Comparative epidemic expansion of SARS-CoV-2 variants Delta and Omicron in the Brazilian State of Amazonas

• Published in: Nature communications Vol. 14; no. 1; p. 2048
• Main Authors: Arantes, Ighor, Bello, Gonzalo, Nascimento, Valdinete, Souza, Victor, da Silva, Arlesson, Silva, Dejanane, Nascimento, Fernanda, Mejía, Matilde, Brandão, Maria Júlia, Gonçalves, Luciana, Silva, George, da Costa, Cristiano Fernandes, Abdalla, Ligia, Santos, João Hugo, Ramos, Tatyana Costa Amorim, Piantham, Chayada, Ito, Kimihito, Siqueira, Marilda Mendonça, Resende, Paola Cristina, Wallau, Gabriel Luz, Delatorre, Edson, Gräf, Tiago, Naveca, Felipe Gomes
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 11-04-2023; Nature Publishing Group; Nature Portfolio
• Subjects: 45/23; 45/77; 45/88; 45/90; 631/208/212; 631/326/596/2562; 631/326/596/4130; 692/700/478/174; Adaptive Immunity; Brazil; Coronaviruses; COVID-19; Dynamics; Epidemics; Genomes; Herd immunity; Humanities and Social Sciences; Humans; Immunity; multidisciplinary; Phenotypes; SARS-CoV-2; Science; Science (multidisciplinary); Severe acute respiratory syndrome coronavirus 2; Viral diseases; Brazil
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-023-37541-6

The SARS-CoV-2 variants of concern (VOCs) Delta and Omicron spread globally during mid and late 2021, respectively. In this study, we compare the dissemination dynamics of these VOCs in the Amazonas state, one of Brazil’s most heavily affected regions. We sequenced the virus genome from 4128 patients collected in Amazonas between July 1st, 2021, and January 31st, 2022, and investigated the viral dynamics using a phylodynamic approach. The VOCs Delta and Omicron BA.1 displayed similar patterns of phylogeographic spread but different epidemic dynamics. The replacement of Gamma by Delta was gradual and occurred without an upsurge of COVID-19 cases, while the rise of Omicron BA.1 was extremely fast and fueled a sharp increase in cases. Thus, the dissemination dynamics and population-level impact of new SARS-CoV-2 variants introduced in the Amazonian population after mid-2021, a setting with high levels of acquired immunity, greatly vary according to their viral phenotype.
The Amazonas region has been the most heavily affected by COVID-19 in Brazil. In this study, the authors conduct phylodynamic analyses to assess SARS-CoV-2 lineage replacement dynamics in the region and infer the impact of population immunity on the spread and severity of the Delta and Omicron variants.