Detection of SARS-CoV-2 lineage P.1 in patients from a region with exponentially increasing hospitalisation rate, February 2021, Rio Grande do Sul, Southern Brazil

Martins, Andreza Francisco; Zavascki, Alexandre Prehn; Wink, Priscila Lamb; Volpato, Fabiana Caroline Zempulski; Monteiro, Francielle Liz; Rosset, Clévia; de‐Paris, Fernanda; Ramos, Álvaro; Barth, Afonso Luís

doi:10.2807/1560-7917.es.2021.26.12.2100276

Cited by 56 publications

(79 citation statements)

References 4 publications

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“…Genomic surveillance and early data sharing by teams worldwide have led to the rapid detection and characterization of SARS-CoV-2 and new variants of concern (VOCs) ( 25 ), yet such surveillance is still limited in many settings. The P.1 lineage is spreading rapidly across Brazil ( 55 ), and this lineage has now been detected in >36 countries ( 56 ). But existing virus genome sampling strategies are often inadequate for determining the true extent of VOCs in Brazil, and more detailed data are needed to address the impact of different epidemiological and evolutionary processes in their emergence.…”

Section: Discussionmentioning

confidence: 99%

Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil

Faria

Mellan

Whittaker

et al. 2021

Science

1,252

1,110

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Cases of SARS-CoV-2 infection in Manaus, Brazil, resurged in late 2020, despite previously high levels of infection. 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. 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 receptor. Molecular clock analysis shows that P.1 emergence occurred around mid-November 2020 and was preceded by a period of faster molecular evolution. Using a two-category dynamical model that integrates genomic and mortality data, we estimate that P.1 may be 1.7–2.4-fold more transmissible, and that previous (non-P.1) infection provides 54–79% of the protection against infection with P.1 that it provides against non-P.1 lineages. Enhanced global genomic surveillance of variants of concern, which may exhibit increased transmissibility and/or immune evasion, is critical to accelerate pandemic responsiveness.

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Section: Discussionmentioning

confidence: 99%

Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil

Faria

Mellan

Whittaker

et al. 2021

Science

1,252

1,110

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“…This variant probably emerged between late November and early December 2020 in Amazonas, northern Brazil, with rapid dissemination to other regions and other countries [1]. The introduction of this variant was temporally associated with increased transmissibility of covid-19 causing a critical epidemiological scenario in different places where it was detected as the Amazonas, in the north region, and the Paraná and the Rio Grande do Sul (RS) states, in the south of the country [2][3][4][5]. In the Amazonas state, a collapse of the health system was observed, which made it difficult to assess the real impact of the P.1 variant on the lethality by covid-19, which may have increased due to the overload of the health system and not exclusively by the intrinsic characteristics of the variant [2].…”

Section: Introductionmentioning

confidence: 99%

“…Virological surveillance data showed that in February, the variant P.1 corresponded to about 70% of the viruses sequenced in the RS state. [5,7] The exponential increase in the hospitalization rate observed in the RS state could be explained, on one hand, by the P.1 circulation as this variant has being 2.6 times more transmissible (95% Confidence Interval (CI): 2.4-2.8) than the previous one [8]. However, on other hand, studies have suggested that the P.1 variant can also lead to more severe conditions, which would increase the need for hospitalization and contribute to the increase observed in hospitalization rates.…”

Section: Introductionmentioning

confidence: 99%

The increase in the risk of severity and fatality rate of covid-19 in southern Brazil after the emergence of the Variant of Concern (VOC) SARS-CoV-2 P.1 was greater among young adults without pre-existing risk conditions

Freitas

Drq

Beckedorff

et al. 2021

Preprint

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Background The SARS-CoV-2 P.1 variant has been considered as variant of concern (VOC) since the end of 2020 when it was firstly identified in the Brazilian state of Amazonas and from there spread to other regions of Brazil. This variant was associated with an increase in transmissibility and worsening of the epidemiological situation in the places where it was detected. The aim of this study was to analyze the severity profile of covid-19 cases in the Rio Grande do Sul state, southern region of Brazil, before and after the emergence of the P.1 variant, considering also the context of the hospitals overload and the collapse of health services. Methods We analyzed data from the Influenza Epidemiological Surveillance Information System, SIVEP-Gripe (Sistema de Informacao de Vigilancia Epidemiologica da Gripe) and compare two epidemiological periods: the first wave comprised by cases occurred during November and December 2020 (EW 45 to 53) and the second wave with cases occurred in February 2021 (EW 5 to 8), considering that in this month there was a predominance of the new variant P.1. We calculated the proportion of severe forms among the total cases of covid-19, the case fatality rates (CFR) and hospital case fatality rate (hCFR) over both waves time set using the date of onset of symptoms as a reference. We analyzed separately the patients without pre-existing conditions of risk, by age and sex. For comparison between periods, we calculated the Risk Ratio (RR) with their respective 95% confidence intervals and the p-values. Findings We observed that in the second wave there were an increase in the proportion of severe cases and covid-19 deaths among younger age groups and patients without pre-existing conditions of risk. The proportion of people under the age of 60 among the cases that evolved to death raised from 18% (670 deaths) in November and December (1st wave) to 28% (1370 deaths) in February (2nd wave). A higher proportion of patients without pre-existing risk conditions was also observed among those who evolved to death due to covid-19 in the second wave (22%, 1,077 deaths) than in the first one (13%, 489 deaths). The CFR for covid-19 increased overall and in different age groups, in both sexes. The increase occurred in a greatest intensity in the population between 20 and 59 years old and among patients without pre-existing risk conditions. Female 20 to 39 years old, with no pre-existing risk conditions, were at risk of death 5.65 times higher in February (95%CI = 2.9 - 11.03; p <0.0001) and in the age group of 40 and 59 years old, this risk was 7.7 times higher (95%CI = 5.01-11.83; p <0.0001) comparing with November-December. Interpretation Our findings showed an increase in the proportion of young people and people without previous illnesses among severe cases and deaths in the state of RS after the identification of the local transmission of variant P.1 in the state. There was also an increase in the proportion of severe cases and in the CFR, in almost all subgroups analyzed, this increase was heterogeneous in different age groups and sex. As far as we know, these are the first evidences that the P.1 variant can disproportionately increase the risk of severity and deaths among population without pre-existing diseases, suggesting related changes in pathogenicity and virulence profiles. New studies still need to be done to confirm and deepen these findings.

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“…Perhaps the greatest concern when it comes to emerging SARS-CoV-2 variants stems from identification of rapidly expanding lineages with mutations in the RBD that have significant impact on neutralization potency of many RBD-targeting antibodies, including clinical stage antibody therapeutics, as well as natural infection and vaccine-induced antibody responses. In addition to the N501Y mutation, the B.1.351 and P.1 lineages, originating in South Africa and Brazil respectively, also carry mutations E484K and K417N/T (Tegally et al, 2020 Preprint;Martins et al, 2021). Other lineages containing the E484K mutation but not N501Y, such as P.2 (Brazil) and B.1526 (New York), have also been expanding, suggesting that the E484K mutation independent of N501Y may confer sufficient advantages to the virus (Voloch et al, 2020 Preprint;West et al, 2021 Preprint).…”

mentioning

confidence: 99%