Complete genome analysis of a SARS-like bat coronavirus identified in the Republic of Korea - PubMed (original) (raw)

Complete genome analysis of a SARS-like bat coronavirus identified in the Republic of Korea

Yongkwan Kim et al. Virus Genes. 2019 Aug.

Abstract

Bats have been widely known as natural reservoir hosts of zoonotic diseases, such as severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) caused by coronaviruses (CoVs). In the present study, we investigated the whole genomic sequence of a SARS-like bat CoV (16BO133) and found it to be 29,075 nt in length with a 40.9% G+C content. Phylogenetic analysis using amino acid sequences of the ORF 1ab and the spike gene showed that the bat coronavirus strain 16BO133 was grouped with the Beta-CoV lineage B and was closely related to the JTMC15 strain isolated from Rhinolophus ferrumequinum in China. However, 16BO133 was distinctly located in the phylogenetic topology of the human SARS CoV strain (Tor2). Interestingly, 16BO133 showed complete elimination of ORF8 regions induced by a frame shift of the stop codon in ORF7b. The lowest amino acid identity of 16BO133 was identified at the spike region among various ORFs. The spike region of 16BO133 showed 84.7% and 75.2% amino acid identity with Rf1 (SARS-like bat CoV) and Tor2 (human SARS CoV), respectively. In addition, the S gene of 16BO133 was found to contain the amino acid substitution of two critical residues (N479S and T487 V) associated with human infection. In conclusion, we firstly carried out whole genome characterization of the SARS-like bat coronavirus discovered in the Republic of Korea; however, it presumably has no human infectivity. However, continuous surveillance and genomic characterization of coronaviruses from bats are necessary due to potential risks of human infection induced by genetic mutation.

Keywords: Bat; Frame shift; SARS-like coronavirus; Whole genome; Zoonotic disease.

PubMed Disclaimer

Conflict of interest statement

The authors declare that there are no conflicts of interest.

Figures

Fig. 1

Fig. 1

Phylogenetic analysis using whole genome sequences of ORF 1ab with reference strains. The phylogenetic trees were drawn using the neighboring joining method using the maximum composite likelihood model with MEGA 7 software. The bootstrap values were calculated with 1000 replicates. Phylogenetic analysis using whole genome sequences of the spike region with reference strains. The phylogenetic trees were drawn using the neighboring joining method using the maximum composite likelihood model with MEGA 7 software. The bootstrap values were calculated with 1000 replicates

Similar articles

Cited by

References

    1. Brian DA, Baric RS. Coronavirus genome structure and replication. Curr Top Microbiol Immunol. 2005;287:1–30. - PMC - PubMed
    1. Gonzalez JM, Gomez-Puertas P, Cavanagh D, Gorbalenya AE, Enjuanes L. A comparative sequence analysis to revise the current taxonomy of the family Coronaviridae. Arch Virol. 2003;148:2207–2235. doi: 10.1007/s00705-003-0162-1. - DOI - PMC - PubMed
    1. Xu L, Zhang F, Yang W, Jiang T, Lu G, He B, Li X, Hu T, Chen G, Feng Y, Zhang Y, Fan Q, Feng J, Zhang H, Tu C. Detection and characterization of diverse alpha- and betacoronaviruses from bats in China. Virol Sin. 2016;31:69–77. doi: 10.1007/s12250-016-3727-3. - DOI - PMC - PubMed
    1. Kim HK, Yoon SW, Kim DJ, Koo BS, Noh JY, Kim JH, Choi YG, Na W, Chang KT, Song D, Jeong DG. Detection of severe acute respiratory syndrome-like, Middle East respiratory syndrome-like bat coronaviruses and group H rotavirus in faeces of Korean bats. Transbound Emerg Dis. 2016;63:365–372. doi: 10.1111/tbed.12515. - DOI - PMC - PubMed
    1. Yang L, Wu Z, Ren X, Yang F, He G, Zhang J, Dong J, Sun L, Zhu Y, Du J, Zhang S, Jin Q. Novel SARS-like betacoronaviruses in bats, China. Emerg Infect Dis. 2011;19:989–991. - PMC - PubMed

MeSH terms

LinkOut - more resources