Thus far, 221 people have died and 13,921 have been infected, according to the Ministry of Health.
"All the factors that cause cholera remain unaddressed: poverty, deficient sanitary services, lack of drinking water," Umaro Ba, head of the cholera unit at the capital Bissau's Simao Mendes hospital, told IRIN. "And more importantly in the future we need to put in place a strong prevention programme."
At the epidemic's peak in the final week of September, 1,376 new cholera cases were registered and 19 people died, according to the ministry of health, but from 9 to 16 November just 128 new cases and no deaths were reported.
Medical NGO Médecins Sans Frontières-Spain (MSF) is dismantling the tents it set up beside the hospital to isolate and treat cholera victims, and plans to leave the country in the coming weeks.
Why the drop
A decrease in cholera cases is partly due to the end of the rainy season, according to Ba, as the disease is spread by bacteria in contaminated water.
The strong mobilisation from UN agencies, communities, local and international NGOs and donors also helped contain the disease, according to Johannes Mooij, technical adviser at the Simao Mendes hospital.
"This year, we had MSF providing support and UN agencies supplying medicines. This made a clear difference," he said.
But while international agencies were swift to commit resources and expertise to contain the epidemic, Guinea-Bissau personnel were slow to organise, lacking the training and skills to coordinate a response in the early stages, according to Daniel Remartinez, MSF emergency coordinator.
Speed is crucial when stamping out cholera as it is easily treatable if people access proper treatment quickly, he said.
In Antula, one of Bissau's poorest neighbourhoods, the number of cholera cases shot up because locals were sifting through contaminated rubbish. "This could have been avoided if people had simply burned their rubbish," Ba explained. But he said the authorities never coordinated and sent the message out.
"In future we need to be able to quickly mobilise all the necessary personnel once the first case is declared," Ba said.
Source still unknown
After months of battling the epidemic, experts know little about its initial source as Guinea-Bissau has weak epidemiological surveillance capabilities, according to hospital adviser Mooij.
Health Ministry officials say cholera broke out in May in the southern region of Tombali, but they still do not know how it spread to the capital, home to the highest number of victims.
Nor do epidemiologists understand why the isolated Bijagos Islands had the highest per capita caseload.
The US Centers for Disease Control and Prevention (CDC) is studying into the disease's spread across the country.
Preventing future outbreaks
Health Ministry epidemiologist Augostino Betunda is frustrated that past cholera lessons have not been heeded.
At the height of the 2008 outbreak he told IRIN: "After the 2005 cholera outbreak we.made many recommendations to the government [on preventing future outbreaks].but none of them were ever implemented, and so we are left to start all over again."
Government officials are not used to planning big prevention efforts, Mooij said. "Prevention is difficult here. There are no planning capabilities. The government waits for the cholera outbreak before it disinfects and cleans the streets."
"To efficiently fight cholera in the future, we will need future governments to exhibit strong leadership," he added.
In the run-up to Guinea-Bissau's 16 November parliamentary elections many politicians promised to improve access to safe drinking water. Cholera expert Ba said new leaders must live up to their promise. "The politicians' words now need to be turned into reality."