Working Paper Short Note Version 2 This version is not peer-reviewed

Understanding the Origin of ‘BatCoVRaTG13’, a Virus Closest to SARS-CoV-2

Version 1 : Received: 19 May 2020 / Approved: 20 May 2020 / Online: 20 May 2020 (07:08:38 CEST)
Version 2 : Received: 24 May 2020 / Approved: 24 May 2020 / Online: 24 May 2020 (20:02:22 CEST)

A peer-reviewed article of this Preprint also exists.

Journal reference: Front. Public Health 2020
DOI: 10.3389/fpubh.2020.581569

Abstract

Genomic analysis indicates that SARS-CoV-2 is most related to RaTG13, a beta corona virus derived from bats by 96% 1. At present, RaTG13 is only available on the public database in the form of a genome sequence. The genome of RaTG13 (MN996532.1) was sequenced from the RNA of a bat faecal swab collected in 2013 from Yunnan, China, however the exact location is not mentioned. Since RaTG13 is one of the main supports for SARS-CoV-2 to have a natural origin, it is of utmost importance to understand the sample location. RNA dependent RNA polymerase (RdRp) sequence of RaTG13 shows that it is 100% similar to that of bat corona virus BtCoV/4991 and 98.7-98.9% similar to SARS-CoV-2 RdRp 2. BtCoV/4991 was described to be a SARS-like (SL-) corona virus from bat faeces sampled in an abandoned mine from Mojiang 2. Both the publications 1,2 are authored by Dr. Zheng-li Shi (Z-L Shi), who is described as the bat woman of China 3. However, BtCoV/4991 has not been mentioned by Zhou et al 2020 1 where novel corona virus was first described. Based on the RdRp sequence similarities, similarities in sample collection dates, sample locations, and the fact that RaTG13 is mentioned synonymous to BtCoV/4991 on the Chinese bat database, it is predicted that RaTG13 and BtCoV/4991 originate from the same sample. The sample, bat faecal swab was collected in 2013 from an abandoned mineshaft in Mojiang by Dr. Shi and her work group. In 2012, in a Mojiang mineshaft, six mine workers suffered from atypical pneumonia and three of them died. These workers were engaged in the work of clearing debris from a mineshaft which had a lot of bats and bat faeces 3,4. A detailed health investigation indicated that the miners suffered from atypical pneumonia mostly of the viral origin 4. Therefore, in the light of the present Covid-19 caused by SARS-CoV-2, the fact that its phylogenetic neighbour RaTG13 originated from bat faeces collected from a mineshaft, which was also the origin of pneumonia-like disease in miners in 2012, should be noted.

Subject Areas

SARS-CoV-2; RATG13; BtCoV/4991; SARS-like (SL-) corona virus; pneumonia

Comments (3)

Comment 1
Received: 24 May 2020
Commenter: Monali Rahalkar
Commenter's Conflict of Interests: Author
Comment: Added to the abstract (Page 2)
These workers were engaged in the work of clearing debris from a mineshaft which had a lot of bats and bat faeces 3,4. A detailed health investigation indicated that the miners suffered from atypical pneumonia mostly of the viral origin 4. Therefore, in the light of the present Covid-19 caused by SARS-CoV-2, the fact that its phylogenetic neighbour RaTG13 originated from bat faeces collected from a mineshaft, which was also the origin of pneumonia-like disease in miners in 2012, should be noted. 
Page 4 and page 5 added content:
has been also predicted in a preprint 6 and mentioned on a Chinese Database of bat-associated viruses (http://www.mgc.ac.cn/cgi-bin/DBatVir/main.cgi?func=accession&acc=MN996532).
Severe pneumonia cases and deaths in miners working in a mineshaft,Mojiang, Yunnan, ChinaIn April-May 2012, six mineworkers were involved in removing debris from a mineshaft filled with bats and bat faeces, in the Mojiang region, Yunnan, China 4. It was noted that after exposure to the bat faeces for a varying period of time these miners started experiencing fever and signs of severe pneumonia and were admitted to the emergency department affiliated to Kunming Medical University. A master’s thesis entitled ‘The analysis of 6 patients with severe pneumonia caused by unknown viruses’ described the details of diagnosis, treatment and probable causes of the infections and deaths 4. Three of the mineworkers succumbed to the infection and died while three of them survived 4. The cause of the pneumonia was diagnosed to be primarily of a viral origin (related to bats) and secondary infections due to fungus or bacteria were also seen by experts 4. The inferences drawn in the thesis based on the six miners were that the shorter time the workers spent in the mine (clearing the bat faeces) and younger the age, the prognosis of these patients was better and the hospital stay was shorter. The treatment included the use of antiviral, antibacterial, antifungal antibiotics, along with cortico-steroids and antithrombotic drugs (in a few patients).

Page 7 added: Six mine workers who cleared the debris (mainly bat faeces) from the same mineshafts suffered from atypical pneumonia and three of them died. This reference also has not been mentioned in Zhou et al 2020 1. Therefore, in the light of the present Covid-19 caused by SARS-CoV-2, the fact that its phylogenetic neighbour RaTG13 originated from bat faeces collected from a mineshaft, which was also the origin of pneumonia-like disease in miners in 2012, should be noted. Although the genomic composition of SARS-CoV-2 and RaTG13 differ by 4%, it was important to report and refer to the exact sample and conditions from which RaTG13 sequence was derived 1. All these facts should be considered in light of the present Covid-19, by scientists, doctors and academicians.
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Comment 2
Received: 2 September 2020
The commenter has declared there is no conflict of interests.
Comment: I would like to add that the information that the genome of RaTG13 (MN996532.1) was sequenced from the RNA of a bat faecal swab is incorrect. In the current data base, a faecal swab is mentioned as the source material for sequencing (https://bigd.big.ac.cn/gsa/browse/CRA002424/CRX097481). However, if one takes a look to the first version of the entry, one will find out, that the source material for sequencing was extracted from bronchoalveolar lavage fluid. The only explanation is that it was taken from the infected mine workers. So, somebody is trying to hide something?
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Response 1 to Comment 2
Received: 17 September 2020
The commenter has declared there is no conflict of interests.
Comment: Can you please leave the link to the first version showing 4991 came from human sample and the link to the second version showing bat sample. Its not clear in the link above. I d
Suggest saving them in the way back archieve

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