Different Neutralization Profiles After Primary SARS-CoV-2 Omicron BA.1 and BA.2 Infections

Background and MethodsThe SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) Omicron (B.1.1.529) variant is the antigenically most distinct variant to date. As the heavily mutated spike protein enables neutralization escape, we studied serum-neutralizing activities of naïve and vaccinated individuals after Omicron BA.1 or BA.2 sub-lineage infections in live virus neutralization tests with Omicron BA.1, Omicron BA.2, wildtype (WT, B1.1), and Delta (B.1.617.2) strains. Serum samples obtained after WT infections and three-dose mRNA vaccinations with and without prior infection were included as controls.ResultsPrimary BA.1 infections yielded reduced neutralizing antibody levels against WT, Delta, and Omicron BA.2, while samples from BA.2-infected individuals showed almost no cross-neutralization against the other variants. Serum neutralization of Omicron BA.1 and BA.2 variants was detectable after three-dose mRNA vaccinations, but with reduced titers. Vaccination-breakthrough infections with either Omicron BA.1 or BA.2, however, generated equal cross-neutralizing antibody levels against all SARS-CoV-2 variants tested.ConclusionsOur study demonstrates that although Omicron variants are able to enhance cross-neutralizing antibody levels in pre-immune individuals, primary infections with BA.1 or BA.2 induced mostly variant-specific neutralizing antibodies, emphasizing the differently shaped humoral immunity induced by the two Omicron variants. These data thus contribute substantially to the understanding of antibody responses induced by primary Omicron infections or multiple exposures to different SARS-CoV-2 variants and are of particular importance for developing vaccination strategies in the light of future emerging variants

International bottom trawl survey in the Mediterranean. Instruction manual. Version 9

The MEDITS project started in 1994 within the cooperation between several research Institutes from four Mediterranean Member States (France, Greece, Italy, Spain) of the European Union. Along the time, till to the advent of the European framework for the collection and management of fisheries data, new partners from Slovenia, Croatia, Albania, Montenegro, Malta and Cyprus joined the MEDITS project. The target was to conduct a common bottom trawl survey in the Mediterranean in which all the participants use the same gear, the same sampling protocol and the same methodology.   A first manual with the major specifications was prepared at the start of the project. The manual was revised in 1995, following the 1994 survey and taking into account the methodological improvements acquired during the first survey. Along the years, several improvements were introduced. A new version of the manual was issued each time it was felt necessary to make improvements to the previous protocol. In any case, each time the MEDITS Co-ordination Committee ensured that amendments did not disrupt the consistency of the series. The third version of this manual was edited in 1999, while the fourth one served as a manual for the surveys carried out between 2000 and 2006. The fifth version, although issued in 2007, included improvements adopted by the MEDITS group since 2005, and was the protocol followed from 2005 until 2011 surveys.   In 2012 the revision 6 was issued, which included substantial modifications to the MEDITS manual, though not affecting the main characteristics of the protocol regarding the sampling scheme, methods and gear. This new version included changes in the list of target species and faunistic categories, which were both expanded. In addition, the protocol for otolith sampling and measurements of biological parameters was included, while adjusting the storage data formats accordingly.   The version number 7, in continuity with the previous ones, was amending and innovating some aspects, while incorporating more specific and standardised gear checks and proposing a common protocol for the voluntary collection of data on marine litters, in agreements with the requirements of the Marine Strategy Directive Framework (Directive 2008/56/EC).   The version 8 introduced more details on the checks of the MEDITS gear and on the aspects related to the taxonomic list and categories. To ease the MEDITS Handbook consultation, the present version 9 separates out the TM list from the MEDITS Handbook and makes the former available in an electronic format only at the web site: http://www.sibm.it/MEDITS%202011/principale%20project.htm

An Absolutely Conserved Tryptophan in the Stem of the Envelope Protein E of Flaviviruses Is Essential for the Formation of Stable Particles

The major envelope protein E of flaviviruses contains an ectodomain that is connected to the transmembrane domain by the so-called “stem” region. In mature flavivirus particles, the stem is composed of two or three mostly amphipathic α-helices and a conserved sequence element (CS) with an undefined role in the viral life cycle. A tryptophan is the only residue within this region which is not only conserved in all vector-borne flaviviruses, but also in the group with no known vector. We investigated the importance of this residue in different stages of the viral life cycle by a mutagenesis-based approach using tick-borne encephalitis virus (TBEV). Replacing W421 by alanine or histidine strongly reduced the release of infectious virions and their thermostability, whereas fusion-related entry functions and virus maturation were still intact. Serial passaging of the mutants led to the emergence of a same-site compensatory mutation to leucine that largely restored these properties of the wildtype. The conserved tryptophan in CS (or another big hydrophobic amino acid at the same position) is thus essential for the assembly and infectivity of flaviviruses by being part of a network required for conferring stability to infectious particles

Different Cross-Reactivities of IgM Responses in Dengue, Zika and Tick-Borne Encephalitis Virus Infections

Flaviviruses circulate worldwide and cause a number of medically relevant human diseases, such as dengue, Zika, yellow fever, and tick-borne encephalitis (TBE). Serology plays an important role in the diagnosis of flavivirus infections, but can be impeded by antigenic cross-reactivities among flaviviruses. Therefore, serological diagnosis of a recent infection can be insufficiently specific, especially in areas where flaviviruses co-circulate and/or vaccination coverage against certain flaviviruses is high. In this study, we developed a new IgM assay format, which is well suited for the specific diagnosis of TBE, Zika and dengue virus infections. In the case of TBE and Zika, the IgM response proved to be highly specific for the infecting virus. In contrast, primary dengue virus infections induced substantial amounts of cross-reactive IgM antibodies, which is most likely explained by structural peculiarities of dengue virus particles. Despite the presence of cross-reactive IgM, the standardized nature and the quantitative read-out of the assay even allowed the serotype-specific diagnosis of recent dengue virus infections in most instances

Extensive flavivirus E trimer breathing accompanies stem zippering of the post‐fusion hairpin

International audienceFlaviviruses enter cells by fusion with endosomal membranes through a rearrangement of the envelope protein E, a class II membrane fusion protein, into fusogenic trimers. The rod-like E subunits bend into "hairpins" to bring the fusion loops next to the C-terminal transmembrane (TM) anchors, with the TM-proximal "stem" element zippering the E trimer to force apposition of the membranes. The structure of the complete class II trimeric hairpin is known for phleboviruses but not for flaviviruses, for which the stem is only partially resolved. Here, we performed comparative analyses of E-protein trimers from the tick-borne encephalitis fla-vivirus with sequential stem truncations. Our thermostability and antibody-binding data suggest that the stem "zipper" ends at a characteristic flavivirus conserved sequence (CS) that cloaks the fusion loops, with the downstream segment not contributing to trimer stability. We further identified a highly dynamic behavior of E trimers C-terminally truncated upstream the CS, which, unlike fully stem-zippered trimers, undergo rapid deuterium exchange at the trimer interface. These results thus identify important "breathing" intermediates in the E-protein-driven membrane fusion process

Bivalent COVID-19 mRNA booster vaccination (BA.1 or BA.4/BA.5) increases neutralization of matched Omicron variants

Abstract We report SARS-CoV-2 neutralizing antibody titers in sera of triple-vaccinated individuals who received a booster dose of an original monovalent or a bivalent BA.1- or BA.4/BA.5-adapted vaccine or had a breakthrough infection with Omicron variants BA.1, BA.2 or BA.4/BA.5. A bivalent BA.4/BA.5 booster or Omicron-breakthrough infection induced increased Omicron-neutralization titers compared with the monovalent booster. The XBB.1.5 variant effectively evaded neutralizing-antibody responses elicited by current vaccines and/or infection with previous variants

Evolution and activation mechanism of the flavivirus class II membrane-fusion machinery

We thank the staff at beamlines PX1 and PX2 at SOLEIL synchrotron (St. Aubin, France) and at PX beamlines at the ESRF (Grenoble, France); A. Haouz and the staff at the crystallographic facility at Institut Pasteur; F. Agou from the Chemogenomic and Biological Screening platform at Institut Pasteur; P. Guardado Calvo and I. Fernandez for helping for the MALS experiments.International audienceThe flavivirus envelope glycoproteins prM and E drive the assembly of icosahedral, spiky immature particles that bud across the membrane of the endoplasmic reticulum. Maturation into infectious virions in the trans-Golgi network involves an acid-pH-driven rearrangement into smooth particles made of (prM/E)2 dimers exposing a furin site for prM cleavage into "pr" and "M". Here we show that the prM "pr" moiety derives from an HSP40 cellular chaperonin. Furthermore, the X-ray structure of the tick-borne encephalitis virus (pr/E)2 dimer at acidic pH revealed the E 150-loop as a hinged-lid that opens at low pH to expose a positively-charged prbinding pocket at the E dimer interface, inducing (prM/E)2 dimer formation to generate smooth particles in the Golgi. Furin cleavage is followed by lid-closure upon deprotonation in the neutral-pH extracellular environment, expelling pr while the 150-loop takes the relay in fusion loop protection, thus revealing the elusive flavivirus mechanism of fusion activation

Weight-length relationships of 3 demersal fish species from Lebanese marine waters, eastern Mediterranean

International audienceWeight‐length relationships (WLRs) were estimated for 3 demersal species, from the Lebanese marine waters, eastern Mediterranean, namely Coelorinchus caelorhincus (Risso, 1810), Scorpaena elongata Cadenat, 1943 and Stephanolepsis diaspros Fraser‐Brunner, 1940. The specimens were collected using trammel and gill nets from June 2012 to October 2014. The values of parameter b of the WLRs W = aLb ranged from 2.922 to 3.708. Pronounced sexual dimorphism in WLR was observed for S. diaspros and none showed a WLR‐based geographical pattern of distribution. WLRs reported in this study should be applied only within the observed length ranges

Structural basis of potent Zika-dengue virus antibody cross-neutralization

Zika virus is a member of the flavivirus genus that had not been associated with severe disease in humans until the recent outbreaks, when it was linked to microcephaly in newborns in Brazil and to Guillain-Barré syndrome in adults in French Polynesia. Zika virus is related to dengue virus, and we report here that a category of antibodies isolated from dengue patients and targeting a conformational epitope potently neutralize Zika virus. The crystal structure of two of these antibodies in complex with the envelope protein of Zika virus reveals the details of a conserved epitope, which is also the site of interaction of the envelope protein dimer with the precursor prM protein during virus maturation. Comparison of the Zika and dengue virus immunocomplexes provides a lead for rational, epitope-focused design of a universal vaccine capable of eliciting potent cross-neutralizing antibodies to protect against Zika and dengue viruses simultaneously