Genome sequencing and analysis of an emergent SARS-CoV-2 variant characterized by multiple spike protein mutations detected from the Central Visayas Region of the Philippines

  1. Francis A. Tablizo
  2. Kenneth M. Kim
  3. Carlo M. Lapid
  4. Marc Jerrone R. Castro
  5. Maria Sofia L. Yangzon
  6. Benedict A. Maralit
  7. Marc Edsel C. Ayes
  8. Eva Maria Cutiongco-de la Paz
  9. Alethea R. De Guzman
  10. Jan Michael C. Yap
  11. Jo-Hannah S. Llames
  12. Shiela Mae M. Araiza
  13. Kris P. Punayan
  14. Irish Coleen A. Asin
  15. Candice Francheska B. Tambaoan
  16. Asia Louisa U. Chong
  17. Karol Sophia Agape R. Padilla
  18. Rianna Patricia S. Cruz
  19. El King D. Morado
  20. Joshua Gregor A. Dizon
  21. Razel Nikka M. Hao
  22. Arianne A. Zamora
  23. Devon Ray Pacial
  24. Juan Antonio R. Magalang
  25. Marissa Alejandria
  26. Celia Carlos
  27. Anna Ong-Lim
  28. Edsel Maurice Salvaña
  29. John Q. Wong
  30. Jaime C. Montoya
  31. Maria Rosario Singh-Vergeire
  32. Cynthia P. Saloma

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Abstract

The emergence of SARS-CoV-2 variants of concern such as the B.1.1.7, B.1.351 and the P.1 have prompted calls for governments worldwide to increase their genomic biosurveillance efforts. Globally, quarantine and outbreak management measures have been implemented to stem the introduction of these variants and to monitor any emerging variants of potential clinical significance domestically. Here, we describe the emergence of a new SARS-CoV-2 lineage, mainly from the Central Visayas region of the Philippines. This emergent variant is characterized by 13 lineage-defining mutations, including the co-occurrence of the E484K, N501Y, and P681H mutations at the spike protein region, as well as three additional radical amino acid replacements towards the C-terminal end of the said protein. A three-amino acid deletion at positions 141 to 143 (LGV141_143del) in the spike protein was likewise seen in a region preceding the 144Y deletion found in the B.1.1.7 variant. A single amino acid replacement, K2Q, at the N-terminus of ORF8 was also shared by all 33 samples sequenced. The mutation profile of this new virus variant warrants closer investigation due to its potential public health implications. The current distribution of this emergent variant in the Philippines and its transmission are being monitored and addressed by relevant public health agencies to stem its spread in nearby islands and regions in the country.

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  1. ScreenIT

    SciScore for 10.1101/2021.03.03.21252812: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board Statementnot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Mapping and coverage statistics were obtained using Samtools (flagstat and coverage) as well.
    Samtools
    suggested: (SAMTOOLS, RRID:SCR_002105)
    Summary mutation tables and plots were generated using in-house scripts written in Python.
    Python
    suggested: (IPython, RRID:SCR_001658)
    Phylogenetic trees were produced by initially generating a multiple sequence alignment of the local SARS-CoV-2 consensus sequences using the tool MAFFT v7.407 (Katoh et al., 2002), supplemented with publicly available sequences from the EpiCoV database of the Global Initiative for Sharing All Influenza Data (GISAID) platform (Shu and McCauley, 2017).
    MAFFT
    suggested: (MAFFT, RRID:SCR_011811)

    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.

    About SciScore

    SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

  2. Version published to 10.1101/2021.03.03.21252812 on medRxiv