Retrospective BLAST Analysis Detects RaTG13/Ra4991 in the Earliest SARS-CoV-2 Genome Submitted to NCBI GenBank (December 28, 2019)

On December 28, 2019, Dr. Lili Ren submitted a near-complete genome sequence of a novel coronavirus (BetaCoV/Wuhan/IPBCAMS-WH-01/2019) to NCBI GenBank - the earliest known SARS-CoV-2 sequence sent outside China. At the time, GenBank already contained an embargoed partial RdRp sequence of RaTG13/Ra4991 (accession MH615898.1), a strain that would later be recognized as the closest known relative to SARS-CoV-2, deposited in July 2018.

This retrospective BLAST analysis demonstrates that a standard nucleotide search of Dr. Ren’s December 28, 2019, sequence would have produced a strong match of 97.79% identity to the embargoed 2018 fragment. A subsequent keyword search for “Ra4991” would have rapidly linked the emerging virus to the Mojiang mine and the 2012 miner outbreak. These findings strongly suggest that a clear early warning signal would have been detectable in late December 2019 using routine bioinformatics tools and data already available in the NIH GenBank system.