Juliana Schons Gularte¹, Mariana Soares da Silva¹, Meriane Demoliner¹, Alana Witt Hansen¹, Fágner Henrique Heldt¹, Micheli Filippi¹, Vyctoria Malayhka de Abreu Góes Pereira¹, Francine Pereira da Silva¹, Larissa Mallmann¹, Pietra Fink¹, Matheus Nunes Weber¹, Paula Rodrigues de Almeida¹, Juliane Deise Fleck¹, Fernando Rosado Spilki¹
¹Universidade Feevale, Laboratório de Microbiologia Molecular, Rodovia ERS-239, Nº 2755, Prédio Vermelho, Piso 1, sala 103, Vila Nova, CEP 93525-075, Novo Hamburgo, RS, Brazil.
SARS-CoV-2 variant B.1.617.2, also known as the Delta (21A) variant, has quickly spread and detected in many countries 1–3. Since May 11, 2021, it has been classified as a variant of concern (VOC) by WHO 4. In Brazil, the first community sustained transmission chains were reported in Rio de Janeiro on June of 2021 5 and it has been already detected in other states over time 6. In the state of Rio Grande do Sul (RS), the southernmost state of Brazil, the first case was officially reported by local health authorities from a clinical specimen collected on July 12, 2021 7.
Our group have recently reported the whole viral genome sequencing and phylogenetic analysis were performed in 86 naso-oropharyngeal swab samples collected from 12 cities of RS and from travelers at the Salgado Filho International Airport at the state capital, in collaboration with the Municipal Health Department of Porto Alegre. The samples were collected from June 15 to August 9, 2021. Samples analyzed were from cities of Alvorada (1), Campo Bom (3), Canoas (31), Estância Velha (1), Esteio (1), Garibaldi (16), Minas do Leão (1), São Sebastião do Caí (1), Sapucaia do Sul (1), Quaraí (1), Novo Hamburgo (14), and Porto Alegre (11), in addition to travelers from other states. The age of patients ranged from 10 to 93 years and fifty-one samples were from female patients.
According to the Nextclade tool, 75% of the samples were characterized by Gamma variant (20J, V3) and 25% were Delta variant (21A). Detailed analysis using the Pangolin tool, 3.1.11 version, revealed the following distribution in strains: P.1 (56), P.1.7 (5), P.2 (2), P.1.8, (1). In the Delta variant clade, samples were observed in lineage B.1.617.2 (12), AY.4 (9), and AY.12 (1).
Regarding these data, we highlight some specific founds as the detection of Delta variant (Pango lineage B.1.617.2) collected on June 17, 2021, in two patients in the city of Garibaldi, even before the first notifications in the state of RS. We also started to see an increase in the detection of Delta variant over time. In 11 samples collected in the second half of June, 36 % (4) were positive for the Delta variant and 64 % (7) for the Gamma variant. In the month of July, 65 samples were collected being 20% (13) classified as Delta variant and 80 % (52) of the Gamma variant and its derived branches. However, in the 10 most recent samples collected on August, 5 samples (50%) belonged to the Delta variant. The Delta variant and its derived lineages were found in patients’ samples that were collected in the cities of Canoas, Estância Velha, Garibaldi, Novo Hamburgo, and Porto Alegre. As we already know at moment, the Delta variant causes more infections and spreads faster than the other SARS-COV-2 variants 8. Based on genomic characteristics, the delta variant (B.1.617.2) has been divided into sub-lineages that were also detected in our results being AY.4 (alias of B.1.617.2.4, UK lineage) and AY.12 (alias of B.1.617.2.12, Israel lineage) that harbor the L452R spike protein substitution that is a Substitution of Therapeutic Concern according to CDC 9.
Our study also analyzed 8 samples of travelers who landed at the state’s international airport. Six of these samples were positive for the P.1, one for the P.1.7, and another sample, from a passenger from Rio de Janeiro, positive for the AY.4 lineage derived from the Delta variant. We would like to highlight that only six of the 86 samples were from vaccinated individuals, being involved in these cases the lineages AY.12, B.1.617.2 (Delta), P.1.7, and P.1.
Therefore, the data corroborate with recent results found in other Brazilian states of continued evolution and diversification of the Gamma variant 10,11, as well as an increased occurrence of the Delta variant. We emphasize that constant surveillance of the circulation and relative distribution of the different variants is an important tool to fight the pandemic. The genomic surveillance efforts described here will be continued and this post will be updated in the coming weeks.
GISAID accession ID of the samples described in this study:
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