Now, week after week, up to a few dozen new people are appearing on the World Health Organization's weekly report on the situation in West Africa. And public health officials are racing to find out what's driving these pockets of Ebola transmission.
Sierra Leone's chief medical officer, Brima Kargbo, diagnosed part of the problem as an inability to convince some people to not seek treatment from local healers.
“The challenge that we have is that we continue to see people escaping from quarantined homes and move from Kambia to Port Loko and from Port Loko to the Western areas," Kargbo told Voice of America. In recent days, Kargbo said, "we have seen an increasing number of cases in Port Loko and Kambia because people escaped from quarantined homes and they were taken to an herbalist."
He added: "This is how the disease started spreading."
Since the outbreak began in 18 months ago,
The United Nations' Ebola chief said this month that he expects health officials in Sierra Leone might be able to get to zero in a matter of weeks. But in Guinea, David Nabarro told the Associated Press, the challenges are greater, with surprise cases surfacing beyond the known chains of transmission.
"Getting on top of this is difficult,” Nabarro told the AP. “It’s like looking for needles in haystacks — very hard to find the people who are ill and get them under treatment quickly before they perhaps infect others."
Essentially, bringing Ebola to a complete halt is simple public health: Find out who is sick and who those people have been in contact with and monitor all of those people for the full incubation period.
It's a formula Liberia successfully deployed -- eventually in 100 percent of its cases.
But in practice, it's harder than it sounds.
In Guinea, the rising number of cases reflects newly discovered sick people or bodies of people who likely died of Ebola. In many cases, no one knows how they got sick, or who they contracted the virus from and how many other people they may have sickened.
That's a huge problem, said Daniel R. Lucey, a senior scholar with the O'Neill Institute for National and Global Health Law at Georgetown University.
"Someone found dead of Ebola means they've been sick and contagious for certainly quite a few days or quite a few weeks," Lucey -- who treated Ebola patients in West Africa at the height of the epidemic -- told The Washington Post from Conakry, Guinea, this week.
"What the data are telling us, especially from Guinea, is that for as many weeks as I can remember, Guinea has had patients who have been found dead in the community and they turn out to have had Ebola," he said. "Patients who are alive and are diagnosed with Ebola ... they're not on any contact tracing lists. As long as that continues, there are chains of transmission of Ebola virus that we don't know about."
In Guinea in particular, cases are popping up in widely dispersed geographical areas -- some of which are difficult to reach. But more importantly, there's a desperate need for interventions in these communities to be tailored to cultural and social norms.
Public health professionals and community members need to work diligently to establish, maintain and re-establish trust among Guineans if there have any hope of bringing Ebola under control, Lucey said.
Key evidence of a need for more culturally responsive intervention is the continuing practice of unsafe burials. The WHO reported 19 unsafe burials in Guinea in the week that ended June 7. And though none were reported in Sierra Leone, the WHO noted that there is "clear evidence that they are still taking place in some areas."
In Liberia, where Ebola was completely eradicated, the government finally stopped the deadly disease in part by requiring all bodies to be burned for a period of time at the height of the epidemic. In virtually every cultural practice, forced cremation is controversial.
“Cremation is not our culture,” Tolbert Nyensuwah, head of Liberia's Ebola task force, told the Guardian in January. "It was due to necessity that we had to cremate people, but it worked very well."
Soon, there will be another problem that could make stopping the virus even harder: Weather, which will make it even more difficult to travel to far-flung communities to investigate new Ebola cases.
"The rainy season is here, but it's going to be more rainy next month," Lucey said from Guinea's capital. "So it gets harder to do contact tracing. It will make it substantially more difficult to get to zero."
Could Ebola come roaring back? It's possible, though it's more likely that the virus will seep into the bones of the two countries, becoming endemic.
But the U.N.'s Nabarro said he was certain Ebola would be eradicated -- eventually.
"It can be done," he said. "I'm utterly confident it will be done. I just can't tell you how long it will take."