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An injury-time strike by Erleta Memeti propelled 100th-ranked Kosovo to nine points from three matches and gave them their second title in a row.
The image of the flag with the message "we do not surrender" in Serbian went viral when it was shared by Kosovo minister Hajrulla Ceku.
England can clinch qualification for the finals with a win away to the Czech Republic in their next game on Oct. 11.
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