Emergence of a novel SARS-CoV-2 strain in Southern California, USA

 Wenjuan Zhang, Brian D Davis, Stephanie S Chen, Jorge M Sincuir Martinez,  

View ORCID ProfileJasmine T Plummer, Eric Vail

doi: https://doi.org/10.1101/2021.01.18.21249786

This article is a preprint and has not been peer-reviewed [what does this mean?]. It reports new medical research that has yet to be evaluated and so should not be used to guide clinical practice.

PDF: https://www.medrxiv.org/content/10.1101/2021.01.18.21249786v1.full.pdf

Abstract

Since October 2020, novel strains of SARS-CoV-2 including B.1.1.7, have been identified to be of global significance from an infection and surveillance perspective. While this strain (B.1.1.7) may play an important role in increased COVID rates in the UK, there are still no reported strains to account for the spike of cases in Los Angeles (LA) and California as a whole, which currently has some of the highest absolute and per-capita COVID transmission rates in the country. From the early days of the pandemic when LA only had a single viral genome uploaded onto GISAID we have been at the forefront of generating and analyzing the SARS-CoV-2 sequencing data from the LA region. We report a novel strain emerging in Southern California. Most current cases in the catchment population in LA fall into two distinct subclades: 1) 20G (24% of total) is the predominant subclade currently in the United States 2) a relatively novel strain in clade 20C, CAL.20C strain (∼36% of total) is defined by five concurrent mutations. After an analysis of all of the publicly available data and a comparison to our recent sequences, we see a dramatic growth in the relative percentage of the CAL.20C strain beginning in November of 2020. The predominance of this strain coincides with the increased positivity rate seen in this region. Unlike 20G, this novel strain CAL.20C is defined by multiple mutations in the S protein, a characteristic it shares with both the UK and South African strains, both of which are of significant clinical and scientific interest

Competing Interest Statement

The authors have declared no competing interest.

Funding Statement

Internal funding from the Department of Biomedical Sciences, Cedars Sinai Medical Center was awarded for the execution and completion of this work.

https://www.medrxiv.org/content/10.1101/2021.01.18.21249786v1