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@article{Mishra:2021:10.1016/j.eclinm.2021.101064,
author = {Mishra, S and Mindermann, S and Sharma, M and Whittaker, C and Mellan, TA and Wilton, T and Klapsa, D and Mate, R and Fritzsche, M and Zambon, M and Ahuja, J and Howes, A and Miscouridou, X and Nason, GP and Ratmann, O and Semenova, E and Leech, G and Sandkuehler, JF and Rogers-Smith, C and Vollmer, M and Unwin, HJT and Gal, Y and Chand, M and Gandy, A and Martin, J and Volz, E and Ferguson, NM and Bhatt, S and Brauner, JM and Flaxman, S},
doi = {10.1016/j.eclinm.2021.101064},
journal = {EClinicalMedicine},
pages = {1--8},
title = {Changing composition of SARS-CoV-2 lineages and rise of Delta variant in England},
url = {http://dx.doi.org/10.1016/j.eclinm.2021.101064},
volume = {39},
year = {2021}
}

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TY  - JOUR
AB  - BackgroundSince its emergence in Autumn 2020, the SARS-CoV-2 Variant of Concern (VOC) B.1.1.7 (WHO label Alpha) rapidly became the dominant lineage across much of Europe. Simultaneously, several other VOCs were identified globally. Unlike B.1.1.7, some of these VOCs possess mutations thought to confer partial immune escape. Understanding when and how these additional VOCs pose a threat in settings where B.1.1.7 is currently dominant is vital.MethodsWe examine trends in the prevalence of non-B.1.1.7 lineages in London and other English regions using passive-case detection PCR data, cross-sectional community infection surveys, genomic surveillance, and wastewater monitoring. The study period spans from 31st January 2021 to 15th May 2021.FindingsAcross data sources, the percentage of non-B.1.1.7 variants has been increasing since late March 2021. This increase was initially driven by a variety of lineages with immune escape. From mid-April, B.1.617.2 (WHO label Delta) spread rapidly, becoming the dominant variant in England by late May.InterpretationThe outcome of competition between variants depends on a wide range of factors such as intrinsic transmissibility, evasion of prior immunity, demographic specificities and interactions with non-pharmaceutical interventions. The presence and rise of non-B.1.1.7 variants in March likely was driven by importations and some community transmission. There was competition between non-B.1.17 variants which resulted in B.1.617.2 becoming dominant in April and May with considerable community transmission. Our results underscore that early detection of new variants requires a diverse array of data sources in community surveillance. Continued real-time information on the highly dynamic composition and trajectory of different SARS-CoV-2 lineages is essential to future control effortsFundingNational Institute for Health Research, Medicines and Healthcare products Regulatory Agency, DeepMind, EPSRC, EA Funds programme, Open Philanthropy
AU  - Mishra,S
AU  - Mindermann,S
AU  - Sharma,M
AU  - Whittaker,C
AU  - Mellan,TA
AU  - Wilton,T
AU  - Klapsa,D
AU  - Mate,R
AU  - Fritzsche,M
AU  - Zambon,M
AU  - Ahuja,J
AU  - Howes,A
AU  - Miscouridou,X
AU  - Nason,GP
AU  - Ratmann,O
AU  - Semenova,E
AU  - Leech,G
AU  - Sandkuehler,JF
AU  - Rogers-Smith,C
AU  - Vollmer,M
AU  - Unwin,HJT
AU  - Gal,Y
AU  - Chand,M
AU  - Gandy,A
AU  - Martin,J
AU  - Volz,E
AU  - Ferguson,NM
AU  - Bhatt,S
AU  - Brauner,JM
AU  - Flaxman,S
DO  - 10.1016/j.eclinm.2021.101064
EP  - 8
PY  - 2021///
SN  - 2589-5370
SP  - 1
TI  - Changing composition of SARS-CoV-2 lineages and rise of Delta variant in England
T2  - EClinicalMedicine
UR  - http://dx.doi.org/10.1016/j.eclinm.2021.101064
UR  - https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000704058900023&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=1ba7043ffcc86c417c072aa74d649202
UR  - https://www.sciencedirect.com/science/article/pii/S2589537021003448?via%3Dihub
UR  - http://hdl.handle.net/10044/1/105850
VL  - 39
ER  -

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