The Japanese encephalitis virus is “very unlikely” to be eliminated from Australia after an unprecedented outbreak in four states, the Commonwealth deputy chief medical officer says.

Two deaths and 16 other cases of Japanese encephalitis have now been confirmed across NSW, Victoria, Queensland and SA, including a four-month-old baby who was infected around Lake Hume on the Murray River.

The Federal Government last week launched a $69-million response to the mosquito-borne virus, including vaccinating piggery workers and their families, as well as expanding mosquito surveillance.

Speaking on Friday, deputy chief medical officer Dr Sonya Bennett said the funding was for “the short-term response” and the government was planning for ongoing management of the virus.