SARS-CoV-2 genomic surveillance in Rondônia, Brazilian Western Amazon

Abstract

SARS-CoV-2 has spread rapidly around the world, with Brazil currently considered an epicenter of the pandemic. The Northern region has the second highest incidence coefficient, as well as the third highest mortality rate in the country. This study aimed to investigate information about the evolutionary history of epidemic spread and genetic aspects of strains isolated on the Western Amazon, in the State of Rondônia, Brazil. It was possible to detect a total of 22 mutations. Some of these alterations may possibly be related to effects on transmissibility, the fidelity of RNA replication, the ability of cancer patients to respond to infection, beyond a mutation that emerged after the introduction of SARS-CoV-2 in Rondônia. At least two events of introduction were detected, corresponding to the B.1 and B.1.1 European lineages. An introduction was observed possibly through Argentina, where strains originated that circulated in the Minas Gerais and Ceará Brazilian states, prior to Rondônia (B.1.), as well as through the Minas Gerais state and the Federal District, which gave rise to strains that spread to Rondônia, from the capital to more rural parts of the state (B.1.1.). The findings show the need to monitor the genetic epidemiology of COVID-19, in order to surveil the virus's evolution, dispersion and diversity.

Figure 1

Linear regression graphs of temporal signal detection. The graphs show the positive correlation between genetic diversity from root to tip (y-axis) and the sampling time of the included sequences (x-axis). This effect on the relationship of these variables shows the existence of a temporal signal in the analyzed data set, which makes it sufficient for molecular clock analysis. Graphs A and B refer to the analyses in datasets A and B, respectively. The value of R² is shown in the upper left corner of the corresponding graph.

Figure 2

Bayesian phylogenetic analysis to determine evolutionary group. In the generated MCC tree, the phylogenetic relationship was estimated from 49 SARS-CoV-2 sequences included in dataset A. The red taxa correspond to the SS1 group; groups SS2 and SS3 are in green, mixed as previously proposed and; the SS4 group is in blue. The study samples are colored black, as well as the sequence used for rooting the inferred tree. In each node, the subsequent probability rate for supporting the branches in decimal data is shown. The time for the most recent common ancestor (tMRCA) among all variations of SARS-CoV-2 was dated to October 23, 2019 (95% Highest Posterior Density—HPD: July 29 and December 17, 2019), similar to other studies^–, which shows the accuracy of the molecular clock addressed in the present study.

Figure 3

Bayesian phylogenetic tree for detailing the evolutionary path. In the generated MCC tree, the phylogenetic relationship was estimated based on 307 SARS-CoV-2 sequences included in dataset B. (a) The taxa and clades colored in blue correspond to strains belonging to variations of pangolin lineage B.1.1., including: B.1.1., B.1.1.1., B.1.1.10. and B.1.1.9. (b) The green colored taxa and clades correspond to strains belonging to other variations of pangolin lineage B.1., Including: B.1., B.1.3., B.1.5., B.1.5.4., B. 1.67. and B.1.8. The study samples are colored black, along with the sequence used for rooting the inferred tree. In each node, the subsequent probability rate for supporting the branches in decimal data is shown. The tMRCA among all variations of SARS-CoV-2 was dated to November 20, 2019 (95% HPD between October 17 and December 20, 2019), similar to other studies^–, which may show the accuracy of the molecular clock addressed in the present study.

Figure 3

Bayesian phylogenetic tree for detailing the evolutionary path. In the generated MCC tree, the phylogenetic relationship was estimated based on 307 SARS-CoV-2 sequences included in dataset B. (a) The taxa and clades colored in blue correspond to strains belonging to variations of pangolin lineage B.1.1., including: B.1.1., B.1.1.1., B.1.1.10. and B.1.1.9. (b) The green colored taxa and clades correspond to strains belonging to other variations of pangolin lineage B.1., Including: B.1., B.1.3., B.1.5., B.1.5.4., B. 1.67. and B.1.8. The study samples are colored black, along with the sequence used for rooting the inferred tree. In each node, the subsequent probability rate for supporting the branches in decimal data is shown. The tMRCA among all variations of SARS-CoV-2 was dated to November 20, 2019 (95% HPD between October 17 and December 20, 2019), similar to other studies^–, which may show the accuracy of the molecular clock addressed in the present study.