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Virus Bioinformatics 2023

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A special issue of Viruses (ISSN 1999-4915). This special issue belongs to the section "General Virology".

Deadline for manuscript submissions: closed (30 June 2023) | Viewed by 21515

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Special Issue Editors

Dr. Franziska Hufsky

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The European Virus Bioinformatics Center, Friedrich Schiller University Jena, Jena, Germany
Interests: computational metabolomics and mass spectrometry; algorithms in bioinformatics; virus bioinformatics
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Dr. Alba Pérez-Cataluña

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Guest Editor

CSIC - Instituto de Agroquimica y Tecnologia de los Alimentos (IATA), Valencia, Spain
Interests: sewage; food microbiology; fermentation; molecular biology; sanger sequencing; microbial molecular biology
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Prof. Dr. Fernando González-Candelas

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Guest Editor

Unidad Mixta Infección y Salud Pública, Universitat de ValEncia, Valencia, Spain
Interests: molecular evolutionary epidemiology of different pathogens, mainly RNA viruses, such as hepatitis C virus (HCV) and human immunodeficiency virus (HIV), and bacteria, such as Legionella pneumophila, Treponema pallidum, Neisseria gonorrhoeae, Pseudomonas aeruginosa and Klebsiella pneumoniae
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Prof. Dr. Manja Marz

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Guest Editor

The European Virus Bioinformatics Center, Friedrich Schiller University, Jena, Germany
Interests: high throughput sequencing analysis; bioinformatic analysis and system biology of viruses; comparative genomics; identification and annotation of non-coding RNAs; coevolution of proteins and RNAs; algorithmic bioinformatics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue is published alongside the International Virus Bioinformatics Meeting 2023 (ViBioM 2023 https://evbc.uni-jena.de/events/vibiom2023/) taking place in Valencia, Spain, May 24-26, 2023. ViBioM has become synonymous with scientific exchange and dialogue between different disciplines and attracts some of the most influential scientists in virus bioinformatics.

This Special Issue will present original research articles and review papers covering recent advancements and current understanding of computational technology aspects of virology. Scientific results of interdisciplinary research are often difficult to publish in journals in either area. To facilitate publications in the field of virus bioinformatics, the European Virus Bioinformatics Center has been running this recurring special issue since 2019.

We encourage you to publish your work in this Special Issue and present it at ViBioM 2023. However, this is not an obligation for publication.

All papers should be submitted online at https://www.mdpi.com/journal/viruses. Please select the correct Special Issue when submitting your paper to Viruses.

Dr. Franziska Hufsky
Dr. Alba Pérez-Cataluña
Prof. Dr. Fernando González-Candelas
Prof. Dr. Manja Marz
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Viruses is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

virus bioinformatics
software
viral metagenomics and ecology
virus–host interactions
viral diversity and evolution
virus identification

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Published Papers (11 papers)

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Research

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10 pages, 1242 KiB

Open AccessCommunication

Bioinformatic Surveillance Leads to Discovery of Two Novel Putative Bunyaviruses Associated with Black Soldier Fly

by Hunter K. Walt, Emilia Kooienga, Jonathan A. Cammack, Jeffery K. Tomberlin, Heather R. Jordan, Florencia Meyer and Federico G. Hoffmann

Viruses 2023, 15(8), 1654; https://doi.org/10.3390/v15081654 - 29 Jul 2023

Cited by 1 | Viewed by 1265

Abstract

The black soldier fly (Hermetia illucens, BSF) has emerged as an industrial insect of high promise because of its ability to convert organic waste into nutritious feedstock, making it an environmentally sustainable alternative protein source. As global interest rises, rearing efforts have also been upscaled, which is highly conducive to pathogen transmission. Viral epidemics have stifled mass-rearing efforts of other insects of economic importance, such as crickets, silkworms, and honeybees, but little is known about the viruses that associate with BSF. Although BSFs are thought to be unusually resistant to pathogens because of their expansive antimicrobial gene repertoire, surveillance techniques could be useful in identifying emerging pathogens and common BSF microbes. In this study, we used high-throughput sequencing data to survey BSF larvae and frass samples, and we identified two novel bunyavirus-like sequences. Our phylogenetic analysis grouped one in the family Nairoviridae and the other with two unclassified bunyaviruses. We describe these putative novel viruses as BSF Nairovirus-like 1 and BSF uncharacterized bunyavirus-like 1. We identified candidate segments for the full BSF Nairovirus-like 1 genome using a technique based on transcript co-occurrence and only a partial genome for BSF uncharacterized bunyavirus-like 1. These results emphasize the value of routine BSF colony surveillance and add to the number of viruses associated with BSF. Full article

(This article belongs to the Special Issue Virus Bioinformatics 2023)

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10 pages, 7261 KiB

Open AccessArticle

Viral Instant Mutation Viewer: A Tool to Speed Up the Identification and Analysis of New SARS-CoV-2 Emerging Variants and Beyond

by Vincent Wilde, Bruno Canard and François Ferron

Viruses 2023, 15(8), 1628; https://doi.org/10.3390/v15081628 - 26 Jul 2023

Viewed by 906

Abstract

The appearance of genetic variants impacts vaccination efficiency and therapeutic options, generating a need to map and relate mutations observed in the proteome and the genome. We develop an user-friendly web service software (Viral Instant Mutation Viewer or VIMVer) which allows a direct identification of mutations in the genome and its counterpart in the viral proteome. Since its emergence in 2019, the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), responsible for the COVID-19 pandemic, has generated an overwhelming amount of data while becoming one of the most studied viruses of the Nidovirales order. We originally developed this tool during the COVID pandemic; thus, for any SARS-CoV-2 nucleotide sequence, the web service gives a fast identification, mapping, and display of new mutations simultaneously at the nucleotide and amino acid level in comparison to a reference sequence (Wuhan-1). Furthermore, the lineage or the relative position to the known lineage of the variant of interest is available on the link to Phylogenetic Assignment of Named Global Outbreak LINeages (PANGOLIN COVID-19). The workflow presented here is available online. The source code is released under public license and can be easily adapted for further development to other viruses. Full article

(This article belongs to the Special Issue Virus Bioinformatics 2023)

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14 pages, 3603 KiB

Open AccessArticle

Genomic Characterization of a Halovirus Representing a Novel Siphoviral Cluster

by Kaixin Diao, Guohui Li, Xueqin Sun, Hao Yi, Shiying Zhang and Wei Xiao

Viruses 2023, 15(6), 1392; https://doi.org/10.3390/v15061392 - 19 Jun 2023

Viewed by 1496

Abstract

Salt mines are a special type of hypersaline environment. Current research mainly focuses on prokaryotes, and the understanding of viruses in salt mines remains limited. Understanding viruses in hypersaline environments is of great significance for revealing the formation and maintenance of microbial communities, energy flow and element cycling, and host ecological functions. A phage infecting Halomonas titanicae was isolated from Yipinglang Salt Mine in China, designated Halomonas titanicae phage vB_HtiS_YPHTV-1 (YPHTV-1). Transmission electron microscopy revealed that YPHTV-1 had an icosahedral head with a diameter of 49.12 ± 0.15 nm (n = 5) and a long noncontractile tail with a length of 141.7 ± 0.58 nm (n = 5), indicating that it was a siphovirus. The one-step growth curve showed that the burst size of YPHTV-1 was 69 plaque forming units (PFUs) cell⁻¹. The genome of YPHTV-1 was 37,980 bp with a GC content of 36.2%. The phylogenetic analysis of the six conserved proteins indicated that YPHTV-1 formed a cluster with Bacillus phages and was separated from phages infecting Halomonas. The average nucleotide identity (ANI), phylogenetic, and network analyses indicated that the phage YPHTV-1 represented a new genus under Caudoviricetes. In total, 57 open reading frames (ORFs) were predicted in the YPHTV-1 genome, 30 of which could be annotated in the database. Notably, several auxiliary metabolic genes were encoded by YPHTV-1, such as ImmA/IrrE family metalloendopeptidase, mannose-binding lectin (MBL) folding metallohydrolase, M15 family of metal peptidases, MazG-like family protein, O antigen ligase, and acyltransferase. These genes potentially enabled the host bacterium to resist ionizing radiation, ultraviolet light (UV), mitomycin C, β-lactam antibiotic, high osmotic pressure, and nutritional deficiencies. These findings highlight the role of haloviruses in the life cycle of halobacteria. Full article

(This article belongs to the Special Issue Virus Bioinformatics 2023)

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15 pages, 4780 KiB

Open AccessArticle

CoVigator—A Knowledge Base for Navigating SARS-CoV-2 Genomic Variants

by Thomas Bukur, Pablo Riesgo-Ferreiro, Patrick Sorn, Ranganath Gudimella, Johannes Hausmann, Thomas Rösler, Martin Löwer, Barbara Schrörs and Ugur Sahin

Viruses 2023, 15(6), 1391; https://doi.org/10.3390/v15061391 - 17 Jun 2023

Cited by 2 | Viewed by 1639

Abstract

Background: The outbreak of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) resulted in the global COVID-19 pandemic. The urgency for an effective SARS-CoV-2 vaccine has led to the development of the first series of vaccines at unprecedented speed. The discovery of SARS-CoV-2 spike-glycoprotein mutants, however, and consequentially the potential to escape vaccine-induced protection and increased infectivity, demonstrates the persisting importance of monitoring SARS-CoV-2 mutations to enable early detection and tracking of genomic variants of concern. Results: We developed the CoVigator tool with three components: (1) a knowledge base that collects new SARS-CoV-2 genomic data, processes it and stores its results; (2) a comprehensive variant calling pipeline; (3) an interactive dashboard highlighting the most relevant findings. The knowledge base routinely downloads and processes virus genome assemblies or raw sequencing data from the COVID-19 Data Portal (C19DP) and the European Nucleotide Archive (ENA), respectively. The results of variant calling are visualized through the dashboard in the form of tables and customizable graphs, making it a versatile tool for tracking SARS-CoV-2 variants. We put a special emphasis on the identification of intrahost mutations and make available to the community what is, to the best of our knowledge, the largest dataset on SARS-CoV-2 intrahost mutations. In the spirit of open data, all CoVigator results are available for download. The CoVigator dashboard is accessible via covigator.tron-mainz.de. Conclusions: With increasing demand worldwide in genome surveillance for tracking the spread of SARS-CoV-2, CoVigator will be a valuable resource of an up-to-date list of mutations, which can be incorporated into global efforts. Full article

(This article belongs to the Special Issue Virus Bioinformatics 2023)

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13 pages, 1088 KiB

Open AccessArticle

Novel Approach for Identification of Basic and Effective Reproduction Numbers Illustrated with COVID-19

by Tchavdar T. Marinov, Rossitza S. Marinova, Radoslav T. Marinov and Nicci Shelby

Viruses 2023, 15(6), 1352; https://doi.org/10.3390/v15061352 - 11 Jun 2023

Viewed by 1529

Abstract

This paper presents a novel numerical technique for the identification of effective and basic reproduction numbers,

R_{e}

and

R_{0}

, for long-term epidemics, using an inverse problem approach. The method is based on the direct integration of the SIR (Susceptible–Infectious–Removed) system [...] Read more.

This paper presents a novel numerical technique for the identification of effective and basic reproduction numbers,

R_{e}

and

R_{0}

, for long-term epidemics, using an inverse problem approach. The method is based on the direct integration of the SIR (Susceptible–Infectious–Removed) system of ordinary differential equations and the least-squares method. Simulations were conducted using official COVID-19 data for the United States and Canada, and for the states of Georgia, Texas, and Louisiana, for a period of two years and ten months. The results demonstrate the applicability of the method in simulating the dynamics of the epidemic and reveal an interesting relationship between the number of currently infectious individuals and the effective reproduction number, which is a useful tool for predicting the epidemic dynamics. For all conducted experiments, the results show that the local maximum (and minimum) values of the time-dependent effective reproduction number occur approximately three weeks before the local maximum (and minimum) values of the number of currently infectious individuals. This work provides a novel and efficient approach for the identification of time-dependent epidemics parameters. Full article

(This article belongs to the Special Issue Virus Bioinformatics 2023)

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20 pages, 2675 KiB

Open AccessArticle

Idiotope-Driven T-Cell/B-Cell Collaboration-Based T-Cell Epitope Prediction Using B-Cell Receptor Repertoire Sequences in Infectious Diseases

by Yukio Nakamura, Meng Ling Moi, Takashi Shiina, Tadasu Shin-I and Ryuji Suzuki

Viruses 2023, 15(5), 1186; https://doi.org/10.3390/v15051186 - 17 May 2023

Cited by 2 | Viewed by 2633

Abstract

T-cell recognition of antigen epitopes is a crucial step for the induction of adaptive immune responses, and the identification of such T-cell epitopes is, therefore, important for understanding diverse immune responses and controlling T-cell immunity. A number of bioinformatic tools exist that predict T-cell epitopes; however, many of these methods highly rely on evaluating conventional peptide presentation by major histocompatibility complex (MHC) molecules, but they ignore epitope sequences recognized by T-cell receptor (TCR). Immunogenic determinant idiotopes are present on the variable regions of immunoglobulin molecules expressed on and secreted by B-cells. In idiotope-driven T-cell/B-cell collaboration, B-cells present the idiotopes on MHC molecules for recognition by idiotope-specific T-cells. According to the idiotype network theory formulated by Niels Jerne, such idiotopes found on anti-idiotypic antibodies exhibit molecular mimicry of antigens. Here, by combining these concepts and defining the patterns of TCR-recognized epitope motifs (TREMs), we developed a T-cell epitope prediction method that identifies T-cell epitopes derived from antigen proteins by analyzing B-cell receptor (BCR) sequences. This method allowed us to identify T-cell epitopes that contain the same TREM patterns between BCR and viral antigen sequences in two different infectious diseases caused by dengue virus and SARS-CoV-2 infection. The identified epitopes were among the T-cell epitopes detected in previous studies, and T-cell stimulatory immunogenicity was confirmed. Thus, our data support this method as a powerful tool for the discovery of T-cell epitopes from BCR sequences. Full article

(This article belongs to the Special Issue Virus Bioinformatics 2023)

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11 pages, 5249 KiB

Open AccessArticle

Validation of HIV-1 MA Shell Structural Arrangements and Env Protein Interactions Predict a Role of the MA Shell in Viral Maturation

by Tarana A. Mangukia, Joy Ramielle L. Santos, Weijie Sun, Dominik Cesarz, Carlos D. Ortíz Hidalgo and Marcelo Marcet-Palacios

Viruses 2023, 15(4), 893; https://doi.org/10.3390/v15040893 - 30 Mar 2023

Viewed by 1186

Abstract

The molecular structure of the type 1 human immunodeficiency virus (HIV-1) is tightly linked to the mechanism of viral entry. The spike envelope (Env) glycoproteins and their interaction with the underlying matrix (MA) shell have emerged as key components of the entry mechanism. Microscopy evidence suggests that the MA shell does not span the entire inner lipid surface of the virus, producing a region of the virus that completely lacks an MA shell. Interestingly, evidence also suggests that Env proteins cluster during viral maturation and, thus, it is likely that this event takes place in the region of the virus that lacks an MA shell. We have previously called this part of the virus a fusion hub to highlight its importance during viral entry. While the structure of the MA shell is in contention due to the unaddressed inconsistencies between its reported hexagonal arrangement and the physical plausibility of such a structure, it is possible that a limited number of MA hexagons could form. In this study, we measured the size of the fusion hub by analysing the cryo-EM maps of eight HIV-1 particles and measured the size of the MA shell gap to be 66.3 nm ± 15.0 nm. We also validated the feasibility of the hexagonal MA shell arrangement in six reported structures and determined the plausible components of these structures that do not violate geometrical limitations. We also examined the cytosolic domain of Env proteins and discovered a possible interaction between adjacent Env proteins that could explain the stability of cluster formation. We present an updated HIV-1 model and postulate novel roles of the MA shell and Env structure. Full article

(This article belongs to the Special Issue Virus Bioinformatics 2023)

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18 pages, 4147 KiB

Open AccessArticle

Fragment-Based Approaches Identified Tecovirimat-Competitive Novel Drug Candidate for Targeting the F13 Protein of the Monkeypox Virus

by Yasir Ali, Hina Imtiaz, Muhammad Mutaal Tahir, Fouzia Gul, Umair Ali Khan Saddozai, Ashfaq ur Rehman, Zhi-Guang Ren, Saadullah Khattak and Xin-Ying Ji

Viruses 2023, 15(2), 570; https://doi.org/10.3390/v15020570 - 19 Feb 2023

Cited by 11 | Viewed by 2214

Abstract

Monkeypox is a serious public health issue in tropical and subtropical areas. Antivirals that target monkeypox proteins might lead to more effective and efficient therapy. The F13 protein is essential for the growth and maturation of the monkeypox virus. F13 inhibition might be a viable therapeutic target for monkeypox. The in silico fragment-based drug discovery method for developing antivirals may provide novel therapeutic options. In this study, we generated 800 compounds based on tecovirimat, an FDA-approved drug that is efficacious at nanomolar quantities against monkeypox. These compounds were evaluated to identify the most promising fragments based on binding affinity and pharmacological characteristics. The top hits from the chemical screening were docked into the active site of the F13 protein. Molecular dynamics simulations were performed on the top two probable new candidates from molecular docking. The ligand–enzyme interaction analysis revealed that the C2 ligand had lower binding free energy than the standard ligand tecovirimat. Water bridges, among other interactions, were shown to stabilize the C2 molecule. Conformational transitions and secondary structure changes in F13 protein upon C2 binding show more native three-dimensional folding of the protein. Prediction of pharmacological properties revealed that compound C2 may be promising as a drug candidate for monkeypox fever. However, additional in vitro and in vivo testing is required for validation. Full article

(This article belongs to the Special Issue Virus Bioinformatics 2023)

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27 pages, 1852 KiB

Open AccessArticle

Rational Design of Profile HMMs for Sensitive and Specific Sequence Detection with Case Studies Applied to Viruses, Bacteriophages, and Casposons

by Liliane S. Oliveira, Alejandro Reyes, Bas E. Dutilh and Arthur Gruber

Viruses 2023, 15(2), 519; https://doi.org/10.3390/v15020519 - 13 Feb 2023

Cited by 1 | Viewed by 1838

Abstract

Profile hidden Markov models (HMMs) are a powerful way of modeling biological sequence diversity and constitute a very sensitive approach to detecting divergent sequences. Here, we report the development of protocols for the rational design of profile HMMs. These methods were implemented on TABAJARA, a program that can be used to either detect all biological sequences of a group or discriminate specific groups of sequences. By calculating position-specific information scores along a multiple sequence alignment, TABAJARA automatically identifies the most informative sequence motifs and uses them to construct profile HMMs. As a proof-of-principle, we applied TABAJARA to generate profile HMMs for the detection and classification of two viral groups presenting different evolutionary rates: bacteriophages of the Microviridae family and viruses of the Flavivirus genus. We obtained conserved models for the generic detection of any Microviridae or Flavivirus sequence, and profile HMMs that can specifically discriminate Microviridae subfamilies or Flavivirus species. In another application, we constructed Cas1 endonuclease-derived profile HMMs that can discriminate CRISPRs and casposons, two evolutionarily related transposable elements. We believe that the protocols described here, and implemented on TABAJARA, constitute a generic toolbox for generating profile HMMs for the highly sensitive and specific detection of sequence classes. Full article

(This article belongs to the Special Issue Virus Bioinformatics 2023)

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Review

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27 pages, 9557 KiB

Open AccessReview

Navigating the Landscape: A Comprehensive Review of Current Virus Databases

by Muriel Ritsch, Noriko A. Cassman, Shahram Saghaei and Manja Marz

Viruses 2023, 15(9), 1834; https://doi.org/10.3390/v15091834 - 29 Aug 2023

Cited by 1 | Viewed by 2686

Abstract

Viruses are abundant and diverse entities that have important roles in public health, ecology, and agriculture. The identification and surveillance of viruses rely on an understanding of their genome organization, sequences, and replication strategy. Despite technological advancements in sequencing methods, our current understanding of virus diversity remains incomplete, highlighting the need to explore undiscovered viruses. Virus databases play a crucial role in providing access to sequences, annotations and other metadata, and analysis tools for studying viruses. However, there has not been a comprehensive review of virus databases in the last five years. This study aimed to fill this gap by identifying 24 active virus databases and included an extensive evaluation of their content, functionality and compliance with the FAIR principles. In this study, we thoroughly assessed the search capabilities of five database catalogs, which serve as comprehensive repositories housing a diverse array of databases and offering essential metadata. Moreover, we conducted a comprehensive review of different types of errors, encompassing taxonomy, names, missing information, sequences, sequence orientation, and chimeric sequences, with the intention of empowering users to effectively tackle these challenges. We expect this review to aid users in selecting suitable virus databases and other resources, and to help databases in error management and improve their adherence to the FAIR principles. The databases listed here represent the current knowledge of viruses and will help aid users find databases of interest based on content, functionality, and scope. The use of virus databases is integral to gaining new insights into the biology, evolution, and transmission of viruses, and developing new strategies to manage virus outbreaks and preserve global health. Full article

(This article belongs to the Special Issue Virus Bioinformatics 2023)

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Other

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27 pages, 6213 KiB

Open AccessConference Report

The International Virus Bioinformatics Meeting 2023

by Franziska Hufsky, Ana B. Abecasis, Artem Babaian, Sebastian Beck, Liam Brierley, Simon Dellicour, Christian Eggeling, Santiago F. Elena, Udo Gieraths, Anh D. Ha, Will Harvey, Terry C. Jones, Kevin Lamkiewicz, Gabriel L. Lovate, Dominik Lücking, Martin Machyna, Luca Nishimura, Maximilian K. Nocke, Bernard Y. Renard, Shoichi Sakaguchi, Lygeri Sakellaridi, Jannes Spangenberg, Maria Tarradas-Alemany, Sandra Triebel, Yulia Vakulenko, Rajitha Yasas Wijesekara, Fernando González-Candelas, Sarah Krautwurst, Alba Pérez-Cataluña, Walter Randazzo, Gloria Sánchez and Manja Marz Show full author list Hide full author list

Viruses 2023, 15(10), 2031; https://doi.org/10.3390/v15102031 - 30 Sep 2023

Viewed by 1596

Abstract

The 2023 International Virus Bioinformatics Meeting was held in Valencia, Spain, from 24–26 May 2023, attracting approximately 180 participants worldwide. The primary objective of the conference was to establish a dynamic scientific environment conducive to discussion, collaboration, and the generation of novel research ideas. As the first in-person event following the SARS-CoV-2 pandemic, the meeting facilitated highly interactive exchanges among attendees. It served as a pivotal gathering for gaining insights into the current status of virus bioinformatics research and engaging with leading researchers and emerging scientists. The event comprised eight invited talks, 19 contributed talks, and 74 poster presentations across eleven sessions spanning three days. Topics covered included machine learning, bacteriophages, virus discovery, virus classification, virus visualization, viral infection, viromics, molecular epidemiology, phylodynamic analysis, RNA viruses, viral sequence analysis, viral surveillance, and metagenomics. This report provides rewritten abstracts of the presentations, a summary of the key research findings, and highlights shared during the meeting. Full article

(This article belongs to the Special Issue Virus Bioinformatics 2023)

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