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.

Dynamics of a Dual SARS-CoV-2 Lineage Co-Infection on a Prolonged Viral Shedding COVID-19 Case: Insights into Clinical Severity and Disease Duration

“…At the diagnosis (sample P1.1), she displayed 100% of a 20A affiliated haplotype, bearing the basal C241T-C3037T-C14408T-A23403G variants (in relation to the reference sequence), and additional C3140T-G24077T-C295557 variants. The G24077T variant has been extensively observed in Lombardy, Italy ( ) [ 22 ], while the C3140T-C295557 variants were highly observed in Portugal by the time of this patient’s infections, especially so around her geographical region [ 23 ]. This viral haplotype was also obtained from the RNA extracted from the diagnostic sample of her 41-year-old mother.…”

The early dynamics of the SARS-CoV-2 epidemic in Portugal

“…Among these, it is highlighted the increased frequency of the B.1.1 sublineages (roughly corresponding to clade 20B/GR), as well as of the B.1, B.1.5 and B.1.91 lineages (all mostly including 20A/G virus). Of note, the B.1.91 sub-lineage, and part of its ancestor sublineage B.1, correspond to the Spike G614+Y839 variant that massively disseminated in Portugal during the early epidemic (22% and 59% of the sampled genomes from the North and Center regions of Portugal by April 30 th ) ( Borges et al, 2020 ).…”

“…Interestingly, despite the UK, France and Spain having seeded the majority of introductions, at least one seeding event with travel history from Italy generated the largest outbreak recorded in early stages of the COVID-19 epidemic in Portugal (cfr. below) ( Borges et al, 2020 ). We noticed a similar pattern for an introduction from Thailand, however this event had a low supported topology posterior probability ( Figure 5 and 6B; Table S5 ).…”

“…This site gives access to “situation reports of the study and provides interactive data navigation using both Nextstrain (https://nextstrain.org/) ( Hadfield et al, 2018 ) and Microreact (https://microreact.org/) ( Árgimon et al, 2016 ) tools. As of July 23 rd , 2020, genomic and phylogenetic analysis were performed using the SARS-CoV-2 Nextstrain pipeline version from March 23, 2020 (https://github.com/nextstrain/ncov), with slight modifications ( Borges et al, 2020 ). For data navigation, an IQ-TREE-derived ( Nguyen et al, 2015 ) phylogenetic tree enrolling the 1275 studied sequences, and the associated metadata, can be visualized interactively at https://microreact.org/project/cM6KURnU7rUpqdAnBq5DAf/a2d3840e.…”

Investigation of potential safety hazards during medical waste disposal in SARS-CoV-2 testing laboratory

“…Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) as the causative agent of COVID-19 is highly infectious and lethal (Harrison et al 2020 , Koff and Williams 2020 , Phua et al 2020 ). The continuous emergence of variants such as D614G, Spike Y839, and 20A.EU1 make it spread faster (Baric 2020 , Borges et al 2020 , Hodcroft et al 2020 , Kirby 2021 ).…”