Abstract
COVID-19 vaccines were first administered on 15 December 2020, marking an important transition point for the spread of SARS-CoV-2 in the United States (U.S.). Prior to this point in time, the virus spread to an almost completely immunologically naïve population, whereas subsequently, vaccine-induced immune pressure and prior infections might be expected to influence viral evolution. Accordingly, we conducted a study to characterize the spread of SARS-CoV-2 in the U.S. pre-vaccination, investigate the depth and uniformity of genetic surveillance during this period, and measure and otherwise characterize changing viral genetic diversity, including by comparison with more recently emergent variants of concern (VOCs). In 2020, SARS-CoV-2 spread across the U.S. in three phases distinguishable by peaks in the numbers of infections and shifting geographical distributions. Virus was genetically sampled during this period at an overall rate of ~1.2%, though there was a substantial mismatch between case rates and genetic sampling nationwide. Viral genetic diversity tripled over this period but remained low in comparison to other widespread RNA virus pathogens, and although 54 amino acid changes were detected at frequencies exceeding 5%, linkage among them was not observed. Based on our collective observations, our analysis supports a targeted strategy for worldwide genetic surveillance as perhaps the most sensitive and efficient means of detecting new VOCs.
Highlights
The first reported case of COVID-19 in the U.S was on January 20th, 2020 [1]
We provide a detailed characterization of the early spread of SARS-CoV-2 in three phases across the different geographic regions of the U.S and assess the varying levels of genetic surveillance and genetic diversity in each region and phase
Viral spread in the U.S was divided into three phases based on COVID-19 case peaks where the derivative of the trough was approximately zero: Phase 1 of winter–spring
Summary
The first reported case of COVID-19 in the U.S was on January 20th, 2020 [1]. Since that time, through to the beginning of January 2022, there have been more than 57 millionU.S cases (19.3% of global) and 828,000 deaths (15.2% of global) [2]. The first reported case of COVID-19 in the U.S was on January 20th, 2020 [1]. The end of 2020 was marked by the emergence of SARS-CoV-2 variants with greater transmissibility, virulence, and partial resistance to current preventives and treatments [3,4]. Though they share some common genetic features, such ‘variants of concern’ (VOCs) appear to have emerged independently in different regions throughout the world [5,6]. Assessing the spread and genetics of SARSCoV-2 in the U.S in 2020, largely in the absence of immune selection pressure from prior infection or vaccine administration, will allow us and others to contrast these patterns with the surveillance and genetics of the virus in the future, with emphasis on improving the early detection of new variants
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