First Report on the Latvian SARS-CoV-2 Isolate Genetic Diversity

  1. Nikita Zrelovs
  2. Monta Ustinova
  3. Ivars Silamikelis
  4. Liga Birzniece
  5. Kaspars Megnis
  6. Vita Rovite
  7. Lauma Freimane
  8. Laila Silamikele
  9. Laura Ansone
  10. Janis Pjalkovskis
  11. Davids Fridmanis
  12. Baiba Vilne
  13. Marta Priedite
  14. Anastasija Caica
  15. Mikus Gavars
  16. Dmitry Perminov
  17. Jelena Storozenko
  18. Oksana Savicka
  19. Elina Dimina
  20. Uga Dumpis
  21. Janis Klovins

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Abstract

Remaining a major healthcare concern with nearly 29 million confirmed cases worldwide at the time of writing, novel severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has caused more than 920 thousand deaths since its outbreak in China, December 2019. First case of a person testing positive for SARS-CoV-2 infection within the territory of the Republic of Latvia was registered on 2nd of March 2020, 9 days prior to the pandemic declaration by WHO. Since then, more than 277,000 tests were carried out confirming a total of 1,464 cases of coronavirus disease 2019 (COVID-19) in the country as of 12th of September 2020. Rapidly reacting to the spread of the infection, an ongoing sequencing campaign was started mid-March in collaboration with the local testing laboratories, with an ultimate goal in sequencing as much local viral isolates as possible, resulting in first full-length SARS-CoV-2 isolate genome sequences from the Baltics region being made publicly available in early April. With 133 viral isolates representing ~9.1% of the total COVID-19 cases during the “first coronavirus wave” in the country (early March, 2020—mid-September, 2020) being completely sequenced as of today, here, we provide a first report on the genetic diversity of Latvian SARS-CoV-2 isolates.

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  1. Version published to 10.3389/fmed.2021.626000
  2. ScreenIT

    SciScore for 10.1101/2020.09.08.20190504: (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
    Quality controlled reads were then aligned against SARS-CoV-2 isolate Wuhan-Hu-1 reference genome (Accession number: NC_045512.2) with bowtie2 2.3.5.1 [34].
    bowtie2
    suggested: (Bowtie 2, RRID:SCR_016368)
    Average coverage for each of the genomes was calculated using samtools and in-house awk [36] scripts.
    samtools
    suggested: (SAMTOOLS, RRID:SCR_002105)
    Phylogenetic reconstructions: Sequences of the Latvian SARS-CoV-2 isolates and Wuhan-Hu-1 reference sequence were aligned using Clustal-Omega v 1.2.4.
    Clustal-Omega
    suggested: None
    Maximum likelihood phylogeny was performed using IQTREE v 2.0.6 [42] with GTR+F+I as best fit model determined by ModelFinder [43] according to Bayesian Information Criterion (ultrafast bootstrap with 1000 replicates [44]) and assessment of temporal signal associated with the data was performed by importing resulting ML tree into TempEst v1.5.3 [45], parsing sampling dates of isolates and visualizing the root-to-tip divergence.
    ModelFinder
    suggested: None
    TempEst
    suggested: (TempEst, RRID:SCR_017304)
    Bayesian phylogenetic trees were estimated using BEAST v1.10.4 [46], employing GTR nucleotide substitution model with empirical base frequencies and invariant site proportion assuming strict molecular clock.
    BEAST
    suggested: (BEAST, RRID:SCR_010228)
    Tracer v 1.7.1 [49] was used for MCMC trace (log file) inspection to evaluate sufficiency of sampling (all parameters had an ESS of more than 400) and infer substitution rate along with the date of the most recent common ancestor estimate.
    Tracer
    suggested: (Tracer, RRID:SCR_019121)
    To summarize Bayesian phylogenetic inference, maximum clade credibility time-scaled tree was generated in TreeAnnotator v 1.10.4 (distributed with BEAST package) using 10% of the states (5 million) as the burn-in and visualized using FigTree v 1.4.4 [50].
    FigTree
    suggested: (FigTree, RRID:SCR_008515)

    Results from OddPub: Thank you for sharing your data.

    Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

    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.

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  3. Version published to 10.1101/2020.09.08.20190504 on medRxiv