Epidemiological dynamics of SARS-CoV-2 VOC Gamma in Rio de Janeiro, Brazil
| Autor: | Raíssa Mirella dos Santos Cunha da Costa, Amilcar Tanuri, Orlando da Costa Ferreira Júnior, Filipe Romero Rebello Moreira, André F. Santos, Débora S. Faffe, Cássia Cristina Alves Gonçalves, Terezinha M. P. P. Castineiras, Marcelo Calado de Paula Tôrres, Matheus Augusto Calvano Cosentino, Carolina M. Voloch, Alice Laschuk Herlinger, Renato Santana Aguiar, Mirela D’arc, Francine Bittencourt Schiffler, Diana Mariani, Átila Duque Rossi, Rafael Mello Galliez, Isabela de Carvalho Leitão, Thamiris dos Santos Miranda |
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| Rok vydání: | 2021 |
| Předmět: |
medicine.medical_specialty
2019-20 coronavirus outbreak Coronavirus disease 2019 (COVID-19) Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Context (language use) phylogeography Microbiology variant of concern Gamma Virology Environmental health Epidemiology Pandemic medicine AcademicSubjects/MED00860 Molecular clock Cycle threshold SARS-CoV-2 AcademicSubjects/SCI01130 AcademicSubjects/SCI02285 COVID-19 phylodynamics Viral phylodynamics Geography Rio de Janeiro lineage P.1 Brazil Research Article |
| Zdroj: | Virus Evolution |
| ISSN: | 2057-1577 |
| Popis: | The emergence and widespread circulation of severe acute respiratory syndrome coronavirus 2 variants of concern (VOCs) or interest impose an enhanced threat to global public health. In Brazil, one of the countries most severely impacted throughout the pandemic, a complex dynamics involving variants co-circulation and turnover events has been recorded with the emergence and spread of VOC Gamma in Manaus in late 2020. In this context, we present a genomic epidemiology investigation based on samples collected between December 2020 and May 2021 in the second major Brazilian metropolis, Rio de Janeiro. By sequencing 244 novel genomes through all epidemiological weeks in this period, we were able to document the introduction and rapid dissemination of VOC Gamma in the city, driving the rise of the third local epidemic wave. Molecular clock analysis indicates that this variant has circulated locally since the first weeks of 2021 and only 7 weeks were necessary for it to achieve a frequency above 70 per cent, consistent with rates of growth observed in Manaus and other states. Moreover, a Bayesian phylogeographic reconstruction indicates that VOC Gamma spread throughout Brazil between December 2020 and January 2021 and that it was introduced in Rio de Janeiro through at least 13 events coming from nearly all regions of the country. Comparative analysis of reverse transcription-quantitative polymerase chain reaction (RT-qPCR) cycle threshold (Ct) values provides further evidence that VOC Gamma induces higher viral loads (N1 target; mean reduction of Ct: 2.7, 95 per cent confidence interval = ± 0.7). This analysis corroborates the previously proposed mechanistic basis for this variant-enhanced transmissibility and distinguished epidemiological behavior. Our results document the evolution of VOC Gamma and provide independent assessment of scenarios previously studied in Manaus, therefore contributing to the better understanding of the epidemiological dynamics currently being surveyed in other Brazilian regions. |
| Databáze: | OpenAIRE |
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