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

In October of 2020, India was home to the first documented case of severe acute respiratory syndrome coronavirus 2 Delta variant of concern (VOC). The most prevalent SARS-CoV-2 variant in the global coronavirus pandemic of 2019 (COVID-19), was the Delta variant by July 2021.

Brazil discovered its first COVID-19 case in late February 2020 . the Delta variant was discovered in April 2021 in the southern region, which later spread to different regions of Brazil. The spread dynamics of this variant in Brazil is not known since previous studies have focused on Brazil’s two most populous states, Rio de Janeiro, and Sao Paulo.

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

About the study

Brazilian researchers published an article in a preprint on the preprint server. The study aimed to determine the origin and spread of the Delta VOC within different regions of Brazil. The information pertaining to VOC Delta genomes from the COVID-19 Fiocruz Genomic Surveillance network was used to analyze its phylogenetic structure and identify its major dissemination routes across 20 Brazilian states.

To analyze the phylogenetic profiles of 2,264 Delta sequences from Brazil and a subset of 591 non-Brazilian sequences, a combination of maximum likelihood and Bayesian methods was used.

Dissemination major clusters of VOC deltas in different regions of Brazil

The present study identified three major transmission clusters, identified as Brazilian-I (BR-I) (n = 1,560) as well as the BR-II (n=207), and BR-III (n = 497) of Delta variant in Brazil due to founder events. BR-I was the largest cluster containing the Delta variant, which was discovered in the southeastern Brazilian state of Rio de Janerio in April 2021. It was responsible for the spread of the Delta variant to the north-eastern, central region, as well as the northern regions of Brazil. The BR-I cluster also was located in two southern regions, namely the Rio Grande do Sul and Santa Catarina.

BR-II was identified in the state of Parana in the latter part of April 2021. It is thought as the main hub for the expansion of the Delta variant in southern Brazil. Genomic sequencing of BR-II identified three genes: ORF1a A3070V and S T95I. Of these, ORFa, A23V was identified. In addition, ORF3a, A23V was significantly different from other major Brazilian clusters or foreign sequences.

The mutation in ORF3a is A23V. It is a distinct marker that can be found in all sequences in the BR-II cluster. It acts as a molecular Synapomorphy. This gene is an ion transporter of 275 amino acid that is activated by its upregulation and increases fibrinogen production. It is also linked to 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. Cluster BR-III was not widely distributed in other states, and was thus only found in the state of Sao Paulo. The genomes of BR-III showed one molecular synapomorphy, ORF9b: R32L which localizes in the mitochondrial membrane and blocks the production of interferon-1 (IFN-1).

The majority of Delta sequences sampled in the south-eastern and southern regions were subdivided within Brazilian clusters. The northern region was the one with the lowest degree of clustering across samples from between four and six regions and was least represented in the national Delta data set.

Amazonas had the largest Delta cluster and was the most represented state in the northern region. Samples from eight states were located in the north-eastern region. In this region, Paraiba had the largest Delta cluster, followed by Ceara (and Pernambuco)). The level of clustering seen in the north and northern regions was similar at 36 percent, despite a higher number of sequences found in the north-eastern region when compared to the northern region.

Conclusions and limitations

The study revealed that there were different stages of maturity in the Brazilian Delta epidemics. The BR-I, BR-II, and BR-III clusters contribute to the majority of Delta sequences. Therefore, the reduction of transmission clusters in the early stage indicates the effectiveness of the preventive measures implemented in Brazil to prevent the spread of viral infections.

The current study was hindered by the absence of more robust metadata and inadequate sampling in certain Brazilian states. The Delta variants are also susceptible to vaccination. Therefore, information on vaccination status could have helped to identify the possible factors that led to the formation of local clusters in Brazil.

To determine the path for spread and to identify new clusters and to determine the factors that affect suppression at an early stage, more rigorous research should be conducted. This will help identify and limit the spread of new variants and reduce their spread to avoid further outbreaks.

*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.

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Gemma Wilson

Gemma is a journalism graduate with keen interest in covering business news – specifically startups. She has as a keen eye for technologies and has predicted quite a few successful startups over the last couple of years.

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