Within-Host Viral Dynamics: A Window into Viral Evolution

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

Deadline for manuscript submissions: 31 May 2024 | Viewed by 1515

Special Issue Editors


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Guest Editor
School of Medicine, St. Louis University, St. Louis, MO, USA
Interests: viral metagenomics; human genomics; bioinformatics; hepatitis viruses

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Guest Editor
Laboratory for Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium
Interests: hepatitis B virus; blood virome; emerging infectious diseases
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Special Issue Information

Dear Colleagues,

Evolution is the cornerstone in modern biomedicine. However, studying evolution is a challenge in higher organisms owing to their sizable genomes and low mutation rates. Measurable alterations related to evolution can take up to millions of years to develop. Given their tiny genomes, short replication cycles, and high mutation rates, viruses represent an attractive model for studying evolution in vivo. While the entire course of viral infection in hosts can be viewed as an evolutionary episode, our knowledge on underlying mechanisms that drive viral evolution is far from complete. How is the evolutionary process shaped by viral interaction with host innate and adaptive immunity? What is the contribution of the viral intrinsic mutation rate and replication strategy? Does the human microbiome influence viral evolution, and if so, how? Within-host viral dynamics provide an excellent opportunity to study these complex interactions and their roles in infection outcomes. The advent of deep sequencing techniques and other omics approaches now allow an unbiased investigation of the entire viral population in the context of micro- and macroenvironments. These articles will give us deep insights into viral evolution that are relevant to the prevention, diagnosis, and treatment of viral diseases.

Dr. Xiaofeng Fan
Dr. Mahmoud Reza Pourkarim
Guest Editors

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Keywords

  • virome
  • metagenomics
  • phylogenetics
  • viral evolution
  • quasispecies
  • infectious diseases

Published Papers (1 paper)

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Research

15 pages, 3386 KiB  
Article
Intra-Patient Genomic Variations of Human Papillomavirus Type 31 in Cervical Cancer and Precancer
by Gota Kogure, Kohsei Tanaka, Tomoya Matsui, Mamiko Onuki, Koji Matsumoto, Takashi Iwata and Iwao Kukimoto
Viruses 2023, 15(10), 2104; https://doi.org/10.3390/v15102104 - 17 Oct 2023
Cited by 1 | Viewed by 1245
Abstract
Human papillomavirus type 31 (HPV31) is detected less frequently in cervical cancer than two major causative types, HPV16 and HPV18. Here, we report a comprehensive analysis of HPV31 genome sequences in cervical lesions collected from Japanese women. Of 52 HPV31-positive cervical specimens analyzed [...] Read more.
Human papillomavirus type 31 (HPV31) is detected less frequently in cervical cancer than two major causative types, HPV16 and HPV18. Here, we report a comprehensive analysis of HPV31 genome sequences in cervical lesions collected from Japanese women. Of 52 HPV31-positive cervical specimens analyzed by deep sequencing, 43 samples yielded complete genome sequences of around 7900 base pairs and 9 samples yielded partially deleted genome sequences. Phylogenetic analysis showed that HPV31 variant distribution was lineage A in 19 samples (36.5%), lineage B in 28 samples (53.8%), and lineage C in 5 samples (9.6%), indicating that lineage B variants are dominant among HPV31 infections in Japan. Deletions in the viral genome were found in the region from the E1 to L1 genes, but all the deleted genomes retained the E6/E7 genes. Among intra-patient nucleotide variations relative to a consensus genome sequence in each sample, C-to-T substitutions were most frequently detected, followed by T-to-C and C-to-A substitutions. High-frequency, intra-patient mutations (>10%) in cervical cancer samples were found in the E1, E2, and E7 genes, and all of them were nonsynonymous substitutions. The enrichment of high-frequency nonsynonymous substitutions strongly suggests that these intra-patient mutations are positively selected during the development of cervical cancer/precancer. Full article
(This article belongs to the Special Issue Within-Host Viral Dynamics: A Window into Viral Evolution)
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