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Relative Frequency Change By Geographical Region


Last data update: Jun 28, 2020

This tool employs contemporary GISAID data to identify adequately sampled geographical regions and to determine which of those regions are experiencing a significant shift (either up or down) in relative frequency of G614 vs D614 variants of the sequences sampled in that region. D614 was the original form in the Wuhan virus, but G614 is currently the predominant form in most regions; all other changes in Spike are currently very rare.

We are working on a release that will allow tracking of any site using this same strategy in the near future.

Founder effects and non-representative regional sampling can impact the frequency of a variant in any given region. But a consistent pattern of change, with one variant increasing in relative frequency across a range of geographic regions, provides evidence suggesting that a variant may have a selective advantage, or be linked to a site with a selective advantage.

For a change in the relative frequency of a variant to be observed in a geographic region, three requirements must be met:

1. Both variants must at some point be co-circulating in the region
2. Sampling must be over a long enough time to discern a change
3. There must be enough samples available for an observed difference to be statistically significant.

Specifically, for the geographic regions in the chart:

1. We define an "onset" day as the first day for which cumulative number of sequences is at least 15 and each form is represented at least 3 times.
2. We define a "delay" day as two weeks after the onset day, and we require that there be at least 15 sequences available from the post-delay period (ie, from the delay day to the last day of sampling).

A two-sided Fisher's exact test compares the counts in the pre-onset period to the counts in the post-delay period, and provides a p-value against the null hypothesis that the fraction of D614 vs G614 sequences did not change. We require p<0.05 in order to include the region in the bar chart.


S 614 continent


S 614 country


S 614 subcountry


                           Onset    |--Before-|   Delay   |--After--|   Last    Delta   Fisher
                 Location  Date     G/(G+D) G+D   Date    G/(G+D) G+D   Sample  G/(G+D)  p-val
                   Africa  Mar 17   0.861    36   Mar 31  0.962   286   Jun 23   0.10 0.023129
                     Asia  Jan 24   0.016   183   Feb  7  0.485  2899   Oct 15   0.47 0.000000
                   Europe  Jan 29   0.294    17   Feb 12  0.805 26458   Jun 14   0.51 0.000007
            North-America  Feb 28   0.054    92   Mar 13  0.801  8251   Jun 19   0.75 0.000000
                  Oceania  Mar  6   0.070    57   Mar 20  0.672   964   May 24   0.60 0.000000
            South-America  Mar  4   0.632    19   Mar 18  0.959   362   Jun  4   0.33 0.000025

                           Onset    |--Before-|   Delay   |--After--|   Last    Delta   Fisher
                 Location  Date     G/(G+D) G+D   Date    G/(G+D) G+D   Sample  G/(G+D)  p-val
                Australia  Mar  6   0.056    54   Mar 20  0.659   819   May 24   0.60 0.000000
                   Brazil  Mar  4   0.733    15   Mar 18  0.987   154   Apr 30   0.25 0.000559
                   Canada  Mar  4   0.167    18   Mar 18  0.968   280   Apr 29   0.80 0.000000
                    Chile  Mar 10   0.450    20   Mar 24  0.978    46   May  1   0.53 0.000002
                    China  Jan 28   0.014   221   Feb 11  0.162   247   Jun 11   0.15 0.000000
                   France  Feb 26   0.333    18   Mar 11  0.995   201   Apr 17   0.66 0.000000
                  Germany  Feb 27   0.667    15   Mar 12  0.899   139   May 26   0.23 0.022587
                Hong-Kong  Mar 14   0.028   106   Mar 28  0.735    34   May 12   0.71 0.000000
                   ISRAEL  Mar 15   0.788    33   Mar 29  0.966   116   Oct 15   0.18 0.002492
                  Iceland  Mar 11   0.951    61   Mar 25  0.735    49   Mar 29  -0.22 0.002069
                   Israel  Mar 15   0.788    33   Mar 29  0.966   116   Oct 15   0.18 0.002492
                    Italy  Feb 24   0.579    19   Mar  9  1.000    85   Apr 27   0.42 0.000000
                    Japan  Mar 10   0.049    82   Mar 24  0.905    21   May 14   0.86 0.000000
              Netherlands  Mar  1   0.550    20   Mar 15  0.879  1095   May 26   0.33 0.000318
              New-Zealand  Mar 17   0.278    18   Mar 31  0.845    71   Apr 28   0.57 0.000007
                   Norway  Mar 10   0.588    17   Mar 24  1.000    16   May  4   0.41 0.007230
                     Oman  Mar 20   0.312    16   Apr  3  1.000    19   May  9   0.69 0.000010
                   Russia  Mar 23   0.925    53   Apr  6  1.000   121   May  5   0.08 0.007938
             Saudi-Arabia  Mar 23   0.640    25   Apr  6  0.887    62   Apr 20   0.25 0.012756
             South-Africa  Mar 27   0.722    18   Apr 10  0.944    54   Jun  4   0.22 0.020123
                    Spain  Mar  1   0.158    19   Mar 15  0.704   405   May 30   0.55 0.000002
                   Sweden  Mar  3   0.692    26   Mar 17  0.972   251   Jun 11   0.28 0.000008
                 Thailand  Mar  3   0.111    36   Mar 17  0.510    51   May  5   0.40 0.000097
                      USA  Feb 29   0.052   116   Mar 14  0.800  7768   Jun 19   0.75 0.000000
                       UK  Feb 16   0.143    21   Mar  1  0.790 19208   Jun 14   0.65 0.000000

                           Onset    |--Before-|   Delay   |--After--|   Last    Delta   Fisher
                 Location  Date     G/(G+D) G+D   Date    G/(G+D) G+D   Sample  G/(G+D)  p-val
            Australia_NSW  Mar  8   0.111    36   Mar 22  0.669   266   May 24   0.56 0.000000
Australia_South-Australia  Mar 16   0.438    16   Mar 30  0.868    53   May  5   0.43 0.001025
       Australia_Victoria  Mar 10   0.125    24   Mar 24  0.627   169   May 17   0.50 0.000003
           Austria_Vienna  Mar 16   0.948    58   Mar 30  0.733    15   Apr  7  -0.21 0.029079
            Belgium_Liege  Mar 15   0.650    20   Mar 29  0.905   116   May 28   0.26 0.005952
         Brazil_Sao-Paulo  Mar  9   0.800    15   Mar 23  1.000    37   Apr 30   0.20 0.020588
           Canada_Ontario  Mar  7   0.467    15   Mar 21  0.955    88   Apr 29   0.49 0.000010
           Chile_Santiago  Mar 10   0.471    17   Mar 24  0.955    22   Apr 30   0.48 0.000872
        Iceland_Reykjavik  Mar 11   0.951    61   Mar 25  0.735    49   Mar 29  -0.22 0.002069
              India_Delhi  Mar 30   0.733    15   Apr 13  0.000    34   May 21  -0.73 0.000000
            India_Gujarat  Apr 26   0.867    30   May 10  0.975   161   Jun 12   0.11 0.022296
        India_Maharashtra  Mar 26   0.316    19   Apr  9  0.917    24   Apr 27   0.60 0.000060
          India_Telangana  Mar 31   0.176    17   Apr 14  0.812   112   Jun  2   0.64 0.000000
   Netherlands_Gelderland  Mar 20   0.667    15   Apr  3  0.984   126   May 26   0.32 0.000129
      Netherlands_Limburg  Mar 27   0.600    15   Apr 10  0.970    33   May 19   0.37 0.002331
 Netherlands_Zuid-Holland  Mar  6   0.750    16   Mar 20  0.952   147   May 14   0.20 0.013659
              Oman_Muscat  Mar 20   0.333    15   Apr  3  1.000    19   May  9   0.67 0.000023
     Spain_Basque-Country  Mar  5   0.188    16   Mar 19  0.939    33   Apr 12   0.75 0.000000
     Spain_Com-Valenciana  Mar 10   0.108    37   Mar 24  0.768    56   Apr  1   0.66 0.000000
         Sweden_Stockholm  Mar  3   0.773    22   Mar 17  1.000    36   Jun 11   0.23 0.005747
   Sweden_Vastra-Gotaland  Mar 25   0.600    15   Apr  8  1.000    35   Jun  9   0.40 0.000315
                   USA_CA  Mar 11   0.059    51   Mar 25  0.652   706   May 21   0.59 0.000000
         USA_CA_San-Diego  Mar 13   0.200    15   Mar 27  0.964    83   May 19   0.76 0.000000
          USA_Connecticut  Mar 14   0.826    23   Mar 28  0.962   183   May 12   0.14 0.023173
              USA_Florida  Mar 13   0.533    15   Mar 27  0.939    33   Apr 30   0.41 0.002156
             USA_Illinois  Mar 14   0.333    18   Mar 28  0.846    26   Apr 18   0.51 0.001068
             USA_Michigan  Mar 13   0.919    37   Mar 27  0.996   499   May 29   0.08 0.002760
            USA_Minnesota  Mar 12   0.478    23   Mar 26  0.895   248   Jun  3   0.42 0.000005
                   USA_NY  Mar  4   0.750    20   Mar 18  0.957   898   May 10   0.21 0.001820
                 USA_Utah  Mar 12   0.588    17   Mar 26  0.968   311   May 12   0.38 0.000004
             USA_Virginia  Mar 11   0.467    15   Mar 25  0.953   299   May 19   0.49 0.000001
                   USA_WA  Mar  7   0.016   184   Mar 21  0.639  1301   May 30   0.62 0.000000
              USA_WA_King  Mar 13   0.025   121   Mar 27  0.755    94   May  5   0.73 0.000000
            USA_WA_Pierce  Apr  8   0.256    43   Apr 22  1.000    45   May  4   0.74 0.000000
         USA_WA_Snohomish  Mar 28   0.108    37   Apr 11  0.971    68   May  6   0.86 0.000000
         USA_WI_Milwaukee  Mar 23   0.120    25   Apr  6  0.542    24   Apr 26   0.42 0.002292
               UK_England  Feb 25   0.100    30   Mar 10  0.807 12147   Jun 14   0.71 0.000000
        UK_England_Exeter  Mar 26   0.588    17   Apr  9  0.910   133   Jun  3   0.32 0.001527
     UK_England_Liverpool  Mar 23   0.500    20   Apr  6  0.880   468   Jun  7   0.38 0.000065
       UK_England_Norwich  Apr  8   0.774    31   Apr 22  0.932   370   May 28   0.16 0.007020
    UK_England_Nottingham  Mar 14   0.143    21   Mar 28  0.788   537   Jun 14   0.64 0.000000
    UK_England_Portsmouth  Mar 30   0.520    25   Apr 13  0.934    91   May 22   0.41 0.000007
     UK_England_Sheffield  Mar 18   0.500    16   Apr  1  0.940   514   Jun  1   0.44 0.000003
      UK_Northern-Ireland  Mar 17   0.250    16   Mar 31  0.910   210   May  1   0.66 0.000000
                 UK_Wales  Mar 12   0.588    17   Mar 26  0.850  3462   Jun  6   0.26 0.008669




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last modified: Sun Jun 14 16:55 2020



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