Biology subjects

Shah, A. U.

Publications and source records attributed to Shah, A. U..

5 recordsLinked to original sources

bioRxiv2026

Integrated epidemiological and genomic analysis of some respiratory Bovine Coronavirus isolates reveals circulation of GIIb strains and ongoing viral evolution in U.S. Cattle (2020-2025)

Bovine coronavirus (BCoV) is an important contributor to the respiratory disease complex in cattle; however, integrated genomic and epidemiological data describing currently circulating respiratory BCoV strains in the United States remain limited. The objective of this study was to monitor respiratory BCoV at the genomic level and analyze its epidemiological patterns over a five-year period. A total of 4,505 respiratory samples submitted to a diagnostic laboratory between January 2020 and November 2025 were analyzed, of which 693 (15.38%) tested positive for BCoV. Positivity was highest in young calves (0-40 days; 20.0%) and declined significantly with increasing age based on logistic regression analysis. Temporal trend analysis using LOESS smoothing and the Mann-Kendall test showed no significant monotonic change in BCoV detection during the study period. Co-infection analysis indicated that BCoV was commonly detected with other viral respiratory pathogens, while bacterial pathogens predominated in many samples. Lung tissues from infected cattle were screened by RT-PCR, and selected samples with high viral loads were subjected to next-generation sequencing. Complete genome sequencing identified four respiratory BCoV isolates ([~]31 kb), all clustering within genotype GIIb with recent U.S. strains. Comparative genomic analysis revealed several amino acid substitutions in structural and non-structural proteins that may influence viral attachment, replication, and tissue tropism. These findings provide updated epidemiological and genomic insights into respiratory BCoV circulating in U.S. cattle.

microbiology↗

bioRxiv2024

Applications of some artificial intelligence tools in the drug design of some compounds targeting the main viral protease of the Feline Infectious Peritonitis Virus (FIPV) in cats

Feline infectious peritonitis virus (FIPV) is one of cats most serious viral infections. The FIPV infection induces a complicated syndrome in the affected cats, including immunosuppression and severe inflammatory conditions. Unfortunately, these vaccines cannot prevent cats from getting infected with these viral infections. There is ongoing research on preparing antiviral therapies against FIPV in cats. However, these are still in clinical trials and have not been fully approved by the drug authorities in many countries, including the USA. Targeting the main viral proteases is one of the promising trends in the drug design of many viral diseases, including coronaviruses. The main goal of the current study was to repurpose and test the efficacy of some known antiviral drugs to treat FIPV infection in cats by targeting the FIPV-main protease enzyme. To achieve these goals, we used the in-silico prediction and molecular docking tools to screen and identify some drugs targeting FIPV-MPro. We used the docking and binding energies as the main parameters for selecting target compounds (FIPV-MPro). Our results show that out of the 15 antiviral and immunomodulatory compounds, the top-ranked inhibitors for the FIPV-Mpro are (Michael acceptor inhibitors (N3), Sofosbuvir, and methotrexate).In conclusion, our results confirmed the potential applications of the predicted FIPV-Mpro inhibitors either independently or in combination with other immune-modulatory compounds. Further in vitro and in vivo studies are encouraged to test the efficacy of these identified compounds as potent inhibitors for the MPro of the FIPV in cats. This study will pave the way for the development of novel drugs that treat FIPV infection in cats.

microbiology↗

bioRxiv2024

Isolation and molecular characterization of an enteric isolate of the Genotype-I Bovine coronavirus with notable mutations in the receptor binding domain of the spike glycoprotein and deletion downstream the RNA binding domain of the nucleocapsid protein.

Bovine coronavirus (BCoV) continues to be a significant threat to cattle populations despite the implementation of vaccination programs. The continuous circulation of BCoV highlights the necessity for ongoing genomic surveillance to understand better the viruss evolution and its impact on cattle health. The main goal of this study was to do isolation and perform a comprehensive molecular characterization of a new enteric field isolate of the BCoV. To identify any genetic elements in the sequences of this BCoV isolate that could act as genetic markers for BCoV infection in cattle. To achieve these objectives, the newly identified BCoV isolate was propagated on the MDBK cell line for several subsequent blind passages. The immunofluorescence assay verified confirmation of the virus propagation. We plaque purified this isolate and titrated it by plaque assay using the HRT-18 cell line. We examined the viral protein expression using the SDS-PAGE followed by the Western blot using the BCoV/S and BCoV/N and BCoV/S antibodies. Our results show a substantial increase in the viral genome copy number, protein expression, and virus infectivity of this BCoV isolate with the increase in cell culture passages. The full-length genome sequence of this isolate using the NGS was drafted. The vial genome is 31 Kb in length. The viral genome has the typical BCoV organization (5-UTR-Gene- 1- HE-S-M-E-N-UTR-3). Our phylogenetic analysis based on the nucleotide sequences of the (full-length genome, S, HE, and N) showed that the BCoV-13 clustered with other members of the BCoV (genotype I-i). The sequence analysis shows several synonymous mutations among various domains of the S glycoprotein, especially the receptor binding domain. We found nine notable nucleotide deletions immediately downstream of the RNA binding domain of the nucleocapsid gene. Further gene function studies are encouraged to study the function of these mutations on the BCoV molecular pathogenesis and immune regulation/evasion. This research enhances our understanding of BCoV genomics and contributes to improved diagnostic and control measures for BCoV infections in cattle populations.

microbiology↗

bioRxiv2024

The Ex Vivo Infection of the Peripheral Bovine Mononuclear Cells (PBMCs) and the Bovine Spleen Cells with the Bovine Coronavirus (BCoV) Induced a Differential Expression of the Host Cytokine Genes Profiles and Modulates the Virus Replication

The adaptive immune response during BCoV infection of peripheral blood mononuclear cells (PBMCs), the bovine spleen cells, and their isolated T lymphocytes was not studied well. Our study confirmed successful BCoV infection in PBMCs and spleen T cells. This was evidenced by measuring genome copy numbers using real-time PCR, expression levels of BCoV spike and nucleocapsid proteins via western blot and immunofluorescence assays, and virus infectivity titration by plaque assay. In infected PBMCs, CD4 T-cell levels were 1.45-fold higher, and CD8 T-cell levels were 1.6-fold lower compared to sham-infected cells. Conversely, infected splenocytes showed a 0.88-fold decrease in CD4 T-cells and a 1.88-fold increase in CD8 T-cells. The cytokine gene expression analysis revealed that BCoV infection activated type 1 interferon and upregulated IL-6 expression in PBMCs and splenocytes. These findings demonstrate that BCoV successfully infects immune cells from PBMCs and spleen, inducing differential host cytokine gene expression favors virus replication.

microbiology↗

bioRxiv2024

The dual actions of the host miRNA-16a in restricting Bovine coronavirus (BCoV) replication through targeting host cell Furin and in enhancing the host immune response.

1.The roles of host cell miRNAs have not been studied well in the context of BCoV replication and immune regulation. The main aim of this study was to identify some miRNA candidates that regulate essential host genes involved in BCoV replication, tissue tropism, and immune regulation. To achieve these goals, we used two isolates of BCoV (enteric and respiratory) to infect the bovine endothelial cells (BEC) and Madine Darby Bovine Kidney (MDBK) cells. This is in addition to the ex vivo model using the peripheral bovine blood mononuclear cells (PBMC). We determined the miRNA expression profiles in these cells after BCoV infection. miRA-16a is one of the differentially altered during BCoV infection. Our data shows that miRNA-16a is a significantly downregulated miRNA in both in vitro and ex vivo models. We confirmed the miRNA-16a expression profile by the qRT-PCR. Overexpression of the pre-miRNA-16a in BEC and MDBK cell lines resulted in marked inhibition of BCoV infection based on the viral genome copy numbers measured by qRT-PCR, the viral protein expression (S and N) measured by Western blot, and the virus infectivity using plaque assay. Our bioinformatic prediction showed that Furin is a potential target for the miRNA-16a. We checked the Furin protein expression level in the pre-miRNA-16a transfected/BCoV infected cells compared to the pre-miRNA scrambled to validate that. Our data shows marked inhibition of the Furin expression levels on the mRNA levels by qRT-PCR and the protein level by Western blot. The BCoV-S protein expression was markedly inhibited on both the mRNA and protein levels. To further confirm the impacts of the downregulation of the Furin enzyme on the replication of BCoV, we used transfected cells with specific Furin-siRNA parallel to the scrambled siRNA. A marked inhibition of BCoV replication was observed in the Furin-siRNA-treated group. To further validate Furin as a novel target for miRNA-16a, we cloned the 3UTR of the bovine Furin carrying the seed region of the miRNA-16a in the dual luciferase vector. Our data shows luciferase activity in the pre-miRNA-16a transfected cells decreased by more than 50% compared to the cells transfected with the construct carrying the mutated Furin seed region. Our data confirms miRNA-16a inhibits BCoV replication by targeting the host cell Furin and the BCoV-S glycoprotein. It will also enhance the host immune response, which contributes to the inhibition of viral replication. To our knowledge, this is the first study to confirm that Furin is a valid target for the miRNA-16a. Our findings highlight the clinical applications of the host miRNA-16a as a potential miRNA-based vaccine/antiviral therapy.

microbiology↗