IoS Appeal: The civil war has ended – now the war on disease has begun

In the southernmost town of South Sudan, the world's newest country, a hospital backed by the charity Merlin provides healthcare that gives patients real hope of survival

A doctor and nurse clad in green scrubs dash out of an operating theatre carrying what looks like a heap of cloth. As they gingerly place the bundle on a table outside, a fold of material falls back to reveal the face of a baby girl, seconds old and still covered in amniotic fluid.

Struggling to breathe, she has been delivered by caesarean section. Thick mucus blocks her mouth and nose. The nurse begins to pump out the girl's nostrils, until her airways clear and the tiny body splutters with life.

The scene is a familiar one in Britain, but in South Sudan, where a woman has more chance of dying in childbirth than going to secondary school, hospital deliveries of any kind are a rarity. That the hospital in question is fully equipped with trained staff is even more remarkable.

The hospital is in Nimule, the southernmost town in South Sudan. It is being supported by the the medical relief charity Merlin – the subject of this year's Independent on Sunday appeal. Next week, the youngest country in the world will have existed for six months, but South Sudan has a long wait for a health system it can celebrate. After more than two decades of civil war during which it was part of Sudan, it has almost no home-grown doctors and nurses and its clinics are in disarray.

Nurse Jane Kalike, who delivered the girl, says both mother and baby are lucky to be alive. "Imagine what's happening in other areas where there's no access to help. I don't think they would have made it alone."

The baby's mother, Betty Cunyua, 30, from Nimule, is next door being carefully stitched up after the operation. She had been in labour for 24 hours when the doctor opted to perform a caesarean. The baby was in breech, with a racing heartbeat, and Betty's blood pressure had rocketed.

In South Sudan, giving birth often carries the risk of death: one in seven women dies in childbirth, largely because more than 90 per cent of all mothers deliver at home. There are fewer than 10 diploma-holding midwives in the whole country, according to the UN, and that means the most likely person to be at an expectant mother's bedside is an illiterate, untrained traditional birth attendant.

At Nimule, the facilities are basic but the tools are sterilised; the staff are trained, and the rooms are clean. This is helping it to defy national statistics. Of the 2,000 deliveries here in 2011, only one mother died in childbirth – and that was from suspected cancer of the uterus.

The day after Betty gave birth, a malaria test revealed she had unwittingly been suffering from the disease and had passed it on to her baby. In the ward, both of them are now in the grip of a fever. "The baby is feeling so weak and I'm not feeling OK," she whispers, as beads of sweat show on her forehead.

It is yet another hurdle, but the doctors know that, in hospital, the pair are almost certain to survive. Both are put on a quinine drip and, by the next day, they are already looking better. Betty is sitting up and thinking about the future. "After a week we will discuss a name with elders," she says of her unnamed daughter.

The most publicised deaths in South Sudan have been the thousands killed in the conflict with Sudan in the north, but these figures are tiny compared with the numbers who perish every year because of the lack of basic healthcare. The Merlin charity is working here in the hope that it can make stories of survival like Betty's less of a rarity.

Dr David Nyumba Sylvester, medical director at Nimule hospital, said: "The health system here is really bad. There's very limited coverage. Take this hospital: you have to go all the way to Juba before you get to another hospital – and that's four hours away. There are various places with facilities, but the medical personnel are often not qualified."

Dr Sylvester is one of a handful of doctors who qualified during the war when the university in Juba was moved north to Khartoum. He was recruited by Merlin to transform services in Nimule and, if the hospital continues to improve, it will be handed back to national control.

"Merlin came and responded during the crisis in 2004, and now they're building up the health system so that the government can eventually take control," he said. "But they're doing it gradually so that they help the country. Other organisations, when they respond, do one service and then go. There was one NGO at a hospital in Kajo-Keji that just left, and now that hospital has no services. The government was not ready to take over."

Fighting between the Sudanese army and rebel groups continues along the northern border with Sudan, where civilians are terrorised by sustained bomb attacks. But in Nimule, at the opposite end of the country, things are relatively peaceful.

Most of the town's population fled to Uganda during the worst of the conflict in the 1990s. Since the peace agreement was signed with Sudan in 2005, they have been returning home, but their arrival has set the stage for a new conflict. While they were away, internal refugees fleeing the fighting on the northern border arrived and set up homes. These new arrivals were largely from the Dinka tribe, while the indigenous people, now returning to old homes, are Mardis. In the past year there have been three serious incidents of fighting between the groups and five people are known to have died in land disputes.

Dr Sylvester says he often sees victims of this fighting. "People come in injured with machetes. The Mardis feel deprived of their ancestral rights because the Dinka settled on land owned by them."

South Sudan has only nine hospitals, and reaching help is a serious problem. Almost all the roads are dirt and in varying states of disrepair. The US government has paid for the road between Nimule and Juba to be paved, but the construction is unearthing new problems. Landmines laid by troops in the 1990s are being uncovered. The Independent on Sunday was stopped 100 miles outside Juba after an anti-tank mine was found in the centre of the road.

The most lethal legacy of past conflict could be yet to come. The International HIV/Aids Alliance is predicting a rapid rise in HIV infections. A recent report said that, since the war ended, South Sudan "is experiencing a transition from a humanitarian emergency to recovery and development phase, which means that all the conditions favourable for an HIV explosion will be widespread". Today, South Sudan's official HIV prevalence rate is 3 per cent, but in areas such as Nimule, it is already closer to 10 per cent.

A truck stop at the Ugandan border has attracted many female sex workers and is a suspected hub of HIV infection. Merlin has sent community workers there to distribute condoms and encourage women to attend the nearby Nimule hospital for sexual health testing. Most, such as Akulu Susan, come from Uganda. The 28-year-old, who supports three children at home, said: "We came here for the money because in Uganda we have issues with school fees."

She says she uses condoms, but has been persuaded not to – for a price. "Some men come with huge money and say, 'Will you let me without a condom?' If they're offering 50 South Sudanese pounds [£11], I'll say yes." She has a chesty cough and says she has been feeling unwell for a long time. "I want to take a [HIV] test but I've not had one. Maybe I'll come to the hospital now."

Merlin is concentrating on pregnant mothers to protect a new generation from infection. Vicky Lawa, 29, from Nimule found out she was HIV positive when she was pregnant with her son, Lucky Solomon, who is now three months old. "I came to Nimule hospital and tested positive just after I fell pregnant. I had two children that died before. I started taking anti-retroviral drugs when I was seven months pregnant and, because of them, I'm still breastfeeding, and I'm feeling fine now."

Thanks to her treatment, Vicky is unlikely to pass on the infection to her son, which is why she decided to name him Lucky. But the likelihood of Lucky living a long life are not down to chance but the arrival of proper medical care.

Dominic West (actor)

"If, like me, you have been following The Independent on Sunday's Christmas Appeal, you will know that Merlin's health workers strive tirelessly all over the world in some of the toughest places, giving their medical expertise to millions of people.

They work around the clock to tackle disasters such as the food crisis in Kenya. They didn't stop for Christmas. Out of the spotlight, without any fuss, these health workers are saving lives today – in fact, every minute 18 people somewhere are helped by a Merlin health worker. This is why I hope you will join me in supporting The Independent on Sunday's Christmas Appeal on behalf of Merlin."

To make a donation visit: www.merlin.org.uk/independent-on-sunday-appeal or call 0800 035 6035 (24 hour, seven days a week - donation line).