Back in May, when the Ebola virus first crossed over from Guinea into Sierra Leone, among the first to know were staffers working for a US-based charity on a child malnutrition project in the country’s east.

Catholic Relief Services staffers began switching from malnutrition to Ebola prevention when the first cases were confirmed in neighboring Guinea. But with limited resources and knowledge of how to combat the disease, they were outgunned when it came to Sierra Leone.

“It moved from one town to a slightly more major town. Then it was in the next district, where our office is. [We were] watching it creep along,” says CRS country health program manager Meredith Dyson.

“I don’t think that anyone at that point saw where it was going to go or understood the measures that were going to be needed to contain it.”

Now some of the community members that worked on the malnutrition project are dead. CRS’s child nutrition program has been suspended, along with scores of other non-Ebola aid and development projects in Sierra Leone, Guinea, and Liberia – their staff and funds frozen or diverted to the emergency response.

Nearly 4,500 people have died of the Ebola outbreak, virtually of all of them in just three West African countries. At the same time, people are dying of malaria, malnutrition, HIV/AIDS, birth complications, and countless other health problems. Countries are also grappling with low literacy rates, environmental degradation, and hunger.

Still, before the epidemic, generally things were improving, say aid workers. In Liberia, life expectancy rose from 55 years at birth in 2005 to 60.6 in 2013, according to the United Nations Development Fund. Guinea and Sierra Leone also saw improvements in life expectancy over the same period.

Now, if and when Ebola is finally brought under control, that modest progress may have been thrown aside in poor countries that depend almost entirely on foreign aid.

“It’s a big blow,” says Asmare Ayele, country director in Sierra Leone for CARE International, an international aid organization. “Sierra Leone just came out from a 10-year war. It was declared a stable nation at the UN in March.”

Figuring out what is 'essential'

Aid organizations in the region are struggling to balance their desire to keep their projects going with the risk posed to staff and recipients by Ebola.

One major hurdle: Many aid programs depend on gathering people together in one place, which has been banned in the worst affected areas. That means organizations have to think hard about which meetings or events are truly “essential,” says Trevor Hughes, director of risk management and global security for International Relief and Development in Arlington, Va.

He says he would define essential as “everything that you need to have in a society that is somewhat functioning and not going backwards.”

That backward slide has already begun, with warnings of food shortages in some countries. The crops CARE helped support in Sierra Leone have either withered in the fields or in the homes, with no market to bring them to. A CRS malaria program in Sierra Leone is on hold because it’s no longer safe for the community workers to draw blood in the village.

Many existing health programs in West Africa have been retooled to target Ebola directly. HIV/AIDS messaging is now Ebola messaging. Immunization efforts might now be Ebola detection efforts.

But the epidemic has ravaged already weak healthcare systems. According to USAID, only 40 percent of Liberia's public health facilities are operating.

Radio plugs education gap

Still, not all foreign-funded programs have been put on ice. Lisa Hartenberger Toby, an international development specialist with Education Development Center, says their work has expanded. The Massachusetts-based charity does education and health projects around the world, including in Liberia.

Their radio program-based education program, allowing non-traditional students to learn from home, is now being expanded to include primary school age students whose schools have been indefinitely closed.

“It’s always a struggle to make sure [education] is considered as part of the emergency response strategy, not a secondary one,” she says.

Some aid organizations are pushing to restart programs that were suspended, arguing that the epidemic shouldn’t preclude other health interventions. In Sierra Leone, CRS is lobbying the government for the resumption of routine services like immunizations and prenatal care, Ms. Dyson says.

“We really don’t want to lose the gains we’ve made. There’s a lot of [activity] right now to put more focus on those issues.”

Organizations with non-health workers say that they too, are essential, even if they can't help with Ebola treatment. Newly arrived organizations have struggled to penetrate the tight-knit and distrustful communities to teach proper prevention and containment, but those who have been in the country for years have networks and the trust of locals.

While some staff have been evacuated from Ebola-affected countries, others have stayed. Many are in out in the communities getting the word out on prevention, distributing protective equipment, and delivering food and water.

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One of the biggest challenges for organizations is getting workers to admit when it's become too much and they need a break, Mr. Hughes says.

"This is going to be a long-term thing and there is always too much work to do," he says. “It’s extraordinarily demoralizing to reach the end of your tether and get on an airplane and fly home… You see what you left behind and it’s not going to end anytime soon.”