Biology subjects

Mostafa, H. H.

Publications and source records attributed to Mostafa, H. H..

6 recordsLinked to original sources

bioRxiv2025

Emergence of an Antigenically Drifted and Reassorted Influenza B Virus at the end of the 2024-25 Influenza Season

Influenza B virus (IBV) is a significant contributor to annual and severe cases of influenza, particularly in the young and elderly. Late in the 2024-25 Northern Hemisphere influenza season, a surge of IBV cases were identified in the Johns Hopkins Hospital Systems. The IBV responsible for the surge, C.3.1/re, was a clade C.3 virus that had reassorted with clade C.5.1 viruses and acquired the D197N mutation in hemagglutinin restoring a putative N-linked glycan predicted to mask a key neutralizing antibody epitope. The C.3.1/re viruses preferentially infected children but showed no significant change in disease severity. C.3.1/re viruses were poorly neutralized by pre- and post- influenza vaccination serum in a human cohort. Removal of the glycan at residue 197 restored neutralizing antibody recognition. The C.3.1/re IBV genotype that emerged late in the 2024-25 influenza season was antigenically mismatched with IBV vaccine strains for the 2025 and 2026 Southern hemisphere, as well as the 2025-26 Northern Hemisphere influenza seasons. While the 2026-27 Northern Hemisphere vaccine strain is a C.3.1/re, the egg adapted isolate selected (B/Tokyo/EIS13-175/2025) lacks the 197 glycosylation which is predicted to have poor recognition with circulating IBV clades. Phylogenetic analysis of currently circulating IBVs shows a diversification of circulating C.3 clades with multiple reassortment events between C.3 and C.5 clades in addition to independent acquisitions of D197N mutations, suggesting IBV is going through a period of significant antigenic and genetic expansion. IMPORTANCEInfluenza B viruses are undergoing a period of antigenic and genetic expansion, with several reassorted viruses emerging that also contain point mutations in key hemagglutinin antigenic sites proximal to the receptor binding domain. This has important impacts on vaccine strain choice, as only one IBV component is included in current influenza vaccines. We demonstrate a significant shift in the demographics of IBV infected individuals with the emergence of the antigenically drifted and reassorted IBV C.3.1/re. Furthermore, we show that 197 glycosylation of hemagglutinin is critical for C.3.1/re antigenic drift and we document several emergent C.3 reassortments encoding the D197N mutation. With the IBV vaccine component for the Northern Hemisphere 2026-27 season having lost a key N-linked glycan on the hemagglutinin protein, and multiple independent emergences of antigenically drifted and reassorted viruses, attention to IBV infections should be increased in the upcoming Southern and Northern hemisphere influenza seasons.

microbiology↗

bioRxiv2024

SARS-CoV-2 variants from long-term, persistently infected immunocompromised patients have altered syncytia formation, temperature-dependent replication, and serum neutralizing antibody escape

SARS-CoV-2 infection of immunocompromised individuals often leads to prolonged detection of viral RNA and infectious virus in nasal specimens, presumably due to the lack of induction of an appropriate adaptive immune response. Mutations identified in virus sequences obtained from persistently infected patients bear signatures of immune evasion and have some overlap with sequences present in variants of concern. We characterized virus isolates from two COVID-19 patients undergoing immunosuppressive cancer therapy, with all isolates obtained greater than 100 days after the initial COVID-19 diagnoses and compared to an isolate from the start of the infection. Isolates from an individual who never mounted an antibody response specific to SARS-CoV-2 despite the administration of convalescent plasma showed slight reductions in plaque size and some showed temperature-dependent replication attenuation on human nasal epithelial cell culture compared to the virus that initiated infection. An isolate from another patient - who did mount a SARS-CoV-2 IgM response - showed temperature dependent changes in plaque size as well as increased syncytia formation and escape from serum neutralizing antibody. Our results indicate that not all virus isolates from immunocompromised COVID-19 patients display clear signs of phenotypic change, but increased attention should be paid to monitoring virus evolution in this patient population.

microbiology↗

bioRxiv2023

Convergent Evolution of A-Lineage (Clade 19B) SARS-CoV-2 Spike Sequences with B-Lineage Variants of Concern Affects Virus Replication in a Temperature-Dependent Manner on Human Nasal Epithelial Cell Cultures

The first three months of the COVID-19 pandemic was dominated by two SARS-CoV-2 lineages: A-lineages (Clade 19B) and B-lineages (Clade 19A). However, with the emergence of the Spike D614G substitution in B.1 lineages (Clade 20A), both early lineages were outcompeted and remained near-extinction from mid-2020 onwards. In early-2021, there was a re-emergence and persistence of novel A-lineage variants with substitutions in the Spike gene resembling those found in Variants of Concern (VOCs). An early A.3 variant (MD-HP00076/2020) and three A.2.5 variants (MD-HP02153/2021, MD-HP05922/2021 and CA-VRLC091/2021) were isolated and characterized for their genomic sequences, antibody neutralization, and in vitro replication. All A.2.5 isolates had five Spike mutations relative to the A.3 variant sequence: D614G, L452R, {Delta}141-143, D215A, and ins215AGY. Plaque reduction neutralization assays demonstrated that A.2.5 isolates had a 2.5 to 5-fold reduction in neutralization using contemporaneous COVID-19 convalescent plasma when compared to A.3. In vitro viral characterization in VeroE6 cell lines revealed that the A.3 isolate grew faster and spread more than A.2.5. On VeroE6-TMPRSS2 cells, significant syncytia formation was also observed with the A.2.5 isolates, however Spike cleavage efficiency did not explain these differences. In human nasal epithelial cell (hNEC) cultures, the A.2.5 isolates grew significantly faster and to higher total infectious virus titers than A.3. All A.2.5 lineage isolates grew significantly faster at 37{degrees}C than at 33{degrees}C irrespective of cell type, and to higher peak titers except compared to A.3. This suggests A.2.5s adapted to improve replication using similar mutations found in the B-lineage SARS-CoV-2 variants. ImportanceWhile both A- and B-lineage SARS-CoV-2 variants emerged and circulated together during the early months of the pandemic, the B-lineages that acquired Spike D614G eventually outcompeted all other variants. We show that the A-lineage variants eventually evolved mutations including Spike D614G and Spike L452R that improved their in vitro replication in human nasal epithelial cells in a temperature dependent manner, suggesting there are some highly selectable mutation landscapes that SARS-CoV-2 can acquire to adapt to replication and transmission in humans.

microbiology↗

bioRxiv2022

Within-host evolutionary dynamics and tissue compartmentalization during acute SARS-CoV-2 infection

The global evolution of SARS-CoV-2 depends in part upon the evolutionary dynamics within individual hosts with varying immune histories. To characterize the within-host evolution of acute SARS-CoV-2 infection, we deep sequenced saliva and nasal samples collected daily from immune and unvaccinated individuals early during infection. We show that longitudinal sampling facilitates high-confidence genetic variant detection and reveals evolutionary dynamics missed by less-frequent sampling strategies. Within-host dynamics in both naive and immune individuals appeared largely stochastic; however, we identified clear mutational hotspots within the viral genome, consistent with selection and differing between naive and immune individuals. In rare cases, minor genetic variants emerged to frequencies sufficient for forward transmission. Finally, we detected significant genetic compartmentalization of virus between saliva and nasal swab sample sites in many individuals. Altogether, these data provide a high-resolution profile of within-host SARS-CoV-2 evolutionary dynamics.

microbiology↗

bioRxiv2020

A rapid, point of care red blood cell agglutination assay for detecting antibodies against SARS-CoV-2

The COVID-19 pandemic has brought the world to a halt, with cases observed around the globe causing significant mortality. There is an urgent need for serological tests to detect antibodies against SARS-CoV-2, which could be used to assess the prevalence of infection, as well as ascertain individuals who may be protected from future infection. Current serological tests developed for SARS-CoV-2 rely on traditional technologies such as enzyme-linked immunosorbent assays (ELISA) and lateral flow assays, which may lack scalability to meet the demand of hundreds of millions of antibody tests in the coming year. Herein, we present an alternative method of antibody testing that just depends on one protein reagent being added to patient serum/plasma or whole blood and a short five-minute assay time. A novel fusion protein was designed that binds red blood cells (RBC) via a single-chain variable fragment (scFv) against the H antigen and displays the receptor-binding domain (RBD) of SARS-CoV-2 spike protein on the surface of RBCs. Upon mixing of the fusion protein, RBD-scFv with recovered COVID-19 patient serum and RBCs, we observed agglutination of RBCs, indicating the patient developed antibodies against SARS-CoV-2 RBD. Given that the test uses methods routinely used in hospital clinical labs across the world, we anticipate the test can be rapidly deployed with only the protein reagent required at projected manufacturing cost at U.S. cents per test. We anticipate our agglutination assay may find extensive use in low-resource settings for detecting SARS-CoV-2 antibodies.Competing Interest StatementR.L.K. is an inventor on a provisional patent application related to the work described in the manuscript. All other authors have no competing interests.View Full Text

pathology↗

bioRxiv2018

Next-generation sequencing based hospital outbreak investigation yields insight into Klebsiella aerogenes population structure and determinants of carbapenem resistance and virulence

Klebsiella aerogenes is a nosocomial pathogen associated with drug resistance and outbreaks in intensive care units. In a 5-month period in 2017, we experienced an increased incidence of cultures for carbapenem-resistant K. aerogenes (CR-KA) from an adult cardiothoracic intensive care unit (CICU) involving 15 patients. Phylogenomic analysis following whole-genome sequencing (WGS) identified the outbreak CR-KA isolates to group together as a tight clonal cluster (<7 SNPs apart), suggestive of a protracted intra-ward transmission event. No clonal relationships were identified between the CICU CR-KA strains and additional hospital CR-KA patient isolates from different wards and/or previous years. Genes encoding carbapenemases or drug-resistant plasmids were absent in the outbreak strains, and carbapenem resistance was attributed to mutations impacting AmpD activity and membrane permeability. The CICU outbreak strains harbored an integrative conjugative element (ICEKp10), which has been associated with pathogenicity in hypervirulent Klebsiella pneumoniae lineages. Comparative genomics with global K. aerogenes genomes showed our outbreak strains to group closely with global ST4 strains, which along with ST93 likely represent dominant K. aerogenes lineages associated with human infections. WGS is a powerful tool that goes beyond high-resolution tracking of transmission events into identifying the genetic basis of drug-resistance and virulence, which are not part of conventional diagnostic workflows. With an increasing availability of sequenced genomes from across the globe, population structure analysis offers opportunities to identify emerging trends and dominant clones associated with specific syndromes and geographical locations for poorly characterized pathogens.

genomics↗