Continued genomic Surveillance of SARS-CoV-2 in the state of Rio de Janeiro, Brazil, by the Corona-ômica-RJ Network

Continued genomic Surveillance of SARS-CoV-2 in the state of Rio de Janeiro, Brazil, by the Corona-ômica-RJ Network

Alessandra P Lamarca¹, Luiz G P de Almeida¹, Ronaldo da Silva Francisco Junior¹, Liliane Cavalcante¹, Otávio Brustolini¹, Alexandra L Gerber¹, Ana Paula de C Guimarães¹, Thiago Henrique de Oliveira², Érica Ramos dos Santos Nascimento², Cintia Policarpo², Erika Martins de Carvalho³,Mario Sergio Ribeiro4, Silvia Carvalho4, Flávio Dias da Silva5, Marcio Henrique de Oliveira Garcia5, Leandro Magalhães de Souza6, Cristiane Gomes Da Silva6, Caio Luiz Pereira Ribeiro5, Andréa Cony Cavalcanti6, Claudia Maria Braga de Mello4, Amilcar Tanuri², Ana Tereza R Vasconcelos¹*

1-Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis, Brazil.
2-Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
3-Unidades de Apoio ao Diagnóstico da Covid-19, Rio de Janeiro, Brazil.
4-Secretaria Estadual de Saúde do Rio de Janeiro, Rio de Janeiro, Brazil.
5-Secretaria Municipal de Saúde Rio de Janeiro, Rio de Janeiro, Brazil.
6-Laboratório Central de Saúde Pública Noel Nutels, Rio de Janeiro, Brazil.

Corresponding author (*): atrv@lncc.br

The state of Rio de Janeiro plays an important role in the dynamics of SARS-CoV-2 in Brazil. Previous findings showcase that it was the main stage of the emergence of new lineages [1–3] and that the state is a hub for national transmission of the Variant of Concern Delta (B.1.617.2 and its sublineages)[4,5] and the former Variant of Interest Zeta (lineage P.2)[6]. Ongoing monitoring of SARS-CoV-2 genomic diversity in Rio de Janeiro is, therefore, of utmost importance to understand the epidemic in Brazil. Here we present the latest findings by the Corona-ômica-RJ Network.

We randomly selected 375 samples of SARS-CoV-2 obtained from a pool of nasopharyngeal swabs collected by the Noel Nutels Central Laboratory (LACEN-RJ) and Unidades de Apoio ao Diagnóstico da Covid-19 (UNADIG-RJ) to diagnose COVID-19 in residents of the state of Rio de Janeiro between December 22nd of 2021 and January 13rd of 2022. Extraction and library preparation was conducted at the Laboratory of Molecular Virology at Universidade Federal do Rio de Janeiro (LVM-UFRJ). Reads were generated using the NextSeq 500/550 Mid Output Kit v2.5 (300 Cycles) and the DRAGEN COVID Lineage v3.5.1 pipeline was used for sequence analysis, consensus building, and variant calling. All newly sequenced and assembled genomes are publicly available at GISAID (Table S1) and GSA/NGDC (BioProject PRJCA007589) databases. Finally, we used the PangoLEARN v1.2.123 model database to classify the lineage of our newly assembled genomes. We aligned these sequences with MAFFT and reconstructed their evolutionary tree with IQ-TREE. We additionally obtained all Brazilian sequences available in GISAID (Table S2) to evaluate if there was a single or multiple introduction events in the state of Rio de Janeiro. The study was approved by the National Ethics Committee (protocols 30161620.0.1001.5257 and 34025020.0.0000.5257).

From the 375 analyzed sequences, 97.33% (n = 365) were classified as the Omicron variant (lineage B.1.1.529 and its sublineages BA.x). Most of these belonged to lineage BA.1 (n = 306), with the remaining being BA.1.1 (Figure 1). Other lineages detected were AY.34.1, AY.43 and AY.99.2, all from the Delta variant dominant in the state until the end of 2021 (Genomic Surveillance of SARS-CoV-2 in the State of Rio de Janeiro, Brazil: technical briefing - #9 by lgonzaga). We observed that these samples are probably the result of multiple introductions in Rio de Janeiro, as opposed to what happened with the Delta variant in the state. These multiple seeding events indicate that the virus is freely circulating between Brazilian states.

Figure 1. Relationship between SARS-CoV-2 lineages identified in the state of Rio de Janeiro between December 22nd of 2021 and January 13rd of 2022. Colors represent the lineages of the viral samples.

Figure 2. Evolutionary tree of Omicron sequences from Brazil. In color, each of the Brazilian states (AL, Alagoas; AM, Amazonas; BA, Bahia; CE, Ceará; DF, Distrito Federal; ES, Espírito Santo; GO, Goiás; MG, Minas Gerais; PB, Paraíba; PE, Pernambuco; RJ, Rio de Janeiro; RN, Rio Grande do Norte; RS, Rio Grande do Sul; SC, Santa Catarina; SP, São Paulo; TO, Tocantins).

Acknowledgements: We would like to thank all the authors and administrators of the GISAID database, which allowed this study of genomic epidemiology to be conducted properly. A complete list acknowledging the authors publishing data used in this study can be found in Table S2.

This work was developed in the frameworks of Corona-ômica-RJ (FAPERJ = E-26/210.179/2020 e E-26/211.107/2021). We acknowledge the support from the Rede Corona-ômica BR MCTI/FINEP affiliated to RedeVírus/MCTI (FINEP 01.20.0029.000462/20, CNPq 404096/2020-4).

Table S1 (249.8 KB)
Table S2 (120.8 KB)