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Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England
The SARS-CoV-2 lineage B.1.1.7, designated variant of concern (VOC) 202012/01 by Public Health England 1 , was first identified in the UK in late summer to early autumn 2020 2 . Whole-genome SARS-CoV-2 sequence data collected from community-based diagnostic testing for COVID-19 show an extremely rap...
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| Published in: | Nature (London) 2021-05, Vol.593 (7858), p.266-269 |
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| Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
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| creator | Volz, Erik Mishra, Swapnil Chand, Meera Barrett, Jeffrey C. Johnson, Robert Geidelberg, Lily Hinsley, Wes R. Laydon, Daniel J. Dabrera, Gavin O’Toole, Áine Amato, Robert Ragonnet-Cronin, Manon Harrison, Ian Jackson, Ben Ariani, Cristina V. Boyd, Olivia Loman, Nicholas J. McCrone, John T. Gonçalves, Sónia Jorgensen, David Myers, Richard Hill, Verity Jackson, David K. Gaythorpe, Katy Groves, Natalie Sillitoe, John Kwiatkowski, Dominic P. Flaxman, Seth Ratmann, Oliver Bhatt, Samir Hopkins, Susan Gandy, Axel Rambaut, Andrew Ferguson, Neil M. |
| description | The SARS-CoV-2 lineage B.1.1.7, designated variant of concern (VOC) 202012/01 by Public Health England
1
, was first identified in the UK in late summer to early autumn 2020
2
. Whole-genome SARS-CoV-2 sequence data collected from community-based diagnostic testing for COVID-19 show an extremely rapid expansion of the B.1.1.7 lineage during autumn 2020, suggesting that it has a selective advantage. Here we show that changes in VOC frequency inferred from genetic data correspond closely to changes inferred by
S
gene target failures (SGTF) in community-based diagnostic PCR testing. Analysis of trends in SGTF and non-SGTF case numbers in local areas across England shows that B.1.1.7 has higher transmissibility than non-VOC lineages, even if it has a different latent period or generation time. The SGTF data indicate a transient shift in the age composition of reported cases, with cases of B.1.1.7 including a larger share of under 20-year-olds than non-VOC cases. We estimated time-varying reproduction numbers for B.1.1.7 and co-circulating lineages using SGTF and genomic data. The best-supported models did not indicate a substantial difference in VOC transmissibility among different age groups, but all analyses agreed that B.1.1.7 has a substantial transmission advantage over other lineages, with a 50% to 100% higher reproduction number.
Genetic and testing data from England show that the SARS-CoV-2 variant of concern B.1.1.7 has a transmission advantage over other lineages. |
| doi_str_mv | 10.1038/s41586-021-03470-x |
| format | article |
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1
, was first identified in the UK in late summer to early autumn 2020
2
. Whole-genome SARS-CoV-2 sequence data collected from community-based diagnostic testing for COVID-19 show an extremely rapid expansion of the B.1.1.7 lineage during autumn 2020, suggesting that it has a selective advantage. Here we show that changes in VOC frequency inferred from genetic data correspond closely to changes inferred by
S
gene target failures (SGTF) in community-based diagnostic PCR testing. Analysis of trends in SGTF and non-SGTF case numbers in local areas across England shows that B.1.1.7 has higher transmissibility than non-VOC lineages, even if it has a different latent period or generation time. The SGTF data indicate a transient shift in the age composition of reported cases, with cases of B.1.1.7 including a larger share of under 20-year-olds than non-VOC cases. We estimated time-varying reproduction numbers for B.1.1.7 and co-circulating lineages using SGTF and genomic data. The best-supported models did not indicate a substantial difference in VOC transmissibility among different age groups, but all analyses agreed that B.1.1.7 has a substantial transmission advantage over other lineages, with a 50% to 100% higher reproduction number.
Genetic and testing data from England show that the SARS-CoV-2 variant of concern B.1.1.7 has a transmission advantage over other lineages.</description><identifier>ISSN: 0028-0836</identifier><identifier>EISSN: 1476-4687</identifier><identifier>DOI: 10.1038/s41586-021-03470-x</identifier><identifier>PMID: 33767447</identifier><language>eng</language><publisher>London: Nature Publishing Group UK</publisher><subject>45 ; 631/181/457 ; 631/326/596/4130 ; 692/699/255/2514 ; Adolescent ; Adult ; Age ; Age composition ; Age Distribution ; Aged ; Aged, 80 and over ; Autumn ; Basic Reproduction Number ; Biomarkers ; Child ; Child, Preschool ; Coronaviruses ; COVID-19 ; COVID-19 - diagnosis ; COVID-19 - epidemiology ; COVID-19 - transmission ; COVID-19 - virology ; COVID-19 diagnostic tests ; Diagnostic systems ; Disease transmission ; England - epidemiology ; Evolution, Molecular ; Genome, Viral - genetics ; Genomes ; Humanities and Social Sciences ; Humans ; Infant ; Infant, Newborn ; Latent period ; Middle Aged ; multidisciplinary ; Nucleotide sequence ; Phylogeny ; Proteins ; Public health ; S gene ; SARS-CoV-2 - classification ; SARS-CoV-2 - genetics ; SARS-CoV-2 - isolation & purification ; SARS-CoV-2 - pathogenicity ; Science ; Science (multidisciplinary) ; Severe acute respiratory syndrome coronavirus 2 ; Spike Glycoprotein, Coronavirus - analysis ; Spike Glycoprotein, Coronavirus - genetics ; Time Factors ; Trends ; Young Adult</subject><ispartof>Nature (London), 2021-05, Vol.593 (7858), p.266-269</ispartof><rights>The Author(s), under exclusive licence to Springer Nature Limited 2021</rights><rights>COPYRIGHT 2021 Nature Publishing Group</rights><rights>Copyright Nature Publishing Group May 13, 2021</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c687t-d04c67041dbfff045da74129a31a23e04699d109749a116e104f39a4eca08caf3</citedby><cites>FETCH-LOGICAL-c687t-d04c67041dbfff045da74129a31a23e04699d109749a116e104f39a4eca08caf3</cites><orcidid>0000-0001-6268-8937 ; 0000-0003-4270-3321 ; 0000-0003-4337-3707 ; 0000-0002-9981-0649 ; 0000-0002-1154-8093 ; 0000-0002-2477-4217 ; 0000-0002-8057-1844 ; 0000-0002-6777-0451 ; 0000-0002-5023-0176 ; 0000-0003-3734-9081 ; 0000-0002-8759-5902</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>315,783,787,27938,27939</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/33767447$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Volz, Erik</creatorcontrib><creatorcontrib>Mishra, Swapnil</creatorcontrib><creatorcontrib>Chand, Meera</creatorcontrib><creatorcontrib>Barrett, Jeffrey C.</creatorcontrib><creatorcontrib>Johnson, Robert</creatorcontrib><creatorcontrib>Geidelberg, Lily</creatorcontrib><creatorcontrib>Hinsley, Wes R.</creatorcontrib><creatorcontrib>Laydon, Daniel J.</creatorcontrib><creatorcontrib>Dabrera, Gavin</creatorcontrib><creatorcontrib>O’Toole, Áine</creatorcontrib><creatorcontrib>Amato, Robert</creatorcontrib><creatorcontrib>Ragonnet-Cronin, Manon</creatorcontrib><creatorcontrib>Harrison, Ian</creatorcontrib><creatorcontrib>Jackson, Ben</creatorcontrib><creatorcontrib>Ariani, Cristina V.</creatorcontrib><creatorcontrib>Boyd, Olivia</creatorcontrib><creatorcontrib>Loman, Nicholas J.</creatorcontrib><creatorcontrib>McCrone, John T.</creatorcontrib><creatorcontrib>Gonçalves, Sónia</creatorcontrib><creatorcontrib>Jorgensen, David</creatorcontrib><creatorcontrib>Myers, Richard</creatorcontrib><creatorcontrib>Hill, Verity</creatorcontrib><creatorcontrib>Jackson, David K.</creatorcontrib><creatorcontrib>Gaythorpe, Katy</creatorcontrib><creatorcontrib>Groves, Natalie</creatorcontrib><creatorcontrib>Sillitoe, John</creatorcontrib><creatorcontrib>Kwiatkowski, Dominic P.</creatorcontrib><creatorcontrib>Flaxman, Seth</creatorcontrib><creatorcontrib>Ratmann, Oliver</creatorcontrib><creatorcontrib>Bhatt, Samir</creatorcontrib><creatorcontrib>Hopkins, Susan</creatorcontrib><creatorcontrib>Gandy, Axel</creatorcontrib><creatorcontrib>Rambaut, Andrew</creatorcontrib><creatorcontrib>Ferguson, Neil M.</creatorcontrib><creatorcontrib>COVID-19 Genomics UK (COG-UK) consortium</creatorcontrib><creatorcontrib>The COVID-19 Genomics UK (COG-UK) consortium</creatorcontrib><title>Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England</title><title>Nature (London)</title><addtitle>Nature</addtitle><addtitle>Nature</addtitle><description>The SARS-CoV-2 lineage B.1.1.7, designated variant of concern (VOC) 202012/01 by Public Health England
1
, was first identified in the UK in late summer to early autumn 2020
2
. Whole-genome SARS-CoV-2 sequence data collected from community-based diagnostic testing for COVID-19 show an extremely rapid expansion of the B.1.1.7 lineage during autumn 2020, suggesting that it has a selective advantage. Here we show that changes in VOC frequency inferred from genetic data correspond closely to changes inferred by
S
gene target failures (SGTF) in community-based diagnostic PCR testing. Analysis of trends in SGTF and non-SGTF case numbers in local areas across England shows that B.1.1.7 has higher transmissibility than non-VOC lineages, even if it has a different latent period or generation time. The SGTF data indicate a transient shift in the age composition of reported cases, with cases of B.1.1.7 including a larger share of under 20-year-olds than non-VOC cases. We estimated time-varying reproduction numbers for B.1.1.7 and co-circulating lineages using SGTF and genomic data. The best-supported models did not indicate a substantial difference in VOC transmissibility among different age groups, but all analyses agreed that B.1.1.7 has a substantial transmission advantage over other lineages, with a 50% to 100% higher reproduction number.
Genetic and testing data from England show that the SARS-CoV-2 variant of concern B.1.1.7 has a transmission advantage over other lineages.</description><subject>45</subject><subject>631/181/457</subject><subject>631/326/596/4130</subject><subject>692/699/255/2514</subject><subject>Adolescent</subject><subject>Adult</subject><subject>Age</subject><subject>Age composition</subject><subject>Age Distribution</subject><subject>Aged</subject><subject>Aged, 80 and over</subject><subject>Autumn</subject><subject>Basic Reproduction Number</subject><subject>Biomarkers</subject><subject>Child</subject><subject>Child, Preschool</subject><subject>Coronaviruses</subject><subject>COVID-19</subject><subject>COVID-19 - diagnosis</subject><subject>COVID-19 - epidemiology</subject><subject>COVID-19 - transmission</subject><subject>COVID-19 - virology</subject><subject>COVID-19 diagnostic tests</subject><subject>Diagnostic systems</subject><subject>Disease transmission</subject><subject>England - epidemiology</subject><subject>Evolution, Molecular</subject><subject>Genome, Viral - genetics</subject><subject>Genomes</subject><subject>Humanities and Social Sciences</subject><subject>Humans</subject><subject>Infant</subject><subject>Infant, Newborn</subject><subject>Latent period</subject><subject>Middle Aged</subject><subject>multidisciplinary</subject><subject>Nucleotide sequence</subject><subject>Phylogeny</subject><subject>Proteins</subject><subject>Public health</subject><subject>S gene</subject><subject>SARS-CoV-2 - classification</subject><subject>SARS-CoV-2 - genetics</subject><subject>SARS-CoV-2 - isolation & purification</subject><subject>SARS-CoV-2 - pathogenicity</subject><subject>Science</subject><subject>Science (multidisciplinary)</subject><subject>Severe acute respiratory syndrome coronavirus 2</subject><subject>Spike Glycoprotein, Coronavirus - analysis</subject><subject>Spike Glycoprotein, Coronavirus - genetics</subject><subject>Time 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transmissibility of SARS-CoV-2 lineage B.1.1.7 in England</title><author>Volz, Erik ; Mishra, Swapnil ; Chand, Meera ; Barrett, Jeffrey C. ; Johnson, Robert ; Geidelberg, Lily ; Hinsley, Wes R. ; Laydon, Daniel J. ; Dabrera, Gavin ; O’Toole, Áine ; Amato, Robert ; Ragonnet-Cronin, Manon ; Harrison, Ian ; Jackson, Ben ; Ariani, Cristina V. ; Boyd, Olivia ; Loman, Nicholas J. ; McCrone, John T. ; Gonçalves, Sónia ; Jorgensen, David ; Myers, Richard ; Hill, Verity ; Jackson, David K. ; Gaythorpe, Katy ; Groves, Natalie ; Sillitoe, John ; Kwiatkowski, Dominic P. ; Flaxman, Seth ; Ratmann, Oliver ; Bhatt, Samir ; Hopkins, Susan ; Gandy, Axel ; Rambaut, Andrew ; Ferguson, Neil 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Collection</collection><collection>Environmental Science Collection</collection><collection>ProQuest Central Basic</collection><collection>University of Michigan</collection><collection>Genetics Abstracts</collection><collection>SIRS Editorial</collection><collection>Environment Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>Nature (London)</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Volz, Erik</au><au>Mishra, Swapnil</au><au>Chand, Meera</au><au>Barrett, Jeffrey C.</au><au>Johnson, Robert</au><au>Geidelberg, Lily</au><au>Hinsley, Wes R.</au><au>Laydon, Daniel J.</au><au>Dabrera, Gavin</au><au>O’Toole, Áine</au><au>Amato, Robert</au><au>Ragonnet-Cronin, Manon</au><au>Harrison, Ian</au><au>Jackson, Ben</au><au>Ariani, Cristina V.</au><au>Boyd, Olivia</au><au>Loman, Nicholas J.</au><au>McCrone, John T.</au><au>Gonçalves, Sónia</au><au>Jorgensen, David</au><au>Myers, Richard</au><au>Hill, Verity</au><au>Jackson, David K.</au><au>Gaythorpe, Katy</au><au>Groves, Natalie</au><au>Sillitoe, John</au><au>Kwiatkowski, Dominic P.</au><au>Flaxman, Seth</au><au>Ratmann, Oliver</au><au>Bhatt, Samir</au><au>Hopkins, Susan</au><au>Gandy, Axel</au><au>Rambaut, Andrew</au><au>Ferguson, Neil M.</au><aucorp>COVID-19 Genomics UK (COG-UK) consortium</aucorp><aucorp>The COVID-19 Genomics UK (COG-UK) consortium</aucorp><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England</atitle><jtitle>Nature (London)</jtitle><stitle>Nature</stitle><addtitle>Nature</addtitle><date>2021-05-13</date><risdate>2021</risdate><volume>593</volume><issue>7858</issue><spage>266</spage><epage>269</epage><pages>266-269</pages><issn>0028-0836</issn><eissn>1476-4687</eissn><notes>ObjectType-Article-1</notes><notes>SourceType-Scholarly Journals-1</notes><notes>ObjectType-Feature-2</notes><notes>content type line 23</notes><abstract>The SARS-CoV-2 lineage B.1.1.7, designated variant of concern (VOC) 202012/01 by Public Health England
1
, was first identified in the UK in late summer to early autumn 2020
2
. Whole-genome SARS-CoV-2 sequence data collected from community-based diagnostic testing for COVID-19 show an extremely rapid expansion of the B.1.1.7 lineage during autumn 2020, suggesting that it has a selective advantage. Here we show that changes in VOC frequency inferred from genetic data correspond closely to changes inferred by
S
gene target failures (SGTF) in community-based diagnostic PCR testing. Analysis of trends in SGTF and non-SGTF case numbers in local areas across England shows that B.1.1.7 has higher transmissibility than non-VOC lineages, even if it has a different latent period or generation time. The SGTF data indicate a transient shift in the age composition of reported cases, with cases of B.1.1.7 including a larger share of under 20-year-olds than non-VOC cases. We estimated time-varying reproduction numbers for B.1.1.7 and co-circulating lineages using SGTF and genomic data. The best-supported models did not indicate a substantial difference in VOC transmissibility among different age groups, but all analyses agreed that B.1.1.7 has a substantial transmission advantage over other lineages, with a 50% to 100% higher reproduction number.
Genetic and testing data from England show that the SARS-CoV-2 variant of concern B.1.1.7 has a transmission advantage over other lineages.</abstract><cop>London</cop><pub>Nature Publishing Group UK</pub><pmid>33767447</pmid><doi>10.1038/s41586-021-03470-x</doi><tpages>4</tpages><orcidid>https://orcid.org/0000-0001-6268-8937</orcidid><orcidid>https://orcid.org/0000-0003-4270-3321</orcidid><orcidid>https://orcid.org/0000-0003-4337-3707</orcidid><orcidid>https://orcid.org/0000-0002-9981-0649</orcidid><orcidid>https://orcid.org/0000-0002-1154-8093</orcidid><orcidid>https://orcid.org/0000-0002-2477-4217</orcidid><orcidid>https://orcid.org/0000-0002-8057-1844</orcidid><orcidid>https://orcid.org/0000-0002-6777-0451</orcidid><orcidid>https://orcid.org/0000-0002-5023-0176</orcidid><orcidid>https://orcid.org/0000-0003-3734-9081</orcidid><orcidid>https://orcid.org/0000-0002-8759-5902</orcidid><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 0028-0836 |
| ispartof | Nature (London), 2021-05, Vol.593 (7858), p.266-269 |
| issn | 0028-0836 1476-4687 |
| language | eng |
| recordid | cdi_proquest_miscellaneous_2506284021 |
| source | Nature |
| subjects | 45 631/181/457 631/326/596/4130 692/699/255/2514 Adolescent Adult Age Age composition Age Distribution Aged Aged, 80 and over Autumn Basic Reproduction Number Biomarkers Child Child, Preschool Coronaviruses COVID-19 COVID-19 - diagnosis COVID-19 - epidemiology COVID-19 - transmission COVID-19 - virology COVID-19 diagnostic tests Diagnostic systems Disease transmission England - epidemiology Evolution, Molecular Genome, Viral - genetics Genomes Humanities and Social Sciences Humans Infant Infant, Newborn Latent period Middle Aged multidisciplinary Nucleotide sequence Phylogeny Proteins Public health S gene SARS-CoV-2 - classification SARS-CoV-2 - genetics SARS-CoV-2 - isolation & purification SARS-CoV-2 - pathogenicity Science Science (multidisciplinary) Severe acute respiratory syndrome coronavirus 2 Spike Glycoprotein, Coronavirus - analysis Spike Glycoprotein, Coronavirus - genetics Time Factors Trends Young Adult |
| title | Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England |
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