Evolution and epidemic spread of SARS-CoV-2 in Brazil
Candido DS., Claro IM., de Jesus JG., Souza WM., Moreira FRR., Dellicour S., Mellan TA., Plessis LD., Pereira RHM., Sales FCS., Manuli ER., Thézé J., Almeida L., Menezes MT., Voloch CM., Fumagalli MJ., Coletti TM., Silva CAM., Ramundo MS., Amorim MR., Hoeltgebaum H., Mishra S., Gill MS., Carvalho LM., Buss LF., Prete CA., Ashworth J., Nakaya H., Peixoto PS., Brady OJ., Nicholls SM., Tanuri A., Rossi ÁD., Braga CKV., Gerber AL., Guimarães AP., Gaburo N., Alencar CS., Ferreira ACS., Lima CX., Levi JE., Granato C., Ferreira GM., Francisco RS., Granja F., Garcia MT., Moretti ML., Perroud MW., Castineiras TMPP., Lazari CS., Hill SC., de Souza Santos AA., Simeoni CL., Forato J., Sposito AC., Schreiber AZ., Santos MNN., de Sá CZ., Souza RP., Resende-Moreira LC., Teixeira MM., Hubner J., Leme PAF., Moreira RG., Nogueira ML., Ferguson NM., Costa SF., Proenca-Modena JL., Vasconcelos ATR., Bhatt S., Lemey P., Wu C-H., Rambaut A., Loman NJ., Aguiar RS., Pybus OG., Sabino EC., Faria NR.
<jats:title>Abstract</jats:title><jats:p>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 São Paulo and Rio de Janeiro cities show that the reproduction number (<jats:italic>R</jats:italic><jats:sub><jats:italic>t</jats:italic></jats:sub>) 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.</jats:p><jats:sec><jats:title>One Sentence Summary</jats:title><jats:p>Joint analysis of genomic, mobility and epidemiological novel data provide unique insight into the spread and transmission of the rapidly evolving epidemic of SARS-CoV-2 in Brazil.</jats:p></jats:sec>