Massive dissemination of a SARS-CoV-2 Spike Y839 variant in Portugal

Abstract

Genomic surveillance of SARS-CoV-2 was rapidly implemented in Portugal by the National Institute of Health in collaboration with a nationwide consortium of >50 hospitals/laboratories. Here, we track the geotemporal spread of a SARS-CoV-2 variant with a mutation (D839Y) in a potential host-interacting region involving the Spike fusion peptide, which is a target motif of anti-viral drugs that plays a key role in SARS-CoV-2 infectivity. The Spike Y839 variant was most likely imported from Italy in mid-late February and massively disseminated in Portugal during the early epidemic, becoming prevalent in the Northern and Central regions of Portugal where it represented 22% and 59% of the sampled genomes, respectively, by 30 April. Based on our high sequencing sampling during the early epidemics [15.5% (1275/8251) and 6.0% (1500/24987) of all confirmed cases until the end of March and April, respectively], we estimate that, between 14 March and 9 April (covering the epidemic exponential phase) the relative frequency of the Spike Y839 variant increased at a rate of 12.1% (6.1%-18.2%, CI 95%) every three days, being potentially associated with 24.8% (20.8-29.7%, CI 95%; 3177-4542 cases, CI 95%) of all COVID-19 cases in Portugal during this period. Our data supports population/epidemiological (founder) effects contributing to the Y839 variant superspread. The potential existence of selective advantage is also discussed, although experimental validation is required. Despite huge differences in genome sampling worldwide, SARS-CoV-2 Spike D839Y has been detected in 13 countries in four continents, supporting the need for close surveillance and functional assays of Spike variants.

Keywords: COVID-19; D839Y; SARS-CoV-2; Spike; fusion peptide; genetic variant; genomic epidemiology; mutation.

Figure 1.

Overview of the SARS-CoV-2 genome sequencing sampling in Portugal and cumulative relative frequency of the circulating Spike Y839 variant, as of 30 April 2020 (n = 1500). Area plots (left y-axis) reflect the cumulative total number of SARS-CoV-2 genome sequences (gray) and Spike Y839 variant sequences (red) obtained in Portugal during the first two months of the epidemic. Lines (right y-axis) display the cumulative percentage of COVID-19 confirmed cases for which SARS-CoV-2 genome data was generated (“sequencing sampling” – black dash line) and the cumulative proportion of the Spike Y839 variant sequences (red line) detected in Portugal during the same period.

Figure 2.

Landscape of the geotemporal spread of SARS-CoV-2 Spike Y839 variant in Portugal by region, as of 30 April 2020. (A) Distribution of the analysed genome sequences (n = 1500) by date of sample collection and Health Administration region, highlighting COVID-19 cases caused by the Spike Y839 variant (red dots). In y-axis, it is indicated, for each region, the number of sequences analysed (n), the percentage of confirmed cases with SARS-CoV-2 genome data (% cases), the percentage of sequences from each region in the whole dataset (% genomes) and the percentage of Y839 variant sequences (%Y839, in red), as of 30 April, 2020. (B) Radial maximum likelihood phylogenetic tree showing the high proportion of genomes with the Spike D839Y mutation detected in Portugal [about 20% of all sequences collected until the end of March (255/1275) or the end of April (287/1500)]. This dataset covers 15.5% (1275/8251) and 6.0% (1500/24987) of all confirmed cases detected until the end of March and April, respectively. The phylogeny and geotemporal distribution can be visualized interactively at https://microreact.org/project/nDGsJKFv7gQTj1q8CQwwKR/0489f840 (geographic resolution by Region) and https://microreact.org/project/2kh3TRVYB9gWGRpNSJWDW5/b6c659e0 (geographic resolution by District) using Microreact (https://microreact.org/). (C) Distribution of the Spike Y839 variant by Health Administration region, highlighting its high relative frequency in the Northern and Central regions of Portugal, where this variant represented 22% and 59% of the sampled genomes until the end of April 2020, respectively. The size of the pie charts is proportional to the number of sequenced genomes. (D) Cumulative total number of COVID-19 confirmed cases by Health Administration region, showing the Northern region as the “epicenter” of the epidemic during the two first months (source: General Directorate of Health (DGS), https://covid19.min-saude.pt/relatorio-de-situacao/).

Figure 3.

Overview of the SARS-CoV-2 genome sequencing sampling and cumulative relative frequency of the circulating Spike Y839 variant, as of 30 April 2020 (n = 1500), in the Northern (A) and Central (B) regions of Portugal. Area plots (left y-axis) reflect the cumulative total number of COVID-19 confirmed cases (light blue) and SARS-CoV-2 genome sequences (dark blue) detected/generated in each Health Administration region. Lines (right y-axis) display the cumulative percentage of COVID-19 confirmed cases with SARS-CoV-2 genome data, i.e. sequencing sampling (blue dash line) and the cumulative proportion of the Spike Y839 variant sequences (red line) detected in those regions during the same period.

Figure 4.

Increasing trajectory of the Spike Y839 variant and estimated weight of this variant in the total number of COVID-19 confirmed cases in early epidemic. A binomial regression model with logarithmic link function was applied to assess the temporal variation in the proportion of the Y839 variant among sequenced samples (graph in the upper left corner, showing an estimate increase from 13.3% to 33.1%). This model was then applied to extrapolate the evolution of Y839 cases (red line) in the total confirmed case population (gray bars) at each 3-day interval (main graph). Crosses represent the estimated Y839 cases and the shaded region shows the 95% confidence interval. 1-day was assumed as the timeframe delay between sample collection and case notification.

Figure 5.

Detection and circulation of the SARS-CoV-2 Spike D839Y mutation worldwide. SARS-CoV-2 Spike amino acid sequences available at GISAID (https://www.gisaid.org/), as of 23 July 2020, were download, aligned and screened for the presence of mutations in Spike 839 amino acid position. The main plot displays the country and data of collection of 92 Spike sequences with the D839Y mutation (detailed in Table S2). The bar graph in the upper right corner displays the proportion of D839Y sequences in the total number of Spike amino acid sequences available per country. As detailed in Table S2, the D839Y sequence from Estonia indicates March 2020 as the date of collection (31 March 2020 was assumed in this plot). Two genomes (one from United Kingdom and another from India) only had the year of sampling available, thus they were not included in the graph.