Biology subjects

Relich, R. F.

Publications and source records attributed to Relich, R. F..

8 recordsLinked to original sources

bioRxiv2026

Repurposing antiviral drugs as a new avenue for Klebsiella pneumoniae decolonization

Klebsiella pneumoniae (Kp) is a common antibiotic-resistant pathogen that colonizes the gastrointestinal tract and can disseminate to peripheral sites, causing a range of infections including bacteremia, urinary tract infections, and pneumonia. Intestinal colonization with Kp is a risk factor for subsequent infection, as the colonizing strain frequently corresponds to the infecting isolate. Accordingly, targeting Kp prior to dissemination at the site of colonization through decolonization strategies offers a promising approach to mitigate infection risk. In this study, we evaluated the repurposing of existing drugs with previously uncharacterized antibacterial activity as candidates for Kp decolonization. To this end, we screened an antiviral compound library for their activity against Kp. We identified and validated six compounds with previously uncharacterized activity against Kp. Then, we screened a library of clinical Kp strains against a subset of these compounds and found that their activity was strain-specific to degrees that differed based on the compound. Finally, we tested the activity of these compounds in conditions relevant to the human gut. We determined the activity of these candidates was dependent on biological context. Collectively, these findings support further investigation of antiviral drugs as potential gut decolonization therapies for Kp.

microbiology↗

bioRxiv2026

A novel antiviral strategy targeting human metapneumovirus through pH modulation in human airway epithelial cells

Human metapneumovirus (hMPV) is a major cause of respiratory infections, particularly among infants, older adults, and immunocompromised individuals, yet no approved vaccines or targeted antiviral therapies are currently available. pH-regulated processes, including airway epithelial physiology, endosomal acidification, and viral fusion mediated by the fusion (F) protein, are critical for hMPV infection. This study evaluates PHOH-001, an inhaled alkaline buffer, as a potential therapeutic strategy to modulate airway epithelial pH and inhibit hMPV infection. Using a recombinant hMPV expressing green fluorescent protein (rhMPV-GFP), viral replication was assessed in primary human airway epithelial cells (HAECs). PHOH-001 significantly reduced GFP expression at 72 hours post-infection in both submerged and air-liquid interface (ALI) cultures, with effects comparable to those of the endosomal acidification inhibitor bafilomycin A1. In Vero E6 cells, used as a mechanistic in vitro model, PHOH-001 increased extracellular and intracellular pH in a concentration-dependent manner and correspondingly reduced hMPV infection. In HAECs, PHOH-001 reduced viral replication, as measured by TCID50 assays of infectious virus, and inhibited syncytium formation, a key step in viral spread. Furthermore, PHOH-001 altered F protein localization and was associated with changes in actin organization, consistent with impaired viral spread. Collectively, these findings demonstrate that PHOH-001 alters multiple pH-dependent steps in hMPV infection in vitro and support airway pH modulation as a potential antiviral strategy against hMPV.

molecular biology↗

bioRxiv2026

ThermiQuant(TM) MegaScan: High-throughput isothermal reactor with quantitative colorimetric readout for paper-based nucleic acid amplification tests

Isothermal nucleic acid amplification tests (NAATs), such as loop-mediated isothermal amplification (LAMP) implemented on microfluidic paper-based analytical devices ({micro}PADs), enable inexpensive and rapid ([≤]60 min) colorimetric molecular diagnostics; however, no existing instrument supports high-throughput (>100 reactions) quantitative analysis of colorimetric isothermal assays on paper substrates under controlled laboratory conditions. To address this gap, we developed ThermiQuant MegaScan, a scanner- and water-bath-based platform that accommodates a 160-reaction {micro}PAD cartridge, maintains uniform incubation at 65 {+/-} 0.5 {degrees}C, and enables real-time imaging every 30 s. We also developed accompanying software, Amplimetrics, for automated {micro}PAD detection and kinetic colorimetric analysis. Using paper-based colorimetric LAMP targeting the SARS-CoV-2 orf7ab region, the assay achieved a limit of detection at 95% probability (LOD95) of 34 copies per reaction (5 copies/{micro}L) and a limit of quantification (LOQ) of 250 copies per reaction (33 copies/{micro}L) using purified synthetic DNA targets, and achieved 72% sensitivity and 100% specificity relative to digital PCR (dPCR) for diluted human nasopharyngeal (NP) swab virus samples. We further evaluated the effects of viral and universal transport media (VTM/UTM) on assay performance and found that linear calibration derived from synthetic targets do not reliably translate to clinical samples in these media. Together, these results establish ThermiQuant MegaScan as a high-throughput laboratory research platform for standardized evaluation, optimization, and benchmarking of paper-based colorimetric nucleic acid amplification assays.

bioengineering↗

bioRxiv2025

Pseudomonas aeruginosa phenazines dictate site-specific competitive interactions with Klebsiella pneumoniae

Pseudomonas aeruginosa and Klebsiella pneumoniae are Gram-negative opportunistic pathogens that frequently colonize the human body and are major causes of infection. These bacteria are often co-isolated in polymicrobial urinary tract and lung infections, the latter of which is associated with increased disease severity and worse clinical outcomes. Despite their overlapping niches and clinical relevance, little is known about how these two pathogens interact and how those interactions influence human health. Given the growing recognition that microbial interactions are key drivers of disease, we investigated how P. aeruginosa and K. pneumoniae influence one another. We discovered an antagonistic interaction in which P. aeruginosa restricts the growth of K. pneumoniae. This inhibition is driven by phenazine production in P. aeruginosa, specifically the secondary metabolites pyocyanin and pyorubin, which are both necessary and sufficient to suppress K. pneumoniae growth. Using a diverse set of clinical isolates, we found that this antagonism is strain dependent. Both the susceptibility of K. pneumoniae to phenazines and the ability of P. aeruginosa to restrict K. pneumoniae growth varies between strains. Moreover, the necessity of phenazine production is specific to the site of infection. Together, these findings demonstrate that strain background and environmental context are critical determinants of pathogen interactions. Our work underscores the importance of considering these variables when investigating how microbial interactions influence infection and disease outcomes.

microbiology↗

bioRxiv2025

229E- and NL63-like coronaviruses in phyllostomid bats, Belize

We report novel and previously identified alphacoronavirus (-CoV) diversity in three phyllostomid bat species (Desmodus rotundus, Carollia sowelli, and Sturnira parvidens) in Belize. Phylogenetic analysis suggests strong similarity between two Neotropical bat -CoV lineages and human CoVs (229E and NL63) compared to prior bat -CoVs.

ecology↗

bioRxiv2021

Serum from COVID-19 patients early in the pandemic shows limited evidence of cross-neutralization against variants of concern

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) results in a variety of clinical symptoms ranging from no or mild to severe disease. Currently, there are multiple postulated mechanisms that may push a moderate to severe disease into a critical state. Human serum contains abundant evidence of the immune status following infection. Cytokines, chemokines, and antibodies can be assayed to determine the extent to which a patient responded to a pathogen. We examined serum and plasma from a cohort of patients infected with SARS-CoV-2 early in the pandemic and compared them to negative-control sera. Cytokine and chemokine concentrations varied depending on the severity of infection, and antibody responses were significantly increased in severe cases compared to mild to moderate infections. Neutralization data revealed that patients with high titers against an early 2020 isolate had detectable but limited neutralizing antibodies against newly circulating SARS-CoV-2 variants of concern. This study highlights the potential of re-infection for recovered COVID-19 patients.

microbiology↗

bioRxiv2020

Selectomic and Evolvability Analyses of the Highly Pathogenic Betacoronaviruses SARS-CoV-2, SARS-CoV, and MERS-CoV

SARS-CoV-2, the causative agent of COVID-19, is widespread in several countries around the world following its late-2019 emergence in the human population. Rapid development of molecular diagnostic tests and subunit vaccines have been prioritized, and as such evaluating the SARS-CoV-2 genomic plasticity and evolutionary dynamics is an urgent need. We determined the SARS-CoV-2 selectome by calculating rates of pervasive and episodic diversifying selection for every amino acid coding position in the SARS-CoV-2 genome. To provide context for evolutionary dynamics of a highly pathogenic betacoronavirus following a zoonotic spillover into human hosts, we also determined the selectomes of SARS-CoV and MERS-CoV, and performed evolvability calculations for SARS-CoV-2 based on SARS-CoV. These analyses identify the amino acid sites within each coding sequence that have been subjected to pervasive diversifying selection or episodic diversifying selection, and report significantly evolvable sites in the ORF1a polyprotein, the spike protein, and the membrane protein of SARS-CoV-2. These findings provide a comprehensive view of zoonotic, highly pathogenic betacoronavirus evolutionary dynamics that can be directly applied to diagnostic assay and vaccine design for SARS-CoV-2.

microbiology↗

bioRxiv2018

Mechanisms of Host Cell Binding and Neurotropism of Zika Virus

Zika virus (ZIKV) recently emerged in the Western Hemisphere with previously unrecognized or unreported clinical presentations. Here, we identify two distinct binding mechanisms of ancestral and emergent ZIKV strains featuring the envelope (E) protein residue ASN154 and viral phosphatidylserine (PS). Short (20-mer) peptides representing the region containing ASN154 from strains PRVABC59 (Puerto Rico 2015) and MR_766 (Uganda 1947) were exposed to neuronal cells and fibroblasts, expecting interactions to be representative of ZIKV E protein/cell interactions, and bound MDCK or Vero cells and primary neurons significantly above a scrambled PRVABC59 control peptide. Peptides also significantly inhibited Vero cell adsorption by ZIKV strains MR_766 and PRVABC59, indicating that we have identified a binding mechanism of ancestral African ZIKV strains and emergent Western Hemisphere strains.\n\nPretreatment of ZIKV MR_766 and PRVABC59 with the PS-binding protein annexin V significantly inhibited replication of PRVABC59, but not MR_766, suggesting that Western hemisphere strains are additionally utilizing PS-mediated entry to infect host cells. Taken together, these data indicate that we have identified an ancestral binding mechanism of ZIKV, and a secondary binding mechanism utilized by Western Hemisphere strains.

microbiology↗