Genomic and epidemiological updates on SARS-CoV-2 circulation in Brazil

Coronavirus disease 2019 (COVID-19) is a disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that was first detected in China in December 2019. Brazil confirmed the first cases in February 26, 2020, in a patient returning from Italy.

Epidemiological situation in Brazil

Currently, there are 628 confirmed cases across Brazil, with 96 cases confirmed on the 19 March 2020. Of these, 286 cases (45%) of all confirmed cases were reported in the state of São Paulo and 65 cases (10%) were reported in the state of Rio de Janeiro. Please note that these numbers contain information recorded through local media and may not correspond to the numbers reported by the Brazilian Ministry of Health. Please check daily updates provided by the Brazilian Ministry of Health.

The first case in Brazil was confirmed on the 26th of February 2020 (check out our brief report here). Since then, the virus has been detected throughout the five regions of the country. Local transmission has now been confirmed in 6 states (São Paulo, Rio de Janeiro, Espírito Santo, Bahia, Pernambuco, Distrito Federal, Bahia, Santa Catarina) (as of 19 March 2020).

Routes of COVID-19 introduction in Brazil

As the number of imported SARS-CoV-2 cases is on the rise in Brazil, we use incidence and historical air travel data to estimate the most important routes of importation into the country.

Between February and March 2019, Brazil received 841,302 international passengers in a total of 84 cities across the country (Figure 1). São Paulo, the largest city in the country, was the final destination of nearly half (46.1%) of the passengers arriving in Brazil, followed by Rio de Janeiro (21%) and Belo Horizonte (4.1%). More than half of the international passengers started their journey in the USA (50.8%) followed by France (7.9%) and Italy (7.5%). The air-travel routes to airports in Brazil with most passengers were USA-São Paulo (23.3%), USA-Rio de Janeiro (9.8%) and Italy-São Paulo (3.4%).

Potential for COVID-19 importation to Brazil. Panel on the left shows the proportion (%) of passengers for the top-20 routes to Brazilian airports from countries that had reported COVID-19 cases by 5th March 2020. Panel on the right side estimated proportion (%) of importations for the top-20 routes from countries that had reported local COVID-19 by 5th March 2020.

Importantly, with the recent reduction in the number of flights leaving from Italy and 51% of flights to Brazil depart from airports in the USA, we should anticipate for an increasing proportion of infected travelers arriving from the USA. At a time when the number of SARS-CoV-2 cases is steadily growing in Brazil, our findings highlight the high potential for the introduction of new cases in several cities of Brazil, especially in Sao Paulo and Rio de Janeiro metropolises. Rapid identification of locations where clusters of local transmission might first ignite is critical to better coordinate preparedness, readiness and response actions. There is a critical need for epidemiological, human mobility and genetic data to understand virus transmission dynamics across Brazil. Continued integration of these data streams should help guide the deployment of resources to mitigate COVID-19 transmission Brazil.

Check out our scientific publication here. Check also a youtube video from Dr. Chico Camargo explaining our findings (Portuguese)