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

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 DNA 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.

How Cooperative Engagement Programs Strengthen Sequencing Capabilities for Biosurveillance and Outbreak Response

“…However, it showed greater similarity to a coronavirus sequence obtained from bats (19). Interestingly, the spike protein, responsible for viral entry into cells, was more closely related to a separate published coronavirus sequence identified in pangolins (22). This paved the way for a more nuanced understanding of the evolutionary origins of the novel coronavirus responsible for the pandemic.…”

Coronaviruses in humans and animals: the role of bats in viral evolution

“…Full-genome sequencing and phylogenetic analysis of various SARS-CoV2 clusters revealed a variable degree of relationship to other bats coronaviruses (Zhou et al 2020;Boni et al 2020;Yan et al 2020). Coronaviruses of bat origin could closely align with isolates of 32 other host species and possess the highest number of coronaviruses subclades (Zhu et al 2020).…”

“…Moreover, infected bats with CoV produce lower levels of IL-1β secretion and ASC (apoptosis-associated speck-like protein containing a CARD) than other mammals without affecting the viral propagation capacity which makes them ideal reservoir hosts for viruses (Ahn et al 2019;Hall et al 2020). Therefore, bats are considered to be exceptional mammals that provide a large genomic pool for the emerge of novel human coronavirus (Zhu et al 2020). This may be attributed to the extreme genomic flexibility of coronaviruses which makes it difficult to pinpoint the exact reservoir (Bonilla-Aldana et al 2020).…”

“…Although almost all literature consider bats as the source of SARS-CoV2, direct pieces of evidence are still lacking (Lacroix et al 2020). However, enough arguments for bat accusation are available which are based mainly on four argumentative approaches: (1) experience gathered from previous Betacoronavirus (Beta-CoV) epidemics where all known human coronavirus pandemics originated from bats (as discussed above) (Zhu et al 2020); (2) phylogenic relationship of SARS-CoV2 and related clades; (3) data obtained through artificial infection of bats with SARS-CoV2; and (4) computerized models of SARS-CoV2 evolution.…”

“…Recently, it has been shown that bat isolates of coronaviruses are the major parent contributor for fractions of coronavirus sequences (Zhu et al 2020). Full-genome sequencing and phylogenetic analysis of various SARS-CoV2 clusters revealed a variable degree of relationship to other bats coronaviruses (Zhou et al 2020;Boni et al 2020;Yan et al 2020).…”