Update information – samples analysis from late July and early September
Since the last update, we have additionally sequenced a total of 74 SARS-CoV-2 samples collected between late July and early September. The patients were from 14 cities: Alvorada (1), Campo Bom (2), Canoas (31), Garibaldi (8), Novo Hamburgo (11), Picada Café (1), Porto Alegre (4), Rio Grande (1), Santa Cruz do Sul (9), São Leopoldo (1), Sapucaia do Sul (2) e Viamão (1) (RS State); Friburgo (1) (Santa Catarina State) and Macapá (1) (Amapá State). Complete SARS-CoV-2 genomes were first analyzed through online Pangolin tool (https://github.com/hCoV-2019/pangolin) , and characterized as Gamma (P.1, P.1.2 e P.1.9) and Delta (B.1.617.2) lineages. The corresponding frequencies were: 75% of Delta (B.1.617.2) and 25% of Gamma (including P.1, P.1.2 and P.1.9). It is interesting to point out that, in the previous sequencing, the frequencies of the Gamma and Delta lineages had been basically opposite to those found herein. This epidemiological follow-up allowed us to observe the Delta variant emergence and establishment in the RS State. The complete temporal data from the sequencing of SARS-CoV-2 variants in 2021 by our laboratory can be seen in Figure 1. In order to confirm the data obtained, the sequences were aligned with complete SARS-CoV-2 genomes from different lineages through the NextClade online platform and the phylogenetic tree was inferred. The sequences generated herein clearly clustered into two major clades belonging to Gamma and Delta lineages (Figure 2). The constant monitoring of new genomes, as well as the entry and distribution of new lineages are of special relevance, considering the impact caused by lineages such as B.1.1.7 (Alpha), B.1.351 (Beta), P.1, and B .1.617.2 (Delta), in the United Kingdom, South Africa, Brazil and India, respectively.
Figure 1. Temporal SARS-CoV-2 lineages distribution sequenced between 2021 January and September in Rio Grande do Sul State
Figure 2. Phylogenetic tree inferred through online NextClade tool. Delta (green) and Gamma (blue) sequences generated in this genomic surveillance study (sequences IDs according to GISAID database).