SARS-CoV-2 spike protein gene variants with N501T and G142D mutation dominated infections in minks in the US

Cai, H. Y.; Cai, A.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have infected human and animals world wide. Since the first SARS-CoV-2 sequences identified from samples collected in December 2019, the virus has been evolving. Now, in the GISAID database of SARS-CoV-2 genomes as of March 17, 2021, 95.7% (758,684 of 792,388) of the SARS-CoV-2 genome has the D614G mutation in the spike protein gene; and 22% (178,186 of 792.388) had N501Y mutation which occurred in the more virulent UK variants, South Africa variant and Brazil variant. Large number of minks were infected with the virus which containing the Y453F mutation in Europe, causing zoonosis concerns. To evaluate the genetic characteristics of the US mink-derived SARS-CoV-2 sequences, we analyzed all animal-derived (977), all Canadian (19,529) and US (173,277) SARS-CoV-2 sequences deposited in GISAID from December 2019 to March 12, 2021, and identified 2 dominant novel variants, the N501T-G142D variant and N501T-G142D-F486L variant, in the US mink-derived SARS-CoV-2 sequences. These variants were not found in minks from Canada or other countries. The Y453F mutation was not identified in the mink-derive sequences in the US and Canada. The N501T mutation occurred two months earlier in the human than in the minks in the US. The results of our study highlighted the importance of on going monitoring the mutations of the SARS-CoV-2 virus in animals.