![]() ![]() Viral lineages were classified by using the Pangolin ( 26) software tool ( ), nextclade ( ), and standard phylogenetic analysis using complete reference genomes. ![]() S1 to S4), together with other available and published genomes from Brazil for context. Because partial genome sequences can provide useful epidemiological information, particularly regarding virus genetic diversity and lineage composition ( 25), we harnessed information from partial ( n = 41 viral sequences, 25 to 75% genome coverage), as well as near-complete ( n = 95 viral sequences, 75 to 95%) and complete ( n = 48 viral sequences, ≥95%) sequences from Manaus (figs. ![]() We sequenced SARS-CoV-2 genomes from 184 samples from patients seeking COVID-19 testing in two diagnostic laboratories in Manaus between November and December 2020, using the ARTIC V3 multiplexed amplicon scheme ( 24) and the MinION sequencing platform. Before this, only seven SARS-CoV-2 genome sequences from Amazonas were publicly available (SARS-CoV-2 was first detected in Manaus on 13 March 2020) ( 19, 23). 1A), we focused ongoing SARS-CoV-2 genomic surveillance ( 2, 18– 22) on recently collected samples from the city (supplementary materials, materials and methods, and table S2). Enhanced global genomic surveillance of variants of concern, which may exhibit increased transmissibility and/or immune evasion, is critical to accelerate pandemic responsiveness.Īfter a rapid increase in hospitalizations in Manaus caused by severe acute respiratory infection (SARI) in December 2020 ( Fig. Using a two-category dynamical model that integrates genomic and mortality data, we estimate that P.1 may be 1.7- to 2.4-fold more transmissible and that previous (non-P.1) infection provides 54 to 79% of the protection against infection with P.1 that it provides against non-P.1 lineages. Molecular clock analysis shows that P.1 emergence occurred around mid-November 2020 and was preceded by a period of faster molecular evolution. Lineage P.1 acquired 17 mutations, including a trio in the spike protein (K417T, E484K, and N501Y) associated with increased binding to the human ACE2 (angiotensin-converting enzyme 2) receptor. Genome sequencing of viruses sampled in Manaus between November 2020 and January 2021 revealed the emergence and circulation of a novel SARS-CoV-2 variant of concern. Coupled with the emergence of P.1, disease spread was accelerated by stark local inequalities and political upheaval, which compromised a prompt federal response.Ĭases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in Manaus, Brazil, resurged in late 2020 despite previously high levels of infection. ![]() After a period of accelerated evolution, this variant emerged in Brazil during November 2020. tracked the evolution of a new, more aggressive lineage called P.1, which has 17 mutations, including three (K417T, E484K, and N501Y) in the spike protein. In Manaus, transmission reached unprecedented levels after a momentary respite in mid-2020. SARS-CoV-2 circulated undetected in Brazil for more than a month as it spread north from Sã o Paulo. Clusters of deaths before cases became apparent indicated unmitigated spread. analyzed the pattern of spread of COVID-19 cases and deaths in the country from February to October 2020. Using daily data from state health offices, Castro et al. Sabino +69 authors +67 authors +62 authors fewer Authors Info & Affiliationsĭespite an extensive network of primary care availability, Brazil has suffered profoundly during the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. Pybus, Seth Flaxman, Samir Bhatt, and Ester C. Loman, Philippe Lemey, Andrew Rambaut, Nelson A. Pond, Chieh-Hsi Wu, Oliver Ratmann, Neil M. Hay, Mélodie Monod, Xenia Miscouridou, Helen Coupland, Raphael Sonabend, Michaela Vollmer, Axel Gandy, Carlos A. Camilo, Henrique Hoeltgebaum, William M. ![]()
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