The rapid replacement of the SARS-CoV-2 Delta variant by Omicron (B.1.1.529) in England.
The rapid replacement of the SARS-CoV-2 Delta variant by Omicron (B.1.1.529) in England.
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DOI：
10.1126/scitranslmed.abo5395
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发表时间：
2022-07-06
影响因子：
17.1
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B.1.1.529（Omicron）变种的出现引起了国际关注，因为它在南部非洲迅速传播。目前尚不清楚这种变体是否会在引入英国时取代或与当时占主导地位的Delta变体共存（无论是暂时还是长期）。我们开发了一套分层逻辑增长模型来描述S基因靶失败（SGTF）PCR检测频率的变化，这是Omicron的替代指标。SGTF病例的倍增时间在12月5日达到峰值1.56天（95%CI：1.49，1.63），而三重阳性病例每5.82天减半（95%CI：5.11，6.67）进入2021年圣诞节。我们无法用单一比率描述Omicron替代Delta的情况。在12月14日至15日期间，替代率下降了53.56%（95%CrI：45.38，61.01），这意味着Omicron的竞争优势大约减半。在变化点之前，Omicron在接种两剂或更多疫苗的患者中替换Delta的速度快16.24%（95%CrI：9.72，23.41），表明疫苗逃逸是竞争优势的重要组成部分。尽管增长放缓，但在第一例国内测序病例发生后的一个月内，德尔塔在英格兰几乎完全被取代。在Omicron流行的不同阶段，各地区的变化点的同步性表明，由于与菌株竞争相关的生物学机制，生长速率优势并未减弱。替代品的逐步变化可能是由行为变化引起的，可能是由公共卫生信息或政策引起的，这些变化对Omicron产生了不同的影响。尽管于二零二一年十二月中旬更换率约减半，Omicron变体仍于英格兰取代Delta变体。
The emergence of the B.1.1.529 (Omicron) variant caused international concern due to its rapid spread in Southern Africa. It was unknown whether this variant would replace or co-exist with (either transiently or long-term) the then-dominant Delta variant on its introduction to England. We developed a set of hierarchical logistic growth models to describe changes in the frequency of S gene target failure (SGTF) PCR tests, which was a proxy for Omicron. The doubling time of SGTF cases peaked at 1.56 days (95% CI: 1.49, 1.63) on the 5th of December, while triple positive cases were halving every 5.82 days (95% CI: 5.11, 6.67) going into Christmas 2021. We were unable to characterize the replacement of Delta by Omicron with a single rate. The replacement rate decreased by 53.56% (95% CrI: 45.38, 61.01) between the 14th and 15th of December, meaning the competitive advantage of Omicron approximately halved. Preceding the changepoint, Omicron was replacing Delta 16.24% (95% CrI: 9.72, 23.41) faster in those with two or more vaccine doses, indicative of vaccine escape being a substantial component of the competitive advantage. Despite the slowdown, Delta had almost entirely been replaced in England within a month of the first sequenced domestic case. The synchrony of changepoints across regions at various stages of Omicron epidemics suggests that the growth rate advantage was not attenuated due to biological mechanisms related to strain competition. The step-change in replacement could have resulted from behavioral changes, potentially elicited by public health messaging or policies, that differentially affected Omicron. The Omicron variant replaced the Delta variant in England despite the rate of replacement approximately halving in mid-December 2021.
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DOI：
10.1056/nejmoa2119451
发表时间：
2022-04-21
期刊：
The New England journal of medicine
影响因子：
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作者：
Andrews N;Stowe J;Kirsebom F;Toffa S;Rickeard T;Gallagher E;Gower C;Kall M;Groves N;O'Connell AM;Simons D;Blomquist PB;Zaidi A;Nash S;Iwani Binti Abdul Aziz N;Thelwall S;Dabrera G;Myers R;Amirthalingam G;Gharbia S;Barrett JC;Elson R;Ladhani SN;Ferguson N;Zambon M;Campbell CNJ;Brown K;Hopkins S;Chand M;Ramsay M;Lopez Bernal J
通讯作者：
Lopez Bernal J
影响因子：
56.9
作者：
McCallum, Matthew;Czudnochowski, Nadine;Rosen, Laura E.;Zepeda, Samantha K.;Bowen, John E.;Walls, Alexandra C.;Hauser, Kevin;Joshi, Anshu;Stewart, Cameron;Dillen, Josh R.;Powell, Abigail E.;Croll, Tristan, I;Nix, Jay;Virgin, Herbert W.;Corti, Davide;Snell, Gyorgy;Veesler, David
通讯作者：
Veesler, David
影响因子：
64.5
作者：
Liu C;Ginn HM;Dejnirattisai W;Supasa P;Wang B;Tuekprakhon A;Nutalai R;Zhou D;Mentzer AJ;Zhao Y;Duyvesteyn HME;López-Camacho C;Slon-Campos J;Walter TS;Skelly D;Johnson SA;Ritter TG;Mason C;Costa Clemens SA;Gomes Naveca F;Nascimento V;Nascimento F;Fernandes da Costa C;Resende PC;Pauvolid-Correa A;Siqueira MM;Dold C;Temperton N;Dong T;Pollard AJ;Knight JC;Crook D;Lambe T;Clutterbuck E;Bibi S;Flaxman A;Bittaye M;Belij-Rammerstorfer S;Gilbert SC;Malik T;Carroll MW;Klenerman P;Barnes E;Dunachie SJ;Baillie V;Serafin N;Ditse Z;Da Silva K;Paterson NG;Williams MA;Hall DR;Madhi S;Nunes MC;Goulder P;Fry EE;Mongkolsapaya J;Ren J;Stuart DI;Screaton GR
通讯作者：
Screaton GR
DOI：
10.3390/v14020294
发表时间：
2022-01-30
期刊：
Viruses
影响因子：
--
作者：
Grabowski F;Kochańczyk M;Lipniacki T
通讯作者：
Lipniacki T
DOI：
10.1098/rstb.2020.0264
发表时间：
2021-07-19
期刊：
Philosophical transactions of the Royal Society of London. Series B, Biological sciences
影响因子：
--
作者：
Pellis L;Scarabel F;Stage HB;Overton CE;Chappell LHK;Fearon E;Bennett E;Lythgoe KA;House TA;Hall I;University of Manchester COVID-19 Modelling Group
通讯作者：
University of Manchester COVID-19 Modelling Group