![]() ![]() Major SARS-CoV-2 local clades drove the COVID-19 epidemic in Amazonas state These findings clearly show a sharp increase of lineage P.1 prevalence in Manaus, and in the countryside of Amazonas state, during the second epidemic wave. Similar findings were observed when analyses were restricted to the city of Manaus: P.1 lineage in 0% of samples collected in November 2020 ( n = 0/211), in 10.5% of samples from 1 to 15 December 2020 ( n = 32/305), in 45.1% of samples from 16 to 31 December 2020 ( n = 106/235) and in 66.0% of samples from 1 to 15 January 2021 ( n = 163/247). Combining genome sequencing and real-time RT–PCR testing, we found the P.1 lineage in 0% of samples collected in November 2020 ( n = 0/355), in 8.6% of samples from 1 to 15 December 2020 ( n = 33/384), in 50.8% of samples from 16 to 31 December 2020 ( n = 177/348) and in 73.8% of samples from 1 to 15 January 2021 ( n = 487/660) (Fig. However, positive samples for the NSP6 deletion were frequently detected in the second half of December 2020 and in January 2021. None of the SARS-CoV-2-positive samples genotyped by real-time RT–PCR before 16 December was positive for the NSP6 deletion, supporting our sequencing results that indicate a very low prevalence of VOC P.1 before mid-December 2020 in Amazonas. Thus, we evaluated a further 1,232 SARS-CoV-2-positive samples available at the central laboratory of Amazonas state (LACEN-AM) between 1 November 2020 and 31 January 2021. To better estimate the temporal trajectory of the emergence of P.1 in Amazonas state in late 2020 and early 2021, we designed a real-time PCR with reverse transcription (RT–PCR) screening assay to detect the deletion at orf1b (NSP6: S106del, G107del, F108del), which is a genetic signature of VOCs P.1, B.1.1.7 and B.1.351. ![]() The VOC P.1 was first detected on 4 December 2020 in Manaus, and displayed an extremely rapid increase in prevalence up to January 2021. This lineage persisted as the most prevalent from May to December 2020, when the second lineage replacement took place coinciding with the second phase of exponential growth. However, its prevalence gradually decreased after the first epidemic peak in early May and was surpassed by lineage B.1.1.28. The lineage B.1.195 was the most prevalent during the first exponential growth phase. Viral sequences were generated at FIOCRUZ Amazônia, which is part of both the Amazonas state health genomics network (REGESAM) and the consortium FIOCRUZ COVID-19 Genomics Surveillance Network of the Brazilian Ministry of Health ( ). To acquire a more in-depth understanding of the genetic diversity of SARS-CoV-2 variants circulating in Amazonas state since the early epidemic, we generated 250 SARS-CoV-2 high-quality, whole-genome sequences from individuals living in 25 municipalities, between 16 March 2020 and 13 January 2021 (Fig. These data provide insights to understanding the mechanisms underlying the COVID-19 epidemic waves and the risk of dissemination of SARS-CoV-2 VOC P.1 in Brazil and, potentially, worldwide.Įvidence of successive SARS-CoV-2 lineage replacements in Amazonas Our findings support the conclusion that successive lineage replacements in Amazonas were driven by a complex combination of variable levels of social distancing measures and the emergence of a more transmissible VOC P.1 virus. The second wave coincides with the emergence of the variant of concern (VOC) P.1, which evolved from a local B.1.1.28 clade in late November 2020 and replaced the parental lineage in <2 months. Through a genomic epidemiology study based on 250 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes from different Amazonas municipalities sampled between March 2020 and January 2021, we reveal that the first exponential growth phase was driven mostly by the dissemination of lineage B.1.195, which was gradually replaced by lineage B.1.1.28 between May and June 2020. The northern state of Amazonas is among the regions in Brazil most heavily affected by the COVID-19 epidemic and has experienced two exponentially growing waves, in early and late 2020. ![]() Nature Medicine volume 27, pages 1230–1238 ( 2021) Cite this article COVID-19 in Amazonas, Brazil, was driven by the persistence of endemic lineages and P.1 emergence ![]()
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