Special Issue "Viral Genetic Diversity"

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

Deadline for manuscript submissions: closed (30 September 2021).

Special Issue Editors

Dr. Jean-Michel Heraud
E-Mail Website
Guest Editor
Institut Pasteur de Dakar, Virology Department, 36, avenue Pasteur, BP 220, 12500 Dakar, Senegal
Interests: influenza and respiratory viruses; vector-borne viruses; zoonosis; diagnostic; public health
Dr. Anne Lavergne
E-Mail Website
Guest Editor
Institut Pasteur de la Guyane, Laboratoire des Interactions Virus-Hôtes, 23 Avenue Pasteur, BP6010, 97306 Cayenne Cedex, Guyane-Française
Interests: host–virus interaction; co-evolution; speciation; virus ecology; molecular evolution; bats
Dr. Richard Njouom
E-Mail Website
Guest Editor
Center Pasteur du Cameroun, Virology Department, 451 Rue 2005, BP1274, Yaoundé 2, Cameroun
Interests: hepatitis viruses; influenza and respiratory viruses; zoonosis; molecular evolution

Special Issue Information

Dear Colleagues,

With an estimate of 1031 particles present in the biosphere, viruses are the most abundant species on earth. Their incredible genetic diversity has been shaped through evolution, and this propensity to generate genetic diversity is one of the key factors allowing viruses to adapt to new environments and new hosts, leading to the emergence or re-emergence of new viruses and new diseases. One of the most recent examples is the SARS-CoV2 responsible for the second large pandemic of this century.

Studying and decoding viral diversity/virome is a major challenge for a better understanding of its role in health and also of interaction networks linking the different compartments of the ecosystem (individual, population, species, and communities). In this Special Issue, we seek to highlight recent advances in understanding the genetic diversity of viruses. We welcome manuscripts that describe new viruses infecting various hosts, viral etiologies of diseases, studies on viral genetic diversity in the context of viral–host interaction, and what the genetic drivers of viral emergence are.

Dr. Jean-Michel Heraud
Dr. Anne Lavergne
Dr. Richard Njouom
Guest Editors

Manuscript Submission Information

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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 2200 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

  • phage
  • plant viruses
  • fungi viruses
  • animal viruses
  • virome
  • metagenomics
  • ecology
  • richness
  • genetic
  • biodiversity
  • emerging viruses
  • evolution

Published Papers (5 papers)

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Research

Article
The Influence of Habitat on Viral Diversity in Neotropical Rodent Hosts
Viruses 2021, 13(9), 1690; https://0-doi-org.brum.beds.ac.uk/10.3390/v13091690 - 26 Aug 2021
Viewed by 626
Abstract
Rodents are important reservoirs of numerous viruses, some of which have significant impacts on public health. Ecosystem disturbances and decreased host species richness have been associated with the emergence of zoonotic diseases. In this study, we aimed at (a) characterizing the viral diversity [...] Read more.
Rodents are important reservoirs of numerous viruses, some of which have significant impacts on public health. Ecosystem disturbances and decreased host species richness have been associated with the emergence of zoonotic diseases. In this study, we aimed at (a) characterizing the viral diversity in seven neotropical rodent species living in four types of habitats and (b) exploring how the extent of environmental disturbance influences this diversity. Through a metagenomic approach, we identified 77,767 viral sequences from spleen, kidney, and serum samples. These viral sequences were attributed to 27 viral families known to infect vertebrates, invertebrates, plants, and amoeba. Viral diversities were greater in pristine habitats compared with disturbed ones, and lowest in peri-urban areas. High viral richness was observed in savannah areas. Differences in these diversities were explained by rare viruses that were generally more frequent in pristine forest and savannah habitats. Moreover, changes in the ecology and behavior of rodent hosts, in a given habitat, such as modifications to the diet in disturbed vs. pristine forests, are major determinants of viral composition. Lastly, the phylogenetic relationships of four vertebrate-related viral families (Polyomaviridae, Flaviviridae, Togaviridae, and Phenuiviridae) highlighted the wide diversity of these viral families, and in some cases, a potential risk of transmission to humans. All these findings provide significant insights into the diversity of rodent viruses in Amazonia, and emphasize that habitats and the host’s dietary ecology may drive viral diversity. Linking viral richness and abundance to the ecology of their hosts and their responses to habitat disturbance could be the starting point for a better understanding of viral emergence and for future management of ecosystems. Full article
(This article belongs to the Special Issue Viral Genetic Diversity)
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Article
Understanding the Genetic Diversity of Picobirnavirus: A Classification Update Based on Phylogenetic and Pairwise Sequence Comparison Approaches
Viruses 2021, 13(8), 1476; https://0-doi-org.brum.beds.ac.uk/10.3390/v13081476 - 28 Jul 2021
Viewed by 586
Abstract
Picobirnaviruses (PBVs) are small, double stranded RNA viruses with an ability to infect a myriad of hosts and possessing a high degree of genetic diversity. PBVs are currently classified into two genogroups based upon classification of a 200 nt sequence of RdRp. We [...] Read more.
Picobirnaviruses (PBVs) are small, double stranded RNA viruses with an ability to infect a myriad of hosts and possessing a high degree of genetic diversity. PBVs are currently classified into two genogroups based upon classification of a 200 nt sequence of RdRp. We demonstrate here that this phylogenetic marker is saturated, affected by homoplasy, and has high phylogenetic noise, resulting in 34% unsolved topologies. By contrast, full-length RdRp sequences provide reliable topologies that allow ancestralism of members to be correctly inferred. MAFFT alignment and maximum likelihood trees were established as the optimal methods to determine phylogenetic relationships, providing complete resolution of PBV RdRp and capsid taxa, each into three monophyletic groupings. Pairwise distance calculations revealed these lineages represent three species. For RdRp, the application of cutoffs determined by theoretical taxonomic distributions indicates that there are five genotypes in species 1, eight genotypes in species 2, and three genotypes in species 3. Capsids were also divided into three species, but sequences did not segregate into statistically supported subdivisions, indicating that diversity is lower than RdRp. We thus propose the adoption of a new nomenclature to indicate the species of each segment (e.g., PBV-C1R2). Full article
(This article belongs to the Special Issue Viral Genetic Diversity)
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Article
Structure-Function Analyses of New SARS-CoV-2 Variants B.1.1.7, B.1.351 and B.1.1.28.1: Clinical, Diagnostic, Therapeutic and Public Health Implications
Viruses 2021, 13(3), 439; https://0-doi-org.brum.beds.ac.uk/10.3390/v13030439 - 09 Mar 2021
Cited by 30 | Viewed by 3760
Abstract
SARS-CoV-2 (Severe Acute Respiratory Syndrome-Coronavirus 2) has accumulated multiple mutations during its global circulation. Recently, three SARS-CoV-2 lineages, B.1.1.7 (501Y.V1), B.1.351 (501Y.V2) and B.1.1.28.1 (P.1), have emerged in the United Kingdom, South Africa and Brazil, respectively. Here, we have presented global viewpoint on [...] Read more.
SARS-CoV-2 (Severe Acute Respiratory Syndrome-Coronavirus 2) has accumulated multiple mutations during its global circulation. Recently, three SARS-CoV-2 lineages, B.1.1.7 (501Y.V1), B.1.351 (501Y.V2) and B.1.1.28.1 (P.1), have emerged in the United Kingdom, South Africa and Brazil, respectively. Here, we have presented global viewpoint on implications of emerging SARS-CoV-2 variants based on structural–function impact of crucial mutations occurring in its spike (S), ORF8 and nucleocapsid (N) proteins. While the N501Y mutation was observed in all three lineages, the 501Y.V1 and P.1 accumulated a different set of mutations in the S protein. The missense mutational effects were predicted through a COVID-19 dedicated resource followed by atomistic molecular dynamics simulations. Current findings indicate that some mutations in the S protein might lead to higher affinity with host receptors and resistance against antibodies, but not all are due to different antibody binding (epitope) regions. Mutations may, however, result in diagnostic tests failures and possible interference with binding of newly identified anti-viral candidates against SARS-CoV-2, likely necessitating roll out of recurring “flu-like shots” annually for tackling COVID-19. The functional relevance of these mutations has been described in terms of modulation of host tropism, antibody resistance, diagnostic sensitivity and therapeutic candidates. Besides global economic losses, post-vaccine reinfections with emerging variants can have significant clinical, therapeutic and public health impacts. Full article
(This article belongs to the Special Issue Viral Genetic Diversity)
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Article
Epidemiology and Genetic Variability of HHV-8/KSHV among Rural Populations and Kaposi’s Sarcoma Patients in Gabon, Central Africa. Review of the Geographical Distribution of HHV-8 K1 Genotypes in Africa
Viruses 2021, 13(2), 175; https://0-doi-org.brum.beds.ac.uk/10.3390/v13020175 - 25 Jan 2021
Cited by 1 | Viewed by 864
Abstract
Human herpesvirus 8 (HHV-8) is the etiological agent of all forms of Kaposi’s sarcoma (KS). K1 gene studies have identified five major molecular genotypes with geographical clustering. This study described the epidemiology of HHV-8 and its molecular diversity in Gabon among Bantu and [...] Read more.
Human herpesvirus 8 (HHV-8) is the etiological agent of all forms of Kaposi’s sarcoma (KS). K1 gene studies have identified five major molecular genotypes with geographical clustering. This study described the epidemiology of HHV-8 and its molecular diversity in Gabon among Bantu and Pygmy adult rural populations and KS patients. Plasma antibodies against latency-associated nuclear antigens (LANA) were searched by indirect immunofluorescence. Buffy coat DNA samples were subjected to polymerase chain reaction (PCR) to obtain a K1 gene fragment. We studied 1020 persons; 91% were Bantus and 9% Pygmies. HHV-8 seroprevalence was 48.3% and 36.5% at the 1:40 and 1:160 dilution thresholds, respectively, although the seroprevalence of HHV-8 is probably higher in Gabon. These seroprevalences did not differ by sex, age, ethnicity or province. The detection rate of HHV-8 K1 sequence was 2.6% by PCR. Most of the 31 HHV-8 strains belonged to the B genotype (24), while the remaining clustered within the A5 subgroup (6) and one belonged to the F genotype. Additionally, we reviewed the K1 molecular diversity of published HHV-8 strains in Africa. This study demonstrated a high seroprevalence of HHV-8 in rural adult populations in Gabon and the presence of genetically diverse strains with B, A and also F genotypes. Full article
(This article belongs to the Special Issue Viral Genetic Diversity)
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Article
Intra-Host Diversity of SARS-Cov-2 Should Not Be Neglected: Case of the State of Victoria, Australia
Viruses 2021, 13(1), 133; https://0-doi-org.brum.beds.ac.uk/10.3390/v13010133 - 19 Jan 2021
Cited by 10 | Viewed by 2108
Abstract
Since the identification of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) as the etiological agent of the current COVID-19 pandemic, a rapid and massive effort has been made to obtain the genomic sequences of this virus to monitor (in near real time) the [...] Read more.
Since the identification of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) as the etiological agent of the current COVID-19 pandemic, a rapid and massive effort has been made to obtain the genomic sequences of this virus to monitor (in near real time) the phylodynamic and diversity of this new pathogen. However, less attention has been given to the assessment of intra-host diversity. RNA viruses such as SARS-CoV-2 inhabit the host as a population of variants called quasispecies. We studied the quasispecies diversity in four of the main SARS-CoV-2 genes (ORF1a, ORF1b, S and N genes), using a dataset consisting of 210 next-generation sequencing (NGS) samples collected between January and early April of 2020 in the State of Victoria, Australia. We found evidence of quasispecies diversity in 68% of the samples, 76% of which was nonsynonymous variants with a higher density in the spike (S) glycoprotein and ORF1a genes. About one-third of the nonsynonymous intra-host variants were shared among the samples, suggesting host-to-host transmission. Quasispecies diversity changed over time. Phylogenetic analysis showed that some of the intra-host single-nucleotide variants (iSNVs) were restricted to specific lineages, highlighting their potential importance in the epidemiology of this virus. A greater effort must be made to determine the magnitude of the genetic bottleneck during transmission and the epidemiological and/or evolutionary factors that may play a role in the changes in the diversity of quasispecies over time. Full article
(This article belongs to the Special Issue Viral Genetic Diversity)
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