The ongoing COVID-19 epidemic in Minas Gerais, Brazil: insights from epidemiological data and SARS-CoV-2 whole genome sequencing

Abstract

The recent emergence of a coronavirus (SARS-CoV-2), first identified in the Chinese city of Wuhan in December 2019, has had major public health and economic consequences. Although 61,888 confirmed cases were reported in Brazil by 28 April 2020, little is known about the SARS-CoV-2 epidemic in this country. To better understand the recent epidemic in the second most populous state in southeast Brazil - Minas Gerais (MG) - we sequenced 40 complete SARS-CoV-2 genomes from MG cases and examined epidemiological data from three Brazilian states. Both the genome analyses and the geographical distribution of reported cases indicate for multiple independent introductions into MG. Epidemiological estimates of the reproductive number (R) using different data sources and theoretical assumptions suggest the potential for sustained virus transmission despite a reduction in R from the first reported case to the end of April 2020. The estimated date of SARS-CoV-2 introduction into Brazil was consistent with epidemiological data from the first case of a returned traveller from Lombardy, Italy. These findings highlight the nature of the COVID-19 epidemic in MG and reinforce the need for real-time and continued genomic surveillance strategies to better understand and prepare for the epidemic spread of emerging viral pathogens..

Keywords: Minas Gerais; SARS-CoV-2; genomic epidemiology; genomic surveillance; pandemic; sequencing; southeast Brazil.

Figure 1.

Timeline of key events following the first confirmed case of COVID-19 in Brazil. Events below the line occurred in Minas Gerais (MG) state, while national events are presented above the line. Codes in parentheses refer to the identification code (CV#) of the isolates from the cases described in this study.

Figure 2.

SARS-CoV-2 epidemic curve and spatial distribution of cases and deaths reported in the states of Minas Gerais (MG), São Paulo (SP) and Rio de Janeiro (RJ), Brazil. Panel A: Daily confirmed cases of COVID-19 in the state of MG. The X-axis represents the days from the first case in Brazil until 28 April 2020, while the Y-axis (left-hand side) represents the number of cases. The right-hand side of the Y-axis represents the number of deaths related to COVID-19. Y-axis numbers are represented as log10. Panels B and C: Maps with location (municipality) of (B) deaths and case (C) events, coloured by total number of reports. Different background colours highlight the boundaries of the three states: green for SP, purple for MG, blue for RJ.

Figure 3.

Phylogenetic analysis of the SARS-CoV-2 isolated in the state of MG, Brazil. Maximum likelihood phylogeny inferred using 40 genome sequences from SARS-CoV-2 generated in this study (marked with red circles) and 3062 sequences already deposited on the GISAID database. The tree is rooted between lineages A and B. Vertical branch lengths give the number of nucleotide substitutions per site.

Figure 4.

Bayesian analysis of the SARS-CoV-2 isolated in the state of MG, Brazil. (a) Map of the MG state showing the number of SARS-CoV-2 new sequences by patient´s municipality. (b) Molecular clock phylogeny of a subset of lineage A viruses, including one new sequence from MG. (c) Molecular clock phylogeny of a subset of lineage B viruses, including two new sequences from MG. (d) Molecular clock phylogeny of the subset from sublineage B.1, including 37 new sequences from MG. In all cases, the numbers along branches represent posterior probabilities while colours represent different sampling locations.