Biology subjects

Ogando, N. S.

Publications and source records attributed to Ogando, N. S..

4 recordsLinked to original sources

bioRxiv2026

Progressive Post-Acute Gut Microbiome Disruption Following SARS-CoV-2 Infection in Mice

SARS-CoV-2 infection is increasingly recognized to produce long-lasting physiological disturbances that extend beyond the acute phase. The gut microbiome has emerged as a potential contributor to post-infection outcomes, yet the longitudinal progression of microbial disruption following infection remains poorly defined. Here, we used a mouse model of SARS-CoV-2 infection to characterize gut microbiome dynamics at 7 (late acute phase), 14 (early recovery), and 21 (post-COVID condition, PCC) days post-infection (dpi). Viral RNA was detected in the lungs through 21 dpi. Longitudinal microbiome profiling revealed a two-phase restructuring marked by early shifts in Bacillota and Bacteroidota abundance, followed by pronounced post-acute dysbiosis characterized by reduced diversity, expansion of Bacillota, and near-complete loss of Bacteroidota. Functional pathway predictions showed progressive metabolic remodeling, including disruptions in nucleotide turnover, fermentation, and vitamin-related pathways. Together, these findings demonstrate that SARS-CoV-2 infection drives progressive and sustained alterations in gut microbial composition and function after the transition from acute infection through recovery into PCC.

microbiology↗

bioRxiv2021

Structure-function analysis of the nsp14 N7-guanine methyltransferase reveals an essential role in betacoronavirus replication

As coronaviruses (CoVs) replicate in the host cell cytoplasm, they rely on their own capping machinery to ensure the efficient translation of their mRNAs, protect them from degradation by cellular 5 exoribonucleases, and escape innate immune sensing. The CoV nonstructural protein 14 (nsp14) is a bi-functional replicase subunit harboring an N-terminal 3'-to-5' exoribonuclease (ExoN) domain and a C-terminal (N7-guanine)-methyltransferase (N7-MTase) domain that is presumably involved in viral mRNA capping. Here, we aimed to integrate structural, biochemical, and virological data to assess the importance of conserved N7-MTase residues for nsp14s enzymatic activities and virus viability. We revisited the crystal structure of severe acute respiratory syndrome (SARS)-CoV nsp14 to perform an in silico comparative analysis between betacoronaviruses. We identified several residues likely involved in the formation of the N7-MTase catalytic pocket, which presents a fold distinct from the Rossmann fold observed in most known MTases. Next, for SARS-CoV and Middle East respiratory syndrome-CoV, site-directed mutagenesis of selected residues was used to assess their importance for in vitro enzymatic activity. Most of the engineered mutations abolished N7-MTase activity, while not affecting nsp14-ExoN activity. Upon reverse engineering of these mutations into different betacoronavirus genomes, we identified two substitutions (R310A and F426A in SARS-CoV nsp14) abrogating virus viability and one mutation (H424A) yielding a crippled phenotype across all viruses tested. Our results identify the N7-MTase as a critical enzyme for betacoronavirus replication and define key residues of its catalytic pocket that can be targeted to design inhibitors with a potential pan-coronaviral activity spectrum. Significance StatementThe ongoing SARS-CoV-2 pandemic emphasizes the urgent need to develop efficient broad-spectrum anti-CoV drugs. The structure-function characterization of conserved CoV replicative enzymes is key to identifying the most suitable drug targets. Using a multidisciplinary comparative approach and different betacoronaviruses, we characterized the key conserved residues of the nsp14 (N7-guanine)-methyltransferase, a poorly defined subunit of the CoV mRNA-synthesizing machinery. Our study highlights the unique structural features of this enzyme and establishes its essential role in betacoronavirus replication, while identifying two residues that are critical for the replication of the four betacoronaviruses tested, including SARS-CoV-2.

molecular biology↗

bioRxiv2020

Genome-wide mapping of therapeutically-relevant SARS-CoV-2 RNA structures

SARS-CoV-2 is a betacoronavirus with a linear single-stranded, positive-sense RNA genome of [~]30 kb, whose outbreak caused the still ongoing COVID-19 pandemic. The ability of coronaviruses to rapidly evolve, adapt, and cross species barriers makes the development of effective and durable therapeutic strategies a challenging and urgent need. As for other RNA viruses, genomic RNA structures are expected to play crucial roles in several steps of the coronavirus replication cycle. Despite this, only a handful of functionally conserved structural elements within coronavirus RNA genomes have been identified to date. Here, we performed RNA structure probing by SHAPE-MaP to obtain a single-base resolution secondary structure map of the full SARS-CoV-2 coronavirus genome. The SHAPE-MaP probing data recapitulate the previously described coronavirus RNA elements (5' UTR, ribosomal frameshifting element, and 3' UTR), and reveal new structures. Secondary structure-restrained 3D modeling of highly-structured regions across the SARS-CoV-2 genome allowed for the identification of several putative druggable pockets. Furthermore, [~]8% of the identified structure elements show significant covariation among SARS-CoV-2 and other coronaviruses, hinting at their functionally-conserved role. In addition, we identify a set of persistently single-stranded regions having high sequence conservation, suitable for the development of antisense oligonucleotide therapeutics. Collectively, our work lays the foundation for the development of innovative RNA-targeted therapeutic strategies to fight SARS-related infections.

genetics↗

bioRxiv2020

Suramin inhibits SARS-CoV-2 infection in cell culture by interfering with early steps of the replication cycle

The SARS-CoV-2 pandemic that originated from Wuhan, China, in December 2019 has impacted public health, society and economy and the daily lives of billions of people in an unprecedented manner. There are currently no specific registered antiviral drugs to treat or prevent SARS-CoV-2 infections. Therefore, drug repurposing would be the fastest route to provide at least a temporary solution while better, more specific drugs are being developed. Here we demonstrate that the antiparasitic drug suramin inhibits SARS-CoV-2 replication, protecting Vero E6 cells with an EC50 of [~]20 {micro}M, which is well below the maximum attainable level in human serum. Suramin also decreased the viral load by 2-3 logs when Vero E6 cells or cells of a human lung epithelial cell line (Calu-3) were treated. Time of addition and plaque reduction assays showed that suramin acts on early steps of the replication cycle, possibly preventing entry of the virus. In a primary human airway epithelial cell culture model, suramin also inhibited the progression of infection. The results of our preclinical study warrant further investigation and suggest it is worth evaluating whether suramin provides any benefit for COVID-19 patients, which obviously requires well-designed, properly controlled randomized clinical trials.

microbiology↗