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This makes her the first person in the country to be infected with the illness twice, amid growing concerns about the virus' spread.
The woman, who is a tour bus guide in her forties and a resident of Osaka in western Japan, tested positive on Wednesday after developing a sore throat and chest pains.
The government's statement said she had first tested positive in late January and was later discharged from hospital after recovering on 1 February.
Speaking in parliament, Health Minister Katsunobu Kato said the central government would need to review patient lists and keep tabs on the condition of those previously discharged.
Currently, the John Hopkins Center for Systems Science and Engineering's online dashboard shows there have been three deaths in Japan and a further four from on board the Diamond Princess cruise ship, docked in Yokohama.
According to the BBC, there have also been reports of patients in China testing positive again after an initial recovery, as health experts analyse implications of contracting the illness for a second time.
Philip Tierno Jr., Professor of Microbiology and Pathology at NYU School of Medicine, told Reuters: "Once you have the infection, it could remain dormant and with minimal symptoms, and then you can get an exacerbation if it finds its way into the lungs."
He said much remained unknown about the virus.
"I'm not certain that this is not bi-phasic, like anthrax," he added, meaning the disease seems to disappear before recurring.
With this summer's Olympic Games in Tokyo looming, Tierno believes officials should consider postponing the major sporting event if the outbreak continues to prove a global issue.
He said: "The Olympics should be postponed if this continues... There are many people who don't understand how easy it is to spread this infection from one person to another."
Dr Babak Ashrafi, from UK-based online doctor Zava, told the Metro: "Because this strain of coronavirus is new, we don't have enough data to understand how long our immunity lasts after initial infection.
"Experts are busy gathering information from those who have become infected to see how well their immune systems react and how long they'll remain immune.
"We do know that when you catch a virus, your body learns how to fight it off. Even after you've fully recovered your body is left with the ability to battle a virus and avoid developing symptoms again. However, like our minds, our bodies can forget over time how to do this and immunity can wear off over time after initial infection."
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