Escalating combinations of enhanced infectivity and immune escape define SARS-CoV-2 Omicron lineage replacement

Author:

Chen Nicholas F.G.,Pham Kien,Chaguza Chrispin,Lopes RafaelORCID,Klaassen FayetteORCID,Weinberger Daniel M.,Pitzer Virginia E.,Warren Joshua L.,Grubaugh Nathan D.ORCID,Hahn Anne M.ORCID

Abstract

AbstractIn 2022, consecutive sweeps of the highly transmissible SARS-CoV-2 Omicron-family maintained high viral transmission levels despite extensive antigen exposure on the population level resulting from both vaccinations and infections. To better understand variant fitness in the context of the highly dynamic immunity landscape of 2022, we aimed to dissect the interplay between immunity and fitness advantages of emerging SARS-CoV-2 Omicron lineages on the population-level. We evaluated the relative contribution of higher intrinsic transmissibility or immune escape on the fitness of emerging lineages by analyzing data collected through our local genomic surveillance program from Connecticut, USA. We compared growth rates, estimated infections, effective reproductive rates, average viral copy numbers, and likelihood for causing vaccine break-through infections. Using these population-level data, we find that newly emerging Omicron lineages reach dominance through a specific combination of enhanced intrinsic transmissibility and immune escape that varies over time depending on the state of the host-population. Using similar frameworks that integrate whole genome sequencing together with clinical, laboratory, and epidemiological data can advance our knowledge on host-pathogen dynamics in the post-emergence phase that can be applied to other communicable diseases beyond SARS-CoV-2.

Publisher

Cold Spring Harbor Laboratory

同舟云学术

1.学者识别学者识别

2.学术分析学术分析

3.人才评估人才评估

"同舟云学术"是以全球学者为主线,采集、加工和组织学术论文而形成的新型学术文献查询和分析系统,可以对全球学者进行文献检索和人才价值评估。用户可以通过关注某些学科领域的顶尖人物而持续追踪该领域的学科进展和研究前沿。经过近期的数据扩容,当前同舟云学术共收录了国内外主流学术期刊6万余种,收集的期刊论文及会议论文总量共计约1.5亿篇,并以每天添加12000余篇中外论文的速度递增。我们也可以为用户提供个性化、定制化的学者数据。欢迎来电咨询!咨询电话:010-8811{复制后删除}0370

www.globalauthorid.com

TOP

Copyright © 2019-2024 北京同舟云网络信息技术有限公司
京公网安备11010802033243号  京ICP备18003416号-3