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The 14-year-old died in Azerbaijan capital of Baku on January 28. His cousin died from bird flu during an outbreak last year.
The Azeri health ministry said in a statement the sample tested negative for bird flu, citing results from a test conducted by a World Health Organisation laboratory in London.
Earlier tests by an Azeri laboratory were also negative and showed the boy died from an acute form of pneumonia.
The H5N1 bird flu virus is known to have infected 270 people and killed at least 164 worldwide since 2003, most of them in Asia, and more than 200 million birds have died from it or have been killed to prevent its spread. Reuters