How the coronavirus Sars-CoV-2 originated and where it comes from is one of the open questions of the current pandemic. It only seems clear that the ancestors of this virus once developed in bats. A study is now examining how Sars-CoV-2 is related to the known bat coronaviruses and when it could have split off from its closest relative. Accordingly, this virus separated from other bat viruses in the 1960s. However, its spike protein, which is important for docking with human cells, could be even older – and also present in other bat coronaviruses.
Since the first Covid-19 cases became known in Wuhan, China, virologists and epidemiologists have been asking how and from which animal the responsible coronavirus has spread to humans. Relatively early after sequencing the genes of Sars-CoV-2, comparisons with coronaviruses isolated from bats suggested that the new pathogen must also have its origin in this group of animals. The most similar virus strain to date is RaTG13, a type of coronavirus isolated for the first time in 2013 from Java horseshoe bat (Rhinolophus affinis) in the Chinese province of Yunnan. “It matches Sars-CoV-2 in approximately 96 percent of the sequences in almost all genomic regions,” Maciej Boni of Pennsylvania State University and his colleagues report. However, the even greater similarity of the spike protein of Sars-CoV-2, which is crucial for the infestation of human cells, with a coronavirus found in pangolines suggested that these pangolins may also be considered as intermediate hosts for the new virus.
Split off from bat relatives in the 1960s
To provide more clarity, Boni and his team examined and compared the RNA sequences and the recombination of the genes of Sars-CoV-2, Sars-CoV, the bat coronaviruses and other virus strains belonging to the subgroup of these so-called sarbecoviruses. In the first step, they searched for passages in the genome that indicate an intensive gene exchange of the virus variants with each other and with other viruses. It was found that the entire subgroup of these corona viruses is strongly characterized by recombination. In the course of their evolution, these viruses must therefore have exchanged parts of their genetic makeup – which can also make it easier to infect new host species. By comparing longer, little-modified sections of RNA, the researchers conclude that Sars-CoV-2 and RaTG13 go back to a common tribal line. From this line, some coronaviruses, also detected in pangolines, branched off as a sister group. According to this, RaTG13 is the closest relative of Sars-CoV-2 and both developed from a reservoir of similar corona viruses, which are still circulating in horseshoe noses.
Boni and his colleagues were able to determine when the ancestors of RaTG13 and Sars-CoV-2 separated from one another by comparing the RNA sequences and drawing conclusions about the likely rate of mutations and recombinations of these viruses. “According to our most conservative approach, the time to split Sars-CoV-2 and RaTG13 is in 1969,” the researchers report. With two other approaches they came to times around 1948 or 1982. The causative agent of the current pandemic could therefore have arisen almost at the same time as the causative agent of the Sars pandemic of 2002/2003. Because Sars-CoV separated from its bat relatives in 1962, as the scientists determined. “The long separation period of 40 to 70 years suggests that there are other, previously unrecognized virus lines in horseshoe bats that have zoonotic potential,” said Boni and his team. Because both pandemic agents apparently only circulated under bats for decades before they then spread to humans.
Spike protein structure no “reinvention”
As part of their comparative studies, the researchers also took a closer look at the spike protein, the most important part of Sars-CoV-2 for changing hosts. Their comparisons showed that the building instructions for this protein are similar to those of the RaTG13 virus, but show an even better agreement with one of the pangolin viruses. “At first glance, this could suggest that Sars-CoV-2 is the recombinant of an ancestor of Pangolin-2019 and the RaTG13 strain,” said Boni and his team. But closer analyzes revealed that the RaTG13 spike protein shows far more evidence of recombinations, especially in its so-called loop region. In contrast, in Sars-CoV-2 and Pangolin-2019, the deviation patterns for spike protein show little evidence of recombination in the tribal line. “This is remarkable because the loop region contains six key structures for the virus to bind to the ACE2 receptor,” the researchers say.
Boni and his colleagues conclude from these results that the spike protein structure found in Sars-CoV-2 is not a “reinvention” of this virus, but is largely original and was already found in the common ancestors of this and other corona viruses of this subgroup. In their opinion, this also suggests that there could be other potentially pandemic coronaviruses in the horseshoe noses. This underlines the need for close monitoring of new outbreaks that are not due to known pathogens.
Source: Maciej Boni (Pennsylvania State University, University Park) et al., Nature Microbiology, doi: 10.1038 / s41564-020-0771-4