Immune transcriptomes from hospitalized patients infected with the SARS-CoV-2 variants B.1.1.7 and B.1.1.7 carrying the E484K escape mutation.
Hye Kyung Lee, Ludwig Knabl, Ludwig Knabl, Manuel Wieser, Anna Mur, August Zabernigg, Jana Schumacher, Norbert Kaiser, Priscilla A Furth, Lothar Hennighausen
Author Information
Hye Kyung Lee: National Institute of Diabetes, Digestive and Kidney Diseases, Bethesda, MD 20892, USA.
Ludwig Knabl: TyrolPath, Zams, Austria.
Ludwig Knabl: Krankenhaus St. Vinzenz, Zams, Austria.
Manuel Wieser: TyrolPath, Zams, Austria.
Anna Mur: Division of Internal Medicine, Krankenhaus Kufstein, Kufstein, Austria.
August Zabernigg: Division of Internal Medicine, Krankenhaus Kufstein, Kufstein, Austria.
Jana Schumacher: Division of Internal Medicine, Krankenhaus St. Johann, St. Johann, Austria.
Norbert Kaiser: Division of Internal Medicine, Krankenhaus St. Johann, St. Johann, Austria.
Priscilla A Furth: Departments of Oncology & Medicine, Georgetown University, Washington, DC, USA.
Lothar Hennighausen: National Institute of Diabetes, Digestive and Kidney Diseases, Bethesda, MD 20892, USA.
Fast-spreading variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) energize the COVID-19 pandemic. B.1.1.7 (VOC-202012/01) has become the predominant variant in many countries and a new lineage (VOC-202102/02) harboring the E484K escape mutation in the B.1.1.7 background emerged in February 2021 . This variant is of concern due to reduced neutralizing activity by vaccine-elicited antibodies . However, it is not known whether this single amino acid change leads to an altered immune response. Here, we investigate differences in the immune transcriptome in hospitalized patients infected with either B.1.1.7 (n=28) or B.1.1.7+E484K (n=12). RNA-seq conducted on PBMCs isolated within five days after the onset of COVID symptoms demonstrated elevated activation of specific immune pathways, including JAK-STAT signaling, in B.1.1.7+E484K patients as compared to B.1.1.7. Longitudinal transcriptome studies demonstrated a delayed dampening of interferon-activated pathways in B.1.1.7+E484K patients. Prior vaccination with BNT162b vaccine (n=8 one dose; n=1 two doses) reduced the transcriptome inflammatory response to B.1.1.7+E484K infection relative to unvaccinated patients. Lastly, the immune transcriptome of patients infected with additional variants (B.1.258, B.1.1.163 and B.1.7.7) displayed a reduced activation compared to patients infected with B.1.1.7. Acquisition of the E484K substitution in the B.1.1.7 background elicits an altered immune response, which could impact disease progression.
References
Bioinformatics. 2015 Jan 15;31(2):166-9
[PMID: 25260700]
