An in-depth assessment into origin and spread of SARS-CoV-2 Delta variant in Brazil

There has been a steady rise in the number of coronavirus disease (COVID-19) cases due to the Delta variant in Brazil. This was alarming, especially following the emergence of the P.1 (Gamma) variant of concern (VOC), which spread radically throughout the country since January 2021, accounting for more than 90% of the weekly cases.

The Delta severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) VOC, which originated in India, has now spread worldwide and contributed to a relevant rise in hospitalizations and deaths. However, its origin and dissemination in Brazil still remain unclear.

Study: SARS-CoV-2 Delta variant of concern in Brazil -multiple introductions, communitary transmission, and early signs of local evolution. Image Credit: malazzama / Shutterstock.com

The lack of information on the activity of the Delta variant in Brazil is despite frequent reports of isolated cases from different Brazilian states like São Paulo (SP), Rio de Janeiro (RJ), Minas Gerais (MG), Rio Grande do Sul (RS), Tocantins (TO), Paraná (PR), Goiás (GO), and Maranhão (MA).

Brazilian researchers from different educational institutions collaborated to characterize the dissemination of the Delta VOC in Brazil and assess its emergence within the global Delta phylogeny. The researchers of this study, which was published on the preprint server medRxiv*, also characterized the mutational profile of the largest clade within the Brazilian Delta VOCs, with a focus on samples obtained in the State of São Paulo, especially in the city of São Paulo, which is the largest metropolis of South America, as well as a national and international transportation hub.

The emergence of the Delta VOC in Brazil and its phylogenetic assessment

Researchers obtained all SARS-CoV-2 positive samples from the Laboratory Platform for Coronavirus Diagnosis, which was established by the Butantan Institute. The researchers then randomly selected and sequenced around 7-10% from each epidemiological week (epiweek) for genotyping with cycle threshold (Ct) values up to 35. Following this, the researchers extracted the messenger ribonucleic acid (mRNA) material from the samples and performed molecular diagnoses to evaluate the VOCs.

The first reported cases of Delta VOC infections in Brazil were traced to a cargo ship that departed from Malaysia on March 27, 2021, and had a connection in South Africa that had arrived in Brazil by May 14, 2021. This ship carried over 20 crewmen, six of which were positive for Delta. It was also traced to have caused community transmission.

The researchers detected at least four independent community transmission chains state-wise, one each in RJ, GO, MA, PR. They simultaneously observed that some samples from the same state belonged to different clades. For example, SP samples in clades III and V, whereas  RJ was detected in clades III and VI and PR in clades I and V. Taken together, these findings suggest multiple modes of introduction in the Brazilian population.

Sao Paulo, which is the largest city of the American continents, had positive samples mainly from its northern districts. The first collected sample in the city of Sao Paulo from late June 2021 was from the south-eastern region of the Great São Paulo, where it was assumed to have arrived through the Taubate Regional Health Department from RJ. Until epiweek 29, 84 samples were detected in six distinct Regional Health Departments along with the state of Sao Paulo, thus indicating the Delta VOC is constantly on the rise, taxing the country’s healthcare system, and evading vaccine-based neutralization.

Study implications

Upon analyzing the impact of the spread of the Delta VOC in Brazil, the researchers concluded that there were at least 10 different Delta VOC introductions that had spread over eight Brazilian states in the first semester of 2021. Four apparently unrelated transmission chains were identified in the states of São Paulo, Paraná, Goiás, and Maranhão, which validated the presence and transmission of the Delta VOC in Brazil.

Finally, the locally fixed mutation (ORF1ab: T4087I) which changed a hydrophilic amino acid for a hydrophobic one, was also observed in a previously published report. This finding suggests the emergence of local variants that could potentially cause more damage by evading vaccine-based protection.

Even though preliminary analyses indicate that SARS-CoV-2 vaccines used nationwide may offer protection against the Delta VOC, the introduction of any VOC in a country demands significant attention. Such assessments concerning the emergence, evolution, and community-based dissemination of Delta VOC in Brazil would be a good example for future studies on other VOCs in different parts of the world. Taken together, these findings will help to reduce the burden on the healthcare system and improve vaccination strategies.

*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

Written by

Sreetama Dutt

Sreetama Dutt has completed her B.Tech. in Biotechnology from SRM University in Chennai, India and holds an M.Sc. in Medical Microbiology from the University of Manchester, UK. Initially decided upon building her career in laboratory-based research, medical writing and communications happened to catch her when she least expected it. Of course, nothing is a coincidence.