Genomic recombination events may reveal the evolution of coronavirus and the origin of SARS-CoV-2

Zhenglin Zhu,Geng Meng,Kaiwen Meng

doi:10.1038/s41598-020-78703-6

Zhenglin Zhu, Geng Meng + Show 1 more

Open Access

https://doi.org/10.1038/s41598-020-78703-6

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Abstract

To trace the evolution of coronaviruses and reveal the possible origin of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes the coronavirus disease 2019 (COVID-19), we collected and thoroughly analyzed 29,452 publicly available coronavirus genomes, including 26,312 genomes of SARS-CoV-2 strains. We observed coronavirus recombination events among different hosts including 3 independent recombination events with statistical significance between some isolates from humans, bats and pangolins. Consistent with previous records, we also detected putative recombination between strains similar or related to Bat-CoV-RaTG13 and Pangolin-CoV-2019. The putative recombination region is located inside the receptor-binding domain (RBD) of the spike glycoprotein (S protein), which may represent the origin of SARS-CoV-2. Population genetic analyses provide estimates suggesting that the putative introduced genetic sequence within the RBD is undergoing directional evolution. This may result in the adaptation of the virus to hosts. Unsurprisingly, we found that the putative recombination region in S protein was highly diverse among strains from bats. Bats harbor numerous coronavirus subclades that frequently participate in recombination events with human coronavirus. Therefore, bats may provide a pool of genetic diversity for the origin of SARS-CoV-2.

Highlights

To trace the evolution of coronaviruses and reveal the possible origin of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes the coronavirus disease 2019 (COVID-19), we collected and thoroughly analyzed 29,452 publicly available coronavirus genomes, including 26,312 genomes of SARS-CoV-2 strains
Pangolin coronavirus was previously considered to have no direct relationship with SARS-CoV-28, viral communication was observed between Malayan pangolins (Manis javanica) and other hosts[9]
It has been proposed that the receptor-binding domain (RBD) of the S protein in SARS-CoV-2 might be resulted from recombination between a virus similar or related to Bat-CoVRaTG13 and a virus similar or related to Pangolin-CoV-201911,12,14,15

Summary

Introduction

To trace the evolution of coronaviruses and reveal the possible origin of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes the coronavirus disease 2019 (COVID-19), we collected and thoroughly analyzed 29,452 publicly available coronavirus genomes, including 26,312 genomes of SARS-CoV-2 strains. Population genetic analyses provide estimates suggesting that the putative introduced DNA within the RBD is undergoing directional evolution This may result in the adaptation of the virus to hosts. Bats may provide a pool of genetic diversity for the origin of SARS-CoV-2 Since it was first identified in Wuhan, C hina[1,2,3], severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become a global pandemic. Indepth statistical analyses of genomic recombination among coronaviruses from different hosts, especially between pangolin coronaviruses and bat coronaviruses, should be important for tracing the origin of SARS-CoV-2 and may reveal interesting subsequent evolutionary patterns. Our results revealed genomic recombination events between coronaviruses from different hosts and provided further evidence for the origin of SARS-CoV-2 via a recombination event between Bat-CoV-RaTG13 and Pangolin-CoV-2019 related s trains[11,12,14]

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