In total, 41 people in Wuhan have been diagnosed with a novel coronavirus, a family of viruses that can cause both the common cold and more severe diseases like SARS and MERS.
The 69-year-old man had been admitted to hospital with abnormal renal function and severe damage to multiple organs, the Wuhan municipal health commission announced. As of late Thursday, 12 patients have been cured and discharged and five were being treated for acute conditions.
In Wuhan 763 people have been put under observation after coming into close contact with known patients, health authorities have said.
No human-to-human transmission of the virus behind the Wuhan outbreak has been confirmed so far, but the health commission has said the possibility "cannot be excluded".
After the second death was reported, online discussion spread in China over the severity of the Wuhan coronavirus - and how much information the government is hiding from the public.
The first confirmed fatality was a 61-year-old man in Wuhan who died of pneumonia after testing positive for the virus.
"This is the first domestic discovery of a pneumonia case related to the new coronavirus", the ministry said in a statement.
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The man in Japan said he did not visit the market, leaving it unclear how he got the virus. The market has since been shut down for investigation and disinfection.
Two patients in Thailand and another in Japan have been diagnosed with the virus.
The Chinese woman, 74, had been quarantined since her arrival on Monday and was found to be infected with the newly identified coronavirus, said Mr Sukhum Karnchanapimai, permanent secretary of the Public Health Ministry.
The woman diagnosed in Thailand had not reported visiting the seafood market, the World Health Organization said on Tuesday.
The Japanese man developed a fever and cough on January 3 while in Wuhan, returned to Japan on January 6, and was hospitalized four days later as the symptoms persisted, with his X-ray image showing signs of pneumonia, the Japanese Ministry of Health, Labor and Welfare said Thursday. He has since been released from the hospital after his condition improved.
The Wuhan health commission said one man who had been diagnosed worked at Huanan Seafood Wholesale Market, but his wife, who also had the virus, reported "no history of exposure" at the facility.