Viral Genomics and Metagenomics

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Viral Genomics".

Deadline for manuscript submissions: 20 October 2024 | Viewed by 4158

Special Issue Editor


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Guest Editor
School of Medicine, Jiangsu University, Zhenjiang 212013, China
Interests: metagenomics; next-generation sequencing; virome; virus evolution; infectious diseases; viral genomics

Special Issue Information

Dear Colleagues,

Viruses are the main pathogens that cause diseases. In recent years, many novel pathogenic viruses have emerged and caused disease epidemics worldwide (e.g., Zika virus, Ebola virus, SARS-CoV-2). This seriously hinders the development of the world economy and poses a threat to people’s health and lives.

Viral metagenomics has the potential advantage of uncovering new viral pathogens or recombinant/reassortant types. It makes it possible to circumvent the steps of virus isolation and culture, to take the environmental virome as the research object, and to be combined with next-generation high-throughput sequencing technology to obtain all the virome information in the sample in a short period of time. At present, viral metagenomics is also used for exploring the correlation between viruses and diseases in clinical disease diagnosis. Using viral metagenomics to discover novel viruses as early as possible and understand their genome information is of great significance for disease prevention and treatment.

This Special Issue aims to analyze the virome of human, animal or environment using metagenomic approaches, and to clarify the pathogenic relationships between viruses and animals or humans through the subsequent research of virus etiology and epidemiology. This is applicable to, but not limited to, the report of metagenomics approaches as well as etiology and epidemiology research related to viral diseases.

Dr. Shixing Yang
Guest Editor

Manuscript Submission Information

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Keywords

  • metagenomics
  • next-generation sequencing
  • virome
  • virus evolution
  • infectious diseases
  • viral genomics

Published Papers (2 papers)

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Research

20 pages, 6461 KiB  
Article
Shotgun Metagenomic Sequencing Reveals Virome Composition of Mosquitoes from a Transition Ecosystem of North-Northeast Brazil
by Carine Fortes Aragão, Sandro Patroca da Silva, Bruna Laís Sena do Nascimento, Fábio Silva da Silva, Joaquim Pinto Nunes Neto, Valéria Cristina Soares Pinheiro and Ana Cecília Ribeiro Cruz
Genes 2023, 14(7), 1443; https://doi.org/10.3390/genes14071443 - 14 Jul 2023
Cited by 2 | Viewed by 1530
Abstract
A wide diversity of pathogenic mosquito-borne viruses circulate in the Brazilian Amazon, and the intense deforestation can contribute to the spread of these viruses. In this context, this study aimed to investigate the viral diversity in mosquitoes of the genera Aedes, Culex [...] Read more.
A wide diversity of pathogenic mosquito-borne viruses circulate in the Brazilian Amazon, and the intense deforestation can contribute to the spread of these viruses. In this context, this study aimed to investigate the viral diversity in mosquitoes of the genera Aedes, Culex, Haemagogus, and Sabethes from a transition area between the Amazon, Cerrado, and Caatinga biomes in Brazil. Metagenomic high-throughput sequencing was used to characterize the virome of 20 mosquito pools. A total of 15 virus-like genomes were identified, comprising species genomically close to insect-specific viruses of the families Iflaviridae, Metaviridae, Lispiviridae, Rhabdoviridae, Xinmoviridae, and Parvoviridae and species of plant viruses of the families Solemoviridae, Virgaviridae, and Partitiviridae. However, sequences of viruses associated with human and animal diseases were not detected. Most of the recovered genomes were divergent from those previously described. These findings reveal that there are a large number of unknown viruses to be explored in the middle-north of Brazil. Full article
(This article belongs to the Special Issue Viral Genomics and Metagenomics)
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10 pages, 2510 KiB  
Article
SARS-CoV-2 Omicron Variant Genomic and Phylogenetic Analysis in Iraqi Kurdistan Region
by Sevan Omer Majed, Suhad Asad Mustafa, Paywast Jamal Jalal, Mohammed Hassan Fatah, Monika Miasko, Zanko Jawhar and Abdulkarim Yasin Karim
Genes 2023, 14(1), 173; https://doi.org/10.3390/genes14010173 - 09 Jan 2023
Cited by 2 | Viewed by 2299
Abstract
Omicron variants have been classified as Variants of Concern (VOC) by the World Health Organization (WHO) ever since they first emerged as a result of a significant mutation in this variant, which showed to have an impact on transmissibility and virulence of the [...] Read more.
Omicron variants have been classified as Variants of Concern (VOC) by the World Health Organization (WHO) ever since they first emerged as a result of a significant mutation in this variant, which showed to have an impact on transmissibility and virulence of the virus, as evidenced by the ongoing modifications in the SARS-CoV-2 virus. As a global pandemic, the Omicron variant also spread among the Kurdish population. This study aimed to analyze different strains from different cities of the Kurdistan region of Iraq to show the risk of infection and the impact of the various mutations on immune responses and vaccination. A total of 175 nasopharyngeal/oropharyngeal specimens were collected at West Erbil Emergency Hospital and confirmed for SARS-CoV-2 infection by RT-PCR. The genomes of the samples were sequenced using the Illumina COVID-Seq Method. The genome analysis was established based on previously published data in the GISAID database and compared to previously detected mutations in the Omicron variants, and that they belong to the BA.1 lineage and include most variations determined in other studies related to transmissibility, high infectivity and immune escape. Most of the mutations were found in the RBD (receptor binding domain), the region related to the escape from humoral immunity. Remarkably, these point mutations (G339D, S371L, S373P, S375F, T547K, D614G, H655Y, N679K and N969K) were also determined in this study, which were unique, and their impact should be addressed more. Overall, the Omicron variants were more contagious than other variants. However, the mortality rate was low, and most infectious cases were asymptomatic. The next step should address the potential of Omicron variants to develop the next-generation COVID-19 vaccine. Full article
(This article belongs to the Special Issue Viral Genomics and Metagenomics)
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