Tim J. Sloan Andrew Bosworth Stephanie Hutchings Hannah M. Pymont Anna Casey Liz Ratcliffe Christopher R. Jones Bridget A. Knight Tanzina Haque Jennifer Hart Dianne Irish-Tavares Eric Witele Craig Mower Louisa K. Watson Jennifer Collins Gary Eltringham Dorian Crudgington Ben Macklin Miren Iturriza-Gomara Anita O. Lucaci Patrick C. McClure Matthew Carlile Nadine Holmes Christopher Moore Nathaniel Storey Stefan Rooke Gonzalo Yebra Noel Craine Malorie Perry Nabil-Fareed Alikhan Stephen Bridgett Kate F. Cook Christopher Fearn Salman Goudarzi Ronan A. Lyons Thomas Williams Sam T. Haldenby Robert M. Davies Rahul Batra Beth Blane Moira J. Spyer Perminder Smith Mehmet Yavus Rachel J. Williams Adhyana I. K. Mahanama Buddhini Samaraweera Sophia T. Girgis Samantha E. Hansford Angie Green Katherine L. Bellis Matthew J. Dorman Joshua Quick Radoslaw Poplawski Nicola Reynolds Andrew Mack Arthur Morriss Thomas Whalley Bindi Patel Iliana Georgana Myra Hosmillo Malte L. Pinckert Joanne Stockton John H. Henderson Amy Hollis William Stanley Wen C. Yew Richard Myers Alicia Thornton Alexander Adams Tara Annett Hibo Asad Alec Birchley Jason Coombes Johnathan M. Evans Laia Fina Bree Gatica-Wilcox Lauren Gilbert Lee Graham Jessica Hey Ember Hilvers Sophie Jones Hannah Jones Sara Kumziene-Summerhayes Caoimhe McKerr Jessica Powell Georgia Pugh Sarah Taylor Alexander J. Trotter Charlotte A. Williams Leanne M. Kermack Benjamin H. Foulkes Marta Gallis Hailey R. Hornsby Stavroula F. Louka Manoj Pohare Paige Wolverson Peijun Zhang George MacIntyre-Cockett Amy Trebes Robin J. Moll Lynne Ferguson Emily J. Goldstein Alasdair Maclean Rachael Tomb Igor Starinskij Laura Thomson Joel Southgate Moritz U. G. Kraemer Jayna Raghwani Alex E. Zarebski Olivia Boyd Lily Geidelberg Chris J. Illingworth Chris Jackson David Pascall Sreenu Vattipally Timothy M. Freeman Sharon N. Hsu Benjamin B. Lindsey Jaime M. Tovar-Corona MacGregor Cox Khalil Abudahab Mirko Menegazzo Ben E. W. Taylor Corin A. Yeats Afrida Mukaddas Derek W. Wright Leonardo de Oliveira Martins Rachel Colquhoun Verity Hill Ben Jackson J. T. McCrone Nathan Medd Emily Scher Jon-Paul Keatley Tanya Curran Sian Morgan Patrick Maxwell Ken Smith Sahar Eldirdiri Anita Kenyon Alison H. Holmes James R. Price Tim Wyatt Alison E. Mather Timofey Skvortsov John A. Hartley Martyn Guest Christine Kitchen Ian Merrick Robert Munn Beatrice Bertolusso Jessica Lynch Gabrielle Vernet Stuart Kirk Elizabeth Wastnedge Rachael Stanley Giles Idle Declan T. Bradley Jennifer Poyner Matilde Mori Owen Jones Victoria Wright Ellena Brooks Carol M. Churcher Mireille Fragakis Katerina Galai Andrew Jermy Sarah Judges Georgina M. McManus Kim S. Smith Elaine Westwick Stephen W. Attwood Frances Bolt Alisha Davies Elen De Lacy Fatima Downing Sue Edwards Lizzie Meadows Sarah Jeremiah Nikki Smith Themoula Charalampous Amita Patel Louise Berry Tim Boswell Vicki M. Fleming Hannah C. Howson-Wells Amelia Joseph Manjinder Khakh Michelle M. Lister Paul W. Bird Karlie Fallon Thomas Helmer Claire L. McMurray Mina Odedra Jessica Shaw Julian W. Tang Nicholas J. Willford Victoria Blakey Veena Raviprakash Nicola Sheriff Lesley-Anne Williams Theresa Feltwell Luke Bedford James S. Cargill Warwick Hughes Jonathan Moore Susanne Stonehouse Laura Atkinson Jack C. D. Lee Divya Shah Adela Alcolea Natasha Ohemeng-Kumi John Ramble Jasveen Sehmi Rebecca Williams Wendy Chatterton Monika Pusok William Everson Anibolina Castigador Emily Macnaughton Kate El Bouzidi Temi Lampejo Malur Sudhanva Cassie Breen Graciela Sluga Shazaad S. Y. Ahmad Ryan P. George Nicholas W. Machin Debbie Binns Victoria James Rachel Blacow Lindsay Coupland Louise Smith Edward Barton Debra Padgett Garren Scott Aidan Cross Mariyam Mirfenderesky Jane Greenaway Kevin Cole Phillip Clarke Nichola Duckworth Sarah Walsh Kelly Bicknell Robert Impey Sarah Wyllie Richard Hopes Chloe Bishop Vicki Chalker Laura Gifford Zoltan Molnar Cressida Auckland Cariad Evans Kate Johnson David G. Partridge Mohammad Raza Paul Baker Stephen Bonner Sarah Essex Leanne J. Murray Andrew I. Lawton Shirelle Burton-Fanning Brendan A. I. Payne Sheila Waugh Andrea N. Gomes Maimuna Kimuli Darren R. Murray Paula Ashfield Donald Dobie Fiona Ashford Angus Best Liam Crawford Nicola Cumley Megan Mayhew Oliver Megram Jeremy Mirza Emma Moles-Garcia Benita Percival Leah Ensell Helen L. Lowe Laurentiu Maftei Matteo Mondani Nicola J. Chaloner Benjamin J. Cogger Lisa J. Easton Hannah Huckson Jonathan Lewis Sarah Lowdon Cassandra S. Malone Florence Munemo Manasa Mutingwende Roberto Nicodemi Olga Podplomyk Thomas Somassa Andrew Beggs Alex Richter Claire Cormie Joana Dias Sally Forrest Ellen E. Higginson Mailis Maes Jamie Young Rose K. Davidson Kathryn A. Jackson Lance Turtle Alexander J. Keeley Jonathan Ball Timothy Byaruhanga Joseph G. Chappell Jayasree Dey Jack D. Hill Emily J. Park Arezou Fanaie Rachel A. Hilson Geraldine Yaze Safiah Afifi Robert Beer Joshua Maksimovic Kathryn McCluggage Masters Karla Spellman Catherine Bresner William Fuller Angela Marchbank Trudy Workman Ekaterina Shelest Johnny Debebe Fei Sang Marina Escalera Zamudio Sarah Francois Bernardo Gutierrez Tetyana I. Vasylyeva Flavia Flaviani Manon Ragonnet-Cronin Katherine L. Smollett Alice Broos Daniel Mair Jenna Nichols Kyriaki Nomikou Lily Tong Ioulia Tsatsani Sarah O’Brien Steven Rushton Roy Sanderson Jon Perkins Seb Cotton Abbie Gallagher Elias Allara Clare Pearson David Bibby Gavin Dabrera Nicholas Ellaby Eileen Gallagher Jonathan Hubb Angie Lackenby David Lee Nikos Manesis Tamyo Mbisa Steven Platt Katherine A. Twohig Mari Morgan Alp Aydin David J. Baker Ebenezer Foster-Nyarko Sophie J. Prosolek Steven Rudder Chris Baxter Sílvia F. Carvalho Deborah Lavin Arun Mariappan Clara Radulescu Aditi Singh Miao Tang Helen Morcrette Nadua Bayzid Marius Cotic Carlos E. Balcazar Michael D. Gallagher Daniel Maloney Thomas D. Stanton Kathleen A. Williamson Robin Manley Michelle L. Michelsen Christine M. Sambles David J. Studholme Joanna Warwick-Dugdale Richard Eccles Matthew Gemmell Richard Gregory Margaret Hughes Charlotte Nelson Lucille Rainbow Edith E. Vamos Hermione J. Webster Mark Whitehead Claudia Wierzbicki Adrienn Angyal Luke R. Green Max Whiteley Iraad F. Bronner Ben W. Farr Stefanie V. Lensing Shane A. McCarthy Michael A. Quail Nicholas M. Redshaw Scott A. J. Thurston Will Rowe Amy Gaskin Thanh Le-Viet Jennifier Liddle Ewan Birney Erik Volz Sebastian Funk Dominic Kwiatkowski Meera Chand Inigo Martincorena Jeffrey C. Barrett Moritz Gerstung (The Wellcome Sanger Institute COVID-19 Surveillance Team) (The COVID-19 Genomics UK (COG-UK) Consortium*) (Funding acquisition, leadership and supervision, metadata curation, project administration, samples and logistics, sequencing and analysis, software and analysis tools, and visualization) (Funding acquisition, leadership and supervision, metadata curation, project administration, samples and logistics, sequencing and analysis, and software and analysis tools) (Leadership and supervision, metadata curation, project administration, samples and logistics, sequencing and analysis, software and analysis tools, and visualization) (Funding acquisition, leadership and supervision, metadata curation, samples and logistics, sequencing and analysis, and visualization) (Funding acquisition, leadership and supervision, project administration, samples and logistics, sequencing and analysis, and software and analysis tools) (Funding acquisition, leadership and supervision, project administration, sequencing and analysis, software and analysis tools, and visualization) (Funding acquisition, metadata curation, project administration, samples and logistics, sequencing and analysis, and software and analysis tools) (Leadership and supervision, metadata curation, project administration, samples and logistics, software and analysis tools, and visualization) (Funding acquisition, leadership and supervision, metadata curation, project administration, and samples and logistics) (Funding acquisition, leadership and supervision, metadata curation, samples and logistics, and sequencing and analysis) (Funding acquisition, leadership and supervision, metadata curation, sequencing and analysis, and software and analysis tools) (Funding acquisition, leadership and supervision, project administration, samples and logistics, and sequencing and analysis) (Leadership and supervision, metadata curation, project administration, samples and logistics, and sequencing and analysis) (Leadership and supervision, metadata curation, project administration, samples and logistics, and visualization) (Leadership and supervision, metadata curation, project administration, sequencing and analysis, and software and analysis tools) (Leadership and supervision, metadata curation, samples and logistics, sequencing and analysis, and visualization) (Leadership and supervision, metadata curation, sequencing and analysis, software and analysis tools, and visualization) (Metadata curation, project administration, samples and logistics, sequencing and analysis, and software and analysis tools) (Funding acquisition, samples and logistics, sequencing and analysis, and visualization) (Funding acquisition, leadership and supervision, metadata curation and project administration) (Funding acquisition, leadership and supervision, metadata curation, and samples and logistics) (Funding acquisition, leadership and supervision, metadata curation, and sequencing and analysis) (Funding acquisition, leadership and supervision, project administration, and samples and logistics) (Funding acquisition, leadership and supervision, sequencing and analysis, and visualization) (Leadership and supervision, metadata curation, project administration, and sequencing and analysis) (Leadership and supervision, metadata curation, project administration, and samples and logistics) (Leadership and supervision, metadata curation, samples and logistics, and sequencing and analysis) (Leadership and supervision, metadata curation, samples and logistics, and visualization) (Leadership and supervision, metadata curation, sequencing and analysis, and software and analysis tools) (Leadership and supervision, project administration, samples and logistics, and sequencing and analysis) (Leadership and supervision, sequencing and analysis, software and analysis tools, and visualization) (Metadata curation, project administration, samples and logistics, and sequencing and analysis) (Metadata curation, project administration, sequencing and analysis, and software and analysis tools) (Metadata curation, samples and logistics, sequencing and analysis, and software and analysis tools) (Metadata curation, samples and logistics, sequencing and analysis, and visualization) (Metadata curation, sequencing and analysis, software and analysis tools, and visualization) (Project administration, sequencing and analysis, software and analysis tools, and visualization) (Funding acquisition, leadership and supervision, and metadata curation) (Funding acquisition, leadership and supervision, and project administration) (Funding acquisition, leadership and supervision, and samples and logistics) (Funding acquisition, leadership and supervision, and sequencing and analysis) (Leadership and supervision, metadata curation and project administration) (Leadership and supervision, metadata curation, and samples and logistics) (Leadership and supervision, metadata curation, and sequencing and analysis) (Leadership and supervision, project administration, and samples and logistics) (Leadership and supervision, project administration, and sequencing and analysis) (Leadership and supervision, samples and logistics, and sequencing and analysis) (Leadership and supervision, sequencing and analysis, and software and analysis tools) (Leadership and supervision, sequencing and analysis, and visualization) (Metadata curation, project administration, and samples and logistics) (Metadata curation, project administration, and sequencing and analysis) (Metadata curation, project administration, and software and analysis tools) (Metadata curation, project administration and visualization) (Metadata curation, samples and logistics, and sequencing and analysis) (Metadata curation, samples and logistics, and visualization) (Metadata curation, sequencing and analysis, and software and analysis tools) (Metadata curation, sequencing and analysis, and visualization) (Project administration, samples and logistics, and sequencing and analysis) (Project administration, samples and logistics, and visualization) (Samples and logistics, software and analysis tools, and visualization) (Sequencing and analysis, software and analysis tools, and visualization) (Funding acquisition, and leadership and supervision) (Funding acquisition and project administration) (Leadership and supervision, and metadata curation) (Leadership and supervision, and project administration) (Leadership and supervision, and samples and logistics) (Leadership and supervision, and sequencing and analysis) (Metadata curation, and samples and logistics) (Metadata curation, and sequencing and analysis) (Metadata curation, and software and analysis tools) (Project administration, and samples and logistics) (Project administration, and sequencing and analysis) (Project administration, and software and analysis tools) (Samples and logistics, and sequencing and analysis) (Samples and logistics, and software and analysis tools) (Sequencing and analysis, and software and analysis tools) (Sequencing and analysis, and visualization) (Software and analysis tools, and visualization) (Leadership and supervision) (Metadata curation) (Project administration) (Samples and logistics) (Sequencing and analysis) (Software and analysis tools) Ronan Lyons |
format |
Journal article |
container_title |
Nature |
container_volume |
600 |
container_issue |
7889 |
container_start_page |
506 |
publishDate |
2021 |
institution |
Swansea University |
issn |
0028-0836 1476-4687 |
doi_str_mv |
10.1038/s41586-021-04069-y |
publisher |
Springer Science and Business Media LLC |
college_str |
Faculty of Medicine, Health and Life Sciences |
hierarchytype |
|
hierarchy_top_id |
facultyofmedicinehealthandlifesciences |
hierarchy_top_title |
Faculty of Medicine, Health and Life Sciences |
hierarchy_parent_id |
facultyofmedicinehealthandlifesciences |
hierarchy_parent_title |
Faculty of Medicine, Health and Life Sciences |
department_str |
Swansea University Medical School - Health Data Science{{{_:::_}}}Faculty of Medicine, Health and Life Sciences{{{_:::_}}}Swansea University Medical School - Health Data Science |
document_store_str |
1 |
active_str |
0 |
description |
The evolution of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus leads to new variants that warrant timely epidemiological characterization. Here we use the dense genomic surveillance data generated by the COVID-19 Genomics UK Consortium to reconstruct the dynamics of 71 different lineages in each of 315 English local authorities between September 2020 and June 2021. This analysis reveals a series of subepidemics that peaked in early autumn 2020, followed by a jump in transmissibility of the B.1.1.7/Alpha lineage. The Alpha variant grew when other lineages declined during the second national lockdown and regionally tiered restrictions between November and December 2020. A third more stringent national lockdown suppressed the Alpha variant and eliminated nearly all other lineages in early 2021. Yet a series of variants (most of which contained the spike E484K mutation) defied these trends and persisted at moderately increasing proportions. However, by accounting for sustained introductions, we found that the transmissibility of these variants is unlikely to have exceeded the transmissibility of the Alpha variant. Finally, B.1.617.2/Delta was repeatedly introduced in England and grew rapidly in early summer 2021, constituting approximately 98% of sampled SARS-CoV-2 genomes on 26 June 2021. |
published_date |
2021-12-16T12:29:35Z |
_version_ |
1802741823019417600 |
score |
11.021648 |