Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genetic and structural genome-based survey reveals the low potential for epidemiological expansion of the SARS-CoV-2 XBB.1.5 sublineage.

ABSTRACT:

SUBMITTER: Scarpa F

PROVIDER: S-EPMC9974203 | biostudies-literature | 2023 Jun

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Genetic and structural genome-based survey reveals the low potential for epidemiological expansion of the SARS-CoV-2 XBB.1.5 sublineage.

Scarpa Fabio F Imperia Elena E Azzena Ilenia I Giovanetti Marta M Benvenuto Domenico D Locci Chiara C Casu Marco M Fiori Pier Luigi PL Maruotti Antonello A Ceccarelli Giancarlo G Borsetti Alessandra A Caruso Arnaldo A Cauda Roberto R Cassone Antonio A Via Allegra A Pascarella Stefano S Sanna Daria D Ciccozzi Massimo M

The Journal of infection 20230301 6

PMID: 36863537

Similar Datasets

Molecular In-Depth on the Epidemiological Expansion of SARS-CoV-2 XBB.1.5.

Project description:Since the beginning of the pandemic, the generation of new variants periodically recurs. The XBB.1.5 SARS-CoV-2 variant is one of the most recent. This research was aimed at verifying the potential hazard of this new subvariant. To achieve this objective, we performed a genome-based integrative approach, integrating results from genetic variability/phylodynamics with structural and immunoinformatic analyses to obtain as comprehensive a viewpoint as possible. The Bayesian Skyline Plot (BSP) shows that the viral population size reached the plateau phase on 24 November 2022, and the number of lineages peaked at the same time. The evolutionary rate is relatively low, amounting to 6.9 × 10-4 subs/sites/years. The NTD domain is identical for XBB.1 and XBB.1.5 whereas their RBDs only differ for the mutations at position 486, where the Phe (in the original Wuhan) is replaced by a Ser in XBB and XBB.1, and by a Pro in XBB.1.5. The variant XBB.1.5 seems to spread more slowly than sub-variants that have caused concerns in 2022. The multidisciplinary molecular in-depth analyses on XBB.1.5 performed here does not provide evidence for a particularly high risk of viral expansion. Results indicate that XBB.1.5 does not possess features to become a new, global, public health threat. As of now, in its current molecular make-up, XBB.1.5 does not represent the most dangerous variant.

| S-EPMC10142263 | biostudies-literature

XBB.1.5 Kraken cracked: Gibbs energies of binding and biosynthesis of the XBB.1.5 variant of SARS-CoV-2.

Project description:The SARS-CoV-2 Hydra with many heads (variants) has been causing the COVID-19 pandemic for 3 years. The appearance of every new head (SARS-CoV-2 variant) causes a new pandemic wave. The last in the series is the XBB.1.5 "Kraken" variant. In the general public (social media) and in the scientific community (scientific journals), during the last several weeks since the variant has appeared, the question was raised of whether the infectivity of the new variant will be greater. This article attempts to provide the answer. Analysis of thermodynamic driving forces of binding and biosynthesis leads to the conclusion that infectivity of the XBB.1.5 variant could be increased to a certain extent. The pathogenicity of the XBB.1.5 variant seems to be unchanged compared to the other Omicron variants.

| S-EPMC9928726 | biostudies-literature

Coding-Complete Genome Sequences of 40 SARS-CoV-2 Omicron XBB, XBB.1, and XBB.2 Sublineage Strains in Bangladesh.

Project description:Here, we report the coding-complete genome sequences of 40 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains of the newly emerged recombinant Omicron variants XBB, XBB.1, and XBB.2. The strains were isolated from nasopharyngeal swab samples that had been collected from symptomatic patients in Bangladesh between September and October 2022 and were sequenced using an Oxford Nanopore Technologies (ONT) system.

| S-EPMC10019308 | biostudies-literature

First identification of the SARS-COV-2/XBB.1.5 sublineage among indigenous COVID-19 cases through the influenza sentinel surveillance system in Niger

Project description: Not available

| S-EPMC10637901 | biostudies-literature

SARS-CoV-2 pseudovirus strain:XBB.1.5

Project description:SARS-CoV-2 XBB.1.5 RBD-only pseudovirus based deep mutational scanning libraries

| PRJNA1035795 | ENA

SARS-CoV-2 pseudovirus strain:XBB.1.5

Project description:XBB.1.5 spike DMS for infant sera

| PRJNA1210606 | ENA

Virological characteristics of the SARS-CoV-2 Omicron XBB.1.5 variant.

Project description:Circulation of SARS-CoV-2 Omicron XBB has resulted in the emergence of XBB.1.5, a new Variant of Interest. Our phylogenetic analysis suggests that XBB.1.5 evolved from XBB.1 by acquiring the S486P spike (S) mutation, subsequent to the acquisition of a nonsense mutation in ORF8. Neutralization assays showed similar abilities of immune escape between XBB.1.5 and XBB.1. We determine the structural basis for the interaction between human ACE2 and the S protein of XBB.1.5, showing similar overall structures between the S proteins of XBB.1 and XBB.1.5. We provide the intrinsic pathogenicity of XBB.1 and XBB.1.5 in hamsters. Importantly, we find that the ORF8 nonsense mutation of XBB.1.5 resulted in impairment of MHC suppression. In vivo experiments using recombinant viruses reveal that the XBB.1.5 mutations are involved with reduced virulence of XBB.1.5. Together, our study identifies the two viral functions defined the difference between XBB.1 and XBB.1.5.

| S-EPMC10853506 | biostudies-literature

SARS-CoV-2 XBB.1.5 mRNA booster vaccination elicits limited mucosal immunity.

Project description:Current COVID-19 vaccines provide robust protection against severe disease but minimal protection against acquisition of infection. Intramuscularly administered COVID-19 vaccines induce robust serum neutralizing antibodies (NAbs), but their ability to boost mucosal immune responses remains to be determined. In this study, we show that the XBB.1.5 messenger RNA (mRNA) boosters result in increased serum neutralization to multiple severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants in humans, including the dominant circulating variant JN.1. In contrast, we found that the XBB.1.5 mRNA booster did not augment mucosal NAbs or mucosal IgA responses, although acute SARS-CoV-2 XBB infection substantially increased mucosal antibody responses. These data demonstrate that current XBB.1.5 mRNA boosters substantially enhance peripheral antibody responses but do not robustly increase mucosal antibody responses. Our data highlight a separation between the peripheral and mucosal immune systems in humans and emphasize the importance of developing next-generation vaccines to augment mucosal immunity to protect against respiratory virus infections.

| S-EPMC11542980 | biostudies-literature

An updated review of epidemiological characteristics, immune escape, and therapeutic advances of SARS-CoV-2 Omicron XBB.1.5 and other mutants.

Project description:The rapid evolution of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has led to the emergence of new variants with different genetic profiles, with important implications for public health. The continued emergence of new variants with unique genetic features and potential changes in biological properties poses significant challenges to public health strategies, vaccine development, and therapeutic interventions. Omicron variants have attracted particular attention due to their rapid spread and numerous mutations in key viral proteins. This review aims to provide an updated and comprehensive assessment of the epidemiological characteristics, immune escape potential, and therapeutic advances of the SARS-CoV-2 Omicron XBB.1.5 variant, as well as other variants.

| S-EPMC10752979 | biostudies-literature

Bivalent mRNA vaccine-elicited SARS-CoV-2 specific T cells recognise the omicron XBB sublineage.

Project description: Not available

| S-EPMC10038665 | biostudies-literature