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 <!DOCTYPE article PUBLIC "-//NLM//DTD JATS (Z39.96) Journal Publishing DTD v1.0 20120330//EN" "http://jats.nlm.nih.gov/publishing/1.0/JATS-journalpublishing1.dtd"> <article xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" article-type="research-article" dtd-version="1.0" xml:lang="en">
  <front>
    <journal-meta>
      <journal-id journal-id-type="publisher-id">JVAT</journal-id>
      <journal-title-group>
        <journal-title>Journal of Current Viruses and Treatment Methodologies</journal-title>
      </journal-title-group>
      <issn pub-type="epub">2691-8862</issn>
      <publisher>
        <publisher-name>Open Access Pub</publisher-name>
        <publisher-loc>United States</publisher-loc>
      </publisher>
    </journal-meta>
    <article-meta>
      <article-id pub-id-type="doi">10.14302/issn.2691-8862.jvat-21-3991</article-id>
      <article-id pub-id-type="publisher-id">JVAT-21-3991</article-id>
      <article-categories>
        <subj-group>
          <subject>research-article</subject>
        </subj-group>
      </article-categories>
      <title-group>
        <article-title>Characterizing the Dynamics of Covid-19 Based on Data </article-title>
        <alt-title alt-title-type="running-head">data driven discovery of covid-19 dynamics</alt-title>
      </title-group>
      <contrib-group>
        <contrib contrib-type="author">
          <name>
            <surname>Raúl</surname>
            <given-names>Isea</given-names>
          </name>
          <xref ref-type="aff" rid="idm1843332764">1</xref>
          <xref ref-type="aff" rid="idm1843334132">*</xref>
        </contrib>
      </contrib-group>
      <aff id="idm1843332764">
        <label>1</label>
        <addr-line>Fundación Instituto de Estudios             Avanzados, Hoyo de la Puerta, Baruta, Venezuela. </addr-line>
      </aff>
      <aff id="idm1843334132">
        <label>*</label>
        <addr-line>Corresponding author</addr-line>
      </aff>
      <contrib-group>
        <contrib contrib-type="editor">
          <name>
            <surname>Qianqian</surname>
            <given-names>Song</given-names>
          </name>
          <xref ref-type="aff" rid="idm1843470196">1</xref>
        </contrib>
      </contrib-group>
      <aff id="idm1843470196">
        <label>1</label>
        <addr-line>Wake Forest School of Medicine, Wake Forest Baptist Comprehensive Cancer               Center, Medical Center Boulevard, Winston-Salem, NC 27157.</addr-line>
      </aff>
      <author-notes>
        <corresp>Correspondence: Raúl Isea, Fundación Instituto de Estudios Avanzados, Hoyo de la Puerta, Baruta, Venezuela. Email: <email>raul.isea@gmail.com</email></corresp>
        <fn fn-type="conflict" id="idm1850787660">
          <p>The authors have declared that no competing interests exist.</p>
        </fn>
      </author-notes>
      <pub-date pub-type="epub" iso-8601-date="2021-11-20">
        <day>20</day>
        <month>11</month>
        <year>2021</year>
      </pub-date>
      <volume>1</volume>
      <issue>3</issue>
      <fpage>25</fpage>
      <lpage>30</lpage>
      <history>
        <date date-type="received">
          <day>10</day>
          <month>10</month>
          <year>2021</year>
        </date>
        <date date-type="accepted">
          <day>18</day>
          <month>11</month>
          <year>2021</year>
        </date>
        <date date-type="online">
          <day>20</day>
          <month>11</month>
          <year>2021</year>
        </date>
      </history>
      <permissions>
        <copyright-statement>© </copyright-statement>
        <copyright-year>2021</copyright-year>
        <copyright-holder>Raúl Isea</copyright-holder>
        <license xlink:href="http://creativecommons.org/licenses/by/4.0/" xlink:type="simple">
          <license-p>This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.</license-p>
        </license>
      </permissions>
      <self-uri xlink:href="http://openaccesspub.org/jvat/article/1736">This article is available from http://openaccesspub.org/jvat/article/1736</self-uri>
      <abstract>
        <p>The objective of this paper is to apply   datadriven discovery of dynamics modeling to obtain a system of differential equations that            allows us to describe the transmission dynamics of Covid-19, based on the number of confirmed cases and deaths reported daily. This methodology was applied in four different countries: Brazil, Colombia, Venezuela, and the United States. The main advantage is that only one differential equation is needed to characterize the dynamic of Covid-19 without any mathematical assumption.</p>
      </abstract>
      <kwd-group>
        <kwd>Covid-19</kwd>
        <kwd>Data driven</kwd>
        <kwd>SINDy</kwd>
        <kwd>Model</kwd>
        <kwd>SARS-CoV-2.</kwd>
      </kwd-group>
      <counts>
        <fig-count count="3"/>
        <table-count count="1"/>
        <page-count count="6"/>
      </counts>
    </article-meta>
  </front>
  <body>
    <sec id="idm1843192812" sec-type="intro">
      <title>Introduction </title>
      <p>There is a great effort to explain the                 transmission dynamics of Covid-19 with                      mathematical models after it was declared a                    pandemic in March 2020 <xref ref-type="bibr" rid="ridm1849913780">1</xref>.  In fact, a search in Google Scholar (to cite an example) using the                 keywords: "<italic>Mathematics + Covid-19</italic>", obtained 17,900 different results from 2020 as those of November 2021. All of it indicates the great diversity of results obtained in this important field of work.</p>
      <p>Most of these papers are dedicated to                  describe the outbreak in some places of the world. For example, Isea described the dynamics on                 Venezuela <xref ref-type="bibr" rid="ridm1849917884">2</xref>, Tang <italic>et al</italic> on Brazil <xref ref-type="bibr" rid="ridm1849927180">3</xref>, and so on. For that reason, it is necessary to develop a methodology that allows describing the epidemic by Covid-19 based on the data, and principally with only a                mathematical model.</p>
      <p>In the last decade, computational                     methodologies have been developed for obtaining the non-linear differential equations that rule a                    dynamical system. One of the techniques to do so is called datadriven discovery of dynamics modeling                <xref ref-type="bibr" rid="ridm1849984916">4</xref><xref ref-type="bibr" rid="ridm1849774956">5</xref><xref ref-type="bibr" rid="ridm1849778988">6</xref><xref ref-type="bibr" rid="ridm1849763684">7</xref>, which is based on Sparse Identification of        Nonlinear Dynamics (SINDy). This computational               implementation is usually done in Python <xref ref-type="bibr" rid="ridm1849758860">8</xref> or                    Mathematical <xref ref-type="bibr" rid="ridm1849753060">9</xref>.</p>
      <p>In fact, the SINDy methodology applied to               Covid-19 has already been reported in the scientific              literature <sup>see for example 10</sup>, but unlike those                publications, we obtained a polynomial differential                equation based on confirmed cases and deaths reported daily as described in the next section.</p>
    </sec>
    <sec id="idm1843193532" sec-type="methods">
      <title>Methodology</title>
      <p>The data driven discovery of equations is a             computational methodology where applied techniques of Data Science and Machine Learningare used, and also              Artificial Intelligence as shown by Bruton <italic>et al</italic><xref ref-type="bibr" rid="ridm1849763684">7</xref>. This methodology is displayed in <xref ref-type="fig" rid="idm1843183844">Figure 1</xref>, where only            solutions of polynomial functions are considered. </p>
      <p>As can be seen in <xref ref-type="fig" rid="idm1843183844">Figure 1</xref>, a matrix whose                 columns are the time dependent input data are built, <italic>i.e.</italic>, the number of confirmed cases (I) and deaths (D) reported daily. The next step was to build a library of coefficients of nonlinear functions based on polynomial function                  indicated as in the figure, where the degree of a polynomial is represented by U.  For example, U=2, it means will be [1, I,D,I<sup>2</sup>,D<sup>2</sup>,ID] (1 in these                  expressions represents a constant value).</p>
      <fig id="idm1843183844">
        <label>Figure 1.</label>
        <caption>
          <title> Schematic illustration of the methodology to calculate the differential equations (T means                  transpose).  </title>
        </caption>
        <graphic xlink:href="images/image1.jpg" mime-subtype="jpg"/>
      </fig>
      <p>The dynamics will be described by the following equation (the point in X represents the derivative respect to the time), and the sparse coefficients vector will be equal to [x<sub>1,</sub> x<sub>2</sub>,], which correspond to the values of [I, D], respectively (accordingly to Bruton’s methodology)<xref ref-type="bibr" rid="ridm1849763684">7</xref>. </p>
      <p>The third step is an optimization process where the parameters are calculated by Least Absolute Shrinkage and Selection Operator (abbreviated as LASSO) <xref ref-type="bibr" rid="ridm1849738156">14</xref>.               Remember that LASSO regression is also known as           L1-norm regression. In future papers other methods will be implemented such as Scaled Sequential Threshold Least Squares (S<xref ref-type="bibr" rid="ridm1849917884">2</xref>TLS) algorithm <xref ref-type="bibr" rid="ridm1849736212">15</xref> to compare results. This step is really the most import of them all.  In fact, the degree (U) in the library coefficients is obtained automatically by the program according to the minimization of the error in the optimization step.</p>
      <p>Finally, the last step is to obtain the differential equation. For the case in which U=2, this would be</p>
      <fig id="idm1843181756">
        <graphic xlink:href="images/image2.png" mime-subtype="png"/>
      </fig>
      <p>where a<sub>i</sub> and b<sub>i</sub> (i from 1 to 6) are the constant coefficients to be calculated for each of the countries.</p>
    </sec>
    <sec id="idm1843164532" sec-type="results">
      <title>Results</title>
      <p>The data was obtained from the Johns Hopkins University portal, available at coronavirus.jhu.edu. Four countries were selected: Brazil, Colombia, Venezuela, and the United States, and in each country the numberof              contagions (I) and deaths (D) is obtained, from March 27, 2020 until June 14, 2021 (a total of 445 records) were     retrieved.</p>
      <p>The next step was to normalize the data according to standard deviation, and the results are shown in               <xref ref-type="fig" rid="idm1843109812">figure 2</xref>, <italic>i.e.</italic>, this normalization consisted of subtracting by the mean value and divided by the standard deviation, where the data was represented by symbols in blue color, and the results obtained in dashedblack line. It is                 interesting to see the result in Brazil by the dispersion of the data.</p>
      <fig id="idm1843109812">
        <label>Figure 2.</label>
        <caption>
          <title> Daily cases records versus time (t) on the United States, Brazil, Colombia, and Venezuela  represented with a blue point, and with dash line shows the results obtained in the normalization of the data. </title>
        </caption>
        <graphic xlink:href="images/image3.jpg" mime-subtype="jpg"/>
      </fig>
      <p>The next step was to calculate the parameters with the normalization data according to with the              methodology described in <xref ref-type="fig" rid="idm1843183844">Figure 1</xref>, where the library of coefficients of nonlinear functions is based on a                     polynomial function.  The coefficients obtained in each country are shown in <xref ref-type="table" rid="idm1843107580">Table 1</xref>. The degree of differential equations obtained in all countries wasthree (U=3, error less than 0.001).  In addition, it is interesting to note how different are the parameters obtained in this table,                because each result depends on country response measures to Covid-19.</p>
      <table-wrap id="idm1843107580">
        <label>Table 1.</label>
        <caption>
          <title> Coefficients obtained in the differential equations system (1) on Brazil (BRA), United States (USA), Venezuela (VEN), and Colombia (COL), divided into two sections corresponding to dI/dt and dD/dt, respectively. </title>
        </caption>
        <table rules="all" frame="box">
          <tbody>
            <tr>
              <td>
                <inline-graphic xlink:href="images/image4.png" mime-subtype="png"/>
              </td>
              <td>
                <inline-graphic xlink:href="images/image5.png" mime-subtype="png"/>
              </td>
              <td><inline-graphic xlink:href="images/image6.png" mime-subtype="png"/>D</td>
              <td><inline-graphic xlink:href="images/image7.png" mime-subtype="png"/>I</td>
              <td>
                <inline-graphic xlink:href="images/image8.png" mime-subtype="png"/>
              </td>
              <td>
                <inline-graphic xlink:href="images/image9.png" mime-subtype="png"/>
              </td>
              <td>
                <inline-graphic xlink:href="images/image10.png" mime-subtype="png"/>
              </td>
              <td>
                <inline-graphic xlink:href="images/image11.png" mime-subtype="png"/>
              </td>
              <td>
                <inline-graphic xlink:href="images/image12.png" mime-subtype="png"/>
              </td>
              <td>
                <inline-graphic xlink:href="images/image13.png" mime-subtype="png"/>
              </td>
              <td>
                <inline-graphic xlink:href="images/image14.png" mime-subtype="png"/>
              </td>
            </tr>
            <tr>
              <td>BRA</td>
              <td>0,15</td>
              <td>0,34</td>
              <td>0,04</td>
              <td>15,8</td>
              <td>14,0</td>
              <td>-29,8</td>
              <td>63,3</td>
              <td>-55,1</td>
              <td>-24,0</td>
              <td>15,8</td>
            </tr>
            <tr>
              <td>USA</td>
              <td>0,10</td>
              <td>0,24</td>
              <td>3,00</td>
              <td> </td>
              <td>-1,43</td>
              <td> </td>
              <td>4,88</td>
              <td>-2,01</td>
              <td>-3,03</td>
              <td>0,22</td>
            </tr>
            <tr>
              <td>VEN</td>
              <td> </td>
              <td>-3,66</td>
              <td>7,97</td>
              <td>-7,46</td>
              <td>13,3</td>
              <td>-8,73</td>
              <td>17,3</td>
              <td>-26,6</td>
              <td> </td>
              <td>9,90</td>
            </tr>
            <tr>
              <td>COL</td>
              <td>0,02</td>
              <td>10,0</td>
              <td>-8,13</td>
              <td>-58,1</td>
              <td>-66,5</td>
              <td>123,5</td>
              <td>-657,9</td>
              <td>664,2</td>
              <td>-224,2</td>
              <td>218,2</td>
            </tr>
            <tr>
              <td colspan="11"> </td>
            </tr>
            <tr>
              <td>
                <inline-graphic xlink:href="images/image15.png" mime-subtype="png"/>
              </td>
              <td>
                <inline-graphic xlink:href="images/image16.png" mime-subtype="png"/>
              </td>
              <td><inline-graphic xlink:href="images/image17.png" mime-subtype="png"/>D</td>
              <td><inline-graphic xlink:href="images/image18.png" mime-subtype="png"/>I</td>
              <td>
                <inline-graphic xlink:href="images/image19.png" mime-subtype="png"/>
              </td>
              <td>
                <inline-graphic xlink:href="images/image20.png" mime-subtype="png"/>
              </td>
              <td>
                <inline-graphic xlink:href="images/image21.png" mime-subtype="png"/>
              </td>
              <td>
                <inline-graphic xlink:href="images/image22.png" mime-subtype="png"/>
              </td>
              <td>
                <inline-graphic xlink:href="images/image23.png" mime-subtype="png"/>
              </td>
              <td>
                <inline-graphic xlink:href="images/image24.png" mime-subtype="png"/>
              </td>
              <td>
                <inline-graphic xlink:href="images/image25.png" mime-subtype="png"/>
              </td>
            </tr>
            <tr>
              <td>BRA</td>
              <td>0,34</td>
              <td>1,64</td>
              <td>-2,52</td>
              <td>14,3</td>
              <td>13,3</td>
              <td>-26,7</td>
              <td>10,7</td>
              <td>-5,52</td>
              <td>-5,29</td>
              <td> </td>
            </tr>
            <tr>
              <td>USA</td>
              <td>0,10</td>
              <td>0,20</td>
              <td>-0,77</td>
              <td>-2,55</td>
              <td>-2,99</td>
              <td>6,54</td>
              <td> </td>
              <td>-0,46</td>
              <td>0,002</td>
              <td>0,18</td>
            </tr>
            <tr>
              <td>VEN</td>
              <td> </td>
              <td>-4,10</td>
              <td>7,17</td>
              <td>-1,82</td>
              <td>18,5</td>
              <td>-18,5</td>
              <td>15,8</td>
              <td>-24,0</td>
              <td> </td>
              <td>8,59</td>
            </tr>
            <tr>
              <td>COL</td>
              <td>0,04</td>
              <td>14,8</td>
              <td>-13,3</td>
              <td>-58,4</td>
              <td>-72,3</td>
              <td>130,0</td>
              <td>644,9</td>
              <td>-641,5</td>
              <td>-217,3</td>
              <td>214,</td>
            </tr>
          </tbody>
        </table>
      </table-wrap>
      <p>Finally, <xref ref-type="fig" rid="idm1842991188">figure 3</xref> depicts the result obtained in (A) the United States of America and (B) Venezuela according to the results obtained in <xref ref-type="table" rid="idm1843107580">Table 1</xref> (the results are shown with a red line).  The results show that this methodology is not capable to make accurate predictions when there is a lot of difference in the number of cases (see for example the US case), while the prediction for Venezuela better reproduces the observed cases. </p>
      <fig id="idm1842991188">
        <label>Figure 3.</label>
        <caption>
          <title> Results obtained in (A) the United States, and (B) Venezuela. Daily cases record are shown in blue point, the result obtained with the SINDy methodology in dashed black line (represented as SG), and the values obtained according to the coefficients indicated in Table 1in red. </title>
        </caption>
        <graphic xlink:href="images/image26.jpg" mime-subtype="jpg"/>
      </fig>
    </sec>
    <sec id="idm1843083108" sec-type="conclusions">
      <title>Conclusion</title>
      <p>This paper proposes a system of differential    equations of the polynomial type that allows                         characterizing the transmission dynamics of Covid-19 in any country since the beginning of the pandemic. The main advantage of this methodology is that it is possible to derive only one differential equation to explain the                dynamics of contagion by SARS-CoV-2. It only remains to indicate that it is necessary to develop numerical                    calculations to be able to generalize these conclusions.</p>
    </sec>
    <sec id="idm1843082316">
      <title>Acknowledgment</title>
      <p>I’d like to acknowledgment to Rafael Mayo-Garcia and Jesus Isea for your comments in this manuscript.</p>
    </sec>
    <sec id="idm1843080804">
      <title>Dedication</title>
      <p>This paper is dedicated to the memory to Gloria Teresa Villegas who died on 21th October 2021. Her               husband, Raimundo Villegas, also died on October 21. Thank you for your friendship.</p>
    </sec>
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