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Pathogens
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Emerging Viruses and the Role of the Virome in Human...
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Emerging Viruses and the Role of the Virome in Human Health and Diseases

A special issue of Pathogens (ISSN 2076-0817). This special issue belongs to the section "Emerging Pathogens".

Deadline for manuscript submissions: closed (31 January 2024) | Viewed by 7726

Special Issue Editors

Prof. Dr. Wen Zhang

E-Mail Website
Guest Editor
School of Medicine, Jiangsu University, Zhenjiang, China
Interests: virome; emerging viruses; virus evolution; biosafety
Dr. Yanpeng Li

E-Mail Website
Guest Editor
Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
Interests: virome; emerging viruses; virus evolution; virus–host relationship
Dr. Eda Altan

E-Mail Website
Guest Editor
Institute of Biomedicine Research Center Infections and Immunity, University of Turku, Turku, Finland
Interests: novel virus discovery; virus–host interactions; virus kinetics

Special Issue Information

Dear Colleagues,

This Special Issue of Pathogens will cover the topic of “Emerging Viruses and the Role of the Virome in Human Health and Diseases”.

Viruses are one of the most abundant but understudied components of the world’s biodiversity, and are present in almost all biological niches. The last few decades have witnessed outbreaks of novel and deadly viruses that have had massive health, social and economic impacts, e.g., SARS-CoV-2, highlighting a global vulnerability to emerging viral diseases. Viral discovery, including viral diversity, evolution, and ecological traits, is needed in order to unveil global virome profiles, identify those viruses with similar genetic characteristics to known pathogenic viruses, and determine the transmission history or evolutionary trajectory of essential viruses. Metadata on the viral ecology of transmission interfaces for wildlife, livestock, and humans, as well as the behavioral patterns of animals and humans, would be helpful in predicting and reducing potential viral spillovers. Additionally, these databases will help other scientists to expand virus discovery studies and will be available to be used as a data source in a possible emergency. 

Human and animal bodies are also colonized by a remarkable diversity of viruses (the human virome), including both pathogenic and/or resident/commensal viruses, and different viral communities are present in various body compartments. Similar to the bacterial microbiome, it is increasingly recognized that the human virome could be associated with the host immune response and could determine or influence physiology and disease status. Specific viral components are recognized as potential biomarkers of disease outcomes. However, the human virome is still largely neglected and understudied, and little is known about the interactions between the human virome and our host. Hopefully, this Special Issue will offer an opportunity for researchers to share their experiences and research in this field, and will forward our understanding of the human virome in health and diseases. 

This Special Issue of Pathogens calls for all types of research articles, reviews, and short letters related to virome studies, including the evolution, transmission pathways, and pathogenesis of emerging viruses, virus discovery, virus–host interactions, and basic and clinical research related to the human virome. We look forward to your contributions.

Prof. Dr. Wen Zhang
Dr. Yanpeng Li
Dr. Eda Altan
Guest Editors

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. Pathogens 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

  • virome
  • emerging viruses
  • virus evolution
  • biosafety
  • virus–host interaction

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Published Papers (3 papers)

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Research

9 pages, 1789 KiB  
Communication
Virome Profiling of an Eastern Roe Deer Reveals Spillover of Viruses from Domestic Animals to Wildlife
by Yue Sun, Lanshun Sun, Sheng Sun, Zhongzhong Tu, Yang Liu, Le Yi, Changchun Tu and Biao He
Pathogens 2023, 12(2), 156; https://doi.org/10.3390/pathogens12020156 - 18 Jan 2023
Cited by 3 | Viewed by 2123
Abstract
Eastern roe deer (Capreolus pygargus) is a small ruminant and is widespread across China. This creature plays an important role in our ecological system. Although a few studies have been conducted to investigate pathogens harbored by this species, our knowledge of [...] Read more.
Eastern roe deer (Capreolus pygargus) is a small ruminant and is widespread across China. This creature plays an important role in our ecological system. Although a few studies have been conducted to investigate pathogens harbored by this species, our knowledge of the virus diversity is still very sparse. In this study, we conducted the whole virome profiling of a rescue-failed roe deer, which revealed a kobuvirus (KoV), a bocaparvovirus (BoV), and multiple circular single-stranded viruses. These viruses were mainly recovered from the rectum, but PCR detection showed systematic infection of the KoV. Particularly, the KoV and BoV exhibited closely genetic relationships with bovine and canine viruses, respectively, highly suggesting the spillover of viruses from domestic animals to wildlife. Although these viruses were unlikely to have been responsible for the death of the animal, they provide additional data to understand the virus spectrum harbored by roe deer. The transmission of viruses between domestic animals and wildlife highlights the need for extensive investigation of wildlife viruses. Full article
(This article belongs to the Special Issue Emerging Viruses and the Role of the Virome in Human Health and Diseases)
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13 pages, 1376 KiB  
Article
Investigation of the Virome and Characterization of Issyk-Kul Virus from Swedish Myotis brandtii Bats
by Harindranath Cholleti, Johnny de Jong, Anne-Lie Blomström and Mikael Berg
Pathogens 2023, 12(1), 12; https://doi.org/10.3390/pathogens12010012 - 21 Dec 2022
Cited by 2 | Viewed by 2751
Abstract
Bats are reservoirs for many different viruses, including some that can be transmitted to and cause disease in humans and/or animals. However, less is known about the bat-borne viruses circulating in Northern European countries such as in Sweden. In this study, saliva from [...] Read more.
Bats are reservoirs for many different viruses, including some that can be transmitted to and cause disease in humans and/or animals. However, less is known about the bat-borne viruses circulating in Northern European countries such as in Sweden. In this study, saliva from Myotis brandtii bats, collected from south-central Sweden, was analyzed for viruses. The metagenomic analysis identified viral sequences belonging to different viral families, including, e.g., Nairoviridae, Retroviridae, Poxviridae, Herpesviridae and Siphoviridae. Interestingly, through the data analysis, the near-complete genome of Issyk-Kul virus (ISKV), a zoonotic virus within the Nairoviridae family, was obtained, showing 95–99% protein sequence identity to previously described ISKVs. This virus is believed to infect humans via an intermediate tick host or through contact with bat excrete. ISKV has previously been found in bats in Europe, but not previously in the Nordic region. In addition, near full-length genomes of two novel viruses belonging to Picornavirales order and Tymoviridae family were characterized. Taken together, our study has not only identified novel viruses, but also the presence of a zoonotic virus not previously known to circulate in this region. Thus, the results from these types of studies can help us to better understand the diversity of viruses circulating in bat populations, as well as identify viruses with zoonotic potential that could possibly be transmitted to humans. Full article
(This article belongs to the Special Issue Emerging Viruses and the Role of the Virome in Human Health and Diseases)
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10 pages, 2124 KiB  
Article
Viral Metagenomics Reveals a Putative Novel HPV Type in Anogenital Wart Tissues
by Huimin Hu, Yu Ling, Xuan Wang, Hao Wang, Niannan Zhu, Yumei Li and Hui Xu
Pathogens 2022, 11(12), 1452; https://doi.org/10.3390/pathogens11121452 - 1 Dec 2022
Cited by 1 | Viewed by 2101
Abstract
Viral metagenomics is widely employed to identify novel viruses in biological samples. Recently, although numerous novel human papillomavirus (HPV) types have been identified in clinical samples including anogenital warts (AGWs), many novel HPV sequences remain to be discovered. In this study, a putative [...] Read more.
Viral metagenomics is widely employed to identify novel viruses in biological samples. Recently, although numerous novel human papillomavirus (HPV) types have been identified in clinical samples including anogenital warts (AGWs), many novel HPV sequences remain to be discovered. In this study, a putative novel HPV type designated as HPV-JDFY01 was discovered from library GW05 with 63 sequence reads by the viral metagenomic technique. Its complete genomic sequence was determined by PCR to bridge the gaps between contigs combining Sanger sequencing. The complete genome of HPV-JDFY01 is a 7186 bp encoding 7 open reading frames (ORFs) (E6, E7, E1, E2, E4, L2 and L1) and contains a 487 bp long control region (LCR) between L1 and E6. Sequence and phylogeny analysis indicated that HPV-JDFY01 shared the highest sequence identity of 74.2% with HPV-mSK_244 (MH777383) and well clustered into the genus Gammapapillomavirus. It has the classical genomic organization of Gammapapillomaviruses. Epidemiological investigation showed that one out of the 413 AGW tissue samples was positive for HPV-JDFY01. Further research with large size and different type of samples should be performed to elucidate the epidemiologic status of HPV-JDFY01. Full article
(This article belongs to the Special Issue Emerging Viruses and the Role of the Virome in Human Health and Diseases)
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