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Viruses
Special Issues
Viral Genetic Variation
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Viral Genetic Variation

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

Deadline for manuscript submissions: closed (31 March 2024) | Viewed by 9116

Special Issue Editor

Dr. Tatsuo Shioda

E-Mail Website
Guest Editor
Center for Infectious Disease Education and Research, Department of Viral Infections, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
Interests: HIV; restriction factors; dengue virus; chikungunya virus; SARS-CoV-2; genetic diversity; pathogenesis

Special Issue Information

Dear Colleagues,

Viral genetic variation can be seen when viruses begin to adapt to new host species. Viral genetic variation can be driven by infection- or vaccine-induced host immunity. Viral genetic variation can be driven by specific antiviral therapies, such as inhibitors for virus enzymes or therapeutic antibodies. Furthermore, viral genetic variation can affect the species specificity, tissue tropism, or receptor usage of viruses. Viral genetic variation can also affect pathogenicity, interferon sensitivity, or replicative capability, either upward or downward, in a host. Viral genetic variation in a host population may prevent the formation of herd immunity and affect therapeutic efficacy as well as diagnosis sensitivity. Finally, viral genetic variation can even affect its evolution rate.

In this Special Issue, we welcome a wide range of articles, including original research, short communications, and reviews, that focus on any kind of viral genetic variation.

We look forward to receiving your submissions for this Special Issue.

Dr. Tatsuo Shioda
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.

Keywords

  • emerging and re-emerging viruses
  • adaptation
  • tropism
  • receptor usage
  • immune escape
  • drug resistance
  • evolution rate

Published Papers (5 papers)

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Research

22 pages, 5646 KiB  
Article
Epidemiological Features of Human Norovirus Genotypes before and after COVID-19 Countermeasures in Osaka, Japan
by Tatsuya Shirai, Juthamas Phadungsombat, Yumi Ushikai, Kunihito Yoshikaie, Tatsuo Shioda and Naomi Sakon
Viruses 2024, 16(4), 654; https://doi.org/10.3390/v16040654 - 22 Apr 2024
Viewed by 367
Abstract
We investigated the molecular epidemiology of human norovirus (HuNoV) in all age groups using samples from April 2019 to March 2023, before and after the COVID-19 countermeasures were implemented. GII.2[P16] and GII.4[P31], the prevalent strains in Japan before COVID-19 countermeasures, remained prevalent during [...] Read more.
We investigated the molecular epidemiology of human norovirus (HuNoV) in all age groups using samples from April 2019 to March 2023, before and after the COVID-19 countermeasures were implemented. GII.2[P16] and GII.4[P31], the prevalent strains in Japan before COVID-19 countermeasures, remained prevalent during the COVID-19 pandemic, except from April to November 2020; in 2021, the prevalence of GII.2[P16] increased among children. Furthermore, there was an increase in the prevalence of GII.4[P16] after December 2022. Phylogenetic analysis of GII.P31 RdRp showed that some strains detected in 2022 belonged to a different cluster of other strains obtained during the present study period, suggesting that HuNoV strains will evolve differently even if they have the same type of RdRp. An analysis of the amino acid sequence of VP1 showed that some antigenic sites of GII.4[P16] were different from those of GII.4[P31]. The present study showed high infectivity of HuNoV despite the COVID-19 countermeasures and revealed changes in the prevalent genotypes and mutations of each genotype. In the future, we will investigate whether GII.4[P16] becomes more prevalent, providing new insights by comparing the new data with those analyzed in the present study. Full article
(This article belongs to the Special Issue Viral Genetic Variation)
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18 pages, 8631 KiB  
Article
Genetic Diversity, Evolutionary Dynamics, and Ongoing Spread of Pedilanthus Leaf Curl Virus
by Zafar Iqbal, Muhammad Shafiq, Muhammad Naeem Sattar, Irfan Ali, Muhammad Khurshid, Umer Farooq and Muhammad Munir
Viruses 2023, 15(12), 2358; https://doi.org/10.3390/v15122358 - 30 Nov 2023
Viewed by 843
Abstract
Pedilanthus leaf curl virus (PeLCV) is a monopartite begomovirus (family Geminiviridae) discovered just a few decades ago. Since then, it has become a widely encountered virus, with reports from ca. 25 plant species across Pakistan and India, indicative of its notable evolutionary [...] Read more.
Pedilanthus leaf curl virus (PeLCV) is a monopartite begomovirus (family Geminiviridae) discovered just a few decades ago. Since then, it has become a widely encountered virus, with reports from ca. 25 plant species across Pakistan and India, indicative of its notable evolutionary success. Viruses mutate at such a swift rate that their ecological and evolutionary behaviors are inextricably linked, and all of these behaviors are imprinted on their genomes as genetic diversity. So, all these imprints can be mapped by computational methods. This study was designed to map the sequence variation dynamics, genetic heterogeneity, regional diversity, phylogeny, and recombination events imprinted on the PeLCV genome. Phylogenetic and network analysis grouped the full-length genome sequences of 52 PeLCV isolates into 7 major clades, displaying some regional delineation but lacking host-specific demarcation. The progenitor of PeLCV was found to have originated in Multan, Pakistan, in 1977, from where it spread concurrently to India and various regions of Pakistan. A high proportion of recombination events, distributed unevenly throughout the genome and involving both inter- and intraspecies recombinants, were inferred. The findings of this study highlight that the PeLCV population is expanding under a high degree of genetic diversity (π = 0.073%), a high rate of mean nucleotide substitution (1.54 × 10−3), demographic selection, and a high rate of recombination. This sets PeLCV apart as a distinctive begomovirus among other begomoviruses. These factors could further exacerbate the PeLCV divergence and adaptation to new hosts. The insights of this study that pinpoint the emergence of PeLCV are outlined. Full article
(This article belongs to the Special Issue Viral Genetic Variation)
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11 pages, 1833 KiB  
Article
Genetic Diversity of Domestic Cat Hepadnavirus in Southern Taiwan
by Benji Brayan Ilagan Silva, Jin-Yang Chen, Brian Harvey Avanceña Villanueva, Zi-Ying Lu, Hua-Zhen Hsing, Andrew D. Montecillo, Maya Shofa, Hoang Minh, Jen-Pin Chuang, Huai-Ying Huang, Akatsuki Saito and Kuo-Pin Chuang
Viruses 2023, 15(10), 2128; https://doi.org/10.3390/v15102128 - 20 Oct 2023
Cited by 1 | Viewed by 1678
Abstract
Domestic cat hepadnavirus (DCH) is an infectious disease associated with chronic hepatitis in cats, which suggests a similarity with hepatitis B virus infections in humans. Since its first identification in Australia in 2018, DCH has been reported in several countries with varying prevalence [...] Read more.
Domestic cat hepadnavirus (DCH) is an infectious disease associated with chronic hepatitis in cats, which suggests a similarity with hepatitis B virus infections in humans. Since its first identification in Australia in 2018, DCH has been reported in several countries with varying prevalence rates, but its presence in Taiwan has yet to be investigated. In this study, we aimed to identify the presence and genetic diversity of DCH infections in Taiwan. Among the 71 samples tested, eight (11.27%) were positive for DCH. Of these positive cases, three cats had elevated levels of alanine transaminase (ALT) and aspartate transaminase (AST), suggesting an association between DCH infection and chronic hepatitis. Four DCH-positive samples were also tested for feline immunodeficiency virus (FIV) and feline leukemia virus (FeLV) coinfection. One sample (25%) was positive for FIV, whereas there was no positive sample for FeLV (0%). In addition, we performed whole genome sequencing on six samples to determine the viral genome sequences. Phylogenetic analyses identified a distinct lineage compared with previously reported sequences. This study highlights the importance of continuous surveillance of DCH and further research to elucidate the pathophysiology and transmission route of DCH. Full article
(This article belongs to the Special Issue Viral Genetic Variation)
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16 pages, 2656 KiB  
Article
Genomic Diversity and Evolution of SARS-CoV-2 Lineages in Pakistan
by Muhammad Waqar Aziz, Nadia Mukhtar, Aftab Ahamd Anjum, Muhammad Hassan Mushtaq, Muhammad Adnan Ashraf, Amar Nasir, Muhammad Furqan Shahid, Muhammad Nawaz, Muhammad Zubair Shabbir, Noreen Sarwar, Rabia Tanvir and Tahir Yaqub
Viruses 2023, 15(7), 1450; https://doi.org/10.3390/v15071450 - 27 Jun 2023
Viewed by 1307
Abstract
The emergence of SARS-CoV-2 variants has posed a challenge to disease control efforts worldwide. This study explored the genomic diversity and phylogenetic relationship of SARS-CoV-2 variants reported in Pakistan. Our objective was to understand the transmission dynamics of different lineages within the country. [...] Read more.
The emergence of SARS-CoV-2 variants has posed a challenge to disease control efforts worldwide. This study explored the genomic diversity and phylogenetic relationship of SARS-CoV-2 variants reported in Pakistan. Our objective was to understand the transmission dynamics of different lineages within the country. We retrieved and analyzed spike protein sequences from Pakistan and compared them with reference sequences reported worldwide. Our analysis revealed the clustering of Pakistan-origin isolates in nine different clades representing different regions worldwide, suggesting the transmission of multiple lineages within the country. We found 96 PANGO lineages of SARS-CoV-2 in Pakistan, and 64 of these corresponded to 4 WHO-designated variants: Alpha, Beta, Delta, and Omicron. The most dominant variants in Pakistan were Alpha (B.1.1.7), Beta (B.1.351), Delta (B.1.617.2, AY.108), and Omicron (BA.2.75, BA.5.2), and the N-terminal domain and receptor binding regions were the most hypervariable regions of the spike gene. Compared to the reference strain, characteristic substitutions were found in dominant variants. Our findings emphasize the importance of continuously monitoring and assessing nucleotide and residue substitutions over time to understand virus evolutionary trends better and devise effective disease control interventions. Full article
(This article belongs to the Special Issue Viral Genetic Variation)
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16 pages, 1301 KiB  
Article
Genetic Analysis of Dengue Virus in Severe and Non-Severe Cases in Dhaka, Bangladesh, in 2018–2022
by Rummana Rahim, Abu Hasan, Juthamas Phadungsombat, Nazmul Hasan, Nikhat Ara, Suma Mita Biswas, Emi E. Nakayama, Mizanur Rahman and Tatsuo Shioda
Viruses 2023, 15(5), 1144; https://doi.org/10.3390/v15051144 - 10 May 2023
Cited by 3 | Viewed by 4044
Abstract
Dengue virus (DENV) infections have unpredictable clinical outcomes, ranging from asymptomatic or minor febrile illness to severe and fatal disease. The severity of dengue infection is at least partly related to the replacement of circulating DENV serotypes and/or genotypes. To describe clinical profiles [...] Read more.
Dengue virus (DENV) infections have unpredictable clinical outcomes, ranging from asymptomatic or minor febrile illness to severe and fatal disease. The severity of dengue infection is at least partly related to the replacement of circulating DENV serotypes and/or genotypes. To describe clinical profiles of patients and the viral sequence diversity corresponding to non-severe and severe cases, we collected patient samples from 2018 to 2022 at Evercare Hospital Dhaka, Bangladesh. Serotyping of 495 cases and sequencing of 179 cases showed that the dominant serotype of DENV shifted from DENV2 in 2017 and 2018 to DENV3 in 2019. DENV3 persisted as the only representative serotype until 2022. Co-circulation of clades B and C of the DENV2 cosmopolitan genotype in 2017 was replaced by circulation of clade C alone in 2018 with all clones disappearing thereafter. DENV3 genotype I was first detected in 2017 and was the only genotype in circulation until 2022. We observed a high incidence of severe cases in 2019 when the DENV3 genotype I became the only virus in circulation. Phylogenetic analysis revealed clusters of severe cases in several different subclades of DENV3 genotype I. Thus, these serotype and genotype changes in DENV may explain the large dengue outbreaks and increased severity of the disease in 2019. Full article
(This article belongs to the Special Issue Viral Genetic Variation)
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