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. Owing to limited available data, assessments of the impact of non-pharmaceutical interventions (NPIs) on virus spread remain challenging. Using a mobility-driven transmission model, we show that NPIs reduced the reproduction number from >3 to 1–1.6 in São Paulo and Rio de Janeiro. Sequencing of 427 new genomes and analysis of a geographically representative genomic dataset identified >100 international virus introductions in Brazil. We estimate that most (76%) of the Brazilian strains fell in three clades that were introduced from Europe between 22 February11 March 2020. During the early epidemic phase, we found that SARS-CoV-2 spread mostly locally and within-state borders. After this period, despite sharp decreases in air travel, we estimated multiple exportations from large urban centers that coincided with a 25% increase in average travelled distances in national flights. This study sheds new light on the epidemic transmission and evolutionary trajectories of SARS-CoV-2 lineages in Brazil, and provide evidence that current interventions remain insufficient to keep virus transmission under control in the country.

SARS-CoV-2 genomic and quasispecies analyses in cancer patients reveal relaxed intrahost virus evolution

“…The viral genomes also displayed sequence features of other already characterized Brazilian viruses, consistent with the hypothesis of local, community transmission rather than virus importation from abroad. In fact, the timeframe of the analyzed infections (from April 7 th to May 5 th , 2020) is consistent with a period in Brazil where community virus transmission was already established and ongoing [18]. Moreover, as a public and free hospital in the Brazilian Public Health System, INCA is also likely to admit patients with low socioeconomic resources who are mostly unable to travel abroad and most likely acquired viral infections from local sources.…”

Improvements to the ARTIC multiplex PCR method for SARS-CoV-2 genome sequencing using nanopore

“…Viral genomes can be used to estimate the rate of viral evolution, monitor circulating lineages as well as identifying any signs of adaptation to hosts, treatments or vaccines. Genome sequencing of SARS-CoV-2 has provided epidemiological insights into the early outbreak [7][8][9] and a number of studies have adopted our method [8,[10][11][12][13][14][15][16][17] . Rapid data sharing allows sequences to be compared across labs or public health authorities and can provide insight into routes of transmission and effectiveness of containment measures [18] .…”

ReumaCoV Brasil Registry: Brazilian Study of Patients with Immuno-mediated Chronic Inflammatory Diseases Infected by SARS-CoV-2 

“…The Coronavirus Disease (COVID-19) was declared as pandemic in March, 11 th , 2020 by World Health Organization (WHO) [1] and Brazil was the rst Latin American country to have a con rmed case of COVID-19 in February 26 th , 2020 [2]. Heretofore, almost 3 millions of cases and more than 90,000 deaths have been con rmed in our country by July, 31 th 2020 [3].…”