-
Tytuł:
-
Exploration of hosts and transmission traits for SARS-CoV-2 based on the k-mer natural vector.
-
Autorzy:
-
Zhang Y; School of Information Engineering, Suihua University, Suihua 152061, China.
Wen J; School of Information Engineering, Suihua University, Suihua 152061, China; Warshel Institute for Computational Biology, The Chinese University of Hong Kong (Shenzhen), Shenzhen 518172, China. Electronic address: .
Li X; Tianjin International Joint Research Center for Neural Engineering, Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin 30072, China.
Li G; Yingkou Institute of Technology, Yingkou 115014, China.
-
Źródło:
-
Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases [Infect Genet Evol] 2021 Sep; Vol. 93, pp. 104933. Date of Electronic Publication: 2021 May 20.
-
Typ publikacji:
-
Journal Article; Research Support, Non-U.S. Gov't
-
Język:
-
English
-
Imprint Name(s):
-
Original Publication: Amsterdam ; New York : Elsevier Science, c2001-
-
MeSH Terms:
-
Host-Pathogen Interactions*
Phylogeny*
COVID-19/*transmission
SARS-CoV-2/*genetics
SARS-CoV-2/*pathogenicity
Animals ; Biological Evolution ; COVID-19/epidemiology ; China ; Chiroptera/virology ; Coronavirus/genetics ; Genome, Viral ; Pangolins/virology ; Spike Glycoprotein, Coronavirus/genetics ; Viral Zoonoses/transmission ; Viverridae/virology
-
Contributed Indexing:
-
Keywords: Bayesian; Cross-species; Intermediate host; K-mer model; Phylogenetic analysis
-
Substance Nomenclature:
-
0 (Spike Glycoprotein, Coronavirus)
0 (spike protein, SARS-CoV-2)
-
Entry Date(s):
-
Date Created: 20210523 Date Completed: 20210913 Latest Revision: 20210913
-
Update Code:
-
20240105
-
PubMed Central ID:
-
PMC8136293
-
DOI:
-
10.1016/j.meegid.2021.104933
-
PMID:
-
34023511
-
A severe respiratory pneumonia COVID-19 has raged all over the world, and a coronavirus named SARS-CoV-2 is blamed for this global pandemic. Despite intensive research into the origins of the COVID-19 pandemic, the evolutionary history of its agent SARS-CoV-2 remains unclear, which is vital to control the pandemic and prevent another round of outbreak. Coronaviruses are highly recombinogenic, which are not well handled with alignment-based method. In addition, deletions have been found in the genomes of several SARS-CoV-2, which cannot be resolved with current phylogenetic methods. Therefore, the k-mer natural vector is proposed to explore hosts and transmission traits for SARS-CoV-2 using strict phylogenetic reconstruction. SARS-CoV-2 clustering with bat-origin coronaviruses strongly suggests bats to be the natural reservoir of SARS-CoV-2. By building bat-to-human transmission route, pangolin is identified as an intermediate host, and civet is predicted as a possible candidate. We speculate that SARS-CoV-2 undergoes cross-species recombination between bat and pangolin coronaviruses. This study also demonstrates transmission mode and features of SARS-CoV-2 in the COVID-19 pandemic when it broke out early around the world.
(Copyright © 2021 Elsevier B.V. All rights reserved.)
