Unique SARS-CoV-2 variant found in public sequence data of Antarctic soil samples collected in 2018-2019 (preprint)

ABSTRACT

The COVID-19 pandemic has been going on for two years now and although many hypotheses have been put forward, its origin remain obscure. We investigated whether the huge public sequencing data archives’ samples collected earlier than the earliest known cases of the pandemic might contain traces of SARS-CoV-2. Here we report the bioinformatic analysis of a metagenome sample set collected from soil on King George Island, Antarctica between 2018-12-24 and 2019-01-13. It contains sequence fragments matching the SARS-CoV-2 reference genome with altogether more than half million nucleotides, covering the complete genome on average 17×. Preliminary phylogeny analysis places the sample close to the known earliest cases. The high sequence coverage rules out chance alignments from other species but possible laboratory contamination cannot be excluded. The sequence harbours a unique combination of mutations, unseen in other samples, so whatever its origin, it can add important piece of information to the puzzle of the ongoing pandemic.