Evolution and spread of SARS-CoV-2 likely to be affected by climate

  1. Priyanka Bajaj
  2. Prakash Chandra Arya

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Abstract

COVID-19 pandemic has been extensively studied by many researchers. However, it is still unclear why it was restricted to higher latitudes during the initial days and later cascaded in the tropics. Here, we analyzed 176 SARS-CoV-2 genomes across different latitudes and climate (Koppen’s climate) that provided insights about within species virus evolution and its relation to abiotic factors. Two genetically variant groups, named as G1 and G2 were identified, well defined by four mutations. The G1 group (ancestor), is mainly restricted to warm and moist, temperate climate (Koppen’s C climate) while its descendent G2 group surpasses the climatic restrictions of G1, initially cascading into neighboring cold climate (D) of higher latitudes and later into hot climate of the tropics (A). It appears that the gradation of temperate climate (Cfa-Cfb) to cold climate (Dfa-Dfb) drives the evolution of G1 into G2 variant group which later adapted to tropical climate (A) as well. It seems this virus followed inverse latitudinal gradient in the beginning due to its preference towards temperate (C) and cold climate (D). Our work elucidates virus evolutionary studies combined with climatic studies can provide crucial information about the pathogenesis and natural spreading pathways in such outbreaks which is hard to achieve through individual studies. Mutational insights gained may help design an efficacious vaccine.

Graphical Abstract

In Brief

The authors elucidate adaptation of SARS-CoV-2 to different climates by studying phylogenetics and the distribution of strains on Koppen’s climate map.

Highlights

  • Phylogenetic network divides SARS-CoV-2 strains into two variant groups, G1 and G2.

  • G1 strains is restricted to Koppen’s “temperate” climate (mainly Cfa-Cfb ).

  • G2 strains has evolved from G1 to sustain in other climates mainly “ humid-continental” (Dfa-Dfb) and “ tropical-savannah” (Aw) climate.

Article activity feed

  1. Version published to 10.1101/2020.06.18.147074v3 on bioRxiv
  2. Version published to 10.1101/2020.06.18.147074v2 on bioRxiv
  3. ScreenIT

    SciScore for 10.1101/2020.06.18.147074: (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
    The aligned sequences were used to construct a phylogenetic tree using MEGA X35.
    MEGA
    suggested: (Mega BLAST, RRID:SCR_011920)
    Statistical analysis: Two-tailed paired t-test & Chi-square test were performed in Microsoft Excel (2016) to test null hypothesis H1, H2, H3 & H4 related to latitudinal preference (H1), climatic preference (H2 & H3) & regional preference (H4) of SARS-CoV-2.
    Microsoft Excel
    suggested: (Microsoft Excel, RRID:SCR_016137)

    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: Please consider improving the rainbow (“jet”) colormap(s) used on page 32. At least one figure is not accessible to readers with colorblindness and/or is not true to the data, i.e. not perceptually uniform.

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

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  4. Version published to 10.1101/2020.06.18.147074v1 on bioRxiv