Geographic and Phylodynamic Distribution of SARS-CoV-2 from Environmental Origin

  1. Elijah Kolawole Oladipo
  2. Emmanuel Oluwatobi Dairo
  3. Ayodele Eugene Ayeni
  4. Boluwatife Ayobami Irewolede
  5. Moyosoluwa Precious Oyewole
  6. Charles Oluwaseun Adetunji
  7. Julius Kola Oloke

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Abstract

The coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread globally. Understanding the transmission dynamics of SARS-CoV-2 contamination in the environment is essential for infection control policies. This study aims to provide a phylodynamic analysis and distribution pattern of SARS-CoV-2 from the environment in terms of Source, clades, lineages, and their location. Ninety (90) retrieved whole-genome sequences of environmental sources from GISAID were investigated to determine the evolutionary process of SARS-CoV-2 and mutation in the isolated nucleotide sequences. The analysis was carried out using R, MAFFT, and MEGA X software. Out of the five countries studied, Austria has the highest distribution with sixty-five samples (72.2%), and the highest isolates of 68 (75.6%) were from raw sewage. The highest clade in circulation as obtained from the study is G with lineages B. The phylogeny of SARS-CoV-2 whole-genome sequences from Austria, the United States, China, Brazil, and Liechtenstein indicated that the SARS-CoV-2 viruses were all clustered together, irrespective of sequence geographic location. The study concluded by demonstrating a clear interconnection between the phylogeny of SARS-CoV-2 isolates from various geographic locations, all of which were locked in the same cluster regardless of their environment specimen. Thus, depicting the possibility of their origination from a common ancestor.

Highlight

  • Environmental sources of specimen isolated from raw sewage have the highest occurring specimen sequence, while those from breathing air, door handle, and wastewater have the lowest sequence.

  • Environmental surveillance of SARS-CoV-2 is of great importance to control the spread of the virus. Untreated raw sewage should be of more priority for the environmental surveillance of the virus.

  • Eighteen (18) nucleotide sequences from this study’s multiple sequence alignment shared a 90% similarity with the Wuhan-Hu-1 reference genome, indicating a common evolutionary origin.

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    SciScore for 10.1101/2021.09.13.21263432: (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
    Multiple sequence alignment and evolutionary Analysis: The complete genome sequences of 90 SARS-CoV-2 obtained were aligned using MAFFT version 7 (https://mafft.cbrc.jp/alignment/server/) against the Wuhan-Hu-1 reference genome (Accession number: NC_0455122), with all parameters set at default (Katoh et al., 2019; Kuraku et al., 2013).
    MAFFT
    suggested: (MAFFT, RRID:SCR_011811)
    Based on the whole genome sequences, a maximum likelihood tree was constructed using MEGA X with 50 bootstraps resampling to ascertain the common antecedent among each strain (Tingting et al., 2020).
    MEGA
    suggested: (Mega BLAST, RRID:SCR_011920)

    Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

    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.

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

    About SciScore

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  2. Version published to 10.1101/2021.09.13.21263432v1 on medRxiv