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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 06; 92(6):688-692.JM

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.

Authors+Show Affiliations

Laboratory of Agrobiotechnology, National Council of Science and Technology (CONACYT)-University of Colima, Colima, Colima, Mexico.University Center for Biomedical Research, National Council of Science and Technology (CONACYT)-University of Colima, Colima, Colima, Mexico.Laboratory of Agrobiotechnology, University of Colima, Colima, Colima, Mexico.Laboratory of Agrobiotechnology, National Council of Science and Technology (CONACYT)-University of Colima, Colima, Colima, Mexico.Laboratory of Agrobiotechnology, National Council of Science and Technology (CONACYT)-University of Colima, Colima, Colima, Mexico.

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

32167166

Citation

Cárdenas-Conejo, Yair, et al. "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)." Journal of Medical Virology, vol. 92, no. 6, 2020, pp. 688-692.
Cárdenas-Conejo Y, Liñan-Rico A, García-Rodríguez DA, et al. 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;92(6):688-692.
Cárdenas-Conejo, Y., Liñan-Rico, A., García-Rodríguez, D. A., Centeno-Leija, S., & Serrano-Posada, H. (2020). 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). Journal of Medical Virology, 92(6), 688-692. https://doi.org/10.1002/jmv.25758
Cárdenas-Conejo Y, et al. 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;92(6):688-692. PubMed PMID: 32167166.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - 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). AU - Cárdenas-Conejo,Yair, AU - Liñan-Rico,Andrómeda, AU - García-Rodríguez,Daniel Alejandro, AU - Centeno-Leija,Sara, AU - Serrano-Posada,Hugo, Y1 - 2020/03/20/ PY - 2020/02/26/received PY - 2020/03/09/accepted PY - 2020/3/14/pubmed PY - 2020/7/1/medline PY - 2020/3/14/entrez KW - SARS KW - SARS-CoV-2 KW - Wuhan KW - coronavirus KW - pp1ab protein KW - virus SP - 688 EP - 692 JF - Journal of medical virology JO - J Med Virol VL - 92 IS - 6 N2 - 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. SN - 1096-9071 UR - https://www.unboundmedicine.com/medline/citation/32167166/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__ L2 - https://doi.org/10.1002/jmv.25758 DB - PRIME DP - Unbound Medicine ER -