This seemed like a interesting mental exercise. Here's my take:

#!/usr/bin/env perl

use 5.010;
use strict;
use warnings;

my (%incl, %excl);

while (<DATA>) {
    my ($id, $loc_list) = split;
    my @locs = split /,/ => $loc_list;
    @{$incl{$id}}{@locs} = (1) x @locs;
}

for my $in (keys %incl) {
    for my $ex (keys %incl) {
        $excl{$in}{$ex} = [ grep { ! $incl{$ex}{$_} } keys %{$incl{$in
+}} ];
    }
}

say join qq{\t} => q{ID}, sort(keys %incl);

for my $id (sort keys %incl) {
    say join qq{\t} => $id, map { scalar @{$excl{$id}{$_}} } sort keys
+ %incl;
}

__DATA__
Name1  USA,Canada,Yemen 
Name2  Canada,Portugal,India
Name3  China,HongKong,Canada
Name4  London,Amsterdam,Ireland,USA
Name5  India,USA,Canada
[download]

Output:

ID      Name1   Name2   Name3   Name4   Name5
Name1   0       2       2       2       1
Name2   2       0       2       3       1
Name3   2       2       0       3       2
Name4   3       4       4       0       3
Name5   1       1       2       2       0
[download]