Evidence map›Paper›PMID 32645523›Full record

ArticleGenomics2020

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

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

Open access · greenAbstract readComparative Study
PubMed Full text at PMC Publisher
In one paragraph

Article in Genomics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.

0numbers the graph read from it
0cells of the map it votes in
18citing papers in PubMed
2.8field-weighted citation impact, top 9% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

18 citing papers in PubMed, 38 citations in OpenAlex.

  1. Article
  2. Review
  3. Review
  4. Review
  5. Review
  6. Article
  7. Review
  8. Review
  9. Article
  10. Review
  11. Article
  12. Article
  13. Review
  14. Article
  15. New methodology for repetitive sequences identification inBiomedical signal processing and control · 2021
    Article
  16. Article
  17. Chaos game representation and its applications in bioinformatics.Computational and structural biotechnology journal · 2021
    Review
  18. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

8 authors at 5 institutions in 1 country.

Rabeb TouatiUniversity of Tunis El Manar, LR99ES10 Human Genetics Laboratory, Faculty of Medicine of Tunis, Tunisia; University of Tunis El Manar, SITI Laboratory, National School of Engineers of Tunis, BP 37, le Belvédère, 1002 Tunis, Tunisie. Electronic address: rabeb.touati@enit.utm.tn.
Sondes Haddad-BoubakerUniversity of Tunis El Manar, Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for EMRO region, Institut Pasteur de Tunis, 13 place Pasteur, BP74 1002 le Belvédère, Tunis, Tunisie.
Imen FerchichiUniversity of Tunis El Manar, LR99ES10 Human Genetics Laboratory, Faculty of Medicine of Tunis, Tunisia.
Imen MessaoudiUniversity of Carthage, Higher Institute of Information Technologies and Communications, Industrial Computing Department, Tunisia; University of Tunis El Manar, SITI Laboratory, National School of Engineers of Tunis, BP 37, le Belvédère, 1002 Tunis, Tunisie.
Afef Elloumi OuesletiUniversity of Carthage, National School of Engineers of Carthage, Electrical Engineering Department, Tunisia; University of Tunis El Manar, SITI Laboratory, National School of Engineers of Tunis, BP 37, le Belvédère, 1002 Tunis, Tunisie.
Henda TrikiUniversity of Tunis El Manar, Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for EMRO region, Institut Pasteur de Tunis, 13 place Pasteur, BP74 1002 le Belvédère, Tunis, Tunisie.
Zied LachiriUniversity of Tunis El Manar, SITI Laboratory, National School of Engineers of Tunis, BP 37, le Belvédère, 1002 Tunis, Tunisie.
Maher KharratUniversity of Tunis El Manar, LR99ES10 Human Genetics Laboratory, Faculty of Medicine of Tunis, Tunisia.
Faculté de médecine de TunisInstitut Pasteur de Tunis · TNUniversity of Carthage · TNNational Engineering School of Tunis · TNTunis University · TN

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Coronaviruses are responsible on respiratory diseases in animal and human. The combination of numerical encoding techniques and digital signal processing methods are becoming increasingly important in handling large genomic data. In this paper, we propose to analyze the SARS-CoV-2 genomic signature using the combination of different nucleotide representations and signal processing tools in the aim to identify its genetic origin. The sequence of SARS-CoV-2 was compared with 21 relevant sequences including Bat, Yak and Pangolin coronavirus sequences. In addition, we developed a new algorithm to locate the nucleotide modifications. The results show that the Bat and Pangolin coronaviruses were the most related to SARS-CoV-2 with 96% and 86% of identity all along the genome. Within the S gene sequence, the Pangolin sequence presents local highest nucleotide identity. Those findings suggest genesis of SARS-Cov-2 through evolution from Bat and Pangolin strains. This study offers new ways to automatically characterize viruses.

Indexed as

Recombination, GeneticAlgorithmsAnimalsChiropteraCoronavirusGenome, ViralGenomicsHumansPangolinsSARS-CoV-2BatCOVID19Genome signaturePangolinSARS-CoV-2Yak

Identifiers

PMID32645523
PMCPMC7336935
OpenAlexW3039910690

What OpenQuestion holds

Textmetadata
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.