Viral by Matt Ridley

Author:Matt Ridley
Language: eng
Format: epub, mobi
Publisher: Harper
Published: 2021-10-08T00:00:00+00:00

Natural insertions

In their March 2020 ‘Proximal Origin’ paper, Dr Andersen’s group had confidently predicted that a bat virus with a similar furin cleavage site to SARS-CoV-2’s would soon turn up: ‘Given the level of genetic variation in the spike, it is likely that SARS-CoV-2-like viruses with partial or full polybasic cleavage sites will be discovered in other species.’ Shortly afterwards, a bat virus was found and given a lot of publicity for at least seeming to prove that it did appear to possibly have a natural insertion at the S1/S2 boundary of its spike, although not one that acted as a furin cleavage site. It was a sarbecovirus, in which some parts of its genome were very closely related to their counterparts in SARS-CoV-2.

Its name is RmYN02. Rm stands for Rhinolophus malayanus, the Malayan horseshoe bat; YN stands for Yunnan. The story behind RmYN02 is that between May and October 2019, scientists from the Key Laboratory of Etiology and Epidemiology of Emerging Infectious Diseases in Shandong and the Center for Integrative Conservation at the Xishuangbanna Tropical Botanical Garden caught 227 bats of twenty species in Mengla County in the far south of Yunnan, very near the border with Laos. This is yet another team of scientists that was catching bats in southern China in search of viruses. This far south in China, as well as two widespread species of horseshoe bat, R. sinicus and pearsonii, they found horseshoe bat species that are more typical of Indochina and not found further north, including malayanus. The bats were sampled for viruses and the samples sequenced and analysed. Different tissue and faecal samples were merged into pools for sequencing, with each pool containing as many as eleven samples. Although the approach was cost effective, this meant that when the team found signs of a SARS-like virus, which they dubbed RmYN01 and RmYN02, they had to then figure out which of the eleven samples in the pool contained these two viruses. Only one of the samples, number 123, collected on 25 June 2019, tested positive for both sequences. From this sample, the scientists were only able to verify parts of the RmYN02 genomic sequence but not that the sequenced parts were necessarily from the same virus. RmYN02 looks very similar to SARS-CoV-2 over most of its genome but its spike gene is very different – only a 72 per cent genetic match. Could the spike gene or part of it have come from some other virus lurking in the same sample?

It is in this distantly related spike of RmYN02 that another sequence, ‘PAA’, is found, which the Shandong scientists called a natural insertion similar to that of ‘PRRA’ in SARS-CoV-2. For this reason, they called the similarity ‘strongly suggestive of a natural zoonotic origin of SARS-CoV-2’. However, upon a closer look, this S1/S2 segment of RmYN02’s genome is shorter even compared with most of the close relatives to SARS-CoV-2, let alone SARS-CoV-2 with its four amino acid insertion. As Mr Deigin and Dr Segreto

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