tetano
Editor, Senior Moderator
Infect Genet Evol
. 2021 May 20;104933.
doi: 10.1016/j.meegid.2021.104933. Online ahead of print.
Exploration of hosts and transmission traits for SARS-CoV-2 based on the k-mer natural vector
Yuyan Zhang[SUP] 1 [/SUP], Jia Wen[SUP] 2 [/SUP], Xin Li[SUP] 3 [/SUP], Guizhi Li[SUP] 4 [/SUP]
Affiliations
Abstract
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 methods. In addition, several SARS-CoV-2 isolates have been found deletions in their genomes, which cannot be resolved with current phylogenetic methods. Therefore, the k-mer natural vector is proposed to explore hosts and transmitting 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 transmitting 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 before transmitting to Human. 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.
Keywords: Bayesian; Cross-species; Intermediate host; K-mer model; Phylogenetic analysis.
. 2021 May 20;104933.
doi: 10.1016/j.meegid.2021.104933. Online ahead of print.
Exploration of hosts and transmission traits for SARS-CoV-2 based on the k-mer natural vector
Yuyan Zhang[SUP] 1 [/SUP], Jia Wen[SUP] 2 [/SUP], Xin Li[SUP] 3 [/SUP], Guizhi Li[SUP] 4 [/SUP]
Affiliations
- PMID: 34023511
- DOI: 10.1016/j.meegid.2021.104933
Abstract
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 methods. In addition, several SARS-CoV-2 isolates have been found deletions in their genomes, which cannot be resolved with current phylogenetic methods. Therefore, the k-mer natural vector is proposed to explore hosts and transmitting 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 transmitting 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 before transmitting to Human. 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.
Keywords: Bayesian; Cross-species; Intermediate host; K-mer model; Phylogenetic analysis.