Molecular dynamics of the COVID-19 pandemic in Espirito Santo (Brazil) and border States

Abstract

This study represents the first overview of the epidemiological dynamics of SARS-CoV-2 in Espirito Santo (ES) State, Brazil, filling in knowledge on this topic, observing data collected in the State, and aiming at understanding the epidemiological dynamics of the virus in ES, as well as its possible routes of transmission and dissemination. . Our results highlight that, so far, nine lineages have been identified with ES State. The B.1.1.33 lineage was the first with the highest occurrence in ES, remaining predominant until September 2020. The second predominant lineage was Gamma, representing 45% of the samples. The Delta lineage appears on the State scene, proving to be the next dominant lineage. This research allowed us to understand how the lineages advanced and were distributed in the State, which is important for future work, also making it possible to guide sanitary control measures. Data analyses were made through the GISAID database for ES State showed that the pandemic in the State has been evolving dynamically with lineage replacements over the months since the first notification.

Figure 1. Emergence of lineages in ES State over time.

Figure 2. Phylogenetic tree inferred by the Maximum Likelihood (ML) of 202 complete SARS-CoV-2 genomes from ES, BA, MG and RJ States.

Figure 3. Highlighting of interesting points on the phylogenetic tree: (A) Relationship between the genome of Delta lineage virions collected in ES, MG and RJ States; (B) The first sample referring to the Delta variant in ES State, collected on July 19, 2021 (EPI_ISL_3801883); (C) Single sample from ES State, lineage B.1.1.7 that make up the database.