Introduction

The world is facing one of the the biggest health, economic and social crisis. A minuscule, 50-nanometer in diameter structure is putting the most powerful world economies on their knees, and hundred of thousands are tragically succumbing to COVID-19.

This article is an invitation to governments to embrace GNU Health and Libre Software for the sake of their public healthcare system in the context of the COVID-19 pandemic.

For those of you who already use GNU Health, take this article as some sort of guideline to optimize your implementation and day-by-day usage. Even though it focuses on COVID-19 disease, most topics will apply to any GNU Health implementation.

People before patients: Demographics and health infrastructure

Information is power. Good quality and timely data is crucial to tackle the COVID-19 pandemic. GNU Health has been designed on Social medicine. That is, instead of dealing directly with patients, GNU Health works first on the main pillars of a society. As a result, the government will have better tools for health promotion and disease prevention. The government will be better prepared to fight this pandemic and future outbreaks.

Domiciliary Units : DU are houses, apartments and buildings where people live. GNU Health DU model stores the infrastructure, sanitary conditions as well as the people who is living at anytime at that dwelling, in realtime. This feature is key to track possible contacts of an infected individual. Moreover, the infrastructure, surface and number of rooms provides great information in terms of possible overcrowding conditions that would facilitate the spreading of the disease. Each domiciliary unit can be georeferenced, thanks to GNU Health link OpenStreetMap.

Domiciliary Unit in GNU Health: conditions, members and its geolocation linked to OSM

Operational Areas: GNU Health can divide a country in administrative areas and sectors (provinces, cities, neighborhoods,..) composed by domiciliary units and health institutions. GNU health can do real-time epidemiological reporting based on these sectors. Understanding this concept is key for COVID-19 contention or mitigation programs, since it would be able to identify early outbreaks in new areas, or focus on sections of relevant incidence. Operational areas and sectors allow us to find correlations from many indicators (ethnicity, sex, age, income, education level, population density) in the COVID-19 incidence, prevalence, susceptibility of infection or disease progression.

Health institutions: GNU Health can keep track and manage health institutions across the country. Human resources, financial and stock management, pharmacies and laboratories. In the context of the COVID-19 pandemic, you can do reporting on occupation levels of those institutions, number of beds, operating rooms, devices such as ventilators, number of health professionals and their specialties, the incidence, prevalence and mortality per institution, average time of hospitalization, and many other studies. Of course, you need to have the institutions set up.

GNU Health institution model

Health professionals : In crises such the COVID-19, GNU Health allows the Ministry of health to know each health professional, their specialties, the health institution where they work and where are they located (operational sectors). Time is precious and keeping updated information of the professionals will allow rapid assignment.

Person Demographics: Age, address and domiciliary units, work and insurance. Make sure this information is stored. Age is a factor on this epidemics, as COVID-19 is particularly pernicious with the elderly population. The profession of the person is also important. For instance, health professionals are highest infected group. Demographics will also help to identify people without health coverage, unemployed, homeless and other underprivileged groups that are particularly vulnerable.

Person contacts: For each person, GNU Health keeps record of their contacts and their relations (work, classmates, friends, classmates). In the scenario of a positive case for COVID-19, this information would allow to call the patient close contacts. It is key to have this information updated. Remember to fill in all possible contact mechanisms for each person (email, mobile phone, Telegram, …). Tracking and getting in touch with the person close contacts is vital.

Person Universal ID: This is one key feature of GNU Health, specially in the context of the GNU Health Federation. The person Unique ID (Federation Account) would be valid not only for the region or country, but across the world. The clinical information could be available and updated in any health institution across the country or region, immediately available for the rest.

Screening

The World Health Organization (WHO) keeps saying “test,test,test” the population. The earlier we test the population, the better we can control the spread of the disease in the community. Special population groups, such as health professionals, the elderly or those with existing health conditions should have priority.

There are rapid, point-of-care tests available in many countries that can deliver the results in less than 30 minutes. Some of them around 10 minutes. In GNU Health, you can use the SARS-CoV-2 antibodies lab test type.

GNU Health workstations can be deployed at the mobile test stations, and send the information in real-time to the Ministry of Health, with the result, signed and validated.

SARS-CoV-2 antibodies lab request

GNU Health report SARS-CoV-2 result

If the person has tested positive for IgM antibodies, it means she is in the early stage of the infection. IgG antibodies build up later in the infection and are part of the “immunological memory”. If IgM is positive, you must update the health conditions, include the following ICD10 code and activate the COVID-19 protocol for patient isolation and contact tracking.

The ICD10 code for COVID-19 is U07.1

U07.1 : 2019-nCoV acute respiratory disease COVID-19 : In GNU Health, the U07.1 condition (COVID-19) belongs to the infectious, respiratory and notifiable disease groups.

Indicate the lab test type and order in the related condition.

GNU Health patient screen sample, including critical information related to COVID-19 disease

Clinical Management

If the patient is tested positive but is asymptomatic or mild clinical, the patient might be sent home for home care. Please verify at that moment if the Domiciliary Unit meets the requirements (ventilation, number of rooms, number of people in the house, … ).

If the person has tested positive and/or presents signs to warrant her hospitalization, admit her to the health facility and assign her a bed in the appropriate ward. A new inpatient record will be created, with the corresponding in charge physician, treatment and nutrition plan. When admitting a patient suffering from COVID-19 is important to enter its code (U07.1 : 2019-nCoV acute respiratory disease COVID-19) as the reason of admission and discharge. This will be very valuable for statistics.

Medical History: The patient medical history is ready in GNU Health, from all the patient evaluations in the different health institutions. In the context of the COVID-19, this information is key, especially for people with chronic health conditions, such as cardiovascular disease or diabetes. The current and past medication is also stored in GNU Health, as well as surgeries.

Roundings: For each rounding, enter the vital signs, the medication provided,  assess the environment and the “Six P’s” and record all the procedures done in the rounding itself.  In addition, if the patient is on Intensive Care Unit (“ICU” tab), record relevant information on nervous, respiratory, cardiovascular, urinary and digestive systems, as well as any signs of infection.

The vital signs can be taken in different contexts. They can be assessed in an outpatient evaluation, inpatient nurse rounding or ICU setting.

Intensive Care Unit: If the disease progression is life threatening, the patient will be admitted to the Intensive Care Unit. GNU Health has an Intensive Care Unit module. After recording the main information of the rounding, move to the “ICU” tab for a detailed assessment of the patient in this unit. Scores such as Glasgow Coma Scale and Apache II are available.   For each ICU rounding the health professional should record both the basic information as well as a detailed RoS. GNU Health allows to enter ECG information and the copy of the ECG strip per rounding, if needed.

A percentage of hospitalized patients by COVID-19 will need mechanical ventilation. GNU Health records the type and duration of the intubation, per patient on each institution. This information is very valuable for both clinical management as well as for statistics. Most countries are facing today is the shortage of mechanical ventilators. GNU Health permits to know the incidence of hospitalizations due to COVID-19, as well as the discharge rate.

Medical Imaging and Laboratory tests

Radiological findings of many COVID-19 patients are compatible with atypical pneumonia. Streaky opacities, specially at the bases are common findings. Many people with mild disease won’t show any radiological signs.

GNU Health provides different types of Dx tests. Images and observations are recorded in the system and linked to the patient history. In addition to the standard GNU health radiology package, the Intensive Care module also permits to add Xray images on each rounding to evaluate and compare the disease progression.

For large images and studies, such MRI or CT scans, we highly recommend the GNU Health Orthanc package. Orthanc is a fantastic Libre DICOM server and GNU Health can interoperate with it, thanks to the magic of the Free Software philosophy.

GNU Health radiology. Findings compatible with atypical pneumonia in a COVID-19 patient

In addition to the standard lab test types (CBC, renal and liver function …..), there are markers that can predict COVID-19 progression and severity. For instance, high ferritin levels, low platelet number and a high ESR are common in patients who develop severe disease and the cytokine storm syndrome.

GNU Health LIMS showing a Complete Blood Count sample

All the lab test results can be exported to different formats. In the context of the GNU Health Federation a new POL (Page of Life) is created and the information can be exchanged directly in JSON format. The following pictures show the same lab test report in PDF and JSON format from the GNU Health Federation message server (“Thalamus”)

GNU Health generated CBC Lab test report in pdf

Lab test JSON format from the GNU Health Federation

In addition to the tests done in hospitalized patients, remember that GNU Health LIMS package can be used in diagnostic and population screening, as in the case of PCR and rapid tests.

Death Certificates

The death certificate is a key document, since it has legal, administrative, demographic and epidemiological significance.

The following is an example of how we could use the GNU Health Vital Record System to generate a death certificate associated to the COVID-19 disease.

Person Death certificate related to COVID-19 disease

Digitally signing the digital certificate with the health professional and/or civil officer will make it a legal document. GNU Health uses GNUPG (GNU Privacy Guard) to digitally sign and encrypt documents.

Digital signature section of the death certificate

Research

Although the respiratory system is the most affected in patients with COVID-19, other organs can be impacted. The ACE2 receptor (cell’s entry point for SARS-CoV-2) is expressed in other tissues in addition than lungs, such colon and heart. Not surprisingly, gastrointestinal symptoms and cardiac involvement, as acute myocarditis, have been reported. Recording all findings will help to improve the management of the disease of the patient, but also to share information with colleagues from the scientific community.

Sharing the patient treatments and individual outcomes will help speed up clinical trials and response to possible therapeutic agents (eg, remdesivir, lopinavir/ritonavir, hydroxychloroquine, tocilizumab…)

The GNU Health Federation connects thousands of nodes from health and research institutions

To be able to achieve such breakthroughs in science and in our society, we need our politicians and governments to embrace open science, open data and Libre software.

A call for Open Science, Open Data and Libre Software

The current COVID-19 pandemic is a terrible tragedy for human kind, but opens an opportunity to cooperation, to join forces and to our innate resilience.There are many gray areas and many uncertainties in the origin of the virus, disease progression and therapeutic approaches. On the other hand, the GNU Health Federation allows the scientific community to come together and tackle this beast. We can securely  share huge, anonymized amount of information from all over the world to find not only the molecular basis of the COVID-19 disease, but environmental and social factors that impact on the susceptibility and disease progression.

I am returning from Japan, where I was invited to give a lecture at Kyoto university Medical Innovation Center (MIC). It was an honor to share ideas with students and professionals from a leading institution on molecular biology and biomedicine. Although I talked about GNU Health in cancer research, my presentation focused on the importance of Libre Health informatics, open science, open data in Public Health. It was surprisingly exciting the great level of engagement of the audience in these topics.

A robust, sustainable public health infrastructure must be based in cooperation. Cooperation involves open knowledge and open science. I am convinced that true evolution comes from cooperation, and not from competition. In this sense, we as members of the scientific community should share our work, whether is a computer program source code, the discovery of a protein natural variant or the development of a new therapeutic molecule.

GNU Health uses the GPL license (General Public License), which permits downloading the program, study the source code, adapt it to your center needs and share it with the community.

Keep in mind that libre software not only provides collective freedom, but is the only way to achieve privacy in healthcare. Proprietary, non-libre programs are blackboxes that jeopardize both personal privacy and public health information. In addition to that, using proprietary software in Public Health is an obscene contradiction.

To accomplish collective freedom, every single component must be Free/Libre. That is, the operating systems (both for servers and clients) as well as the applications around. We will need to share information among colleagues around the world, so the format that we use in the corresponding files should also be open.

In the meantime, stay safe. Stay home !

Update: Last year (May 2018), the FSF asked me to write a post about GNU Health. Finally, here it is !

May 2018

Health is a non-negotiable human right. Access to quality healthcare must be public and universal.

I am back from my trip to India, where I spent a week with the team of All India Institute of Medical Sciences – AIIMS –, the largest public hospital in Asia and a leading research institution. They have taken the decision to adopt GNU Health, the Free Hospital and Health Information System.

One key aspect in Free Software is ownership. From the moment they adopted GNU Health, it now also belongs to AIIMS. They have full control over it. They can download and upgrade the system; access the source code; customize it to fit their needs; and contribute back to the community. This is the definition of Free Software.

The definition of Free Software is universal. GNU Health is equally valid for very large institutions, national public health networks and small, rural or primary care centers. The essence is the same.

GNU Health as a social movement: GNU Health is a social project with technology behind. It’s about Social Medicine and delivering universal healthcare. It’s about social activism. One of the main reasons that led me to create GNU Health were the tremendous inequalities in access to healthcare. Over 20000 children die every day from preventable, social diseases. To name a few : malnutrition, contaminated water, child slavery, prostitution, war, malaria, HIV-AIDS, tuberculosis, dengue and other neglected tropical diseases. These are causes and/or results of social diseases, conditions that have a higher impact and higher prevalence on the poor and the underprivileged.

Studying and getting a deeper understanding on the living conditions of people in rural areas and in urban ghettos around the world, reinforced my intention to write a system that included the socio-economic determinants of health and disease. Most of the time, health (and the lack of) is determined by the environment, and biology plays a lesser role. Proper nutrition, housing, sanitation, access to education and to primary healthcare are key for the dignity, development and health of the individual, family and society at large. I like to summarize it as “people before patients”.

GNU Health implementation at Laos CMR Public Health hospital (CC BY-SA 4.0 GNU Solidario )

Nature and Nurture: Having Social Medicine on its DNA does not stop GNU Health from also working on the molecular basis of health and disease, precision medicine, bioinformatics and genetics. For instance, we incorporate state-of-the-art information from Unitprot containing thousands of gene natural variants involved in human disease. The bio-psycho-social GNU Health approach makes personalized medicine possible, and it builds the bridge between the clinician and the research institution, to better understand and fight multifactorial conditions such as Alzheimer’s disease or cancer. Both nature and nurture are present in GNU Health.

GNU Health – Freedom and Equity in Healthcare

Trans-disciplinary team: GNU Health works at different levels. Social workers doing prevention in the field; health professionals taking care of the patients; Administrative team dealing with stock, human resources, finances and other internal health institution processes; and the ministry of health improving health campaigns based on the collected data. All these processes and tasks are interconnected, and the result of others.

The fight for Public Health System: I am observing how many countries are dismantling the Public Health system in favor of private corporations. This is not only sad, it is a crime. The only way we can guarantee proper and universal health care is by maintaining the Public Health system. Privatization of the public healthcare is evil, creates a health system for the rich, and excludes the underprivileged that can not afford insurance costs. Let me be very clear: healthcare is just a business for the corporation. Dr. René Favaloro said “Medicine without humanism is unworthy of being practiced”. I am not against the small private doctor office, that is complementary to the public health system. I am condemning the destruction of the current public health system, and putting it on the hands of large corporations that only care about money.

GNU Solidario first project. Santiago del Estero 2006 . (CC BY-SA 4.0 Luis Falcon)

Public Health is a public good, so, as a result, anything related to public health should also be public. It is a contradiction to have proprietary software running in the public health system. Not only is contradictory and unethical, it poses many dangers to privacy and security of the individual health information. Private software is a black box. We don’t know what happens when a medical evaluation is recorded. Where else does this data go? Who can access it ? We simply don’t know, because we can not see the code behind the action.

Children in a Cameroon rural school (2018 CC BY-SA 4.0 Luis Falcon)

Collective Freedom and ethical software: Free software is a philosophy based on community, cooperation and solidarity. We all benefit from the work, effort and talent of others. GNU Health uses many Free Software (operating systems, programming languages, database engines, encryption libraries, etc.). Moreover, GNU Health is today the result of the contribution of many people and institutions. We must be grateful to the community, and make sure that nobody breaks the evolution chain. This is where the concept I call “collective freedom” comes into play. People or companies that take the work of others, and purposely make it non-free are breaking the chain of evolution. They have taken advantage of the good will from the community to lock-in them in. Purposely obfuscating the code, not providing upgrade scripts, hiding documentation are ways violating the “collective freedom” and making a system non-ethical. That is one of the reasons we differentiate between Free Software philosophy, which is ethical by definition, from “Open Source”, that has a more pragmatic approach to programming. Richard Stallman wrote an article “When Free Software depends on nonfree” (https://www.gnu.org/philosophy/when-free-depends-on-nonfree) , related to this concept. For Spanish speakers, you can read my article “El Software Libre no se Mancha” (http://www.rebelion.org/noticia.php?id=233717 ), also related to this concept of Collective Freedom.

Ten years of Freedom and Equity in Healthcare: During this 10-year period, we have seen GNU Health adopted in many different scenarios: Primary care centers and academic institutions in Argentina; in the tropical rainforest of Cameroon; Infectious diseases laboratory in Gabon; the eHealth system in Jamaica Ministry of Public Health; The Center for Physical Rehabilitation in Laos taking care of UXO victims; Red Cross hospitals in Mexico or the largest public hospital in India and Asia. They are all different contexts and peculiarities, yet they all share the same spirit, that is, delivering Freedom and Equity in healthcare to the people.

GNU Health at the United Nations – International Institute for Global Health

Let’s celebrate this 10 years of GNU Health, a social movement with technology behind. Let’s keep on fighting for health to be a non-negotiable human right.