diff --git a/lib/db/install.xml b/lib/db/install.xml
index a26be81259d..b64a07fa29c 100644
--- a/lib/db/install.xml
+++ b/lib/db/install.xml
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8" ?>
-<XMLDB PATH="lib/db" VERSION="20161119" COMMENT="XMLDB file for core Moodle tables"
+<XMLDB PATH="lib/db" VERSION="20170207" COMMENT="XMLDB file for core Moodle tables"
     xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
     xsi:noNamespaceSchemaLocation="../../lib/xmldb/xmldb.xsd"
 >
@@ -545,8 +545,9 @@
         <KEY NAME="primary" TYPE="primary" FIELDS="id"/>
       </KEYS>
       <INDEXES>
-        <INDEX NAME="useridto" UNIQUE="false" FIELDS="useridto"/>
         <INDEX NAME="useridfromtodeleted" UNIQUE="false" FIELDS="useridfrom, useridto, timeuserfromdeleted, timeusertodeleted"/>
+        <INDEX NAME="useridfrom_timeuserfromdeleted_notification" UNIQUE="false" FIELDS="useridfrom, timeuserfromdeleted, notification"/>
+        <INDEX NAME="useridto_timeusertodeleted_notification" UNIQUE="false" FIELDS="useridto, timeusertodeleted, notification"/>
       </INDEXES>
     </TABLE>
     <TABLE NAME="message_read" COMMENT="Stores all messages that have been read">
@@ -573,9 +574,10 @@
         <KEY NAME="primary" TYPE="primary" FIELDS="id"/>
       </KEYS>
       <INDEXES>
-        <INDEX NAME="useridto" UNIQUE="false" FIELDS="useridto"/>
         <INDEX NAME="useridfromtodeleted" UNIQUE="false" FIELDS="useridfrom, useridto, timeuserfromdeleted, timeusertodeleted"/>
         <INDEX NAME="notificationtimeread" UNIQUE="false" FIELDS="notification, timeread"/>
+        <INDEX NAME="useridfrom_timeuserfromdeleted_notification" UNIQUE="false" FIELDS="useridfrom, timeuserfromdeleted, notification"/>
+        <INDEX NAME="useridto_timeusertodeleted_notification" UNIQUE="false" FIELDS="useridto, timeusertodeleted, notification"/>
       </INDEXES>
     </TABLE>
     <TABLE NAME="message_contacts" COMMENT="Maintains lists of relationships between users">
diff --git a/lib/db/upgrade.php b/lib/db/upgrade.php
index 20e304f71cc..edd29a24de4 100644
--- a/lib/db/upgrade.php
+++ b/lib/db/upgrade.php
@@ -2465,5 +2465,65 @@ function xmldb_main_upgrade($oldversion) {
         upgrade_main_savepoint(true, 2016122800.00);
     }
 
+    if ($oldversion < 2017020200.01) {
+
+        // Define index useridfrom_timeuserfromdeleted_notification (not unique) to be added to message.
+        $table = new xmldb_table('message');
+        $index = new xmldb_index('useridfrom_timeuserfromdeleted_notification', XMLDB_INDEX_NOTUNIQUE, array('useridfrom', 'timeuserfromdeleted', 'notification'));
+
+        // Conditionally launch add index useridfrom_timeuserfromdeleted_notification.
+        if (!$dbman->index_exists($table, $index)) {
+            $dbman->add_index($table, $index);
+        }
+
+        // Define index useridto_timeusertodeleted_notification (not unique) to be added to message.
+        $index = new xmldb_index('useridto_timeusertodeleted_notification', XMLDB_INDEX_NOTUNIQUE, array('useridto', 'timeusertodeleted', 'notification'));
+
+        // Conditionally launch add index useridto_timeusertodeleted_notification.
+        if (!$dbman->index_exists($table, $index)) {
+            $dbman->add_index($table, $index);
+        }
+
+        $index = new xmldb_index('useridto', XMLDB_INDEX_NOTUNIQUE, array('useridto'));
+
+        // Conditionally launch drop index useridto.
+        if ($dbman->index_exists($table, $index)) {
+            $dbman->drop_index($table, $index);
+        }
+
+        // Main savepoint reached.
+        upgrade_main_savepoint(true, 2017020200.01);
+    }
+
+    if ($oldversion < 2017020200.02) {
+
+        // Define index useridfrom_timeuserfromdeleted_notification (not unique) to be added to message_read.
+        $table = new xmldb_table('message_read');
+        $index = new xmldb_index('useridfrom_timeuserfromdeleted_notification', XMLDB_INDEX_NOTUNIQUE, array('useridfrom', 'timeuserfromdeleted', 'notification'));
+
+        // Conditionally launch add index useridfrom_timeuserfromdeleted_notification.
+        if (!$dbman->index_exists($table, $index)) {
+            $dbman->add_index($table, $index);
+        }
+
+        // Define index useridto_timeusertodeleted_notification (not unique) to be added to message_read.
+        $index = new xmldb_index('useridto_timeusertodeleted_notification', XMLDB_INDEX_NOTUNIQUE, array('useridto', 'timeusertodeleted', 'notification'));
+
+        // Conditionally launch add index useridto_timeusertodeleted_notification.
+        if (!$dbman->index_exists($table, $index)) {
+            $dbman->add_index($table, $index);
+        }
+
+        $index = new xmldb_index('useridto', XMLDB_INDEX_NOTUNIQUE, array('useridto'));
+
+        // Conditionally launch drop index useridto.
+        if ($dbman->index_exists($table, $index)) {
+            $dbman->drop_index($table, $index);
+        }
+
+        // Main savepoint reached.
+        upgrade_main_savepoint(true, 2017020200.02);
+    }
+
     return true;
 }
diff --git a/message/output/popup/db/install.xml b/message/output/popup/db/install.xml
index e915f8fc3e6..6a92e563b01 100644
--- a/message/output/popup/db/install.xml
+++ b/message/output/popup/db/install.xml
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8" ?>
-<XMLDB PATH="message/output/popup/db" VERSION="20160729" COMMENT="XMLDB file for Moodle message/output/popup"
+<XMLDB PATH="message/output/popup/db" VERSION="20161221" COMMENT="XMLDB file for Moodle message/output/popup"
     xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
     xsi:noNamespaceSchemaLocation="../../../../lib/xmldb/xmldb.xsd"
 >
@@ -15,6 +15,7 @@
       </KEYS>
       <INDEXES>
         <INDEX NAME="messageid-isread" UNIQUE="true" FIELDS="messageid, isread"/>
+        <INDEX NAME="isread" UNIQUE="false" FIELDS="isread"/>
       </INDEXES>
     </TABLE>
   </TABLES>
diff --git a/message/output/popup/db/upgrade.php b/message/output/popup/db/upgrade.php
index ae50d394ab8..a0b031b85a4 100644
--- a/message/output/popup/db/upgrade.php
+++ b/message/output/popup/db/upgrade.php
@@ -74,5 +74,20 @@ function xmldb_message_popup_upgrade($oldversion) {
     // Automatically generated Moodle v3.2.0 release upgrade line.
     // Put any upgrade step following this.
 
+    if ($oldversion < 2016122100) {
+
+        // Define index isread (not unique) to be added to message_popup.
+        $table = new xmldb_table('message_popup');
+        $index = new xmldb_index('isread', XMLDB_INDEX_NOTUNIQUE, array('isread'));
+
+        // Conditionally launch add index isread.
+        if (!$dbman->index_exists($table, $index)) {
+            $dbman->add_index($table, $index);
+        }
+
+        // Popup savepoint reached.
+        upgrade_plugin_savepoint(true, 2016122100, 'message', 'popup');
+    }
+
     return true;
 }
diff --git a/message/output/popup/version.php b/message/output/popup/version.php
index 5d39cce018f..3313805cb1c 100644
--- a/message/output/popup/version.php
+++ b/message/output/popup/version.php
@@ -24,6 +24,6 @@
 
 defined('MOODLE_INTERNAL') || die();
 
-$plugin->version   = 2016120500;        // The current plugin version (Date: YYYYMMDDXX)
+$plugin->version   = 2016122100;        // The current plugin version (Date: YYYYMMDDXX)
 $plugin->requires  = 2016112900;        // Requires this Moodle version
 $plugin->component = 'message_popup';  // Full name of the plugin (used for diagnostics)
diff --git a/version.php b/version.php
index a7955651778..35b002a4dec 100644
--- a/version.php
+++ b/version.php
@@ -29,7 +29,7 @@
 
 defined('MOODLE_INTERNAL') || die();
 
-$version  = 2017020200.00;              // YYYYMMDD      = weekly release date of this DEV branch.
+$version  = 2017020200.02;              // YYYYMMDD      = weekly release date of this DEV branch.
                                         //         RR    = release increments - 00 in DEV branches.
                                         //           .XX = incremental changes.