Study explores the emergence and spread of SARS-CoV-2 Delta variant across Brazil

In October 2020, the first case of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Delta variant of concern (VOC) was identified in India. By July 2021, the Delta variant was the most represented SARS-CoV-2 lineage in the global coronavirus disease 2019 (COVID-19) pandemic profile.

Brazil reported its first COVID-19 case in late February 2020 and the Delta variant was identified in April 2021 in the southern region, which later spread to different regions of Brazil.  Since previous studies of the Delta variant in Brazil focus on Rio de Janeiro and São Paulo, which are the most populated states in this country, information on the dissemination dynamics of the Delta variant in other Brazilian states is inadequate.

Study: Emergence and Spread of the SARS-CoV-2 Variant of Concern Delta Across Different Brazilian Regions. Image Credit: 3dartistav /

About the study

In a preprint study published on the medRxiv* preprint server, Brazilian researchers aimed to determine the emergence and spread of the Delta VOC in different regions in Brazil. The data relating to VOC Delta genomes from the COVID-19 Fiocruz Genomic Surveillance network was used to analyze its phylogenetic profile and determine its major dissemination routes across 20 Brazilian states.

A combination of maximum likelihood (ML) and Bayesian methods was implicated to analyze the phylogenetic profile of 2,264 Delta sequences from Brazil and a subset of 591 non-Brazilian sequences.

Dissemination of major clusters of VOC Delta in different regions in Brazil

The current study identified three main transmission clusters, which were identified as Brazilian-I (BR-I) (n = 1,560), BR-II (n=207), and BR-III (n = 497) of Delta variant in Brazil due to founder events. BR-I was the largest cluster of the Delta variant found in the southeastern state of Rio de Janerio in late April 2021 and was identified to be primarily responsible for the dissemination of the Delta variant in the northern, north-eastern, and central-western regions in Brazil. The BR-I cluster was also found in two southern regions, namely the Rio Grande do Sul and Santa Catarina.

BR-II was identified in the state of Parana in late April 2021 and is known to be the primary hub for the expansion of the Delta variant in southern Brazil. Genomic sequencing of BR-II found three genes of ORF1a: A3070V, S: T95I, and ORFa: A23V, among which ORF3a: A23V was found to be significantly different with respect to other major Brazilian clusters and foreign sequences.

The mutation in ORF3a: A23V is a distinctive marker found in all sequences within the BR-II cluster and acts as a molecular synapomorphy. This gene is an ion transporter of 275 amino acids that, following its up-regulation, increases fibrinogen secretion that is linked to the COVID-19 cytokine storm.

BR-III is the most recently emerged cluster among the three Delta clusters found in Brazil and was found in Sao Paulo state in early June 2021. The spread of cluster BR-III in other states was limited and was therefore mostly confined to Sao Paulo state. BR-III genomes displayed one molecular synapomorphy, ORF9b: R32L which localizes in the mitochondrial membrane and inhibits the secretion of interferon-1 (IFN-1).

The majority of Delta sequences sampled in the south-eastern and southern regions were sub-divided within Brazilian clusters. The northern region showed the lowest level of clusterization among samples from four to six regions and was least represented in the national Delta dataset.

Amazonas had the largest Delta cluster and was the most represented state in the northern region. The north-eastern region of Brazil harbored samples from eight states, in which Paraiba displayed the largest Delta cluster followed by Ceara and Pernambuco. The clusterization level observed in the northern and north-eastern regions was similar at 36%, despite a larger number of sequences in the north-eastern as compared to the northern region.

Conclusions and limitations

The study findings portrayed different stages of maturity in the Delta epidemics in Brazil. The BR-I, BR-II, and BR-III clusters contribute to the majority of Delta sequences. Therefore, the suppression of transmission clusters at the initial stage indicates the effectiveness of the preventive measures implemented in Brazil to prevent viral transmission.

The current study was limited by the lack of more robust metadata and inadequate sampling in some Brazilian states. The Delta variants are also susceptive to vaccines; therefore, information on vaccination status might have provided clarity on potential factors responsible for the development of local clusters in Brazil.  

More vigorous studies should be conducted to determine the dissemination path and identification of new clusters and the factors affecting suppression at an early stage. This could help identify and mitigate new variant introductions and further limit their dissemination to prevent more significant outbreaks in the future.

*Important notice

medRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.

Journal reference:
Susha Cheriyedath

Written by

Susha Cheriyedath

Susha has a Bachelor of Science (B.Sc.) degree in Chemistry and Master of Science (M.Sc) degree in Biochemistry from the University of Calicut, India. She always had a keen interest in medical and health science. As part of her masters degree, she specialized in Biochemistry, with an emphasis on Microbiology, Physiology, Biotechnology, and Nutrition. In her spare time, she loves to cook up a storm in the kitchen with her super-messy baking experiments.


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