An exclusive 42 amino acid signature in pp1ab protein provides insights into the evolutive history of the 2019 novel human-pathogenic coronavirus (SARS-CoV-2)

J Med Virol. 2020 Jun;92(6):688-692. doi: 10.1002/jmv.25758. Epub 2020 Mar 20.

Abstract

The city of Wuhan, Hubei province, China, was the origin of a severe pneumonia outbreak in December 2019, attributed to a novel coronavirus (severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2]), causing a total of 2761 deaths and 81109 cases (25 February 2020). SARS-CoV-2 belongs to genus Betacoronavirus, subgenus Sarbecovirus. The polyprotein 1ab (pp1ab) remains unstudied thoroughly since it is similar to other sarbecoviruses. In this short communication, we performed phylogenetic-structural sequence analysis of pp1ab protein of SARS-CoV-2. The analysis showed that the viral pp1ab has not changed in most isolates throughout the outbreak time, but interestingly a deletion of 8 aa in the virulence factor nonstructural protein 1 was found in a virus isolated from a Japanese patient that did not display critical symptoms. While comparing pp1ab protein with other betacoronaviruses, we found a 42 amino acid signature that is only present in SARS-CoV-2 (AS-SCoV2). Members from clade 2 of sarbecoviruses have traces of this signature. The AS-SCoV2 located in the acidic-domain of papain-like protein of SARS-CoV-2 and bat-SL-CoV-RatG13 guided us to suggest that the novel 2019 coronavirus probably emerged by genetic drift from bat-SL-CoV-RaTG13. The implication of this amino acid signature in papain-like protein structure arrangement and function is something worth to be explored.

Keywords: SARS; SARS-CoV-2; Wuhan; coronavirus; pp1ab protein; virus.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Animals
  • Base Sequence
  • Betacoronavirus / classification
  • Betacoronavirus / genetics*
  • Betacoronavirus / isolation & purification
  • Betacoronavirus / pathogenicity
  • COVID-19
  • Chiroptera / microbiology
  • Computational Biology / methods
  • Coronavirus Infections / epidemiology*
  • Coronavirus Infections / transmission
  • Coronavirus Infections / virology
  • Coronavirus Papain-Like Proteases
  • Evolution, Molecular
  • Gene Expression
  • Humans
  • Pandemics*
  • Papain / genetics
  • Phylogeny*
  • Pneumonia, Viral / epidemiology*
  • Pneumonia, Viral / transmission
  • Pneumonia, Viral / virology
  • Polyproteins
  • SARS Virus / classification
  • SARS Virus / genetics*
  • SARS Virus / pathogenicity
  • SARS-CoV-2
  • Sequence Alignment
  • Sequence Homology, Amino Acid
  • Viral Nonstructural Proteins / genetics
  • Viral Proteins / genetics*

Substances

  • ORF1ab polyprotein, SARS-CoV-2
  • Polyproteins
  • Viral Nonstructural Proteins
  • Viral Proteins
  • Coronavirus Papain-Like Proteases
  • Papain