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Repressions continued under a second Soviet occupation that replaced the 1941-1944 Nazi occupation. An attempt to restore the Republic of Estonia was suppressed by the Red Army on 18.-22. September 1944 and most members of a newly formed Estonian Government were arrested. Some were later shot while others were imprisoned and sent to Siberia. During 1944-1945, some 10.000 Estonian people were imprisoned and most died in less than two years. According to sources, 25.000-30.000 people were transported to labor and prison camps during 1944-53 and 11.000 did not return. The fear of Communist terror forced 70.000 Estonians to flee the country and only a handful of refugees later returned to Soviet-occupied Estonia. Some 10% of refugees never reached their destination. The gravest shipwreck of the Baltic Sea dates from 22. September 1944 when refugee ship Moero with 2300-2700 persons on board was sunk by Soviet air force. According to Soviet data, more than 2000 Estonian „forest brother" resistance fighters were killed during 1944-53 and 9870 were arrested; half of the latter were later shot or died in camps. The last known resistance fighter died in a shootout with security forces in 1978. On 25. March 1949, simultaneous mass deportations were carried out in Estonia, Latvia and Lithuania to suppress resistance and induce the creation of collective farms. At least 20.072 Estonians were deported to Siberia for life, most of them women, children and the elderly. Of 23.000 persons deported after the war, some 3000 perished. All ethnic Germans remaining in Estonia after the war were deported and deportations also targeted religious groups such as Jehovah's Witnesses.
After restoring the Soviet rule, Estonia's economy was fully nationalized. In addition, peasant farmers were forced into collective farms in 1949, delivering a heavy blow to agricultural production and rural life in general. Estonian culture fell under strong pressure. During the 1950-51 campaign against „bourgeois nationalists", thousands of cultural workers, researchers and teachers lost their job. Estonia's independent cultural life was virtually frozen.