Scientists determine the origin and transmission rates of SARS-CoV-2 strains

A team of Brazilian and European scientists has determined the transmission rates and out-of-country origins of predominant SARS-CoV-2 strains currently circulating in Brazil, which harbors one of the fastest growing COVID-19 epidemics in the world.

Although the researchers show that non-pharmaceutical interventions initially reduced viral transmission, the continued increases in both cases and deaths in the country suggest that these interventions remain insufficient to control SARS-CoV-2 transmission.

Their findings could help inform additional strategies to address the virus' spread, including contact tracing, quarantining of new cases, rapid and accessible diagnostic screening, and coordinated social distancing measures across the country, the authors say.

Reaching around 1,800,827 cases as of July 12, 2020, Brazil currently holds the second largest number of SARS-CoV-2 cases in the world.

Despite these concerning numbers, the dearth of available data on real-time viral transmission - due to delays in reporting cases and inconsistent access to testing across populations - has prevented comprehensive assessment of SARS-CoV-2's spread in the country, the authors say.

Here, Darlan da Silva Candido and colleagues used data on individual mobility and reported deaths due to severe acute respiratory infections to perform model simulations on SARS-CoV-2 transmission.

They showed that school and store closures in mid to late March reduced the reproduction number, or the expected number of cases arising from a single infector, from greater than 3 cases to roughly 1 case in São Paulo and Rio de Janeiro, the two largest cities in Brazil.

To investigate how SARS-CoV-2 became established in the country, the authors ran PCR assays on 26,732 viral genomes taken from a network of genomic laboratories they had established using harmonized protocols.

They found 29% of the samples positive for SARS-CoV-2. Sequencing 427 of these SARS-CoV-2 genomes, the researchers identified more than 100 internationally-sourced virus introductions into Brazil, estimating that more than 75% of Brazilian SARS-CoV-2 strains fell under three clades introduced from Europe between February 28 and March 11.

Modeling the spread of these viral strains, the scientists discovered there were ample opportunities for SARS-CoV-2 to "export" from large urban centers to the rest of the country during the early stage of the epidemic, due an overall 25% increase in average traveled distances via domestic flights before the introduction of air travel restrictions.

The authors further postulate that this increase in long-distance flights likely dispersed the virus to remote parts of Brazil, which counteracted reductions in virus transmission that may have otherwise resulted from an overall reduction in air travel after restrictions were implemented.

Together, these quantifications suggest Brazil requires more extensive interventions to stifle SARS-CoV-2 transmission moving forward.