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Viral and Host Factors Driving the Emergence and the Evolution...
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Viral and Host Factors Driving the Emergence and the Evolution of the SARS-CoV-2 and Other Coronaviruses

A special issue of Viruses (ISSN 1999-4915). This special issue belongs to the section "SARS-CoV-2 and COVID-19".

Deadline for manuscript submissions: closed (30 April 2022) | Viewed by 28356

Special Issue Editor

Dr. Corinne Ronfort

E-Mail Website
Guest Editor
1. Animal Health Department UMR IVPC, University of Lyon I, French National Research Institute for Agriculture, Food and Environment, 69007 Lyon, France
2. AIOVA sas, University of Grenoble, 570 rue de la Chimie, 38300 Saint Martin d’Hèyres, France
Interests: infectiology; molecular and cellular biology; virology; emerging and re-emerging viral infections; vaccines; SARS-CoV; retro- and lentiviruses; influenza; gene therapy; gene transfer vectors

Special Issue Information

Dear Colleagues,

Eighteen months ago, humanity was facing the emergence of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the causative agent of the COVID-19 pandemic. This emergence, from an animal reservoir, is the third in just two decades after the SARS-CoV-1 in 2002 and the MERS in 2012. Thus, new SARS pandemics are likely to occur in the future.

SARS viruses undergo continuous genetic changes. Thousands of SARS-CoV-2 variants have been detected by laboratory screening. Four of them (from United Kingdom, South Africa, Brazil and India) that may have enhanced transmission and pathogenicity are emerging and are of great concern. Regarding the vaccines authorized to date for an emergency use, there is also concern about the reduction in vaccine-induced immune protection to emerging variants.

The complex questions to explore are : (i) what makes a SARS virus transmissible from one species to another, and (ii) which factors drive mutation, evolution and emergence of SARS. Understanding these questions will provide us with better tools to controlling COVID.

The aim of this special issue is to provide data on the viral, cellular and host factors involved in the emergence and evolution of the SARS viruses. Several factors are in question such as the viral dynamic, the RNA nature of the virus - ability to mutate, the role of co-infections and recombinations -, host and cellular restriction factors as well as host immunity and immune escape.

Papers focusing on animal coronaviruses that may be relevant to SARS-CoV-2 are welcome.

Dr. Corinne Ronfort
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

  • COVID-19
  • SARS-CoV-2, SARS, MERS
  • biology of SARS CoV-2 and other coronaviruses
  • emergence
  • viral evolution, variants
  • host factors
  • innate and adaptive immunity
  • crossing of the species barrier

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Published Papers (7 papers)

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Editorial

Jump to: Research, Review

3 pages, 174 KiB  
Editorial
Special Issue “Viral and Host Factors Driving the Emergence and the Evolution of the SARS-CoV-2 and Other Coronaviruses”
by Corinne Ronfort
Viruses 2022, 14(8), 1705; https://doi.org/10.3390/v14081705 - 2 Aug 2022
Viewed by 1371
Abstract
Two and half years ago, humanity was facing the emergence of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the causal agent of the COVID-19 pandemics that significantly impact public health, society and the global economy [...] Full article
(This article belongs to the Special Issue Viral and Host Factors Driving the Emergence and the Evolution of the SARS-CoV-2 and Other Coronaviruses)

Research

Jump to: Editorial, Review

17 pages, 3676 KiB  
Article
Contrasting Epidemiology and Population Genetics of COVID-19 Infections Defined by Multilocus Genotypes in SARS-CoV-2 Genomes Sampled Globally
by Felicia Hui Min Chan, Ricardo Ataide, Jack S. Richards and Charles A. Narh
Viruses 2022, 14(7), 1434; https://doi.org/10.3390/v14071434 - 29 Jun 2022
Cited by 9 | Viewed by 2488
Abstract
Since its emergence in 2019, SARS-CoV-2 has spread and evolved globally, with newly emerged variants of concern (VOCs) accounting for more than 500 million COVID-19 cases and 6 million deaths. Continuous surveillance utilizing simple genetic tools is needed to measure the viral epidemiological [...] Read more.
Since its emergence in 2019, SARS-CoV-2 has spread and evolved globally, with newly emerged variants of concern (VOCs) accounting for more than 500 million COVID-19 cases and 6 million deaths. Continuous surveillance utilizing simple genetic tools is needed to measure the viral epidemiological diversity, risk of infection, and distribution among different demographics in different geographical regions. To help address this need, we developed a proof-of-concept multilocus genotyping tool and demonstrated its utility to monitor viral populations sampled in 2020 and 2021 across six continents. We sampled globally 22,164 SARS-CoV-2 genomes from GISAID (inclusion criteria: available clinical and demographic data). They comprised two study populations, “2020 genomes” (N = 5959) sampled from December 2019 to September 2020 and “2021 genomes” (N = 16,205) sampled from 15 January to 15 March 2021. All genomes were aligned to the SARS-CoV-2 reference genome and amino acid polymorphisms were called with quality filtering. Thereafter, 74 codons (loci) in 14 genes including orf1ab polygene (N = 9), orf3a, orf8, nucleocapsid (N), matrix (M), and spike (S) met the 0.01 minimum allele frequency criteria and were selected to construct multilocus genotypes (MLGs) for the genomes. At these loci, 137 mutant/variant amino acids (alleles) were detected with eight VOC-defining variant alleles, including N KR203&204, orf1ab (I265, F3606, and L4715), orf3a H57, orf8 S84, and S G614, being predominant globally with > 35% prevalence. Their persistence and selection were associated with peaks in the viral transmission and COVID-19 incidence between 2020 and 2021. Epidemiologically, older patients (≥20 years) compared to younger patients (<20 years) had a higher risk of being infected with these variants, but this association was dependent on the continent of origin. In the global population, the discriminant analysis of principal components (DAPC) showed contrasting patterns of genetic clustering with three (Africa, Asia, and North America) and two (North and South America) continental clusters being observed for the 2020 and 2021 global populations, respectively. Within each continent, the MLG repertoires (range 40–199) sampled in 2020 and 2021 were genetically differentiated, with ≤4 MLGs per repertoire accounting for the majority of genomes sampled. These data suggested that the majority of SARS-CoV-2 infections in 2020 and 2021 were caused by genetically distinct variants that likely adapted to local populations. Indeed, four GISAID clade-defined VOCs - GRY (Alpha), GH (Beta), GR (Gamma), and G/GK (Delta variant) were differentiated by their MLG signatures, demonstrating the versatility of the MLG tool for variant identification. Results from this proof-of-concept multilocus genotyping demonstrates its utility for SARS-CoV-2 genomic surveillance and for monitoring its spatiotemporal epidemiology and evolution, particularly in response to control interventions including COVID-19 vaccines and chemotherapies. Full article
(This article belongs to the Special Issue Viral and Host Factors Driving the Emergence and the Evolution of the SARS-CoV-2 and Other Coronaviruses)
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13 pages, 1755 KiB  
Article
Infectious Bronchitis Coronavirus: Genome Evolution in Vaccinated and Non-Vaccinated SPF Chickens
by Alexandre Flageul, Chantal Allée, Céline Courtillon, Véronique Béven, Hélène Quenault, Yannick Blanchard, Michel Amelot, David Courtois, Sjaak De Wit, Nicolas Eterradossi, Béatrice Grasland and Paul A. Brown
Viruses 2022, 14(7), 1392; https://doi.org/10.3390/v14071392 - 25 Jun 2022
Cited by 7 | Viewed by 2263
Abstract
Infectious Bronchitis virus (IBV) continues to cause significant economic losses for the chicken industry despite the use of many live IBV vaccines around the world. Several authors have suggested that vaccine-induced partial protection may contribute to the emergence of new IBV strains. In [...] Read more.
Infectious Bronchitis virus (IBV) continues to cause significant economic losses for the chicken industry despite the use of many live IBV vaccines around the world. Several authors have suggested that vaccine-induced partial protection may contribute to the emergence of new IBV strains. In order to study this hypothesis, three passages of a challenge IBV were made in SPF chickens sham inoculated or vaccinated at day of age using a live vaccine heterologous to the challenge virus. All birds that were challenged with vaccine heterologous virus were positive for viral RNA. NGS analysis of viral RNA in the unvaccinated group showed a rapid selection of seven genetic variants, finally modifying the consensus genome of the viral population. Among them, five were non-synonymous, modifying one position in NSP 8, one in NSP 13, and three in the Spike protein. In the vaccinated group, one genetic variant was selected over the three passages. This synonymous modification was absent from the unvaccinated group. Under these conditions, the genome population of an IBV challenge virus evolved rapidly in both heterologous vaccinated and non-vaccinated birds, while the genetic changes that were selected and the locations of these were very different between the two groups. Full article
(This article belongs to the Special Issue Viral and Host Factors Driving the Emergence and the Evolution of the SARS-CoV-2 and Other Coronaviruses)
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15 pages, 2155 KiB  
Article
A Pre-Vaccination Baseline of SARS-CoV-2 Genetic Surveillance and Diversity in the United States
by Adam A. Capoferri, Wei Shao, Jon Spindler, John M. Coffin, Jason W. Rausch and Mary F. Kearney
Viruses 2022, 14(1), 104; https://doi.org/10.3390/v14010104 - 7 Jan 2022
Cited by 1 | Viewed by 2142
Abstract
COVID-19 vaccines were first administered on 15 December 2020, marking an important transition point for the spread of SARS-CoV-2 in the United States (U.S.). Prior to this point in time, the virus spread to an almost completely immunologically naïve population, whereas subsequently, vaccine-induced [...] Read more.
COVID-19 vaccines were first administered on 15 December 2020, marking an important transition point for the spread of SARS-CoV-2 in the United States (U.S.). Prior to this point in time, the virus spread to an almost completely immunologically naïve population, whereas subsequently, vaccine-induced immune pressure and prior infections might be expected to influence viral evolution. Accordingly, we conducted a study to characterize the spread of SARS-CoV-2 in the U.S. pre-vaccination, investigate the depth and uniformity of genetic surveillance during this period, and measure and otherwise characterize changing viral genetic diversity, including by comparison with more recently emergent variants of concern (VOCs). In 2020, SARS-CoV-2 spread across the U.S. in three phases distinguishable by peaks in the numbers of infections and shifting geographical distributions. Virus was genetically sampled during this period at an overall rate of ~1.2%, though there was a substantial mismatch between case rates and genetic sampling nationwide. Viral genetic diversity tripled over this period but remained low in comparison to other widespread RNA virus pathogens, and although 54 amino acid changes were detected at frequencies exceeding 5%, linkage among them was not observed. Based on our collective observations, our analysis supports a targeted strategy for worldwide genetic surveillance as perhaps the most sensitive and efficient means of detecting new VOCs. Full article
(This article belongs to the Special Issue Viral and Host Factors Driving the Emergence and the Evolution of the SARS-CoV-2 and Other Coronaviruses)
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22 pages, 3845 KiB  
Article
Circulation and Evolution of SARS-CoV-2 in India: Let the Data Speak
by Sanket Limaye, Sunitha M. Kasibhatla, Mukund Ramtirthkar, Meenal Kinikar, Mohan M. Kale and Urmila Kulkarni-Kale
Viruses 2021, 13(11), 2238; https://doi.org/10.3390/v13112238 - 8 Nov 2021
Cited by 13 | Viewed by 4639
Abstract
The COVID-19 pandemic is a global challenge that impacted 200+ countries. India ranks in the second and third positions in terms of number of reported cases and deaths. Being a populous country with densely packed cities, SARS-CoV-2 spread exponentially. India sequenced ≈0.14% isolates [...] Read more.
The COVID-19 pandemic is a global challenge that impacted 200+ countries. India ranks in the second and third positions in terms of number of reported cases and deaths. Being a populous country with densely packed cities, SARS-CoV-2 spread exponentially. India sequenced ≈0.14% isolates from confirmed cases for pandemic surveillance and contributed ≈1.58% of complete genomes sequenced globally. This study was designed to map the circulating lineage diversity and to understand the evolution of SARS-CoV-2 in India using comparative genomics and population genetics approaches. Despite varied sequencing coverage across Indian States and Union Territories, isolates belonging to variants of concern (VoC) and variants of interest (VoI) circulated, persisted, and diversified during the first seventeen months of the pandemic. Delta and Kappa lineages emerged in India and spread globally. The phylogenetic tree shows lineage-wise monophyletic clusters of VoCs/VoIs and diversified tree topologies for non-VoC/VoI lineages designated as ‘Others’ in this study. Evolutionary dynamics analyses substantiate a lack of spatio-temporal clustering, which is indicative of multiple global and local introductions. Sites under positive selection and significant variations in spike protein corroborate with the constellation of mutations to be monitored for VoC/VoI as well as substitutions that are characteristic of functions with implications in virus–host interactions, differential glycosylation, immune evasion, and escape from neutralization. Full article
(This article belongs to the Special Issue Viral and Host Factors Driving the Emergence and the Evolution of the SARS-CoV-2 and Other Coronaviruses)
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15 pages, 7207 KiB  
Article
Mutation in a SARS-CoV-2 Haplotype from Sub-Antarctic Chile Reveals New Insights into the Spike’s Dynamics
by Jorge González-Puelma, Jacqueline Aldridge, Marco Montes de Oca, Mónica Pinto, Roberto Uribe-Paredes, José Fernández-Goycoolea, Diego Alvarez-Saravia, Hermy Álvarez, Gonzalo Encina, Thomas Weitzel, Rodrigo Muñoz, Álvaro Olivera-Nappa, Sergio Pantano and Marcelo A. Navarrete
Viruses 2021, 13(5), 883; https://doi.org/10.3390/v13050883 - 11 May 2021
Cited by 8 | Viewed by 6457
Abstract
The emergence of SARS-CoV-2 variants, as observed with the D614G spike protein mutant and, more recently, with B.1.1.7 (501Y.V1), B.1.351 (501Y.V2) and B.1.1.28.1 (P.1) lineages, represent a continuous threat and might lead to strains of higher infectivity and/or virulence. We report on the [...] Read more.
The emergence of SARS-CoV-2 variants, as observed with the D614G spike protein mutant and, more recently, with B.1.1.7 (501Y.V1), B.1.351 (501Y.V2) and B.1.1.28.1 (P.1) lineages, represent a continuous threat and might lead to strains of higher infectivity and/or virulence. We report on the occurrence of a SARS-CoV-2 haplotype with nine mutations including D614G/T307I double-mutation of the spike. This variant expanded and completely replaced previous lineages within a short period in the subantarctic Magallanes Region, southern Chile. The rapid lineage shift was accompanied by a significant increase of cases, resulting in one of the highest incidence rates worldwide. Comparative coarse-grained molecular dynamic simulations indicated that T307I and D614G belong to a previously unrecognized dynamic domain, interfering with the mobility of the receptor binding domain of the spike. The T307I mutation showed a synergistic effect with the D614G. Continuous surveillance of new mutations and molecular analyses of such variations are important tools to understand the molecular mechanisms defining infectivity and virulence of current and future SARS-CoV-2 strains. Full article
(This article belongs to the Special Issue Viral and Host Factors Driving the Emergence and the Evolution of the SARS-CoV-2 and Other Coronaviruses)
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Review

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27 pages, 11448 KiB  
Review
Evolutionary Dynamics and Epidemiology of Endemic and Emerging Coronaviruses in Humans, Domestic Animals, and Wildlife
by Ariful Islam, Jinnat Ferdous, Shariful Islam, Md. Abu Sayeed, Shusmita Dutta Choudhury, Otun Saha, Mohammad Mahmudul Hassan and Tahmina Shirin
Viruses 2021, 13(10), 1908; https://doi.org/10.3390/v13101908 - 23 Sep 2021
Cited by 33 | Viewed by 7179
Abstract
Diverse coronavirus (CoV) strains can infect both humans and animals and produce various diseases. CoVs have caused three epidemics and pandemics in the last two decades, and caused a severe impact on public health and the global economy. Therefore, it is of utmost [...] Read more.
Diverse coronavirus (CoV) strains can infect both humans and animals and produce various diseases. CoVs have caused three epidemics and pandemics in the last two decades, and caused a severe impact on public health and the global economy. Therefore, it is of utmost importance to understand the emergence and evolution of endemic and emerging CoV diversity in humans and animals. For diverse bird species, the Infectious Bronchitis Virus is a significant one, whereas feline enteric and canine coronavirus, recombined to produce feline infectious peritonitis virus, infects wild cats. Bovine and canine CoVs have ancestral relationships, while porcine CoVs, especially SADS-CoV, can cross species barriers. Bats are considered as the natural host of diverse strains of alpha and beta coronaviruses. Though MERS-CoV is significant for both camels and humans, humans are nonetheless affected more severely. MERS-CoV cases have been reported mainly in the Arabic peninsula since 2012. To date, seven CoV strains have infected humans, all descended from animals. The severe acute respiratory syndrome coronaviruses (SARS-CoV and SARS-CoV-2) are presumed to be originated in Rhinolopoid bats that severely infect humans with spillover to multiple domestic and wild animals. Emerging alpha and delta variants of SARS-CoV-2 were detected in pets and wild animals. Still, the intermediate hosts and all susceptible animal species remain unknown. SARS-CoV-2 might not be the last CoV to cross the species barrier. Hence, we recommend developing a universal CoV vaccine for humans so that any future outbreak can be prevented effectively. Furthermore, a One Health approach coronavirus surveillance should be implemented at human-animal interfaces to detect novel coronaviruses before emerging to humans and to prevent future epidemics and pandemics. Full article
(This article belongs to the Special Issue Viral and Host Factors Driving the Emergence and the Evolution of the SARS-CoV-2 and Other Coronaviruses)
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