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Viruses
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Caliciviruses
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Caliciviruses

A special issue of Viruses (ISSN 1999-4915). This special issue belongs to the section "Human Virology and Viral Diseases".

Deadline for manuscript submissions: closed (31 August 2024) | Viewed by 7506

Special Issue Editor

Dr. Miranda De Graaf

E-Mail Website
Guest Editor
Department of Viroscience, Erasmus MC, 3015 Rotterdam, The Netherlands
Interests: norovirus; cross-species transmission; tropism; phylogeny; RNA viruses; virus evolution; virus attachment

Special Issue Information

Dear Colleagues,

We are pleased to announce the launch of a Special Issue of Viruses dedicated to the in-depth exploration of the family Caliciviridae. This Special Issue aims to enhance our understanding of this diverse family, which currently encompasses eleven genera. The family Caliciviridae has been detected in a wide range of animals, with seven genera infecting mammals (Lagovirus, Norovirus, Nebovirus, Recovirus, Sapovirus, Valovirus, and Vesivirus), two infecting birds (Bavovirus and Nacovirus), and two infecting fish (Minovirus and Salovirus). Additionally, several unclassified caliciviruses have been identified.

Advancements in metagenomics and novel in vivo and in vitro infection model systems have significantly expanded our understanding of the diversity of the family Caliciviridae and its interactions with host organisms. In recent years, significant progress has been made in understanding the calicivirus life cycle, the biology of infections in humans and animals, epidemiology, and immunity. Notably, new transmission routes have been discovered for noroviruses, as well as genotype-specific differences in virus–host interactions, and ongoing efforts are being made to develop treatment strategies and vaccines to control acute and chronic infections.

Therefore, we invite the submission of various types of manuscripts, including reviews, research articles, and short communications, that explore novel discoveries in the field of calicivirus research. Specifically, we encourage investigations related to epidemiology, evolution, replication, and virus–host interactions, although other relevant topics are also welcome.

We look forward to receiving your contributions to this Special Issue.

Dr. Miranda De Graaf
Guest Editor

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.

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Published Papers (4 papers)

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Research

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13 pages, 2599 KiB  
Article
Genomic Characterization and Molecular Evolution of Sapovirus in Children under 5 Years of Age
by Xiaolei Ji, Chen Guo, Yaoyao Dai, Lu Chen, Yujia Chen, Shifang Wang and Yihua Sun
Viruses 2024, 16(1), 146; https://doi.org/10.3390/v16010146 - 19 Jan 2024
Cited by 4 | Viewed by 1785
Abstract
Sapovirus (SaV) is a type of gastroenteric virus that can cause acute gastroenteritis. It is highly contagious, particularly among children under the age of 5. In this study, a total of 712 stool samples from children under the age of 5 with acute [...] Read more.
Sapovirus (SaV) is a type of gastroenteric virus that can cause acute gastroenteritis. It is highly contagious, particularly among children under the age of 5. In this study, a total of 712 stool samples from children under the age of 5 with acute gastroenteritis were collected. Out of these samples, 28 tested positive for SaV, resulting in a detection rate of 3.93% (28/712). Samples with Ct < 30 were collected for library construction and high-throughput sequencing, resulting in the acquisition of nine complete genomes. According to Blast, eight of them were identified as GI.1, while the remaining one was GI.6. The GI.6 strain sequence reported in our study represents the first submission of the GI.6 strain complete genome sequence from mainland China to the Genbank database, thus filling the data gap in our country. Sequence identity analysis revealed significant nucleotide variations between the two genotypes of SaV and their corresponding prototype strains. Phylogenetic and genetic evolution analyses showed no evidence of recombination events in the obtained sequences. Population dynamics analysis demonstrated potential competitive inhibition between two lineages of GI.1. Our study provides insights into the molecular epidemiological and genetic evolution characteristics of SaV prevalent in the Nantong region of China, laying the foundation for disease prevention and control, as well as pathogen tracing related to SaV in this area. Full article
(This article belongs to the Special Issue Caliciviruses)
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Review

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17 pages, 1893 KiB  
Review
The Disorderly Nature of Caliciviruses
by Vivienne L. Young, Alice M. McSweeney, Matthew J. Edwards and Vernon K. Ward
Viruses 2024, 16(8), 1324; https://doi.org/10.3390/v16081324 - 19 Aug 2024
Cited by 2 | Viewed by 1912
Abstract
An intrinsically disordered protein (IDP) or region (IDR) lacks or has little protein structure but still maintains function. This lack of structure creates flexibility and fluidity, allowing multiple protein conformations and potentially transient interactions with more than one partner. Caliciviruses are positive-sense ssRNA [...] Read more.
An intrinsically disordered protein (IDP) or region (IDR) lacks or has little protein structure but still maintains function. This lack of structure creates flexibility and fluidity, allowing multiple protein conformations and potentially transient interactions with more than one partner. Caliciviruses are positive-sense ssRNA viruses, containing a relatively small genome of 7.6–8.6 kb and have a broad host range. Many viral proteins are known to contain IDRs, which benefit smaller viral genomes by expanding the functional proteome through the multifunctional nature of the IDR. The percentage of intrinsically disordered residues within the total proteome for each calicivirus type species can range between 8 and 23%, and IDRs have been experimentally identified in NS1-2, VPg and RdRP proteins. The IDRs within a protein are not well conserved across the genera, and whether this correlates to different activities or increased tolerance to mutations, driving virus adaptation to new selection pressures, is unknown. The function of norovirus NS1-2 has not yet been fully elucidated but includes involvement in host cell tropism, the promotion of viral spread and the suppression of host interferon-λ responses. These functions and the presence of host cell-like linear motifs that interact with host cell caspases and VAPA/B are all found or affected by the disordered region of norovirus NS1-2. The IDRs of calicivirus VPg are involved in viral transcription and translation, RNA binding, nucleotidylylation and cell cycle arrest, and the N-terminal IDR within the human norovirus RdRP could potentially drive liquid–liquid phase separation. This review identifies and summarises the IDRs of proteins within the Caliciviridae family and their importance during viral replication and subsequent host interactions. Full article
(This article belongs to the Special Issue Caliciviruses)
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27 pages, 3518 KiB  
Review
Highs and Lows in Calicivirus Reverse Genetics
by Ángel L. Álvarez, Aroa Arboleya, Fábio A. Abade dos Santos, Alberto García-Manso, Inés Nicieza, Kevin P. Dalton, Francisco Parra and José M. Martín-Alonso
Viruses 2024, 16(6), 866; https://doi.org/10.3390/v16060866 - 28 May 2024
Cited by 1 | Viewed by 1887
Abstract
In virology, the term reverse genetics refers to a set of methodologies in which changes are introduced into the viral genome and their effects on the generation of infectious viral progeny and their phenotypic features are assessed. Reverse genetics emerged thanks to advances [...] Read more.
In virology, the term reverse genetics refers to a set of methodologies in which changes are introduced into the viral genome and their effects on the generation of infectious viral progeny and their phenotypic features are assessed. Reverse genetics emerged thanks to advances in recombinant DNA technology, which made the isolation, cloning, and modification of genes through mutagenesis possible. Most virus reverse genetics studies depend on our capacity to rescue an infectious wild-type virus progeny from cell cultures transfected with an “infectious clone”. This infectious clone generally consists of a circular DNA plasmid containing a functional copy of the full-length viral genome, under the control of an appropriate polymerase promoter. For most DNA viruses, reverse genetics systems are very straightforward since DNA virus genomes are relatively easy to handle and modify and are also (with few notable exceptions) infectious per se. This is not true for RNA viruses, whose genomes need to be reverse-transcribed into cDNA before any modification can be performed. Establishing reverse genetics systems for members of the Caliciviridae has proven exceptionally challenging due to the low number of members of this family that propagate in cell culture. Despite the early successful rescue of calicivirus from a genome-length cDNA more than two decades ago, reverse genetics methods are not routine procedures that can be easily extrapolated to other members of the family. Reports of calicivirus reverse genetics systems have been few and far between. In this review, we discuss the main pitfalls, failures, and delays behind the generation of several successful calicivirus infectious clones. Full article
(This article belongs to the Special Issue Caliciviruses)
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Other

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21 pages, 5143 KiB  
Perspective
Conformational Flexibility in Capsids Encoded by the Caliciviridae
by Charlotte B. Lewis, Lee Sherry, Michaela J. Conley, Masaaki Nakashima, Shirin Akbar, Nithya Govindan, Margaret J. Hosie and David Bhella
Viruses 2024, 16(12), 1835; https://doi.org/10.3390/v16121835 - 26 Nov 2024
Viewed by 1157
Abstract
Caliciviruses are a diverse group of non-enveloped, positive-sense RNA viruses with a wide range of hosts and transmission routes. Norovirus is the most well-known member of the Caliciviridae; the acute gastroenteritis caused by human norovirus (HuNoV), for example, frequently results in closures [...] Read more.
Caliciviruses are a diverse group of non-enveloped, positive-sense RNA viruses with a wide range of hosts and transmission routes. Norovirus is the most well-known member of the Caliciviridae; the acute gastroenteritis caused by human norovirus (HuNoV), for example, frequently results in closures of hospital wards and schools during the winter months. One area of calicivirus biology that has gained increasing attention over the past decade is the conformational flexibility exhibited by the protruding (P) domains of the major capsid protein VP1. This was observed in structure analyses of capsids encoded by many species and is often a consequence of environmental cues such as metal ions, changes to pH, or receptor/co-factor engagement. This review summarises the current understanding of P-domain flexibility, discussing the role this region plays in caliciviral infection and immune evasion, and highlighting potential avenues for further investigation. Full article
(This article belongs to the Special Issue Caliciviruses)
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