1
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Jaworski E, Langsjoen RM, Mitchell B, Judy B, Newman P, Plante JA, Plante KS, Miller AL, Zhou Y, Swetnam D, Sotcheff S, Morris V, Saada N, Machado RR, McConnell A, Widen SG, Thompson J, Dong J, Ren P, Pyles RB, Ksiazek TG, Menachery VD, Weaver SC, Routh AL. Tiled-ClickSeq for targeted sequencing of complete coronavirus genomes with simultaneous capture of RNA recombination and minority variants. eLife 2021; 10:68479. [PMID: 34581669 PMCID: PMC8478411 DOI: 10.7554/elife.68479] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 09/08/2021] [Indexed: 12/13/2022] Open
Abstract
High-throughput genomics of SARS-CoV-2 is essential to characterize virus evolution and to identify adaptations that affect pathogenicity or transmission. While single-nucleotide variations (SNVs) are commonly considered as driving virus adaption, RNA recombination events that delete or insert nucleic acid sequences are also critical. Whole genome targeting sequencing of SARS-CoV-2 is typically achieved using pairs of primers to generate cDNA amplicons suitable for next-generation sequencing (NGS). However, paired-primer approaches impose constraints on where primers can be designed, how many amplicons are synthesized and requires multiple PCR reactions with non-overlapping primer pools. This imparts sensitivity to underlying SNVs and fails to resolve RNA recombination junctions that are not flanked by primer pairs. To address these limitations, we have designed an approach called ‘Tiled-ClickSeq’, which uses hundreds of tiled-primers spaced evenly along the virus genome in a single reverse-transcription reaction. The other end of the cDNA amplicon is generated by azido-nucleotides that stochastically terminate cDNA synthesis, removing the need for a paired-primer. A sequencing adaptor containing a Unique Molecular Identifier (UMI) is appended to the cDNA fragment using click-chemistry and a PCR reaction generates a final NGS library. Tiled-ClickSeq provides complete genome coverage, including the 5’UTR, at high depth and specificity to the virus on both Illumina and Nanopore NGS platforms. Here, we analyze multiple SARS-CoV-2 isolates and clinical samples to simultaneously characterize minority variants, sub-genomic mRNAs (sgmRNAs), structural variants (SVs) and D-RNAs. Tiled-ClickSeq therefore provides a convenient and robust platform for SARS-CoV-2 genomics that captures the full range of RNA species in a single, simple assay.
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Affiliation(s)
- Elizabeth Jaworski
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, United States.,ClickSeq Technologies LLC, Galveston, United States
| | - Rose M Langsjoen
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, United States
| | - Brooke Mitchell
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, United States.,Department of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, United States
| | - Barbara Judy
- Department of Pediatrics, University of Texas Medical Branch, Galveston, United States
| | - Patrick Newman
- Department of Pediatrics, University of Texas Medical Branch, Galveston, United States
| | - Jessica A Plante
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, United States.,Department of Pathology, University of Texas Medical Branch, Galveston, United States.,Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, United States
| | - Kenneth S Plante
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, United States.,Department of Pathology, University of Texas Medical Branch, Galveston, United States.,Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, United States
| | - Aaron L Miller
- Department of Pediatrics, University of Texas Medical Branch, Galveston, United States
| | - Yiyang Zhou
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, United States
| | - Daniele Swetnam
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, United States
| | - Stephanea Sotcheff
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, United States
| | - Victoria Morris
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, United States
| | - Nehad Saada
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, United States.,Department of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, United States
| | - Rafael Rg Machado
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, United States.,Department of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, United States
| | - Allan McConnell
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, United States.,Department of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, United States
| | - Steven G Widen
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, United States.,Next-Generation Sequencing Core, The University of Texas Medical Branch, Galveston, United States
| | - Jill Thompson
- Next-Generation Sequencing Core, The University of Texas Medical Branch, Galveston, United States
| | - Jianli Dong
- Department of Pediatrics, University of Texas Medical Branch, Galveston, United States.,Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, United States
| | - Ping Ren
- Department of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, United States
| | - Rick B Pyles
- Department of Pediatrics, University of Texas Medical Branch, Galveston, United States
| | - Thomas G Ksiazek
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, United States.,Department of Pathology, University of Texas Medical Branch, Galveston, United States
| | - Vineet D Menachery
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, United States.,Department of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, United States.,Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, United States
| | - Scott C Weaver
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, United States.,Department of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, United States.,Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, United States
| | - Andrew L Routh
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, United States.,Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, United States.,Sealy Centre for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, United States
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2
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Jaworski E, Langsjoen RM, Mitchell B, Judy B, Newman P, Plante JA, Plante KS, Miller AL, Zhou Y, Swetnam D, Sotcheff S, Morris V, Saada N, Machado R, McConnell A, Widen S, Thompson J, Dong J, Ren P, Pyles RB, Ksiazek T, Menachery VD, Weaver SC, Routh A. Tiled-ClickSeq for targeted sequencing of complete coronavirus genomes with simultaneous capture of RNA recombination and minority variants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.03.10.434828. [PMID: 33758846 PMCID: PMC7987005 DOI: 10.1101/2021.03.10.434828] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
High-throughput genomics of SARS-CoV-2 is essential to characterize virus evolution and to identify adaptations that affect pathogenicity or transmission. While single-nucleotide variations (SNVs) are commonly considered as driving virus adaption, RNA recombination events that delete or insert nucleic acid sequences are also critical. Whole genome targeting sequencing of SARS-CoV-2 is typically achieved using pairs of primers to generate cDNA amplicons suitable for Next-Generation Sequencing (NGS). However, paired-primer approaches impose constraints on where primers can be designed, how many amplicons are synthesized and requires multiple PCR reactions with non-overlapping primer pools. This imparts sensitivity to underlying SNVs and fails to resolve RNA recombination junctions that are not flanked by primer pairs. To address these limitations, we have designed an approach called 'Tiled-ClickSeq', which uses hundreds of tiled-primers spaced evenly along the virus genome in a single reverse-transcription reaction. The other end of the cDNA amplicon is generated by azido-nucleotides that stochastically terminate cDNA synthesis, removing the need for a paired-primer. A sequencing adaptor containing a Unique Molecular Identifier (UMI) is appended to the cDNA fragment using click-chemistry and a PCR reaction generates a final NGS library. Tiled-ClickSeq provides complete genome coverage, including the 5'UTR, at high depth and specificity to the virus on both Illumina and Nanopore NGS platforms. Here, we analyze multiple SARS-CoV-2 isolates and clinical samples to simultaneously characterize minority variants, sub-genomic mRNAs (sgmRNAs), structural variants (SVs) and D-RNAs. Tiled-ClickSeq therefore provides a convenient and robust platform for SARS-CoV-2 genomics that captures the full range of RNA species in a single, simple assay.
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Affiliation(s)
- Elizabeth Jaworski
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX, USA
- ClickSeq Technologies LLC, Galveston, TX, USA
| | - Rose M. Langsjoen
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Brooke Mitchell
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA
- Department of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Barbara Judy
- Department of Pediatrics, University of Texas Medical Branch, Galveston, TX, USA
| | - Patrick Newman
- Department of Pathology, University of Texas Medical Branch, Galveston TX, USA
| | - Jessica A. Plante
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA
- Department of Pathology, University of Texas Medical Branch, Galveston TX, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
| | - Kenneth S. Plante
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA
- Department of Pathology, University of Texas Medical Branch, Galveston TX, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
| | - Aaron L. Miller
- Department of Pediatrics, University of Texas Medical Branch, Galveston, TX, USA
| | - Yiyang Zhou
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Daniele Swetnam
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Stephanea Sotcheff
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Victoria Morris
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Nehad Saada
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA
- Department of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Rafael Machado
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA
- Department of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Allan McConnell
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA
- Department of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Steve Widen
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX, USA
- Next-Generation Sequencing Core, The University of Texas Medical Branch, Galveston, TX, USA
| | - Jill Thompson
- Next-Generation Sequencing Core, The University of Texas Medical Branch, Galveston, TX, USA
| | - Jianli Dong
- Department of Pediatrics, University of Texas Medical Branch, Galveston, TX, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
| | - Ping Ren
- Department of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Rick B. Pyles
- Department of Pediatrics, University of Texas Medical Branch, Galveston, TX, USA
| | - Thomas Ksiazek
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA
- Department of Pathology, University of Texas Medical Branch, Galveston TX, USA
| | - Vineet D. Menachery
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA
- Department of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, TX, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
| | - Scott C. Weaver
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA
- Department of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, TX, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
| | - Andrew Routh
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
- Sealy Centre for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas, USA
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3
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McCarthy KR, Rennick LJ, Nambulli S, Robinson-McCarthy LR, Bain WG, Haidar G, Duprex WP. Recurrent deletions in the SARS-CoV-2 spike glycoprotein drive antibody escape. Science 2021. [PMID: 33536258 DOI: 10.1101/2020.11.19.389916] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Zoonotic pandemics, such as that caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), can follow the spillover of animal viruses into highly susceptible human populations. The descendants of these viruses have adapted to the human host and evolved to evade immune pressure. Coronaviruses acquire substitutions more slowly than other RNA viruses. In the spike glycoprotein, we found that recurrent deletions overcome this slow substitution rate. Deletion variants arise in diverse genetic and geographic backgrounds, transmit efficiently, and are present in novel lineages, including those of current global concern. They frequently occupy recurrent deletion regions (RDRs), which map to defined antibody epitopes. Deletions in RDRs confer resistance to neutralizing antibodies. By altering stretches of amino acids, deletions appear to accelerate SARS-CoV-2 antigenic evolution and may, more generally, drive adaptive evolution.
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Affiliation(s)
- Kevin R McCarthy
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Laboratory of Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Linda J Rennick
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Sham Nambulli
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | | | - William G Bain
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Internal Medicine, UPMC, Pittsburgh, PA, USA
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- VA Pittsburgh Healthcare System, Pittsburgh, PA, USA
| | - Ghady Haidar
- Division of Infectious Disease, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Division of Infectious Disease, Department of Internal Medicine, UPMC, Pittsburgh, PA, USA
| | - W Paul Duprex
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
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4
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Everett J, Hokama P, Roche AM, Reddy S, Hwang Y, Kessler L, Glascock A, Li Y, Whelan JN, Weiss SR, Sherrill-Mix S, McCormick K, Whiteside SA, Graham-Wooten J, Khatib LA, Fitzgerald AS, Collman RG, Bushman F. SARS-CoV-2 Genomic Variation in Space and Time in Hospitalized Patients in Philadelphia. mBio 2021; 12:e03456-20. [PMID: 33468702 PMCID: PMC7829343 DOI: 10.1128/mbio.03456-20] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 12/11/2020] [Indexed: 01/18/2023] Open
Abstract
The severe acute respiratory coronavirus 2 (SARS-CoV-2) is the cause of the global outbreak of COVID-19. The epidemic accelerated in Philadelphia, PA, in the spring of 2020, with the city experiencing a first peak of infections on 15 April, followed by a decline through midsummer. Here, we investigate spread of the epidemic in the first wave in Philadelphia using full-genome sequencing of 52 SARS-CoV-2 samples obtained from 27 hospitalized patients collected between 30 March and 17 July 2020. Sequences most commonly resembled lineages circulating at earlier times in New York, suggesting transmission primarily from this location, though a minority of Philadelphia genomes matched sequences from other sites, suggesting additional introductions. Multiple genomes showed even closer matches to other Philadelphia isolates, suggestive of ongoing transmission within Philadelphia. We found that all of our isolates contained the D614G substitution in the viral spike and belong to lineages variously designated B.1, Nextstrain clade 20A or 20C, and GISAID clade G or GH. There were no viral sequence polymorphisms detectably associated with disease outcome. For some patients, genome sequences were determined longitudinally or concurrently from multiple body sites. In both cases, some comparisons showed reproducible polymorphisms, suggesting initial seeding with multiple variants and/or accumulation of polymorphisms after infection. These results thus provide data on the sources of SARS-CoV-2 infection in Philadelphia and begin to explore the dynamics within hospitalized patients.IMPORTANCE Understanding how SARS-CoV-2 spreads globally and within infected individuals is critical to the development of mitigation strategies. We found that most lineages in Philadelphia had resembled sequences from New York, suggesting infection primarily but not exclusively from this location. Many genomes had even nearer neighbors within Philadelphia, indicating local spread. Multiple genome sequences were available for some subjects and in a subset of cases could be shown to differ between time points and body sites within an individual, indicating heterogeneous viral populations within individuals and raising questions on the mechanisms responsible. There was no evidence that different lineages were associated with different outcomes in patients, emphasizing the importance of individual-specific vulnerability.
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Affiliation(s)
- John Everett
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Pascha Hokama
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Aoife M Roche
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Shantan Reddy
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Young Hwang
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Lyanna Kessler
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Abigail Glascock
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Yize Li
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jillian N Whelan
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Susan R Weiss
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Scott Sherrill-Mix
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Kevin McCormick
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Samantha A Whiteside
- Pulmonary, Allergy and Critical Care Division, Department of Medicine; University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Jevon Graham-Wooten
- Pulmonary, Allergy and Critical Care Division, Department of Medicine; University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Layla A Khatib
- Pulmonary, Allergy and Critical Care Division, Department of Medicine; University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Ayannah S Fitzgerald
- Pulmonary, Allergy and Critical Care Division, Department of Medicine; University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Ronald G Collman
- Pulmonary, Allergy and Critical Care Division, Department of Medicine; University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Frederic Bushman
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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5
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Mykytyn AZ, Breugem TI, Riesebosch S, Schipper D, van den Doel PB, Rottier RJ, Lamers MM, Haagmans BL. SARS-CoV-2 entry into human airway organoids is serine protease-mediated and facilitated by the multibasic cleavage site. eLife 2021; 10:e64508. [PMID: 33393462 PMCID: PMC7806259 DOI: 10.7554/elife.64508] [Citation(s) in RCA: 93] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 12/31/2020] [Indexed: 01/19/2023] Open
Abstract
Coronavirus entry is mediated by the spike protein that binds the receptor and mediates fusion after cleavage by host proteases. The proteases that mediate entry differ between cell lines, and it is currently unclear which proteases are relevant in vivo. A remarkable feature of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike is the presence of a multibasic cleavage site (MBCS), which is absent in the SARS-CoV spike. Here, we report that the SARS-CoV-2 spike MBCS increases infectivity on human airway organoids (hAOs). Compared with SARS-CoV, SARS-CoV-2 entered faster into Calu-3 cells and, more frequently, formed syncytia in hAOs. Moreover, the MBCS increased entry speed and plasma membrane serine protease usage relative to cathepsin-mediated endosomal entry. Blocking serine proteases, but not cathepsins, effectively inhibited SARS-CoV-2 entry and replication in hAOs. Our findings demonstrate that SARS-CoV-2 enters relevant airway cells using serine proteases, and suggest that the MBCS is an adaptation to this viral entry strategy.
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Affiliation(s)
- Anna Z Mykytyn
- Viroscience Department, Erasmus University Medical CenterRotterdamNetherlands
| | - Tim I Breugem
- Viroscience Department, Erasmus University Medical CenterRotterdamNetherlands
| | - Samra Riesebosch
- Viroscience Department, Erasmus University Medical CenterRotterdamNetherlands
| | - Debby Schipper
- Viroscience Department, Erasmus University Medical CenterRotterdamNetherlands
| | | | - Robbert J Rottier
- Department of Pediatric Surgery, Erasmus University Medical Center - Sophia Children's HospitalRotterdamNetherlands
| | - Mart M Lamers
- Viroscience Department, Erasmus University Medical CenterRotterdamNetherlands
| | - Bart L Haagmans
- Viroscience Department, Erasmus University Medical CenterRotterdamNetherlands
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6
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Xiang Y, Nambulli S, Xiao Z, Liu H, Sang Z, Duprex WP, Schneidman-Duhovny D, Zhang C, Shi Y. Versatile, Multivalent Nanobody Cocktails Efficiently Neutralize SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020. [PMID: 32869034 PMCID: PMC7457627 DOI: 10.1101/2020.08.24.264333] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The outbreak of COVID-19 has severely impacted global health and the economy. Cost-effective, highly efficacious therapeutics are urgently needed. Here, we used camelid immunization and proteomics to identify a large repertoire of highly potent neutralizing nanobodies (Nbs) to the SARS-CoV-2 spike (S) protein receptor-binding domain (RBD). We discovered multiple elite Nbs with picomolar to femtomolar affinities that inhibit viral infection at sub-ng/ml concentration, more potent than some of the best human neutralizing antibodies. We determined a crystal structure of such an elite neutralizing Nb in complex with RBD. Structural proteomics and integrative modeling revealed multiple distinct and non-overlapping epitopes and indicated an array of potential neutralization mechanisms. Structural characterization facilitated the bioengineering of novel multivalent Nb constructs into multi-epitope cocktails that achieved ultrahigh neutralization potency (IC50s as low as 0.058 ng/ml) and may prevent mutational escape. These thermostable Nbs can be rapidly produced in bulk from microbes and resist lyophilization, and aerosolization. These promising agents are readily translated into efficient, cost-effective, and convenient therapeutics to help end this once-in-a-century health crisis.
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Affiliation(s)
| | - Sham Nambulli
- Center for Vaccine Research.,Department of Microbiology and Molecular Genetics School of Medicine
| | | | - Heng Liu
- Department of Pharmacology and Chemical Biology University of Pittsburgh, Pittsburgh, PA, USA
| | - Zhe Sang
- Department of Cell Biology.,Pitt/CMU Program for Computational Biology
| | - W Paul Duprex
- Center for Vaccine Research.,Department of Microbiology and Molecular Genetics School of Medicine
| | - Dina Schneidman-Duhovny
- School of Computer Science and Engineering, Institute of Life Sciences, The Hebrew University of Jerusalem, Israel
| | - Cheng Zhang
- Department of Pharmacology and Chemical Biology University of Pittsburgh, Pittsburgh, PA, USA
| | - Yi Shi
- Department of Cell Biology.,Pitt/CMU Program for Computational Biology
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