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Viruses
Special Issues
Coronavirus Genome Evolution, Recombination and Phylogeny
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Coronavirus Genome Evolution, Recombination and Phylogeny

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 (31 July 2023) | Viewed by 12089

Special Issue Editor

Dr. Alexandre Hassanin

E-Mail Website
Guest Editor
Institut Systématique Evolution Biodiversité (ISYEB), Sorbonne Université, MNHN, CNRS, EPHE, UA, 57 rue Cuvier, CP 51, 75005 Paris, France
Interests: molecular evolution; phylogeny; genome; reservoir hosts; viruses; coevolution; ecology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Coronaviruses are enveloped viruses with a positive-sense single-stranded RNA genome of about 25–32 kb that are currently classified into four genera within the subfamily Coronavirinae (Alphacoronavirus, Betacoronavirus, Deltacoronavirus, and Gammacoronavirus). In mammals and birds they can cause respiratory tract infections, as well as liver, intestinal tract, and brain infections. In humans they include some cases of the common cold, as well as emerging pathogens involved in the SARS, MERS, and COVID-19 epidemics. Bats and birds are the natural reservoirs of most coronaviruses. With the development of metagenomic studies, more and more new coronaviruses are described, particularly in tropical regions, where the species diversity of their natural reservoirs is much more important than in temperate regions. Understanding the origin and evolution of coronaviruses through phylogenetic and molecular dating analyses remains, however, challenging due to their variable rates of nucleotide substitutions and genome recombination, as well as their high capacity for interspecies transmission (host jump).

The purpose of this Special Issue is to bring together a series of original research and review articles related to the evolution of coronavirus genomes. Areas of interest include, but are not limited to, the following topics: evolution of recombination, impact of recombination on phylogenetic inferences, characterization of recombinant genomes (including those identified between SARS-CoV-2 lineages), description of new animal coronaviruses, and the spatial and temporal evolution of coronaviruses.

Dr. Alexandre Hassanin
Guest Editor

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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. Viruses is an international peer-reviewed open access monthly journal published by MDPI.

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Keywords

  • coronavirus
  • RNA genome
  • evolution
  • recombination
  • phylogeny
  • reservoir hosts
  • bats
  • birds
  • ecology
  • emerging pathogens

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Published Papers (5 papers)

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Research

13 pages, 2084 KiB  
Article
Emergence of Genomic Diversity in the Spike Protein of the “Omicron” Variant
by Surajit Basak, Pratanu Kayet, Manisha Ghosh, Joyeeta Chatterjee and Shanta Dutta
Viruses 2023, 15(10), 2132; https://doi.org/10.3390/v15102132 - 21 Oct 2023
Cited by 2 | Viewed by 1840
Abstract
SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus) has constantly been evolving into different forms throughout its spread in the population. Emerging SARS-CoV-2 variants, predominantly the variants of concern (VOCs), could have an impact on the virus spread, pathogenicity, and diagnosis. The recently emerged “Omicron” [...] Read more.
SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus) has constantly been evolving into different forms throughout its spread in the population. Emerging SARS-CoV-2 variants, predominantly the variants of concern (VOCs), could have an impact on the virus spread, pathogenicity, and diagnosis. The recently emerged “Omicron” variant has exhibited rapid transmission and divergence. The spike protein of SARS-CoV-2 has consistently been appearing as the mutational hotspot of all these VOCs. In order to determine a deeper understanding of the recently emerged and extremely divergent “Omicron”, a study of amino acid usage patterns and their substitution patterns was performed and compared with those of the other four successful variants of concern (“Alpha”, “Beta”, “Gamma”, and “Delta”). We observed that the amino acid usage of “Omicron” has a distinct pattern that distinguishes it from other VOCs and is significantly correlated with the increased hydrophobicity in spike proteins. We observed an increase in the non-synonymous substitution rate compared with the other four VOCs. Considering the phylogenetic relationship, we hypothesized about the functional interdependence between recombination and the mutation rate that might have resulted in a shift in the optimum of the mutation rate for the evolution of the “Omicron” variant. The results suggest that for improved disease prevention and control, more attention should be given to the significant genetic differentiation and diversity of newly emerging variants. Full article
(This article belongs to the Special Issue Coronavirus Genome Evolution, Recombination and Phylogeny)
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14 pages, 4407 KiB  
Article
SARS-CoV-2 Recombination and Coinfection Events Identified in Clinical Samples in Russia
by Ekaterina N. Chernyaeva, Andrey A. Ayginin, Alexey V. Kosenkov, Svetlana V. Romanova, Anastasia V. Tsypkina, Andrey R. Luparev, Ivan F. Stetsenko, Natalia I. Gnusareva, Alina D. Matsvay, Yulia A. Savochkina and German A. Shipulin
Viruses 2023, 15(8), 1660; https://doi.org/10.3390/v15081660 - 30 Jul 2023
Viewed by 2238
Abstract
Recombination is one of the mechanisms of SARS-CoV-2 evolution along with the occurrence of point mutations, insertions, and deletions. Recently, recombinant variants of SARS-CoV-2 have been registered in different countries, and some of them have become circulating forms. In this work, we performed [...] Read more.
Recombination is one of the mechanisms of SARS-CoV-2 evolution along with the occurrence of point mutations, insertions, and deletions. Recently, recombinant variants of SARS-CoV-2 have been registered in different countries, and some of them have become circulating forms. In this work, we performed screening of SARS-CoV-2 genomic sequences to identify recombination events and co-infections with various strains of the SARS-CoV-2 virus detected in Russia from February 2020 to March 2022. The study included 9336 genomes of the COVID-19 pathogen obtained as a result of high-throughput sequencing on the Illumina platform. For data analysis, we used an algorithm developed by our group that can identify viral recombination variants and cases of co-infections by estimating the frequencies of characteristic substitutions in raw read alignment files and VCF files. The detected cases of recombination were confirmed by alternative sequencing methods, principal component analysis, and phylogenetic analysis. The suggested approach allowed for the identification of recombinant variants of strains BA.1 and BA.2, among which a new recombinant variant was identified, as well as a previously discovered one. The results obtained are the first evidence of the spread of recombinant variants of SARS-CoV-2 in Russia. In addition to cases of recombination we identified cases of coinfection: eight of them contained the genome of the Omicron line as one of the variants, six of them the genome of the Delta line, and two with the genome of the Alpha line. Full article
(This article belongs to the Special Issue Coronavirus Genome Evolution, Recombination and Phylogeny)
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12 pages, 2218 KiB  
Article
Rooting and Dating Large SARS-CoV-2 Trees by Modeling Evolutionary Rate as a Function of Time
by Xuhua Xia
Viruses 2023, 15(3), 684; https://doi.org/10.3390/v15030684 - 5 Mar 2023
Cited by 1 | Viewed by 2066
Abstract
Almost all published rooting and dating studies on SARS-CoV-2 assumed that (1) evolutionary rate does not change over time although different lineages can have different evolutionary rates (uncorrelated relaxed clock), and (2) a zoonotic transmission occurred in Wuhan and the culprit was immediately [...] Read more.
Almost all published rooting and dating studies on SARS-CoV-2 assumed that (1) evolutionary rate does not change over time although different lineages can have different evolutionary rates (uncorrelated relaxed clock), and (2) a zoonotic transmission occurred in Wuhan and the culprit was immediately captured, so that only the SARS-CoV-2 genomes obtained in 2019 and the first few months of 2020 (resulting from the first wave of the global expansion from Wuhan) are sufficient for dating the common ancestor. Empirical data contradict the first assumption. The second assumption is not warranted because mounting evidence suggests the presence of early SARS-CoV-2 lineages cocirculating with the Wuhan strains. Large trees with SARS-CoV-2 genomes beyond the first few months are needed to increase the likelihood of finding SARS-CoV-2 lineages that might have originated at the same time as (or even before) those early Wuhan strains. I extended a previously published rapid rooting method to model evolutionary rate as a linear function instead of a constant. This substantially improves the dating of the common ancestor of sampled SARS-CoV-2 genomes. Based on two large trees with 83,688 and 970,777 high-quality and full-length SARS-CoV-2 genomes that contain complete sample collection dates, the common ancestor was dated to 12 June 2019 and 7 July 2019 with the two trees, respectively. The two data sets would give dramatically different or even absurd estimates if the rate was treated as a constant. The large trees were also crucial for overcoming the high rate-heterogeneity among different viral lineages. The improved method was implemented in the software TRAD. Full article
(This article belongs to the Special Issue Coronavirus Genome Evolution, Recombination and Phylogeny)
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13 pages, 1587 KiB  
Article
Dynamics of Early Establishment of SARS-CoV-2 VOC Omicron Lineages in Minas Gerais, Brazil
by Mariane Talon de Menezes, Filipe Romero Rebello Moreira, Charles Whittaker, Franciele Martins Santos, Daniel Costa Queiroz, Victor Geddes, Paula Luize Camargos Fonseca, Jaqueline Góes de Jesus, Franciane Mendes-Oliveira, Valquíria Reis-Souza, Bibiana Santos, Danielle Alves Gomes Zauli, Aline Brito de Lima, Cristiane de Brito Mendonça, Luige Biciati Alvim, Joice do Prado Silva, Frederico Scott Varella Malta, Alessandro Clayton de Souza Ferreira, Nuno R. Faria, Ester Cerdeira Sabino and Renato Santana Aguiaradd Show full author list remove Hide full author list
Viruses 2023, 15(2), 585; https://doi.org/10.3390/v15020585 - 20 Feb 2023
Cited by 4 | Viewed by 2817
Abstract
Brazil is one of the nations most affected by Coronavirus disease 2019 (COVID-19). The introduction and establishment of new virus variants can be related to an increase in cases and fatalities. The emergence of Omicron, the most modified SARS-CoV-2 variant, caused alarm for [...] Read more.
Brazil is one of the nations most affected by Coronavirus disease 2019 (COVID-19). The introduction and establishment of new virus variants can be related to an increase in cases and fatalities. The emergence of Omicron, the most modified SARS-CoV-2 variant, caused alarm for the public health of Brazil. In this study, we examined the effects of the Omicron introduction in Minas Gerais (MG), the second-most populous state of Brazil. A total of 430 Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) samples from November 2021 to June 2022 from Belo Horizonte (BH) city were sequenced. These newly sequenced genomes comprise 72% of all previously available SARS-CoV-2 genomes for the city. Evolutionary analysis of novel viral genomes reveals that a great diversity of Omicron sublineages have circulated in BH, a pattern in-keeping with observations across Brazil more generally. Bayesian phylogeographic reconstructions indicate that this diversity is a product of a large number of international and national importations. As observed previously, São Paulo state is shown as a significant hub for viral spread throughout the country, contributing to around 70% of all viral Omicron introductions detected in MG. Full article
(This article belongs to the Special Issue Coronavirus Genome Evolution, Recombination and Phylogeny)
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21 pages, 2961 KiB  
Article
Retracing Phylogenetic, Host and Geographic Origins of Coronaviruses with Coloured Genomic Bootstrap Barcodes: SARS-CoV and SARS-CoV-2 as Case Studies
by Alexandre Hassanin and Opale Rambaud
Viruses 2023, 15(2), 406; https://doi.org/10.3390/v15020406 - 31 Jan 2023
Cited by 4 | Viewed by 2045
Abstract
Phylogenetic trees of coronaviruses are difficult to interpret because they undergo frequent genomic recombination. Here, we propose a new method, coloured genomic bootstrap (CGB) barcodes, to highlight the polyphyletic origins of human sarbecoviruses and understand their host and geographic origins. The results indicate [...] Read more.
Phylogenetic trees of coronaviruses are difficult to interpret because they undergo frequent genomic recombination. Here, we propose a new method, coloured genomic bootstrap (CGB) barcodes, to highlight the polyphyletic origins of human sarbecoviruses and understand their host and geographic origins. The results indicate that SARS-CoV and SARS-CoV-2 contain genomic regions of mixed ancestry originating from horseshoe bat (Rhinolophus) viruses. First, different regions of SARS-CoV share exclusive ancestry with five Rhinolophus viruses from Southwest China (RfYNLF/31C: 17.9%; RpF46: 3.3%; RspSC2018: 2.0%; Rpe3: 1.3%; RaLYRa11: 1.0%) and 97% of its genome can be related to bat viruses from Yunnan (China), supporting its emergence in the Rhinolophus species of this province. Second, different regions of SARS-CoV-2 share exclusive ancestry with eight Rhinolophus viruses from Yunnan (RpYN06: 5.8%; RaTG13: 4.8%; RmYN02: 3.8%), Laos (RpBANAL103: 3.3%; RmarBANAL236: 1.7%; RmBANAL52: 1.0%; RmBANAL247: 0.7%), and Cambodia (RshSTT200: 2.3%), and 98% of its genome can be related to bat viruses from northern Laos and Yunnan, supporting its emergence in the Rhinolophus species of this region. Although CGB barcodes are very useful in retracing the origins of human sarbecoviruses, further investigations are needed to better take into account the diversity of coronaviruses in bats from Cambodia, Laos, Myanmar, Thailand and Vietnam. Full article
(This article belongs to the Special Issue Coronavirus Genome Evolution, Recombination and Phylogeny)
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