Early Emergence Phase of SARS-CoV-2 Delta Variant in Florida, US

Abstract

SARS-CoV-2, the causative agent of COVID-19, emerged in late 2019. The highly contagious B.1.617.2 (Delta) variant of concern (VOC) was first identified in October 2020 in India and subsequently disseminated worldwide, later becoming the dominant lineage in the US. Understanding the local transmission dynamics of early SARS-CoV-2 introductions may inform actionable mitigation efforts during subsequent pandemic waves. Yet, despite considerable genomic analysis of SARS-CoV-2 in the US, several gaps remain. Here, we explore the early emergence of the Delta variant in Florida, US using phylogenetic analysis of representative Florida and globally sampled genomes. We find multiple independent introductions into Florida primarily from North America and Europe, with a minority originating from Asia. These introductions led to three distinct clades that demonstrated varying relative rates of transmission and possessed five distinct substitutions that were 3-21 times more prevalent in the Florida sample as compared to the global sample. Our results underscore the benefits of routine viral genomic surveillance to monitor epidemic spread and support the need for more comprehensive genomic epidemiology studies of emerging variants. In addition, we provide a model of epidemic spread of newly emerging VOCs that can inform future public health responses.

Keywords: Delta; Florida; SARS-CoV-2; early emergence; phylogenetic analysis.

Figure 1

Infection distribution over time in the context of SARS-CoV-2 lineages and vaccination. (A) Distribution (y-axes) of previously considered variants of concern (VOCs) over time (x-axis) in terms of number of weekly confirmed cases (top), count of sequenced isolates stratified by VOC (middle), and the proportion of VOC (bottom). Remaining lineages are grouped into “Other”. (B) Vaccinated individuals (defined as ”incomplete” for a single dose of Moderna or Pfizer and ”fully” for two doses of Moderna or Pfizer and a single dose of Johnson&Johnson, top) and cumulative number of weekly confirmed cases (bottom) over time (x-axis).

Figure 2

Distribution of spike protein substitutions among Florida SARS-CoV-2 Delta (B.1.617.2) variant genomes. The x-axis shows the coordinates of the region encoding the spike protein and the y-axis shows the proportion of genomes carrying the substitution. Substitutions with a prevalence greater than 2% are annotated. The inlaid table includes the Delta variant characterizing substitutions in spike protein region, the prevalence among Florida genomes, and the prevalence among worldwide Delta genomes sampled from GISAID (*) (https://outbreak.info/compare-lineages?pango=B.1.617.2&gene=S&threshold=0.2 (accessed on 13 July 2021)).

Figure 3

Sources of viral exchanges (imports and exports) in and outside Florida. Movement was inferred using ancestral reconstruction of geographic states within the phylogenetic tree of genomic samples. (A). Total number of viral introductions over time into Florida. (B). Graphical representation of the estimated number of migration events between the geographic areas; introductions into the state of Florida are outlined in black.

Figure 4

Time-resolved maximum-likelihood trees containing high-quality Delta SARS-CoV-2 near-full-genome sequences. (A). Full time-resolved maximum-likelihood tree for all sequence data. The three clades identified as being well-supported using bootstrap (BS) analysis (BS > 70) are highlighted in light purple (referred to as clades I–III). A pie chart indicating the location distribution is located on top of each of the three clades. (B–D). Maximum-clade credibility tree reconstruction for the three clades (I–III) individually. Tree tips are colored according to their location (continent) and the color legend is on the top right of the figure.