H5N1

How we used machine learning to look where Ebola may strike

Via ProPublica: How We Used Machine Learning to Look Where Ebola May Strike. Excerpt:

ProPublica spent months teaching a computer to analyze past Ebola outbreaks linked to deforestation. What we found reveals a weakness in the way that governments and public health experts are preparing for future pandemics. 

The bright spots on the map struck us like a lightning bolt. 

We had spent months teaching a computer about the Ebola virus –– feeding it information about the landscapes and populations in places where the disease had previously emerged, showing it how to analyze those outbreaks for patterns, and then instructing it to flag other areas that looked similarly perilous.   

Some of the highlighted spots were predictable; the virus had repeatedly ravaged one of those countries.  

But we didn’t expect our model to light up Nigeria, the most populous country in Africa. The West African nation and international travel hub has never seeded an Ebola outbreak, but just a year ago, it served as the springboard for another virus to travel into Europe and the Americas and spread across the globe. However that virus, mpox, originally known as monkeypox, is rarely fatal.  

What if it had been Ebola, which kills about half of the people it infects?  

We asked Nigerian public health officials whether they were concerned.  

“Ebola is not part of our top concerns any more,” said Oyeladun Okunromade, the director of surveillance and epidemiology at the Nigeria Centre for Disease Control.  

In the aftermath of the 2014 West African Ebola epidemic, the worst on record, Nigerian officials were on high alert. But last year, they took the virus off the list of the top infectious diseases the country needed to prepare for, downgrading Ebola in relation to threats like mpox, which Nigeria was actively fighting.  

The disjoint between how our model sees Nigeria’s risk and how the nation’s health officials view it reveals a weakness in the way that governments and public health experts are preparing for future pandemics. The methods many countries use to rank threats focus mainly on factors that occur after an outbreak has already begun, such as the potential economic impact of an epidemic. Or they rely on past cases, looking at where a pathogen has previously struck.  

Neither approach considers the root causes.  

We’ve spent more than a year digging into the question of what causes outbreaks and what the world can do to prevent them. And we’ve learned that while science has advanced so we’re starting to understand the complex factors that trigger an outbreak, the world is not doing nearly enough to try to head off the next big one.

Kirundo-Muyinga: A mysterious disease with symptoms resembling those of the Ebola virus appears

Via SOS Médias Burundi, a March 27 report: Kirundo-Muyinga: a mysterious disease with symptoms resembling those of the Ebola virus appears. The Google translation:

An as yet unidentified disease killed three people in three days in the commune of Gitobe in the province of Kirundo and in the commune of Butihinda in the province of Muyinga (north-eastern Burundi). 

Symptoms developed by patients suffering from this disease resemble those of Ebola hemorrhagic virus or Marburg virus disease. In the case of Kirundo, the governor and the provincial doctor are waiting for the results of samples taken by specialists from the INSP (National Institute of Public Health) to decide.  

The ministry in charge of health has already confirmed for that of Muyinga that it is neither the Marburg virus disease nor Ebola. (SOS Media Burundi) This disease, not yet identified but having signs similar to those of Ebola, has just claimed the lives of two people in the commune of Gitobe. Both people died within 24 hours of showing the signs. All the patients come from the same Migwa hill, in the Baziro area.  

According to witnesses on the spot, "the symptoms include abdominal pain, nasal bleeding which increases after death, acute headaches, high fever, vomiting and dizziness". This disease kills very quickly, noted a nurse interviewed by SOS Media Burundi.  

“It's a disease that kills quickly. Within 24 hours, the infected person dies. It's terrible, we are all waiting for death," said a panicked nurse from the Migwa health center in the Gashoho health district in Muyinga province where patients were sent, including two women who died there.

When the population of Baziro wanted to bring the third person there, the population of Migwa blocked the entrances, fearing the spread of the disease. For the moment no one can leave the area of ​​Baziro which, it seems, has been confined. 

Samples were taken by the INSP to identify which disease it is.  

But until now the disease is not yet detected, according to doctors.  

In the morning of Friday, the governor of Kirundo, Albert Hatungimana, accompanied by the provincial doctor, carried out a raid in the commune of Gitobe, but they made no forecast.  

"We are awaiting the results of the swabs," a member of the governor's cabinet said.  

The population is worried because, she says, "So far no real prevention strategy against this disease has been communicated".  

“Apart from washing your hands and avoiding greeting each other, there are no strict measures, which can promote contamination,” residents insisted.  

Note that at Kirundo hospital, the first case was also admitted on Friday evening. In the commune of Ntega (same province), people with the same symptoms were reported on the same Friday evening.  

The population of the urban center of Kirundo lives in panic fear. She asks the government to declare the epidemic so that there is a rapid intervention.  

Another case was recorded in Giteranyi commune, Muyinga province (neighboring Kirundo). A student from Kobero Basic School not far from the border with Tanzania, died of this disease last Thursday.  

Tanzania declared a Marburg virus epidemic on March 21. A cousin of Ebola, this “filovirus” causes high fevers accompanied by virulent haemorrhages. So far, there is no vaccine or antiviral treatment for this disease, which can also attack primates. It is suspected that it is the Marburg virus which has spread in the Burundian provinces bordering Tanzania, the epidemic having been detected in the Kagera region in the north-west of Tanzania not far from Burundi and Rwanda .

Uganda: Family denies exhuming body of Ebola casualty

Via The Monitor, which has done an excellent job of covering the outbreak: Family denies exhuming body of Ebola casualty. Excerpt:

The family of an Ebola Virus Disease (EVD) victim, whose body was allegedly exhumed by unknown people, have asked the Ministry of Health and the security agencies to investigate the incident.  

The incident took place in Kitongo Village, Kalwana Sub-county Kassanda District about a month ago, according to district health officials.  

While meeting the Kassanda District Ebola taskforce, Health Minister Jane Ruth Aceng, and other officials at Kassanda District headquarters on Wednesday, a family representative, Mr Mubarak Muwade Kawuki, denied claims that they exhumed the body to perform Muslim burial rituals on it.  

He added that they are now being stigmatised, “causing a lot of distress to our family”.   

“Our own investigation reveals that nobody tampered with the grave,” he said.  

Mr Kawuki insisted that the rituals and the preparation of the grave were performed prior to their loved one being buried.  

He added that the interment was done by the burial team from the government.     

“There was no single reason as family members to have the body of a person presumed to have died of Ebola exhumed in the name of performing a religious burial,” he said.   

He added: “It is also interesting that when we asked the police to investigate the incident, they have failed to give us a report.”  

The family has asked the government to institute a special investigation to examine the grave and possibly exhume the body to find out if it was tampered with.  

But in an earlier interview with this paper, the Kassanda Resident District Commissioner, Ms Phoebe Namulindwa, revealed that the health officials have recovered some evidence but did not give any more details on the matter.  

She added that some people had also confessed to exhuming the body.  

“I only request the community to stop stigmatising the family because we are all focused on fighting the Ebola Virus Disease in Kassanda District,” she said.  

Meanwhile Dr Aceng urged the family to join the fight against Ebola and forget the past.  

“I will call the team and interact with them to find out what really happened. We have had some challenges in Kassanda District as we fight the Ebola pandemic. We should work as a team to stop the spread of Ebola,” she said.  

It was revealed at the meeting that the cumulative confirmed Ebola cases is now 50, while the cumulative death cases are now 18 in Kassanda District.

Uganda: MSF responds to Ebola outbreak

Via Doctors Without Borders USA: Uganda: MSF responds to Ebola outbreak.

NEW YORK, SEPTEMBER 23, 2022—Following the September 20 declaration of an Ebola outbreak in Uganda in the country’s central Mubende district, the ministry of health has asked the international medical humanitarian organization Doctors Without Borders/Médecins Sans Frontières (MSF) to support its efforts in the fight against the spread of the disease.  

On September 21, an MSF team of six people—including doctors and logisticians—traveled to the town of Mubende to carry out an assessment of the situation and the needs at the regional referral hospital, where the first case was detected. The virus has been confirmed to be the rarer Sudan strain of Ebola for which there is no approved vaccine or treatment, unlike the Zaire strain that caused the last several outbreaks in the Democratic Republic of Congo.  

Since carrying out this assessment, MSF has begun setting up an Ebola isolation and treatment center in the Mubende hospital to help improve patient care. Teams are also exploring the possibility of setting up a second center in the town of Madudu, which is approximately 25 kilometers [15 miles] north of where the first person who died from Ebola originated and where several suspicious cases are reported.  

MSF is currently putting together a team of health workers, epidemiologists, and logisticians with experience in hemorrhagic fevers to start work next week.  

The last Ebola outbreak in the country occurred in 2019. MSF intervened at that time to support the Ugandan health authorities in the management of people who had been in contact with these confirmed cases, the establishment of an Ebola treatment unit, and the improvement of infection prevention and control measures in health facilities.

The Ugandan Ministry of Health has tweeted an update:

Uganda: Second suspected Ebola victim dies

Uganda's new Ebola outbreak hit the news yesterday, but it seems to have started several weeks ago. Via New Vision: Second suspected Ebola victim dies.

Another man suspected to be infected with Ebola has died at Mubende Regional Referral Hospital.  

He was part of the 14 people who checked into Mubende Regional Referral Hospital with symptoms of Ebola on September 20, 2022.  

Emmanuel Ainebyoona, the health ministry spokesperson, confirmed the death of suspected victim.  

"Yes, there is a child who died yesterday but we are waiting for test results  from UVRI. It is a suspected death at the moment," he said.  

According to Mubende RDC Rosemary Byabashaijja, a man from Madudu Sub County in Mubende died yesterday (September 20) after he was admitted at Mubende Regional Referral Hospital.  

The RDC is heading the Mubende Rapid Response team, which is working with Ministry of Health to track down contacts for the person who died on Monday and investigate the six deaths that occurred earlier in the month.  

The six deaths occurred suddenly and the local people say they died of strange illness.  

Byabashaijja said they had identified 14 contacts of the person who died on September 19, 2022. They included 10 people from Madudu Sub county including the one who passed on yesterday (September 20) and four people from neighbouring Kyegegwa district in Toro.  

“Since we registered the first case, we sent a surveillance team which goes around where they even sensitize the people. In Madudu, we have been asking those who were in touch with first victims to willingly come up and be tested and we are happy that some are turning up,” she said.  

On September 20, the team of medics took away the body of the first victims from Mubende hospital and buried. The body of the person who died on September 20 is awaiting burial today (September 21), according to sources.  

Byabashaijja noted that the six people expected to have died of Ebola form Madudu died because of self-medication.  

An isolation center has been set up at Mubende Regional Referral Hospital where suspected cases are being quarantined pending the results from samples picked from them.

August 2022 Ebola case in DRC linked to 2018-2020 Nord Kivu EVD outbreak

Thanks to Helen Branswell for tweeting the link to this excellent report at Virological.org: August 2022 EVD case in DRC linked to 2018-2020 Nord Kivu EVD outbreak. Excerpt:

The new case of Ebola Virus Disease in Beni is genetically linked to the 2018-2020 Nord Kivu/Ituri EVD outbreak and does not represent a new spillover event.**  

Context  

On Monday, August 15, 2022, the Institut National de Recherche Biomédicale (INRB) Beni mobile laboratory received an oropharyngeal secretion sample taken from a deceased patient who was being treated at the Beni General Reference Hospital (HGR-Beni). The sample tested positive for Ebola virus (EBOV) using the Cepheid Xpert Ebola assay with ct- values of 32.5 for viral glycoprotein (GP), and 28.2 for viral nucleoprotein (NP). For quality control and confirmation, samples were sent to the Rodolphe Mérieux INRB-Goma Laboratory on Tuesday August 16, 2022, where the analysis confirmed the EVD case.  

The patient was admitted on July 23, 2022 to the Internal Medicine department of the HGR-Beni for cough, headache, polyarthralgia, intense physical asthenia dating back several days and for which she had self-medicated with non-specified drugs. She was HIV-positive on antiretroviral treatment, and she had also presented with tuberculosis for which she was receiving anti-tuberculosis treatment.  

On August 13, 2022, her health condition deteriorated with the onset of bronchial congestion and kidney failure, which prompted her transfer to the intensive care unit for better care. She died on August 15, 2022. In total her hospitalization lasted 23 days. The body was collected by the family the same day for burial.  

On August 17, 2022, 131 contacts were listed, including 60 front-line healthcare workers and 71 co-patients. Of the 131 pre-listed contacts, 59 of the 60 HCWs are vaccinated. The vaccination status of the index case and 71 co-patients is not yet known.

The Democratic Republic of the Congo declares 14th Ebola outbreak over

Via WHO AFRO: The Democratic Republic of the Congo declares 14th Ebola outbreak over. Excerpt:

Brazzaville/Kinshasa – The Democratic Republic of the Congo today declared the end of the Ebola outbreak that erupted less than three months ago in Mbandaka, the capital of Equateur Province in the northwest. It was the third outbreak in the province since 2018 and the country’s 14th overall.  

With greater experience in Ebola control, national emergency teams, with the support from World Health Organization (WHO) and partners, mounted a swift response soon after the outbreak was declared on 23 April, rolling out key counter measures including testing, contact tracing, infection prevention and control, treatmentand community engagement. Vaccination – a crucial protective measure – was launched just four days after the outbreak was declared.  

In all, there were four confirmed cases and one probable case – all of whom died. In the previous outbreak in Equateur Province that lasted from June to November 2020, there were 130 confirmed cases and 55 deaths.  

“Thanks to the robust response by the national authorities, this outbreak has been brought to an end swiftly with limited transmission of the virus,” said Dr Matshidiso Moeti, WHO Regional Director for Africa. “Crucial lessons have been learned from past outbreaks and they have been applied to devise and deploy an ever more effective Ebola response.”  

The just ended outbreak saw a total of 2104 people vaccinated, including 302 contacts and 1307 frontline workers. To facilitate the vaccination rollout, an ultra-cold chain freezer was installed in Mbandaka which allowed for vaccine doses to be stored locally and safely and be delivered effectively.  

The Democratic Republic of the Congo has now recorded 14 Ebola outbreaks since 1976, six of which have occurred since 2018.  

“Africa is seeing an increase in Ebola and other infectious diseases that jump from animals to humans impacting large urban areas,” said Dr Moeti. “We need to be ever more vigilant to ensure we catch cases quickly. This outbreak response shows that by bolstering preparedness, disease surveillance and swift detection, we can stay a step ahead.”

Ebola in Mbandaka: Death of a 4th confirmed case

Via Radio Okapi: Ebola in Mbandaka: death of a 4th confirmed case. The Google translation, with my bolding:

The fourth confirmed case of the Ebola virus disease died on Friday May 20 in Mbandaka. This is the fourth recorded since the outbreak of the epidemic on April 21. He was discovered on Thursday in the Maman Balako health area, Wangata health zone and commune.  

Only 24 hours after his discovery, the patient died, after having dragged around the community for a long time without proper care.  

Medical sources claim that the victim was a 12-year-old child in the Maman Balako health area. Since May 14, he had been developing symptoms of Ebola, including fever, fatigue, blackish vomit.  

For five days, he was cared for at home, until Thursday, May 19; date on which he was taken to a medical center in the Mbandaka II district. The results of the analysis of the samples taken on the same day from the child were found to be positive for the Ebola virus disease.  

But the family resisted and brought the child home on Thursday evening, where he passed away on Friday morning.  

Sources add that another 9-year-old child died with the same symptoms, in the same neighborhood, on May 6 and buried, without post-mortem collection or a dignified and secure burial. This raises fears of a multiplication of cases.  

The response teams are preparing for the decontamination of different places, through which the deceased child passed. They seek the cooperation of the populations around the case and in the health area concerned.  

They also invite the inhabitants to appropriate all the preventive measures recently enacted by the provincial authority, in order to avoid a large-scale spread of the disease. Among these measures, there is a compulsory post-mortem sample before any burial of bodies in the city.

Ebola in Mbandaka: No new confirmed case for a week

Via Provinces 26 RDC: DRC-Ebola in Mbandaka: no new confirmed case for a week. The Google translation, slightly edited:

No new confirmed case of the Ebola virus disease has been recorded for a week, to the day, in the city of Mbandaka in Equateur province. The last case was recorded on April 25, and died a day later.  

The latest data made public by the health authorities show a total of 2 confirmed cases, a man and a woman [all deceased], in the health zone of Mbandaka alone. 

Since Wednesday April 27, the vaccination campaign against Ebola has been launched. It concerns people who have come into contact with a patient suffering from Ebola, as well as front-line workers.  

So far, 175 people have been vaccinated. The total number of contacts listed is 334 people.  

Meanwhile, the Governor of Equateur calls on the population to be vigilant and to respect the health measures enacted, in order to stop the spread of this epidemic.  

In a message made public, Governor Bobo Boloko asks residents to immediately refer suspected cases within their various entities to nearby health structures for appropriate care.  

"Our province is now in an epidemic of the Ebola virus disease. I want to inform you that it is a very dangerous, contagious and often fatal disease. It is transmitted by direct contact with blood, urine, stool, vomit, saliva, semen, vaginal secretions, sweat and manipulation of the body of a patient with or who has died of Ebola. And by the consumption of wild and domestic animals found dead. In case of headache, fever, abdominal pain, hiccups, vomiting, diarrhea, rash, red eyes and sometimes bleeding. This is why before eating, preparing, breastfeeding and changing babies' diapers, after the toilet, on returning home, we wash our hands with soap and clean water. 

Note that this 14th Ebola epidemic has been officially declared in Mbandaka. This is the third outbreak in this province since 2018.

Mbandaka: ISTM takes measures to secure its students against the new Ebola epidemic

Via Radio Okapi, we learn that the first Ebola case was a medical student: Mbandaka: ISTM takes measures to secure its students against the new Ebola epidemic. The Google translation:

The Higher Institute of Medical Techniques (ISTM) took measures, including vaccination, to secure its students and limit the spread of Ebola, 48 hours after the declaration of the epidemic in Mbandaka by the central government.   

The first confirmed and deceased case was student Yange Bononga, enrolled in the 3rd Nutrition graduate, for the 2021-2022 academic year.   

Thus the management committee meeting on Monday, April 25 asked for the cooperation of the students and the support of the competent services.   

Among these measures taken, there is the awareness of students on the existence of the disease, the respect of barrier gestures and the obligation to present themselves free of charge to the hospital in the event of illness.   

In addition to the installation of washbasins in front of the strategic corners of the institute, the committee also requested the vaccination of the entire ISTM community, particularly the students of the 3rd Nutrition graduate.      

In addition, the ISTM has launched an appeal to public health services and humanitarian organizations to help build its capacity in information and protective equipment. Thus, a conference-debate on the resurgence of the Ebola virus disease in Ecuador is planned this week.   

All these measures are taken, continues the management committee, following the instructions of the minister in charge, to help curb the epidemic.    

Some students unfortunately had contact with the victim during his final moments.   

The management committee clarified, however, that the victim would have contracted the disease during his return trip from the holidays of Boende, where he is from.   

Although he probably arrived on April 10 in Mbandaka, he was directly admitted to health centers without attending the institute. This, until his hospitalization at the Wangata General Reference Hospital, then at the Ebola treatment center, where he passed away.