ArticleMicrobiology spectrum2022
Spread of Gamma (P.1) Sub-Lineages Carrying Spike Mutations Close to the Furin Cleavage Site and Deletions in the N-Terminal Domain Drives Ongoing Transmission of SARS-CoV-2 in Amazonas, Brazil.
Article in Microbiology spectrum, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers, 2 of them syntheses that pooled it.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
30 citing papers in PubMed, 2 syntheses or guidelines pooled it, 52 citations in OpenAlex.
- New variants of COVID-19 (XBB.1.5 and XBB.1.16, the "Arcturus"): A review of highly questioned concerns, a brief comparison between different peaks in the COVID-19 pandemic, with a focused systematic review on expert recommendations for prevention, vaccination, and treatment measures in the general population and at-risk groups.Immunity, inflammation and disease · 2024Pooled it
- SARS-CoV-2 Genomic Surveillance in Brazil: A Systematic Review with Scientometric Analysis.Viruses · 2022Pooled it
- Effectiveness of CoronaVac in a pioneer risk-based allocation clinical trial during the COVID-19 pandemic.PloS one · 2026Trial
- Immunogenicity, Effectiveness, and Safety of Inactivated Virus (CoronaVac) Vaccine in a Two-Dose Primary Protocol and BNT162b2 Heterologous Booster in Brazil (Immunita-001): A One Year Period Follow Up Phase 4 Study.Frontiers in immunology · 2022Trial
- Incidence of and Risk Factors for SARS-CoV-2 Infection Among Vaccinated Healthcare Workers During Emergence of SARS-CoV-2 Gamma Variant in the Amazon Region, Brazil, 2021.Clinical infectious diseases : an official publication of the Infectious Diseases Society of America · 2025Article
- Unveiling the Dynamics of SARS-CoV-2 Gamma and Delta Waves in Paraná, Brazil - Delta Displacing a Persistent Gamma Through Alternative Routes of Dispersal.Journal of medical virology · 2025Article
- Article
- Long-term surveillance of SARS-CoV-2 in the school community from Campo Grande, Brazil.BMC public health · 2024Article
- Spatiotemporal transmission of SARS-CoV-2 lineages during 2020-2021 in Pernambuco-Brazil.Microbiology spectrum · 2024Article
- Haplotypic Distribution of SARS-CoV-2 Variants in Cases of Intradomiciliary Infection in the State of Rondônia, Western Amazon.Bioinformatics and biology insights · 2024Article
- Targeting Viral ORF3a Protein: A New Approach to Mitigate COVID-19 Induced Immune Cell Apoptosis and Associated Respiratory Complications.Advanced pharmaceutical bulletin · 2023Review
- SARS-CoV-2 Rapid Antigen Test Based on a New Anti-Nucleocapsid Protein Monoclonal Antibody: Development and Real-Time Validation.Microorganisms · 2023Article
- Assessment of clinical characteristics and viral load in individuals infected by Delta and Omicron variants of SARS-CoV-2.Heliyon · 2023Article
- Reduced Pathogenicity and Transmission Potential of Omicron BA.1 and BA.2 Sublineages Compared with the Early Severe Acute Respiratory Syndrome Coronavirus 2 D614G Variant in Syrian Hamsters.The Journal of infectious diseases · 2023Article
- SARS-CoV-2 intra-host diversity, antibody response, and disease severity after reinfection by the variant of concern Gamma in Brazil.Scientific reports · 2023Article
- Comparative epidemic expansion of SARS-CoV-2 variants Delta and Omicron in the Brazilian State of Amazonas.Nature communications · 2023Article
- Clinical Profile and Risk Factors for Severe COVID-19 in Hospitalized Patients from Rio de Janeiro, Brazil: Comparison between the First and Second Pandemic Waves.Journal of clinical medicine · 2023Article
- Implementing a provisional overarching intervention for COVID-19 monitoring and control in the Brazil-Colombia-Peru frontier.Frontiers in public health · 2023Article
- SARS-CoV-2 Spike Protein Mutations in Different Variants: A Comparison Between Vaccinated and Unvaccinated Population in Western Amazonia.Bioinformatics and biology insights · 2023Article
- The emergence of Omicron VOC and its rapid spread and persistence in the Western Amazon.PloS one · 2023Article
Corrections and comments
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Authors and funding
43 authors at 8 institutions in 1 country.
Funding
Abstract
The Amazonas was one of the most heavily affected Brazilian states by the COVID-19 epidemic. Despite a large number of infected people, particularly during the second wave associated with the spread of the Variant of Concern (VOC) Gamma (lineage P.1), SARS-CoV-2 continues to circulate in the Amazonas. To understand how SARS-CoV-2 persisted in a human population with a high immunity barrier, we generated 1,188 SARS-CoV-2 whole-genome sequences from individuals diagnosed in the Amazonas state from 1st January to 6th July 2021, of which 38 were vaccine breakthrough infections. Our study reveals a sharp increase in the relative prevalence of Gamma plus (P.1+) variants, designated Pango Lineages P.1.3 to P.1.6, harboring two types of additional Spike changes: deletions in the N-terminal (NTD) domain (particularly Δ144 or Δ141-144) associated with resistance to anti-NTD neutralizing antibodies or mutations at the S1/S2 junction (N679K or P681H) that probably enhance the binding affinity to the furin cleavage site, as suggested by our molecular dynamics simulations. As lineages P.1.4 (S:N679K) and P.1.6 (S:P681H) expanded (Re > 1) from March to July 2021, the lineage P.1 declined (Re < 1) and the median Ct value of SARS-CoV-2 positive cases in Amazonas significantly decreases. Still, we did not find an increased incidence of P.1+ variants among breakthrough cases of fully vaccinated patients (71%) in comparison to unvaccinated individuals (93%). This evidence supports that the ongoing endemic transmission of SARS-CoV-2 in the Amazonas is driven by the spread of new local Gamma/P.1 sublineages that are more transmissible, although not more efficient to evade vaccine-elicited immunity than the parental VOC. Finally, as SARS-CoV-2 continues to spread in human populations with a declining density of susceptible hosts, the risk of selecting more infectious variants or antibody evasion mutations is expected to increase.
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