Comparative genomic signature representations of the emerging COVID-19 coronavirus and other coronaviruses: High identity and possible recombination between Bat and Pangolin coronaviruses

Touati, Rabeb; Haddad-Boubaker, Sondès; Ferchichi, Imen; Messaoudi, Imen; Ouesleti, Afef Elloumi; Triki, Henda; Lachiri, Zied; Kharrat, Maher

doi:10.1016/j.ygeno.2020.07.003

Cited by 32 publications

(45 citation statements)

References 30 publications

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“…Another study, which supports the results of present finding, showed that the bat and pangolin coronaviruses were the most related to SARS-CoV-2 with 96% and 86% of identity all along the genome [ 57 ]. The comparison study from bat and pangolin by Li and his friends explains that BetaCoV/bat/Yunnan/RaTG13/2013 virus was more similar to the SARS-CoV-2 virus than the coronavirus obtained from the two pangolin samples (SRR10168377 and SRR10168378).…”

Section: Resultssupporting

confidence: 90%

Sequence Analysis and Structure Prediction of SARS-CoV-2 Accessory Proteins 9b and ORF14: Evolutionary Analysis Indicates Close Relatedness to Bat Coronavirus

Baruah¹,

Devi²,

Sharma

2020

BioMed Research International

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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has a single-stranded RNA genome that encodes 14 open reading frames (ORFs), eight of which encode accessory proteins that allow the virus to infect the host and promote virulence. The genome expresses around 29 structural and nonstructural protein products. The accessory proteins of SARS-CoV-2 are not essential for virus replication but do affect viral release, stability, and pathogenesis and finally contribute to virulence. This paper has attempted the structure prediction and functional analysis of two such accessory proteins, 9b and ORF14, in the absence of experimental structures. Sequence analysis, structure prediction, functional characterization, and evolutionary analysis based on the UniProtKB reviewed the amino acid sequences of SARS-CoV-2 9b (P0DTD2) and ORF14 (P0DTD3) proteins. Modeling has been presented with the introduction of hybrid comparative and ab initio modeling. QMEANDisCo 4.0.0 and ProQ3 for global and local (per residue) quality estimates verified the structures as high quality, which may be attributed to structure-based drug design targets. Tunnel analysis revealed the presence of 1-2 highly active tunneling sites, perhaps which will able to provide certain inputs for advanced structure-based drug design or to formulate potential vaccines in the absence of a complete experimental structure. The evolutionary analysis of both proteins of human SARS-CoV-2 indicates close relatedness to the bat coronavirus. The whole-genome phylogeny indicates that only the new bat coronavirus followed by pangolin coronaviruses has a close evolutionary relationship with the novel SARS-CoV-2.

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Section: Resultssupporting

confidence: 90%

Sequence Analysis and Structure Prediction of SARS-CoV-2 Accessory Proteins 9b and ORF14: Evolutionary Analysis Indicates Close Relatedness to Bat Coronavirus

Baruah¹,

Devi²,

Sharma

2020

BioMed Research International

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“…In terms of recombination events, our analysis revealed a plausible past recombination between animal CoVs from pangolin and bat, which has been also confirmed by similar analyses (i.e., Simplot and Recombination Identification Program (RIP) tool for recombination detection) [17,22,23]. Interestingly, we uncovered possible recombination events between sparrow and Rhinolophus blasii (bat), and the hCoV-HKU1 genome with hedgehog (Erinaceus), shedding light on another possible scenario about the origins of SARS-CoV-2.…”

Section: Discussionsupporting

confidence: 82%

Population Genomics Insights into the First Wave of COVID-19

Vasilarou

Alachiotis

Garefalaki

et al. 2021

Life

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Full-genome-sequence computational analyses of the SARS-coronavirus (CoV)-2 genomes allow us to understand the evolutionary events and adaptability mechanisms. We used population genetics analyses on human SARS-CoV-2 genomes available on 2 April 2020 to infer the mutation rate and plausible recombination events between the Betacoronavirus genomes in nonhuman hosts that may have contributed to the evolution of SARS-CoV-2. Furthermore, we localized the targets of recent and strong, positive selection during the first pandemic wave. The genomic regions that appear to be under positive selection are largely co-localized with regions in which recombination from nonhuman hosts took place. Our results suggest that the pangolin coronavirus genome may have contributed to the SARS-CoV-2 genome by recombination with the bat coronavirus genome. However, we find evidence for additional recombination events that involve coronavirus genomes from other hosts, i.e., hedgehogs and sparrows. We further infer that recombination may have recently occurred within human hosts. Finally, we estimate the parameters of a demographic scenario involving an exponential growth of the size of the SARS-CoV-2 populations that have infected European, Asian, and Northern American cohorts, and we demonstrate that a rapid exponential growth in population size from the first wave can support the observed polymorphism patterns in SARS-CoV-2 genomes.

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“…This transformation is called “DNA coding”. In this work, we opted for a special coding technique called “Order 2 Frequency Chaos Game Signal” (FCGS 2 ) [ 23 , 24 ]. The FCGS 2 coding is a statistical representation of DNA.…”

Section: Methodsmentioning

confidence: 99%

New methodology for repetitive sequences identification in human X and Y chromosomes

Touati

Tajouri

Mesaoudi

et al. 2021

Biomedical Signal Processing and Control

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Comparative genomic signature representations of the emerging COVID-19 coronavirus and other coronaviruses: High identity and possible recombination between Bat and Pangolin coronaviruses

Cited by 32 publications

References 30 publications

Sequence Analysis and Structure Prediction of SARS-CoV-2 Accessory Proteins 9b and ORF14: Evolutionary Analysis Indicates Close Relatedness to Bat Coronavirus

Sequence Analysis and Structure Prediction of SARS-CoV-2 Accessory Proteins 9b and ORF14: Evolutionary Analysis Indicates Close Relatedness to Bat Coronavirus

Population Genomics Insights into the First Wave of COVID-19

New methodology for repetitive sequences identification in human X and Y chromosomes

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