Model-based evaluation of transmissibility and reinfection for the P.1 variant of the SARS-CoV-2

  title={Model-based evaluation of transmissibility and reinfection for the P.1 variant of the SARS-CoV-2},
  author={Renato Mendes Coutinho and Flavia Maria Darcie Marquitti and Leonardo Souto Ferreira and M. E. Borges and R P Silva and O. Canton and Tatiana Pineda Portella and Silas P. Lyra and Caroline Franco and A. da Silva and Roberto Andr{\'e} Kraenkel and Maria Am{\'e}lia Veras and Paulo In{\'a}cio Prado},
The variant of concern (VOC) P.1 emerged in the Amazonas state (Brazil) and was sequenced for the 1st time on 6-Jan-2021 by the Japanese National Institute of Infectious Diseases. It contains a constellation of mutations, ten of them in the spike protein. Consequences of these mutations at the populational level have been poorly studied so far. From December-2020 to February-2021, Manaus was devastated by four times more cases compared to the previous peak (April-2020). Here, data from the… Expand
The new SARS-CoV-2 variant and reinfection in the resurgence of COVID-19 outbreaks in Manaus, Brazil
This work revisits claims that the first wave of COVID-19 infected over three quarters of the population in Manaus based on routine blood donor data, and the second wave was largely due to reinfection with a new variant named P1 strain, and model the two waves with a two-strain model without a significant proportion of reinfections. Expand
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
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 can disproportionately increase the risk of severity and deaths among population without pre-existing diseases, suggesting related changes in pathogenicity and virulence profiles. Expand
Phylogenetic-based inference reveals distinct transmission dynamics of SARS-CoV-2 variant of concern Gamma and lineage P.2 in Brazil
Although the epicenter of the lineage P.2 dissemination in Brazil was the heavily interconnected Southeastern region, it displayed a slower rate of spatial spread than the VOC Gamma, which originated in the more isolated Northern Brazilian region, although the viral Re of the V OC varied according to the geographic context. Expand
Up State of the SARS-COV-2 Spike Homotrimer Favors an Increased Virulence for New Variants
The COVID-19 pandemic has spread worldwide. However, as soon as the first vaccines—the only scientifically verified and efficient therapeutic option thus far—were released, mutations combined intoExpand
Standardised, quantitative neutralisation responses to SARS-CoV-2 Variants of Concern by convalescent anti-sera from first wave infections of UK Health Care Workers and Patients
A significant reduction in the ability of first wave convalescent plasma to neutralise the VOCs is demonstrated and widespread use of the WHO International Standard by laboratories in different countries will allow for cross-laboratory comparisons, to benchmark and to establish thresholds of protection against SARS-CoV-2 and levels of immunity in different settings and countries. Expand
Detection of SARS-CoV-2 lineage P.1 in patients from a region with exponentially increasing hospitalization rates in February 2021, Rio Grande do Sul, Southern Brazil
Whole-genome sequencing revealed that the previously undetected P.1 lineage accounted for 88.9% of specimens collected from patients at a referral COVID-19 hospital, which raises concerns regarding a possible association between lineage P. 1 and rapid growth in cases and hospitalizations. Expand
COVID-19 in northeast Brazil: first year of the pandemic and uncertainties to come
The Brazilian NE and the country are in increasingly complicated health, social and economic situations, and it is necessary to speed up vaccinations and maintain non-pharmacological measures: face masks, social distancing measures and hygiene care, in addition to policies to protect workers who have lost their incomes and to subsidize small business owners. Expand
The next phase of SARS-CoV-2 surveillance: real-time molecular epidemiology.
A systematic approach is needed to link global genomic surveillance and timely assessment of the phenotypic characteristics of novel variants, which will support the development and updating of diagnostics, vaccines, therapeutics and nonpharmaceutical interventions. Expand
Emerging SARS-CoV-2 Variants: A Review of Its Mutations, Its Implications and Vaccine Efficacy
The different SARS-CoV-2 variants are discussed, emphasizing variants of concern circulating the world and how these mutations affect the characteristics of the virus. Expand
The COVID-19 Vaccination Strategy in Brazil—A Case Study
Brazil is among the countries which have faced two devastating infection waves of COVID-19 in the past year. Despite the fact the country has one of the world’s leading immunization programs, BrazilExpand


Genomics and epidemiology of a novel SARS-CoV-2 lineage in Manaus, Brazil
A novel SARS-CoV-2 variant of concern, lineage P.1, that acquired 17 mutations, including a trio in the spike protein associated with increased binding to the human ACE2 receptor, is identified in Manaus, Brazil. Expand
COVID-19 epidemic in the Brazilian state of Amazonas was driven by long-term persistence of endemic SARS-CoV-2 lineages and the recent emergence of the new Variant of Concern P.1
Findings support 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.1.1 virus. Expand
Covid-19: Is Manaus the final nail in the coffin for natural herd immunity?
A second crisis has stunned the city of Manaus, and raises questions around a new variant and the likelihood of natural herd immunity. Expand
Nowcasting by Bayesian Smoothing: A flexible, generalizable model for real-time epidemic tracking
A smooth Bayesian nowcasting approach that produces accurate estimates that capture the time evolution of the epidemic curve and outperform a previous approach in the literature is presented. Expand
Phylogenetic relationship of SARS-CoV-2 sequences from Amazonas with emerging Brazilian variants harboring mutations E484K and N501Y in the Spike protein
  • Virological
  • 2021
Brief report: New Variant Strain of SARS-CoV-2 Identified in Travelers from Brazil. Coronavirus disease 4
    COVID-19 epidemic in the Brazilian state of Amazonas was driven by long-term persistence of endemic SARS-CoV-2 lineages and the recent emergence of the new Variant of Concern P.1. Research Square
      Plots from Rede Genômica Fiocruz website