use strict;
use warnings;

my %siteInfo;

while (<DATA>) {
    chomp;

    my @parts = split;
    my $site  = ($siteInfo{"Site$."} = {});

    @{$site}{qw(region country city)} = @parts;
    $site->{totalS5s} = $site->{totalVulns} = ++$site->{totalDevices};
}

my @sorted = sort {
    my $siteA = $siteInfo{$a};
    my $siteB = $siteInfo{$b};

       $siteA->{region} cmp $siteB->{region}
    or $siteA->{country} cmp $siteB->{country}
    or $siteA->{city} cmp $siteB->{city}
    } keys %siteInfo;

for my $site1 (@sorted) {
    my $site = $siteInfo{$site1};
    print "$site->{region},$site->{country},$site1,$site->{totalDevices}, ,$site->{totalVulns},$site->{totalS5s}\n";
}

__DATA__
...