Evolution and epidemic spread of SARS-CoV-2 in Brazil

Abstract

Brazil currently has one of the fastest growing SARS-CoV-2 epidemics in the world. Due to limited available data, assessments of the impact of non-pharmaceutical interventions (NPIs) on virus transmission and epidemic spread remain challenging. We investigate the impact of NPIs in Brazil using epidemiological, mobility and genomic data. Mobility-driven transmission models for Sao Paulo and Rio de Janeiro cities show that the reproduction number (Rt) reached below 1 following NPIs but slowly increased to values between 1 to 1.3 (1.0 - -1.6). Genome sequencing of 427 new genomes and analysis of a geographically representative genomic dataset from 21 of the 27 Brazilian states identified >100 international introductions of SARS-CoV-2 in Brazil. We estimate that three clades introduced from Europe emerged between 22 and 27 February 2020, and were already well-established before the implementation of NPIs and travel bans. During this first phase of the epidemic establishment of SARS-CoV-2 in Brazil, we find that the virus spread mostly locally and within-state borders. Despite sharp decreases in national air travel during this period, we detected a 25% increase in the average distance travelled by air passengers during this time period. This coincided with the spread of SARS-CoV-2 from large urban centers to the rest of the country. In conclusion, our results shed light on the role of large and highly connected populated centres in the rapid ignition and establishment of SARS-CoV-2, and provide evidence that current interventions remain insufficient to keep virus transmission under control in Brazil.

Phylogenomics reveals multiple introductions and early spread of SARS-CoV-2 into Peru

“…These observations are in line with the known epidemiology of the pandemic (5). Furthermore, the analysis of genomic data has shown that Peruvian isolates were widely distributed across the phylogenetic tree suggesting multiple, independent introductions, designed as nodes (1)(2)(3)(4)(5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15)(16)(17)(18) with over 70% of statistical support from ML ( Figure 1A and Table 1). Similar to these introductions it has been reported in other countries such as Brazil (6), Colombia (7) and the USA (8).…”

“…In addition, most introductions into South America countries (e.g. Colombia or Brazil) included European B lineages isolates (6,7,12). However, any other factors might be involved including uneven sampling, chance and epidemiology reasons (13).…”

SARS-CoV-2 spread across the Colombian-Venezuelan border

“…An average of 113,821.3 reads were obtained per sample reaching 960.52× of average depth of coverage in the genomes analyzed. We found that two of the SARS-CoV-2 genomes obtained (VEN-89312 and VEN-95072) were identical and belonged to the B1 lineage, while the third (VEN-95070) belonged to the B.1.13 lineage, suggesting two separate introductions ( da Candido et al, 2020 ; Ramirez et al, 2020 ). Phylogenetic analysis revealed that two of the Venezuelan SARS-CoV-2 genomes (VEN-95070 and VEN-95072) closely resembled genomes from neighboring Colombia (Cesar and Norte de Santander Departments) ( Ramirez et al, 2020 ) while the third (VEN-89312) was related to genomes from Brazil ( Fig.…”

“…Phylogenetic analysis revealed that two of the Venezuelan SARS-CoV-2 genomes (VEN-95070 and VEN-95072) closely resembled genomes from neighboring Colombia (Cesar and Norte de Santander Departments) ( Ramirez et al, 2020 ) while the third (VEN-89312) was related to genomes from Brazil ( Fig. 1 C) ( da Candido et al, 2020 ).…”

Comparisons of the genome of SARS-CoV-2 and those of other betacoronaviruses

“…1B) can be inferred using published estimates of the evolutionary rate of the SARS-2 population in the human population, assuming that the pre-and post-emergence rates are the same (Rodríguez-Román and Gibbs, 2020). Various estimates of the SARS-2 evolutionary rate have been published recently; 1.126 x 10 -3 (95 % BCI: 1.03-1.23 x 10 -3 ) substitutions per site per year (s/s/y) (Candido et al, 2020), 1.1×10 −3 s/s/y (95% CI 7.03×10 −4 and 1.5×10 −3 s/s/y) (Duchêne et al, 2020), 9.41×10 -4 s/s/y +/-4.99×10 -5 (Pybus et al, 2020) and 8 x 10 -4 s/s/y (Resende et al, 2020).…”