Circulation of 21A (Delta) SARS-CoV-2 variant in Rio Grande do Sul, Southern Brazil

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:

EPI_ISL_3492502
EPI_ISL_3492513
EPI_ISL_3492501
EPI_ISL_3492512
EPI_ISL_3492511
EPI_ISL_3492510
EPI_ISL_3492509
EPI_ISL_3492508
EPI_ISL_3492507
EPI_ISL_3492506
EPI_ISL_3492505
EPI_ISL_3492504
EPI_ISL_3492515
EPI_ISL_3492503
EPI_ISL_3492514
EPI_ISL_3492483
EPI_ISL_3492494
EPI_ISL_3492493
EPI_ISL_3492492
EPI_ISL_3492491
EPI_ISL_3492490
EPI_ISL_3492489
EPI_ISL_3492500
EPI_ISL_3492488
EPI_ISL_3492499
EPI_ISL_3492487
EPI_ISL_3492498
EPI_ISL_3492486
EPI_ISL_3492497
EPI_ISL_3492485
EPI_ISL_3492496
EPI_ISL_3492484
EPI_ISL_3492495
EPI_ISL_3461109
EPI_ISL_3461105
EPI_ISL_3461106
EPI_ISL_3461107
EPI_ISL_3461108
EPI_ISL_3461101
EPI_ISL_3461102
EPI_ISL_3461103
EPI_ISL_3461104
EPI_ISL_3461097
EPI_ISL_3461098
EPI_ISL_3461099
EPI_ISL_3461100
EPI_ISL_3461058
EPI_ISL_3461059
EPI_ISL_3461053
EPI_ISL_3461064
EPI_ISL_3461054
EPI_ISL_3461065
EPI_ISL_3461055
EPI_ISL_3461066
EPI_ISL_3461056
EPI_ISL_3461067
EPI_ISL_3461060
EPI_ISL_3461061
EPI_ISL_3461062
EPI_ISL_3461063
EPI_ISL_3456070
EPI_ISL_3456061
EPI_ISL_3456063
EPI_ISL_3456062
EPI_ISL_3456065
EPI_ISL_3456064
EPI_ISL_3456067
EPI_ISL_3456066
EPI_ISL_3456069
EPI_ISL_3456068
EPI_ISL_3460258
EPI_ISL_3460248
EPI_ISL_3460249
EPI_ISL_3460254
EPI_ISL_3460255
EPI_ISL_3460256
EPI_ISL_3460257
EPI_ISL_3460250
EPI_ISL_3460251
EPI_ISL_3460252
EPI_ISL_3460253

References

  1. Public Health England. SARS-CoV-2 Variants of Concern and Variants under Investigation in England.; 2021.

  2. Li B, Deng A, Li K, et al. Viral infection and transmission in a large, well-traced outbreak caused by the SARS-CoV-2 Delta variant. medRxiv. Published online 2021:2021.07.07.21260122. https://www.medrxiv.org/content/10.1101/2021.07.07.21260122v2 https://www.medrxiv.org/content/10.1101/2021.07.07.21260122v2.abstract

  3. Bolze A, Cirulli ET, Luo S, et al. SARS-CoV-2 variant Delta rapidly displaced variant Alpha in the United States and led to higher viral loads. medRxiv. Published online 2021:2021.06.20.21259195. https://www.medrxiv.org/content/10.1101/2021.06.20.21259195v3 https://www.medrxiv.org/content/10.1101/2021.06.20.21259195v3.abstract

  4. World Health Organization. Tracking SARS-CoV-2 variants. Published 2021. Accessed August 18, 2021. Tracking SARS-CoV-2 variants

  5. Lamarca AP, Almeida LGP De, Francisco S, et al. Genomic surveillance tracks the first communitary outbreak of Delta (B.1.617.2) variant in Brazil. Virological.org. Published online 2021:2-5. Genomic surveillance tracks the first communitary outbreak of Delta (B.1.617.2) variant in Brazil

  6. Ministério da Saúde. Boletim epidemiológico especial - Doença Pelo Novo Coronavírus – COVID-19.; 2021.

  7. Srcretaria da Saúde do Rio Grande do Sul. Confirmados dois primeiros casos da variante Delta no RS. Published 2021. https://saude.rs.gov.br/confirmados-dois-primeiros-casos-da-variante-delta-no-rs

  8. Centers for Disease Control and Prevention (CDC). COVID-19 Delta Variant : What We Know About the Science. CDC. Published 2021. Accessed August 19, 2021. Delta Variant: What We Know About the Science | CDC

  9. Centers for Disease Control and Prevention (CDC). SARS-CoV-2 Variant Classifications and Definitions. CDC. Published 2021. Accessed August 19, 2021. https://www.cdc.gov/coronavirus/2019-ncov/cases-updates/variant-surveillance/variant-info.html https://www.cdc.gov/coronavirus/2019-ncov/cases-updates/variant-surveillance/variant-info.html#print

  10. Demoliner M, Soares M, Hansen AW, Fink P. Predominance of SARS-CoV-2 P . 1 ( Gamma ) lineage inducing the recent wave in southern Brazil and the finding of an additional S : D614A mutation. Res Sq . 2021;1:1-13. doi:Predominance of SARS-CoV-2 P.1 (Gamma) lineage inducing the recent wave in southern Brazil and the finding of an additional S: D614A mutation | Research Square License:

  11. Naveca F, Nascimento V, Souza V, et al. Emergence and spread of SARS-CoV-2 P . 1 ( Gamma ) lineage variants carrying Spike mutations ? 141-144 , N679K or P681H during persistent viral circulation in. Virological. 2021;1(July):0-2. Emergence and spread of SARS-CoV-2 P.1 (Gamma) lineage variants carrying Spike mutations 𝚫141-144, N679K or P681H during persistent viral circulation in Amazonas, Brazil

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Update information – samples analysis from July 24, 2021, to August 13, 2021.

Our group has recently reported the whole viral genome sequencing and phylogenetic analysis performed in 29 naso-oropharyngeal swab samples collected from 4 cities of RS. The material included for analysis was collected between July 24, 2021, and August 13, 2021.

The general analysis for the whole period revealed 13 samples classified as Gamma variant (20J, V3), and 16 cases of Delta variant (21A) according to the Nextclade tool. Detailed analysis using the Pangolin tool, 3.1.11 version, revealed the following distribution in strains: 9 samples of P.1, 3 samples of P.1.1, and 1 sample of P.1.8. In the Delta variant clade, 9 samples were observed in lineage B.1.617.2, 1 sample of AY.4, and 6 samples of AY.6.

Regarding these data generated by samples collected from July to August, we highlight some interesting founds:

  • The finding of 2 cases of the Delta variant in the municipality of Campo Bom in sample collected on August 11, as well as additional cases of this same variant for the other cities.
  • Of the 10 samples collected between July 24 and August 1, 2021, 4 were positive for the Delta variant (40%) while in the samples analyzed between August 6 and August 13, 2021, the rate increase to 63.15% (12/19 samples), confirming the upward trend already observed by the Corona-Ômica.BR-MCTI Network for the region.

The results complement recent work carried out in the region and the data are being shared with health authorities. We reinforce that surveillance of the circulation and relative distribution of SARS-CoV-2 variants is an important tool for combating the COVID-19 pandemic. We further inform that the genomes obtained in this study will be deposited in international databases in the coming days.

Update information – samples analysis from July 24, 2021, to August 13, 2021

GISAID accession ID of the samples described in this study:

EPI_ISL_3756569
EPI_ISL_3756579
EPI_ISL_3756578
EPI_ISL_3756577
EPI_ISL_3756576
EPI_ISL_3756575
EPI_ISL_3756574
EPI_ISL_3756573
EPI_ISL_3756572
EPI_ISL_3756571
EPI_ISL_3756582
EPI_ISL_3756570
EPI_ISL_3756581
EPI_ISL_3756580
EPI_ISL_3806777
EPI_ISL_3806778
EPI_ISL_3806775
EPI_ISL_3806776
EPI_ISL_3806773
EPI_ISL_3806784
EPI_ISL_3806774
EPI_ISL_3806771
EPI_ISL_3806782
EPI_ISL_3806772
EPI_ISL_3806783
EPI_ISL_3806780
EPI_ISL_3806770
EPI_ISL_3806781
EPI_ISL_3806779