Distinct immune signatures discriminate SARS-CoV-2 vaccine combinations

Several vaccines have been found effective against COVID-19, usually administered in homologous regimens, with the same vaccine used for the prime and boost doses. However, recent studies have demonstrated improved protection via heterologous mix-and-match COVID-19 vaccine combinations, and a direct comparison among these regimens is needed to identify the best employment strategies. Here, we show a single-cohort comparison of changes to the humoral and cellular immune compartments following five different COVID-19 vaccines spanning three technologies (adenoviral, mRNA and inactivated vaccines). These vaccines were administered in a combinatorial fashion, resulting in sixteen different homologous and heterologous regimens. SARS-CoV-2-targeting antibody titres were highest when the boost dose consisted of mRNA-1273, independent of the vaccine used for priming. Priming with BBIBP-CorV induced less class-switching among spike-binding memory B cells and the highest antigen-specific T cell responses in heterologous combinations. These were generally more immunogenic in terms of specific antibodies and cellular responses compared to homologous regimens. Finally, single-cell analysis of 754 samples revealed specific B and T cell signatures of the vaccination regimens, indicating distinctive differences in the immune responses. These data provide new insights on the immunological effects of COVID-19 vaccine combinations and a framework for the design of improved vaccination strategies for other pathogens and cancer. ### Competing Interest Statement The authors have declared no competing interest. ### Clinical Trial NCT04988048 ### Funding Statement This project has received funding from the European Research Council (ERC) under the European Unions Horizon 2020 research and innovation programme grant agreement No 882424 the Swiss National Science Foundation (733 310030 170320 310030 188450 and CRSII5 183478 to B.B.) Sinergia 183478 and The Loop Zurich Medical Research Center Agencia Nacional de Promocion Cientifica y Tecnica (PICT 2021 CAI-I #00051) and Fondo para la Investigacion Cientifica y Tecnologica (FONCyT) [PICT IP COVID 19-464 2020] School of Medical Sciences National University of Cordoba Argentina and the Ministry of Health of Cordoba Province Argentina. N.G.N. is a recipient of a University Research Priority Program (URPP) postdoctoral fellowship. S.K. and T.W. are recipients of a postdoctoral research fellowship of the German Research Foundation (DFG). ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: Volunteers (age range 18-82 years old) were enrolled in a randomized, open Phase IIB clinical trial (ECEHeVac, [NCT04988048][1]) aimed at comparing the immunogenicity and reactogenicity of heterologous and homologous vaccination regimens available in Cordoba, Argentina. The study received ethical approval by the Registro Provincial de Investigacion en Salud (Provincial Registry of Health Research, REPIS-Cba #4371) I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable. Yes All data produced in the present study are available upon reasonable request to the authors All data produced in the present work are contained in the manuscript All data produced are available online at [1]: /lookup/external-ref?link_type=CLINTRIALGOV&access_num=NCT04988048&atom=%2Fmedrxiv%2Fearly%2F2022%2F09%2F06%2F2022.09.05.22279572.atom