Rapid spread and high impact of the variant of concern P.1 in the largest city of Brazil

Barbosa, Gabriela; Moreira, Luiz Vinícius Leão; Justo, Alberto Fernando Oliveira; Perosa, Ana Helena; Luna, Luciano Kleber de Souza; Chaves, Ana Paula Cunha; Bueno, Marília; Conte, D.; Carvalho, Joseane Mayara Almeida; Prates, Janesly; Dantas, Patrícia Sousa; Faíco-Filho, Klinger Soares; Camargo, Clarice Neves; Resende, Paola Cristina; Siqueira, Marilda Mendonça; Bellei, Nancy

doi:10.1016/j.jinf.2021.04.008

Cited by 15 publications

(15 citation statements)

References 3 publications

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“…Since mid-November, there has been a new surge in COVID-19 cases in Brazil, prompting the delimitation of a second phase of the pandemic in the country. This sharp increase in cases is attributed to the emergence of P.1 lineage, which has been reported in several cities in Brazil since December [15][16][17][18][19][20]. Unfortunately, lineage pervasiveness and genomic diversity are still unknown or outdated in several Brazilian states.…”

Section: Introductionmentioning

confidence: 99%

Genomic surveillance of SARS-CoV-2 tracks early interstate transmission of P.1 lineage and diversification within P.2 clade in Brazil

et al. 2021

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The sharp increase of COVID-19 cases in late 2020 has made Brazil the new epicenter of the ongoing SARS-CoV-2 pandemic. The novel viral lineages P.1 (Variant of Concern Gamma) and P.2, respectively identified in the Brazilian states of Amazonas and Rio de Janeiro, have been associated with potentially higher transmission rates and antibody neutralization escape. In this study, we performed the whole-genome sequencing of 185 samples isolated from three out of the five Brazilian regions, including Amazonas (North region), Rio Grande do Norte, Paraíba and Bahia (Northeast region), and Rio de Janeiro (Southeast region) in order to monitor the spread of SARS-CoV-2 lineages in Brazil in the first months of 2021. Here, we showed a widespread dispersal of P.1 and P.2 across Brazilian regions and, except for Amazonas, P.2 was the predominant lineage identified in the sampled states. We estimated the origin of P.2 lineage to have happened in February, 2020 and identified that it has differentiated into new clades. Interstate transmission of P.2 was detected since March, but reached its peak in December, 2020 and January, 2021. Transmission of P.1 was also high in December and its origin was inferred to have happened in August 2020. We also confirmed the presence of lineage P.7, recently described in the southernmost region of Brazil, to have spread across the Northeastern states. P.1, P.2 and P.7 are descended from the ancient B.1.1.28 strain, which co-dominated the first phase of the pandemic in Brazil with the B.1.1.33 strain. We also identified the occurrence of a new lineage descending from B.1.1.33 that convergently carries the E484K mutation, N.9. Indeed, the recurrent report of many novel SARS-CoV-2 genetic variants in Brazil could be due to the absence of effective control measures resulting in high SARS-CoV2 transmission rates. Altogether, our findings provided a landscape of the critical state of SARS-CoV-2 across Brazil and confirm the need to sustain continuous sequencing of the SARS-CoV-2 isolates worldwide in order to identify novel variants of interest and monitor for vaccine effectiveness.

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Section: Introductionmentioning

confidence: 99%

Genomic surveillance of SARS-CoV-2 tracks early interstate transmission of P.1 lineage and diversification within P.2 clade in Brazil

et al. 2021

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“…These findings show that the variant P.1 spread rapidly across Brazilian territory and may be one of the factors responsible for the high hospitalization and mortality of younger people. Among the main states with high hCFR proportion in the T6 period, variant P.1 was detected in Minas Gerais, Paraná, Rio Grande do Sul, Santa Catarina and São Paulo states in that period 6,27 . In fact, Brazil is experiencing a numerical explosion of hospitalizations and deaths by COVID-19 in the 20-59 years age group, especially in the state of São Paulo, with a similar proportion of hospitalizations but higher proportion of deaths compared to the first wave.…”

Section: Discussionmentioning

confidence: 95%

“…It should be considered that São Paulo is the most populous state in Brazil with an estimated population of nearly 27 million people aged 20-59 years in 2020 28 . A recent study showed that of the 52 sequenced samples from COVID-19 patients in the São Paulo city, 84.4% were P.1 variant, that is more transmissible and infectious 27 . Also taking into account that São Paulo state has a population of ≈70% in working age, these factors could justify the results obtained for the age group of 20-59 years in the state, since they are numerically majority and more exposed to coronavirus due to economic needs.…”

Section: Discussionmentioning

confidence: 99%

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Young adults vulnerability to COVID-19 in Brazil: an overview across the country

Souza

Hojo-Souza

Oliveira

et al. 2021

Preprint

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Brazil is a country of continental dimensions, where many smaller countries would fit. In addition to demographic, socioeconomic, and cultural differences, hospital infrastructure and healthcare varies across all 27 federative units. Therefore, the evolution of COVID-19 pandemic did not manifest itself in a homogeneous and predictable trend across the nation. In late 2020 and early 2021, new waves of the COVID-19 outbreak have caused an unprecedented sanitary collapse in Brazil. Unlike the first COVID-19 wave, in subsequent waves, preliminary evidence has pointed to an increase in the daily reported cases among younger people being hospitalized, overloading the healthcare system. In this comprehensive retrospective study, confirmed cases of hospitalization, ICU admission, IMV requirement and in-hospital death from Brazilian COVID-19 patients throughout 2020 until the beginning of 2021 were analyzed through a spatio-temporal study for patients aged 20-59 years. All Brazilian federative units had their data disaggregated in six periods of ten epidemiological weeks each. We found that there is a wide variation in the waves dynamic due to SARS-CoV-2 infection, both in the first and in subsequent outbreaks in different federative units over the analyzed periods. As a result, atypical waves can be seen in the Brazil data as a whole. The analysis showed that Brazil is experiencing a numerical explosion of hospitalizations and deaths for patients aged 20-59 years, especially in the state of Sao Paulo, with a similar proportion of hospitalizations for this age group but higher proportion of deaths compared to the first wave.

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“…Both lineages exhibit the E484K mutation and descendant of the B.1.1.28 strain ( Faria et al, 2021 ; Voloch et al, 2021 )⁠. Over time, the P.2 lineage was almost completely replaced by Gamma ( De Almeida et al, 2021 ; Barbosa et al, 2021 )⁠. Since few mutations can change virus fitness, the aim of this research was to investigate the lineages that were circulating in the beginning of 2021 in Rio Grande do Sul State (RS) , southern Brazil, to better understand the possible virus-related causes of this major health crisis caused by SARS-CoV-2 in the region, searching also possible additional SARS-CoV-2 mutations.…”

Section: Introductionmentioning

confidence: 99%

Predominance of SARS-CoV-2 P.1 (Gamma) lineage inducing the recent COVID-19 wave in southern Brazil and the finding of an additional S: D614A mutation

Demoliner

Silva

Gularte

et al. 2021

Infection, Genetics and Evolution

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Rapid spread and high impact of the variant of concern P.1 in the largest city of Brazil

Cited by 15 publications

References 3 publications

Genomic surveillance of SARS-CoV-2 tracks early interstate transmission of P.1 lineage and diversification within P.2 clade in Brazil

Genomic surveillance of SARS-CoV-2 tracks early interstate transmission of P.1 lineage and diversification within P.2 clade in Brazil

Young adults vulnerability to COVID-19 in Brazil: an overview across the country

Predominance of SARS-CoV-2 P.1 (Gamma) lineage inducing the recent COVID-19 wave in southern Brazil and the finding of an additional S: D614A mutation

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