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Article ; Online: Publisher Correction: Genomic epidemiology reveals multiple introductions of SARS-CoV-2 from mainland Europe into Scotland.

da Silva Filipe, Ana / Shepherd, James G / Williams, Thomas / Hughes, Joseph / Aranday-Cortes, Elihu / Asamaphan, Patawee / Ashraf, Shirin / Balcazar, Carlos / Brunker, Kirstyn / Campbell, Alasdair / Carmichael, Stephen / Davis, Chris / Dewar, Rebecca / Gallagher, Michael D / Gunson, Rory / Hill, Verity / Ho, Antonia / Jackson, Ben / James, Edward /

Jesudason, Natasha / Johnson, Natasha / McWilliam Leitch, E Carol / Li, Kathy / MacLean, Alasdair / Mair, Daniel / McAllister, David A / McCrone, John T / McDonald, Sarah E / McHugh, Martin P / Morris, A Keith / Nichols, Jenna / Niebel, Marc / Nomikou, Kyriaki / Orton, Richard J / O'Toole, Áine / Palmarini, Massimo / Parcell, Benjamin J / Parr, Yasmin A / Rambaut, Andrew / Rooke, Stefan / Shaaban, Sharif / Shah, Rajiv / Singer, Joshua B / Smollett, Katherine / Starinskij, Igor / Tong, Lily / Sreenu, Vattipally B / Wastnedge, Elizabeth / Holden, Matthew T G / Robertson, David L / Templeton, Kate / Thomson, Emma C

Nature microbiology

2021 Volume 6, Issue 2, Page(s) 271

Language	English
Publishing date	2021-01-18
Publishing country	England
Document type	Published Erratum
ISSN	2058-5276
ISSN (online)	2058-5276
DOI	10.1038/s41564-021-00865-4
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Genetic epidemiology of SARS-CoV-2 transmission in renal dialysis units - A high risk community-hospital interface.

Li, Kathy K / Woo, Y Mun / Stirrup, Oliver / Hughes, Joseph / Ho, Antonia / Filipe, Ana Da Silva / Johnson, Natasha / Smollett, Katherine / Mair, Daniel / Carmichael, Stephen / Tong, Lily / Nichols, Jenna / Aranday-Cortes, Elihu / Brunker, Kirstyn / Parr, Yasmin A / Nomikou, Kyriaki / McDonald, Sarah E / Niebel, Marc / Asamaphan, Patawee /

The Journal of infection

2021 Volume 83, Issue 1, Page(s) 96–103

Abstract: Objectives: Patients requiring haemodialysis are at increased risk of serious illness with SARS-CoV-2 infection. To improve the understanding of transmission risks in six Scottish renal dialysis units, we utilised the rapid whole-genome sequencing data ... ...

Abstract	Objectives: Patients requiring haemodialysis are at increased risk of serious illness with SARS-CoV-2 infection. To improve the understanding of transmission risks in six Scottish renal dialysis units, we utilised the rapid whole-genome sequencing data generated by the COG-UK consortium. Methods: We combined geographical, temporal and genomic sequence data from the community and hospital to estimate the probability of infection originating from within the dialysis unit, the hospital or the community using Bayesian statistical modelling and compared these results to the details of epidemiological investigations. Results: Of 671 patients, 60 (8.9%) became infected with SARS-CoV-2, of whom 16 (27%) died. Within-unit and community transmission were both evident and an instance of transmission from the wider hospital setting was also demonstrated. Conclusions: Near-real-time SARS-CoV-2 sequencing data can facilitate tailored infection prevention and control measures, which can be targeted at reducing risk in these settings.
MeSH term(s)	Bayes Theorem ; COVID-19 ; Hospitals ; Humans ; Molecular Epidemiology ; Renal Dialysis/adverse effects ; SARS-CoV-2
Language	English
Publishing date	2021-04-22
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	424417-5
ISSN	1532-2742 ; 0163-4453
ISSN (online)	1532-2742
ISSN	0163-4453
DOI	10.1016/j.jinf.2021.04.020
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Author Correction: Genomic epidemiology reveals multiple introductions of SARS-CoV-2 from mainland Europe into Scotland.

Nature microbiology

2021 Volume 6, Issue 3, Page(s) 414

Language	English
Publishing date	2021-01-28
Publishing country	England
Document type	Published Erratum
ISSN	2058-5276
ISSN (online)	2058-5276
DOI	10.1038/s41564-021-00869-0
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Genomic epidemiology reveals multiple introductions of SARS-CoV-2 from mainland Europe into Scotland.

Nature microbiology

2020 Volume 6, Issue 1, Page(s) 112–122

Abstract: Coronavirus disease 2019 (COVID-19) was first diagnosed in Scotland on 1 March 2020. During the first month of the outbreak, 2,641 cases of COVID-19 led to 1,832 hospital admissions, 207 intensive care admissions and 126 deaths. We aimed to identify the ... ...

Abstract	Coronavirus disease 2019 (COVID-19) was first diagnosed in Scotland on 1 March 2020. During the first month of the outbreak, 2,641 cases of COVID-19 led to 1,832 hospital admissions, 207 intensive care admissions and 126 deaths. We aimed to identify the source and number of introductions of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) into Scotland using a combined phylogenetic and epidemiological approach. Sequencing of 1,314 SARS-CoV-2 viral genomes from available patient samples enabled us to estimate that SARS-CoV-2 was introduced to Scotland on at least 283 occasions during February and March 2020. Epidemiological analysis confirmed that early introductions of SARS-CoV-2 originated from mainland Europe (the majority from Italy and Spain). We identified subsequent early outbreaks in the community, within healthcare facilities and at an international conference. Community transmission occurred after 2 March, 3 weeks before control measures were introduced. Earlier travel restrictions or quarantine measures, both locally and internationally, would have reduced the number of COVID-19 cases in Scotland. The risk of multiple reintroduction events in future waves of infection remains high in the absence of population immunity.
MeSH term(s)	Adult ; Aged ; COVID-19/epidemiology ; COVID-19/virology ; Europe/epidemiology ; Genome, Viral ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; Middle Aged ; Molecular Epidemiology ; Phylogeny ; SARS-CoV-2/genetics ; SARS-CoV-2/isolation & purification ; Spain/epidemiology ; Travel/statistics & numerical data
Language	English
Publishing date	2020-12-21
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2058-5276
ISSN (online)	2058-5276
DOI	10.1038/s41564-020-00838-z
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Genetic epidemiology of SARS-CoV-2 transmission in renal dialysis units - a high risk community-hospital interface

Woo, Y. Mun / Stirrup, Oliver / Li, Kathy / Hughes, Joseph / Ho, Antonia / Da Silva Filipe, Ana / Johnson, Natasha / Smollett, Katherine / Mair, Daniel / Carmichael, Stephen / Tong, Lily / Nichols, Jenna / Aranday-Cortes, Elihu / Brunker, Kirstyn / Parr, Yasmin A. / Nomikou, Kyriaki / McDonald, Sarah E / Niebel, Marc / Asamaphan, Patawee /

Sreenu, Vattipally B / Robertson, David L / Taggart, Aislynn / Jesudason, Natasha / Shah, Rajiv / Shepherd, James G / Singer, Josh / Taylor, Alison HM / Cousland, Zoe / Price, Jonathan / Lees, Jennifer / Jones, Timothy P.W. PW / Lopez, Carlos Varon / MacLean, Alasdair / Starinskij, Igor / Gunson, Rory / Morris, Scott T.W. / Thomson, Peter C. / Geddes, Colin C / Traynor, Jamie P. / Breuer, Judith G / The COVID-19 Genomics UK (COG-UK) consortium / Thomson, Emma C / Mark, Patrick B

medRxiv

Abstract	Objectives: Patients requiring haemodialysis are at increased risk of serious illness with SARS-CoV-2 infection. To improve the understanding of transmission risks in six Scottish renal dialysis units, we utilised the rapid whole-genome sequencing data generated by the COG-UK consortium. Methods: We combined geographical, temporal and genomic sequence data from the community and hospital to estimate the probability of infection originating from within the dialysis unit, the hospital or the community using Bayesian statistical modelling and compared these results to the details of epidemiological investigations. Results: Of 671 patients, 60 (8.9%) became infected with SARS-CoV-2, of whom 16 (27%) died. Within-unit and community transmission were both evident and an instance of transmission from the wider hospital setting was also demonstrated. Conclusions: Near-real-time SARS-CoV-2 sequencing data can facilitate tailored infection prevention and control measures, which can be targeted at reducing risk in these settings. Key words: SARS-CoV-2, COVID-19, haemodialysis, renal dialysis unit, infection control, rapid sequencing, outbreak, nosocomial Key words: SARS-CoV-2, COVID-19, haemodialysis, renal dialysis unit, infection control, rapid sequencing, outbreak, nosocomial
Keywords	covid19
Language	English
Publishing date	2021-03-26
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2021.03.24.21253587
Database	COVID19

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Article ; Online: Genomic epidemiology of SARS-CoV-2 spread in Scotland highlights the role of European travel in COVID-19 emergence

Filipe, Ana Da Silva / Shepherd, James / Williams, Thomas / Hughes, Joseph / Aranday-Cortes, Elihu / Asamaphan, Patawee / Balcazar, Carlos / Brunker, Kirstyn / Carmichael, Stephen / Dewar, Rebecca / Gallagher, Michael D / Gunson, Rory / Ho, Antonia / Jesudason, Natasha / Johnson, Natasha / Leitch, E. Carol McWilliam / Li, Kathy / MacLean, Alasdair / Mair, Daniel /

medRxiv

Abstract: Abstract SARS-CoV-2, the causative agent of COVID-19, emerged in Wuhan, China in December 2019 and spread rapidly throughout the world. Understanding the introductions of this new coronavirus in different settings may assist control efforts and the ... ...

Abstract	Abstract SARS-CoV-2, the causative agent of COVID-19, emerged in Wuhan, China in December 2019 and spread rapidly throughout the world. Understanding the introductions of this new coronavirus in different settings may assist control efforts and the establishment of frameworks to support rapid response in future infectious disease outbreaks. We investigated the first four weeks of emergence of the SARS-CoV-2 virus in Scotland after the first case reported on the 1st March 2020. We obtained full genome sequences from 452 individuals with a laboratory-confirmed diagnosis of COVID-19, representing 20% of all cases until 1st April 2020 (n=2310). This permitted a genomic epidemiology approach to study the introductions and spread of the SARS-2 virus in Scotland. From combined phylogenetic and epidemiological analysis, we estimated at least 113 introductions of SARS-CoV-2 into Scotland during this period. Clusters containing multiple sequences suggestive of onward transmission occurred in 48/86 (56%). 42/86 (51%) clusters had no known international travel history indicating undetected introductions. The majority of viral sequences were most closely related to those circulating in other European countries, including Italy, Austria and Spain. Travel-associated introductions of SARS-CoV-2 into Scotland predated travel restrictions in the UK and other European countries. The first local transmission occurred three days after the first case. A shift from travel-associated to sustained community transmission was apparent after only 11 days. Undetected introductions occurred prior to the first known case of COVID-19. Earlier travel restrictions and quarantine measures might have resulted in fewer introductions into Scotland, thereby reducing the number of cases and the subsequent burden on health services. The high number of introductions and transmission rates were likely to have impacted on national contact tracing efforts. Our results also demonstrate that local real-time genomic epidemiology can be used to monitor transmission clusters and facilitate control efforts to restrict the spread of COVID-19.
Keywords	covid19
Language	English
Publishing date	2020-06-09
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2020.06.08.20124834
Database	COVID19

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Article ; Online: Epidemic waves of COVID-19 in Scotland: a genomic perspective on the impact of the introduction and relaxation of lockdown on SARS-CoV-2

Lycett, Samantha J / Hughes, Joseph / McHugh, Martin P / Filipe, Ana Da Silva / Dewar, Rebecca / Lu, Lu / Doherty, Thomas / Shepherd, Amy / Inward, Rhys / Rossi, Gianluigi / Balaz, Daniel / Kao, Rowland R / Rooke, Stefan / Cotton, Seb / Gallagher, Michael D / Balcazar-Lopez, Carlos E / O'Toole, Aine / Scher, Emily / Hill, Verity /

McCrone, John T / Colquhoun, Rachel M / Jackson, Ben / Williams, Thomas C / Williamson, Kathleen A / Johnson, Natasha / Smollett, Katherine / Mair, Daniel / Carmichael, Stephen / Tong, Lily / Nichols, Jenna / Brunker, Kirstyn / Shepherd, James G / Li, Kathy / Aranday-Cortes, Elihu / Parr, Yasmin A / Broos, Alice / Nomikou, Kyriaki / McDonald, Sarah E / Niebel, Marc / Asamaphan, Patawee / Starinskij, Igor / Jesudason, Natasha / Shah, Rajiv / Sreenu, Vattipally B / Stanton, Tom / Shaaban, Sharif / MacLean, Alasdair / The COVID-19 Genomics UK (COG-UK) consortium / Woolhouse, Mark / Gunson, Rory / Templeton, Kate / Thomson, Emma C / Rambaut, Andrew / Holden, Matthew TG / Robertson, David L

medRxiv

Abstract: The second SARS virus, SARS-CoV-2, emerged in December 2019, and within a month was globally distributed. It was first introduced into Scotland in February 2020 associated with returning travellers and visitors. By March it was circulating in communities ...

Abstract	The second SARS virus, SARS-CoV-2, emerged in December 2019, and within a month was globally distributed. It was first introduced into Scotland in February 2020 associated with returning travellers and visitors. By March it was circulating in communities across the UK, and to control COVID-19 cases, and prevent overwhelming of the National Health Service (NHS), a 9lockdown9 was introduced on 23rd March 2020 with a restriction of people9s movements. To augment the public health efforts a large-scale genome epidemiology effort (as part of the COVID-19 Genomics UK (COG-UK) consortium) resulted in the sequencing of over 5000 SARS-CoV-2 genomes by 18th August 2020 from Scottish cases, about a quarter of the estimated number of cases at that time. Here we quantify the geographical origins of the first wave introductions into Scotland from abroad and other UK regions, the spread of these SARS-CoV-2 lineages to different regions within Scotland (defined at the level of NHS Health Board) and the effect of lockdown on virus 9success9. We estimate that approximately 300 introductions seeded lineages in Scotland, with around 25% of these lineages composed of more than five viruses, but by June circulating lineages were reduced to low levels, in line with low numbers of recorded positive cases. Lockdown was, thus, associated with a dramatic reduction in infection numbers and the extinguishing of most virus lineages. Unfortunately since the summer cases have been rising in Scotland in a second wave, with >1000 people testing positive on a daily basis, and hospitalisation of COVID-19 cases on the rise again. Examining the available Scottish genome data from the second wave, and comparing it to the first wave, we find that while some UK lineages have persisted through the summer, the majority of lineages responsible for the second wave are new introductions from outside of Scotland and many from outside of the UK. This indicates that, while lockdown in Scotland is directly linked with the first wave case numbers being brought under control, travel-associated imports (mostly from Europe or other parts of the UK) following the easing of lockdown are responsible for seeding the current epidemic population. This demonstrates that the impact of stringent public health measures can be compromised if following this, movements from regions of high to low prevalence are not minimised.
Keywords	covid19
Language	English
Publishing date	2021-01-20
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2021.01.08.20248677
Database	COVID19

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Article ; Online: Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity

Volz, Erik / Hill, Verity / McCrone, John T. / Price, Anna / Jorgensen, David / O’Toole, Áine / Southgate, Joel / Johnson, Robert / Jackson, Ben / Nascimento, Fabricia F. / Rey, Sara M. / Nicholls, Samuel M. / Colquhoun, Rachel M. / da Silva Filipe, Ana / Shepherd, James / Pascall, David J. / Shah, Rajiv / Jesudason, Natasha / Li, Kathy /

Jarrett, Ruth / Pacchiarini, Nicole / Bull, Matthew / Geidelberg, Lily / Siveroni, Igor / Goodfellow, Ian / Loman, Nicholas J. / Pybus, Oliver G. / Robertson, Dave / Thomson, Emma C. / Rambaut, Andrew / Connor, Thomas R. / Koshy, Cherian / Wise, Emma / Cortes, Nick / Lynch, Jessica / Kidd, Stephen / Mori, Matilde / Fairley, Derek J. / Curran, Tanya / McKenna, James P. / Adams, Helen / Fraser, Christophe / Golubchik, Tanya / Bonsall, David / Moore, Catrin / Caddy, Sarah L. / Khokhar, Fahad A. / Wantoch, Michelle / Reynolds, Nicola / Warne, Ben / Maksimovic, Joshua / Spellman, Karla / McCluggage, Kathryn / John, Michaela / Beér, Robert / Afifi, Safiah / Morgan, Siân / Marchbank, Angela / Kitchen, C. / Gulliver, Huw / Merrick, Ian / Guest, Martyn / Munn, Robert / Workman, Trudy / Fuller, William / Bresner, Catherine / Snell, Luke B. / Charalampous, Themoula / Nebbia, Gaia / Batra, Rahul / Edgeworth, Jonathan / Robson, Samuel C. / Beckett, Angela / Loveson, Katie F. / Aanensen, David M. / Underwood, Anthony P. / Yeats, Corin A. / Abudahab, Khalil / Taylor, Ben E.W. / Menegazzo, Mirko / Clark, Gemma / Smith, Wendy / Khakh, Manjinder / Fleming, Vicki M. / Lister, Michelle M. / Howson-Wells, Hannah C. / Berry, Louise / Boswell, Tim / Joseph, Amelia / Willingham, Iona / Bird, Paul / Helmer, Thomas / Fallon, Karlie / Holmes, Christopher / Tang, Julian / Raviprakash, Veena / Campbell, Sharon / Sheriff, Nicola / Loose, Matthew W. / Holmes, Nadine / Moore, Christopher / Carlile, Matthew / Wright, Victoria / Sang, Fei / Debebe, Johnny / Coll, Francesc / Signell, Adrian W. / Betancor, Gilberto / Wilson, Harry D. / Feltwell, Theresa / Houldcroft, Charlotte J. / Eldirdiri, Sahar / Kenyon, Anita / Davis, Thomas / Pybus, Oliver / Du Plessis, L. / Zarebski, Alex / Raghwani, Jayna / Kraemer, Moritz / Francois, Sarah / Attwood, Stephen / Vasylyeva, Tetyana / Török, Estée / Hamilton, William L. / Goodfellow, Ian G. / Hall, Grant / Jahun, Aminu S. / Chaudhry, Yasmin / Hosmillo, Myra / Pinckert, Malte L. / Georgana, Iliana / Yakovleva, Anna / Meredith, Luke W. / Moses, S. / Lowe, Hannah / Ryan, Felicity / Fisher, Chloe L. / Awan, Ali R. / Boyes, John / Breuer, Judith / Harris, Kathryn Ann / Brown, Julianne Rose / Shah, Divya / Atkinson, Laura / Lee, Jack C.D. / Alcolea-Medina, Adela / Moore, Nathan / Cortes, Nicholas / Williams, Rebecca / Chapman, Michael R. / Levett, Lisa J. / Heaney, Judith / Smith, Darren L. / Bashton, Matthew / Young, Gregory R. / Allan, John / Loh, Joshua / Randell, Paul A. / Cox, Ali / Madona, Pinglawathee / Holmes, Alison / Bolt, Frances / Price, James / Mookerjee, Siddharth / Rowan, Aileen / Taylor, Graham P. / Ragonnet-Cronin, Manon / Johnson, Rob / Boyd, Olivia / Volz, Erik M. / Brunker, Kirstyn / Smollett, Katherine L. / Quick, Joshua / McMurray, Claire / Stockton, Joanne / Nicholls, Sam / Rowe, William / Poplawski, Radoslaw / Martinez-Nunez, Rocio T. / Mason, Jenifer / Robinson, Trevor I. / O'Toole, Elaine / Watts, Joanne / Breen, Cassie / Cowell, Angela / Ludden, Catherine / Sluga, Graciela / Machin, Nicholas W. / Ahmad, Shazaad S.Y. / George, Ryan P. / Halstead, Fenella / Sivaprakasam, Venkat / Shepherd, James G. / Asamaphan, Patawee / Niebel, Marc O. / Li, Kathy K. / Shah, Rajiv N. / Jesudason, Natasha G. / Parr, Yasmin A. / Tong, Lily / Broos, Alice / Mair, Daniel / Nichols, Jenna / Carmichael, Stephen N. / Nomikou, Kyriaki / Aranday-Cortes, Elihu / Johnson, NaTasha / Starinskij, Igor / Orton, Richard J. / Hughes, Joseph / Vattipally, Sreenu / Singer, Joshua B. / Hale, Antony D. / Macfarlane-Smith, Louissa R. / Harper, Katherine L. / Taha, Yusri / Payne, Brendan A.I. / Burton-Fanning, Shirelle / Waugh, Sheila / Collins, Jennifer / Eltringham, Gary / Templeton, Kate E. / McHugh, Martin P. / Dewar, Rebecca / Wastenge, Elizabeth / Dervisevic, Samir / Stanley, Rachael / Prakash, Reenesh / Stuart, Claire / Elumogo, Ngozi / Sethi, Dheeraj K. / Meader, Emma J. / Coupland, Lindsay J. / Potter, Will / Graham, Clive / Barton, Edward / Padgett, Debra / Scott, Garren / Swindells, Emma / Greenaway, Jane / Nelson, Andrew / Yew, Wen C. / Resende Silva, Paola C. / Andersson, Monique / Shaw, Robert / Peto, Timothy / Justice, Anita / Eyre, David / Crooke, Derrick / Hoosdally, Sarah / Sloan, Tim J. / Duckworth, Nichola / Walsh, Sarah / Chauhan, Anoop J. / Glaysher, Sharon / Bicknell, Kelly / Wyllie, Sarah / Butcher, Ethan / Elliott, Scott / Lloyd, Allyson / Impey, Robert / Levene, Nick / Monaghan, Lynn / Bradley, Declan T. / Allara, Elias / Pearson, Clare / Muir, Peter / Vipond, Ian B. / Hopes, Richard / Pymont, Hannah M. / Hutchings, Stephanie / Curran, Martin D. / Parmar, Surendra / Lackenby, Angie / Mbisa, Tamyo / Platt, Steven / Miah, Shâhjahân / Bibby, David / Manso, Carmen / Hubb, Jonathan / Chand, Meera / Dabrera, Gavin / Ramsay, Mary / Bradshaw, Daniel / Thornton, Alicia / Myers, Richard / Schaefer, Ulf / Groves, Natalie / Gallagher, Eileen / Lee, David / Williams, David / Ellaby, Nicholas / Harrison, Ian / Hartman, Hassan / Manesis, Nikos / Patel, Vineet / Bishop, Chloe / Chalker, Vicki / Osman, Husam / Bosworth, Andrew / Robinson, Esther / Holden, Matthew T.G. / Shaaban, Sharif / Birchley, Alec / Adams, Alexander / Davies, Alisha / Gaskin, Amy / Plimmer, Amy / Gatica-Wilcox, Bree / McKerr, Caoimhe / Moore, Catherine / Williams, Chris / Heyburn, David / De Lacy, Elen / Hilvers, Ember / Downing, Fatima / Shankar, Giri / Jones, Hannah / Asad, Hibo / Coombes, Jason / Watkins, Joanne / Evans, Johnathan M. / Fina, Laia / Gifford, Laura / Gilbert, Lauren / Graham, Lee / Perry, Malorie / Morgan, Mari / Cronin, Michelle / Craine, Noel / Jones, Rachel / Howe, Robin / Corden, Sally / Rey, Sara / Kumziene-Summerhayes, Sara / Taylor, Sarah / Cottrell, Simon / Jones, Sophie / Edwards, Sue / O’Grady, Justin / Page, Andrew J. / Wain, John / Webber, Mark A. / Mather, Alison E. / Baker, David J. / Rudder, Steven / Yāsir, Muḥammad / Thomson, Nicholas M. / Aydin, Alp / Tedim, Ana P. / Kay, Gemma L. / Trotter, Alexander J. / Gilroy, Rachel A.J. / Alikhan, Nabil-Fareed / de Oliveira Martins, Leonardo / Le-Viet, Thanh / Meadows, Lizzie / Kolyva, Anastasia / Diaz, Maria / Bell, Andrew / Gutierrez, Ana Victoria / Charles, Ian G. / Adriaenssens, Evelien M. / Kingsley, Robert A. / Casey, Anna / Simpson, D. A. / Molnár, Zoltán / Thompson, Thomas / Acheson, Erwan / Masoli, Jane A.H. / Knight, Bridget A. / Hattersley, Andrew / Ellard, Sian / Auckland, Cressida / Mahungu, Tabitha W. / Irish-Tavares, Dianne / Haque, Tanzina / Bourgeois, Yann / Scarlett, Garry P. / Partridge, David G. / Raza, Mohammad / Evans, Cariad / Johnson, Kate / Liggett, Steven / Baker, Paul / Essex, Sarah / Lyons, Ronan A. / Caller, Laura G. / Castellano, Sergi / Williams, Rachel J. / Kristiansen, Mark / Roy, Sunando / Williams, Charlotte A. / Dyal, Patricia L. / Tutill, Helena J. / Panchbhaya, Yasmin N. / Forrest, Leysa M. / Niola, Paola / Findlay, Jacqueline / Brooks, Tony T. / Gavriil, Artemis / Mestek-Boukhibar, Lamia / Weeks, Sam / Pandey, Sarojini / Berry, Lisa / Jones, K. E. / Richter, Alex / Beggs, Andrew / Smith, Colin P. / Bucca, Giselda / Hesketh, Andrew R. / Harrison, Ewan M. / Peacock, Sharon J. / Eser, Sophie / Churcher, Carol M. / Bellis, Katherine L. / Girgis, Sophia T. / Naydenova, Plamena / Blane, Beth / Sridhar, Sushmita / Ruis, Chris / Forrest, Sally / Cormie, Claire / Gill, Harmeet K. / Dias, Joana / Higginson, Ellen E. / Maes, Mailis / Young, Jamie / Kermack, Leanne M. / Hadjirin, Nazreen F. / Aggarwal, Dinesh / Griffith, Luke / Swingler, Tracey / Davidson, Rose K. / Williams, Thomas / Balcazar, Carlos E. / Gallagher, Michael D. / O'Toole, Áine / Rooke, Stefan / Colquhoun, Rachel / Ashworth, Jordan / McCrone, J.T. / Scher, Emily / Yu, Xiaoyu / Williamson, Kathleen A. / Stanton, Thomas D. / Michell, Stephen L. / Bewshea, Claire M. / Temperton, Ben / Michelsen, Michelle L. / Warwick-Dugdale, Joanna / Manley, Robin / Farbos, Audrey / Harrison, James W. / Sambles, Christine M. / Studholme, David J. / Jeffries, Aaron R. / Darby, Alistair C. / Hiscox, Julian A. / Paterson, Steve / Iturriza-Gomara, Miren / Jackson, Kathryn A. / Lucaci, Anita O. / Vamos, Edith E. / Hughes, Margaret / Rainbow, Lucille / Eccles, Richard / Nelson, Charlotte / Whitehead, Mark / Turtle, Lance / Haldenby, Sam T. / Gregory, Richard / Gemmell, Matthew / Kwiatkowski, Dominic / de Silva, Thushan I. / Smith, Nikki / Angyal, Adrienn / Lindsey, Benjamin B. / Groves, Danielle C. / Green, Luke R. / Wang, Dennis / Freeman, Timothy M. / Parker, Matthew D. / Keeley, Alexander J. / Parsons, Paul J. / Tucker, Rachel M. / Brown, Rebecca / Wyles, Matthew / Constantinidou, Chrystala / Unnikrishnan, Meera / Ott, Sascha / Cheng, Jeffrey K.J. / Bridgewater, Hannah E. / Frost, Lucy R. / Taylor-Joyce, Grace / Stark, Richard / Baxter, Laura / Alam, Mohammad T. / Brown, Paul E. / McClure, Patrick C. / Chappell, Joseph G. / Tsoleridis, Theocharis / Ball, Jonathan / Gramatopoulos, Dimitris / Buck, David / Todd, John A. / Green, Angie / Trebes, Amy / MacIntyre-Cockett, George / de Cesare, Mariateresa / Langford, Cordelia / Alderton, Alex / Amato, Roberto / Goncalves, Sonia / Jackson, David K. / Johnston, Ian / Sillitoe, John / Palmer, Steve / Lawniczak, Mara / Berriman, Matt / Danesh, John / Livett, Rich / Shirley, Lesley / Farr, Ben / Quail, Mike / Thurston, Scott / Park, Naomi / Betteridge, Emma / Weldon, Danni / Goodwin, Scott / Nelson, Rachel / Beaver, Charlotte / Letchford, Laura / Jackson, David A. / Foulser, Luke / McMinn, Liz / Prestwood, Liam / Kay, Sally / Kane, Leanne / Dorman, Matthew J. / Martincorena, Inigo / Puethe, Christoph / Keatley, Jon-Paul / Tonkin-Hill, Gerry / Smith, Christen / Jamrozy, Dorota / Beale, Mathew A. / Patel, Minal / Ariani, Cristina / Spencer-Chapman, Michael / Drury, Eleanor / Lo, Stephanie / Rajatileka, Shavanthi / Scott, Carol / James, Keith / Buddenborg, Sarah K. / Berger, Duncan J. / Patel, Gaurang / Garcia-Casado, Maria V. / Dibling, Thomas / McGuigan, Samantha / Rogers, Hazel A. / Hunter, Adam D. / Souster, Emily / Neaverson, Alexandra S.

Cell. 2021 Jan. 07, v. 184, no. 1 p.64-75.e11

2021

Abstract: Global dispersal and increasing frequency of the SARS-CoV-2 spike protein variant D614G are suggestive of a selective advantage but may also be due to a random founder effect. We investigate the hypothesis for positive selection of spike D614G in the ... ...

Institution	COG-UK Consortium
Abstract	Global dispersal and increasing frequency of the SARS-CoV-2 spike protein variant D614G are suggestive of a selective advantage but may also be due to a random founder effect. We investigate the hypothesis for positive selection of spike D614G in the United Kingdom using more than 25,000 whole genome SARS-CoV-2 sequences. Despite the availability of a large dataset, well represented by both spike 614 variants, not all approaches showed a conclusive signal of positive selection. Population genetic analysis indicates that 614G increases in frequency relative to 614D in a manner consistent with a selective advantage. We do not find any indication that patients infected with the spike 614G variant have higher COVID-19 mortality or clinical severity, but 614G is associated with higher viral load and younger age of patients. Significant differences in growth and size of 614G phylogenetic clusters indicate a need for continued study of this variant.
Keywords	COVID-19 infection ; Severe acute respiratory syndrome coronavirus 2 ; data collection ; founder effect ; genetic analysis ; genome ; mortality ; mutation ; pathogenicity ; phylogeny ; viral load ; United Kingdom ; COVID-19 ; SARS-CoV-2 ; evolution ; epidemiology ; spike
Language	English
Dates of publication	2021-0107
Size	p. 64-75.e11.
Publishing place	Elsevier Inc.
Document type	Article ; Online
Note	NAL-AP-2-clean
ZDB-ID	187009-9
ISSN	1097-4172 ; 0092-8674
ISSN (online)	1097-4172
ISSN	0092-8674
DOI	10.1016/j.cell.2020.11.020
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Publisher Correction: Genomic epidemiology reveals multiple introductions of SARS-CoV-2 from mainland Europe into Scotland.

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Article ; Online: Genetic epidemiology of SARS-CoV-2 transmission in renal dialysis units - A high risk community-hospital interface.

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Article ; Online: Author Correction: Genomic epidemiology reveals multiple introductions of SARS-CoV-2 from mainland Europe into Scotland.

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Article ; Online: Genomic epidemiology reveals multiple introductions of SARS-CoV-2 from mainland Europe into Scotland.

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Article ; Online: Genetic epidemiology of SARS-CoV-2 transmission in renal dialysis units - a high risk community-hospital interface

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Article ; Online: Genomic epidemiology of SARS-CoV-2 spread in Scotland highlights the role of European travel in COVID-19 emergence

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Article ; Online: Epidemic waves of COVID-19 in Scotland: a genomic perspective on the impact of the introduction and relaxation of lockdown on SARS-CoV-2

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Article ; Online: Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity

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