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Viruses
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Population Genomics of Human Viruses
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Population Genomics of Human Viruses

A special issue of Viruses (ISSN 1999-4915). This special issue belongs to the section "Human Virology and Viral Diseases".

Deadline for manuscript submissions: closed (31 March 2023) | Viewed by 16543

Special Issue Editors

Dr. Manuela Sironi

E-Mail Website
Guest Editor
Scientific Insitute IRCCS Eugenio Medea, Bosisio Parini, Italy
Interests: human virus evolution; virus population genetics; geographic structure of viral populations; virus origin; arenavirus genetic diversity; herpesvirus genetics; coronavirus evolution
Dr. Rachele Cagliani

E-Mail Website
Guest Editor
Scientific Insitute IRCCS Eugenio Medea, Bosisio Parini, Italy
Interests: host-pathogen interactions; pathogenic potential of human viruses; human virus evolution; coronavirus genetics

Special Issue Information

Dear Colleagues,

In recent years, the advent of high-throughput sequencing approaches and the parallel increase in the sophistication and quality of computational tools for storing and mining large sequence datasets have greatly enhanced our ability to genetically characterize viral populations. The enormous potential of these developments has become more than clear during the SARS-CoV-2 pandemic, but the large-scale sequencing of other human viruses has also provided invaluable information about their epidemiology and evolutionary dynamics. It is thus becoming evident that the genetic diversity of viral populations is determined by viral intrinsic features, but also influenced by host factors, by human population interactions among themselves, and by anthropic changes to the natural environment.

This Special Issue “Population Genomics of Human Viruses”, is intended for original papers and reviews that further our insight into human virus genetic diversity, evolution, and ecology using population genomics approaches. Computational tools to characterize viral populations, track their spread and analyze their spatial/temporal structure will also be welcome, together with original databases of viral genome diversity and relevant metadata. 

Dr. Manuela Sironi
Dr. Rachele Cagliani
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. 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

  • human viruses
  • viral populations
  • evolutionary genomics
  • virus genetic diversity
  • spatial/temporal population structure
  • computational tools
  • epidemiology
  • viral ecology

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Published Papers (5 papers)

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Research

18 pages, 3946 KiB  
Article
Genomic Expedition: Deciphering Human Adenovirus Strains from the 2023 Outbreak in West Bengal, India: Insights into Viral Evolution and Molecular Epidemiology
by Ananya Chatterjee, Uttaran Bhattacharjee, Rudrak Gupta, Ashis Debnath, Agniva Majumdar, Ritubrita Saha, Mamta Chawla-Sarkar, Alok Kumar Chakrabarti and Shanta Dutta
Viruses 2024, 16(1), 159; https://doi.org/10.3390/v16010159 - 21 Jan 2024
Cited by 1 | Viewed by 2086
Abstract
Understanding the genetic dynamics of circulating Human Adenovirus (HAdV) types is pivotal for effectively managing outbreaks and devising targeted interventions. During the West Bengal outbreak of 2022–2023, an investigation into the genetic characteristics and outbreak potential of circulating HAdV types was conducted. Twenty-four [...] Read more.
Understanding the genetic dynamics of circulating Human Adenovirus (HAdV) types is pivotal for effectively managing outbreaks and devising targeted interventions. During the West Bengal outbreak of 2022–2023, an investigation into the genetic characteristics and outbreak potential of circulating HAdV types was conducted. Twenty-four randomly selected samples underwent whole-genome sequencing. Analysis revealed a prevalent recombinant strain, merging type 3 and type 7 of human mastadenovirus B1 (HAd-B1) species, indicating the emergence of recent strains of species B in India. Furthermore, distinctions in VA-RNAs and the E3 region suggested that current circulating strains of human mastadenovirus B1 (HAd-B1) possess the capacity to evade host immunity, endure longer within hosts, and cause severe respiratory infections. This study underscores the significance of evaluating the complete genome sequence of HAdV isolates to glean insights into their outbreak potential and the severity of associated illnesses. Full article
(This article belongs to the Special Issue Population Genomics of Human Viruses)
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13 pages, 1480 KiB  
Article
Genetic Diversity and Dispersal of DENGUE Virus among Three Main Island Groups of the Philippines during 2015–2017
by Ava Kristy Sy, Carmen Koo, Kristine J. R. Privaldos, Mary Ann T. Quinones, Mary A. U. Igoy, Sharon Y. A. M. Villanueva, Martin L. Hibberd, Lee Ching Ng and Hapuarachchige C. Hapuarachchi
Viruses 2023, 15(5), 1079; https://doi.org/10.3390/v15051079 - 28 Apr 2023
Cited by 4 | Viewed by 4019
Abstract
Dengue has been one of the major public health concerns in the Philippines for more than a century. The annual dengue case burden has been increasing in recent years, exceeding 200,000 in 2015 and 2019. However, there is limited information on the molecular [...] Read more.
Dengue has been one of the major public health concerns in the Philippines for more than a century. The annual dengue case burden has been increasing in recent years, exceeding 200,000 in 2015 and 2019. However, there is limited information on the molecular epidemiology of dengue in the Philippines. We, therefore, conducted a study to understand the genetic composition and dispersal of DENV in the Philippines from 2015 to 2017 under UNITEDengue. Our analyses included 377 envelope (E) gene sequences of all 4 serotypes obtained from infections in 3 main island groups (Luzon, Visayas, and Mindanao) of the Philippines. The findings showed that the overall diversity of DENV was generally low. DENV-1 was relatively more diverse than the other serotypes. Virus dispersal was evident among the three main island groups, but each island group demonstrated a distinct genotype composition. These observations suggested that the intensity of virus dispersal was not substantive enough to maintain a uniform heterogeneity among island groups so that each island group behaved as an independent epidemiological unit. The analyses suggested Luzon as one of the major sources of DENV emergence and CAR, Calabarzon, and CARAGA as important hubs of virus dispersal in the Philippines. Our findings highlight the importance of virus surveillance and molecular epidemiological analyses to gain deep insights into virus diversity, lineage dominance, and dispersal patterns that could assist in understanding the epidemiology and transmission risk of dengue in endemic regions. Full article
(This article belongs to the Special Issue Population Genomics of Human Viruses)
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16 pages, 4514 KiB  
Article
Phylogenetic Characterization of HIV-1 Sub-Subtype A1 in Karachi, Pakistan
by Uroosa Tariq, Jamirah Nazziwa, Sviataslau Sasinovich, Sharaf Ali Shah, Sadaf Naeem, Syed Hani Abidi and Joakim Esbjörnsson
Viruses 2022, 14(10), 2307; https://doi.org/10.3390/v14102307 - 20 Oct 2022
Cited by 2 | Viewed by 2257
Abstract
(1) Background: HIV-1 sub-subtype A1 is common in parts of Africa, Russia, former Soviet Union countries, and Eastern Europe. In Pakistan, sub-subtype A1 is the predominant HIV-1 subtype. Preliminary evidence suggests that distinct strains of HIV-1 sub-subtype A1 are circulating in Pakistan; however, [...] Read more.
(1) Background: HIV-1 sub-subtype A1 is common in parts of Africa, Russia, former Soviet Union countries, and Eastern Europe. In Pakistan, sub-subtype A1 is the predominant HIV-1 subtype. Preliminary evidence suggests that distinct strains of HIV-1 sub-subtype A1 are circulating in Pakistan; however, an in-depth molecular phylogenetic characterization of HIV-1 sub-subtype A1 strains in Pakistan have not been presented. We performed a detailed characterization of the HIV-1 sub-subtype A1 epidemic in Pakistan using state-of-the-art molecular epidemiology and phylodynamics. (2) Methods: A total of 143 HIV-1 sub-subtype A1 gag sequences, including 61 sequences generated specifically for this study from PLHIVs part of our cohort, representing all sub-subtype A1 gag sequences from Pakistan, were analyzed. Maximum-likelihood phylogenetic cluster analysis was used to determine the relationship between Pakistani sub-subtype A1 strains and pandemic sub-subtype A1 strains. Furthermore, we used signature variation, charge distribution, selection pressures, and epitope prediction analyses to characterize variations unique to Pakistani HIV-1 strains and establish the association between signature variations and Gag epitope profile. (3) Results: The HIV-1 sub-subtype A1 sequences from Pakistan formed three main clusters: two that clustered with Kenyan sequences (7 and 10 sequences, respectively) and one that formed a Pakistan-specific cluster of 123 sequences that were much less related to other sub-subtype A1 sequences available in the database. The sequences in the Pakistan-specific cluster and the Kenyan reference strains exhibited several signature variations, especially at amino acid positions 312, 319, 331, 372, 373, 383, and 402. Structural protein modeling suggested that amino acid changes in these positions result in alterations of the Gag protein structure as well as in Gag-specific T-cell epitopes. (4) Conclusions: Our results suggest that the majority of the Pakistan HIV-1 sub-subtype A1 strains were unique to Pakistan and with a specific mutation pattern in Gag. Full article
(This article belongs to the Special Issue Population Genomics of Human Viruses)
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11 pages, 888 KiB  
Article
Dating the Emergence of Human Endemic Coronaviruses
by Diego Forni, Rachele Cagliani, Uberto Pozzoli, Alessandra Mozzi, Federica Arrigoni, Luca De Gioia, Mario Clerici and Manuela Sironi
Viruses 2022, 14(5), 1095; https://doi.org/10.3390/v14051095 - 19 May 2022
Cited by 8 | Viewed by 4540
Abstract
Four endemic coronaviruses infect humans and cause mild symptoms. Because previous analyses were based on a limited number of sequences and did not control for effects that affect molecular dating, we re-assessed the timing of endemic coronavirus emergence. After controlling for recombination, selective [...] Read more.
Four endemic coronaviruses infect humans and cause mild symptoms. Because previous analyses were based on a limited number of sequences and did not control for effects that affect molecular dating, we re-assessed the timing of endemic coronavirus emergence. After controlling for recombination, selective pressure, and molecular clock model, we obtained similar tMRCA (time to the most recent common ancestor) estimates for the four coronaviruses, ranging from 72 (HCoV-229E) to 54 (HCoV-NL63) years ago. The split times of HCoV-229E and HCoV-OC43 from camel alphacoronavirus and bovine coronavirus were dated ~268 and ~99 years ago. The split times of HCoV-HKU1 and HCoV-NL63 could not be calculated, as their zoonoticic sources are unknown. To compare the timing of coronavirus emergence to that of another respiratory virus, we recorded the occurrence of influenza pandemics since 1500. Although there is no clear relationship between pandemic occurrence and human population size, the frequency of influenza pandemics seems to intensify starting around 1700, which corresponds with the initial phase of exponential increase of human population and to the emergence of HCoV-229E. The frequency of flu pandemics in the 19th century also suggests that the concurrence of HCoV-OC43 emergence and the Russian flu pandemic may be due to chance. Full article
(This article belongs to the Special Issue Population Genomics of Human Viruses)
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22 pages, 2461 KiB  
Article
Variability in Codon Usage in Coronaviruses Is Mainly Driven by Mutational Bias and Selective Constraints on CpG Dinucleotide
by Josquin Daron and Ignacio G. Bravo
Viruses 2021, 13(9), 1800; https://doi.org/10.3390/v13091800 - 10 Sep 2021
Cited by 6 | Viewed by 2587
Abstract
The Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the third human-emerged virus of the 21st century from the Coronaviridae family, causing the ongoing coronavirus disease 2019 (COVID-19) pandemic. Due to the high zoonotic potential of coronaviruses, it is critical to unravel their [...] Read more.
The Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the third human-emerged virus of the 21st century from the Coronaviridae family, causing the ongoing coronavirus disease 2019 (COVID-19) pandemic. Due to the high zoonotic potential of coronaviruses, it is critical to unravel their evolutionary history of host species breadth, host-switch potential, adaptation and emergence, to identify viruses posing a pandemic risk in humans. We present here a comprehensive analysis of the composition and codon usage bias of the 82 Orthocoronavirinae members, infecting 47 different avian and mammalian hosts. Our results clearly establish that synonymous codon usage varies widely among viruses, is only weakly dependent on their primary host, and is dominated by mutational bias towards AU-enrichment and by CpG avoidance. Indeed, variation in GC3 explains around 34%, while variation in CpG frequency explains around 14% of total variation in codon usage bias. Further insight on the mutational equilibrium within Orthocoronavirinae revealed that most coronavirus genomes are close to their neutral equilibrium, the exception being the three recently infecting human coronaviruses, which lie further away from the mutational equilibrium than their endemic human coronavirus counterparts. Finally, our results suggest that, while replicating in humans, SARS-CoV-2 is slowly becoming AU-richer, likely until attaining a new mutational equilibrium. Full article
(This article belongs to the Special Issue Population Genomics of Human Viruses)
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