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Escalera A, Laporte M, Turner S, Karakus U, Gonzalez-Reiche AS, van de Guchte A, Farrugia K, Khalil Z, van Bakel H, Smith D, García-Sastre A, Aydillo T. The impact of S2 mutations on Omicron SARS-CoV-2 cell surface expression and fusogenicity. Emerg Microbes Infect 2024; 13:2297553. [PMID: 38112266 PMCID: PMC10866063 DOI: 10.1080/22221751.2023.2297553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 12/17/2023] [Indexed: 12/21/2023]
Abstract
SARS-CoV-2 Omicron subvariants are still emerging and spreading worldwide. These variants contain a high number of polymorphisms in the spike (S) glycoprotein that could potentially impact their pathogenicity and transmission. We have previously shown that the S:655Y and P681H mutations enhance S protein cleavage and syncytia formation. Interestingly, these polymorphisms are present in Omicron S protein. Here, we characterized the cleavage efficiency and fusogenicity of the S protein of different Omicron sublineages. Our results showed that Omicron BA.1 subvariant is efficiently cleaved but it is poorly fusogenic compared to previous SARS-CoV-2 strains. To understand the basis of this phenotype, we generated chimeric S protein using combinations of the S1 and S2 domains from WA1, Delta and Omicron BA.1 variants. We found that the S2 domain of Omicron BA.1 hindered efficient cell-cell fusion. Interestingly, this domain only contains six unique polymorphisms never detected before in ancestral SARS-CoV-2 variants. WA1614G S proteins containing the six individuals S2 Omicron mutations were assessed for their fusogenicity and S surface expression after transfection in cells. Results showed that the S:N856K and N969K substitutions decreased syncytia formation and impacted S protein cell surface levels. However, we observed that "first-generation" Omicron sublineages that emerged subsequently, had convergently evolved to an enhanced fusogenic activity and S expression on the surface of infected cells while "second-generation" Omicron variants have highly diverged and showed lineage-specific fusogenic properties. Importantly, our findings could have potential implications in the improvement and redesign of COVID-19 vaccines.
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Affiliation(s)
- Alba Escalera
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Manon Laporte
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sam Turner
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, UK
| | - Umut Karakus
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ana S. Gonzalez-Reiche
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Adriana van de Guchte
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Keith Farrugia
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Zain Khalil
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Harm van Bakel
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Derek Smith
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, UK
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Teresa Aydillo
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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2
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Fernbach S, Spieler EE, Busnadiego I, Karakus U, Lkharrazi A, Stertz S, Hale BG. Restriction factor screening identifies RABGAP1L-mediated disruption of endocytosis as a host antiviral defense. Cell Rep 2022; 38:110549. [PMID: 35320721 PMCID: PMC8939003 DOI: 10.1016/j.celrep.2022.110549] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 01/31/2022] [Accepted: 03/01/2022] [Indexed: 11/26/2022] Open
Abstract
Host interferons (IFNs) powerfully restrict viruses through the action of several hundred IFN-stimulated gene (ISG) products, many of which remain uncharacterized. Here, using RNAi screening, we identify several ISG restriction factors with previously undescribed contributions to IFN-mediated defense. Notably, RABGAP1L, a Tre2/Bub2/Cdc16 (TBC)-domain-containing protein involved in regulation of small membrane-bound GTPases, robustly potentiates IFN action against influenza A viruses (IAVs). Functional studies reveal that the catalytically active TBC domain of RABGAP1L promotes antiviral activity, and the RABGAP1L proximal interactome uncovered its association with proteins involved in endosomal sorting, maturation, and trafficking. In this regard, RABGAP1L overexpression is sufficient to disrupt endosomal function during IAV infection and restricts an early post-attachment, but pre-fusion, stage of IAV cell entry. Other RNA viruses that enter cells primarily via endocytosis are also impaired by RABGAP1L, while entry promiscuous SARS-CoV-2 is resistant. Our data highlight virus endocytosis as a key target for host defenses.
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Affiliation(s)
- Sonja Fernbach
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland; Life Science Zurich Graduate School, ETH and University of Zurich, 8057 Zurich, Switzerland
| | - Eva E Spieler
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland; Life Science Zurich Graduate School, ETH and University of Zurich, 8057 Zurich, Switzerland
| | - Idoia Busnadiego
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
| | - Umut Karakus
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
| | - Anouk Lkharrazi
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
| | - Silke Stertz
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
| | - Benjamin G Hale
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland.
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3
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Friedrich N, Stiegeler E, Glögl M, Lemmin T, Hansen S, Kadelka C, Wu Y, Ernst P, Maliqi L, Foulkes C, Morin M, Eroglu M, Liechti T, Ivan B, Reinberg T, Schaefer JV, Karakus U, Ursprung S, Mann A, Rusert P, Kouyos RD, Robinson JA, Günthard HF, Plückthun A, Trkola A. Distinct conformations of the HIV-1 V3 loop crown are targetable for broad neutralization. Nat Commun 2021; 12:6705. [PMID: 34795280 PMCID: PMC8602657 DOI: 10.1038/s41467-021-27075-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 11/03/2021] [Indexed: 12/14/2022] Open
Abstract
The V3 loop of the HIV-1 envelope (Env) protein elicits a vigorous, but largely non-neutralizing antibody response directed to the V3-crown, whereas rare broadly neutralizing antibodies (bnAbs) target the V3-base. Challenging this view, we present V3-crown directed broadly neutralizing Designed Ankyrin Repeat Proteins (bnDs) matching the breadth of V3-base bnAbs. While most bnAbs target prefusion Env, V3-crown bnDs bind open Env conformations triggered by CD4 engagement. BnDs achieve breadth by focusing on highly conserved residues that are accessible in two distinct V3 conformations, one of which resembles CCR5-bound V3. We further show that these V3-crown conformations can, in principle, be attacked by antibodies. Supporting this conclusion, analysis of antibody binding activity in the Swiss 4.5 K HIV-1 cohort (n = 4,281) revealed a co-evolution of V3-crown reactivities and neutralization breadth. Our results indicate a role of V3-crown responses and its conformational preferences in bnAb development to be considered in preventive and therapeutic approaches.
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Affiliation(s)
- Nikolas Friedrich
- grid.7400.30000 0004 1937 0650Institute of Medical Virology, University of Zurich (UZH), Zurich, Switzerland
| | - Emanuel Stiegeler
- grid.7400.30000 0004 1937 0650Institute of Medical Virology, University of Zurich (UZH), Zurich, Switzerland ,grid.424277.0Present Address: Roche Diagnostics GmbH, Nonnenwald 2, 82377 Penzberg, Deutschland
| | - Matthias Glögl
- grid.7400.30000 0004 1937 0650Institute of Medical Virology, University of Zurich (UZH), Zurich, Switzerland
| | - Thomas Lemmin
- grid.7400.30000 0004 1937 0650Institute of Medical Virology, University of Zurich (UZH), Zurich, Switzerland ,grid.5801.c0000 0001 2156 2780Department of Computer Science, ETH Zurich, Zurich, Switzerland ,grid.29078.340000 0001 2203 2861Present Address: Euler Institute, Faculty of Biomedicine, Università della Svizzera italiana (USI), Lugano, Switzerland
| | - Simon Hansen
- grid.7400.30000 0004 1937 0650Department of Biochemistry, University of Zurich (UZH), Zurich, Switzerland ,Present Address: NGM Bio, 333 Oysterpoint Blvd, South San Francisco, CA 94080 USA
| | - Claus Kadelka
- grid.34421.300000 0004 1936 7312Department of Mathematics, Iowa State University, Ames, IA USA
| | - Yufan Wu
- grid.7400.30000 0004 1937 0650Department of Biochemistry, University of Zurich (UZH), Zurich, Switzerland ,Present Address: Innovent Biologics Inc, 168 Dongping Street, Suzhou Industrial Park, 215123 China
| | - Patrick Ernst
- grid.7400.30000 0004 1937 0650Department of Biochemistry, University of Zurich (UZH), Zurich, Switzerland ,grid.7400.30000 0004 1937 0650Present Address: Office Research and Teaching, Medical Faculty, University of Zurich, Zurich, Switzerland
| | - Liridona Maliqi
- grid.7400.30000 0004 1937 0650Institute of Medical Virology, University of Zurich (UZH), Zurich, Switzerland
| | - Caio Foulkes
- grid.7400.30000 0004 1937 0650Institute of Medical Virology, University of Zurich (UZH), Zurich, Switzerland
| | - Mylène Morin
- grid.7400.30000 0004 1937 0650Department of Chemistry, University of Zurich (UZH), Zurich, Switzerland ,Present Address: BeiGene Switzerland GmbH, Aeschengraben 27, 4051 Basel, Switzerland
| | - Mustafa Eroglu
- grid.7400.30000 0004 1937 0650Institute of Medical Virology, University of Zurich (UZH), Zurich, Switzerland ,Present Address: Janssen Vaccines AG, Rehhagstrasse 79, 3018 Bern, Switzerland
| | - Thomas Liechti
- grid.7400.30000 0004 1937 0650Institute of Medical Virology, University of Zurich (UZH), Zurich, Switzerland ,grid.419681.30000 0001 2164 9667Present Address: ImmunoTechnology Section, Vaccine Research Center, NIAID, NIH, Bethesda, MD USA
| | - Branislav Ivan
- grid.7400.30000 0004 1937 0650Institute of Medical Virology, University of Zurich (UZH), Zurich, Switzerland ,grid.410567.1Present Address: Laboratory Medicine, Division of Clinical Chemistry, University Hospital Basel, Basel, Switzerland
| | - Thomas Reinberg
- grid.7400.30000 0004 1937 0650Department of Biochemistry, University of Zurich (UZH), Zurich, Switzerland
| | - Jonas V. Schaefer
- grid.7400.30000 0004 1937 0650Department of Biochemistry, University of Zurich (UZH), Zurich, Switzerland ,grid.419481.10000 0001 1515 9979Present Address: Novartis Institutes for BioMedical Research, Chemical Biology & Therapeutics (CBT), Novartis Pharma AG, Virchow 16, 4056 Basel, Switzerland
| | - Umut Karakus
- grid.7400.30000 0004 1937 0650Institute of Medical Virology, University of Zurich (UZH), Zurich, Switzerland
| | - Stephan Ursprung
- grid.7400.30000 0004 1937 0650Institute of Medical Virology, University of Zurich (UZH), Zurich, Switzerland ,grid.5335.00000000121885934Present Address: University of Cambridge School of Clinical Medicine, Department of Radiology, Cambridge, CB2 0QQ UK
| | - Axel Mann
- grid.7400.30000 0004 1937 0650Institute of Medical Virology, University of Zurich (UZH), Zurich, Switzerland ,Present Address: Roche Innovation Center Zurich, Roche Pharmaceutical Research and Early Development (pRED), Wagistrasse 10, 8952 Schlieren, Switzerland
| | - Peter Rusert
- grid.7400.30000 0004 1937 0650Institute of Medical Virology, University of Zurich (UZH), Zurich, Switzerland
| | - Roger D. Kouyos
- grid.7400.30000 0004 1937 0650Institute of Medical Virology, University of Zurich (UZH), Zurich, Switzerland ,grid.412004.30000 0004 0478 9977Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich (USZ), Zurich, Switzerland
| | - John A. Robinson
- grid.7400.30000 0004 1937 0650Department of Chemistry, University of Zurich (UZH), Zurich, Switzerland
| | - Huldrych F. Günthard
- grid.7400.30000 0004 1937 0650Institute of Medical Virology, University of Zurich (UZH), Zurich, Switzerland ,grid.412004.30000 0004 0478 9977Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich (USZ), Zurich, Switzerland
| | - Andreas Plückthun
- grid.7400.30000 0004 1937 0650Department of Biochemistry, University of Zurich (UZH), Zurich, Switzerland
| | - Alexandra Trkola
- Institute of Medical Virology, University of Zurich (UZH), Zurich, Switzerland.
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4
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Lanz C, Schotsaert M, Magnus C, Karakus U, Hunziker A, Sempere Borau M, Martínez-Romero C, Spieler EE, Günther SC, Moritz E, Hale BG, Trkola A, García-Sastre A, Stertz S. IFITM3 incorporation sensitizes influenza A virus to antibody-mediated neutralization. J Exp Med 2021; 218:212014. [PMID: 33882122 PMCID: PMC8072448 DOI: 10.1084/jem.20200303] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 02/02/2021] [Accepted: 03/04/2021] [Indexed: 12/17/2022] Open
Abstract
The disease severity of influenza is highly variable in humans, and one genetic determinant behind these differences is the IFITM3 gene. As an effector of the interferon response, IFITM3 potently blocks cytosolic entry of influenza A virus (IAV). Here, we reveal a novel level of inhibition by IFITM3 in vivo: We show that incorporation of IFITM3 into IAV particles competes with incorporation of viral hemagglutinin (HA). Decreased virion HA levels did not reduce infectivity, suggesting that high HA density on IAV virions may be an antagonistic strategy used by the virus to prevent direct inhibition. However, we found that IFITM3-mediated reduction in HA content sensitizes IAV to antibody-mediated neutralization. Mathematical modeling predicted that this effect decreases and delays peak IAV titers, and we show that, indeed, IFITM3-mediated sensitization of IAV to antibody-mediated neutralization impacts infection outcome in an in vivo mouse model. Overall, our data describe a previously unappreciated interplay between the innate effector IFITM3 and the adaptive immune response.
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Affiliation(s)
- Caroline Lanz
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland.,Life Sciences Zurich Graduate School, Eidgenössische Technische Hochschule Zurich and University of Zurich, Zurich, Switzerland
| | - Michael Schotsaert
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY.,Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Carsten Magnus
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland.,Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule Zurich, Basel, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Umut Karakus
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Annika Hunziker
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland.,Life Sciences Zurich Graduate School, Eidgenössische Technische Hochschule Zurich and University of Zurich, Zurich, Switzerland
| | - Milagros Sempere Borau
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland.,Life Sciences Zurich Graduate School, Eidgenössische Technische Hochschule Zurich and University of Zurich, Zurich, Switzerland
| | - Carles Martínez-Romero
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY.,Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Eva E Spieler
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland.,Life Sciences Zurich Graduate School, Eidgenössische Technische Hochschule Zurich and University of Zurich, Zurich, Switzerland
| | - Sira C Günther
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland.,Life Sciences Zurich Graduate School, Eidgenössische Technische Hochschule Zurich and University of Zurich, Zurich, Switzerland
| | - Eva Moritz
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Benjamin G Hale
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Alexandra Trkola
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY.,Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY.,Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY.,The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Silke Stertz
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
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5
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Pohl MO, Busnadiego I, Kufner V, Glas I, Karakus U, Schmutz S, Zaheri M, Abela I, Trkola A, Huber M, Stertz S, Hale BG. SARS-CoV-2 variants reveal features critical for replication in primary human cells. PLoS Biol 2021; 19:e3001006. [PMID: 33760807 PMCID: PMC8021179 DOI: 10.1371/journal.pbio.3001006] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 04/05/2021] [Accepted: 03/02/2021] [Indexed: 02/07/2023] Open
Abstract
Since entering the human population, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2; the causative agent of Coronavirus Disease 2019 [COVID-19]) has spread worldwide, causing >100 million infections and >2 million deaths. While large-scale sequencing efforts have identified numerous genetic variants in SARS-CoV-2 during its circulation, it remains largely unclear whether many of these changes impact adaptation, replication, or transmission of the virus. Here, we characterized 14 different low-passage replication-competent human SARS-CoV-2 isolates representing all major European clades observed during the first pandemic wave in early 2020. By integrating viral sequencing data from patient material, virus stocks, and passaging experiments, together with kinetic virus replication data from nonhuman Vero-CCL81 cells and primary differentiated human bronchial epithelial cells (BEpCs), we observed several SARS-CoV-2 features that associate with distinct phenotypes. Notably, naturally occurring variants in Orf3a (Q57H) and nsp2 (T85I) were associated with poor replication in Vero-CCL81 cells but not in BEpCs, while SARS-CoV-2 isolates expressing the Spike D614G variant generally exhibited enhanced replication abilities in BEpCs. Strikingly, low-passage Vero-derived stock preparation of 3 SARS-CoV-2 isolates selected for substitutions at positions 5/6 of E and were highly attenuated in BEpCs, revealing a key cell-specific function to this region. Rare isolate-specific deletions were also observed in the Spike furin cleavage site during Vero-CCL81 passage, but these were rapidly selected against in BEpCs, underscoring the importance of this site for SARS-CoV-2 replication in primary human cells. Overall, our study uncovers sequence features in SARS-CoV-2 variants that determine cell-specific replication and highlights the need to monitor SARS-CoV-2 stocks carefully when phenotyping newly emerging variants or potential variants of concern.
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Affiliation(s)
- Marie O. Pohl
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Idoia Busnadiego
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Verena Kufner
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Irina Glas
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
- Life Science Zurich Graduate School, ETH and University of Zurich, Zurich, Switzerland
| | - Umut Karakus
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Stefan Schmutz
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Maryam Zaheri
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Irene Abela
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Alexandra Trkola
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Michael Huber
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Silke Stertz
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Benjamin G. Hale
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
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6
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Abstract
Influenza viruses are constantly circulating among humans, in which they cause seasonal epidemics of severe respiratory disease. Additionally, these zoonotic viruses infect different mammals and birds, from which new antigenic variants are occasionally transmitted to humans leading to devastating global pandemics. Surveillance programs, in which viruses from the main reservoir (waterfowl), intermediate hosts (like pigs and other farm animals), and other affected species are isolated and characterized, are crucial for the global influenza prevention strategy. This chapter gives an overview of the most commonly used methods for the propagation and titration of influenza viruses, which are key steps in surveillance procedures, as well as in vaccine development and basic research. Depending on the host and the viral strain, primary isolates are obtained from biological samples of different origin and subsequently amplified in embryonated chicken eggs or cell cultures. These propagation procedures are the focus of the first part of this chapter. Once the initial isolates have been amplified, virus titration methods based on particular characteristics of influenza viruses, such as their ability to agglutinate red blood cells (RBCs) or to induce cytopathic effects (CPE) in cell monolayers, are used to estimate the amount of viral particles. Such approaches, like the hemagglutination assay (HA assay), 50% tissue culture infectious dose (TCID50), or plaque assay, are included in the second part of this chapter. Although they are simple and cost-effective, some of these techniques have been partially replaced by faster and more sensitive methods based on the quantification of viral genomes, such as the quantitative real-time reverse transcription PCR (RT-qPCR), which is presented at the end of this section. The different protocols are explained in detail in order to facilitate the preparation and quantification of infectious virus stocks.
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Affiliation(s)
- Umut Karakus
- Institute of Medical Virology, University of Zurich, Zürich, Switzerland
| | - Michel Crameri
- Institute of Medical Virology, University of Zurich, Zürich, Switzerland
| | - Caroline Lanz
- Institute of Medical Virology, University of Zurich, Zürich, Switzerland
| | - Emilio Yángüez
- Institute of Medical Virology, University of Zurich, Zürich, Switzerland.
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