Prevalence of SARS-CoV-2 Omicron Sublineages and Spike Protein Mutations Conferring Resistance against Monoclonal Antibodies in a Swedish Cohort during 2022–2023
Jonathan Haars, Navaneethan Palanisamy, Frans Wallin, Paula Mölling, Johan Lindh, Martin Sundqvist, Patrik Ellström, René Kaden, Johan Lennerstrand
Microorganisms, doi:10.3390/microorganisms11102417
Monoclonal antibodies (mAbs) are an important treatment option for COVID-19 caused by SARS-CoV-2, especially in immunosuppressed patients. However, this treatment option can become ineffective due to mutations in the SARS-CoV-2 genome, mainly in the receptor binding domain (RBD) of the spike (S) protein. In the present study, 7950 SARS-CoV-2 positive samples from the Uppsala and Örebro regions of central Sweden, collected between March 2022 and May 2023, were whole-genome sequenced using amplicon-based sequencing methods on Oxford Nanopore GridION, Illumina MiSeq, Illumina HiSeq, or MGI DNBSEQ-G400 instruments. Pango lineages were determined and all single nucleotide polymorphism (SNP) mutations that occurred in these samples were identified. We found that the dominant sublineages changed over time, and mutations conferring resistance to currently available mAbs became common. Notable ones are R346T and K444T mutations in the RBD that confer significant resistance against tixagevimab and cilgavimab mAbs. Further, mutations conferring a high-fold resistance to bebtelovimab, such as the K444T and V445P mutations, were also observed in the samples. This study highlights that resistance mutations have over time rendered currently available mAbs ineffective against SARS-CoV-2 in most patients. Therefore, there is a need for continued surveillance of resistance mutations and the development of new mAbs that target more conserved regions of the RBD.
The repeated events of evolved resistance to mAbs means that the development of new mAbs and other antiviral treatments remains important for patients infected with SARS-CoV-2. The rapid increase in resistance to tixagevimab and cilgavimab highlights that these changes need to be communicated quickly by labs and scientists to the public. Therefore, the continued surveillance of SARS-CoV-2 through whole-genome sequencing is essential for understanding the evolution of the virus and for providing scientists, physicians, patients, decision makers, and drug manufacturers with correct and updated information for curbing this infection in the population.
Supplementary Materials: The following supporting information can be downloaded at: https: //www.mdpi.com/article/10.3390/microorganisms11102417/s1, Figure S1 Author Contributions: Conceptualization, J.H., N.P. and J.L. (Johan Lennerstrand); methodology, J.H. and J.L. (Johan Lennerstrand); software, J.H. and R.K.; formal analysis, J.H.; investigation, J.H., F.W., P.M., P.E., R.K. and J.L. (Johan Lennerstrand); resources, J.L. (Johan Lindh), M.S. and R.K.; data curation, J.H. and F.W.; writing-original draft preparation, J.H.; writing-review and editing, J.H., N.P., F.W., P.M., P.E., J.L. (Johan Lindh), M.S., R.K. and J.L. (Johan Lennerstrand); visualization, J.H.; supervision, R.K. and J.L. (Johan Lennerstrand); funding acquisition, J.L. (Johan Lennerstrand). All authors have read and agreed to the published version of the..
References
Astrazeneca, A Phase I/III Randomized, Double Blind Study to Evaluate the Safety, Efficacy and Neutralizing Activity of AZD5156/AZD3152 for Pre Exposure Prophylaxis of COVID 19 in Participants With Conditions Causing Immune Impairment. Sub-Study: Phase II Open Label Sub-Study to Evaluate the Safety, PK, and Neutralizing Activity of AZD3152 for Pre-Exposure Prophylaxis of COVID-19
Barnes, Jette, Abernathy, Dam, Esswein et al., SARS-CoV-2 Neutralizing Antibody Structures Inform Therapeutic Strategies, Nature,
doi:10.1038/s41586-020-2852-1Bbmap, None
Cao, Jian, Wang, Yu, Song et al., Imprinted SARS-CoV-2 Humoral Immunity Induces Convergent Omicron RBD Evolution, Nature,
doi:10.1038/s41586-022-05644-7Casadevall, Focosi, SARS-CoV-2 Variants Resistant to Monoclonal Antibodies in Immunocompromised Patients Constitute a Public Health Concern, J. Clin. Investig,
doi:10.1172/JCI168603Davis, Long, Christensen, Olsen, Olson et al., Analysis of the ARTIC Version 3 and Version 4 SARS-CoV-2 Primers and Their Impact on the Detection of the G142D Amino Acid Substitution in the Spike Protein, Microbiol. Spectr,
doi:10.1128/Spectrum.01803-21Ema, EMA Issues Advice on Use of Antibody Combination (Bamlanivimab/Etesevimab)
Evusheld, None
Focosi, Novazzi, Genoni, Dentali, Gasperina et al., Emergence of SARS-COV-2 Spike Protein Escape Mutation Q493R after Treatment for COVID-19, Emerg. Infect. Dis,
doi:10.3201/eid2710.211538Freed, Vlková, Faisal, Silander, Rapid and Inexpensive Whole-Genome Sequencing of SARS-CoV-2 Using 1200 Bp Tiled Amplicons and Oxford Nanopore Rapid Barcoding, Biol. Methods Protoc,
doi:10.1093/biomethods/bpaa014Garrison, Marth, Haplotype-Based Variant Detection from Short-Read Sequencing
Gisaid-Gisaid, None
Gms-Artic, None
Grubaugh, Gangavarapu, Quick, Matteson, De Jesus et al., An Amplicon-Based Sequencing Framework for Accurately Measuring Intrahost Virus Diversity Using PrimalSeq and iVar, Genome Biol,
doi:10.1186/s13059-018-1618-7Gupta, Konnova, Smet, Berkell, Savoldi et al., Host Immunological Responses Facilitate Development of SARS-CoV-2 Mutations in Patients Receiving Monoclonal Antibody Treatments, J. Clin. Investig,
doi:10.1172/JCI166032Jünemann, Sedlazeck, Prior, Albersmeier, John et al., Updating Benchtop Sequencing Performance Comparison, Nat. Biotechnol,
doi:10.1038/nbt.2522Kaden, Early Phylogenetic Diversification of SARS-CoV-2: Determination of Variants and the Effect on Epidemiology, Immunology, and Diagnostics, J. Clin. Med,
doi:10.3390/jcm9061615Lennerstrand, Palanisamy, Global Prevalence of Adaptive and Prolonged Infections' Mutations in the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein, Viruses,
doi:10.3390/v13101974Lyke, Atmar, Islas, Posavad, Szydlo et al., Rapid Decline in Vaccine-Boosted Neutralizing Antibodies against SARS-CoV-2 Omicron Variant, Cell Rep. Med,
doi:10.1016/j.xcrm.2022.100679Mannsverk, Bergholm, Palanisamy, Ellström, Kaden et al., SARS-CoV-2 Variants of Concern and Spike Protein Mutational Dynamics in a Swedish Cohort during 2021, Studied by Nanopore Sequencing, Virol. J,
doi:10.1186/s12985-022-01896-xMeng, Abdullahi, Ferreira, Goonawardane, Saito et al., Altered TMPRSS2 Usage by SARS-CoV-2 Omicron Impacts Infectivity and Fusogenicity, Nature,
doi:10.1038/s41586-022-04474-xMercatelli, Triboli, Fornasari, Ray, Giorgi, Coronapp: A Web Application to Annotate and Monitor SARS-CoV-2 Mutations, J. Med. Virol,
doi:10.1002/jmv.26678O'toole, Scher, Underwood, Jackson, Hill et al., Assignment of Epidemiological Lineages in an Emerging Pandemic Using the Pangolin Tool, Virus Evol,
doi:10.1093/ve/veab064Owen, Allerton, Anderson, Aschenbrenner, Avery et al., An Oral SARS-CoV-2 Mpro Inhibitor Clinical Candidate for the Treatment of COVID-19, Science,
doi:10.1126/science.abl4784Quick, Sequencing Protocol v3 (LoCost)
Rambaut, Holmes, O'toole, Hill, Mccrone et al., A Dynamic Nomenclature Proposal for SARS-CoV-2 Lineages to Assist Genomic Epidemiology, Nat. Microbiol,
doi:10.1038/s41564-020-0770-5Regkirona, None
Schmutz, Pango Lineage Translator
Starr, Greaney, Dingens, Bloom, Complete Map of SARS-CoV-2 RBD Mutations That Escape the Monoclonal Antibody LY-CoV555 and Its Cocktail with LY-CoV016, Cell Rep. Med,
doi:10.1016/j.xcrm.2021.100255Sydow, Lindqvist, Asghar, Johansson, Sundqvist et al., Comparison of SARS-CoV-2 Whole Genome Sequencing Using Tiled Amplicon Enrichment and Bait Hybridization, Sci. Rep,
doi:10.1038/s41598-023-33168-1Tai, He, Zhang, Pu, Voronin et al., Characterization of the Receptor-Binding Domain (RBD) of 2019 Novel Coronavirus: Implication for Development of RBD Protein as a Viral Attachment Inhibitor and Vaccine, Cell Mol. Immunol,
doi:10.1038/s41423-020-0400-4Tamura, Ito, Uriu, Zahradnik, Kida et al., Virological Characteristics of the SARS-CoV-2 XBB Variant Derived from Recombination of Two Omicron Subvariants, Nat. Commun,
doi:10.1038/s41467-023-38435-3Truffot, Andréani, Le Maréchal, Caporossi, Epaulard et al., SARS-CoV-2 Variants in Immunocompromised Patient Given Antibody Monotherapy, Emerg. Infect. Dis,
doi:10.3201/eid2710.211509Tyson, James, Stoddart, Sparks, Wickenhagen et al., Improvements to the ARTIC Multiplex PCR Method for SARS-CoV-2 Genome Sequencing Using Nanopore, bioRxiv,
doi:10.1101/2020.09.04.283077Töpfer, Cbg-Ethz, /ConsensusFixer: Computes a Consensus Sequence with Wobbles, Ambiguous Bases, and in-Frame Insertions, from a NGS Read Alignment
Vellas, Trémeaux, Bello, Latour, Jeanne et al., Resistance Mutations in SARS-CoV-2 Omicron Variant in Patients Treated with Sotrovimab, Clin. Microbiol. Infect,
doi:10.1016/j.cmi.2022.05.002Viana, Moyo, Amoako, Tegally, Scheepers et al., Rapid Epidemic Expansion of the SARS-CoV-2 Omicron Variant in Southern Africa, Nature,
doi:10.1038/s41586-022-04411-yWang, Iketani, Li, Liu, Guo et al., Alarming Antibody Evasion Properties of Rising SARS-CoV-2 BQ and XBB Subvariants, Cell,
doi:10.1016/j.cell.2022.12.018Zhao, Lu, Peng, Chen, Meng et al., SARS-CoV-2 Omicron Variant Shows Less Efficient Replication and Fusion Activity When Compared with Delta Variant in TMPRSS2-Expressed Cells, Emerg. Microbes Infect,
doi:10.1080/22221751.2021.2023329
