Pervasive transmission of E484K and emergence of VUI-NP13L with evidence of SARS-CoV-2 co-infection events by two different lineages in Rio Grande do Sul, Brazil

Abstract

Emergence of novel SARS-CoV-2 lineages are under the spotlight of the media, scientific community and governments. Recent reports of novel variants in the United Kingdom, South Africa and Brazil (B.1.1.28-E484K) have raised intense interest because of a possible higher transmission rate or resistance to the novel vaccines. Nevertheless, the spread of B.1.1.28 (E484K) and other variants in Brazil is still unknown. In this work, we investigated the population structure and genomic complexity of SARS-CoV-2 in Rio Grande do Sul, the southernmost state in Brazil. Most samples sequenced belonged to the B.1.1.28 (E484K) lineage, demonstrating its widespread dispersion. We were the first to identify two independent events of co-infection caused by the occurrence of B.1.1.28 (E484K) with either B.1.1.248 or B.1.91 lineages. Also, clustering analysis revealed the occurrence of a novel cluster of samples circulating in the state (named VUI-NP13L) characterized by 12 lineage-defining mutations. In light of the evidence for E484K dispersion, co-infection and emergence of VUI-NP13 L in Rio Grande do Sul, we reaffirm the importance of establishing strict and effective social distancing measures to counter the spread of potentially more hazardous SARS-CoV-2 strains.

Keywords: COVID-19; Co-infection; E484K; Genomic surveillance; Mutation; P13L.

Fig. 1

Genomic characterization and variant mapping of SARS-CoV-2 in Rio Grande do Sul, Brazil. A) Distribution of single-nucleotide variants (SNVs) throughout the SARS-CoV-2 genome. Each peak represents the allele frequency of each variant across the 92 samples sequenced. In green, we highlighted the top 5 kilobases with the highest mutation rate. Density plot shows the accumulation of variants in the viral genome. B) Clustering analysis using k-means algorithm with high-frequency SNVs shows six distinct clusters.

Fig. 2

Evolutionary relationships between newly described Rio Grande do Sul samples. A) Maximum likelihood tree inferred with 1037 SARS-CoV-2 genomes. Clade highlights indicate the monophyletic grouping for each cluster while the color coded outer ring indicates annotated lineages for each genome based on the Pangolin web application tool. Terminal tip color indicates genome locality by country and southern states of Brazil. In detail, ultrafast bootstrap support for each clade highlighted in A.

Fig. 3

Population structure and intra-host variation. A) Genetic profiling considering clusterization patterns and lineage classification. Bars represent the frequency of SARS-CoV-2 lineages according to Pangolin for each sample using high- and low-frequency variants. The allele frequency pattern observed in samples 38398 and 38158 unveiled two different lineages in both samples. B-C) Intra-host genetic variation analysis in sample 38398 and 38158 showed distinct frequencies of SNVs suggesting the existence of at least two haplotypes. Nucleotides highlighted in bold corresponded to alternative alleles in sites that characterized each lineage.