SARS-CoV-2 genomic surveillance in Taiwan revealed novel ORF8-deletion mutant and clade possibly associated with infections in Middle East

Emerg Microbes Infect. 2020 Dec;9(1):1457-1466. doi: 10.1080/22221751.2020.1782271.


Taiwan experienced two waves of imported infections with Coronavirus Disease 2019 (COVID-19). This study aimed at investigating the genomic variation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Taiwan and compared their evolutionary trajectories with the global strains. We performed culture and full-genome sequencing of SARS-CoV-2 strains followed by phylogenetic analysis. A 382-nucleotides deletion in open reading frame 8 (ORF8) was found in a Taiwanese strain isolated from a patient on February 4, 2020 who had a travel history to Wuhan. Patients in the first wave also included several sporadic, local transmission cases. Genomes of 5 strains sequenced from clustered infections were classified into a new clade with ORF1ab-V378I mutation, in addition to 3 dominant clades ORF8-L84S, ORF3a-G251V and S-D614G. This highlighted clade also included some strains isolated from patients who had a travel history to Turkey and Iran. The second wave mostly resulted from patients who had a travel history to Europe and Americas. All Taiwanese viruses were classified into various clades. Genomic surveillance of SARS-CoV-2 in Taiwan revealed a new ORF8-deletion mutant and a virus clade that may be associated with infections in the Middle East, which contributed to a better understanding of the global SARS-CoV-2 transmission dynamics.

Keywords: COVID-19; ORF8 deletion; Phylogeny; SARS-CoV-2; genome sequencing.

MeSH terms

  • Animals
  • Betacoronavirus / classification
  • Betacoronavirus / genetics*
  • Betacoronavirus / isolation & purification
  • COVID-19
  • Cell Line
  • Chlorocebus aethiops
  • Coronavirus Infections / virology*
  • Genome, Viral*
  • Haemophilus parainfluenzae / isolation & purification
  • Humans
  • Middle East
  • Open Reading Frames
  • Pandemics
  • Phylogeny
  • Pneumonia, Viral / virology*
  • RNA, Viral
  • SARS-CoV-2
  • Sequence Deletion
  • Taiwan
  • Travel
  • Vero Cells
  • Virus Cultivation
  • Whole Genome Sequencing


  • RNA, Viral