A. L. Greninger

Variant mutation in SARS-CoV-2 nucleocapsid enhances viral infection via altered genomic encapsidation

The paper identifies a mutation in the SARS-CoV-2 nucleocapsid protein that enhances viral infection by promoting dimer formation and altering virion structure.

Treponema pallidum periplasmic and membrane proteins are recognized by circulating and skin CD4+ T cells

The paper identifies Tp-specific CD4+ T cell responses in blood and skin of syphilis patients, showing persistence after treatment and highlighting potential vaccine targets.

Age-dependent heterogeneity in the antigenic effects of mutations to influenza hemagglutinin

The paper maps how HA mutations affect neutralization by serum from different age groups, showing age-dependent antigenic effects and implications for viral evolution.

Early antiviral CD4 and CD8 T cell responses and antibodies are associated with upper respiratory tract clearance of SARS-CoV-2

The paper examines early T cell and antibody responses in COVID-19 patients and finds they correlate with reduced SARS-CoV-2 viral RNA in the upper respiratory tract.

Influenza A virus resistance to 4-fluorouridine coincides with viral attenuation in vitro and in vivo

This study identifies mutations conferring resistance to 4-fluorouridine in influenza viruses and shows that resistant variants are attenuated in vivo and can be overcome by higher drug doses.

Therapeutic mitigation of measles-like immune amnesia and exacerbated disease after prior respiratory virus infections in ferrets

This study shows that prior respiratory virus infections worsen measles severity in ferrets and that antiviral treatment can mitigate immune amnesia and disease outcomes regardless of treatment timing.

Within-host rhinovirus evolution in upper and lower respiratory tract highlights capsid variability and mutation-independent compartmentalization

This study tracks HRV evolution in immunocompromised patients, finding no genetic adaptation for URT to LRT progression and highlighting capsid variability and mutation-independent compartmentalization.

Treponema pallidum subsp. pallidum with an Artificially Impaired TprK Antigenic Variation System is Attenuated in the Rabbit Model of Syphilis

This study creates a T. pallidum strain with impaired TprK antigenic variation and shows it is attenuated in a rabbit syphilis model.

Paxlovid-like nirmatrelvir/ritonavir fails to block SARS-CoV-2 transmission in ferrets

This study compares the efficacy of paxlovid and molnupiravir in preventing SARS-CoV-2 transmission in ferrets, finding that molnupiravir reduces transmission while paxlovid does not.

High-throughput nanopore sequencing of Treponema pallidum tandem repeat genes arp and tp0470 reveals clade-specific patterns and recapitulates global whole genome phylogeny

The paper uses nanopore sequencing to analyze repeat regions in T. pallidum genes, revealing clade-specific patterns that align with whole genome phylogeny.

Narrow transmission bottlenecks and limited within-host viral diversity during a SARS-CoV-2 outbreak on a fishing boat

This study investigates SARS-CoV-2 transmission on a fishing boat, finding low within-host viral diversity and limited viral evolution during the outbreak.

SARS-CoV-2 variant of concern type and biological sex affect efficacy of molnupiravir in dwarf hamster model of severe COVID-19

This study evaluates molnupiravir efficacy against SARS-CoV-2 variants in different models, finding VOC-dependent efficacy and sex-based differences in dwarf hamsters.

Replicating RNA platform enables rapid response to the SARS-CoV-2 Omicron variant and elicits enhanced protection in naïve hamsters compared to ancestral vaccine

A bifluorescent-based assay for the identification of neutralizing antibodies against SARS-CoV-2 variants of concern in vitro and in vivo

This paper develops a bifluorescent-based assay to identify neutralizing antibodies against SARS-CoV-2 variants in vitro and in vivo, showing it accurately reflects viral neutralization.

Longitudinal accumulation of in vivo and in vitro-grown Treponema pallidum subsp. pallidum TprK variants in the presence and absence of immune pressure

This study shows that T. pallidum generates TprK sequence diversity both under immune pressure and in vitro without immune selection, highlighting the role of gene conversion in antigenic variation.

SARS-CoV-2 B.1.1.7 and B.1.351 variants of concern induce lethal disease in K18-hACE2 transgenic mice despite convalescent plasma therapy

This study compares the pathogenicity and immune response of SARS-CoV-2 variants B.1.1.7 and B.1.351 with WA-1 in mice, showing reduced protection from convalescent plasma against the variants.

In vivo generation of BK and JC polyomavirus defective viral genomes in human urine samples associated with higher viral loads

The paper identifies defective viral genomes (DVGs) in clinical urine samples of BK and JC polyomaviruses, showing their association with higher viral loads and genomic rearrangements.

A human coronavirus evolves antigenically to escape antibody immunity

This study shows that human coronavirus 229E evolves antigenically to escape antibody immunity, suggesting the need for periodic vaccine updates.

Rapid adaptation to human protein kinase R by a unique genomic rearrangement in rhesus cytomegalovirus.

This paper shows that RhCMV adapts to human PKR by acquiring a genomic duplication that enhances rTRS1 expression and PKR pathway inhibition, improving replication in human cells.

Estimation of Full-Length TprK Diversity in Treponema pallidum subspecies pallidum

This study uses deep sequencing to characterize full-length TprK diversity in T. pallidum strains from human infections, revealing near-complete sequence divergence and estimating high antigenic variation potential.

In vivo antiviral host response to SARS-CoV-2 by viral load, sex, and age

This study examines how SARS-CoV-2 induces antiviral host responses, showing differences by viral load, age, and sex in gene expression profiles from infected individuals.

SARS-CoV-2 ORF6 disrupts nucleocytoplasmic transport through interactions with Rae1 and Nup98

This paper shows SARS-CoV-2 ORF6 interacts with Rae1 and Nup98 to disrupt nucleocytoplasmic transport, reducing reporter expression and causing nuclear mRNA accumulation, more strongly than SARS-CoV ORF6.

Comparative Genomics and Full-Length TprK Profiling of Treponema pallidum subsp. pallidum Reinfection

The paper compares genomic sequences and full-length TprK profiles of two T. pallidum isolates from the same patient to understand reinfection genetics and immune evasion mechanisms.

DIRECT RT-qPCR DETECTION OF SARS-CoV-2 RNA FROM PATIENT NASOPHARYNGEAL SWABS WITHOUT AN RNA EXTRACTION STEP

This paper tests a direct RT-qPCR method for detecting SARS-CoV-2 RNA in nasal swabs without RNA extraction, achieving 92% accuracy on blinded samples.

A comparative 'omics approach to candidate pathogenicity factor discovery in the brain-eating amoeba Naegleria fowleri

This study uses -omics approaches to identify candidate pathogenicity factors in Naegleria fowleri by comparing it to its non-pathogenic relative Naegleria gruberi.

Sensitive detection of highly fragmented cytomegalovirus nucleic acid in human cfDNA

The paper detects highly fragmented CMV nucleic acid in maternal cfDNA and shows its distinct fragment length distribution compared to human cfDNA, which may explain discrepancies in qPCR measurements.

Inactivation of genes in oxidative respiration and iron acquisition pathways in pediatric clinical isolates of small-colony variant Enterobactericeae

This study identifies genetic lesions in oxidative respiration and iron acquisition pathways in small-colony variant (SCV) clinical isolates of Gram-negative bacteria, showing their role in virulence attenuation and persistence in vivo.

A novel qacA allele results in an elevated chlorhexidine gluconate minimum inhibitory concentration in cutaneous Staphylococcus epidermidis isolates

The paper identifies a novel qacA allele, qacA4, associated with elevated chlorhexidine gluconate MICs in Staphylococcus epidermidis isolates from pediatric oncology patients.

Cooperating H3N2 influenza virus variants are not detectable in primary clinical samples

The paper investigates whether a cooperative mutation in H3N2 influenza virus, observed in cell culture, is present in unpassaged clinical samples using deep sequencing.

Validation and Implementation of CLIA-Compliant Whole Genome Sequencing (WGS) in Public Health Laboratory

This paper validates whole genome sequencing in public health labs according to CLIA guidelines and develops tools for quality assurance and reporting.