The Variant-Based Dynamics of SARS-CoV-2 and Other Viral Diseases

A special issue of Vaccines (ISSN 2076-393X). This special issue belongs to the section "COVID-19 Vaccines and Vaccination".

Deadline for manuscript submissions: closed (21 June 2022) | Viewed by 32133

Special Issue Editors

CIRAD, University of Montpellier, Montpellier, France
Interests: emerging diseases; infectious diseases; microbiology; genomics; virus evolution; dynamics of infectious diseases
Special Issues, Collections and Topics in MDPI journals
Department of Animal Biology, Universitat de Barcelona, Barcelona, Spain
Interests: the peculiar ecology of bats (roosting behavior, habitat utilization, and flight mode) and the hosts and transmission pathways that can lead to bat exposure to and infection with Ebola viruses

Special Issue Information

Dear Colleagues,

The COVID-19 crisis has stressed the crucial role of virus variants in the progression of an epidemic or pandemic. The expansion of a virus epidemic/pandemic through a succession of variants is a common process. Nevertheless, there are still many unknowns, and this process is leading to many questions relating to several disciplines. Understanding the role of variants in an epidemic/pandemic is essential to understand the dynamics of these diseases which, in turn, is crucial for developing efficient prevention approaches. A priority is to understand what a variant is from both an evolutionary and functional standpoint. It is essential to characterize this process of generation and succession of variants from different angles, i.e., genetics, evolution, selection adaptation, function, transmissibility, virulence, epidemiology, host interaction, host range, multi-host dynamics, modeling, interaction with the immune system, etc.

Virus variants represent a significant threat to vaccines. There is a risk that new variants may overcome the protection offered by a vaccine. Investigating virus variant selection and evolution in regard to vaccines is thus another key issue to be addressed.

This Special Issue aims to gather works addressing all aspects of viral variant analysis. This Special Issue will welcome all kinds of articles, e.g., reviews, short reports, hypotheses, research articles, opinions, and comments, on all families of viruses. 

Prof. Dr. Roger Frutos
Dr. Jordi Serra-Cobo
Guest Editors

Manuscript Submission Information

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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. Vaccines 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 2700 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

  • variants
  • virus
  • evolution
  • epidemic
  • pandemic
  • viral disease
  • COVID-19
  • epidemiology

Published Papers (5 papers)

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Research

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10 pages, 1407 KiB  
Article
Genome Similarities between Human-Derived and Mink-Derived SARS-CoV-2 Make Mink a Potential Reservoir of the Virus
by Mohammad Khalid, Anas Alshishani and Yousef Al-ebini
Vaccines 2022, 10(8), 1352; https://0-doi-org.brum.beds.ac.uk/10.3390/vaccines10081352 - 19 Aug 2022
Cited by 3 | Viewed by 1358
Abstract
SARS-CoV-2 has RNA as the genome, which makes the virus more prone to mutations. Occasionally, mutations help a virus to cross the species barrier. SARS-CoV-2 infections in humans and minks (Neovison vison) are examples of zoonotic spillover. Many studies on the [...] Read more.
SARS-CoV-2 has RNA as the genome, which makes the virus more prone to mutations. Occasionally, mutations help a virus to cross the species barrier. SARS-CoV-2 infections in humans and minks (Neovison vison) are examples of zoonotic spillover. Many studies on the mutational analysis of human-derived SARS-CoV-2 have been published, but insight into the mink-derived SARS-CoV-2 genome of mutations is still required. Here, we performed a mutation analysis of the mink-derived SARS-CoV-2 genome sequences. We analyzed all available full-length mink-derived SARS-CoV-2 genome sequences on GISAID (214 genome sequences from the Netherlands and 133 genome sequences from Denmark). We found a striking resemblance between human-derived and mink-derived SARS-CoV-2. Our study showed that mutation patterns in the SARS-CoV-2 genome samples from the Netherlands and Denmark were different. Out of the 201 mutations we found, only 13 mutations were shared by the Netherlands’ and Denmark’s mink-derived samples. We found that six mutations were prevalent in the mink-derived SARS-CoV-2 genomes, and these six mutations are also known to be prevalent in human-derived SARS-CoV-2 variants. Our study reveals that the G27948T mutation in SARS-CoV-2 leads to truncation of ORF8, which was also reported in human-derived SARS-CoV-2, thus indicating that the virus can replicate without the full-length ORF8. These resemblances between mink-derived and human-derived SARS-CoV-2 enable the virus to cross the species barrier and suggest mink a potential reservoir for the virus. Full article
(This article belongs to the Special Issue The Variant-Based Dynamics of SARS-CoV-2 and Other Viral Diseases)
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20 pages, 3842 KiB  
Article
Comparison of COVID-19 Resilience Index and Its Associated Factors across 29 Countries during the Delta and Omicron Variant Periods
by Le Duc Huy, Chung-Liang Shih, Yao-Mao Chang, Nhi Thi Hong Nguyen, Phan Thanh Phuc, Tsong-Yih Ou and Chung-Chien Huang
Vaccines 2022, 10(6), 940; https://0-doi-org.brum.beds.ac.uk/10.3390/vaccines10060940 - 13 Jun 2022
Cited by 3 | Viewed by 2520
Abstract
Our study aims to compare the pandemic resilience index and explore the associated factors during the Delta and Omicron variant periods. In addition, the study aims to identify the characteristics of countries that had good performances. We analyzed observation data among 29 countries [...] Read more.
Our study aims to compare the pandemic resilience index and explore the associated factors during the Delta and Omicron variant periods. In addition, the study aims to identify the characteristics of countries that had good performances. We analyzed observation data among 29 countries over the first eight weeks during the two periods of Delta and Omicron variant dominance. Data were extracted from open public databases. The Omicron variant caused a lowered mortality rate per 100,000 COVID-19 patients; however, it is still imposing a colossal burden on health care systems. We found the percentage of the population fully vaccinated and high government indices were significantly associated with a better resilience index in both the Delta and Omicron periods. In contrast, the higher death rate of cancers and greater years lived with disability (YLD) caused by low bone density were linked with poor resilience index in the Omicron periods. Over two periods of Delta and Omicron, countries with good performance had a lower death rate from chronic diseases and lower YLD caused by nutrition deficiency and PM2.5. Our findings suggest that governments need to keep enhancing the vaccine coverage rates, developing interventions for populations with chronic diseases and nutrition deficiency to mitigate COVID-19 impacts on these targeted vulnerable cohorts. Full article
(This article belongs to the Special Issue The Variant-Based Dynamics of SARS-CoV-2 and Other Viral Diseases)
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13 pages, 4237 KiB  
Article
Could SARS-CoV-2 Have Bacteriophage Behavior or Induce the Activity of Other Bacteriophages?
by Carlo Brogna, Barbara Brogna, Domenico Rocco Bisaccia, Francesco Lauritano, Giuliano Marino, Luigi Montano, Simone Cristoni, Marina Prisco and Marina Piscopo
Vaccines 2022, 10(5), 708; https://0-doi-org.brum.beds.ac.uk/10.3390/vaccines10050708 - 29 Apr 2022
Cited by 23 | Viewed by 23575
Abstract
SARS-CoV-2 has become one of the most studied viruses of the last century. It was assumed that the only possible host for these types of viruses was mammalian eukaryotic cells. Our recent studies show that microorganisms in the human gastrointestinal tract affect the [...] Read more.
SARS-CoV-2 has become one of the most studied viruses of the last century. It was assumed that the only possible host for these types of viruses was mammalian eukaryotic cells. Our recent studies show that microorganisms in the human gastrointestinal tract affect the severity of COVID-19 and for the first time provide indications that the virus might replicate in gut bacteria. In order to further support these findings, in the present work, cultures of bacteria from the human microbiome and SARS-CoV-2 were analyzed by electron and fluorescence microscopy. The images presented in this article, in association with the nitrogen (15N) isotope-labeled culture medium experiment, suggest that SARS-CoV-2 could also infect bacteria in the gut microbiota, indicating that SARS-CoV-2 could act as a bacteriophage. Our results add new knowledge to the understanding of the mechanisms of SARS-CoV-2 infection and fill gaps in the study of the interactions between SARS-CoV-2 and non-mammalian cells. These findings could be useful in suggesting specific new pharmacological solutions to support the vaccination campaign. Full article
(This article belongs to the Special Issue The Variant-Based Dynamics of SARS-CoV-2 and Other Viral Diseases)
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Review

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15 pages, 541 KiB  
Review
A Systematic Review on the Emergence of Omicron Variant and Recent Advancement in Therapies
by Beyau M. Konyak, Mohan Sharma, Shabnam Kharia, Ramendra Pati Pandey and Chung-Ming Chang
Vaccines 2022, 10(9), 1468; https://0-doi-org.brum.beds.ac.uk/10.3390/vaccines10091468 - 05 Sep 2022
Cited by 6 | Viewed by 2206
Abstract
With the ongoing COVID-19 pandemic, the emergence of the novel Omicron variant in November 2021 has created chaos around the world. Despite mass vaccination, Omicron has spread rapidly, raising concerns around the globe. The Omicron variant has a vast array of mutations, as [...] Read more.
With the ongoing COVID-19 pandemic, the emergence of the novel Omicron variant in November 2021 has created chaos around the world. Despite mass vaccination, Omicron has spread rapidly, raising concerns around the globe. The Omicron variant has a vast array of mutations, as compared to another variant of concern, with a total of 50 mutations, 30 of which are present on its spike protein alone. These mutations have led to immune escape and more transmissibility compared to other variants, including the Delta variant. A cluster of mutations (H655Y, N679K, and P681H) present in the Omicron spike protein could aid in transmission. Currently, no virus-specific data are available to predict the efficacy of the anti-viral and mAbs drugs. However, two monoclonal antibody drugs, Sotrovimab and Evusheld, are authorized for emergency use in COVID-19 patients. This virus is not fading away soon. The easiest solution and least expensive measure to fight against this pandemic are to follow the appropriate COVID-19 protocols. There is a need to strengthen the level of research for the development of potential vaccines and anti-viral drugs. It is also important to monitor and expand the genomic surveillance to keep track of the emergence of new variants, thus avoiding the spread of new diseases worldwide. This article highlights the emergence of the new SARS-CoV-2 variant of concern, Omicron (B.1.1.529), and the vast number of mutations in its protein. In addition, recent advancements in drugs approved by FDA to treat COVID patients have been listed and focused in this paper. Full article
(This article belongs to the Special Issue The Variant-Based Dynamics of SARS-CoV-2 and Other Viral Diseases)
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Other

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16 pages, 1741 KiB  
Perspective
On the Origins of Omicron’s Unique Spike Gene Insertion
by A. J. Venkatakrishnan, Praveen Anand, Patrick J. Lenehan, Rohit Suratekar, Bharathwaj Raghunathan, Michiel J. M. Niesen and Venky Soundararajan
Vaccines 2022, 10(9), 1509; https://0-doi-org.brum.beds.ac.uk/10.3390/vaccines10091509 - 09 Sep 2022
Cited by 11 | Viewed by 1826
Abstract
The emergence of a heavily mutated SARS-CoV-2 variant (Omicron; Pango lineage B.1.1.529 and BA sublineages) and its rapid spread to over 75 countries raised a global public health alarm. Characterizing the mutational profile of Omicron is necessary to interpret its clinical phenotypes which [...] Read more.
The emergence of a heavily mutated SARS-CoV-2 variant (Omicron; Pango lineage B.1.1.529 and BA sublineages) and its rapid spread to over 75 countries raised a global public health alarm. Characterizing the mutational profile of Omicron is necessary to interpret its clinical phenotypes which are shared with or distinctive from those of other SARS-CoV-2 variants. We compared the mutations of the initially circulating Omicron variant (now known as BA.1) with prior variants of concern (Alpha, Beta, Gamma, and Delta), variants of interest (Lambda, Mu, Eta, Iota, and Kappa), and ~1500 SARS-CoV-2 lineages constituting ~5.8 million SARS-CoV-2 genomes. Omicron’s Spike protein harbors 26 amino acid mutations (23 substitutions, 2 deletions, and 1 insertion) that are distinct compared to other variants of concern. While the substitution and deletion mutations appeared in previous SARS-CoV-2 lineages, the insertion mutation (ins214EPE) was not previously observed in any other SARS-CoV-2 lineage. Here, we consider and discuss various mechanisms through which the nucleotide sequence encoding for ins214EPE could have been acquired, including local duplication, polymerase slippage, and template switching. Although we are not able to definitively determine the mechanism, we highlight the plausibility of template switching. Analysis of the homology of the inserted nucleotide sequence and flanking regions suggests that this template-switching event could have involved the genomes of SARS-CoV-2 variants (e.g., the B.1.1 strain), other human coronaviruses that infect the same host cells as SARS-CoV-2 (e.g., HCoV-OC43 or HCoV-229E), or a human transcript expressed in a host cell that was infected by the Omicron precursor. Full article
(This article belongs to the Special Issue The Variant-Based Dynamics of SARS-CoV-2 and Other Viral Diseases)
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