Virome and Viral Diseases

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

Deadline for manuscript submissions: closed (15 December 2021) | Viewed by 9982

Special Issue Editor

Lab of Virology, Pad Baglivi, INMI L Spallanzani, Via Portuense, 292, 00149 Rome, Italy
Interests: HPV; HIV; viral hepatitis; virus molecular evolution; host–pathogen interaction; zoonoses
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Special Issue Information

Dear Colleagues,

Since 2003, when the term “virome” appeared in a scientific paper, many efforts have been made to understand viral diversity and pathogenicity. There has been an increasing number of findings that underline the relevance of viromes in human diseases such as bowel disease, type I diabetes, graft-versus-host disease and HIV. However, knowledge of the viruses considered to directly infect humans remains incomplete. Metagenomics assays can theoretically detect all pathogens, but often they fail to detect viruses because of their low viral load and small genome. The presence of bacterial and fungal genomes can be accurately detected through consensus PCR approaches that target the 16S rRNA and internal transcribed spacer (ITS) loci, respectively. Conversely, there are no analogous conserved sequences in any virus. Thus, viral sequences found in metagenomic analysis must be aligned with both nucleotide and amino acid levels in a large reference database of viral sequences, and the amplicon pairwise results are often not suitable for proper virus identification. In most virome studies, more than 50% of sequences in virus-enriched preparation had shown sequences with no similarity to any known reference sequences. These unalignable sequences, referred to as “dark matter”, could include new viruses, but the conventional alignment methods are not able to classify them. Thus, virome studies currently present only a partial description of the real virome in a specimen because the dark matter sequences are often ignored. Another bias in virome analysis is the focus on only sequencing of DNA. This is due to the fact that the bacterial microbiome is the primary objective of many metagenomics studies, so that, in experimental protocols, DNA is extracted from nucleic acids without regard to either preserve or recover the RNA. This could lead to incomplete or incorrect conclusions about the real composition of viromes. The main objectives of this Special Issue are to describe the utility of the metagenomics approach to identify new viruses, the virome relationship with human diseases and the description of bioinformatics tools that are suitable to better analyze the viral populations in NGS studies.

Dr. Anna Rosa Garbuglia
Guest Editor

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Keywords

  • metagenomics
  • viromics
  • metaviromics
  • virus
  • next-generation sequencing
  • dark matter sequences
  • bioinformatics tools

Published Papers (2 papers)

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Research

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15 pages, 22560 KiB  
Article
Full Genome of batCoV/MinFul/2018/SriLanka, a Novel Alpha-Coronavirus Detected in Miniopterus fuliginosus, Sri Lanka
by Therese Muzeniek, Thejanee Perera, Sahan Siriwardana, Dilara Bas, Fatimanur Kaplan, Mizgin Öruc, Beate Becker-Ziaja, Inoka Perera, Jagathpriya Weerasena, Shiroma Handunnetti, Franziska Schwarz, Gayani Premawansa, Sunil Premawansa, Wipula Yapa, Andreas Nitsche and Claudia Kohl
Viruses 2022, 14(2), 337; https://0-doi-org.brum.beds.ac.uk/10.3390/v14020337 - 07 Feb 2022
Cited by 6 | Viewed by 2358
Abstract
Coronaviruses (CoV) are divided into the genera α-CoVs, β-CoVs, γ-CoVs and δ-CoVs. Of these, α-CoVs and β-CoVs are solely capable of causing infections in humans, resulting in mild to severe respiratory symptoms. Bats have been identified as natural reservoir hosts for CoVs belonging [...] Read more.
Coronaviruses (CoV) are divided into the genera α-CoVs, β-CoVs, γ-CoVs and δ-CoVs. Of these, α-CoVs and β-CoVs are solely capable of causing infections in humans, resulting in mild to severe respiratory symptoms. Bats have been identified as natural reservoir hosts for CoVs belonging to these two genera. Consequently, research on bat populations, CoV prevalence in bats and genetic characterization of bat CoVs is of special interest to investigate the potential transmission risks. We present the genome sequence of a novel α-CoV strain detected in rectal swab samples of Miniopterus fuliginosus bats from a colony in the Wavul Galge cave (Koslanda, Sri Lanka). The novel strain is highly similar to Miniopterus bat coronavirus 1, an α-CoV located in the subgenus of Minunacoviruses. Phylogenetic reconstruction revealed a high identity of the novel strain to other α-CoVs derived from Miniopterus bats, while human-pathogenic α-CoV strains like HCoV-229E and HCoV-NL63 were more distantly related. Comparison with selected bat-related and human-pathogenic strains of the β-CoV genus showed low identities of ~40%. Analyses of the different genes on nucleotide and amino acid level revealed that the non-structural ORF1a/1b are more conserved among α-CoVs and β-CoVs, while there are higher variations in the structural proteins known to be important for host specificity. The novel strain was named batCoV/MinFul/2018/SriLanka and had a prevalence of 50% (66/130) in rectal swab samples and 58% (61/104) in feces samples that were collected from Miniopterus bats in Wavul Galge cave. Based on the differences between strain batCoV/MinFul/2018/SriLanka and human-pathogenic α-CoVs and β-CoVs, we conclude that there is a rather low transmission risk to humans. Further studies in the Wavul Galge cave and at other locations in Sri Lanka will give more detailed information about the prevalence of this virus. Full article
(This article belongs to the Special Issue Virome and Viral Diseases)
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Review

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29 pages, 2014 KiB  
Review
The Human Virome: Viral Metagenomics, Relations with Human Diseases, and Therapeutic Applications
by Geng-Hao Bai, Sheng-Chieh Lin, Yi-Hsiang Hsu and Shih-Yen Chen
Viruses 2022, 14(2), 278; https://0-doi-org.brum.beds.ac.uk/10.3390/v14020278 - 28 Jan 2022
Cited by 29 | Viewed by 6804
Abstract
The human body is colonized by a wide range of microorganisms. The field of viromics has expanded since the first reports on the detection of viruses via metagenomic sequencing in 2002. With the continued development of reference materials and databases, viral metagenomic approaches [...] Read more.
The human body is colonized by a wide range of microorganisms. The field of viromics has expanded since the first reports on the detection of viruses via metagenomic sequencing in 2002. With the continued development of reference materials and databases, viral metagenomic approaches have been used to explore known components of the virome and discover new viruses from various types of samples. The virome has attracted substantial interest since the outbreak of the coronavirus disease 2019 (COVID-19) pandemic. Increasing numbers of studies and review articles have documented the diverse virome in various sites in the human body, as well as interactions between the human host and the virome with regard to health and disease. However, there have been few studies of direct causal relationships. Viral metagenomic analyses often lack standard references and are potentially subject to bias. Moreover, most virome-related review articles have focused on the gut virome and did not investigate the roles of the virome in other sites of the body in human disease. This review presents an overview of viral metagenomics, with updates regarding the relations between alterations in the human virome and the pathogenesis of human diseases, recent findings related to COVID-19, and therapeutic applications related to the human virome. Full article
(This article belongs to the Special Issue Virome and Viral Diseases)
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