Four new coronavirus relatives discovered in wild bats

No, the direct ancestor of the coronavirus SARS-CoV-2 has not yet been found. But researchers are getting closer. The coronavirus RpYN06 is genetically at least slightly more similar to the virus that is now causing the pandemic in humans than the previous candidate RaTG13. The new virus’s similarity to SARS-CoV-2 now stands at 97.17 percent — nearly half a percent more than the old closeness record, write Chinese researchers in the trade magazine Cell.

After all, RpYN06 should finish in second place after RaTG13, because the total genome is just a few percent less resembles the human coronavirus (94.48 instead of 96.10 percent). But the researchers reason that for an evolutionary comparison they do not need to include the code of the spike gene, because it may have ended up in SARS-CoV-2 through combination of different viruses. In this way the authors arrive at a new record with some creative calculations.

bat dung

The added value of the research lies more in the observation that SARS-CoV-2-like viruses circulate on an unexpectedly large scale in different species of horseshoe bats. The virus RaTG13 was detected once in a sample of the horseshoe bat in 2013 Rhinolophus affinis, captured at the Mojiang Mine in Tongguan, Yunnan Province. The find seemed almost a fluke, such a single virus that during years of sampling bats in the same mine was only seen once. The virologists’ investigation at the mine had begun after six miners suddenly developed severe pneumonia in the summer of 2012 after clearing bat dung. Three of the men died, without it being clear what the cause of their illness was. Remembering the deadly SARS outbreak in 2002, Wuhan virologists began a long-term study of viruses in bats in the mine. The virus they found in 2013 received little attention because it was not closely related to SARS. That changed in 2020 when it became clear that it was related to SARS-CoV-2.

The pandemic virus’s close relative now discovered, RpYN06, comes from another species of horseshoe bat, Rhinolophus pusillus. The discovery was again in Yunnan province, but now in Xishuangbanna Botanical Garden (the size of a nature park) near the border with Laos.

In addition to RpYN06, the researchers found three more SARS-CoV-2-like viruses in a total of nine horseshoe bats belonging to three different species. The samples were collected recently, between May and July 2020. Together with the finding of a SARS-CoV-2-like virus in Thailand in June 2020, this makes it clear that viruses related to the pandemic virus are still circulating in wild bats, the researchers write. Incidentally, they also found three different SARS-like viruses in the 411 samples collected from 381 bats.

Hunting in the forest

Many species of horseshoe bats can carry SARS- and SARS-CoV-2-like coronaviruses that can vary by location. According to the researchers, this is apparent from all virus inventories that have been carried out on bats to date. Because these are species that hunt insects in a wooded area, it is unlikely that they spread over great distances.

At the same time, the research also shows that different species of bats can transmit a virus to each other. According to the researchers, the area in which to search for the natural source of SARS-CoV-2 covers an enormous area. It runs from Indonesia to Japan, formed by the overlapping habitats of the different types of horseshoe noses. The hotspot, with sometimes up to 23 species of horseshoe bats at the same time in one place, is located in the area of ​​Laos, Vietnam and southern China.

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