tldr RaTG13, the virus most closely related to SARS-CoV-2 was discovered by the WIV in a bat cave in 2013 where 6 miners contracted a viral infection leading to severe pneumonia. 3 died. The virus pathogen was never identified. thetimes.co.uk/article/seven-…
Although the medical and research teams could not exactly determine what virus had killed the miners, the medical thesis published in 2013 from Kunming hospital concluded that it was "a Sars-like coronavirus from a bat."
Based on this diagnosis, WIV mined the same cave in Tongguan, Yunnan several times in 2012-2013 for bat coronaviruses. The only SARS-like CoV they found in that cave was RaTG13 - collected on July 2013, also the last time they visited that cave.
They interviewed Peter Daszak, president of EcoHealth, who works closely with the WIV and Shi Zhengli's group. Daszak said that RaTG13 was only sequenced for the RdRp in 2013 and thrown in the freezer in Wuhan for the next 6 years until COVID-19 broke out.
However, according to Daszak, after sequencing the full genome for RaTG13, the sample "disintegrated". So there is no more RaTG13 sample for independent research groups to verify.
But I think Daszak was misinformed because the amplicon sequencing data on NCBI clearly shows that the WIV accessed the sample repeatedly in 2017 and 2018. 
In my tweetorial about how the WIV characterizes new CoVs from bat caves, the data shows that they had begun the CoV characterization pipeline for RaTG13 in 2017. It wasn't just sitting forgotten in a freezer for 6 years (2013-2020).
More than a year passed between the sequencing of the RaTG13 RdRp/Orf8 (June 2017) and the spike (late 2018). Notably in Sep 2018, more closely related viruses had been discovered by another group, which could've helped with primer design. ncbi.nlm.nih.gov/pmc/articles/P…
Within a year, the most similar CoV spike RBD to that of SARS-CoV-2 was sequenced from smuggled pangolins confiscated in March, 2019 in Guangdong province. The sequences were registered on NCBI in September, 2019. ncbi.nlm.nih.gov/bioproject/?te…
Although it is unclear how these smuggled pangolins contracted the CoV (maybe even from their human smugglers), it seems plausible that SARS2-like viruses were emerging in Southern China (Yunnan, RaTG13; Guangdong and Guangxi, 2 pangolin CoVs; Zhejiang, ZXC21 and ZC45).
The question is, how did SARS-CoV-2 get to Wuhan, "the sprawling capital of Central China’s Hubei province", a commercial center where there is no detectable exposure to SARS-related CoVs according to Shi Zhengli's own study. ncbi.nlm.nih.gov/pmc/articles/P…
This RaTG13 situation, similar to that of the Guangdong pangolin CoV, presents a conundrum to researchers who want to use these genomes for their analysis. Scientific discourse requires trust - that experiments were performed properly and results are reported accurately.
In the cases of RaTG13 and the GD pangolin CoV, it's not clear to readers where these samples came from and how (and when) the genomes were assembled (how were the gaps filled?). Were there attempts to culture/isolate these viruses?
It's a dead end because no one else has access to these virus samples that have apparently disintegrated after serving their purpose of being published in Nature.
Besides the fact that RaTG13 continued to be studied in 2017 and 2018, and that the sample has suddenly disintegrated this year, this story also raises the question: What is the EcoHealth/WIV workflow when they discover a cluster of SARS-like cases with an unidentified pathogen?
The first big text visible on the EcoHealth Alliance website reads "Who stands between you and the next pandemic?" ecohealthalliance.org
The pandemic prevention workflow for discovering a novel SARS virus in a cave where miners got ill with a SARS-like pneumonia can't be to throw the virus in a freezer until a pandemic from a closely related virus breaks out.
