The Spread of SARS-CoV-2 Variant Omicron with a Doubling Time of 2.0-3.3 Days Can Be Explained by Immune Evasion.
The Spread of SARS-CoV-2 Variant Omicron with a Doubling Time of 2.0-3.3 Days Can Be Explained by Immune Evasion.
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DOI：
10.3390/v14020294
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发表时间：
2022-01-30
期刊：
影响因子：
--
通讯作者：
Lipniacki T
中科院分区：
文献类型：
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作者：
Grabowski F;Kochańczyk M;Lipniacki T
Omicron是一种新型高度突变的SARS-CoV-2关注变体（VOC， Pango谱系B.1.1.529），于2021年11月初首次在南非收集到。到2021年11月底，该病已在南非蔓延并接近固定，并已在各大洲发现。我们分析了Omicron在南非人口最多的两个省（豪登省和夸祖鲁-纳塔尔省）四周内的指数增长，分别得出了3.3天（95% CI: 3.2-3.4天）和2.7天（95% CI: 2.3-3.3天）的倍增时间估计。在澳大利亚（3.0天）、纽约州（2.5天）、英国（2.4天）和丹麦（2.0天）等其他地方也观察到类似或更短的翻倍时间。对数线性回归表明，疫情于2021年10月11日左右在豪登省开始传播；然而，由于初始传播的可能随机性，这种估计可能不准确。基于系统发育学的分析表明，Omicron菌株在2021年10月6日至10月29日之间开始分化。我们估计，Omicron与Delta之比的周增长率在7.2-10.2之间，大大高于Delta与Alpha之比的周增长率（估计在2.5-4.2之间）和Alpha与已有菌株的周增长率（估计在1.8-2.7之间）。较高的相对生长并不一定意味着较高的组粒传染性。双菌株SEIR模型表明，Omicron的生长优势可能源于免疫逃避，这使得这种VOC既可以感染恢复的个体，也可以感染完全接种过疫苗的个体。正如我们在模型中所证明的那样，免疫逃避比增加的传播性更令人担忧，因为它可能促进更大规模的流行病爆发。
Omicron, the novel highly mutated SARS-CoV-2 Variant of Concern (VOC, Pango lineage B.1.1.529) was first collected in early November 2021 in South Africa. By the end of November 2021, it had spread and approached fixation in South Africa, and had been detected on all continents. We analyzed the exponential growth of Omicron over four-week periods in the two most populated of South Africa’s provinces, Gauteng and KwaZulu-Natal, arriving at the doubling time estimates of, respectively, 3.3 days (95% CI: 3.2–3.4 days) and 2.7 days (95% CI: 2.3–3.3 days). Similar or even shorter doubling times were observed in other locations: Australia (3.0 days), New York State (2.5 days), UK (2.4 days), and Denmark (2.0 days). Log–linear regression suggests that the spread began in Gauteng around 11 October 2021; however, due to presumable stochasticity in the initial spread, this estimate can be inaccurate. Phylogenetics-based analysis indicates that the Omicron strain started to diverge between 6 October and 29 October 2021. We estimated that the weekly growth of the ratio of Omicron to Delta is in the range of 7.2–10.2, considerably higher than the growth of the ratio of Delta to Alpha (estimated to be in in the range of 2.5–4.2), and Alpha to pre-existing strains (estimated to be in the range of 1.8–2.7). High relative growth does not necessarily imply higher Omicron infectivity. A two-strain SEIR model suggests that the growth advantage of Omicron may stem from immune evasion, which permits this VOC to infect both recovered and fully vaccinated individuals. As we demonstrated within the model, immune evasion is more concerning than increased transmissibility, because it can facilitate larger epidemic outbreaks.
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影响因子：
64.5
作者：
Garcia-Beltran WF;St Denis KJ;Hoelzemer A;Lam EC;Nitido AD;Sheehan ML;Berrios C;Ofoman O;Chang CC;Hauser BM;Feldman J;Roederer AL;Gregory DJ;Poznansky MC;Schmidt AG;Iafrate AJ;Naranbhai V;Balazs AB
通讯作者：
Balazs AB
DOI：
10.1056/nejmoa2108891
发表时间：
2021-08-12
期刊：
The New England journal of medicine
影响因子：
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作者：
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通讯作者：
Ramsay M
DOI：
10.1016/s2666-5247(21)00267-6
发表时间：
2022-01
期刊：
The Lancet. Microbe
影响因子：
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作者：
Cromer D;Steain M;Reynaldi A;Schlub TE;Wheatley AK;Juno JA;Kent SJ;Triccas JA;Khoury DS;Davenport MP
通讯作者：
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影响因子：
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作者：
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DOI：
10.3390/v13030392
发表时间：
2021-03-01
期刊：
Viruses
影响因子：
--
作者：
Grabowski F;Preibisch G;Giziński S;Kochańczyk M;Lipniacki T
通讯作者：
Lipniacki T