Abstract
Following the worldwide emergence of the p.Asp614Gly shift in the Spike (S) gene of SARS-CoV-2, there have been few recurring pathogenic shifts occurring during 2020, as assessed by genomic sequencing. This situation has evolved in the last several months with the emergence of several distinct variants (first identified in the United Kingdom and South Africa, respectively) that illustrate multiple changes in the S gene, particularly p.Asn501Tyr (N501Y), that likely have clinical impact. We report here the emergence in Columbus, Ohio in December 2020 of two novel SARS-CoV-2 clade 20G variants. One variant, that has become the predominant virus found in nasopharyngeal swabs in the December 2020-January 2021 period, harbors S p.Gln677His (Q677H) membrane glycoprotein (M) p.Ala85Ser (A85S) and nucleocapsid (N) p.Asp377Tyr (D377Y) mutations, with additional S mutations in subsets. The other variant present in two samples, contains S N501Y, which is a marker of the UK-B.1.1.7 (clade 20I/501Y.V1) strain, but lacks all other mutations from that virus. It is from a different clade and shares multiple mutations with the clade 20G viruses circulating in Ohio prior to December 2020. These two SARS-CoV-2 viruses emerging now in several parts of the United States add to the diversity of S gene shifts occurring worldwide and support multiple independent acquisition of S N501Y (in likely contrast to the unitary S D614G shift) occurring first during this period of the pandemic.
Competing Interest Statement
The authors have declared no competing interest.
Footnotes
We report an additional S N501Y-bearing virus in our data set; update Table 1b with the expanded set of associated variants. We compare Clade 20G viruses recently submitted to GISAID.org that also contain S N501Y and additional shared mutations, from other areas of the United States. This data in Table 1B and the Discussion supports grouping these viruses as an emerging strain. We mentioned recently described Clade 20G viruses that also contain S Q677H mutations, from other areas of the United States. This data supports grouping these viruses as a new strain common in the United States. There is an updated Table 1A listing the proportion of COH.20G/677H viruses with each of the recurrent mutations. There is a revised Figure 1 legend to provide more data.