COVID-19 in South Sudan: Do you leave, or do you stay?

Sweat, fear, perseverance. Epidemiologist Laura shares a fly-on-the-wall account of how a team more accustomed to malaria and malnutrition took on the pandemic.

Laura and members of the MSF team in Juba, South Sudan

“So we’re all here together for this, right? If we stay as a team, we can manage.”

I was three weeks into my first assignment with Médecins Sans Frontières / Doctors Without Borders (MSF) as Epidemiology Activity Manager, sitting in the Country Director’s office with the rest of the coordination team. We were in Juba, the capital of South Sudan.

It was early March, 2020. We had gathered together for a meeting to plan for “contingency measures” and what would classify as the different phases of what we could assume would happen in the coming months.

At the time of the COVID-19 outbreak there was no ICU capacity in the country, even in the capital city

Pandemic had just been declared. Europe was in uproar as cases and deaths began to skyrocket from a disease that no one knew much about, and people “believed in” even less.

COVID-19 had come to most every country and every continent, though no confirmed positive patient had been declared in South Sudan - yet. The realities of how this would look for the people of South Sudan, as well as for us as a medical organization, were still very uncertain.

The context

South Sudan’s health care system is quite weak even in the most stable of times. MSF is one of the largest health care providers in the country, providing essential treatments for malaria, malnutrition, respiratory infections, war wounds, and a host of tropical or neglected diseases ranging from the common (measles, meningitis) to the rare (kala azar, yellow fever).

MSF is also responsible for providing access to safe deliveries for mothers, medical services to survivors of sexual violence, and many other such services. The work is broad and needed everywhere.

All these supplies that were being discussed as “the” ways to combat COVID-19 medically, were simply not possible here

Stories from countries with larger outbreaks early on were of overflowing intensive care units (ICUs), with ventilators and oxygen needed to keep patients alive. In South Sudan, with most healthcare coming from foreign NGOs, ensuring even the basics of healthcare can be challenging, both in terms of medical tools and the workforce to support it.

At the time of the COVID-19 outbreak there was no ICU capacity in the country, even in the capital city of Juba. There were zero beds available for any “severe” patients, a shortage of oxygen, and absolutely no ventilators, or respiratory therapists who would know how to work them.

After weeks of scrambling, the national laboratory was able to procure supplies for what amounted to about 200 COVID-19 tests, for a country of 11 million people.

All these supplies that were being discussed internationally as “the” ways to combat COVID-19 medically, were simply not possible in South Sudan.

Furthermore, the preventative measures of social distancing, working from home, masking and hand hygiene were likewise not at all possible in a country where most people live with their whole family in one-room dwellings, and live hand to mouth.

How were people to eat if they were to “stay home”? As for hand hygiene and masking – where were people supposed to get this water from, with so many already facing water scarcity and difficulties of access, and no money for luxuries like soap or mask?

Even the extra water needed to wash one’s face-masks would be a luxury that was out of reach for most.


The whiteboards with the different projects and staff mapped out

The plan

In this COVID-19 planning meeting, we got a print-out of the names of every senior staff member across each of our projects and taped them to magnets. Then we got two whiteboards. On one we drew out the criteria for the different “phases” of the COVID response: phase 1,2,3.

In phase one all projects would continue operating mostly as normal.

Phase two would be a large scale-down or closure of projects depending on personnel. Meaning the loss or reduction of access to healthcare for thousands of people, at a time when it would be needed most.

In the short time we were in that meeting, the wider situation in South Sudan shifted

Phase three would be large-scale closures with only a skeleton team remaining. A “skeleton team” would be comprised of perhaps 1-2 key coordination people keeping track of things on the ground, but likely little to no medical activities occurring, and many of our local staff being out of work for some time.

So, what would constitute the transition through these phases?

Mass human resource gaps with large exoduses of international staff or loss of local staff, international border closures, inability to receive personal protective equipment (PPE) such as masks, inability to receive essential medical tools, martial law, and many other factors that we suspected could happen.

The shift

While we were mapping this out on the whiteboard, text messages and emails were coming in. We read them aloud to each other, each one sparking a new discussion and a new set of concerns.

“All international borders around South Sudan are now closed”.

With most food coming in from other countries such as Uganda and Kenya, how would the price or access to food, fuel and other essential items be impacted? Would MSF become a target for looting if this got bad enough?

“Oh this one is saying flights out of Juba unlikely after the coming days.”

If international staff wanted to go home, this would now be quite difficult, what about medical evacuation if a staff member gets COVID, or even breaks their leg? The quality of care simply could not be verified. It meant that international staff who were here – would need to be ready to stay for the foreseeable future.

“I just received an email from HQ – With the global shortages of PPE it will be difficult to ensure an adequate supply to South Sudan for all of our health care workers.”

With border closures and global shortages, where would these essential supplies come from, how could MSF continue providing care for patients when it would be so dangerous to the staff to do so?

“This WhatsApp message says the President will likely be declaring a state of lockdown this evening.”

How would people work, how would  they have money for food, and furthermore how would that then impact security? What would this mean for our own staff coming to work and providing care to those who need it? Would they be able to move around and get to the hospitals or health facilities in a safe way?

In the short time we were in that meeting, the wider situation in South Sudan shifted, with the criteria moving from phase one, to phase two, to phase three. Reactions to the disease were much the same as other places in the world, but the repercussions for these in South Sudan were the true fear.

The question

It was at that moment that our Deputy Country Director – whiteboard marker in one hand and cell phone in the other, turned to the team and asked the question.

“We’re all here together for this right? If we stay as a team, we can manage this.”

He went around the room as one by one the team said, yes… we are here for this.

“Staggering gaps”

In the following months there was a mass exodus of senior staff who were from outside of South Sudan. Within my team alone of the 112 senior positions held largely by international staff, there was 68 gaps, with only six new staff able to enter the country in the four months following that day in early March.

Activities and medical care were maintained and managed by the many excellent South Sudanese staff within the projects. However, the gaps in personnel were staggering, especially in the medical team – as many had returned to their countries of origin to assist in their own countries COVID responses.

Working under tough conditions is what we signed up for. However, sometimes there is a limit, and for many this was one...

Other international staff left due to pre-existing conditions that made them high risk. Some feared being stuck in South Sudan with no way home anytime soon. For some it was a natural limit of “it is simply not where I want to be for this”.

At an unprecedented time in global history, it made sense to return to loved ones and home, for the uncertain period ahead.  

For those in MSF, working under tough conditions or in uncertain settings is expected, this is what we signed up for in fact. However sometimes there is a limit, and for many this was one.

In addition to the staffing gaps left by departing international staff, the pandemic had consequences for our local staffing too. Due to the fears of COVID-19 on public transportation or because of expected large-scale community transmission, several local staff positions were also downsized and people were asked to remain at home, or only work part time (with pay) until it was safer to return to work.

Three or four jobs per person

Though the remaining team members, both South Sudanese and international, worked hard to manage the work of continued access to healthcare, the result of these gaps was that many members of the team had to take on the jobs of 2-3 other people.

A first-assignment learning and development staff member was left to act as the HR Coordinator, with only one administrator assisting during a time of very complex movements and continually changing rules and safety measures.    

The team stayed to care for the war-wounded patients, and the many malnourished and malaria-sick children...

A nurse from the Medical Academy, a section of MSF specifically focused on teaching and building capacity of medical personnel in the project locations, resigned to take on the very needed role of medical team leader in one of the project sites. While there she also took on the responsibilities of three other senior medical supervisory positions. 

Commitment, ability, strength

One emergency project usually dealing with conflict, malnutrition or flooding, was left with too few medical personnel to cover the senior roles in an already difficult context. The solution was to move into “remote management”, relying on the dedicated local staff to run the project with only off-site managerial support.  

When conflict hit the area a few weeks after remote management was implemented, the team stayed to care for the many war-wounded patients, and provide support for the many malnourished and malaria sick children in the area.

Enough of a team remained in place to keep operations running. This meant women still had access to safe and assisted births, children were still able to receive life-saving vaccinations...

This strategy was a testament to the commitment, ability, and strength of MSF’s local staff. As one silver lining, I personally hope this can serve as an example to future projects and operational plans.

Stress and fear

Though the response never did escalate to “phase 3”, there were many challenges ahead.

Through the gaps enough of a team remained in place to keep operations running. This meant women still had access to safe and assisted births, children were still able to receive life-saving vaccinations, the thousands of children per month that contract malaria were still treated.

The continuity of these essential services was of utmost importance above “responding to COVID”, though many of the team were reading reports and warnings from the World Health Organization and others warning of the “severe impact COVID could have in Sub-Saharan Africa due to the other co-morbidities in the region”.

You still see death tolls, of any type of morbidity, and think “but these are still people, how can we reach them all?”

Fears that years of malnutrition or COVID-19 in malaria-endemic areas would have a staggering impact on fatality rates. MSF had to make a decision and in the context of South Sudan, and after much analysis it was determined that the loss of life would be much higher from these other health concerns than from what was expected for COVID-19.

In providing these essential services however, staff often had to go to work with not enough PPE to protect them should a COVID-19 case come in, and little ability to treat patients or staff should they fall critically ill due to the limitations of healthcare in the country. The reality of the global lack of PPE had not changed, and the borders were still closed – for the foreseeable future.  It was a constant battle of “duty of care”. I was present in meetings where the stress and fear were palpable, where discussions of how to treat patients, let alone protect staff, was debated in frenzied terms.

My role

As an epidemiologist I would love to write about how in this moment I was able to use my training to shine, of all the things I was able to contribute to the response in South Sudan. But making calculations with not a lot of information, and based on not a lot of data (as we were constantly learning more and more about this disease), to determine the type and extent of a response to a global pandemic is something no one feels totally comfortable to do.

I questioned all my work, my numbers, my estimates. You still see death tolls, of any type of morbidity and think “but these are still people, how can we reach them all?”

I was still able to do my part. I was able to make detailed projections for our projects, and risk assessments for importation and transmission through different areas of the country.


Laura and David Gama, MSF Data Processing Officer

This information was used to prioritize this scarce PPE to the areas most in need, and allow for shifting of our healthcare staff to areas where they could have the biggest impact.

I was also able to conduct large-scale health facility assessments and community leader interviews in Juba – where MSF does not currently provide healthcare services. This helped us learn about barriers to health care access in Juba, how they had been exacerbated by COVID-19, and the real impact this was having on the local people.

“Surveillance” is the term epidemiologists use for tracking cases of a disease, and constraints to an effective surveillance system for COVID-19 abounded. A lack of testing kits, lab equipment that was prone to breakdowns, alert systems that people were both afraid to call and also didn’t believe would be answered if they did.

I feel honored to have been part of the global response to COVID-19.

These issues were all secondary to the fear, mistrust and rumors that abounded within communities, making the real impact of COVID-19 in the country all but untraceable.

I don’t think we will every really know how many people fell sick or died from COVID-19 in South Sudan, but I can hope that MSF and my part of this team did our part to at least reduce any extra deaths from lack of access to healthcare.

One small part

After nine months of hard work, my assignment here is soon coming to an end. While reflecting on my activities and some of the stories, I come to really appreciate my amazing colleagues I was able to work beside in a time where all we had was each other to hold on to. They had such an impact on me personally and professionally, and I hope I can return to them again someday here in South Sudan.

I also reflect on the work done, the piece each of us play doing our part, the small things we can do that can have a large impact. Of course, with this comes many feelings of “what could I have done better?”, or “if only I knew then what I know now”, but I think these feelings are normal, especially when a response is far from perfect.  

I come to really appreciate my amazing colleagues I was able to work beside in a time where all we had was each other to hold on to

I feel honored to have been part of the global response to COVID-19. Though I was one small part, I do feel like I was able to offer and bring a vital service to South Sudan at a time when, so few people were able to.

That question that was asked of me in that meeting in March still comes back to me from time to time… will you stay?

In the moment it was asked I was terrified, there were many moments after in which I was so frustrated I doubted my decision.

Through the ups and downs of these last months, I can honestly say I am so glad that I said “yes”.


Read more: Stories about the COVID-19 response

COVID-19 in South Sudan: "We can do this, together"

South Sudan: "This is what we signed up for"