Viruses

18 pages, 1382 KiB

Open AccessArticle

A Genetic Study of Spillovers in the Bean Common Mosaic Subgroup of Potyviruses

by Mohammad Hajizadeh, Karima Ben Mansour and Adrian J. Gibbs

Viruses 2024, 16(9), 1351; https://doi.org/10.3390/v16091351 (registering DOI) - 23 Aug 2024

Nine viruses of the bean common mosaic virus subgroup of potyviruses are major international crop pathogens, but their phylogenetically closest relatives from non-crop plants have mostly been found only in SE Asia and Oceania, which is thus likely to be their “centre of emergence”. We have compared over 700 of the complete genomic ORFs of the crop pandemic and the non-crop viruses in various ways. Only one-third of crop virus genomes are non-recombinant, but more than half the non-crop virus genomes are. Four of the viruses were from crops domesticated in the Old World (Africa to SE Asia), and the other five were from New World crops. There was a temporal signal in only three of the crop virus datasets, but it confirmed that the most recent common ancestors of all the crop viruses were before inter-continental marine trade started after 1492 CE, whereas all the crown clusters of the phylogenies are from after that date. The non-crop virus datasets are genetically more diverse than those of the crop viruses, and Tajima’s D analyses showed that their populations were contracting, and only one of the crop viruses had a significantly expanding population. dN/dS analyses showed that most of the genes and codons in all the viruses were under significant negative selection, and the few that were under significant positive selection were mostly in the PIPO-encoding region of the P3 protein, or the PIPO protein itself. Interestingly, more positively selected codons were found in non-crop than in crop viruses, and, as the hosts of the former were taxonomically more diverse than the latter, this may indicate that the positively selected codons are involved in host range determination; AlphaFold3 modelling was used to investigate this possibility. Full article

(This article belongs to the Special Issue Plant Virus Spillovers)

8 pages, 781 KiB

Open AccessBrief Report

Honeysuckle-Derived miR2911 Inhibits Replication of Porcine Reproductive and Respiratory Syndrome Virus by Targeting Viral Gene Regions

by Xinyan Cao, Jiaxi Xue, Adnan Ali, Manyi Zhang, Jinliang Sheng, Yanming Sun and Yanbing Zhang

Viruses 2024, 16(9), 1350; https://doi.org/10.3390/v16091350 (registering DOI) - 23 Aug 2024

Abstract

The highly abundant and stable antiviral small RNA derived from honeysuckle, known as miR2911, has been shown to play a key role in inhibiting influenza virus infection and SARS-CoV-2 infection. However, whether miR2911 inhibits the replication of porcine reproductive and respiratory syndrome virus (PRRSV) remains unknown. Hence, this study investigated the mechanisms underlying the action of miR2911 during PRRSV infection. Six targets of miR2911 within the PRRSV orf1 (Nsp2: 2459 to 2477, 1871 to 1892, 954 to 977, and 1271 to 1292; Nsp1: 274 to 296 and 822 to 841) were successfully identified by using the miRanda v1.0b software. The miR2911 target sequence was analyzed by target sequence comparison, and only individual base mutations existed in different prevalent strains, and the miR2911 target region was highly conserved among different strains. Subsequently, through the dual luciferase reporter gene assay and miR2911 overexpression assay, it was demonstrated that miR2911 significantly inhibits the replication of PRRSV by targeting regions of PRRSV Nsp1 and Nsp2. These findings offer new insights for the development of novel anti-PRRSV drugs. Full article

(This article belongs to the Special Issue Porcine Viruses 2024)

5 pages, 491 KiB

Open AccessCommunication

SCANellome V2: Update of the Primate Anellovirus Reference Sequences Database

by Florian Laubscher, Laurent Kaiser and Samuel Cordey

Viruses 2024, 16(9), 1349; https://doi.org/10.3390/v16091349 (registering DOI) - 23 Aug 2024

Abstract

Anelloviruses are ubiquitous in humans and represent a major component of the human virome. Its best-known representative is Torque teno virus (i.e., the Alphatorquevirus genus), which is considered a potential immunity biomarker. Recent metagenomic investigations revealed not only the extraordinary genomic diversity of anellovirus sequences, but also that co-detection of genera, genotypes, or species seems to be the rule in humans. SCANellome was developed to represent a user-friendly tool to analyze the primate (both human and non-human) anellovirus composition at the genus, species, and genotype level from metagenomics data based on an up-to-date database. This SCANellome update includes >900 additional reference sequences from GenBank. Using a clustering at 90% identity, the FASTA database was updated and generated 134 new representative sequences. Based on ORF1, the analysis of these new sequences indicates the presence of 206 potential new species, including four nonhuman primates, and adds four new non-human primate species which will be the subject of a proposal to the International Committee on Taxonomy of Viruses (ICTV). In addition, SCANellome V2 provides now the user with an interactive up-to-date phylogenetic analysis (of ORF1) to show the distribution among the 12 human and nonhuman primate genera of these new potential species. Finally, the Anelloviridae taxonomy was updated to rename species names in binomial format as required by the ICTV. Full article

(This article belongs to the Special Issue Virus Discovery, Classification and Characterization)

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16 pages, 2557 KiB

Open AccessReview

Phage against the Machine: The SIE-ence of Superinfection Exclusion

by Michael J. Bucher and Daniel M. Czyż

Viruses 2024, 16(9), 1348; https://doi.org/10.3390/v16091348 (registering DOI) - 23 Aug 2024

Abstract

Prophages can alter their bacterial hosts to prevent other phages from infecting the same cell, a mechanism known as superinfection exclusion (SIE). Such alterations are facilitated by phage interactions with critical bacterial components involved in motility, adhesion, biofilm production, conjugation, antimicrobial resistance, and immune evasion. Therefore, the impact of SIE extends beyond the immediate defense against superinfection, influencing the overall fitness and virulence of the bacteria. Evaluating the interactions between phages and their bacterial targets is critical for leading phage therapy candidates like Pseudomonas aeruginosa, a Gram-negative bacterium responsible for persistent and antibiotic-resistant opportunistic infections. However, comprehensive literature on the mechanisms underlying SIE remains scarce. Here, we provide a compilation of well-characterized and potential mechanisms employed by Pseudomonas phages to establish SIE. We hypothesize that the fitness costs imposed by SIE affect bacterial virulence, highlighting the potential role of this mechanism in the management of bacterial infections. Full article

(This article belongs to the Special Issue Bacteriophages and Biofilms 2.0)

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9 pages, 3011 KiB

Open AccessArticle

Life-Threatening Conditions in Children with Bocavirus Infection-Case Series and Mini Review of the Literature

by Elena Tătăranu, Felicia Galos, Liliana Anchidin-Norocel, Roxana Axinte, Florin Filip, Sorin Axinte, Adrian Tătăranu, Monica Terteliu and Smaranda Diaconescu

Viruses 2024, 16(9), 1347; https://doi.org/10.3390/v16091347 (registering DOI) - 23 Aug 2024

Abstract

In this study, we present four cases of Human Bocavirus (HBoV) infection in children aged between 1 month and 4 years. Among these cases, two siblings were hospitalized with similar symptoms. Among the four pediatric cases of patients with HBoV infection, three were associated with acute respiratory failure and spontaneous pneumothorax, and two of these presented with subcutaneous emphysema. The presented patients were young children, aged between 1 month and 4 years, two of whom were siblings, suggesting a possible intrafamilial transmission of HBoV1 infection. These cases highlight the importance of considering HBoV as a differential diagnosis in pediatric patients with respiratory and gastrointestinal symptoms. Early recognition and appropriate medical care are important in treating HBoV infection in young children. Full article

(This article belongs to the Section Human Virology and Viral Diseases)

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Viruses, Volume 16, Issue 9 (September 2024) – 5 articles

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