Re-emergence of Gamma-like-II and emergence of Gamma-S:E661D SARS-CoV-2 lineages in the south of Brazil after the 2021 outbreak

  1. Mauro M. Oliveira
  2. Michelle O. Schemberger
  3. Andreia A. Suzukawa
  4. Irina N. Riediger
  5. Maria do Carmo Debur
  6. Guilherme Becker
  7. Paola Cristina Resende
  8. Tiago Gräf
  9. Eduardo Balsanelli
  10. Valter Antônio de Baura
  11. Emanuel M. de Souza
  12. Fábio O. Pedrosa
  13. Lysangela R. Alves
  14. Lucas Blanes
  15. Sheila Cristina Nardelli
  16. Alessandra M. Aguiar
  17. Letusa Albrecht
  18. Dalila Zanette
  19. Andréa R. Ávila
  20. Luis Gustavo Morello
  21. Fabricio K. Marchini
  22. Hellen G. dos Santos
  23. Fabio Passetti
  24. Bruno Dallagiovanna
  25. Helisson Faoro

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Abstract

Background

We report a genomic surveillance of SARS-CoV-2 lineages circulating in Paraná, southern Brazil, from March 2020 to April 2021. Our analysis, based on 333 genomes, revealed that the first variants detected in the state of Paraná in March 2020 were the B.1.1.33 and B.1.1.28 variants. The variants B.1.1.28 and B.1.1.33 were predominant throughout 2020 until the introduction of the variant P.2 in August 2020 and a variant of concern (VOC), Gamma (P.1), in January 2021. The VOC Gamma, a ramification of the B.1.1.28 lineage first detected in Manaus (northern Brazil), has grown rapidly since December 2020 and was thought to be responsible for the deadly second wave of COVID-19 throughout Brazil.

Methods

The 333 genomic sequences of SARS-CoV-2 from March 2020 to April 2021 were generated as part of the genomic surveillance carried out by Fiocruz in Brazil Genomahcov Fiocruz. SARS-CoV-2 sequencing was performed using representative samples from all geographic areas of Paraná. Phylogenetic analyses were performed using the 333 genomes also included other SARS-CoV-2 genomes from the state of Paraná and other states in Brazil that were deposited in the GISAID. In addition, the time-scaled phylogenetic tree was constructed with up to 3 random sequences of the Gamma variant from each state in Brazil in each month of 2021. In this analysis we also added the sequences identified as the B.1.1.28 lineage of the Amazonas state and and the Gamma-like-II (P.1-like-II) lineage identified in different regions of Brazil.

Results

Phylogenetic analyses of the SARS-CoV-2 genomes that were previously classified as the VOC Gamma lineage by WHO/PANGO showed that some genomes from February to April 2021 branched in a monophyletic clade and that these samples grouped together with genomes recently described with the lineage Gamma-like-II. Additionally, a new mutation (E661D) in the spike (S) protein has been identified in nearly 10% of the genomes classified as the VOC Gamma from Paraná in March and April 2021.Finally, we analyzed the correlation between the lineage and the Gamma variant frequency, age group (patients younger or older than 60 years old) and the clinical data of 86 cases from the state of Paraná.

Conclusions

Our results provided a reliable picture of the evolution of the SARS-CoV-2 pandemic in the state of Paraná characterized by the dominance of the Gamma strain, as well as a high frequencies of the Gamma-like-II lineage and the S:E661D mutation. Epidemiological and genomic surveillance efforts should be continued to unveil the biological relevance of the novel mutations detected in the VOC Gamma in Paraná.

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  1. Version published to 10.1186/s12985-021-01690-1
  2. ScreenIT

    SciScore for 10.1101/2021.07.14.21260508: (What is this?)

    Please note, not all rigor criteria are appropriate for all manuscripts.

    Table 1: Rigor

    NIH rigor criteria are not applicable to paper type.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Variants were identified after read mapping in the reference genome for SARS-CoV-2 (RefSeq accession number NC_045512), and the analysis was performed on the Pangolin and Nextclade platforms.
    RefSeq
    suggested: (RefSeq, RRID:SCR_003496)
    The reads were trimmed with Trimmomatic v0.39 (5) and assembled using the tools SPAdes v3.14.1 (4) and MEGAHIT v1.2.9 (26).
    Trimmomatic
    suggested: (Trimmomatic, RRID:SCR_011848)
    SPAdes
    suggested: (SPAdes, RRID:SCR_000131)
    MEGAHIT
    suggested: (MEGAHIT, RRID:SCR_018551)
    The scaffolds were built with RagTag v1.1.1 (1), ABACAS v1.3.1 (3) using the SARS-CoV-2 isolate Wuhan-Hu-1 as a template (NC_045512 RefSeq).
    RagTag
    suggested: None
    ABACAS
    suggested: (ABACAS, RRID:SCR_015852)
    Using this approach, we generated consensus sequences with a mean of 95% coverage (QUAST v5.0.2) (22).
    QUAST
    suggested: (QUAST, RRID:SCR_001228)
    The two groups of sequences were aligned using MAFFT v7.475 (24).
    MAFFT
    suggested: (MAFFT, RRID:SCR_011811)
    The datasets were subjected to a maximum likelihood (ML) and a phylogenetic analysis using IQ-TREE v2.1.2 (31) under the GTR+G4+F nucleotide substitution model, and branch support was assessed by the approximate likelihood-ratio test based on the Shimodaira–Hasegawa-like procedure (SH-aLRT) with 1,000 replicates.
    IQ-TREE
    suggested: (IQ-TREE, RRID:SCR_017254)
    Time-scaled phylogenetic analysis: The time-scale phylogenetic tree was built using the Bayesian Markov Chain Monte Carlo (MCMC) approach implemented in BEAST 1.10.4 with the BEAGLE v3.1.0 library to optimize the computational time.
    BEAST
    suggested: (BEAST, RRID:SCR_010228)
    BEAGLE
    suggested: (BEAGLE, RRID:SCR_001789)
    Convergence (effective sample size> 200) in parameter estimates was assessed using TRACER v1.7.2.
    TRACER
    suggested: (Tracer, RRID:SCR_019121)
    The maximum clade credibility (MCC) tree was summarized with TreeAnnotator v1.10.4 ML, and MCC trees were visualized using FigTree v1.4.4 (18, 19).
    FigTree
    suggested: (FigTree, RRID:SCR_008515)

    Results from OddPub: Thank you for sharing your code and data.

    Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
    A limitation of our study includes the impossibility of follow-up in the cases to make a more precise correlation between the variants and the clinical out-comes, and, for the association analysis, clinical severity was determined from the data from the laboratory that provided the samples. Therefore, we infer, based on the available data, that the P.1 variant may not be related to a higher severity of COVID-19, although further studies should be carried out to carefully explore this issue. Our phylogenetic analysis performed with the P.1 variant genomes identified in the state of Paraná and in the other states of Brazil showed that the recently described lineage P.1- like-II (21) was also present at moderate frequencies in the state of Paraná (Figure 3 and 5). The P.1- like-II lineage presents 15 of the 22 mutations of the P.1 variant, including the three main mutations in the RBD domain of the S protein: K417T, E484K and N501Y. On the other hand, they present some unique substitutions: ORF1ab: C8905T, C16954T and A20931G; NSP4:D2980H, intergenic region E/M A26492T and N:P383 L. The analysis of the mutations in the first 11 P.1- like-II genomes from Paraná identified 3 of the 4 unique substitutions of the P.1- like-II lineage (C8905T, C16954T, A26492T) in addition to the N:P383 L and ORF1a:D2980H mutations. However, we also identified some unique substitutions, which were not yet described, for the P.1 variant and P.1- like-II lineage, and these substitutions included ORF1a:...

    Results from TrialIdentifier: No clinical trial numbers were referenced.

    Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

    Results from JetFighter: We did not find any issues relating to colormaps.

    Results from rtransparent:
    • Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
    • Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
    • No protocol registration statement was detected.

    Results from scite Reference Check: We found no unreliable references.

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  3. Version published to 10.1101/2021.07.14.21260508v1 on medRxiv