An Exploratory Bioinformatic Investigation of Cats’ Susceptibility to Coronavirus-Deriving Epitopes

Coronaviruses are highly transmissible and pathogenic viruses for humans and animals. The vast quantity of information collected about SARS-CoV-2 during the pandemic helped to unveil details of the mechanisms behind the infection, which are still largely elusive. Recent research demonstrated that different class I/II human leukocyte antigen (HLA) alleles might define an individual susceptibility to SARS-CoV-2 spreading, contributing to the differences in the distribution of the infection through different populations; additional studies suggested that the homolog of the HLA in cats, the feline leukocyte antigen (FLA), plays a pivotal role in the transmission of viruses. With these premises, this study aimed to exploit a bioinformatic approach for the prediction of the transmissibility potential of two distinct feline coronaviruses (FCoVs) in domestic cats (feline enteric coronavirus (FeCV) and feline infectious peritonitis virus (FIPV)) using SARS-CoV-2 as the reference model. We performed an epitope mapping of nonapeptides deriving from SARS-CoV-2, FeCV, and FIPV glycoproteins and predicted their affinities for different alleles included in the three main loci in class I FLAs (E, H, and K). The predicted complexes with the most promising affinities were then subjected to molecular docking and molecular dynamics simulations to provide insights into the stability and binding energies in the cleft. Results showed the FLA proteins encoded by alleles in the FLA-I H (H*00501 and H*00401) and E (E*01001 and E*00701) loci are largely responsive to several epitopes deriving from replicase and spike proteins of the analyzed coronaviruses. The analysis of the most affine epitope sequences resulting from the prediction can stimulate the development of anti-FCoV immunomodulatory strategies based on peptide drugs

Coronaviruses Research in BRICS Countries

SARS-CoV-2 has infected more than 105 million people worldwide. During this pandemic, researchers and clinicians have been working to understand the molecular mechanisms that underpin viral pathogenesis by studying viral–host interactions. Now, with the global rollout of various COVID-19 vaccines—based on the neutralization of the spike protein using different technologies—viral immunology and cell-based immunity are being investigated. Researchers are also studying how various SARS-CoV-2 genetic mutations will impact the efficacy of these COVID-19 vaccines. At the same time, various antiviral drugs have been identified or repurposed that have potential as anti-SARS-CoV-2 treatments. BRICS (Brazil, Russia, India, China, and South Africa) is the acronym used to associate five major emerging national economies. The BRICS countries are known for their significant influence on regional affairs, including being leaders in scientific and clinical research and innovation. This Special Issue includes researchers from BRICS countries, in particular South Africa, involved in the study of SARS-CoV-2 and COVID-19. Original articles, as well as new perspectives or reviews on the matter, were welcomed. Research in the fields of vaccine studies, pathogenesis, genetic mutations, viral immunology, and antiviral drugs were especially encouraged

Computational and Molecular Biology Approaches to Viral Replication and Pathogenesis

The primary objective of this dissertation was to combine the power of bioinformatics with synthetic genomics, reverse genetics, and molecular genetic approaches to generate a platform technology, with which to empirically test well-informed hypotheses towards understanding complex mechanisms of viral pathogenesis and replication. This integrative strategy was used to: 1) identify unique sequence signatures that were associated with aberrant or altered gene function, focusing on replicase and structural proteins of the Coronavirus family and the capsid protein of the Norovirus family; 2) use these sequence signatures to generate hypotheses and predictions about gene function or evolution; and then 3) empirically test these models using reverse genetics, synthetic biology, molecular genetics, and biochemistry in the laboratory setting. Applying this integrative strategy allowed us to generate three informative models. First, we generated an informative model for the pleiotropic role of a Coronavirus non-structural protein 10 in replication and proteolytic processing, by demonstrating that this protein regulates RNA transcription during replication, in addition to an essential role in polyprotein processing. Second, we demonstrated that the receptor-binding domain of the Coronavirus spike protein is the minimal domain requiring adaptation for host range switching, which helps explain the evolutionary epidemiology of SARS-CoV emergence from zoonotic reservoirs. And finally, we generated an informative model for the molecular mechanisms governing the persistence of the GII.4 noroviruses in human populations, whereby we demonstrated that these viruses persist by evolving unique epitopes on the capsid protein surface to circumvent herd immunity and mediate receptor switching

Advances in Parvovirus Research 2020

Viruses of the Parvoviridae family constitute a most diverse and intriguing field of research. Parvoviruses can differ widely in their structure, genome organization and expression, virus–cell interactions, and impact on hosts. The translational implication of research on parvoviruses is relevant, since many viruses are important human and veterinary pathogens, while other viruses can be engineered as tools for oncolytic therapy or as sophisticated gene delivery vectors. Exploring the diversity and inherent complexity in the biology of these apparently simple viruses is a still challenging topic for the scientific community. The Special Issue of Viruses is a collection of recent contributions in the field of parvovirus research, encompassing many aspects of basic and translational research on viruses of the family Parvoviridae, including on their structure, replication, and gene expression in addition to virus–host interactions and the development of vaccines and viral vectors

One Health EJP Annual Scientific Meeting 2021 ; 9-11 June in Copenhagen, Denmark and online: Abstract Book

This event is organized by the European Joint Programme One Health EJP, which has received funding from the European Union’s Horizon 2020 research and innovation programme under Grant Agreement No 773830

Fleas of fleas: The potential role of bacteriophages in Salmonella diversity and pathogenicity.

Non-typhoidal salmonellosis is an important foodborne and zoonotic infection, that causes significant global public health concern. Diverse serovars are multidrug-resistant and encode several virulence indicators, however, little is known on the role prophages play in driving these characteristics. Here, we extracted prophages from 75 Salmonella genomes, which represent the 15 most important serovars in the United Kingdom. We analysed the genomes of the intact prophages for the presence of virulence factors which were associated with; diversity, evolution and pathogenicity of Salmonella and to establish their genomic relationships. We identified 615 prophage elements from the Salmonella genomes, from which 195 prophages are intact, 332 being incomplete while 88 are questionable. The average prophage carriage was found to be more prevalent in S. Heidelberg, S. Inverness and S. Newport (10.2-11.6 prophages/strain), compared to S. Infantis, S. Stanley, S. Typhimurium and S. Virchow (8.2-9 prophages/strain) and S. Agona, S. Braenderup, S. Bovismorbificans, S. Choleraesuis, S. Dublin, and S. Java (6-7.8 prophages/strain), and S. Javiana and S. Enteritidis (5.8 prophages/strain). Cumulatively, 2760 virulence factors were detected from the intact prophages and associated with cellular functionality being linked to effector delivery/secretion system (73%), adherence (22%), magnesium uptake (2.7%), resistance to antimicrobial peptides (0.94%), stress/survival (0.4%), exotoxins (0.32%) and antivirulence (0.18%). Close and distant clusters were formed among the prophage genomes suggesting different lineages and associations with bacteriophages of other Enterobacteriaceae. We show that diverse repertoire of Salmonella prophages are associated with numerous virulence factors, and may contribute to diversity, pathogenicity and success of specific serovars

Fleas of fleas: The potential role of bacteriophages in Salmonella diversity and pathogenicity.

Non-typhoidal salmonellosis is an important foodborne and zoonotic infection, that causes significant global public health concern. Diverse serovars are multidrug-resistant and encode several virulence indicators, however, little is known on the role prophages play in driving these characteristics. Here, we extracted prophages from 75 Salmonella genomes, which represent the 15 most important serovars in the United Kingdom. We analysed the genomes of the intact prophages for the presence of virulence factors which were associated with; diversity, evolution and pathogenicity of Salmonella and to establish their genomic relationships. We identified 615 prophage elements from the Salmonella genomes, from which 195 prophages are intact, 332 being incomplete while 88 are questionable. The average prophage carriage was found to be more prevalent in S. Heidelberg, S. Inverness and S. Newport (10.2-11.6 prophages/strain), compared to S. Infantis, S. Stanley, S. Typhimurium and S. Virchow (8.2-9 prophages/strain) and S. Agona, S. Braenderup, S. Bovismorbificans, S. Choleraesuis, S. Dublin, and S. Java (6-7.8 prophages/strain), and S. Javiana and S. Enteritidis (5.8 prophages/strain). Cumulatively, 2760 virulence factors were detected from the intact prophages and associated with cellular functionality being linked to effector delivery/secretion system (73%), adherence (22%), magnesium uptake (2.7%), resistance to antimicrobial peptides (0.94%), stress/survival (0.4%), exotoxins (0.32%) and antivirulence (0.18%). Close and distant clusters were formed among the prophage genomes suggesting different lineages and associations with bacteriophages of other Enterobacteriaceae. We show that diverse repertoire of Salmonella prophages are associated with numerous virulence factors, and may contribute to diversity, pathogenicity and success of specific serovars

Emerg Infect Dis

Emerging Infectious Diseases is providing access to these abstracts on behalf of the ICEID 2022 program committee (http://www.iceid.org), which performed peer review. ICEID is organized by the Centers for Disease Control and Prevention and Task Force for Global Health, Inc.Emerging Infectious Diseases has not edited or proofread these materials and is not responsible for inaccuracies or omissions. All information is subject to change. Comments and corrections should be brought to the attention of the authors.Suggested citation: Authors. Title [abstract]. International Conference on Emerging Infectious Diseases 2022 poster and oral presentation abstracts. Emerg Infect Dis. 2022 Sep [date cited]. http://www.cdc.gov/EID/pdfs/ICEID2022.pdf2022PMC94238981187

A Meeting of Minds: In Recognition of the Contributions of Randall J. Cohrs

A Special Issue in memory of Randall J. Cohrs, Ph.D. Topics include original research reports on a variety of viruses as well as reviews and commentaries on Randy’s contributions to many investigations