Caractérisation fonctionnelle de la protéine S du SARS-CoV-2 et de la formation de syncytia

The SARS-CoV-2 spike (S) protein is a highly antigenic viral fusogen that triggers viral entry upon interaction with cellular receptors and proteases. The S protein also facilitates the formation of syncytia which are large multinucleated cells formed through the fusion of individual cells. Several coronaviruses including the currently pandemic SARS-CoV-2 form syncytia. Severe cases of COVID'19 are associated with extensive lung damage and the presence of infected syncytial pneumocytes. Syncytia may represent a pathological substrate that contributes to viral dissemination, immune evasion, cytopathicity and the inflammatory response. Here we characterized the role of the SARS-CoV-2 S protein in mediating fusion. We show that SARS-CoV-2 induce syncytia when the S protein expressed on the cell surface interacts with the angiotensin-converting enzyme 2 (ACE2) receptor on the surface of neighbouring cells. The transmembrane protease serine 2 (TMPRSS2) protease further augments syncytia formation. Viral infection triggers the production of interferon (IFN) and subsequent expression of a wide array of interferon-stimulated-genes, including interferon-induced transmembrane (IFITM) proteins. IFITMs restrict the cellular entry of a broad spectrum of enveloped viruses, possibly by altering the biomechanically properties of the plasma membrane in ways that are unfavorable to fusion. We found that IFITMs effectively restrict SARS-CoV-2 S protein-mediated syncytia formation. However, this restriction is effectively reverted by the TMPRSS2 protease. As the pandemic progressed, the ancestral Wuhan strain has been replaced by SARS-CoV-2 variants containing several mutations within the S protein. We characterized the Alpha, Beta and Delta variant S proteins in terms of the syncytia formation potential. We report that they induce more fusion than the early D614G variant and the ancestral strain. The fusogenicity of the variants partly correlates with their ACE2 binding potential. The individual mutations associated with the variants differentially modulate syncytia formation. Mutations P681H, D1118H, and D215G augment cell-cell fusion while the antibody escape mutation E484K, K417N and '242-244 are restrictive. IFITMs effectively limit syncytia formation induced by variant S proteins. We also investigated the syncytia formatting potential of the commonly circulating coronaviruses. We found that hCoV-HKU1 S protein induces syncytia only when adjacent cells express catalytically active TMPRSS2. Human IFITM1 restricted HKU1 S mediated syncytia formation. However, mouse IFITM1 increased fusion. Interestingly, while TMPRSS2 accelerates syncytia formation by SARS-CoV-2 and counteracted the restrictive effects of IFITMs, it does not interfere with the restriction of HKU1-S fusion by IFITM1. In summary, we have characterized the mechanisms of S protein-mediated syncytia formation and its regulation by components of the humoral and innate immune response. Our results provide preliminary insights into the cytopathic effect and pathology induced by SARS-CoV-2La protéine de spicule (S) du SARS-CoV-2 est un fusogène viral hautement antigénique qui déclenche l'entrée virale lors de l'interaction avec les récepteurs et protéases cellulaires. La protéine S facilite également la formation de syncytia qui sont de grandes cellules multinucléées formées par la fusion de cellules individuelles. Plusieurs coronavirus, dont le SARS-CoV-2 actuellement pandémique, forment des syncytia. Les cas graves de COVID-19 sont associés à des lésions pulmonaires étendues et à la présence de pneumocytes syncytial infectés. Les syncytia peuvent contribuer à la dissémination virale, à l'évasion immunitaire, à la cytopathie et à la réponse inflammatoire. Ici, nous avons caractérisé le rôle de la protéine S du SARS-CoV-2 dans la médiation de la fusion. Nous montrons que le SARS-CoV-2 induit des syncytia lorsque la protéine S exprimée à la surface cellulaire interagit avec le récepteur de l'enzyme de conversion de l'angiotensine 2 (ACE2) à la surface des cellules voisines. La protéase transmembranaire sérine 2 (TMPRSS2) augmente aussi la formation de syncytia. L'infection virale déclenche la production d'interféron (IFN) et l'expression subséquente d'un large éventail de gènes, y compris les protéines transmembranaires induites par l'interféron (IFITM). Les IFITM restreignent l'entrée cellulaire d'un large spectre de virus enveloppés, possiblement en modifiant les propriétés biomécaniques de la membrane plasmique de manière défavorable à la fusion. Nous avons constaté que les IFITM restreignent efficacement la formation de syncytia médiée par la protéine S du SARS-CoV-2. Cependant, cette restriction est inversée par la protéase TMPRSS2. Au fur et à mesure de la progression de la pandémie, la souche ancestrale de Wuhan a été remplacée par des variants du SARS-CoV-2 contenant plusieurs mutations au sein de la protéine S. Nous avons caractérisé les protéines variantes S Alpha, Beta et Delta par rapport à leur potentiel de formation de syncytia. Nous démontrons que la protéine S de ces variants induisent plus de fusion que le variant précoce D614G et que la souche ancestrale. La fusogénicité des variants est en partie corrélée à leur potentiel de liaison à l'ACE2. De plus, les mutations individuelles associées aux variants modulent de manière différentielle la formation de syncytia. Les mutations P681H, D1118H et D215G augmentent la fusion cellule-cellule tandis que les mutations d'échappement aux anticorps E484K, K417N et '242-244 sont restrictives. Par ailleurs, les IFITM limitent efficacement la formation de syncytia induite par les protéines variantes S. Nous avons également étudié le potentiel de formation de syncytia des coronavirus communément en circulation. Nous avons constaté que la protéine S du hCoV-HKU1 induit des syncytia uniquement lorsque les cellules adjacentes expriment la TMPRSS2 sous sa forme catalytiquement active. Nous montrons aussi que l'IFITM1 humain restreint la formation de syncytia médié par la protéine S du hCov-HKU1 alors que l'IFITM1 murin augmente la fusion. Fait intéressant, alors que la protéase TMPRSS2 accélère la formation de syncytia médiée par le SARS-CoV-2 et contrecarre les effets restrictifs des IFITM, elle n'interfère pas avec la restriction de la fusion HKU1-S médiée par l'IFITM1. En résumé, nous avons caractérisé les mécanismes de la formation de syncytia médiée par la protéine S et sa régulation par des composants de la réponse immunitaire humorale et innée. Nos résultats fournissent ainsi des informations préliminaires sur l'effet cytopathique et la pathologie induite par le SARS-CoV-

Caractérisation fonctionnelle de la protéine S du SARS-CoV-2 et de la formation de syncytia

La protéine de spicule (S) du SARS-CoV-2 est un fusogène viral hautement antigénique qui déclenche l'entrée virale lors de l'interaction avec les récepteurs et protéases cellulaires. La protéine S facilite également la formation de syncytia qui sont de grandes cellules multinucléées formées par la fusion de cellules individuelles. Plusieurs coronavirus, dont le SARS-CoV-2 actuellement pandémique, forment des syncytia. Les cas graves de COVID-19 sont associés à des lésions pulmonaires étendues et à la présence de pneumocytes syncytial infectés. Les syncytia peuvent contribuer à la dissémination virale, à l'évasion immunitaire, à la cytopathie et à la réponse inflammatoire. Ici, nous avons caractérisé le rôle de la protéine S du SARS-CoV-2 dans la médiation de la fusion. Nous montrons que le SARS-CoV-2 induit des syncytia lorsque la protéine S exprimée à la surface cellulaire interagit avec le récepteur de l'enzyme de conversion de l'angiotensine 2 (ACE2) à la surface des cellules voisines. La protéase transmembranaire sérine 2 (TMPRSS2) augmente aussi la formation de syncytia. L'infection virale déclenche la production d'interféron (IFN) et l'expression subséquente d'un large éventail de gènes, y compris les protéines transmembranaires induites par l'interféron (IFITM). Les IFITM restreignent l'entrée cellulaire d'un large spectre de virus enveloppés, possiblement en modifiant les propriétés biomécaniques de la membrane plasmique de manière défavorable à la fusion. Nous avons constaté que les IFITM restreignent efficacement la formation de syncytia médiée par la protéine S du SARS-CoV-2. Cependant, cette restriction est inversée par la protéase TMPRSS2. Au fur et à mesure de la progression de la pandémie, la souche ancestrale de Wuhan a été remplacée par des variants du SARS-CoV-2 contenant plusieurs mutations au sein de la protéine S. Nous avons caractérisé les protéines variantes S Alpha, Beta et Delta par rapport à leur potentiel de formation de syncytia. Nous démontrons que la protéine S de ces variants induisent plus de fusion que le variant précoce D614G et que la souche ancestrale. La fusogénicité des variants est en partie corrélée à leur potentiel de liaison à l'ACE2. De plus, les mutations individuelles associées aux variants modulent de manière différentielle la formation de syncytia. Les mutations P681H, D1118H et D215G augmentent la fusion cellule-cellule tandis que les mutations d'échappement aux anticorps E484K, K417N et '242-244 sont restrictives. Par ailleurs, les IFITM limitent efficacement la formation de syncytia induite par les protéines variantes S. Nous avons également étudié le potentiel de formation de syncytia des coronavirus communément en circulation. Nous avons constaté que la protéine S du hCoV-HKU1 induit des syncytia uniquement lorsque les cellules adjacentes expriment la TMPRSS2 sous sa forme catalytiquement active. Nous montrons aussi que l'IFITM1 humain restreint la formation de syncytia médié par la protéine S du hCov-HKU1 alors que l'IFITM1 murin augmente la fusion. Fait intéressant, alors que la protéase TMPRSS2 accélère la formation de syncytia médiée par le SARS-CoV-2 et contrecarre les effets restrictifs des IFITM, elle n'interfère pas avec la restriction de la fusion HKU1-S médiée par l'IFITM1. En résumé, nous avons caractérisé les mécanismes de la formation de syncytia médiée par la protéine S et sa régulation par des composants de la réponse immunitaire humorale et innée. Nos résultats fournissent ainsi des informations préliminaires sur l'effet cytopathique et la pathologie induite par le SARS-CoV-2The SARS-CoV-2 spike (S) protein is a highly antigenic viral fusogen that triggers viral entry upon interaction with cellular receptors and proteases. The S protein also facilitates the formation of syncytia which are large multinucleated cells formed through the fusion of individual cells. Several coronaviruses including the currently pandemic SARS-CoV-2 form syncytia. Severe cases of COVID'19 are associated with extensive lung damage and the presence of infected syncytial pneumocytes. Syncytia may represent a pathological substrate that contributes to viral dissemination, immune evasion, cytopathicity and the inflammatory response. Here we characterized the role of the SARS-CoV-2 S protein in mediating fusion. We show that SARS-CoV-2 induce syncytia when the S protein expressed on the cell surface interacts with the angiotensin-converting enzyme 2 (ACE2) receptor on the surface of neighbouring cells. The transmembrane protease serine 2 (TMPRSS2) protease further augments syncytia formation. Viral infection triggers the production of interferon (IFN) and subsequent expression of a wide array of interferon-stimulated-genes, including interferon-induced transmembrane (IFITM) proteins. IFITMs restrict the cellular entry of a broad spectrum of enveloped viruses, possibly by altering the biomechanically properties of the plasma membrane in ways that are unfavorable to fusion. We found that IFITMs effectively restrict SARS-CoV-2 S protein-mediated syncytia formation. However, this restriction is effectively reverted by the TMPRSS2 protease. As the pandemic progressed, the ancestral Wuhan strain has been replaced by SARS-CoV-2 variants containing several mutations within the S protein. We characterized the Alpha, Beta and Delta variant S proteins in terms of the syncytia formation potential. We report that they induce more fusion than the early D614G variant and the ancestral strain. The fusogenicity of the variants partly correlates with their ACE2 binding potential. The individual mutations associated with the variants differentially modulate syncytia formation. Mutations P681H, D1118H, and D215G augment cell-cell fusion while the antibody escape mutation E484K, K417N and '242-244 are restrictive. IFITMs effectively limit syncytia formation induced by variant S proteins. We also investigated the syncytia formatting potential of the commonly circulating coronaviruses. We found that hCoV-HKU1 S protein induces syncytia only when adjacent cells express catalytically active TMPRSS2. Human IFITM1 restricted HKU1 S mediated syncytia formation. However, mouse IFITM1 increased fusion. Interestingly, while TMPRSS2 accelerates syncytia formation by SARS-CoV-2 and counteracted the restrictive effects of IFITMs, it does not interfere with the restriction of HKU1-S fusion by IFITM1. In summary, we have characterized the mechanisms of S protein-mediated syncytia formation and its regulation by components of the humoral and innate immune response. Our results provide preliminary insights into the cytopathic effect and pathology induced by SARS-CoV-

Caractérisation fonctionnelle de la protéine S du SARS-CoV-2 et de la formation de syncytia

The SARS-CoV-2 spike (S) protein is a highly antigenic viral fusogen that triggers viral entry upon interaction with cellular receptors and proteases. The S protein also facilitates the formation of syncytia which are large multinucleated cells formed through the fusion of individual cells. Several coronaviruses including the currently pandemic SARS-CoV-2 form syncytia. Severe cases of COVID'19 are associated with extensive lung damage and the presence of infected syncytial pneumocytes. Syncytia may represent a pathological substrate that contributes to viral dissemination, immune evasion, cytopathicity and the inflammatory response. Here we characterized the role of the SARS-CoV-2 S protein in mediating fusion. We show that SARS-CoV-2 induce syncytia when the S protein expressed on the cell surface interacts with the angiotensin-converting enzyme 2 (ACE2) receptor on the surface of neighbouring cells. The transmembrane protease serine 2 (TMPRSS2) protease further augments syncytia formation. Viral infection triggers the production of interferon (IFN) and subsequent expression of a wide array of interferon-stimulated-genes, including interferon-induced transmembrane (IFITM) proteins. IFITMs restrict the cellular entry of a broad spectrum of enveloped viruses, possibly by altering the biomechanically properties of the plasma membrane in ways that are unfavorable to fusion. We found that IFITMs effectively restrict SARS-CoV-2 S protein-mediated syncytia formation. However, this restriction is effectively reverted by the TMPRSS2 protease. As the pandemic progressed, the ancestral Wuhan strain has been replaced by SARS-CoV-2 variants containing several mutations within the S protein. We characterized the Alpha, Beta and Delta variant S proteins in terms of the syncytia formation potential. We report that they induce more fusion than the early D614G variant and the ancestral strain. The fusogenicity of the variants partly correlates with their ACE2 binding potential. The individual mutations associated with the variants differentially modulate syncytia formation. Mutations P681H, D1118H, and D215G augment cell-cell fusion while the antibody escape mutation E484K, K417N and '242-244 are restrictive. IFITMs effectively limit syncytia formation induced by variant S proteins. We also investigated the syncytia formatting potential of the commonly circulating coronaviruses. We found that hCoV-HKU1 S protein induces syncytia only when adjacent cells express catalytically active TMPRSS2. Human IFITM1 restricted HKU1 S mediated syncytia formation. However, mouse IFITM1 increased fusion. Interestingly, while TMPRSS2 accelerates syncytia formation by SARS-CoV-2 and counteracted the restrictive effects of IFITMs, it does not interfere with the restriction of HKU1-S fusion by IFITM1. In summary, we have characterized the mechanisms of S protein-mediated syncytia formation and its regulation by components of the humoral and innate immune response. Our results provide preliminary insights into the cytopathic effect and pathology induced by SARS-CoV-2La protéine de spicule (S) du SARS-CoV-2 est un fusogène viral hautement antigénique qui déclenche l'entrée virale lors de l'interaction avec les récepteurs et protéases cellulaires. La protéine S facilite également la formation de syncytia qui sont de grandes cellules multinucléées formées par la fusion de cellules individuelles. Plusieurs coronavirus, dont le SARS-CoV-2 actuellement pandémique, forment des syncytia. Les cas graves de COVID-19 sont associés à des lésions pulmonaires étendues et à la présence de pneumocytes syncytial infectés. Les syncytia peuvent contribuer à la dissémination virale, à l'évasion immunitaire, à la cytopathie et à la réponse inflammatoire. Ici, nous avons caractérisé le rôle de la protéine S du SARS-CoV-2 dans la médiation de la fusion. Nous montrons que le SARS-CoV-2 induit des syncytia lorsque la protéine S exprimée à la surface cellulaire interagit avec le récepteur de l'enzyme de conversion de l'angiotensine 2 (ACE2) à la surface des cellules voisines. La protéase transmembranaire sérine 2 (TMPRSS2) augmente aussi la formation de syncytia. L'infection virale déclenche la production d'interféron (IFN) et l'expression subséquente d'un large éventail de gènes, y compris les protéines transmembranaires induites par l'interféron (IFITM). Les IFITM restreignent l'entrée cellulaire d'un large spectre de virus enveloppés, possiblement en modifiant les propriétés biomécaniques de la membrane plasmique de manière défavorable à la fusion. Nous avons constaté que les IFITM restreignent efficacement la formation de syncytia médiée par la protéine S du SARS-CoV-2. Cependant, cette restriction est inversée par la protéase TMPRSS2. Au fur et à mesure de la progression de la pandémie, la souche ancestrale de Wuhan a été remplacée par des variants du SARS-CoV-2 contenant plusieurs mutations au sein de la protéine S. Nous avons caractérisé les protéines variantes S Alpha, Beta et Delta par rapport à leur potentiel de formation de syncytia. Nous démontrons que la protéine S de ces variants induisent plus de fusion que le variant précoce D614G et que la souche ancestrale. La fusogénicité des variants est en partie corrélée à leur potentiel de liaison à l'ACE2. De plus, les mutations individuelles associées aux variants modulent de manière différentielle la formation de syncytia. Les mutations P681H, D1118H et D215G augmentent la fusion cellule-cellule tandis que les mutations d'échappement aux anticorps E484K, K417N et '242-244 sont restrictives. Par ailleurs, les IFITM limitent efficacement la formation de syncytia induite par les protéines variantes S. Nous avons également étudié le potentiel de formation de syncytia des coronavirus communément en circulation. Nous avons constaté que la protéine S du hCoV-HKU1 induit des syncytia uniquement lorsque les cellules adjacentes expriment la TMPRSS2 sous sa forme catalytiquement active. Nous montrons aussi que l'IFITM1 humain restreint la formation de syncytia médié par la protéine S du hCov-HKU1 alors que l'IFITM1 murin augmente la fusion. Fait intéressant, alors que la protéase TMPRSS2 accélère la formation de syncytia médiée par le SARS-CoV-2 et contrecarre les effets restrictifs des IFITM, elle n'interfère pas avec la restriction de la fusion HKU1-S médiée par l'IFITM1. En résumé, nous avons caractérisé les mécanismes de la formation de syncytia médiée par la protéine S et sa régulation par des composants de la réponse immunitaire humorale et innée. Nos résultats fournissent ainsi des informations préliminaires sur l'effet cytopathique et la pathologie induite par le SARS-CoV-

The Mechanism and Consequences of SARS-CoV-2 Spike-Mediated Fusion and Syncytia Formation

International audienceSyncytia are formed when individual cells fuse. SARS-CoV-2 induces syncytia when the viral spike (S) protein on the surface of an infected cell interacts with receptors on neighboring cells. Syncytia may potentially contribute to pathology by facilitating viral dissemination, cytopathicity, immune evasion, and inflammatory response. SARS-CoV-2 variants of concern possess several mutations within the S protein that enhance receptor interaction, fusogenicity and antibody binding. In this review, we discuss the molecular determinants of S mediated fusion and the antiviral innate immunity components that counteract syncytia formation. Several interferon-stimulated genes, including IFITMs and LY6E act as barriers to S protein-mediated fusion by altering the composition or biophysical properties of the target membrane. We also summarize the effect that the mutations associated with the variants of concern have on S protein fusogenicity. Altogether, this review contextualizes the current understanding of Spike fusogenicity and the role of syncytia during SARS-CoV-2 infection and pathology

The Spike-Stabilizing D614G Mutation Interacts with S1/S2 Cleavage Site Mutations To Promote the Infectious Potential of SARS-CoV-2 Variants

International audienceSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) remained genetically stable during the first 3 months of the pandemic, before acquiring a D614G spike mutation that rapidly spread worldwide and then generating successive waves of viral variants with increasingly high transmissibility. We set out to evaluate possible epistatic interactions between the early-occurring D614G mutation and the more recently emerged cleavage site mutations present in spike of the Alpha, Delta, and Omicron variants of concern. The P681H/R mutations at the S1/S2 cleavage site increased spike processing and fusogenicity but limited its incorporation into pseudoviruses. In addition, the higher cleavage rate led to higher shedding of the spike S1 subunit, resulting in a lower infectivity of the P681H/R-carrying pseudoviruses compared to those expressing the Wuhan wild-type spike. The D614G mutation increased spike expression at the cell surface and limited S1 shedding from pseudovirions. As a consequence, the D614G mutation preferentially increased the infectivity of P681H/R-carrying pseudoviruses. This enhancement was more marked in cells where the endosomal route predominated, suggesting that more stable spikes could better withstand the endosomal environment. Taken together, these findings suggest that the D614G mutation stabilized S1/S2 association and enabled the selection of mutations that increased S1/S2 cleavage, leading to the emergence of SARS-CoV-2 variants expressing highly fusogenic spikes. IMPORTANCE The first SARS-CoV-2 variant that spread worldwide in early 2020 carried a D614G mutation in the viral spike, making this protein more stable in its cleaved form at the surface of virions. The Alpha and Delta variants, which spread in late 2020 and early 2021, respectively, proved increasingly transmissible and pathogenic compared to the original strain. Interestingly, Alpha and Delta both carried the mutations P681H/R in a cleavage site that made the spike more cleaved and more efficient at mediating viral fusion. We show here that variants with increased spike cleavage due to P681H/R were even more dependent on the stabilizing effect of the D614G mutation, which limited the shedding of cleaved S1 subunits from viral particles. These findings suggest that the worldwide spread of the D614G mutation was a prerequisite for the emergence of more pathogenic SARS-CoV-2 variants with highly fusogenic spikes

Syncytia formation by SARS‐CoV‐2‐infected cells

We thank members of the Virus and Immunity Unit for discussions and help, Mauro Giacca for discussion and sharing unpublished results, Nathalie Aulner and the UtechS Photonic BioImaging (UPBI) core facility (Institut Pasteur), a member of the France BioImaging network, for image acquisition and analysis, and Nicolas Escriou for the kind gift of anti-SARS-CoV-2 antibodies.International audienceSevere cases of COVID-19 are associated with extensive lung damage and the presence of infected multinucleated syncytial pneumocytes. The viral and cellular mechanisms regulating the formation of these syncytia are not well understood. Here, we show that SARS-CoV-2-infected cells express the Spike protein (S) at their surface and fuse with ACE2-positive neighboring cells. Expression of S without any other viral proteins triggers syncytia formation. Interferon-induced transmembrane proteins (IFITMs), a family of restriction factors that block the entry of many viruses, inhibit S-mediated fusion, with IFITM1 being more active than IFITM2 and IFITM3. On the contrary, the TMPRSS2 serine protease, which is known to enhance infectivity of cell-free virions, processes both S and ACE2 and increases syncytia formation by accelerating the fusion process. TMPRSS2 thwarts the antiviral effect of IFITMs. Our results show that SARS-CoV-2 pathological effects are modulated by cellular proteins that either inhibit or facilitate syncytia formation

SARS‐CoV‐2 Alpha, Beta, and Delta variants display enhanced Spike‐mediated syncytia formation

International audienceSevere COVID-19 is characterized by lung abnormalities, including the presence of syncytial pneumocytes. Syncytia form when SARS-CoV-2 spike protein expressed on the surface of infected cells interacts with the ACE2 receptor on neighboring cells. The syncytia forming potential of spike variant proteins remain poorly characterized. Here, we first assessed Alpha (B.1.1.7) and Beta (B.1.351) spread and fusion in cell cultures, compared with the ancestral D614G strain. Alpha and Beta replicated similarly to D614G strain in Vero, Caco-2, Calu-3, and primary airway cells. However, Alpha and Beta formed larger and more numerous syncytia. Variant spike proteins displayed higher ACE2 affinity compared with D614G. Alpha, Beta, and D614G fusion was similarly inhibited by interferon-induced transmembrane proteins (IFITMs). Individual mutations present in Alpha and Beta spikes modified fusogenicity, binding to ACE2 or recognition by monoclonal antibodies. We further show that Delta spike also triggers faster fusion relative to D614G. Thus, SARS-CoV-2 emerging variants display enhanced syncytia formation

The Atlastin ER-shaping proteins facilitate Zika virus replication

International audienceThe endoplasmic reticulum (ER) is the site for Zika virus (ZIKV) replication and is central to the cytopathic effects observed in infected cells. ZIKV induces the formation of ER-derived large cytoplasmic vacuoles followed by “implosive” cell death. Little is known about the nature of the ER factors that regulate flavivirus replication. Atlastins (ATL1, -2, and -3) are dynamin-related GTPases that control the structure and the dynamics of the ER membrane. We show here that ZIKV replication is significantly decreased in the absence of ATL proteins. The appearance of infected cells is delayed, the levels of intracellular viral proteins and released virus are reduced, and the cytopathic effects are strongly impaired. We further show that ATL3 is recruited to viral replication sites and interacts with the nonstructural viral proteins NS2A and NS2B3. Thus, proteins that shape and maintain the ER tubular network ensure efficient ZIKV replication.IMPORTANCE Zika virus (ZIKV) is an emerging virus associated with Guillain-Barré syndrome, and fetal microcephaly as well as other neurological complications. There is no vaccine or specific antiviral treatment against ZIKV. We found that endoplasmic reticulum (ER)-shaping atlastin proteins (ATL1, -2, and -3), which induce ER membrane fusion, facilitate ZIKV replication. We show that ATL3 is recruited to the viral replication site and colocalize with the viral proteins NS2A and NS2B3. The results provide insights into host factors used by ZIKV to enhance its replication

Reduced sensitivity of SARS-CoV-2 variant Delta to antibody neutralization

International audienceThe SARS-CoV-2 B.1.617 lineage was identified in October 2020 in India1,2,3,4,5. Since then, it has become dominant in some regions of India and in the UK, and has spread to many other countries6. The lineage includes three main subtypes (B1.617.1, B.1.617.2 and B.1.617.3), which contain diverse mutations in the N-terminal domain (NTD) and the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein that may increase the immune evasion potential of these variants. B.1.617.2—also termed the Delta variant—is believed to spread faster than other variants. Here we isolated an infectious strain of the Delta variant from an individual with COVID-19 who had returned to France from India. We examined the sensitivity of this strain to monoclonal antibodies and to antibodies present in sera from individuals who had recovered from COVID-19 (hereafter referred to as convalescent individuals) or who had received a COVID-19 vaccine, and then compared this strain with other strains of SARS-CoV-2. The Delta variant was resistant to neutralization by some anti-NTD and anti-RBD monoclonal antibodies, including bamlanivimab, and these antibodies showed impaired binding to the spike protein. Sera collected from convalescent individuals up to 12 months after the onset of symptoms were fourfold less potent against the Delta variant relative to the Alpha variant (B.1.1.7). Sera from individuals who had received one dose of the Pfizer or the AstraZeneca vaccine had a barely discernible inhibitory effect on the Delta variant. Administration of two doses of the vaccine generated a neutralizing response in 95% of individuals, with titres three- to fivefold lower against the Delta variant than against the Alpha variant. Thus, the spread of the Delta variant is associated with an escape from antibodies that target non-RBD and RBD epitopes of the spike protein