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Visualization of SARS-CoV-2 using Immuno RNA-Fluorescence In Situ Hybridization
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Genomic Study of COVID-19 Corona Virus Excludes Its Origin from Recombination or Characterized Biological Sources and

Ahmed M El-Shehawi1,2, Saqer S Alotaibi1, Mona M Elseehy2

  • 1Department of Biotechnology, College of Science, Taif University, P.O. Box 11099 21944 Taif, Saudi Arabia.

Cytology and Genetics
|January 25, 2021
PubMed

Insights

This study analyzed 38 COVID-19 isolates, revealing it as a new viral strain with an undetected biological source. Variations in open reading frames (ORFs) suggest diverse virus-human interactions and potential roles for human endogenous retroviruses (HERVs).

Area of Science:

  • Virology
  • Genomics
  • Epidemiology

Background:

  • The COVID-19 pandemic, originating in Wuhan, China in December 2019, lacks a confirmed biological source.
  • Genomic sequencing of isolates is crucial for understanding viral evolution and transmission.
  • The emergence of SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) necessitates rapid scientific investigation.

Purpose of the Study:

  • To analyze the genomic sequences of 38 COVID-19 isolates.
  • To investigate the phylogenetic relationships and genetic diversity among different isolates.
  • To explore potential biological sources and host-virus interactions, including the role of human endogenous retroviruses (HERVs).

Main Methods:

  • Obtained 38 full genomic sequences of COVID-19 isolates.
  • Performed nucleotide (nt) sequence alignment using Clustal Omega.
  • Analyzed phylogenetic relationships and open reading frame (ORF) patterns.

Main Results:

  • Phylogenetic analysis confirmed COVID-19 as a new viral strain with an undetected biological source.
  • Significant differences in ORF patterns were observed among isolates from various locations and compared to SARS-CoV and bat CoV.
  • All isolates shared five main ORFs (1ab, S, M, N, E), but accessory ORFs varied.

Conclusions:

  • COVID-19 represents a novel viral strain, and its definitive biological origin remains elusive.
  • Variations in ORF patterns indicate diverse virus-human interactions influencing infection and severity.
  • The potential role of human endogenous retroviruses (HERVs) in modulating COVID-19 infection and symptoms warrants further investigation.

Keywords:
COVID-19Human endogenous retroviruses (HERVs)genomenucleotide sequence alignment

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