Emergence and spread of a sub-lineage of SARS-CoV-2 Alpha variant B.1.1.7 in Europe, and with further evolution of spike mutation accumulations shared with the Beta and Gamma variants

Marlena Stadtmüller; Alexa Laubner; Fabian Rost; Sylke Winkler; Eva Patrasová; Lenka Šimůnková; Susanne Reinhardt; Johanna Beil; Alexander H Dalpke; Buqing Yi

doi:10.1093/ve/veac010

Emergence and spread of a sub-lineage of SARS-CoV-2 Alpha variant B.1.1.7 in Europe, and with further evolution of spike mutation accumulations shared with the Beta and Gamma variants

Virus Evol. 2022 Feb 14;8(1):veac010. doi: 10.1093/ve/veac010. eCollection 2022.

Authors

Marlena Stadtmüller, Alexa Laubner¹, Fabian Rost², Sylke Winkler³, Eva Patrasová⁴, Lenka Šimůnková⁴, Susanne Reinhardt², Johanna Beil³, Alexander H Dalpke¹, Buqing Yi¹

Affiliations

¹ Institute of Medical Microbiology and Virology, University Hospital Carl Gustav Carus, Technische Universität Dresden, Fetscherstraße 74, Dresden, Saxony 01307, Germany.
² DRESDEN concept Genome Center, Technische Universität Dresden, Fetscherstraße 105, Dresden, Saxony 01307, Germany.
³ Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany and DRESDEN concept Genome Center, Technische Universität Dresden, Pfotenhauerstraße 108, Dresden, Saxony 01307, Germany.
⁴ Department of Epidemiology, Regional Public Health Authority for Ustecky Kraj, Moskevská 15, Ústí nad Labem 400 01, Czech Republic.

Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) evolution plays a significant role in shaping the dynamics of the coronavirus disease 2019 pandemic. To monitor the evolution of SARS-CoV-2 variants, through international collaborations, we performed genomic epidemiology analyses on a weekly basis with SARS-CoV-2 samples collected from a border region between Germany, Poland, and the Czech Republic in a global background. For identified virus mutant variants, active viruses were isolated and functional evaluations were performed to test their replication fitness and neutralization sensitivity against vaccine-elicited serum neutralizing antibodies. Thereby we identified a new B.1.1.7 sub-lineage carrying additional mutations of nucleoprotein G204P and open-reading-frame-8 K68stop. Of note, this B.1.1.7 sub-lineage is the predominant B.1.1.7 variant in several European countries such as Czech Republic, Austria, and Slovakia. The earliest samples belonging to this sub-lineage were detected in November 2020 in a few countries in the European continent, but not in the UK. We have also detected its further evolution with extra spike mutations D138Y and A701V, which are signature mutations shared with the Gamma and Beta variants, respectively. Antibody neutralization assay of virus variant isolations has revealed that the variant with extra spike mutations is 3.2-fold less sensitive to vaccine-elicited antibodies as compared to the other B.1.1.7 variants tested, indicating potential for immune evasion, but it also exhibited reduced replication fitness, suggesting lower transmissibility. The wide spread of this B.1.1.7 sub-lineage was related to the pandemic waves in early 2021 in various European countries. These findings about the emergence, spread, evolution, infection, and transmission abilities of this B.1.1.7 sub-lineage add to our understanding about the pandemic development in Europe and highlight the importance of international collaboration on virus mutant surveillance.

Keywords: immune evasion; molecular evolution; pathogens; phylogeny; transmission; viral infection.