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COVID-19 trajectories among 57 million adults in England: a cohort study using electronic health records

Johan H Thygesen Orcid Logo, Christopher Tomlinson Orcid Logo, Sam Hollings, Mehrdad Mizani Orcid Logo, Alex Handy Orcid Logo, Ashley Akbari Orcid Logo, Amitava Banerjee Orcid Logo, Jennifer Cooper Orcid Logo, Alvina Lai Orcid Logo, Ken Li, Bilal Mateen Orcid Logo, Naveed Sattar Orcid Logo, Reecha Sofat Orcid Logo, Ana Torralbo Orcid Logo, Honghan Wu Orcid Logo, Angela Wood Orcid Logo, Jonathan A C Sterne Orcid Logo, Christina Pagel Orcid Logo, William Whiteley Orcid Logo, Cathie Sudlow Orcid Logo, Harry Hemingway Orcid Logo, Spiros Denaxas Orcid Logo, Hoda Abbasizanjani, Nida Ahmed, Badar Ahmed, Ashley Akbari, Abdul Qadr Akinoso-Imran, Elias Allara, Freya Allery, Emanuele Di Angelantonio, Mark Ashworth, Vandana Ayyar-Gupta, Sonya Babu-Narayan, Seb Bacon, Steve Ball, Ami Banerjee, Mark Barber, Jessica Barrett, Marion Bennie, Colin Berry, Jennifer Beveridge, Ewan Birney, Lana Bojanić, Thomas Bolton, Anna Bone, Jon Boyle, Tasanee Braithwaite, Ben Bray, Norman Briffa, David Brind, Katherine Brown, Maya Buch, Dexter Canoy, Massimo Caputo, Raymond Carragher, Alan Carson, Genevieve Cezard, Jen-Yu Amy Chang, Kate Cheema, Richard Chin, Yogini Chudasama, Jennifer Cooper, Emma Copland, Rebecca Crallan, Rachel Cripps, David Cromwell, Vasa Curcin, Gwenetta Curry, Caroline Dale, John Danesh, Jayati Das-Munshi, Ashkan Dashtban, Alun Davies, Joanna Davies, Gareth Davies, Neil Davies, Joshua Day, Antonella Delmestri, Spiros Denaxas, Rachel Denholm, John Dennis, Alastair Denniston, Salil Deo, Baljean Dhillon, Annemarie Docherty, Tim Dong, Abdel Douiri, Johnny Downs, Alexandru Dregan, Elizabeth A Ellins, Martha Elwenspoek, Fabian Falck, Florian Falter, Yat Yi Fan, Joseph Firth, Lorna Fraser, Rocco Friebel, Amir Gavrieli, Moritz Gerstung, Ruth Gilbert, Clare Gillies, Myer Glickman, Ben Goldacre, Raph Goldacre, Felix Greaves, Mark Green, Luca Grieco, Rowena Griffiths, Deepti Gurdasani, Julian Halcox, Nick Hall, Tuankasfee Hama, Alex Handy, Anna Hansell, Pia Hardelid, Flavien Hardy, Daniel Harris, Camille Harrison, Katie Harron, Abdelaali Hassaine, Lamiece Hassan, Russell Healey, Harry Hemingway, Angela Henderson, Naomi Herz, Johannes Heyl, Mira Hidajat, Irene Higginson, Rosie Hinchliffe, Julia Hippisley-Cox, Frederick Ho, Mevhibe Hocaoglu, Sam Hollings, Elsie Horne, David Hughes, Ben Humberstone, Mike Inouye, Samantha Ip, Nazrul Islam, Caroline Jackson, David Jenkins, Xiyun Jiang, Shane Johnson, Umesh Kadam, Costas Kallis, Zainab Karim, Jake Kasan, Michalis Katsoulis, Kim Kavanagh, Frank Kee, Spencer Keene, Seamus Kent, Sara Khalid, Anthony Khawaja, Kamlesh Khunti, Richard Killick, Deborah Kinnear, Rochelle Knight, Ruwanthi Kolamunnage-Dona, Evan Kontopantelis, Amanj Kurdi, Ben Lacey, Alvina Lai, Andrew Lambarth, Milad Nazarzadeh Larzjan, Deborah Lawler, Thomas Lawrence, Claire Lawson, Qiuju Li, Ken Li, Miguel Bernabeu Llinares, Paula Lorgelly, Deborah Lowe, Jane Lyons, Ronan Lyons, Pedro Machado, Mary Joan Macleod, John Macleod, Evaleen Malgapo, Mamas Mamas, Mohammad Mamouei, Sinduja Manohar, Rutendo Mapeta, Javiera Leniz Martelli, David Moreno Martos, Bilal Mateen, Aoife McCarthy, Craig Melville, Rebecca Milton, Mehrdad Mizani, Marta Pineda Moncusi, Daniel Morales, Ify Mordi, Lynn Morrice, Carole Morris, Eva Morris, Yi Mu, Tanja Mueller, Lars Murdock, Vahé Nafilyan, George Nicholson, Elena Nikiphorou, John Nolan, Tom Norris, Ruth Norris, Laura North, Teri-Louise North, Dan O'Connell, Dominic Oliver, Adejoke Oluyase, Abraham Olvera-Barrios, Efosa Omigie, Sarah Onida, Sandosh Padmanabhan, Tom Palmer, Laura Pasea, Riyaz Patel, Rupert Payne, Jill Pell, Carmen Petitjean, Arun Pherwani, Owen Pickrell, Livia Pierotti, Munir Pirmohamed, Rouven Priedon, Dani Prieto-Alhambra, Alastair Proudfoot, Terry Quinn, Jennifer Quint, Elena Raffetti, Kazem Rahimi, Shishir Rao, Cameron Razieh, Brian Roberts, Caroline Rogers, Jennifer Rossdale, Safa Salim, Nilesh Samani, Naveed Sattar, Christian Schnier, Roy Schwartz, David Selby, Olena Seminog, Sharmin Shabnam, Ajay Shah, Jon Shelton, James Sheppard, Shubhra Sinha, Mirek Skrypak, Martina Slapkova, Katherine Sleeman, Craig Smith, Reecha Sofat, Filip Sosenko, Matthew Sperrin, Sarah Steeg, Jonathan Sterne, Serban Stoica, Maria Sudell, Cathie Sudlow, Luanluan Sun, Arun Karthikeyan Suseeladevi, Michael Sweeting, Matt Sydes, Rohan Takhar, Howard Tang, Johan Thygesen, George Tilston, Claire Tochel, Clea du Toit, Christopher Tomlinson, Renin Toms, Fatemeh Torabi, Ana Torralbo, Julia Townson, Adnan Tufail, Tapiwa Tungamirai, Susheel Varma, Sebastian Vollmer, Venexia Walker, Tianxiao Wang, Huan Wang, Alasdair Warwick, Ruth Watkinson, Harry Watson, William Whiteley, Hannah Whittaker, Harry Wilde, Tim Wilkinson, Gareth Williams, Michelle Williams, Richard Williams, Eloise Withnell, Charles Wolfe, Angela Wood, Lucy Wright, Honghan Wu, Jinge Wu, Jianhua Wu, Tom Yates, Francesco Zaccardi, Haoting Zhang, Huayu Zhang, Luisa Zuccolo

The Lancet Digital Health, Volume: 4, Issue: 7, Pages: e542 - e557

Swansea University Author: Ashley Akbari Orcid Logo

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DOI (Published version): 10.1016/s2589-7500(22)00091-7

Abstract

BackgroundUpdatable estimates of COVID-19 onset, progression, and trajectories underpin pandemic mitigation efforts. To identify and characterise disease trajectories, we aimed to define and validate ten COVID-19 phenotypes from nationwide linked electronic health records (EHR) using an extensible f...

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Published in: The Lancet Digital Health
ISSN: 2589-7500
Published: Elsevier BV 2022
Online Access: Check full text

URI: https://cronfa.swan.ac.uk/Record/cronfa58863
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fullrecord <?xml version="1.0"?><rfc1807><datestamp>2022-07-25T16:28:52.0746744</datestamp><bib-version>v2</bib-version><id>58863</id><entry>2021-12-01</entry><title>COVID-19 trajectories among 57 million adults in England: a cohort study using electronic health records</title><swanseaauthors><author><sid>aa1b025ec0243f708bb5eb0a93d6fb52</sid><ORCID>0000-0003-0814-0801</ORCID><firstname>Ashley</firstname><surname>Akbari</surname><name>Ashley Akbari</name><active>true</active><ethesisStudent>false</ethesisStudent></author></swanseaauthors><date>2021-12-01</date><deptcode>HDAT</deptcode><abstract>BackgroundUpdatable estimates of COVID-19 onset, progression, and trajectories underpin pandemic mitigation efforts. To identify and characterise disease trajectories, we aimed to define and validate ten COVID-19 phenotypes from nationwide linked electronic health records (EHR) using an extensible framework.MethodsIn this cohort study, we used eight linked National Health Service (NHS) datasets for people in England alive on Jan 23, 2020. Data on COVID-19 testing, vaccination, primary and secondary care records, and death registrations were collected until Nov 30, 2021. We defined ten COVID-19 phenotypes reflecting clinically relevant stages of disease severity and encompassing five categories: positive SARS-CoV-2 test, primary care diagnosis, hospital admission, ventilation modality (four phenotypes), and death (three phenotypes). We constructed patient trajectories illustrating transition frequency and duration between phenotypes. Analyses were stratified by pandemic waves and vaccination status.FindingsAmong 57&#x2009;032&#x2009;174 individuals included in the cohort, 13&#x2009;990&#x2009;423 COVID-19 events were identified in 7&#x2009;244&#x2009;925 individuals, equating to an infection rate of 12&#xB7;7% during the study period. Of 7&#x2009;244&#x2009;925 individuals, 460&#x2009;737 (6&#xB7;4%) were admitted to hospital and 158&#x2009;020 (2&#xB7;2%) died. Of 460&#x2009;737 individuals who were admitted to hospital, 48&#x2009;847 (10&#xB7;6%) were admitted to the intensive care unit (ICU), 69&#x2009;090 (15&#xB7;0%) received non-invasive ventilation, and 25&#x2009;928 (5&#xB7;6%) received invasive ventilation. Among 384&#x2009;135 patients who were admitted to hospital but did not require ventilation, mortality was higher in wave 1 (23&#x2009;485 [30&#xB7;4%] of 77&#x2009;202 patients) than wave 2 (44&#x2009;220 [23&#xB7;1%] of 191&#x2009;528 patients), but remained unchanged for patients admitted to the ICU. Mortality was highest among patients who received ventilatory support outside of the ICU in wave 1 (2569 [50&#xB7;7%] of 5063 patients). 15&#x2009;486 (9&#xB7;8%) of 158&#x2009;020 COVID-19-related deaths occurred within 28 days of the first COVID-19 event without a COVID-19 diagnoses on the death certificate. 10&#x2009;884 (6&#xB7;9%) of 158&#x2009;020 deaths were identified exclusively from mortality data with no previous COVID-19 phenotype recorded. We observed longer patient trajectories in wave 2 than wave 1.InterpretationOur analyses illustrate the wide spectrum of disease trajectories as shown by differences in incidence, survival, and clinical pathways. We have provided a modular analytical framework that can be used to monitor the impact of the pandemic and generate evidence of clinical and policy relevance using multiple EHR sources.</abstract><type>Journal Article</type><journal>The Lancet Digital Health</journal><volume>4</volume><journalNumber>7</journalNumber><paginationStart>e542</paginationStart><paginationEnd>e557</paginationEnd><publisher>Elsevier BV</publisher><placeOfPublication/><isbnPrint/><isbnElectronic/><issnPrint>2589-7500</issnPrint><issnElectronic/><keywords/><publishedDay>1</publishedDay><publishedMonth>7</publishedMonth><publishedYear>2022</publishedYear><publishedDate>2022-07-01</publishedDate><doi>10.1016/s2589-7500(22)00091-7</doi><url/><notes/><college>COLLEGE NANME</college><department>Health Data Science</department><CollegeCode>COLLEGE CODE</CollegeCode><DepartmentCode>HDAT</DepartmentCode><institution>Swansea University</institution><apcterm/><funders>British Heart Foundation Data Science Centre, led by Health Data Research UK.</funders><projectreference/><lastEdited>2022-07-25T16:28:52.0746744</lastEdited><Created>2021-12-01T15:56:12.1908707</Created><path><level id="1">Faculty of Medicine, Health and Life Sciences</level><level id="2">Swansea University Medical School - Medicine</level></path><authors><author><firstname>Johan H</firstname><surname>Thygesen</surname><orcid>0000-0002-7479-3459</orcid><order>1</order></author><author><firstname>Christopher</firstname><surname>Tomlinson</surname><orcid>0000-0002-0903-5395</orcid><order>2</order></author><author><firstname>Sam</firstname><surname>Hollings</surname><order>3</order></author><author><firstname>Mehrdad</firstname><surname>Mizani</surname><orcid>0000-0002-2441-895x</orcid><order>4</order></author><author><firstname>Alex</firstname><surname>Handy</surname><orcid>0000-0002-3739-1530</orcid><order>5</order></author><author><firstname>Ashley</firstname><surname>Akbari</surname><orcid>0000-0003-0814-0801</orcid><order>6</order></author><author><firstname>Amitava</firstname><surname>Banerjee</surname><orcid>0000-0001-8741-3411</orcid><order>7</order></author><author><firstname>Jennifer</firstname><surname>Cooper</surname><orcid>0000-0001-9364-7353</orcid><order>8</order></author><author><firstname>Alvina</firstname><surname>Lai</surname><orcid>0000-0001-8960-8095</orcid><order>9</order></author><author><firstname>Ken</firstname><surname>Li</surname><order>10</order></author><author><firstname>Bilal</firstname><surname>Mateen</surname><orcid>0000-0003-4423-6472</orcid><order>11</order></author><author><firstname>Naveed</firstname><surname>Sattar</surname><orcid>0000-0002-1604-2593</orcid><order>12</order></author><author><firstname>Reecha</firstname><surname>Sofat</surname><orcid>0000-0002-0242-6115</orcid><order>13</order></author><author><firstname>Ana</firstname><surname>Torralbo</surname><orcid>0000-0003-2738-8503</orcid><order>14</order></author><author><firstname>Honghan</firstname><surname>Wu</surname><orcid>0000-0002-0213-5668</orcid><order>15</order></author><author><firstname>Angela</firstname><surname>Wood</surname><orcid>0000-0002-7937-304x</orcid><order>16</order></author><author><firstname>Jonathan A C</firstname><surname>Sterne</surname><orcid>0000-0001-8496-6053</orcid><order>17</order></author><author><firstname>Christina</firstname><surname>Pagel</surname><orcid>0000-0002-2857-1628</orcid><order>18</order></author><author><firstname>William</firstname><surname>Whiteley</surname><orcid>0000-0002-4816-8991</orcid><order>19</order></author><author><firstname>Cathie</firstname><surname>Sudlow</surname><orcid>0000-0002-7725-7520</orcid><order>20</order></author><author><firstname>Harry</firstname><surname>Hemingway</surname><orcid>0000-0003-2279-0624</orcid><order>21</order></author><author><firstname>Spiros</firstname><surname>Denaxas</surname><orcid>0000-0001-9612-7791</orcid><order>22</order></author><author><firstname>Hoda</firstname><surname>Abbasizanjani</surname><order>23</order></author><author><firstname>Nida</firstname><surname>Ahmed</surname><order>24</order></author><author><firstname>Badar</firstname><surname>Ahmed</surname><order>25</order></author><author><firstname>Ashley</firstname><surname>Akbari</surname><order>26</order></author><author><firstname>Abdul Qadr</firstname><surname>Akinoso-Imran</surname><order>27</order></author><author><firstname>Elias</firstname><surname>Allara</surname><order>28</order></author><author><firstname>Freya</firstname><surname>Allery</surname><order>29</order></author><author><firstname>Emanuele 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ame>Kee</surname><order>150</order></author><author><firstname>Spencer</firstname><surname>Keene</surname><order>151</order></author><author><firstname>Seamus</firstname><surname>Kent</surname><order>152</order></author><author><firstname>Sara</firstname><surname>Khalid</surname><order>153</order></author><author><firstname>Anthony</firstname><surname>Khawaja</surname><order>154</order></author><author><firstname>Kamlesh</firstname><surname>Khunti</surname><order>155</order></author><author><firstname>Richard</firstname><surname>Killick</surname><order>156</order></author><author><firstname>Deborah</firstname><surname>Kinnear</surname><order>157</order></author><author><firstname>Rochelle</firstname><surname>Knight</surname><order>158</order></author><author><firstname>Ruwanthi</firstname><surname>Kolamunnage-Dona</surname><order>159</order></author><author><firstname>Evan</firstname><surname>Kontopantelis</surname><order>160</order></author><author><firstname>Amanj</firstname><surname>Kurdi</surname><order>161</order></author><author><firstname>Ben</firstname><surname>Lacey</surname><order>162</order></author><author><firstname>Alvina</firstname><surname>Lai</surname><order>163</order></author><author><firstname>Andrew</firstname><surname>Lambarth</surname><order>164</order></author><author><firstname>Milad Nazarzadeh</firstname><surname>Larzjan</surname><order>165</order></author><author><firstname>Deborah</firstname><surname>Lawler</surname><order>166</order></author><author><firstname>Thomas</firstname><surname>Lawrence</surname><order>167</order></author><author><firstname>Claire</firstname><surname>Lawson</surname><order>168</order></author><author><firstname>Qiuju</firstname><surname>Li</surname><order>169</order></author><author><firstname>Ken</firstname><surname>Li</surname><order>170</order></author><author><firstname>Miguel Bernabeu</firstname><surname>Llinares</surname><order>171</order></author><author><firstname>Paula</firstname><surname>Lorgelly</surname><order>172</order></author><author><firstname>Deborah</firstname><surname>Lowe</surname><order>173</order></author><author><firstname>Jane</firstname><surname>Lyons</surname><order>174</order></author><author><firstname>Ronan</firstname><surname>Lyons</surname><order>175</order></author><author><firstname>Pedro</firstname><surname>Machado</surname><order>176</order></author><author><firstname>Mary Joan</firstname><surname>Macleod</surname><order>177</order></author><author><firstname>John</firstname><surname>Macleod</surname><order>178</order></author><author><firstname>Evaleen</firstname><surname>Malgapo</surname><order>179</order></author><author><firstname>Mamas</firstname><surname>Mamas</surname><order>180</order></author><author><firstname>Mohammad</firstname><surname>Mamouei</surname><order>181</order></author><author><firstname>Sinduja</firstname><surname>Manohar</surname><order>182</order></author><author><firstname>Rutendo</firstname><surname>Mapeta</surname><order>183</order></author><author><firstname>Javiera Leniz</firstname><surname>Martelli</surname><order>184</order></author><author><firstname>David Moreno</firstname><surname>Martos</surname><order>185</order></author><author><firstname>Bilal</firstname><surname>Mateen</surname><order>186</order></author><author><firstname>Aoife</firstname><surname>McCarthy</surname><order>187</order></author><author><firstname>Craig</firstname><surname>Melville</surname><order>188</order></author><author><firstname>Rebecca</firstname><surname>Milton</surname><order>189</order></author><author><firstname>Mehrdad</firstname><surname>Mizani</surname><order>190</order></author><author><firstname>Marta Pineda</firstname><surname>Moncusi</surname><order>191</order></author><author><firstname>Daniel</firstname><surname>Morales</surname><order>192</order></author><author><firstname>Ify</firstname><surname>Mordi</surname><order>193</order></author><author><firstname>Lynn</firstname><surname>Morrice</surname><order>194</order></author><author><firstname>Carole</firstname><surname>Morris</surname><order>195</order></author><author><firstname>Eva</firstname><surname>Morris</surname><order>196</order></author><author><firstname>Yi</firstname><surname>Mu</surname><order>197</order></author><author><firstname>Tanja</firstname><surname>Mueller</surname><order>198</order></author><author><firstname>Lars</firstname><surname>Murdock</surname><order>199</order></author><author><firstname>Vah&#xE9;</firstname><surname>Nafilyan</surname><order>200</order></author><author><firstname>George</firstname><surname>Nicholson</surname><order>201</order></author><author><firstname>Elena</firstname><surname>Nikiphorou</surname><order>202</order></author><author><firstname>John</firstname><surname>Nolan</surname><order>203</order></author><author><firstname>Tom</firstname><surname>Norris</surname><order>204</order></author><author><firstname>Ruth</firstname><surname>Norris</surname><order>205</order></author><author><firstname>Laura</firstname><surname>North</surname><order>206</order></author><author><firstname>Teri-Louise</firstname><surname>North</surname><order>207</order></author><author><firstname>Dan</firstname><surname>O'Connell</surname><order>208</order></author><author><firstname>Dominic</firstname><surname>Oliver</surname><order>209</order></author><author><firstname>Adejoke</firstname><surname>Oluyase</surname><order>210</order></author><author><firstname>Abraham</firstname><surname>Olvera-Barrios</surname><order>211</order></author><author><firstname>Efosa</firstname><surname>Omigie</surname><order>212</order></author><author><firstname>Sarah</firstname><surname>Onida</surname><order>213</order></author><author><firstname>Sandosh</firstname><surname>Padmanabhan</surname><order>214</order></author><author><firstname>Tom</firstname><surname>Palmer</surname><order>215</order></author><author><firstname>Laura</firstname><surname>Pasea</surname><order>216</order></author><author><firstname>Riyaz</firstname><surname>Patel</surname><order>217</order></author><author><firstname>Rupert</firstname><surname>Payne</surname><order>218</order></author><author><firstname>Jill</firstname><surname>Pell</surname><order>219</order></author><author><firstname>Carmen</firstname><surname>Petitjean</surname><order>220</order></author><author><firstname>Arun</firstname><surname>Pherwani</surname><order>221</order></author><author><firstname>Owen</firstname><surname>Pickrell</surname><order>222</order></author><author><firstname>Livia</firstname><surname>Pierotti</surname><order>223</order></author><author><firstname>Munir</firstname><surname>Pirmohamed</surname><order>224</order></author><author><firstname>Rouven</firstname><surname>Priedon</surname><order>225</order></author><author><firstname>Dani</firstname><surname>Prieto-Alhambra</surname><order>226</order></author><author><firstname>Alastair</firstname><surname>Proudfoot</surname><order>227</order></author><author><firstname>Terry</firstname><surname>Quinn</surname><order>228</order></author><author><firstname>Jennifer</firstname><surname>Quint</surname><order>229</order></author><author><firstname>Elena</firstname><surname>Raffetti</surname><order>230</order></author><author><firstname>Kazem</firstname><surname>Rahimi</surname><order>231</order></author><author><firstname>Shishir</firstname><surname>Rao</surname><order>232</order></author><author><firstname>Cameron</firstname><surname>Razieh</surname><order>233</order></author><author><firstname>Brian</firstname><surname>Roberts</surname><order>234</order></author><author><firstname>Caroline</firstname><surname>Rogers</surname><order>235</order></author><author><firstname>Jennifer</firstname><surname>Rossdale</surname><order>236</order></author><author><firstname>Safa</firstname><surname>Salim</surname><order>237</order></author><author><firstname>Nilesh</firstname><surname>Samani</surname><order>238</order></author><author><firstname>Naveed</firstname><surname>Sattar</surname><order>239</order></author><author><firstname>Christian</firstname><surname>Schnier</surname><order>240</order></author><author><firstname>Roy</firstname><surname>Schwartz</surname><order>241</order></author><author><firstname>David</firstname><surname>Selby</surname><order>242</order></author><author><firstname>Olena</firstname><surname>Seminog</surname><order>243</order></author><author><firstname>Sharmin</firstname><surname>Shabnam</surname><order>244</order></author><author><firstname>Ajay</firstname><surname>Shah</surname><order>245</order></author><author><firstname>Jon</firstname><surname>Shelton</surname><order>246</order></author><author><firstname>James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Karthikeyan</firstname><surname>Suseeladevi</surname><order>262</order></author><author><firstname>Michael</firstname><surname>Sweeting</surname><order>263</order></author><author><firstname>Matt</firstname><surname>Sydes</surname><order>264</order></author><author><firstname>Rohan</firstname><surname>Takhar</surname><order>265</order></author><author><firstname>Howard</firstname><surname>Tang</surname><order>266</order></author><author><firstname>Johan</firstname><surname>Thygesen</surname><order>267</order></author><author><firstname>George</firstname><surname>Tilston</surname><order>268</order></author><author><firstname>Claire</firstname><surname>Tochel</surname><order>269</order></author><author><firstname>Clea 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spelling 2022-07-25T16:28:52.0746744 v2 58863 2021-12-01 COVID-19 trajectories among 57 million adults in England: a cohort study using electronic health records aa1b025ec0243f708bb5eb0a93d6fb52 0000-0003-0814-0801 Ashley Akbari Ashley Akbari true false 2021-12-01 HDAT BackgroundUpdatable estimates of COVID-19 onset, progression, and trajectories underpin pandemic mitigation efforts. To identify and characterise disease trajectories, we aimed to define and validate ten COVID-19 phenotypes from nationwide linked electronic health records (EHR) using an extensible framework.MethodsIn this cohort study, we used eight linked National Health Service (NHS) datasets for people in England alive on Jan 23, 2020. Data on COVID-19 testing, vaccination, primary and secondary care records, and death registrations were collected until Nov 30, 2021. We defined ten COVID-19 phenotypes reflecting clinically relevant stages of disease severity and encompassing five categories: positive SARS-CoV-2 test, primary care diagnosis, hospital admission, ventilation modality (four phenotypes), and death (three phenotypes). We constructed patient trajectories illustrating transition frequency and duration between phenotypes. Analyses were stratified by pandemic waves and vaccination status.FindingsAmong 57 032 174 individuals included in the cohort, 13 990 423 COVID-19 events were identified in 7 244 925 individuals, equating to an infection rate of 12·7% during the study period. Of 7 244 925 individuals, 460 737 (6·4%) were admitted to hospital and 158 020 (2·2%) died. Of 460 737 individuals who were admitted to hospital, 48 847 (10·6%) were admitted to the intensive care unit (ICU), 69 090 (15·0%) received non-invasive ventilation, and 25 928 (5·6%) received invasive ventilation. Among 384 135 patients who were admitted to hospital but did not require ventilation, mortality was higher in wave 1 (23 485 [30·4%] of 77 202 patients) than wave 2 (44 220 [23·1%] of 191 528 patients), but remained unchanged for patients admitted to the ICU. Mortality was highest among patients who received ventilatory support outside of the ICU in wave 1 (2569 [50·7%] of 5063 patients). 15 486 (9·8%) of 158 020 COVID-19-related deaths occurred within 28 days of the first COVID-19 event without a COVID-19 diagnoses on the death certificate. 10 884 (6·9%) of 158 020 deaths were identified exclusively from mortality data with no previous COVID-19 phenotype recorded. We observed longer patient trajectories in wave 2 than wave 1.InterpretationOur analyses illustrate the wide spectrum of disease trajectories as shown by differences in incidence, survival, and clinical pathways. We have provided a modular analytical framework that can be used to monitor the impact of the pandemic and generate evidence of clinical and policy relevance using multiple EHR sources. Journal Article The Lancet Digital Health 4 7 e542 e557 Elsevier BV 2589-7500 1 7 2022 2022-07-01 10.1016/s2589-7500(22)00091-7 COLLEGE NANME Health Data Science COLLEGE CODE HDAT Swansea University British Heart Foundation Data Science Centre, led by Health Data Research UK. 2022-07-25T16:28:52.0746744 2021-12-01T15:56:12.1908707 Faculty of Medicine, Health and Life Sciences Swansea University Medical School - Medicine Johan H Thygesen 0000-0002-7479-3459 1 Christopher Tomlinson 0000-0002-0903-5395 2 Sam Hollings 3 Mehrdad Mizani 0000-0002-2441-895x 4 Alex Handy 0000-0002-3739-1530 5 Ashley Akbari 0000-0003-0814-0801 6 Amitava Banerjee 0000-0001-8741-3411 7 Jennifer Cooper 0000-0001-9364-7353 8 Alvina Lai 0000-0001-8960-8095 9 Ken Li 10 Bilal Mateen 0000-0003-4423-6472 11 Naveed Sattar 0000-0002-1604-2593 12 Reecha Sofat 0000-0002-0242-6115 13 Ana Torralbo 0000-0003-2738-8503 14 Honghan Wu 0000-0002-0213-5668 15 Angela Wood 0000-0002-7937-304x 16 Jonathan A C Sterne 0000-0001-8496-6053 17 Christina Pagel 0000-0002-2857-1628 18 William Whiteley 0000-0002-4816-8991 19 Cathie Sudlow 0000-0002-7725-7520 20 Harry Hemingway 0000-0003-2279-0624 21 Spiros Denaxas 0000-0001-9612-7791 22 Hoda Abbasizanjani 23 Nida Ahmed 24 Badar Ahmed 25 Ashley Akbari 26 Abdul Qadr Akinoso-Imran 27 Elias Allara 28 Freya Allery 29 Emanuele Di Angelantonio 30 Mark Ashworth 31 Vandana Ayyar-Gupta 32 Sonya Babu-Narayan 33 Seb Bacon 34 Steve Ball 35 Ami Banerjee 36 Mark Barber 37 Jessica Barrett 38 Marion Bennie 39 Colin Berry 40 Jennifer Beveridge 41 Ewan Birney 42 Lana Bojanić 43 Thomas Bolton 44 Anna Bone 45 Jon Boyle 46 Tasanee Braithwaite 47 Ben Bray 48 Norman Briffa 49 David Brind 50 Katherine Brown 51 Maya Buch 52 Dexter Canoy 53 Massimo Caputo 54 Raymond Carragher 55 Alan Carson 56 Genevieve Cezard 57 Jen-Yu Amy Chang 58 Kate Cheema 59 Richard Chin 60 Yogini Chudasama 61 Jennifer Cooper 62 Emma Copland 63 Rebecca Crallan 64 Rachel Cripps 65 David Cromwell 66 Vasa Curcin 67 Gwenetta Curry 68 Caroline Dale 69 John Danesh 70 Jayati Das-Munshi 71 Ashkan Dashtban 72 Alun Davies 73 Joanna Davies 74 Gareth Davies 75 Neil Davies 76 Joshua Day 77 Antonella Delmestri 78 Spiros Denaxas 79 Rachel Denholm 80 John Dennis 81 Alastair Denniston 82 Salil Deo 83 Baljean Dhillon 84 Annemarie Docherty 85 Tim Dong 86 Abdel Douiri 87 Johnny Downs 88 Alexandru Dregan 89 Elizabeth A Ellins 90 Martha Elwenspoek 91 Fabian Falck 92 Florian Falter 93 Yat Yi Fan 94 Joseph Firth 95 Lorna Fraser 96 Rocco Friebel 97 Amir Gavrieli 98 Moritz Gerstung 99 Ruth Gilbert 100 Clare Gillies 101 Myer Glickman 102 Ben Goldacre 103 Raph Goldacre 104 Felix Greaves 105 Mark Green 106 Luca Grieco 107 Rowena Griffiths 108 Deepti Gurdasani 109 Julian Halcox 110 Nick Hall 111 Tuankasfee Hama 112 Alex Handy 113 Anna Hansell 114 Pia Hardelid 115 Flavien Hardy 116 Daniel Harris 117 Camille Harrison 118 Katie Harron 119 Abdelaali Hassaine 120 Lamiece Hassan 121 Russell Healey 122 Harry Hemingway 123 Angela Henderson 124 Naomi Herz 125 Johannes Heyl 126 Mira Hidajat 127 Irene Higginson 128 Rosie Hinchliffe 129 Julia Hippisley-Cox 130 Frederick Ho 131 Mevhibe Hocaoglu 132 Sam Hollings 133 Elsie Horne 134 David Hughes 135 Ben Humberstone 136 Mike Inouye 137 Samantha Ip 138 Nazrul Islam 139 Caroline Jackson 140 David Jenkins 141 Xiyun Jiang 142 Shane Johnson 143 Umesh Kadam 144 Costas Kallis 145 Zainab Karim 146 Jake Kasan 147 Michalis Katsoulis 148 Kim Kavanagh 149 Frank Kee 150 Spencer Keene 151 Seamus Kent 152 Sara Khalid 153 Anthony Khawaja 154 Kamlesh Khunti 155 Richard Killick 156 Deborah Kinnear 157 Rochelle Knight 158 Ruwanthi Kolamunnage-Dona 159 Evan Kontopantelis 160 Amanj Kurdi 161 Ben Lacey 162 Alvina Lai 163 Andrew Lambarth 164 Milad Nazarzadeh Larzjan 165 Deborah Lawler 166 Thomas Lawrence 167 Claire Lawson 168 Qiuju Li 169 Ken Li 170 Miguel Bernabeu Llinares 171 Paula Lorgelly 172 Deborah Lowe 173 Jane Lyons 174 Ronan Lyons 175 Pedro Machado 176 Mary Joan Macleod 177 John Macleod 178 Evaleen Malgapo 179 Mamas Mamas 180 Mohammad Mamouei 181 Sinduja Manohar 182 Rutendo Mapeta 183 Javiera Leniz Martelli 184 David Moreno Martos 185 Bilal Mateen 186 Aoife McCarthy 187 Craig Melville 188 Rebecca Milton 189 Mehrdad Mizani 190 Marta Pineda Moncusi 191 Daniel Morales 192 Ify Mordi 193 Lynn Morrice 194 Carole Morris 195 Eva Morris 196 Yi Mu 197 Tanja Mueller 198 Lars Murdock 199 Vahé Nafilyan 200 George Nicholson 201 Elena Nikiphorou 202 John Nolan 203 Tom Norris 204 Ruth Norris 205 Laura North 206 Teri-Louise North 207 Dan O'Connell 208 Dominic Oliver 209 Adejoke Oluyase 210 Abraham Olvera-Barrios 211 Efosa Omigie 212 Sarah Onida 213 Sandosh Padmanabhan 214 Tom Palmer 215 Laura Pasea 216 Riyaz Patel 217 Rupert Payne 218 Jill Pell 219 Carmen Petitjean 220 Arun Pherwani 221 Owen Pickrell 222 Livia Pierotti 223 Munir Pirmohamed 224 Rouven Priedon 225 Dani Prieto-Alhambra 226 Alastair Proudfoot 227 Terry Quinn 228 Jennifer Quint 229 Elena Raffetti 230 Kazem Rahimi 231 Shishir Rao 232 Cameron Razieh 233 Brian Roberts 234 Caroline Rogers 235 Jennifer Rossdale 236 Safa Salim 237 Nilesh Samani 238 Naveed Sattar 239 Christian Schnier 240 Roy Schwartz 241 David Selby 242 Olena Seminog 243 Sharmin Shabnam 244 Ajay Shah 245 Jon Shelton 246 James Sheppard 247 Shubhra Sinha 248 Mirek Skrypak 249 Martina Slapkova 250 Katherine Sleeman 251 Craig Smith 252 Reecha Sofat 253 Filip Sosenko 254 Matthew Sperrin 255 Sarah Steeg 256 Jonathan Sterne 257 Serban Stoica 258 Maria Sudell 259 Cathie Sudlow 260 Luanluan Sun 261 Arun Karthikeyan Suseeladevi 262 Michael Sweeting 263 Matt Sydes 264 Rohan Takhar 265 Howard Tang 266 Johan Thygesen 267 George Tilston 268 Claire Tochel 269 Clea du Toit 270 Christopher Tomlinson 271 Renin Toms 272 Fatemeh Torabi 273 Ana Torralbo 274 Julia Townson 275 Adnan Tufail 276 Tapiwa Tungamirai 277 Susheel Varma 278 Sebastian Vollmer 279 Venexia Walker 280 Tianxiao Wang 281 Huan Wang 282 Alasdair Warwick 283 Ruth Watkinson 284 Harry Watson 285 William Whiteley 286 Hannah Whittaker 287 Harry Wilde 288 Tim Wilkinson 289 Gareth Williams 290 Michelle Williams 291 Richard Williams 292 Eloise Withnell 293 Charles Wolfe 294 Angela Wood 295 Lucy Wright 296 Honghan Wu 297 Jinge Wu 298 Jianhua Wu 299 Tom Yates 300 Francesco Zaccardi 301 Haoting Zhang 302 Huayu Zhang 303 Luisa Zuccolo 304 58863__24733__2ba7a3d8cfee48e0b58a0d26e4e7467e.pdf 58863.pdf 2022-07-25T16:27:33.2764592 Output 1269785 application/pdf Version of Record true © 2022 The Author(s). This is an Open Access article under the CC BY 4.0 license true eng https://creativecommons.org/licenses/by/4.0/
title COVID-19 trajectories among 57 million adults in England: a cohort study using electronic health records
spellingShingle COVID-19 trajectories among 57 million adults in England: a cohort study using electronic health records
Ashley Akbari
title_short COVID-19 trajectories among 57 million adults in England: a cohort study using electronic health records
title_full COVID-19 trajectories among 57 million adults in England: a cohort study using electronic health records
title_fullStr COVID-19 trajectories among 57 million adults in England: a cohort study using electronic health records
title_full_unstemmed COVID-19 trajectories among 57 million adults in England: a cohort study using electronic health records
title_sort COVID-19 trajectories among 57 million adults in England: a cohort study using electronic health records
author_id_str_mv aa1b025ec0243f708bb5eb0a93d6fb52
author_id_fullname_str_mv aa1b025ec0243f708bb5eb0a93d6fb52_***_Ashley Akbari
author Ashley Akbari
author2 Johan H Thygesen
Christopher Tomlinson
Sam Hollings
Mehrdad Mizani
Alex Handy
Ashley Akbari
Amitava Banerjee
Jennifer Cooper
Alvina Lai
Ken Li
Bilal Mateen
Naveed Sattar
Reecha Sofat
Ana Torralbo
Honghan Wu
Angela Wood
Jonathan A C Sterne
Christina Pagel
William Whiteley
Cathie Sudlow
Harry Hemingway
Spiros Denaxas
Hoda Abbasizanjani
Nida Ahmed
Badar Ahmed
Ashley Akbari
Abdul Qadr Akinoso-Imran
Elias Allara
Freya Allery
Emanuele Di Angelantonio
Mark Ashworth
Vandana Ayyar-Gupta
Sonya Babu-Narayan
Seb Bacon
Steve Ball
Ami Banerjee
Mark Barber
Jessica Barrett
Marion Bennie
Colin Berry
Jennifer Beveridge
Ewan Birney
Lana Bojanić
Thomas Bolton
Anna Bone
Jon Boyle
Tasanee Braithwaite
Ben Bray
Norman Briffa
David Brind
Katherine Brown
Maya Buch
Dexter Canoy
Massimo Caputo
Raymond Carragher
Alan Carson
Genevieve Cezard
Jen-Yu Amy Chang
Kate Cheema
Richard Chin
Yogini Chudasama
Jennifer Cooper
Emma Copland
Rebecca Crallan
Rachel Cripps
David Cromwell
Vasa Curcin
Gwenetta Curry
Caroline Dale
John Danesh
Jayati Das-Munshi
Ashkan Dashtban
Alun Davies
Joanna Davies
Gareth Davies
Neil Davies
Joshua Day
Antonella Delmestri
Spiros Denaxas
Rachel Denholm
John Dennis
Alastair Denniston
Salil Deo
Baljean Dhillon
Annemarie Docherty
Tim Dong
Abdel Douiri
Johnny Downs
Alexandru Dregan
Elizabeth A Ellins
Martha Elwenspoek
Fabian Falck
Florian Falter
Yat Yi Fan
Joseph Firth
Lorna Fraser
Rocco Friebel
Amir Gavrieli
Moritz Gerstung
Ruth Gilbert
Clare Gillies
Myer Glickman
Ben Goldacre
Raph Goldacre
Felix Greaves
Mark Green
Luca Grieco
Rowena Griffiths
Deepti Gurdasani
Julian Halcox
Nick Hall
Tuankasfee Hama
Alex Handy
Anna Hansell
Pia Hardelid
Flavien Hardy
Daniel Harris
Camille Harrison
Katie Harron
Abdelaali Hassaine
Lamiece Hassan
Russell Healey
Harry Hemingway
Angela Henderson
Naomi Herz
Johannes Heyl
Mira Hidajat
Irene Higginson
Rosie Hinchliffe
Julia Hippisley-Cox
Frederick Ho
Mevhibe Hocaoglu
Sam Hollings
Elsie Horne
David Hughes
Ben Humberstone
Mike Inouye
Samantha Ip
Nazrul Islam
Caroline Jackson
David Jenkins
Xiyun Jiang
Shane Johnson
Umesh Kadam
Costas Kallis
Zainab Karim
Jake Kasan
Michalis Katsoulis
Kim Kavanagh
Frank Kee
Spencer Keene
Seamus Kent
Sara Khalid
Anthony Khawaja
Kamlesh Khunti
Richard Killick
Deborah Kinnear
Rochelle Knight
Ruwanthi Kolamunnage-Dona
Evan Kontopantelis
Amanj Kurdi
Ben Lacey
Alvina Lai
Andrew Lambarth
Milad Nazarzadeh Larzjan
Deborah Lawler
Thomas Lawrence
Claire Lawson
Qiuju Li
Ken Li
Miguel Bernabeu Llinares
Paula Lorgelly
Deborah Lowe
Jane Lyons
Ronan Lyons
Pedro Machado
Mary Joan Macleod
John Macleod
Evaleen Malgapo
Mamas Mamas
Mohammad Mamouei
Sinduja Manohar
Rutendo Mapeta
Javiera Leniz Martelli
David Moreno Martos
Bilal Mateen
Aoife McCarthy
Craig Melville
Rebecca Milton
Mehrdad Mizani
Marta Pineda Moncusi
Daniel Morales
Ify Mordi
Lynn Morrice
Carole Morris
Eva Morris
Yi Mu
Tanja Mueller
Lars Murdock
Vahé Nafilyan
George Nicholson
Elena Nikiphorou
John Nolan
Tom Norris
Ruth Norris
Laura North
Teri-Louise North
Dan O'Connell
Dominic Oliver
Adejoke Oluyase
Abraham Olvera-Barrios
Efosa Omigie
Sarah Onida
Sandosh Padmanabhan
Tom Palmer
Laura Pasea
Riyaz Patel
Rupert Payne
Jill Pell
Carmen Petitjean
Arun Pherwani
Owen Pickrell
Livia Pierotti
Munir Pirmohamed
Rouven Priedon
Dani Prieto-Alhambra
Alastair Proudfoot
Terry Quinn
Jennifer Quint
Elena Raffetti
Kazem Rahimi
Shishir Rao
Cameron Razieh
Brian Roberts
Caroline Rogers
Jennifer Rossdale
Safa Salim
Nilesh Samani
Naveed Sattar
Christian Schnier
Roy Schwartz
David Selby
Olena Seminog
Sharmin Shabnam
Ajay Shah
Jon Shelton
James Sheppard
Shubhra Sinha
Mirek Skrypak
Martina Slapkova
Katherine Sleeman
Craig Smith
Reecha Sofat
Filip Sosenko
Matthew Sperrin
Sarah Steeg
Jonathan Sterne
Serban Stoica
Maria Sudell
Cathie Sudlow
Luanluan Sun
Arun Karthikeyan Suseeladevi
Michael Sweeting
Matt Sydes
Rohan Takhar
Howard Tang
Johan Thygesen
George Tilston
Claire Tochel
Clea du Toit
Christopher Tomlinson
Renin Toms
Fatemeh Torabi
Ana Torralbo
Julia Townson
Adnan Tufail
Tapiwa Tungamirai
Susheel Varma
Sebastian Vollmer
Venexia Walker
Tianxiao Wang
Huan Wang
Alasdair Warwick
Ruth Watkinson
Harry Watson
William Whiteley
Hannah Whittaker
Harry Wilde
Tim Wilkinson
Gareth Williams
Michelle Williams
Richard Williams
Eloise Withnell
Charles Wolfe
Angela Wood
Lucy Wright
Honghan Wu
Jinge Wu
Jianhua Wu
Tom Yates
Francesco Zaccardi
Haoting Zhang
Huayu Zhang
Luisa Zuccolo
format Journal article
container_title The Lancet Digital Health
container_volume 4
container_issue 7
container_start_page e542
publishDate 2022
institution Swansea University
issn 2589-7500
doi_str_mv 10.1016/s2589-7500(22)00091-7
publisher Elsevier BV
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 - Medicine{{{_:::_}}}Faculty of Medicine, Health and Life Sciences{{{_:::_}}}Swansea University Medical School - Medicine
document_store_str 1
active_str 0
description BackgroundUpdatable estimates of COVID-19 onset, progression, and trajectories underpin pandemic mitigation efforts. To identify and characterise disease trajectories, we aimed to define and validate ten COVID-19 phenotypes from nationwide linked electronic health records (EHR) using an extensible framework.MethodsIn this cohort study, we used eight linked National Health Service (NHS) datasets for people in England alive on Jan 23, 2020. Data on COVID-19 testing, vaccination, primary and secondary care records, and death registrations were collected until Nov 30, 2021. We defined ten COVID-19 phenotypes reflecting clinically relevant stages of disease severity and encompassing five categories: positive SARS-CoV-2 test, primary care diagnosis, hospital admission, ventilation modality (four phenotypes), and death (three phenotypes). We constructed patient trajectories illustrating transition frequency and duration between phenotypes. Analyses were stratified by pandemic waves and vaccination status.FindingsAmong 57 032 174 individuals included in the cohort, 13 990 423 COVID-19 events were identified in 7 244 925 individuals, equating to an infection rate of 12·7% during the study period. Of 7 244 925 individuals, 460 737 (6·4%) were admitted to hospital and 158 020 (2·2%) died. Of 460 737 individuals who were admitted to hospital, 48 847 (10·6%) were admitted to the intensive care unit (ICU), 69 090 (15·0%) received non-invasive ventilation, and 25 928 (5·6%) received invasive ventilation. Among 384 135 patients who were admitted to hospital but did not require ventilation, mortality was higher in wave 1 (23 485 [30·4%] of 77 202 patients) than wave 2 (44 220 [23·1%] of 191 528 patients), but remained unchanged for patients admitted to the ICU. Mortality was highest among patients who received ventilatory support outside of the ICU in wave 1 (2569 [50·7%] of 5063 patients). 15 486 (9·8%) of 158 020 COVID-19-related deaths occurred within 28 days of the first COVID-19 event without a COVID-19 diagnoses on the death certificate. 10 884 (6·9%) of 158 020 deaths were identified exclusively from mortality data with no previous COVID-19 phenotype recorded. We observed longer patient trajectories in wave 2 than wave 1.InterpretationOur analyses illustrate the wide spectrum of disease trajectories as shown by differences in incidence, survival, and clinical pathways. We have provided a modular analytical framework that can be used to monitor the impact of the pandemic and generate evidence of clinical and policy relevance using multiple EHR sources.
published_date 2022-07-01T04:15:43Z
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score 11.037581

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