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. 2023 Mar 30;15(4):888.
doi: 10.3390/v15040888.

The Omicron Lineages BA.1 and BA.2 (Betacoronavirus SARS-CoV-2) Have Repeatedly Entered Brazil through a Single Dispersal Hub

Alessandra P Lamarca  1 , Ueric José Borges de Souza  2 , Filipe Romero Rebello Moreira  3 , Luiz G P de Almeida  1 , Mariane Talon de Menezes  3 , Adrieli Barboza de Souza  4 , Alessandro Clayton de Souza Ferreira  5 , Alexandra L Gerber  1 , Aline B de Lima  5 , Ana Paula de C Guimarães  1 , Andréa Cony Cavalcanti  6 , Aryel B Paz E Silva  7 , Bruna Israel Lima  8 , Cirley Lobato  9 , Cristiane Gomes Da Silva  6 , Cristiane P T B Mendonça  5 , Daniel Costa Queiroz  7 , Danielle Alves Gomes Zauli  5 , Diego Menezes  7 , Fábio Sossai Possebon  10 , Franciano Dias Pereira Cardoso  11 , Frederico Scott Varella Malta  5 , Isabela Braga-Paz  7 , Joice do Prado Silva  5 , Jorge Gomes Goulart Ferreira  7 , Jucimária Dantas Galvão  11 , Leandro Magalhães de Souza  6 , Leonardo Ferreira  4 , Lia Gonçalves Possuelo  12 , Liliane Tavares de Faria Cavalcante  1 , Luige B Alvim  5 , Luiz Fellype Alves de Souza  13 , Luiza C G de Araújo E Santos  7 , Rillery Calixto Dias  7 , Rutilene Barbosa Souza  13 , Thaís Regina Y Castro  14 , Andréia Rosane de Moura Valim  12 , Fabrício Souza Campos  15 , João Pessoa Araujo Jr  10 , Priscila de Arruda Trindade  14 , Renato S Aguiar  7 , Robson Michael Delai  4 , Ana Tereza R de Vasconcelos  1
Affiliations

The Omicron Lineages BA.1 and BA.2 (Betacoronavirus SARS-CoV-2) Have Repeatedly Entered Brazil through a Single Dispersal Hub

Alessandra P Lamarca et al. Viruses. .

Abstract

Brazil currently ranks second in absolute deaths by COVID-19, even though most of its population has completed the vaccination protocol. With the introduction of Omicron in late 2021, the number of COVID-19 cases soared once again in the country. We investigated in this work how lineages BA.1 and BA.2 entered and spread in the country by sequencing 2173 new SARS-CoV-2 genomes collected between October 2021 and April 2022 and analyzing them in addition to more than 18,000 publicly available sequences with phylodynamic methods. We registered that Omicron was present in Brazil as early as 16 November 2021 and by January 2022 was already more than 99% of samples. More importantly, we detected that Omicron has been mostly imported through the state of São Paulo, which in turn dispersed the lineages to other states and regions of Brazil. This knowledge can be used to implement more efficient non-pharmaceutical interventions against the introduction of new SARS-CoV variants focused on surveillance of airports and ground transportation.

Keywords: COVID-19; dispersal; genome; phylodynamics; variant of concern; viral evolution.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Evolution of the COVID-19 pandemic in Brazil between 26 September 2021 and 1 May 2022. In (A) is represented the absolute number of cases in the period, while in (B) this number is presented in relative frequency. In (C), the absolute number of deaths is shown. The circles in (D) indicate the number of cases per thousand people in each Brazilian state since the beginning of the pandemic until September 2022. Colors represent the regions of Brazil: North (green), Central–West (dark blue), Northeast (light blue), Southeast (yellow), and South (pink).
Figure 2
Figure 2
Distribution of SARS-CoV-2 lineages in this study from October 2021 to April 2022. In (A) is represented the absolute number of genomes by lineage and in (B), their relative frequency.
Figure 3
Figure 3
The number of introduction events (A) and dispersal rates (B) of the Omicron lineages BA.1 (left) and BA.2 (right) between Brazilian regions, estimated from the proportional dataset. Colors represent the region of the event’s origin.
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