Washington Nicole L, Gangavarapu Karthik, Zeller Mark, Bolze Alexandre, Cirulli Elizabeth T, Barrett Kelly M Schiabor, Larsen Brendan B, Anderson Catelyn, White Simon, Cassens Tyler, Jacobs Sharoni, Levan Geraint, Nguyen Jason, Ramirez Jimmy M, Rivera-Garcia Charlotte, Sandoval Efren, Wang Xueqing, Wong David, Spencer Emily, Robles-Sikisaka Refugio, Kurzban Ezra, Hughes Laura D, Deng Xianding, Wang Candace, Servellita Venice, Valentine Holly, De Hoff Peter, Seaver Phoebe, Sathe Shashank, Gietzen Kimberly, Sickler Brad, Antico Jay, Hoon Kelly, Liu Jingtao, Harding Aaron, Bakhtar Omid, Basler Tracy, Austin Brett, Isaksson Magnus, Febbo Phillip G, Becker David, Laurent Marc, McDonald Eric, Yeo Gene W, Knight Rob, Laurent Louise C, de Feo Eileen, Worobey Michael, Chiu Charles, Suchard Marc A, Lu James T, Lee William, Andersen Kristian G
Helix, San Mateo, CA.
Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA.
medRxiv. 2021 Feb 7:2021.02.06.21251159. doi: 10.1101/2021.02.06.21251159.
As of January of 2021, the highly transmissible B.1.1.7 variant of SARS-CoV-2, which was first identified in the United Kingdom (U.K.), has gained a strong foothold across the world. Because of the sudden and rapid rise of B.1.1.7, we investigated the prevalence and growth dynamics of this variant in the United States (U.S.), tracking it back to its early emergence and onward local transmission. We found that the RT-qPCR testing anomaly of S gene target failure (SGTF), first observed in the U.K., was a reliable proxy for B.1.1.7 detection. We sequenced 212 B.1.1.7 SARS-CoV-2 genomes collected from testing facilities in the U.S. from December 2020 to January 2021. We found that while the fraction of B.1.1.7 among SGTF samples varied by state, detection of the variant increased at a logistic rate similar to those observed elsewhere, with a doubling rate of a little over a week and an increased transmission rate of 35-45%. By performing time-aware Bayesian phylodynamic analyses, we revealed several independent introductions of B.1.1.7 into the U.S. as early as late November 2020, with onward community transmission enabling the variant to spread to at least 30 states as of January 2021. Our study shows that the U.S. is on a similar trajectory as other countries where B.1.1.7 rapidly became the dominant SARS-CoV-2 variant, requiring immediate and decisive action to minimize COVID-19 morbidity and mortality.
截至2021年1月，新型冠状病毒（SARS-CoV-2）具有高传播性的B.1.1.7变体最早在英国被发现，已在全球站稳脚跟。由于B.1.1.7变体突然迅速出现，我们调查了该变体在美国的流行情况和增长动态，追溯其早期出现及随后的本地传播情况。我们发现，最初在英国观察到的S基因靶点失败（SGTF）的逆转录定量聚合酶链反应（RT-qPCR）检测异常是检测B.1.1.7的可靠指标。我们对2020年12月至2021年1月期间从美国检测机构收集的212个B.1.1.7新型冠状病毒基因组进行了测序。我们发现，虽然SGTF样本中B.1.1.7的比例因州而异，但该变体的检测以类似于其他地方观察到的逻辑速率增加，翻倍率略超过一周，传播率增加35%-45%。通过进行时间感知贝叶斯系统发育动力学分析，我们发现早在2020年11月下旬，B.1.1.7就有几次独立传入美国，到2021年1月，社区传播使该变体至少传播到30个州。我们的研究表明，美国与其他国家处于相似的轨迹，B.1.1.7迅速成为主要的新型冠状病毒变体，需要立即采取果断行动，以尽量减少新冠肺炎的发病率和死亡率。
