A Pre-Vaccination Baseline of SARS-CoV-2 Genetic Surveillance and Diversity in the United States

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.

VIROME OF GRAPEVINE GENETIC COLLECTIONS

Russian vineyards are an underexplored reservoir of viral genetic diversity. The use of metagenomics methods allows to obtain information about the virome of a plant and can be used to establish the etiology of a new disease.

Identification of SARS-CoV-2 recombinant genomes

Viral recombination has the potential to bring about viral genotypes with modified phenotypic characteristics, including transmissibility and virulence. Although the capacity for recombination among Betacoronaviruses is well documented, SARS-CoV-2 has only been circulating in humans for approximately 8 months and thus has had a relatively short window of opportunity for the occurrence of recombination. The ability to detect recombination has further been limited by the relatively low levels of genetic diversity in SARS-CoV-2. Despite this, two studies have reported recombinants among SARS-CoV-2 strains. Here we first revisit these findings with a new analysis approach, arguing that neither presents a clear case of within-SARS-CoV-2 recombination. Applying this same approach to available SARS-CoV-2 sequences, we then identify five recombinant genomes. Each of these genomes contain phylogenetic markers of two distinct SARS-CoV-2 clades. Further, the predicted parent clades of these recombinant genomes were, with one exception, documented to be co-circulating in the country of infection in the two weeks prior to the sample being collected. Our results indicate that recombination among SARS-CoV-2 strains is occurring, but is either not widespread or often remains undetectable given current levels of viral genetic diversity. Efforts to monitor the emergence of new recombinant genomes should therefore be sustained.