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Salmonellosis in Finland 2021: After 450 Cases, How to Prevent the Next Outbreak?

Food safety and quality assessment. Microbiologist testing poultry sample for the presence of salmonella and Escherichia coli,
Image: Microbiologist testing poultry sample for the presence of Salmonella


written by Chandana Balasubramanian

About 150 children in Finland and a total of 450 individuals have fallen ill from Salmonella poisoning. Most affected individuals are from daycare centers in the city of Jyväskylä. The cause of this outbreak is suspected to be lettuce imported from Germany via Sweden [1]. Though Salmonella outbreaks have been declining, the 2021 Finland outbreak is one of many reported worldwide this year. As our world continues to shrink due to globalization, it is getting harder for public health agencies to monitor and prevent Salmonella outbreaks from imported foods

This year, Sweden has also reported a national Salmonella outbreak that affected more than 30 people [2]. In June, melons sourced from Costa Rica, Honduras, or Brazil were the most likely cause of a Salmonella outbreak of 200 people across ten countries, including Finland, Denmark, Belgium, Germany, the Netherlands, Sweden, United Kingdom, Canada, and Switzerland [3]. In the United States, the CDC (Centers for Disease Control and Prevention) initiated a ‘Food Safety Alert’ after detecting 102 infected cases across 14 states due to contaminated seafood that originated in Colorado [4]. 

One of the biggest challenges in catching Salmonella in imports is the fact that the bacteria is mainly found in fresh produce and other foods with a short shelf life. This hurdle is made even more complex because of the popular hub-and-spoke model of centralized food distribution. In this model, one country in a region acts as a centralized hub that processes fresh produce, meat, or poultry. This food is then exported to several countries simultaneously. By the time infections are reported, most of the contaminated inventory may have already been consumed – either on its own or mixed with other batches – or thrown away. This makes it difficult to obtain enough samples to test and trace the country of origin [5]. 


A History of Salmonellosis in Finland

Let’s take a closer look at Finland. At 9.29 cases per 100,000 population, Finland has the highest rate of Salmonellosis among Nordic countries despite its stringent controls and processes [6]. 

Nordic region Salmonellosis rates per 100000 graph
Image: Salmonellosis rates per 100,000 population for Finland, Sweden, Norway, Iceland, and Denmark. Copyright © GIDEON Informatics, Inc.


Before 2021, the biggest Salmonella outbreak in Finland was in 2008. Pre-chopped and ready-to-eat Iceberg lettuce happened to be the prime suspect for the 2008 Salmonella outbreak in Finland. There were 77 confirmed cases, and two elderly patients died [7]. 


Image: Salmonellosis in Finland. Cases from 1969 to 2021. Copyright © GIDEON Informatics, Inc.
Image: Salmonellosis in Finland. Cases from 1969 to 2021. Copyright © GIDEON Informatics, Inc.


Finland has seen a steady decline in Salmonellosis since 1995, when the country initiated its national Salmonella control program. The Finnish national Salmonella control program (FSCP) mandates regular testing of cattle, poultry, and pigs, including eggs and meat. Lab test results are evaluated by the Finnish Food Agency monthly. There are stringent checks and balances included throughout their entire supply chain. 

The FSCP measures have helped lower the rates of homegrown Salmonella. However, like many other countries, Finland needs a faster and more effective way to monitor and prevent the bacteria from being brought in from other countries, either through travel or cross-border food imports [8]. 


List of Prominent Salmonella outbreaks in Finland*: 

  • 1976: 550 cases were reported due to contaminated mayonnaise prepared in Spain and served on four international flights (Las Palmas-Helsinki, Las Palmas-Honover). 
  • 1986: 226 cases from packaged meals offered to train and air passengers. 
  • 1992: 224 cases due to contaminated mung beans.
  • 1994: 210 cases in Southern Finland due to alfalfa seeds.
  • 1995: 242 cases were reported in Finland (and the U.S.) due to alfalfa seeds imported from a Dutch supplier. 
  • 2001 – 2003: 666 cases reported in Norway, Finland, and Swedish tourists infected by contaminated poultry.
      • 2001: 303 cases
      • 2002: 164 cases
      • 2003: 199 cases.
  • 2007: 8,453 cases (almost 30% of the population) due to contaminated water in the town of Nokia, Finland. It is the largest reported water-borne outbreak in Finland [9].   
  • 2008: 107 cases in Newport and Reading, Finland due to contaminated lettuce. 
  • 2015: 122 cases in Finland due to an ice hockey team event in Latvia.
  • 2021: 450 cases due to contaminated lettuce imported from Germany via Sweden. 

*Data sourced from GIDEON – the comprehensive Global Infectious Diseases and Epidemiology Online Network database. The GIDEON platform also lists notable cross-border Salmonellosis events in Finland.

Public health agencies worldwide continue to worry about keeping Salmonellosis cases down in their respective countries. But in this hyper-connected world, it can prove challenging. A comprehensive database such as GIDEON that tracks outbreaks as they happen across the world may be a viable solution. 


Image: Salmonella outbreaks worldwide and list of Salmonella outbreaks in Finland. Copyright © GIDEON Informatics, Inc.
Image: Salmonella outbreaks worldwide and list of Salmonella outbreaks in Finland. Copyright © GIDEON Informatics, Inc.



What is Salmonellosis? What are the Symptoms of Salmonellosis? 

Salmonellosis is the infection acquired from ingesting the zoonotic bacteria Salmonella. The most common way to get Salmonellosis is by eating raw or undercooked meat, eggs, or fruit and vegetables that have not been washed and handled correctly. 

Salmonellosis is highly contagious, and you can get sick from any person, animal, or thing that carries the Salmonella bacteria. The bacteria are transmitted to our mouths from contaminated humans or animals feces fecal-oral transmission). Other risk factors for Salmonella poisoning are travel to high-risk countries with poor sanitation and exposure to birds and reptiles being kept as pets. 

Symptoms of Salmonellosis include: 

  • Diarrhea
  • Stomach cramps
  • Fever

They usually last four to seven days and begin within 12 to 72 hours of consuming the contaminated food [10]. 


Image of profile of sick woman having a stomach ache, left side
Image: a woman experiencing stomach cramps


How is Salmonella poisoning diagnosed?

Here is where local laboratory test results play a significant role in helping curb the spread of Salmonella. Usually, stool or blood samples are used to test for Salmonella. Once detected, many countries have protocols that require these labs to report positive incidences of Salmonella to approved public health laboratories for serotyping and DNA fingerprinting.

Around the world, we can also enable on-ground clinicians to play a stronger role in identifying Salmonella cases early and preventing its spread. Having access to data on outbreaks as they happen can help public health officials detect the origin of infection much sooner and more effectively.  


How To Prevent Salmonellosis? 

Good immunity is the best line of defense against Salmonella. Our natural stomach acid can help fight salmonella poisoning. However, there is a greater risk of infection for those with impaired immune functioning due to: 

  • the overuse of antacids, 
  • effects of antibiotics, 
  • age – infants and the elderly, 
  • pregnant women, and 
  • lowered immunity from chronic illnesses like Irritable Bowel Syndrome (IBS) and other conditions like AIDS, Malarial infections, and more. 

Other ways to minimize the risk of getting Salmonella is to:

  • always wash your hands before you eat, after touching animals, using the toilet, or changing diapers,  
  • clean food preparation areas, and 
  • minimize the intake of raw and uncooked food and meat. If fresh produce is to be consumed raw, then it must be washed thoroughly. 

Note: Foods containing Salmonella do not smell or look different from uncontaminated food. Washing hands and following food safety guidelines is your best bet to mitigate risk.   


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[1]  yle, “Imported lettuce confirmed as cause of Jyväskylä salmonella outbreak,”, 07 07 2021. [Online]. Available: [Accessed 10 10 2021].
[2]  GIDEON Database (Global Infectious Diseases and Epidemiology Online Network), “Salmonellosis in Sweden,” GIDEON, 2021.
[3]  FSN, “Large Salmonella outbreak linked to melons,” Food Safety News, 01 06 2021. [Online]. Available: [Accessed 10 10 2021].
[4]  CDC (Centers for Disease Control and Prevention), “Salmonella Outbreak Linked to Seafood – Food Safety Alert,” CDC, 08 10 2021. [Online]. Available: [Accessed 10 10 2021].
[5]  K. G. J. A. R. O. M. A. M. E. W. B. Rebecca L. Bell, “Recent and emerging innovations in Salmonella detection: a food and environmental perspective,” Microb Biotechnol. , vol. 9, no. 3, p. 279–292, 2016. 
[6]  GIDEON Database (Global Infectious Diseases and Epidemiology Online Network), “Salmonella in Finland – Country Note,” GIDEON, 2021.
[7]  T. N. S. G. A. S. M. K. R. R.-F. TARU LIENEMANN, ” Iceberg Lettuce as Suggested Source of a Nationwide Outbreak Caused by Two Salmonella Serotypes, Newport and Reading, in Finland in 2008.,” Food Prot, vol. 74, no. 6, p. 1035–1040, 2011. 
[8]  J. R. E. S. J. P. Riitta Maijala, “The efficiency of the Finnish Salmonella Control Programme,” Food Control, vol. 16, no. 8, p. 669, 2005. 
[9]  E. H. M. J. V. M. S. J. L. P. R. E. K. R. V. T. P. I. M. J. H. O. L. J. A. J. H. M.-L. H. L. M. J. M. a. M. K. • J. LAINE, “An extensive gastroenteritis outbreak after drinking-water contamination by sewage effluent, Finland,” Epidemiology and Infection, vol. 139, no. 7, pp. 1105-1113, 2011. 
[10]  Centers for Disease Control and Prevention, “Salmonella Homepage,” CDC, 08 10 2021. [Online]. Available: [Accessed 11 10 2021].


Mosquito-borne Diseases Dengue, Zika, and Chikungunya in the United States

Close up newborn aedes albopictus mosquito, pest animal, contagion
Image: Newborn Aedes albopictus mosquito


written by Chandana Balasubramanian

Aedes aegypti and Aedes albopictus mosquito-borne illnesses are not just tropical diseases anymore

There’s Dengue fever in California and reports of Zika, Dengue, and Chikungunya cases in Florida. West Nile cases are on the rise in the US, with two recent deaths reported in Arizona and Los Angeles. What do they have in common? These diseases are all mosquito-borne diseases transmitted by the Aedes aegypti and Aedes albopictus species of mosquitoes.

The Aedes aegypti mosquito can transmit Dengue, Yellow fever, Zika, Chikungunya, West Nile Virus, and Venezuelan Equine Encephalitis Virus. Aedes albopictus can transmit Dengue, Chikungunya, Yellow fever, West Nile, Zika, Japanese encephalitis, and more.

These cases have been high enough to warrant different states taking action to curb the spread of disease. The first genetically modified mosquitoes were released in Florida early this year, designed to suppress the Aedes aegypti mosquito.

Dengue cases and rates in the United States, GIDEON graph
Image: Dengue cases and rates in the United States, 1930 to 2020. Copyright © GIDEON Informatics Inc.



Is the spread of infectious disease mosquitoes to non-tropical countries a recent phenomenon? How are epidemiologists and infectious disease specialists monitoring and predicting the spread? How will the introduction of the Aedes family of mosquitoes affect the population of other species of mosquitoes? How exactly are the viruses maintained in the mosquitoes?

GIDEON Informatics partnered with virologist Dr. Melissa K. Jones at the University of Florida to investigate. Dr. Jones recently moderated an informative webinar on the invasion of the Aedes mosquitoes in the United States, particularly Florida. Experts on the panel were:

  • Guy Hendrickx: Co-founder AVIA-GIS, a Belgian organization focused on spatial mapping and modeling of various topics, including infectious diseases.
  • Stephen Berger MD: experienced practicing physician, infectious diseases specialist, and co-founder of GIDEON, the comprehensive infectious disease database.


Highlights from the webinar

Drs. Hendrickx, Berger, and Jones had a fascinating conversation about Aedes-borne diseases. They began by discussing the spread of the Aedes family of mosquitoes away from its traditional habitat in South and Southeast Asia.

Spread of Aedes Away from the Tropics

  • Politics Makes Strange Bedfellows and Infectious Diseases: Did you know that changing political alliances in the 1960s helped introduce the Aedes albopictus mosquito (also known as the Tiger mosquito) to Europe? In the 1960s, an alliance between China and the former USSR ended. However, Albania, a highly communist country in Europe, continued its ties with China. As a result, they frequently imported equipment from China in containers that also carried an unwanted visitor – the Tiger mosquito. Luckily, as Albania did not permit much travel in and out of the country, the mosquito was contained.
  • The Side-effects of Globalization: The Aedes mosquito first entered the United States in the 1980s due to tire imports from Japan. As Europe began imports from Japan in the 1990s, the mosquito began to spread there as well.

Modeling and Tracking the Spread of Aedes-borne diseases

Dr. Hendrickx shared several significant studies about the spread of mosquito-borne vectors and how his team has been instrumental in tracking and predicting the spread of the Tiger mosquito. He stressed that studying the import of vector-borne diseases is essential to help curb outbreaks.

Comparing Clinical Features of Mosquito-Borne Diseases

Dr. Stephen Berger discussed how it might surprise people to know that mosquito-borne diseases are more common in the United States than people may think. After all, the most common condition affecting all American Presidents is not heart attacks or cancer, but malaria! Even more surprising, almost all (except two) got their malaria within the United States, not from another country.

Dr. Berger stressed the importance of clinicians conducting differential diagnoses to compare clinical symptoms and identify mosquito-borne diseases early. This way, a country can curb import-based outbreaks.

Dr. Berger used the GIDEON differential diagnosis web app for a demonstration. He showed how adding ‘insect bites’ to a list of symptoms can help clinicians narrow down potential diagnoses to arrive at the most probable one.


Image: GIDEON differential diagnosis of mosquito-borne illnesses in the United States. List ranked by probability based on symptoms. Copyright @ GIDEON Informatics Inc.
Image: GIDEON differential diagnosis of mosquito-borne illnesses in the United States. The list is ranked by statistical probability. Copyright @ GIDEON Informatics Inc.



The Need for More Data-Driven Research on Mosquito-Borne Diseases

West Nile virus is one of the most severe mosquito-borne diseases that Dr. Berger treats. He mentioned that West Nile is more common in adults than in children. However, he also stressed that there is still an excellent opportunity for further research on several topics. For example, is West Nile more common in adults solely due to physiology? Or are there social factors – for example, children may not be allowed out at night? This may reduce their exposure to the virus.


West Nile Fever outbreaks map, 1955 to 2020
Image: West Nile Fever World Outbreak Map, 1955 to 2020. Copyright © GIDEON Informatics Inc.



Similarly, St. Louis encephalitis can even be fatal for adults, but children are mainly unaffected. Why is this so? More research in this field can offer greater insight.

Dr. Jones and the panel also discussed the challenges and industry best practices to curb the import and export of vector-borne diseases at different ports of entry.

For more, please watch the GIDEON, Avia-GIS, and the University of Florida collaborative webinar on the Invasive Aedes Mosquitoes: Dengue, Chikungunya, and Zika risks in Florida and the United States.



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New Tetanus Cases Reported. What to Do About This Deadly Infection?


Tetanus is an infectious disease caused by the pathogenic bacteria Clostridium tetani
Image: 3D illustration of Clostridium tetani, the agent of Tetanus


written by Chandana Balasubramanian

There’s an urban legend about Tetanus shots. Many people feel you need them only when you step on a rusty nail or if a splinter pokes you. Like any good myth, there is a tiny bit of truth attached to it. Yes, stepping on a nail is a good reason to get a Tetanus shot – but not because of the rust. Once your skin barrier is ruptured, Tetanus bacterial spores from contaminated items can easily enter your body.

The truth is there are many ways to get Tetanus. Spores of the bacteria that cause Tetanus, Clostridium tetani, are commonly found in the soil, dust, and intestines, and feces of several household animals and herbivores, and even humans. However, it does not spread from one person to another. The best way to control Tetanus infections is to prevent them from occurring entirely.


Tetanus Epidemiology: Recent and Older Outbreaks

Worldwide, Tetanus cases have declined rapidly due to mass immunization drives by various governments and public health agencies. However, Russia recently reported its first case of Tetanus in nearly two decades in September 2021 [1]. In India, a 12-year-old boy recently survived a severe case of Tetanus [2]. He had not been vaccinated against it. In Northern Kazakhstan, a 53-year-old man died due to Tetanus, and it is not known if he was vaccinated [3].

One potential reason for these new reports of this highly preventable infection is COVID-19.  In July 2020, WHO and UNICEF warned of disruptions to life-saving immunization services across the world due to the pandemic. Healthcare workers and social workers have been unable to follow standard vaccination schedules for many reasons, including:

  • Lockdowns and social distancing,
  • Disruption to transportation,
  • Fear or reluctance to visit hospitals or clinics for non-urgent health services,
  • More healthcare workers diverted towards COVID-19 and emergency services, and
  • A lower number of available auxiliary nursing midwives (ANMs) to drive regional vaccination for children.

Before the pandemic, two notable Tetanus outbreaks occurred in Indonesia during the devastating tsunami in 2005 and an earthquake in 2006. People hurt in disasters are, in general, at a much higher risk of getting infected with Tetanus. In certain parts of Indonesia, a lack of adequate transportation, access to health facilities, and awareness about Tetanus protocols led to many people dying from Tetanus. Another instance of a Tetanus outbreak was after the 2005 earthquake that struck Pakistan [4].


Tetanus worldwide cases and rates
Image: Worldwide Tetanus cases and rates, 1980 to 2020. Copyright © GIDEON Informatics, Inc.


What Causes Tetanus? What are the Symptoms of Tetanus?

Tetanus is one of the deadliest microbial toxins. It is caused by the bacteria Clostridium tetani and has a high fatality rate. Approximately 10-20% of cases are fatal.

Tetanus is also commonly known as lockjaw. Spores of the bacterium, Clostridium tetani, enter our bodies and spread all over the central nervous system. The spores produce a toxin called tetanospasmin that blocks nerve signals from the spinal cord to the rest of the muscles. The condition is also commonly known as lockjaw because it often causes muscle spasms in the jaw and neck, though it may spread to the rest of the body.

Other symptoms are fever, sweats, a rise in blood pressure, and an elevated heart rate. A common complication of Tetanus is when vocal cords begin to spasm, causing breathing difficulties. Infected individuals can also break their bones or spines based on the severity and frequency of convulsions caused by Tetanus [5].


About Clostridium Tetani

Tetanus spores cannot be killed easily. They are found everywhere and can resist extreme conditions like high heat and strong disinfectants. They can remain inactive but infectious for more than 40 years.

Clostridium tetani is an anaerobic bacterium; it does not live or grow in the presence of oxygen. As a result, there is a higher risk of infection with injury sites that do not receive a strong oxygen supply. This includes deep wounds, burns, needle punctures, and surgical procedures performed without adequate hygiene protocols.

While a Tetanus infection can have serious effects, it is now rare in most developed countries. The United States reports an average of 20 cases per year, mostly in unvaccinated individuals. Though most cases are found in developing countries, many of them now maintain rigorous vaccination programs and made great strides in eliminating or minimizing the incidence of Tetanus. Anyone can get infected, but children and newborns are the most susceptible.


Image: Clostridium tetani. Anatomy of the cell with terminal spore, and vegetative cell. Structure of the terminal spore: core, cortex, and spore coat.
Image: Clostridium tetani. Anatomy of the cell with terminal spore, and vegetative cell. Structure of the terminal spore: core, cortex, and spore coat.


What is the Incubation Period for Tetanus?

The incubation period for Tetanus is anywhere from three to twenty-one days, with an average of ten days. The incubation period varies based on how far the injury site is from the central nervous system. Symptoms can last for weeks and even months. They are higher in unvaccinated individuals and older people for whom immunity is lowered.

Is there a Cure for Tetanus?

There is no cure for Tetanus, but the Tetanus vaccine is highly effective in preventing infection. Once infected, however, symptoms are managed until the effects of the toxin diminish. Chances of survival are lower if muscle spasms develop within five days of getting infected.

There are no blood or laboratory tests to diagnose Tetanus. The most common initial symptom is ‘trismus’ or lockjaw due to facial muscle spasms.

Tetanus can be confused with certain other conditions, which makes it more important to educate frontline clinicians about confirming their own initial assessments either with experts or a platform like GIDEON that factors epidemiology data into differential diagnosis.

How to Treat Tetanus?

Tetanus is considered a medical emergency, and hospital care is required. Treatment is often medication called Tetanus Immune Globulin (TIG), also known as Tetanus antitoxin. It is usually administered as a preventive measure for high-risk wounds and injuries. It is also part of the treatment protocol, together with muscle relaxants and antibiotics like penicillin. When required, proper wound cleaning and debridement are also essential to minimize the risk of Tetanus infections. Patients with difficulty swallowing may also need a breathing tube or ventilator [6].

Preventing the Rise of Tetanus Infections

The best prevention is to ensure newborns, children, and adults receive their Tetanus vaccine doses according to the recommended schedule.

Vaccines for Tetanus are often combined with those for other diseases:

  • DT Vaccines: Diphtheria and Tetanus
  • DTaP or DTP Vaccine: Diphtheria, Tetanus, and Pertussis (whooping cough)
  • Td Vaccine: Tetanus and Diphtheria
  • Tetanus Immune Globulin (TIG)

It is important to note that Tetanus vaccines do not offer lifetime immunity. Many people may need booster shots to continue receiving protection against Clostridium tetani. Additionally, building awareness about improved infection control measures for childbirth, surgery, and other medical protocols in developing and under-resourced nations can make a difference.


WHO-UNICEF estimated vaccine coverage of Tetanus
Image: WHO-UNICEF estimated vaccine coverage of Tetanus graph, 1980 – 2019. Copyright © GIDEON Informatics, Inc.



[1] Outbreak News Today, “Russia: First Tetanus case reported in Sverdlovsk in nearly two decades,” 19 09 2021. [Online]. Available: [Accessed 29 09 2021].
[2] Times of India, “12-yr-old with rare Tetanus survives at GMCH after 37 days on ventilator,” 17 09 2021. [Online]. Available: [Accessed 29 09 2021].
[3] Outbreak News Today, “Tetanus death reported in Northern Kazakhstan,” 4 09 2021. [Online]. Available: [Accessed 09 29 2021].
[4] New York Times, “Twenty-two Tetanus deaths reported in Pakistan quake zone,” NY Times, 27 10 2005. [Online]. Available: [Accessed 29 09 2021].
[5] H. Bjørnar, “Tetanus: pathophysiology, treatment, and the possibility of using botulinum toxin against Tetanus-induced rigidity and spasms.,” Toxins (Basel), vol. 5, no. 1, pp. 73-83, 2013.
[6] Centers for Disease Control and Prevention, “Tetanus for Clinicians,” CDC, [Online]. Available: [Accessed 29 09 2021].



Lymphatic Filariasis: Everything You Need To Know About This Neglected Tropical Disease

Image: Brugia malayi in blood, a roundworm nematode, one of the causative agents of lymphatic filariasis, 3D illustration showing the presence of sheath around the worm and two non-continuous nuclei in the tail
Image: Brugia malayi in blood, a roundworm nematode, one of the causative agents of lymphatic filariasis, 3D illustration showing the presence of sheath around the worm and two non-continuous nuclei in the tail


written by Chandana Balasubramanian


Lymphatic Filariasis, commonly known as Elephantiasis, is considered a Neglected Tropical Disease (NTD). This is unfortunate because it is the second leading cause of permanent and long-term disability in the world! [1] As of 2019, it continues to be a threat to over 859 million people in over 70 countries. 

Like other Neglected Tropical Diseases, it is endemic to low-income regions of the globe that deal with poor water quality, sanitation, and limited access to healthcare. India accounts for 47% of chronic Filariasis and 39% of the at-risk population [2]. The good news is that it is considered “potentially eradicable” and can be prevented through timely treatment. Disease spread can be controlled through mosquito control measures [3]. 

But what is this disease? What are the different types of Lymphatic Filariasis? Where is it found? How do we treat it? 


What is Lymphatic Filariasis? 

Lymphatic Filariasis is an infectious tropical disease caused by parasitic roundworms (nematodes) transmitted by mosquitoes. The disease is named after the family of worms, Filariodidea.  

The disease affects the lymphatic system – the intricate network in our body that is an integral part of our circulatory and immune systems. It can cause severe swelling and disfigurement; body parts may swell up to abnormal proportions. 

Because of the resulting disfigurement and pain, people suffering from Lymphatic Filariasis often face social isolation and loss of income, leading to mental health issues and greater poverty. 

In recent years, the World Health Organization (WHO) and high-risk countries, have organized mass treatment of all eligible people against Lymphatic Filariasis. This type of preventable chemotherapy has successfully proven to help stop the spread of infection [4].  


What are the types of Lymphatic Filariasis? 

There are three types of Lymphatic Filariasis based on the type of pathogen that causes the disease – Bancroftian, Brugia malayi, and Brugia timori.

1. Bancroftian Lymphatic Filariasis

Bancroftian Lymphatic Filariasis comprises 90% of all lymphatic filariasis cases around the world. It is caused by a worm called the Wuchereria bancrofti (W. bancrofti). The earliest descriptions of Bancroftian Filariasis dates as far back as 600 B.C. in India! The disease is named after the dynamic father-son duo of eminent Australian doctors and parasitologists Dr. Joseph Bancroft and Dr. Thomas Bancroft. 

The W.bancrofti worm needs two hosts to complete its life cycle. It sexually reproduces in humans and matures in Anopheles mosquitoes. This has a long incubation period of anywhere from 5 – 18 months, making it harder to detect early without preventive care in high-risk areas.


Image: Advanced Elephantiasis - a patient in the Philippines
Image: Advanced Elephantiasis – a patient in the Philippines


2. Brugia malayi

The Brugia malayi is a type of roundworm that relies on Mansonia and Aedes mosquitoes as vectors. The adult worms that grow in a human’s lymphatic system are similar but smaller to the W.bancrofti. Human infection often includes swollen lymphatics of the neck, groin, or axilla. 

Brugia malayi is endemic to South and Southeast Asia. It usually takes many bites from mosquitoes carrying the Brugia malayi pathogen before a human can be infected. This is why high-risk countries need to improve their sanitation and water quality standards. Additionally, they need to periodically perform proactive mass drug treatments proven to be effective against Lymphatic Filariasis. 

3. Brugia Timori

Brugia timori is a roundworm that uses the Anopheles mosquito as its vector. The life cycle of this worm is similar to the W.bancrofti and Brugia malayi. The prevalence of this variety of Lymphatic Filariasis is much less compared to the other two. It is usually limited to Timor and the Lesser Sunda archipelago of southeast Indonesia [5]. 

A review of Brugia timori on the GIDEON (Global Infectious Diseases and Epidemiology Online Network) database shows that the number of people infected by Brugia timori is estimated to be less than 800,000. 

There are many similarities in symptoms of the three types of Lymphatic Filariasis, but differences do exist. Below is a dynamic comparison chart generated by the GIDEON platform for symptoms of W.bancrofti, Brugia malayi, and Brugia timori infections.


Comparison chart for clinical findings related to Bancroftian, Brugia malayi, and Brugia timori Lymphatic Filariasis. Copyright © GIDEON Informatics, Inc.
Image: Comparison chart for clinical findings related to Bancroftian, Brugia malayi, and Brugia timori Lymphatic Filariasis. Copyright © GIDEON Informatics, Inc.


What is the Best Treatment for Lymphatic Filariasis?  

Treatment for Lymphatic Filariasis is concentrated around large-scale chemotherapy known as mass drug administration (MDA). WHO recommends an annual dose of preventive chemotherapy drugs to high-risk populations:

  • Albendazole (400 mg) alone twice per year for areas co-endemic with loiasis
  • Ivermectin (200 mcg/kg) with albendazole (400 mg) in countries with onchocerciasis
  • Diethylcarbamazine citrate (DEC) (6 mg/kg) and albendazole (400 mg) in countries without onchocerciasis [4]. The United States falls in this category. 

In countries without onchocerciasis (river blindness, another type of Filariasis), WHO also recommends ivermectin (200 mcg/kg) together with diethylcarbamazine citrate (DEC) (6 mg/kg) and albendazole (400 mg) in certain settings. 

A graph illustrating the number of people targeted for mass drug administration (MDA) for Filariasis worldwide.
Image: The global number of people targeted for mass drug administration (MDA) for Filariasis. Copyright © GIDEON Informatics, Inc.


Some studies have shown that Doxycycline administered over six weeks significantly improved the severity of Lymphatic Filariasis in patients with and without active infection. Doxycycline worked to revert or halt the progression of early stages of Lymphatic Filariasis (1-3), not later ones [6]. Doxycycline is an antibiotic often touted as a ‘wonder drug’ because it can kill various pathogens in situations where other antibiotics may fail, like for malaria and against Yersinia pestis, the bacteria responsible for the Plague. The effects of Doxycycline last for a while, so it is effective for both treatment and prevention. 


Image: A graph illustrating countries enrolled on mass treatment programs for Filariasis
Image: A graph illustrating countries enrolled on mass treatment programs for Filariasis. Copyright © GIDEON Informatics, Inc.


How to Prevent the Spread of Lymphatic Filariasis? 

Apart from MDA methods, stringent vector control is essential to eliminate or reduce the incidence of Lymphatic Filariasis. Studies show that vector control after MDA is extremely effective in reducing the resurgence of the disease and preventing spread. Vector control includes bed nets and the regular spraying of insecticides to prevent mosquito bites [7]. 

Additionally, more researchers are beginning to incorporate the epidemiological impact of infectious diseases in their studies. For example, over 20 research papers used GIDEON epidemiology data on infectious diseases as part of their parasitology-focused papers in the past three years alone. This is a welcome trend that can raise awareness about neglected tropical diseases, preventive measures and help drive much-needed resources towards mitigating the devastating effects of these parasites. 


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[1]  CDC (Centers for Disease Control and Prevention), “Hygiene-related diseases: Lymphatic Filariasis,” 2 08 2016. [Online]. Available: [Accessed 15 09 2021].
[2]  GIDEON Database (Global Infectious Diseases and Epidemiology Online Network), “Filariasis – Bancroftian worldwide distribution,” GIDEON Informatics, Inc, 2021.
[3]  PAHO (Pan American Health Organization), “,” PAHO, [Online]. Available: [Accessed 15 09 2021].
[4]  WHO (World Health Organization), “,” WHO, 18 05 2021. [Online]. Available: [Accessed 15 09 2021].
[5]  P. Fischer, T. Supali and R. M. Maizels, “Lymphatic filariasis and Brugia timori: prospects for elimination,” Trends Parasitol, vol. 20, no. 8, pp. 351-5, 2004. 
[6]  S. Mand, A. Y. Debrah, U. Klarman, L. Batsa, Y. Marfo-Debrekyei, A. Kwarteng, S. Specht, A. Belda-Domene, R. Fimmers, M. Taylor, O. Adjei and A. Hoerauf, “Doxycycline Improves Filarial Lymphedema Independent of Active Filarial Infection: A Randomized Controlled Trial,” Clin Infect Dis., vol. 55, no. 5, p. 621–630, 2012. 
[7]  E. L. Davis, J. Prada, L. J. Reimer and T. D. Hollingsworth, “Modelling the Impact of Vector Control on Lymphatic Filariasis Programs: Current Approaches and Limitations,” Clinical Infectious Diseases, vol. 72, no. Supplement_3, p. S152–S157, 2021. 

Epidemiology Terms Explained: Incidence, Prevalence, Seroprevalence, Morbidity, Mortality, Outbreaks, Epidemics, and Pandemics

Abstract word cloud for Epidemiology with related tags and terms

Written by Chandana Balasubramanian


Whether you are a student of nursing, health sciences, public health, or another specialty, you may be interested in expanding your knowledge of epidemiology. Today, the study of infectious diseases is not limited to specialists in the field or researchers. This is because, in our ever-shrinking world, an emerging disease can turn from a small outbreak in one country to a global pandemic in a few weeks. Additionally, shrinking forests and greater urbanization increase the risk of zoonotic transmission of pathogens (transfer of an infectious virus or bacteria to humans from animals). 

Understanding the spread of diseases and epidemiological data can help clinicians and nurses detect and curtail infections early, and public health and government agencies prevent the spread of emerging infectious diseases on their shores.  

Here are the most common epidemiological metrics to help you get started.



Incidence refers to the probability of a disease occurring in a given population in a specific time period. The incidence measures new cases that develop or are diagnosed in a month or a year. 

For example, compare the two GIDEON maps below color-coded based on incidence. The first map is an outbreak map for the plague and the second is that for SARS-COV-2 or COVID-19. Between the two, even at first glance, we can identify the higher incidence of COVID-19 versus the current endemicity of the Plague.


Plague global outbreaks map, illustrating disease incidence between the years 1348 to 2021. Copyright © GIDEON Informatics, Inc
Plague global outbreaks map, years 1348 to 2021. Copyright © GIDEON Informatics, Inc.




Image: COVID-19 global outbreaks map, illustrating disease incidence between the years 2019 to 2021. Copyright © GIDEON Informatics, Inc.
Image: COVID-19 global outbreaks map, years 2019 to 2021. Copyright © GIDEON Informatics, Inc.



Prevalence includes all the people who suffer from a specific condition in a population during a specified period. 

Incidence Versus Prevalence

Incidence refers to newly developed cases of a disease or illness within a specific time frame, while prevalence tells us the total number of individuals who are living with it. 

Let’s look at infections from COVID-19 (SARS-COV-2) as an example. In December 2019, when the first outbreak happened, incidence and prevalence numbers worldwide were low. By March 2020, incidence numbers (newly diagnosed cases) were high. Global prevalence numbers were still low because the virus hadn’t spread to the larger population as yet. But by July 2021, due to highly infectious variants, worldwide incidence and prevalence numbers were high. 


Seroprevalence refers to the number of people in a population who test positive antibodies to a pathogen (infectious virus or bacteria). Seroprevalence to an antibody to a virus or pathogen can give us an idea of the number of people infected with the virus. 

Seroprevalence is expressed as the percentage of people with antibodies to an infectious agent. 

Seroprevalence Survey or Serosurvey

A seroprevalence survey involves blood serum testing of a population and monitoring whether a particular substance is present or absent. These seroprevalence surveys can be tailored based on how widespread or localized infection is. These studies help public health officials and epidemiologists understand how an infectious agent or pathogen is spreading across a specific population over time. 


Image: COVID-19 United States Seroprevalence studies list screenshot, Country Note from GIDEON database. Copyright © GIDEON Informatics, Inc.
Image: COVID-19 United States Seroprevalence studies list screenshot, Country Note from GIDEON database. Copyright © GIDEON Informatics, Inc.



Morbidity Rate

Morbidity means disease. Morbidity Rate measures how often a specific disease or illness occurs in a given population and includes acute and chronic conditions. The metric is used by public health officials, governments, healthcare systems, epidemiologists, and many more to estimate the overall health of a given population. A higher morbidity proportion indicates a greater number of people suffering from illnesses or diseases.  

The Morbidity Rate is expressed as a percentage of the number of cases of a specific disease or condition in a given population. 


Image: Anthrax (Bacillus Anthracis) annual cases in the United States, 1930 - 2020. GIDEON database. Copyright © GIDEON Informatics, Inc
Image: Anthrax (Bacillus anthracis) annual cases in the United States, 1930 – 2020. Copyright © GIDEON Informatics, Inc.



Attack Rate (AR) or Incidence Proportion

The Attack Rate measures the proportion of people who develop a specific condition or illness in a population that was initially free from that disease or illness. This metric is commonly used in epidemiology to track disease outbreaks. Public health officials use the metric to estimate how many individuals may be infected during an outbreak, epidemic, or pandemic. 

The Attack Rate or Incidence Proportion is calculated as the number of new cases of an infection in the total at-risk population. It is expressed as a percentage. 

Secondary Attack Rate (SAR)

The Secondary Attack Rate estimates the spread of infection from an individual to people in their household, residential area, or to another specified group of people who are at risk of getting infected (like hospital staff). SAR is an important metric during contact tracing for infectious diseases.   

Just like the Attack Rate, the Secondary Attack Rate is expressed as a percentage. It is the number of new cases of an infection developed among a person’s contacts out of their total number of contacts. 

Incidence Rate (IR) or Incidence Density Rate or Person-Time Incidence Rate

Incidence rate measures the number of new cases of a disease occurring in a given population during a specified timeframe. 

Incidence Rate is often expressed as the number of new cases per 100,000 population. 



Mortality Rate (MR)

Mortality refers to death. The Mortality Rate or Death Rate helps us understand how frequently death occurs in a given population in a specific amount of time. 

The metric is expressed as deaths per 1,000 individuals per year or 100,000 individuals per year. 


Image: Dengue Mortality Rates for India, GIDEON screenshot. Copyright © GIDEON Informatics, Inc.
Image: Dengue Mortality Rates for India, 1991 – 2020. Copyright © GIDEON Informatics, Inc.


Crude Mortality Rate

Crude Mortality Rate measures the total number of deaths in a population during a specific period of time. It is called ‘crude’ because the number includes all deaths and is used to provide a high-level estimate of deaths during a humanitarian crisis. 

It can be expressed as deaths per 1,000 or 100,000 individuals per year. 

Case-fatality Rate (CFR) or Case-fatality Proportion

The case-fatality rate is used to understand the severity of a disease, evaluate new therapies, and predict how a disease will continue to affect a given population. It estimates the percentage of individuals who die from a specific disease among all people diagnosed with the disease for a given period. It is best applicable for diseases that have specific starts and stops, like acute infections or outbreaks. In reality, it is not a rate but the proportion of deaths due to a specific disease condition. 

It is expressed as a percentage. A higher percentage indicates greater disease severity due to more deaths from the disease. 

Cause-Specific Mortality Rate

Cause-specific Mortality Rate is the number of deaths from a particular cause in a population during a given time interval (usually a calendar year). 

It is expressed as deaths per 100,000 individuals. 

Note: It is different from the case-fatality rate which is not exactly a rate but a proportion of deaths in a population from a particular disease. 

Age-Specific Mortality Rate

The Age-specific Mortality Rate gives us the mortality rate for a specific age group of individuals in a given population. It is also often known as the age-adjusted mortality rate. It is the best way to understand diseases that are highly influenced by age and their impact on a population. This metric is commonly used to understand the rates of heart disease conditions, strokes, diabetes, cancer, and more in a population. 

Age-specific mortality is expressed as deaths per 100,000 in an age range.  

Maternal Mortality Rate (MMR)

The Maternal Mortality Rate is a ratio that helps us understand how many women die from pregnancy-related complications in a population. It is the number of maternal deaths by the total number of live births in a given period. 

The MMR is an important health indicator for a country or a given population because most pregnancy-related deaths are preventable. The biggest pregnancy-related complications include bleeding after childbirth, infections, high blood pressure during pregnancy, and issues that arise during delivery. 

MMR is expressed as deaths per 100,000 live births. 

Infant Mortality Rate (IMR)

The Infant Mortality Rate measures the probability of a child born in a specific period of time dying before it turns one. It helps us understand the likelihood of a newly born infant surviving in a particular population. Since the probability of survival is closely linked to the social structures, economic, and health conditions of a country, it is often a significant indicator of a nation’s health.

It is expressed as deaths per 1,000 live births. 



The term endemic is used to refer to anything that naturally occurs and is confined to a particular location, region, country, or population. For example, from the malaria outbreak map below, we can see that chloroquine-resistant malarial strains are endemic to certain regions in South Asia, Africa, and South America. 

Image: Malaria - current endemicity and historical outbreaks map, illustrating disease incidence between 1866 - 2021. Copyright © GIDEON Informatics, Inc.
Image: Malaria – current endemicity and historical outbreaks map. Copyright © GIDEON Informatics, Inc.


An epidemic affects many people at the same time. In an epidemic, there is a sudden increase in disease infections that spreads in a region or locality where the disease condition is not naturally found. 


An outbreak is a sudden increase in the number of people infected by or diagnosed with a specific disease condition. It is similar to an epidemic but usually restricted to a much smaller locality or geographic location. 


A pandemic is an epidemic that has spread to several countries or continents. It usually affects a much larger group of people than an epidemic. 


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Busy Microbiology Labs Can Detect Infectious Diseases And Biological Threats Faster. Here’s How.

Person in a hazmat suit working in a laboratory setting
Photo by Satheesh Sankaran on Unsplash


written by Chandana Balasubramanian


Could your patient have kissed a camel recently? A new patient may have fallen ill after indulging in a little ‘tari’ (fermented date palm sap) in Southeast Asia. Or could your hospital be in the midst of a Candida Auris outbreak – the multi-drug resistant, severe-illness causing, and often-misidentified yeast?  

When you need to identify an unknown pathogen or biothreat agent, as the title song of the movie ‘Ghostbusters’ goes, “Who you gonna call?” If you’re in Maryland, Sheryl Stuckey and her clinical microbiology lab at the Holy Cross Hospital, Silver Spring, may be the help you need.


The system has been helpful in preparing continuing education for my team.  It helps us with unusual organisms and steering us toward possibilities when people have traveled or reside in other countries.”

Sheryl Stuckey, Manager, Microbiology Lab
Holy Cross Hospital, Silver Spring, Maryland, USA


Accuracy and Efficiency: Challenges of a Busy Clinical Microbiology Lab 

Running a Full-Fledged Lab 

Led by Sheryl Stuckey, the Microbiology lab at the Holy Cross Hospital, Silver Spring, Maryland, has to run with a high level of efficiency. It is usually abuzz with energy from handling a wide range of tasks for the hospital and external agencies. Although the hospital is a community hospital with 450+ beds, it serves patients from all over the world. Even the staff is diverse and represents over 80 countries. But that’s not all. 

Expert in Infectious Diseases and Pathogens 

Sheryl faces an added layer of responsibility – she is the lab tech for clinical microbiology in her hospital, and no one else in her chain of command knows this diagnostic area. Hospitalists (physicians who specialize in treating hospitalized patients) often reach out to Sheryl for help with identifying or confirming a pathogen diagnosis. 

For example, she recently helped a hospitalist identify MERS (Middle East Respiratory Syndrome, also known as ‘camel flu’). While the physician suspected something else, the microbiology lab suggested checking for the patient’s travel history. Says Sheryl, “He hadn’t thought to ask, and when he did, he learned that she had traveled to the Middle East and kissed a camel. Crazy, right?”


Image: GIDEON database MERS worldwide distribution notes. Copyright © GIDEON Informatics, Inc
Image: GIDEON database MERS worldwide distribution notes. Copyright © GIDEON Informatics, Inc


Sentinel Clinical Lab for Biothreat Agents 

The Holy Cross Hospital microbiology lab is also a certified Sentinel Clinical lab to assess suspected agents of bioterrorism, special pathogens, and emerging infectious diseases for their county [1]. The lab packages and ships potential and actual biothreat specimens to the Maryland State Laboratory for special pathogens, surveillance organisms (like COVID-19, Auris, CREs, and more). The lab offers guidance on what specimens to collect and how to collect them safely. The CDC states that Sentinel Laboratories “play a key role in the early detection of biological agents.”  

Partners with Automated Laboratory Team 

The lab is also PPE buddies for their Automated Laboratory Partners for routine testing for potentially infectious pathogens and Person Under Investigation (PUI) for a special pathogen. The PPE buddy system ensures that lab members look out for each other and follow all recommended safety protocols when dealing with infectious (or potentially infectious) pathogens. 

There is little room for error when dealing with infectious diseases, special pathogens, and potential biological threats. Early and accurate detection is critical to prevent or mitigate outbreaks and more widespread devastation.


Using GIDEON for Accurate and Timely Detection of Infectious Diseases and Biological Threats


“I rely on this program because it has everything I need in a pinch.” 

– Sheryl Stuckey


For Microbiology Labs

The Holy Cross Hospital Microbiology Lab appreciates the vast resources that GIDEON offers. GIDEON – the Global Infectious Diseases and Epidemiology Online Network – is a preferred partner for microbiology labs worldwide. 

About GIDEON, Sheryl states, “My favorite features are the organism identification function, information about diseases, comparison of organisms, and now the flowchart function.” She adds, “The system has been helpful in preparing continuing education for my team.  It helps us with unusual organisms and steering us toward possibilities when people have traveled or reside in other countries.”

Designed together with microbiology experts, GIDEON’s lab resources can help:

  • Identify 2000+ pathogens with a few clicks,
  • Generate a ranked pathogen probability list based on Bayesian analysis-based differential analysis,
  • View detailed pathogen outbreak maps, and
  • Elevate training to include dynamic step-by-step decision trees for unknown bacteria projects.


Image: GIDEON microbiology lab diagnosis probability engine and unknown pathogen decision tree. Copyright © GIDEON Informatics, Inc
Image: GIDEON microbiology lab diagnosis probability engine and unknown pathogen decision tree. Copyright © GIDEON Informatics, Inc


For Physicians and Researchers 

An added bonus for hospitals, research hospitals, and teaching institutions is that GIDEON is the most comprehensive database of historical and current infectious disease outbreaks worldwide. Healthcare professionals and researchers can save a lot of time by using the GIDEON one-stop resource for infectious disease and epidemiology research



The GIDEON infectious disease database empowers microbiology labs, hospitals, physicians, and researchers to identify and detect pathogens early and more accurately. 

The platform hosts a wide variety of tools to help busy microbiology labs compare pathogens, analyze the epidemiological impact of patients’ travel histories, use probability engines and decision trees for pathogens and unknown bacteria, mycobacteria, and yeasts.


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[1]  ASM (American Society for Microbiology), “Laboratory Response Network (LRN) Sentinel Level Clinical Laboratory Protocols,” 20 11 2013. [Online]. Available: [Accessed 2021 08 16].

Recent Anthrax Infections: All You Need to Know About the Deadly Bacillus Anthracis


Image: Bacillus anthracis, a gram-positive spore-forming bacteria that causes Anthrax
Image: Bacillus anthracis, a gram-positive spore-forming bacteria that causes Anthrax


written by Chandana Balasubramanian

Trends from past decades can be delightful when they return to inspire today’s music, fashion, and art. However, recently, a dangerous blast from the past reared its ugly head. In early August 2021, China reported a case of the deadly Anthrax pneumonia – its first case after ten years [1]. A few weeks later, local health authorities in another Chinese province discovered nine suspected cases of Anthrax [2]. Around the same time, Russia confirmed a case of Anthrax with a cutaneous infection in a patient involved in butchering cattle meat [3]. 

It’s time to pay more attention to these small outbreaks. 


Anthrax Infections Can Be Serious

While these reported incidents seem to have been related to interactions with domesticated animals, Anthrax has been used as a deadly weapon for more than a hundred years. 

One of the most well-known instances of Anthrax used as a biothreat was in the United States, right after the 9/11 attacks of 2001. Five Americans died, and 17 were severely infected when contaminated letters lined with Anthrax were mailed through the U.S. postal service to senators and members of the media. In response, the Federal Bureau of Investigation or FBI launched ‘Amerithrax’- one of the biggest and most complicated investigations in U.S. history. After conducting more than 10,000 interviews on many continents and collecting over 5,730 environmental samples, they found their suspect. 

Understanding the epidemiology, cross-border transmissions, and the history of this zoonotic pathogen is essential to help encourage safe practices when handling livestock and avert potential threats.


Bacillus Anthracis Infections Are Not Contagious but Serious

Anthrax is caused by the gram-positive bacteria Bacillus Anthracis. The infection is not spread rapidly from person to person through the air like the flu or cold. It can, however, cause severe illness in domestic animals and humans if they interact with infected animals or contaminated animal products. 

The most common natural way people get a Bacillus Anthracis infection is cutaneous, after skin contact with contaminated meat, wool, or leather from infected animals. Cutaneous Anthrax infection can be transferred from one person to another through open lesions. Another form of infection is gastrointestinal Anthrax which is contracted when raw or undercooked contaminated meat is ingested. The most harmful method of Anthrax infection is through inhalation, by breathing in bacterial spores in the air. It is fatal unless treated immediately. 

Inhalation of Bacillus Anthracis spores is not common in nature. Still, this method has been exploited throughout history for bioterrorism purposes. Bacillus Anthracis infections have affected almost every corner of the globe.  

Image: World map of Bacillus Anthracis outbreaks, 1770-2021. Copyright © GIDEON Informatics, Inc.
Image: World map of Bacillus Anthracis outbreaks, 1770-2021. Copyright © GIDEON Informatics, Inc.


Bacillus Anthracis: A Dark History of Bioterrorism

Bacillus Anthracis is effective as a weapon primarily because of its spores. In nature, an infected host sheds the spores on the ground, which then multiply on contact with air. These spores can stay dormant for years, even decades, in the soil waiting for another host [4]. The infection cycle then continues. However, when these microscopic spores can be aerosolized as sprays or powders, they can be released silently and escape detection. Even a small number of spores released in the air can infect massive numbers of people.  

In the United States, the Centers for Disease Control and Prevention (CDC) considers Anthrax as Category A – a Bioterrorism Agent. And indeed, the Bacillus Anthracis has been cultivated and used for bioterrorism from as early as 1915. 

A review of the GIDEON Bioterrorism note for Anthrax shows a long murky past of the pathogen being released by countries during the war, by terrorists to spread fear and destruction, or by accident. 


Image: Snippet of Bacillus Anthracis Bioterrorism Note from GIDEON database. Copyright © GIDEON Informatics, Inc.
Image: Snippet of Bacillus Anthracis Bioterrorism Note from GIDEON database. Copyright © GIDEON Informatics, Inc.


The 2001 U.S. Anthrax incident was more recent. A much larger Anthrax outbreak was an accidental 1979 Anthrax leak. Bacillus Anthracis spores were released from a secret Soviet military research center in Sverdlovsk, Russia. The story has all the intrigue and devastation that is characteristic of the Cold War. 60-70 people are estimated to have died from the accident, now termed the ‘Biological Chernobyl.’ The entire incident and related deaths were covered up and blamed on contaminated meat. It was only almost thirteen years later that a team of expert molecular biologists from Harvard University could investigate the spread of the spores on behalf of the CIA [5]. The team confirmed that aerosolized spores spread through the air and caused the outbreak, not meat. 

WATCH/LISTEN TO PODCAST: Dr. Berger discusses Anthrax infections and the associated bioterrorism history with ‘Outbreaks News’

Symptoms of Bacillus Anthracis Infections

Cutaneous Anthrax Infections

  • Itchy blisters or bumps
  • Painless skin sores that are black in the middle develop after the blisters or bumps 

Gastrointestinal Anthrax Infections

  • Fever and chills
  • Swelling of glands in the neck
  • Sore throat and trouble swallowing
  • Nausea and bloody vomit
  • Headaches
  • Diarrhea 
  • Stomach pain, and more

Inhalation Anthrax or Pulmonary Anthrax Infections

The most deadly but rare form of human anthrax infections. 

  • Fever and chills
  • Difficulty breathing
  • Cough
  • Dizziness 
  • Extreme fatigue
  • Sweats, and more.


This image depicts a man, whose left forearm exhibited a large cutaneous lesion, which had been diagnosed as a case of cutaneous anthrax, caused by the bacterium, Bacillus anthracis. Note the characteristic dark-brown to black-colored eschar that covered the lesion, from which the bacterium derives its name, being that the color resembles that of anthracite coal. The photographed had been captured by Georgian Field Epidemiology Training Program (FETP) resident, Archil Navdarashvili, while at Rustavi Hospital, in the country of Georgia, on August 25, 2012.
Image: This image depicts a man, whose left forearm exhibited a large cutaneous lesion, which had been diagnosed as a case of cutaneous anthrax, caused by the bacterium, Bacillus anthracis. Note the characteristic dark-brown to black-colored eschar that covered the lesion, from which the bacterium derives its name, being that the color resembles that of anthracite coal. The photograph was taken by Georgian Field Epidemiology Training Program (FETP) resident, Archil Navdarashvili, while at Rustavi Hospital, in the country of Georgia, on August 25, 2012.


Mitigating Bacillus Anthracis Infections

Cutaneous anthrax infections comprise the majority of anthrax infections worldwide. They are spread through contact with contaminated animals or animal products. The United States, the U.K., E.U., and many other countries worldwide have implemented better tests and protocols around the way animals are handled. With these processes in place, cutaneous anthrax infections have significantly decreased. 

However, it is extremely easy for anyone to carry an infectious disease endemic to one country and spread it to others. National public health agencies, frontline clinicians, infectious disease specialists, and microbiologists will have to work together to mitigate the effects of dangerous pathogens like the Bacillus Anthracis. Taking epidemiological data into account when diagnosing diseases in Point-of-Care settings can be a great first step towards containing emerging infections. 


Prefer your information in a video format? Here’s a recording of Dr. Berger discussing Anthrax on the ‘Outbreak News’ podcast:


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[1] “China Reports First Human Case of Pulmonary Anthrax in 10 Years,” [Online]. Available: [Accessed: 26-Aug-2021].

[2] Global Times, “Shanxi Province reports 9 suspected anthrax cases, treatment underway,” [Online]. Available: [Accessed: 26-Aug-2021].

[3] Press Release, “Human anthrax case reported in Karabudakhkent region, Russia,”, 10-Aug-2021. [Online]. Available: [Accessed: 26-Aug-2021].

[4] A. Chateau, S. Van der Verren, H. Remaut and A. Fioravanti, “The Bacillus anthracis Cell Envelope: Composition, Physiological Role, and Clinical Relevance”, Microorganisms, vol. 8, no. 12, p. 1864, 2020. Available: 10.3390/microorganisms8121864 [Accessed 26 August 2021].

[5] “Anthrax at Sverdlovsk, 1979”,, 2017. [Online]. Available: [Accessed: 26- Aug- 2021].

Bacterial Unknown Project: Hundreds of Easy Dichotomous Keys for Microbiology Courses

Bacterial Unknown Project - question mark and bacteria photo in the background
Bacterial Unknown Project. Original Photo by CDC on Unsplash


written by Chandana Balasubramanian

Fast, Online Flowcharts for Bacterial Unknown Projects

GIDEON’s Bacterial Unknown Project allows microbiology professors to make and print dynamic dichotomous keys online. Using hundreds of decision trees, you can help your students identify over 2,000 pathogens with a few clicks of your mouse. That’s right. No more drawing elaborate dichotomous key flowcharts by hand or using a clunky word processing program.

GIDEON (Global Infectious Diseases and Epidemiology Online Network) is one of the most well-known reference databases for infectious diseases and a trusted partner for clinicians and microbiologists worldwide. Together with microbiology professors, GIDEON designed an interactive decision tree tool to help identify bacteria, mycobacteria, and yeasts.

Sample screenshot of GIDEON Bacterial Unknown Project decision tree.
Sample screenshots of GIDEON Bacterial Unknown Project, decision tree.


A review from a satisfied customer:

“I was given 2 weeks to prepare the syllabus for two courses I needed to run in the fall semester, one in Public Health and the other in Pathogenic Microbiology. GIDEON was the perfect tool to build activities and learning around it made my job much easier!”

University of South Florida, Dr. Johnny El-Rady, Instructor (Microbiology and Genetics)


Microbiology professors agree that bacterial unknown projects are the ultimate test of a student’s understanding of pathogens in the classroom. Testing microbiology students with “mystery” bacteria allows them to combine their knowledge of pathogen molecular structures and biochemistry with essential laboratory techniques required to identify them.

However, these professors are also unanimous in accepting that preparing dichotomous keys for each class and semester can take time. As a result, students may attempt these active learning tests to identify microbes only once or twice in a semester.


Why Do Students Need to Identify Unknown Bacteria?

Learning through the Bacterial Unknown Project is a great way for microbiology students to get ready for the real world. After all, professionals in the laboratory are counted upon to identify or confirm the presence of pathogens. This expertise is essential whether in a hospital, clinic, or academic research lab. Working knowledge of fundamental laboratory techniques, conducting aseptic transfers, preparing media, and following a systematic flowchart to perform differential testing are invaluable skills.

For example, studying pathogens for further research involves isolating and developing pure colonies to study. This step is critical to make sure the result of further testing is accurate, but new students may find this step difficult and need to practice. This is relevant even though labs are getting more automated than before. To be a professional writer, you have to know the basics of grammar and not rely entirely on auto-correct. Professional musicians need to understand how music notes work together in harmony, even if the software is available to help create music.

Knowing how to perform laboratory techniques correctly will help students identify pathogens in imperfect situations and troubleshoot when things go wrong. Bacterial Unknown Projects are also significant learning assignments because students learn to record and organize their data appropriately, work with their peers, and present their reasoning in written reports. These skills are priceless in a professional setting, private or academic, where we are often asked to defend or explain our work to other teams.

However, since 2020, the learning environment across the globe has changed considerably. Microbiology professors have been facing challenges when it comes to administering Bacterial Unknown Projects online.


How to Conduct Bacterial Unknown Projects Online?

The COVID-19 pandemic inserted a bit of a nonsense mutation in the lives of many microbiology professors. With so much uncertainty, lockdowns, and other restrictions, academic instruction went online. Didactic courses were easier to convert into an online format, but how do bacterial unknown projects translate to remote learning? After all, the very point of a bacterial unknown activity is to train students in a hands-on setting for wet lab techniques.

The Department of Molecular Biosciences at the University of Kansas at Lawrence published their experience in the Journal of Microbiology and Biology Education, March 2021. After administering a test to identify an unknown microbe for about 50 students, they conducted a survey and collected anonymous responses. 80% of students surveyed reported the online bacterial unknown project successful in increasing their skills. The project took over three weeks, with the last week to prepare for oral presentations.

Evaluations focused more on effective student collaborations, arriving at the correct result by asking for the right virtual “tests,” peer evaluations, and communicating their findings in an oral presentation instead of a written report. The entire project was done using images of bacterial stains. The paper discusses how delivering bacterial unknown projects online is not a substitute for wet lab experiences but a complementary teaching method.

Tighter budgets for lab equipment and resources means often having to test students on a limited range of bacteria for in-person wet-lab testing. Creating dynamic dichotomous keys online can help students identify pathogens that are important to learn about but may not be possible to administer in a teaching laboratory.


Using GIDEON’s Bacterial Unknown Decision Trees for Laboratory and Remote Learning

GIDEON’s decision trees for bacterial unknown projects are designed with busy microbiology professors in mind.

Create a dichotomous key in just 3 steps:

Step 1: Specify whether you want to identify a bacteria, mycobacteria, or yeast.

Step 2: If identifying bacteria, select the gram reaction, bacterial shape, respiration, and other laboratory tests by following the intuitive flowchart.

Step 3: Print your key, or export and share with your peers. It’s that simple.

The example below shows the flowchart for Bacillus Subtilis. On the right, you also get a list of the most probable bacteria based on your selections.


Dichotomous key for Bacillus Subtilis. Screenshot from GIDEON's Bacterial Unknown Decision Tree.
Dichotomous key for Bacillus Subtilis. Screenshot from GIDEON’s Bacterial Unknown Decision Tree.



Bacterial Unknown Project is considered to be one of the most effective ways to learn microbiology. Students apply their theoretical knowledge of molecular structure, biochemistry, and lab techniques in a practical wet lab setting. However, the process of preparing dichotomous keys for each test is cumbersome. Microbiology professors who are pressed for time find it challenging to draw decision trees by hand or use a word processing program.

Additionally, when the COVID-19 pandemic began, remote learning became the new normal. While adapting all courses to an online format can be hard, making Bacterial Unknown Project applicable for remote learning is much trickier. Dynamic, online flowcharts and decision trees can help microbiology professors teach their students more effectively in online and wet laboratory settings.


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COVID-19 Vaccine: Do You Need It Even After Surviving COVID-19?

Brown t-shirt with 'I got my COVID vaccine' sticker on the pocket

written by Chandana Balasubramanian

“Should I get the COVID-19 vaccine even if I had COVID?” The answer is yes. Getting COVID-19 in the past is not a guarantee against reinfection.

An August 2021 study out of Kentucky, USA, studied hundreds of residents and found that unvaccinated survivors of COVID-19 had more than double the risk of getting reinfected with COVID-19 compared to the vaccinated group of people. Public health officials, medical professionals, and infectious disease experts worldwide continue to urge more people to get vaccinated as soon as possible. But some individuals who recovered from COVID-19 want to know why.

Wearing safety gear during on-ground combat will not prevent all adverse events. The gear is designed to prioritize and protect a soldier’s brain, heart, spine, and other vital organs from damage. The vaccines are meant to work the same way.

To those on the fence, the decision to get vaccinated or not requires more information. Queries from unvaccinated COVID-19 survivors include:

  • If you already had COVID-19, why are you not protected for life against the virus? After all, with a chickenpox infection, you get lifelong immunity.
  • If people who are vaccinated can still get infected with the Delta variant, why do we need the vaccine?
  • COVID-19 vaccines are currently approved for emergency use. Is this safe?
  • Which COVID-19 vaccine offers maximum protection against COVID-19 and variants like Delta?

Here are answers to these questions to help you choose.

Natural Immunity after COVID-19 varies widely from person to person. Vaccine immunity is more consistent.

Natural immunity from a COVID-19 infection is expected to last 90 days or more in most people. However, the strength of resistance built against COVID-19 varies widely from person to person. It is based on many factors, including viral load (the amount of virus in an infected person’s blood). People who had a light viral load the first time around may not be protected against reinfection. On the other hand, our immune response to the COVID-19 vaccine is more consistent. This is why you are encouraged to get vaccinated even if you had COVID-19.

Different pathogens trigger unique immune responses. The chickenpox virus (Varicella zoster) triggers the production of antibodies with lifelong memories that protect us against reinfection. COVID-19 is new, and so far, there is no data to suggest it offers immunity for life. With the COVID-19 mRNA vaccines, your body gets exposed to a harmless piece of the COVID-19 virus, the spike protein, which is just enough to train our immune system to learn how to fight this particular pathogen.

And for those previously infected with COVID-19, the vaccine can act as added protection, which is necessary to fight emerging variants.

New coronavirus delta variant covid. India mutation of SARS CoV 2, 2019 nCoV new version 2020 2021. Coronavirus new strain. 3D Illustration of viruses with microscope view of sliced virus

The Delta variant is a different beast; natural immunity needs all the help it can get.

The B.1.617.2 variant, or Delta, is significantly more contagious than the original COVID-19 virus from 2020 and all other existing variants. It is also more likely to cause severe disease and death by breaking through our natural immunity and even vaccine-related protections. This applies even if you recovered from COVID-19 in the past.

With the original COVID-19, symptoms took 7 to 14 days to appear. The Delta variant launches its attack on our body much faster. Symptoms could appear within two to three days – which means our immune system has less time to prepare. Additionally, people infected with the Delta variant carry 1000 times more virus than the original COVID-19. The vaccines can boost our natural immunity to strengthen our resistance against the new COVID-19 variants, including the insidious Delta.

It is important to note that the COVID-19 vaccines have proven effective at protecting against severe illness and death. It is still possible to get infected after being vaccinated. But if you are vaccinated, you will most likely experience milder symptoms without extreme damage to your lungs and other organs. In the United States, 97% of hospitalizations from Delta and 99% of associated deaths are due to unvaccinated individuals. These percentages are based on data from January to June and will be updated based on the impact of Delta.

Keep in mind that you are considered fully vaccinated two weeks after your second dose for two-dose vaccines or after one shot for a single-dose vaccine. Even after getting vaccinated, it is advisable to continue following recommended safety protocols.

According to Stephen Berger MD, an experienced doctor, war veteran, and infectious disease specialist, “Those that get vaccinated and then catch an infection, like the Delta variant, may have not yet formed antibodies.” Dr. Berger further stated, “People should still take the usual precautions and wear masks, sanitize their hands, and practice social distancing to help limit the spread of the virus.”

It’s like sending soldiers into battle. The process involves intense preparation and strategy beforehand. However, even the most experienced veteran returning to the call of duty requires armor, like helmets and bulletproof vests, and is trained to follow standard safety measures. The reason for this is because war brings a great deal of uncertainty and high mortality risk. Wearing safety gear during on-ground combat will not prevent all adverse events. The gear is designed to prioritize and protect a soldier’s brain, heart, spine, and other vital organs from damage. The vaccines are meant to work the same way.

The Delta variant may be dashing the world’s hope of reaching herd immunity since vaccinated individuals can spread the virus as much as the uninfected.

This insight makes it more urgent for each individual to get vaccinated and not count on herd immunity or immunity from prior infections to protect them. Professor Sir Andrew Pollard of the Oxford Vaccine Group recently informed that COVID is not like measles where if 95% of the population is vaccinated, the rest are protected. He stated, “…anyone still uninfected at some point will meet the virus.”

Meanwhile, the death knell from COVID-19 and the Delta variant continues to sound.

As of August 10th, 2021, more than 4.3 Million COVID-19-related deaths have been reported to the World Health Organization (WHO). The United States is in the lead with 600,000, followed by 563,000 in Brazil, and over 428,000 in India. In the United States, with only 50% of the population vaccinated, the daily case count now stands at 100,000 and is expected to grow. According to the CDC, the Delta variant is now the cause of 83% of all new cases in the U.S.

While the U.K. reported the highest single-day deaths from COVID-19 on August 11th, 2021 (their highest since March as a result of cases from July), hospitalizations, ICU admissions, and deaths were much lower in this wave than at the beginning of the year. Over 75% of adults in Britain have been fully vaccinated, and 89% have received at least one dose.

In the United States, while the COVID-19 vaccines are under evaluation for safety and efficacy, several have been approved for emergency use.

Portland, OR, USA - Mar 2, 2021: A woman browses the FDA website to learn more about COVID-19 vaccines. FDA has issued emergency use authorization for Janssen vaccine, the third COVID-19 vaccine.


Are vaccines approved under EUA or Emergency Use Authorization safe?

Several countries have granted preliminary approvals for vaccines in light of the devastation caused by COVID-19 and its variants. In the United States, vaccines by Pfizer-BioNTech, Moderna, and Johnson & Johnson (J&J) received EUA approval. Seeing that it is the first time vaccines are being granted EUAs, how effective are the vaccines?

In an ideal world, there would be long-term data and lots of time to analyze and decide whether to get vaccinated. In the future, COVID-19 vaccines may be like the chickenpox and flu vaccine, available for those who need it but not necessary. But right now, like medics on a battlefield, the biggest concern is to stop the bleeding. In the case of COVID-19 and its variants, it means minimizing hospitalizations due to severe illness and deaths. The three vaccines authorized under EUA in the U.S have proven effective against moderate to severe symptomatic disease.

While the EUA is a temporary fast-tracking of potentially life-saving drugs or therapy, it is not granted without reviewing detailed submissions from vaccine manufacturers containing proof of safety and data from clinical trials on more than thousands of willing participants. Another reason for the rapid FDA review and response is that the COVID-19 pandemic is the highest priority. So, resources to evaluate COVID-19 vaccines have been diverted accordingly.

In short, natural immunity will not last forever, the Delta variant is much more capable of breaking through natural immunity, and unvaccinated COVID-19 survivors have a higher likelihood of getting reinfected. If you choose to get vaccinated, here is a comparison of the reported COVID-19 vaccine efficacy against the Delta variant.


Comparison of COVID-19 vaccine protection against the Delta variant

1.    Moderna:

The Moderna vaccine is a two-dose vaccine, taken 28 days apart. It is an mRNA vaccine that makes the spike protein and teaches our body to create antibodies.

Effectiveness against Delta variant:

  • Two doses: 94-95% effective against the Delta variant [1] [2].
  • Single dose: 72% effective.

2.   Pfizer-BioNTech

The Pfizer-BioNTech vaccine is a two-dose vaccine taken 21 days apart. It is also an mRNA vaccine that makes the spike protein.

Effectiveness against Delta variant:

Reports vary between 79 – 95% so let us break them down:

  • A UK study demonstrates 88% overall effectiveness and 96% against hospitalization[3].
  • A Scotland study reported 79% effectiveness [4].
  • A study out of Canada showed 87% effectiveness [1].
  • A study out of Israel showed 90% effectiveness initially but more recently reported 41% effectiveness against symptomatic infections, but 91% effective against severe disease and 88% against hospitalization [5]. A report by the Ministry of Health, Israel, studying confirmed COVID-19 cases from January-July 2021, also showed that vaccinated individuals with pre-existing conditions are better protected against serious illness compared to non-vaccinated individuals without any risk factors [6].
  • A study from France reported 94% overall effectiveness with two doses [7].
  • A New York study stated 94-95% overall effectiveness [2].

3.   Johnson & Johnson – Janssen

The J&J Janssen vaccine is a viral vector vaccine, which uses inactivated and modified Adenovirus as a ‘Trojan horse’ to deliver the gene that encodes the SARS-CoV-2 spike protein. A well-known Bacillus Calmette Guerin (BCG) vaccine works the same way. The vaccine differs from other vaccines on the market in that it requires only one dose.

Effectiveness against Delta variant:

  • 66.9% efficacy in preventing moderate to severe disease. However, the study is small, and some experts now believe a booster may be required [2].

4.   AstraZeneca-Oxford (No EUA in the United States)

The AstraZeneca-Oxford vaccine, similar to the J&J Janssen vaccine, also works as a ‘Trojan Horse’ carrying valuable information to help train our immune system. The AstraZeneca vaccine requires two doses, taken 30 days apart.

Effectiveness against Delta variant:

  • The Public Health England study reported 79% overall effectiveness and 96% effective against severe disease[3].



All around the world, we are waging war against the COVID-19 virus and its variants. The Delta variant is the most dangerous and highly contagious of all emerging variants. Compared to the original COVID-19 and all its other variants, infection due to the Delta is most likely to result in death and severe illness.

Natural immunity gathered from a previous COVID-19 infection is not reliable protection from the Delta. Unvaccinated COVID-19 survivors have double the risk of being reinfected versus vaccinated COVID-19 survivors.

The bottom line is that regardless of the brand or type of vaccine you choose, experts recommend that you get fully vaccinated to protect yourself and your loved ones – even if you had COVID-19 in the past.


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[1] S. N. e. al., “Effectiveness of COVID-19 vaccines against variants of concern, Canada,” Pre-Print, 2021.
[2] T. T. e. al., “Comparison of Neutralizing Antibody Titers Elicited by mRNA and Adenoviral Vector Vaccine against SARS-CoV-2 Variants,” July 19th 2021. [Online]. Available: [Accessed August 11th 2021].
[3] Public Health England, “GOV. U.K.,” June 14th 2021. [Online]. Available: [Accessed 11 August 2021].
[4] Sheikh, Aziz; McMenamin, Jim; Taylor, Bob; Robertson, Chris; Public Health Scotland and EAVE II Collaborators, “SARS-CoV-2 Delta VOC in Scotland: demographics, risk of hospital admission, and vaccine effectiveness,” The Lancet, pp. 2461-2462, June 14th 2021.
[5] Ministry of Health, Israel, “GOV. I.L.,” July 22nd 2021. [Online]. Available: [Accessed 11 August 2021].
[6] Ministry of Health, Israel, “Comparative Review of Confirmed Cases Data from January 2021 and July 2021,”, 2021.
[7] D. Planas, D. Veyer, O. Schwartz and e. al., “Reduced sensitivity of SARS-CoV-2 variant Delta to antibody neutralization,” Nature, vol. 596, p. 276–280, 2021.


Nipah Virus Outbreaks: New Reasons Why the West Needs to Start Caring

Flying Pipistrelle bat (Pipistrellus pipistrellus) action shot of hunting animal on wooden attic of city church. This species is know for roosting and living in urban areas in Europe and Asia.
Image: Flying Pipistrelle bat (Pipistrellus pipistrellus) in the wooden attic of a city church. This species is known for roosting and living in urban areas in Europe and Asia.


written by Chandana Balasubramanian

Nipah virus (NiV) has been detected in several species of bats. While the Pteropus genus of bats has been the reservoir for NiV, new research from Gokhale et al. identified potential NiV infection in Rousettus leschenaultii and Pipistrellus pipistrellus bats in India [1].

Why is this significant?

In the past, the bat-borne Nipah virus has not raised much concern in the West –  since its discovery in the late nineties, outbreaks have been limited to Southeast Asia. However, NiV mutations, zoonotic spillovers, the effects of deforestation, and other factors signify a growing potential for NiV to spread. 

People think of these bat-borne viruses as exotic diseases that are far away. The COVID-19 pandemic illustrates, however, that local spillover of novel viruses can affect the whole world. 

– Stanford epidemiologist Stephen Luby, MD

Additionally, while NiV transmission was previously assumed to be annual or seasonal (primarily winter), a multi-disciplinary study based on six years of data indicates otherwise. Researchers from Stanford, Columbia, Johns Hopkins, and other global partners suggest that bat immunity levels drive NiV infections and that infected bats can shed the virus at any time of year [2].  This article was published in PNAS (Proceedings of the National Academy of Sciences of the United States) and edited by Anthony Fauci, Director of the National Institute of Allergy and Infectious Diseases.

This growing body of Nipah virus research is a bat signal urging the world to pay attention.

The World Health Organization (WHO) prioritized the Nipah virus on their list of epidemic threats that require urgent action. The US National Institutes of Allergy and Infectious Diseases categorizes Nipah at Category C:  “emerging pathogens that could be mass engineered for mass dissemination in the future.” Some governments consider the Nipah virus as a potential agent of bioterrorism and strictly regulate laboratory testing. Several other studies suggest that the NIV virus is a potential pandemic agent [3].

We must track Nipah like a parent that monitors an eight-year-old child in a playground. We do not have to divert all attention and resources urgently, but our eyes and ears need to “stay wide open” for potential issues.

Although NiV is a paramyxovirus – agents primarily responsible for acute respiratory diseases –  transmission from human to human is currently low. The R0 (the number of cases that result from an infected patient) is only 0.48. In comparison, the R0 for SARS-CoV-2 Delta Variant is 5-8, SARS-CoV-2 is 2.5-5.7, SARS-CoV is 2.4, and MERS is 1. Reported case mortality is high at 40 – 70% and is the reason why NiV has not caused mass transmission in a population:  many die before they transmit the disease. Another factor preventing larger outbreaks is that the virus has been detected in villages with a relatively low population density.

But changes are brewing, and we need to track the Nipah virus more closely than before. 

Reasons to Track Nipah Virus (NiV)

1. New Nipah virus mutations

With Nipah, there is no cause for panic just yet. Currently, only a small percentage of infected people transmit NiV. But super-spreaders can infect their loved ones, caregivers, healthcare workers, and others in their community. The incubation period is 5-to-14 days, but in a severe case, it has been reported to extend up to 45 days – sufficient time for an infected person to transmit the virus.

Nipah virus has been confined mainly to Southeast Asian countries with outbreaks in Bangladesh, India, the Philippines, and Malaysia. Still, as new strains continue to be detected, the threat level that NIV poses can potentially escalate. More research is needed in this field, but two distinct strains have been detected – Bangladeshi and Malaysian [2].


Nipah virus outbreaks map, 1998 - 2019
Image: Nipah virus global outbreaks map, 1998 – 2019. Copyright © GIDEON Informatics, Inc.


Consider another bat-borne disease: COVID-19. Since the start of the pandemic, SARS-CoV-2 has mutated quite rapidly. As you read this, variants such as ‘Delta’ (B.1.617.2) continue to wreak global havoc. WHO now categorizes these “mutants” as ‘Variants of Concern’ (VOC) and ‘Variants of Interest’ (VOI).

One concern is that the NIV receptor in humans is ephrin – found in all tissues. As such, infection by a more potent mutant could affect every organ in our body, including our blood and the central nervous system.


2. Potential Zoonotic Spillover: COVID-19 Pandemic Precedent?

As we saw with COVID-19, the spread from a bat to a pangolin and between humans happened extremely rapidly.

NiV was first discovered in pigs but is widely found in bats (Pteropus genus). There is also spillover to horses and other domestic animals. Nikolay et al. report that multiple Nipah spillover events from bats to humans occur in Bangladesh when humans consume raw fermented date palm sap contaminated by infected fruit bats [4]. Another reason for concern is that the Pteropus group of bats is found all over Asia and Australia. If more spillovers continue to occur, the world’s Nipah virus problem may increase quickly [2]. And as discovered in India (and always suspected by NiV experts), more bat species may be infected with NiV [1].

Stanford epidemiologist Stephen Luby MD stated about the Nipah virus, “People think of these bat-borne viruses as exotic diseases that are far away. The COVID-19 pandemic illustrates, however, that local spillover of novel viruses can affect the whole world.”

NiV and SARS-CoV-2 have similarities: both are bat-borne RNA viruses, demonstrate zoonotic spillovers, and cause acute respiratory distress – and without proper medical intervention, can be fatal. Differences include a slower rate of transmission for Nipah versus COVID-19 and its variants, for now. 

Nipah virus and COVID-19 comparison
Image: Comparison between Nipah virus and COVID-19. Copyright © GIDEON Informatics, Inc.


3. Nipah Virus can be transmitted continually

One of the most valuable insights from the Epstein et al. PNAS study was that bats do not transmit NiV annually or seasonally. Instead, there are multi-year cycles of transmission across bat species, which can increase the risk to humans.

Additionally, the study found that the Nipah virus in bats can recrudesce or reinfect the same bat. If an infected bat has high levels of immunity against NIV, it may not shed or transmit the virus. But when immunity levels are low, the same bat may start shedding the virus – even after years! If the immunity of a group of bats drops, an infected bat that immigrates to the flock could reinfect the group. Also, if one bat is persistently infected through recrudescence, NiV may be reintroduced into the bat colony [2].  

4. Ecological Changes Driving Closer Bat-Human Interactions

Generally, most animals prefer to stay away from humans. This is true unless their survival is linked to living closer to humans. In the case of Nipah, the Pteropus medius bat (the predominant host) travels short distances and likes to stay close to home. They pick their homes based on the availability of food in high human population density areas. In Bangladesh, they prefer to live close to humans because of more farmland and the greater availability of silver date palm trees. In Malaysia, fruit trees were planted close to piggeries, which, in turn, are within the range of human habitation. The United Nations projects that by 2050, 60% of the world’s population (4.9 billion people) will live in urban areas, increasing the risk of zoonotic spillovers. Most of this urbanization will occur in Asia and Africa.

Bat feces, called guano, is used as fertilizer in Thailand and Cambodia, and selling it is lucrative. Some people in these areas often encourage fruit bats to live close by for easier access to the droppings.

Deforestation is another strong influencer. Some research suggests that bats shed more virus under stress [6]. Bat populations undergo stressful environmental events such as human encroachment, deforestation, and fires that cause them to flee their natural habitats, searching for new ones. Many of them choose to “cut out the middleman” and roost directly on fruit trees, often planted close to humans and other domesticated or farm animals. 

Two men cutting a tree
Image: Deforestation. Photo by Souro Souvik on Unsplash


Additionally, bats, including Pteropus medius, are gregarious and social animals. Living in a large roost also offers them greater protection from other predators. Pteropus Medius bats prefer to create large roosts in tall trees. But with deforestation on the rise, these bats have been forced to form smaller populations in other locations [7].

Image: Nipah virus infection summary of disease from GIDEON Informatics (Global Infectious Diseases and Epidemiology Network) database.
Image: Nipah virus infection summary. Copyright © GIDEON Informatics, Inc.


Nipah infections are characterized by encephalitis and acute respiratory distress, which are incredibly difficult to treat [5]. The mortality rate is at 40-70%. Since it is found in rural areas with limited lab testing resources and awareness, early detection is often not possible. There are no licensed treatments for Nipah virus infection though some monoclonal antibody therapies are being evaluated. Additionally, there is no vaccine against this virus. According to GAVI, the global vaccine alliance, phase 1 clinical trials are underway.

With COVID-19 being a global public health crisis, investments in vaccine R&D and production have been high from the get-go. But the same mRNA vaccine technology may also be useful in preventing NiV infections.


Nipah virus has been around for 20 years and persists without a vaccine or licensed drug treatment. Though transmission rates are low, mortality rates are high.

The virus has much in common with SARS-COV-2. In particular, both are bat-borne, RNA-based viruses that have spilled over to other animals and humans. The virus of COVID-19, mutating much more often, has spread to every corner of our globe in a full-blown pandemic.

Variant strains of the Nipah virus have been detected. New research also identified more species of bats infected with the NiV virus. Preventing the next pandemic involves equipping researchers and clinicians on the frontlines of emerging disease prevention with the right epidemiological, diagnostic, therapeutic, and preventive tools, right off the bat. 


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[1] M. D. Gokhale, M. Sreelekshmy, A. B. Sudeep, A. Shete, R. Jain, P. D. Yadav, B. Mathapati and D. T. Mourya, “Detection of possible Nipah virus infection in Rousettus leschenaultii and Pipistrellus Pipistrellus bats in Maharashtra, India,” Journal of Infection and Public Health, vol. 14, no. 8, pp. 1010-1012, 2021.
[2] J. H. Epstein, S. J. Anthony, A. Islam, A. M. Kilpatrick, S. Ali Khan, M. D. Balkey, N. Ross, I. Smith, C. Zambrana-Torrelio, Y. Tao, A. Islam, P. Lan Quan, K. J. Olival, M. S. U. Khan, E. S. Gurley, M. J. Hossein, H. E. Field, M. D. Fielder, T. Briese, M. Rahman, C. C. Broder, G. Crameri, L.-F. Wang, S. P. Luby, I. W. Lipkin and P. Daszak, “Nipah virus dynamics in bats and implications for spillover to humans,” PNAS (Proceedings of the National Academy of Sciences of the United States of America, vol. 117, no. 46, pp. 29190-29201, 2020.
[3] P. Devnath and H. M. A. A. Masud, “Nipah virus: a potential pandemic agent in the context of the current severe acute respiratory syndrome coronavirus 2 pandemic,” New Microbes and New Infections, vol. 41, 2021.
[4] B. Nikolay, H. Salje, J. M. Hossain, A. M. Dawlat Khan, H. M. S. Sazzad, M. Rahman, P. Daszak, U. Ströher, J. R. C. Pulliam, A. M. Kilpatrick, S. T. Nichol, J. D. Klena, S. Sultana, S. Afroj, S. P. Luby, S. Cauchemez and E. S. Gurley, “Transmission of Nipah Virus – 14 Years of Investigations in Bangladesh.,” New England Journal of Medicine, vol. 380, no. 19, pp. 1804-1814, 2019.
[5] E. S. Gurley, C. F. Spiropoulou and E. d. Wit, “Twenty years of nipah virus research: Where do we go from here?” J. Infect. Dis., vol. 221, No Supplement_4, p. S359–S362, 2020.
[6] C. M. Davy, M. E. Donaldson, S. Subudhi, N. Rapin, L. Warnecke, J. M. Turner, T. K. Bollinger, C. J. Kyle, N. A. S.-Y. Dorville, E. L. Kunkel, K. J. O. Norquay, Y. A. Dzal, C. K. R. Willis and V. Misra, “White-nose syndrome is associated with increased replication of a naturally persisting coronaviruses in bats,” Scientific Reports, vol. 8, no. 15508, 2018.
[7] C. D. McKee, A. Islam, S. P. Luby, H. Salje, P. J. Hudson, R. K. Plowright and E. S. Gurley, “The ecology of Nipah virus in Bangladesh: a nexus of land use change and opportunistic feeding behavior in bats,” Viruses, vol. 13, no. 169, 2021.