The study traced the trajectory of the epidemics based on genomic data of the SARS-CoV-2 obtained by the sequencing of almost 500 viral isolates from Brazilian patients. The results were crossed with information on aerial travels made in the period and confirmed deaths.

Over 100 different strings of the new coronavirus (SARS-CoV-2) have arrived in Brazil between the month of February and March of 2020, but only three of them – very likely from Europe – continued to expand throughout the country and originated more than 805 thousand cases of COVID-19 confirmed up until June 12th.

These three strings emerged in the states of São Paulo and Rio de Janeiro from the 22nd and the 27th of February and its community transmission was already established in early March, way before the Health Organs recommend the restriction of aerial travels and adopt the “non pharmacological interventions” (NPI) to contain the dissemination of the virus. The Ministry of Health regulated on March 13th the criteria of social distancing and quarantine, which were implemented by governments and mayors about a week after. The terrestrial boarders were only closed on March 19th and the entry of foreigners by international flights was only restricted on the 27th of the same month.

The conclusions are from a study supported by FAPESP and disclosed in the medRxiv platform, still unreviewed by peers.

“Our results demonstrate the existence of two phases of the epidemics in the country. The first is the transmission in short distance, within the state borders of São Paulo and Rio. At the beginning of March there was the start of phase two, of long distance. Meaning, the contaminated people in these two states were already taking the virus to the other regions of the country when the NPIs were adopted”, tells the researcher Ester Sabino, of the Tropical Medicine Institute of the Universidade de São Paulo (IMT-USP), one of the coordinators of the research.

To reach these conclusions, the scientists used a model of oriented transmission by the mobility of the population. Information on aerial travels and on the confirmed deaths by COVID-19 between February and April were crossed with genomic data of the SARS-CoV-2 obtained by the sequencing of almost 500 isolated viruses from patients diagnosed in 21 of the 27 Brazilian states (counting the Distrito Federal). The work was conducted in the scope of the Brazil-UK Center for Discovery, Diagnostics, Genomic & Epidemiology (CADDE).

Although there was a sharp fall in national aerial travels after mid-march, the researchers detected an increase of 25% in the average distance travelled by aerial passengers in the period. Such fact, according to some authors, coincided with the dissemination of the SARS-CoV-2 from the great urban centers to the rest of the country.

“Our results have shed light over the role of great populational centers highly connected in the fast ignition and the establishment of the SARS-CoV-2 and offer evidence the current interventions remain insufficient to keep the transmission of the virus under control in Brazil”, the text states.

The impact of quarantine

Before the social distancing measures were taken, the infection rate of the SARS-CoV-2 in Brazil was around 3. That means every infected person transmitted the virus, on average, to three other people, which favored the exponential growth of the disease.

Although implemented when the community transmission have already been established and the virus had already crossed São Paulo and Rio boarders, the restrictions of the quarantine have managed – in a first moment – to significantly contain the spread of the disease.

The transmission model oriented by the mobility shows the infection rate was below 1 in the cities of São Paulo and Rio de Janeiro soon after the adoption of the NPIs, which avoided the exponential growth of the number in cases and the collapse of the hospitals.

However, when the population acceptance of the social distancing decreased, the infection rate started to slowly increase between 1 and 1.3 and haven’t decreased ever since. Specialists in epidemiology declare only when the infection rate stabilizes under 1 during a few weeks the growth in the number of cases and of deaths will begin to slow down.

Throughout filo geography analyses – which combined the data of sequencing of the viral genome with the information about the place in which the transmission occurred – the researchers identified 104 strains of the SARS-CoV-2 that entered Brazil, mostly from the United States.

From the total of genomes sequenced in Brazil, 75% belong to three strains of European origin: 186 genomes (38%) correspond to the “strain 1”; 161 (33%) are from the “strain 2”; and 19 (4%) are from the “strain 3”.

“It is possible the other strains we identified have not been able to expand because when it entered Brazil there were already social distancing measures in place. But it is very likely, as the isolated virus were sequenced in the country, different strains could be identified. In the United Kingdom, where the sequencing of more than 20 thousand COVID-19 patient samples was made, more than a thousand entries of the new coronavirus were already identified”, tells Sabino.

As the researcher explains, the SARS-CoV-2 genome has about 30 thousand pairs (two opposite nucleotides and complementary connected by hydrogen to form the viral RNA chains). In case the virus infecting an individual suffers a mutation in the position 200 in the RNA chain, for example, every person contaminated through this patient will carry the same mark in the viral genome. “By crossing these data with information about the date and place in which the samples were collected, we were able to trace the trajectory of the pandemic, which is still in its early days”, explains Sabino.

According to the researchers, it is still necessary to sequence more samples in the north region of the country to determinate, for instance, the origin of the strain which was strongly disseminated throughout Amazonas and Pará. “What we already know is the fluvial displacement between the amazonic cities have contributed to spread the virus”, she says.

In Sabino’s evaluation, this kind of study helps understand how a pandemic evolves and which are the main routes of transmission. “This knowledge might serve as a lesson for, in a future situation, measures will be taken earlier and in a more effective way”.

The article Evolution and epidemics spread of SARS-CoV-2 in Brazil can be read here: