Disease Post: Plague

OK, I am going to try for this post. I hope you are ready for a long one.

The plague is my very favorite infectious disease. It is so interesting and the history of it is devastating and fascinating. And what better way to celebrate the month of Halloween than talking about the Black Death? I mean, have you seen plague doctor outfits? They are terrifying (and I LOVE them). And yes, I do have a plague doctor costume, thanks for asking. 

It also helps me be a crazy rat lady since rat fleas (and/or other rodent fleas) are the primary carriers of plague. My rats do not have plague or fleas though, don't worry.

Plague of Marseilles- costumes for plague doctors. Credit- Wellcome Collection and Attribution 4.0 International

Background:

Plague is caused by a bacterium called Yersinia pestis. Y. pestis is a gram-negative (does not have peptidoglycan in its cell walls) rod or coccobacillus (round rod). It is a facultative anaerobe, which means that it "prefers" to have oxygen, but can survive without it by switching to fermentation for energy. This makes them fairly resilient little bugs.

Plague plush from Giant Microbes.

Historically, the plague has caused massive amounts of devastation worldwide and is still present all over the world. I will include a brief history later. 

 

Yersinia pestis is a zoonotic disease, meaning humans get it from animals and/or insects. In this case, the carriers are fleas.

Plague infographic from the WHO

How is it spread?

The infectious dose (or how many bacteria are needed to establish an infection) is not known, but is suspected to be quite low.

 

There are three different forms of plague: pneumonic (respiratory), septicemic, and (the famous) bubonic.

 

Let's start with bubonic plague and septicemic plague because they are similar. People get these by being bitten by an infected flea or by contact with contaminated animal tissue and/or fluid (like skinning or handling a plague-infected animal). Bubonic plague can turn into septicemic plague as the bacteria infiltrates the body and, therefore, the blood stream. And it can become pneumonic plague, too, if the bacteria spread to the lungs. Bubonic and septicemic forms do not spread from person to person.

Pneumonic plague can develop as mentioned above, or can be caught directly through respiratory droplets in the air. If a sick person or animal is coughing (or even just breathing), they release infectious bacteria into the air in tiny respiratory droplets. These can be inhaled by another person or animal, establishing an infection in the lungs. This form can be transmitted person-to-person, but usually requires close contact. You can find more detailed information about transmission from the CDC.

Image from the CDC

Symptoms:

As I mentioned above, there are three forms which will present with different symptoms, though all three will present with a fever, chills, weakness, and (often) headaches. Vomiting, diarrhea, and abdominal pain are seen in some cases, too.

Bubonic plague has an incubation time of seven days or less from infection until the time a person shows symptoms. This form is characterized by the presence of one or more bubos. A bubo is a lymph node that  becomes inflamed, swelling enough to be visible. These are usually located in the neck, armpit, and/or groin. The bubos are tender and painful. From here, the infection can start to infect the bloodstream to develop into septicemic and/or pneumonic plague. Without treatment, estimated death rates are between 50%-70%.

Septicemic plague is the infection of the blood. It is not generally the initial infection that is established, but there are many records of people getting the plague this way. Once the bacteria is in the blood stream it can get just about anywhere. The CDC also notes that people may bleed into the skin or other organs and tissues will start to die and possibly develop gangrene (and turn black=the Black Death). One of my text books (Medical Microbiology by Murray et al.) estimates that 75% of people who have or develop septicemic plague die without treatment.

Pneumonic plague is generally the most worrisome. The incubation is shorter, generally 2-3 days. After the initial symptoms, patients will develop respiratory symptoms within a day or so. According to the CDC, the respiratory symptoms include: shortness of breath, cough, chest pain, and possibly bloody mucous. This is the only form of plague that can spread person-to-person and it is highly infectious. Most sources estimate that the death rate of pneumonic plague is 90% or more if not treated quickly (within 18-24 hours, according to the WHO).

 

Prevention and Treatment:

The good news is that plague is easily treated with a few common antibiotics! However, it needs to be caught as early as possible, especially for pneumonic plague. People do die even with treatment, especially if treatment is too late.

But plague, if there are no bubos, looks like lots of other illnesses. Diagnosis is helped if your doctor knows you have been exposed to fleas or wild rodents, especially in endemic areas (meaning it is "native" to those areas, like much of Asia, Africa--especially Madagascar, and the Southwest United States). 

 

Your pets can also become infected by the same means people can and your pets can spread it to you. Flea control is important and it is best to avoid wild rodents, especially ones that appear ill or have died. Wear gloves while handling dead animals that may be infected.

There is not great prevention besides that. There was a vaccine available in the United States, but not anymore. It did not protect against pneumonic plague. I'm sure there are groups working toward a vaccine, but no one knows if/when one will be available.

The plague of Florence, 1348; a scene from Boccaccio's Decameron. Etching by L. Sabatelli the elder after G. Boccaccio. Credit: the Wellcome Collection and Attribution 4.0 International

Extras 

History:  

The plague has been around for centuries. It was also used in early biological warfare (bodies of plague victims catapulted into cities or enemy camps). Italian Gabriele de'Mussi gave an account of the Black Death origin in 1346: the Mongol army hurled plague-infected cadavers into the city of Caffa. This transmitted plague to the inhabitants, and those who fled took the plague with them towards Europe. This is explained by Mark Wheelis in his paper Biological warfare at the 1346 Siege of Caffa. Ultimately, it is suspected that the Black Death originated somewhere in Asia, though theories of exactly where differ.

There are three main plague pandemics (Perry et al). The first was in the early middle ages (the Plague of Justinian from 541 CE until the mid-700s) and is one of the earliest records we have of the plague. It is suspected to have originated in China and spread to Egypt and then to Constantinople. At the peak of the first pandemic, it is suspected to have killed 10,000 people per day and killed about 40% of citizens. A bit later, in 588 CE, there was another wave that spread it through the Mediterranean and about 100 million people died.

The second pandemic was the one most people are familiar with, from the 14th century to the 19th century. What is known as the Black Death started in this time period. The plague spread from China or somewhere in Asia along the Silk Road, infecting Asia, Europe, and Africa. China lost about half of its population, Europe lost a third to a half of its population, and Africa lost about an eighth of its population. For the record, people at the time did not call the plague the "Black Death," that is a more modern term. They called it the "great pestilence" or the "great mortality" mostly.

The third pandemic was in the 19th and 20th centuries. A wave began in China in 1855 which spread through China, to India, killing more than 12 million people in the two countries. From there, the plague traveled to Russia, causing a large outbreak in Siberia in 1910. It was during this pandemic, in the late 1800s, that the plague bacterium was identified and isolated. Alexandre Yersin is credited with the discovery and the bacteria was eventually named after him.

 

Bioterrorism:

Part of the fear of plague has to do with its potential as a bioterrorism agent. This is part of what keeps this on the select agent list in the United States.

As mentioned above, cadavers of plague victims were intentionally thrown into the city of Caffa, causing an outbreak and causing the disease to spread. This is not the only time that this was done in the history of warfare.

I remember learning about this in history and in my biodefense class. This sentence sums it up fairly well, though it does not go into all the cruel experiments that the Japanese performed on the Chinese. "In World War II, the Japanese military experimented with plague in human subjects at their clandestine biological research facilities in Manchuria, and on several occasions dropped Y. pestis-infested fleas from low-flying planes on Chinese civilian populations, causing limited outbreaks of bubonic plague and initiating cycles of infection in rats" (Dennis, David T. Plague as a Biological Weapon).

The end-goal with Y. pestis as a biological weapon was to successfully aerosolize it, to cause pneumonic plague. I have in my old class notes that "aerosol release of Y. pestis would be odorless, colorless, and likely to be unnoticed until the first victims fell ill," but I have not been able to locate a source yet, so take it with a grain of salt. 

 

It was estimated by a committee of experts that "intentional release of 50 kg of aerosolized Y. pestis over a city of 5 million would... cause 150,000 cases of pneumonic plague and 36,000 deaths...[and] without adequate precautions, an initial outbreak of pneumonic plague involving 50% of a population could result in infection of 90% of the rest of the population in 20–30 days and could cause a case fatality ratio of 60–70%" (Dennis, David T. Plague as a Biological Weapon).

About the bacteria:

I was always interested in the bacteria itself and its interactions with flea and animal hosts. That isn't talked about much because people are concerned with the diseases of people. The flea is initially infected by taking blood from an infected host. I won't get into technical details, but so you know, it does affect the flea by blocking digestion until the flea regurgitates the bacteria when they bite another host. The blocked gut of the flea will eventually kill it. Animal carriers are often symptomatic and can also die of the plague.

There are some genes that the bacteria has that they can switch between based on which host it is in to help it adapt to either the temperature and environment (like pH) of the flea versus animal hosts

The bacteria switches between gene expressions based on the host and the host temperatures. Generally, the bacteria grows best at lower temperatures but can switch gene expression to help them survive and grow at normal human temperatures.

Fun Facts:

The plague doctor mask had the beak which was to be stuffed with flowers, spices, and/or herbs--anything that smelled nice because the belief was that disease traveled through bad smells or miasma.

The plague doctor outfit did actually afford them protection, but not because of the potpourri in the mask. The mask protected their faces from respiratory droplets. They also covered themselves from head to toe in mostly leather, which fleas could not bite through.

Books and Media:

There are several books and such concerning the plague that are great.

For educational purposes, The Black Death: The World's Most Devastating Plague by Dorsey Armstrong from Great Courses is amazing. It goes into details of spread and impacts of the plague (during and after) on society, art, economics, and more. You can get it through Great Courses or through Audible. 

 

This Podcast Will Kill You did a two-part episode on the plague that is very good.

The Great Mortality: An Intimate History of the Black Death, the Most Devastating Plague of All Time by John Kelly is said to be good. I have not read it yet, but I would like to.

The Black Death by Philip Ziegler sounds great, but is another one that I have not read.

Journal of the Plague Year by Daniel Defoe. Arguably, this account is not entirely credible as the author wrote it 57 years after the fact. But he did experience the plague and it is considered to be an accurate account of the time. It was good either way.

Year of Wonders by Geraldine Brooks. This is a historical fiction novel, but it is based on a real town in England that isolated themselves when they found that the plague had reached them. A friend gifted this book to me years ago and it was enjoyable.

The Plague by Albert Camus. I am embarrassed to admit that I have not read this book yet, though I want to, obviously.

 

Crow Boy by Philip Caveney is a fictional story about a modern boy in Edinburgh who travels back in time to 1645, during a plague outbreak. I enjoyed this one, even though the plague doctor was fake and kind of evil.

This is a silly video that will get the original song stuck in your head forever, but it's funny. We watched it at some point during my Masters program: Black Death (Hollaback Girl) aka Fleas on Rats.

There are so many more books that I have not yet read. If anyone has a particularly good suggestion, please drop it in the comments. And if you know of anything about plague doctors, I definitely need to know!

I hope you enjoyed my plague post. If you made it this far, thanks for reading!

 

Sources: 

Perry, Robert D and Fetherston, Jaqueline D. Yersinia pestis--etiologic agent of plague. 1997.

Wheelis, Mark. Biological warfare at the 1346 Siege of Caffa. 2002.

The World Health Organization: Plague

The Centers for Disease Control: Plague 

Medical Microbiology sixth edition by Patrick R. Murray, Ken S. Rosenthal, and Michael A. Pfaller

Armstrong, Dorsey. The Black Death: The World's Most Devastating Plague. 2016. Great Courses.

Reidel, Stefan. Plague: from natural disease to bioterrorism. 2005.

Dennis, David T. Plague as a Biological Weapon. 2009.

Disease Post: Diphtheria

This is a disease that I have always found interesting and horrifying.

Image credit: CDC/Sarah Bailey Cutchin

Background:

The disease diphtheria is caused by a bacteria called Corynebacterium diphtheriae. The part that causes the most problems is the toxin that the bacteria produces (diphtheria toxin). However, not all C. diphtheriae actually have the toxin gene (but this is still infectious and dangerous without the toxin). There are also other Corynebacterium species that can carry the diphtheria toxin, but they cause infections in animals (CDC).

The bacteria is a gram positive (it has a peptidoglycan cell wall) bacillus (rod-shaped bacteria). It is an aerobic bacteria, meaning that it requires oxygen to live.

How is it spread?

There are two different types of diphtheria infection: cutaneous and respiratory.

The cutaneous infection can occur when the bacteria gets in the skin. This can happen if a person comes into physical contact with someone else who has a cutaneous infection, which causes infectious ulcers on the skin. It is also possible to catch it from a surface that has been touched by someone who is infected.

The respiratory infection is the most worrisome type of diphtheria infection. People catch this from inhaling the bacteria via respiratory droplets in the air.

C. diphtheriae is present worldwide. Humans are the only known reservoir, but vaccine non-compliance and the presence of asymptomatic carriers keeps the bacteria around.

Symptoms:

The cutaneous infection is less deadly. The bacteria colonizes the skin and gets deeper into the skin through breaks or cuts. A papule develops and then becomes an ulcer that is usually chronic and slow or non-healing. There can be redness, pain, and swelling according to the Mayo Clinic. The ulcer may be covered with a grayish membrane and is infectious. According to the CDC, this form rarely results in more serious disease.

Diphtheria ulcer on a patient's leg. Image credit: CDC

 

The respiratory infection is the one most people talk and worry about. Symptoms usually start within two to five days of exposure and generally begins with a sore throat, malaise, and low-grade fever (WHO, CDC). The toxin (more on that shortly) causes dead tissue to build up in the throat, eventually forming a "pseudomembrane." According to the CDC, "[The pseudomemebrane] can cover tissues in the nose, tonsils, voice box, and throat, making it very hard to breathe and swallow." As you can imagine, difficulty breathing can lead to many other issues. According to the CDC, without treatment up to half of patients will die of the disease. Even with treatment, the CDC states that one in ten will still die of the disease. And just for the gross out factor: the pseudomembrane can start to slough off and further block your airway. Yuck!

Child with a swollen neck due to diphtheria. Image credit: CDC.

 

The toxin, diphtheria toxin, causes the most problems. The toxin inhibits protein synthesis (keeps cells from making proteins, which are needed for just about everything that happens in your body). "If the toxin gets into the blood stream, it can cause heart, nerve, and kidney damage," according to the CDC. Some of this damage can be long-lasting, even after the infection is cleared.

Prevention and Treatment:

The best prevention for this disease is the vaccine. Keeping up immunization and getting booster shots are the most important ways to keep diphtheria infections to a minimum. The vaccine is a toxoid vaccine, meaning it is actually a vaccine for the toxin, not to the bacteria itself. It is often included with the vaccine for tetanus and/or pertussis: Tdap, DTaP,  DT, and Td vaccines.

For treatment, antibiotics like penicillin or erythromycin can help get rid of the bacteria. But it is important to neutralize the toxin. There is a diphtheria antitoxin available for this and sometimes people will get injections made from the blood of people who have cleared the infection in order to stimulate antibody production to the toxin and bacteria.

So that's C. diphtheriae! I always liked to use diphtheria as a supporting argument for vaccination. Along the lines of: "Do you know what happens to you when you get diphtheria? The skin in your throat sloughs off and then you die."

Sources:

The Centers for Disease Control: Diphtheria

The World Health Organization: Diphtheria

Medical Microbiology sixth edition by Patrick R. Murray, Ken S. Rosenthal, and Michael A. Pfaller

Mayo Clinic: Diphtheria

Disease Post: COVID-19/SARS-2

As we are in the midst of a pandemic, I thought I would do a little post about this disease. I am not an expert on this topic, but I want to try to convey some information to people who are interested.

Background:

Coronaviruses are enveloped viruses. Their genome is RNA, which makes them more prone to mutations, much like the influenza virus. The surface of the envelope is covered with club-shaped spikes or projections which give it a "corona" or crown when looked at under a microscope.

Giant COVID-19 virus from Giant Microbes. Super cute. I want all of their plushy diseases!

Coronaviruses are broken down into four groups: alpha, beta, gamma, and delta. Mostly this helps differentiate the animals the virus originated in: rodents and bats for alpha and beta, birds for gamma and delta. Based on this you can probably gather that coronaviruses are present in several animal species. And you would be correct. Animals all over the world have coronaviruses which usually cause respiratory and/or gastrointestinal diseases. Humans have coronaviruses, too. Some do cause gastrointestinal infections, but many cause upper respiratory infections that are pretty mild. They are usually what we would call a chest cold or viral upper respiratory infection (ie: viral bronchitis). Most people don't have trouble clearing these infections.

But coronaviruses are good at mutating. That means that they have the potential to jump to humans from animal hosts, which is likely how we ended up with SARS, MERS, and SARS-2 (aka COVID-19, SARS-CoV-2, nCoV-19). For the record, SARS stands for "severe acute respiratory syndrome" and MERS stands for "Middle Eastern respiratory syndrome." And real quick before we move on because I have seen bad information spread on social media: COVID stands for "coronavirus disease" and CoV is short for "coronavirus." The number 19 refers to the year 2019 when the first case emerged. SARS could also have been called COVID-02 (2002) and MERS could be called COVID-12 (2012).

The severe coronavirus infections that we hear about cause atypical pneumonia (generally less severe than typical pneumonia). Most coronaviruses do not establish infections deep in the lungs for various reasons (including cell receptors that they need to enter cells and temperature of the upper versus the lower respiratory system). But SARS, SARS-2, and MERS were able to establish infections in the lower respiratory tract which makes them much more dangerous.

According to the WHO, "SARS was more deadly but much less infectious than COVID-19. There have been no outbreaks of SARS anywhere in the world since 2003." But SARS-2 is genetically related to SARS so we might be able to learn more about SARS-2 by studying SARS.

How is it spread?

Respiratory coronaviruses are spread by droplets in the air, gastrointestinal coronaviruses are spread via the fecal-oral route (I know, gross). SARS, SARS-2, and MERS are respiratory and caused by inhaling the virus.

Image from the CDC

These infectious droplets of saliva  or nasal discharges (fluid) are in the air because people cough and sneeze. Even laughing and singing release droplets. This is why the CDC is now recommending that everyone in public wear a mask of some sort (preferably one that is thick enough to stop droplets). It isn't to protect the wearer, it is to protect the people around you. Also, cover your coughs and sneezes. The droplets are heavy, however, and usually settle pretty quickly, which can contaminate surfaces.

It has been thought that the virus can live for a time on surfaces. Here is what the WHO has to say:

It is not certain how long the virus that causes COVID-19 survives on surfaces, but it seems to behave like other coronaviruses. Studies suggest that coronaviruses (including preliminary information on the COVID-19 virus) may persist on surfaces  for a few hours or up to several days. This may vary under different conditions (e.g. type of surface, temperature or humidity of the environment).

If you think a surface may be infected, clean it with simple disinfectant to kill the virus and protect yourself and others. Clean your hands with an alcohol-based hand rub or wash them with soap and water. Avoid touching your eyes, mouth, or nose.

For those worried about catching SARS-2 from animals, the WHO also says, "While there has been one instance of a dog being infected in Hong Kong, to date, there is no evidence that a dog, cat or any pet can transmit COVID-19. COVID-19 is mainly spread through droplets produced when an infected person coughs, sneezes, or speaks. To protect yourself, clean your hands frequently and thoroughly." So don't go dropping your pets off at shelters or (heaven forbid) outside somewhere to fend for themselves. Take care of your animals, they are not going to give you SARS-2. It might be possible for you to give your pet the disease, some animals have lungs much like humans--cats and ferrets for instance. There doesn't seem to be much official information about this and we might not know for a while. Just be cautious. Wash your hands.

It also seems that re-infection with SARS-2 after getting it once is rare if it is happening at all. A couple of papers (Omer et al. and  Bao et al.) indicate that individuals are protected for at least a few months from re-infection with SARS-2. More data needs to be gathered on the subject and we do not know how long the protection might last. But so far, this seems like good news.

Additionally, it appears that the virus does not transmit across the placenta according to an article by Fan et al. Obviously, pregnant and breast-feeding women who are exposed or experiencing symptoms should consult their doctor. More research on this topic is needed, but right now it seems hopeful.

Image from Harvard Coronavirus Resource Center

Symptoms: 

Keep in mind with SARS-2 that some people experience very mild symptoms while others do not. That's part of why this is so dangerous. What doesn't hurt you much could kill someone else. And there is some evidence that there are people who are asymptomatic carriers (they don't feel or appear sick even though they have the disease). However, since they are not showing symptoms (namely coughing) it is more difficult for them to actually spread the disease. Also more difficult to know who is infected. It is a good idea to act as though anyone and everyone might be infected, including yourself.

Within about 7-14 days of infection, people generally show fever, dry cough, tiredness, aches, sore throat and/or shortness of breath. Very few people have reported diarrhea, nausea, and runny nose.

If symptoms get more severe, you should seek medical attention. According to the CDC, if you experience the following: "trouble breathing, persistent pain or pressure in the chest, new confusion or inability to arouse, bluish lips or face" then you should seek emergency medical attention.

I know this is all scary and its still so new that we don't have all of the details, but this is part of why it is important to take care of yourself and keep yourself (and others) healthy. And do keep in mind that many people have more mild infections and recover fine on their own. An article written by Cascella, et. al. reported that about 81% of the cases in China were mild.

Prevention and Treatment:

The WHO recommends the following for prevention:

• Wash your hands regularly with soap and water, or clean them with alcohol-based hand rub.
• Maintain at least 1 metre distance between you and people coughing or sneezing.
• Avoid touching your face.
• Cover your mouth and nose when coughing or sneezing.
• Stay home if you feel unwell.
• Refrain from smoking and other activities that weaken the lungs.
• Practice physical distancing by avoiding unnecessary travel and staying away from large groups of people. 

As of right now, there is not a vaccine or a proven treatment. And I do not want to get political, but Americans: do NOT follow the directions of our president. He is not a medical doctor or a medical professional of any kind. Just because he thinks or "feels" that something might be so, does not mean it is. Please listen to doctors and legitimate medical professionals. It has not been solidly proven that hydroxychloroquine will treat the disease and may cause more harm than good in some cases. There have been lab trials using cell cultures (in vitro) that show decreased levels of disease by SARS-2, but there have been very few good clinical trials. Most have had too small a sampling group to give accurate representation (see Gautret et al.).

I'm not sure what sort of mechanism azithromycin is supposed to use to treat a viral infection. But azithromycin is an antibiotic, meaning it is meant to treat bacterial infections. It could help treat secondary infections people may see with SARS-2 infections, but to my knowledge, will not treat the virus. Please only use antibiotics at the direction of your doctor.

Also, please be aware that development of vaccines and treatments are a long process, usually at least a year if rushed. So scientists are trying to find these things, but please know that it will be a while before these things exist.

As of right now, treatment consists of supportive care.

Extras:

Here is an informational video that has some good information and breakdowns of COVID-19 that might interest you: Ninja Nerd Science: COVID-19 | Coronavirus: Epidemiology, Pathophysiology, Diagnostics and Ninja Nerd Science: COVID-19 | Coronavirus: Treatment, Prognosis, Precautions.

I also highly recommend checking out This Podcast Will Kill You. About two months ago they did a general coronavirus episode and more recently they have done a series all about COVID-19. They are knowledgeable and work with other professionals to get good information out there.

Here is a page that is very important: WHO: Coronavirus disease (COVID-19) advice for the public: Myth busters. Take a look at the information and graphics. I would also like to add a rumor I heard a couple of times: that darker skinned people are less prone (they aren't and also tend to be at a lower socioeconomic status and therefore have less access to treatment and can be more prone to severe disease) and that wearing sunscreen will help protect you from COVID. The virus does not and will not absorb through your skin. Even if there is a break in the skin, I am not sure that coronavirus could properly establish an infection. Covering your skin or having darker skin will not prevent coronoavirus infection.

And I'm sure you know this, but many people have been negatively infected by this pandemic. People have lost friends and family, people have been laid off of work and struggle to make ends meet, our health care professionals and other necessary personnel are worked to the bone. Please keep these people in mind. If it is within your power and means to donate to organizations dedicated to helping these people, please do. Here are a couple of suggestions: your local food banks (like Food Bank of the Rockies), Give Directly, No Kid Hungry, local COVID relief funds, United Way, and many others.

There are local people everywhere doing things to try to help their communities, doing things like delivering food/supplies, giving gift cards to families, and so forth. Also, please keep in mind the homeless populations who also need extra help during these times. Most shelters take food and monetary donations and may need supplies or volunteers. There are people doing good deeds for our health care workers and essential personnel. Remember that many of these people are not being treated well or paid well despite the fact that we actually need them to keep going as a society.

If you can't donate or volunteer, there are still things that you can do: stay home, stay away from people as much as possible, don't travel, and be kind. Kindness doesn't cost anything and empathy is going to help people much more than anger and bitterness. This is difficult for everyone, but please do your part.

Disclaimer: This information is bound to change. We won't know all of the information including complete statistics of infection rates, death rates, and more until this is all over. Scientists and doctors are working all of the time to add to our knowledge of this disease. If any of this changed/changes, feel free to let me know.

Sources: 
Centers for Disease Control: Coronavirus disease 2019 (COVID-19)
World Health Organization: Coronavirus disease 2019
Cascella et al. Features, evaluation and treatment coronavirus.
Gautret et al. Hydroxycholoroquine and azithromycin as a treatment of COVID-19: results of an open-label non-randomized clinical trial.
Omer et al. The COVID-19 Pandemic in the US: A Clinical Update.
Bao et al. Reinfection could notoccur in SARS-CoV-2 infected rhesus macaques. (Please forgive this link, this is the article but the site it was posted on was having problems opening  by the time I was writing this post.) 
Fan et al. Perinatal Transmission of COVID-19 Associated SARS-CoV-2: Should We Worry? 
Emerging Infectious Diseases by Lisa A. Beltz
Medical Microbiology 6th edition by Patrick R. Murray, Ken S. Rosenthal, and Michael A Pfaller

Disease Post: Brucellosis

This is one of my favorite "bugs!"

Background:
Bucellosis is caused by a bacteria from the genus Brucella. There are a few different species that cause disease in animals and humans. For humans, the three species that usually cause disease are suis, abortus, and melitensis.

Brucella colonies on blood agar. Image from Pixnio.

Brucella species are small, anaerobic, gram negative coccobacilli, meaning that they do not require oxygen and do not have peptidoglycan in their cell walls and stain red/pink on a gram stain (bacteria that stain purple are gram positive). Coccobacilli describes the shape--they are between cocci (round) and baccili (rod-shaped).

They are facultative intracellular organisms, which means that they have to be inside another cell for part of their life cycle, but can also live outside of another cell. In the case of Brucella species, the cell they tend to invade is the macrophage. Macrophages are important cells in your immune system. Briefly, they usually "eat" things that are dangerous, like bacteria, and break it up into pieces. Then they take those pieces and display them on the surface of their cells using special cell receptors that will signal other immune cells to look for them. That way, the rest of your immune system can respond to the invaders. Brucella bacteria hiding in these cells, it makes it much more difficult for your body to find and fight off.

How is it spread?
Humans usually get this disease either by being in close contact with an infected animal or by eating contaminated animal products. Namely unpasteurized milk, which is contaminated with the bacteria when an animal is infected (this is why drinking unpasteurized milk is so dangerous). The bacteria can cause infection if inhaled, ingested, or through the skin. Most commonly, it infects via mucous membranes (for example: the eyes, throat, or respiratory tract).

According to the CDC, person-to-person spread is rare, but is most common if a mother is infected, she can infect her breastfeeding infant.

This disease is most worrisome in animals, both wild and agricultural. It is also found world-wide.

The bacteria are not especially hardy, they don't form spores and they can be killed with heat. However, they manage to survive in the environment for several years, if the conditions are right.

The incubation period for this bacteria is about two to four weeks, so there can be quite a delay between getting infected and showing symptoms.

Symptoms:
Many of the symptoms are flu-like: fatigue, fever, sweating, headache, body aches, anorexia, nausea, and malaise (generally not feeling well). According to the CDC, some symptoms can be recurring or persist for a longer period of time. Most commonly these symptoms are: recurrent fever, arthritis, swelling of the heart, neurological problems, chronic fatigue, swelling of the male reproductive system (namely the testes and scrotum), and swelling of the spleen and/or liver.

The good news is that brucellosis is rarely fatal in humans, but it is still considered a potential bioweapon because it can be easily spread and incapacitate people.

The chronic symptoms that are so common with this microbe are due to a couple things: incomplete antibiotic treatment, which causes relapses, and persistent infection by the bacteria in tissues (like bone, spleen, liver, et cetera). It can be difficult to get rid of.

Brucella colonies on serum dextrose. Credit: Royal Veterinary College and Wellcome Collection

Prevention and Treatment:
One way to prevent human infection is by pasteurizing milk and other dairy products. Eating under-cooked meat is not recommended as it could be contaminated with Brucella. There is also a vaccine for herd animals to B. abortus.

People who work with animals like cattle, pigs, goats, and sheep should wear protective clothing, like gloves and goggles.

Because the bacteria hides inside cells, antibiotic treatments can last a long time (often 6 weeks) and often more than one antibiotic is needed. Doxycycline with with rifampicin can be used, or doxycycline with gentamicin. Trimethoprim-sulfamethoxazole can be used for women who are pregnant or for young children.

Miscellaneous Information:
What I find super interesting about this bacteria is that it causes abortion (and infertility), which can lead to further infections in animals. It almost plays off of the maternal instinct. For example, if a cow is infected and it causes the cow to have an abortion, the cow may survive. However, the aborted fetus is infectious. Other cows may come into contact with the aborted fetus as they inspect it and then the bacteria can infect the new animal. A bit evil and fascinating.

Brucellosis is known by many other names, including: Malta fever, Mediterranean fever, Cyprus fever, goat fever, Gibralter fever, to name a few.

Sources:
The Centers for Disease Control: Brucellosis
Microorganisms and Bioterrorism edited by Burt Anderson, Herman Friedman, and Mauro Bendinelli
Emerging Infectious Diseases by Lisa A. Beltz
Medical Microbiology 6th edition by Patrick R. Murray, Ken S. Rosenthal, and Michael A Pfaller

Disease Post: Influenza

I had a few days off around the holidays and I was going to finish this and post it. But I didn't plan on not having access to internet for about six days. Insert facepalm here. So I apologize since I swore I would have this posted in December and ended up not being able to finish and post it until January. It is still relevant though, so I hope you can forgive me.

~*~*~

It's the right time of the year for this post--flu season!

There are a ton of misconceptions about the flu and the flu shot (influenza vaccination). So I will try to clear a bit of that up.

Background:

Influenza (or the "flu") is caused by a virus from the Orthomyxoviridae family. It is an RNA virus but the RNA is segmented into smaller pieces. This is an important feature that we will discuss in a bit.

There are four types of flu virus: A, B, C, and D. C and D cause little to no disease in humans. While humans can get C and D, they are more common in different animals and are usually very mild if a human catches it. A and B are more important for people so we will focus on those.

Influenza B has no subtypes. According to the WHO, there are different lineages and they are traced that way.

Influenza A is the type you will hear the most about. The WHO states, "Only influenza type A viruses are known to have caused pandemics." There are subtypes of this virus determined by proteins on the virus capsid. There are two main glycoproteins: hemagglutinin (or HA) and neuraminidase (NA). Each of these proteins has different forms and each is coded for on a different segment of RNA. There are 18 known HA subtypes and 11 known NA subtypes. And they can be combined in just about any way. This is how they are labeled, and you’ve probably seen or heard the short hand, like H1N1. Those are the HA and NA subtypes. As you can imagine, this allows for all sorts of recombinations and helps explain why the flu changes so much.

Basically, if two flu viruses infect the same host, they can recombine their genomes to create a new flu strain. This is aided by the fact that the genome is in smaller segments. Or if major mutations occur, the HA or NA can change completely. This reassortment or mutation of genes is called “antigenic shift.”

The following image is one taken from a book I have, sorry for the poorer quality. But this shows how recombination can occur with influenza A viruses.

Image from Medical Microbiology 6th Edition by Patrick R. Murray, Ken S. Rosenthal, and Michael A. Pfaller

To make things worse, the influenza A viruses are not very genetically stable and their genomes can go through smaller mutations very easily. This is called “antigenic drift.” Even small changes can alter the HA or NA enough for someone's immune system to not recognize it.

These things mean that even if you are only talking about H3N1, H3 is the variation of HA antigen and there are even different variations of H3. The flu viruses are always changing and that makes it very difficult to keep up with them. It is also why the vaccines have to be updated constantly.

An influenza type A virion. Image from the CDC.

How is it spread?

Influenza is a respiratory disease, though the "flu" has often been incorrectly used by people for other respiratory and stomach diseases, like the "stomach flu." Since it is a respiratory disease, it makes sense that it is spread in the air and infects the nose, throat, and/or lungs. When someone is sick with the flu, they cough or sneeze or speak and droplets that contain the virus are released into the air and another person inhaling the infected droplets can then get the flu.

It is also recommending that anyone who is sick should wash their hands frequently. If they sneeze or cough into their hands, flu can spread that way, too.

The CDC says that people are most contagious in the first three or four days of the illness, but estimate that they can be contagious from one day before symptoms appear and can remain contagious from five to seven days after becoming sick. The CDC also states that, "Some people, especially young children and people with weakened immune systems, might be able to infect others for an even longer time."

Symptoms:

In general, the flu does not have a very long incubation time, meaning that people will start to feel sick pretty quickly after getting it. According to the CDC, the incubation period is about one to four days, with two days being the average.

Symptoms include a fever (but not everyone presents with a fever), chills, cough, sore throat, body aches, congestion, fatigue, and headaches. Rarely, flu can cause vomiting and/or diarrhea, but mostly in children, according to the CDC.

Story time: I got the flu, the actual flu, when I was a senior in high school. I felt a little off for a couple of days, then one day I had a mild fever, and then it hit me like a truck. My fever increased. I couldn't lift my arms to take my hair down. I couldn't stand long enough to shower for a week and when I was getting better, my mom had to put a chair in the shower so I could sit down. I lost my voice and my throat hurt so badly that I couldn't eat and could barely drink. I was completely miserable. It took a good week to start feeling better and another week to get back to my normal energy levels. This is pretty typical of the flu. And I was a young, healthy person. Just think how much worse it would be to be too young or old to have a good immune system. Or to be immunocompromised. That is why these people are usually the most at-risk. A huge part of flu shots is to help protect those at-risk people.

The flu may not sound very serious, but people die from the flu every year. Mostly the people who die are in the at-risk groups. But some flu strains kill people with healthy immune systems, like in the flu pandemic of 1918. Then it was usually the healthy people dying. The flu is no joke.

Prevention and Treatment:

Every year a new flu shot is developed and it is recommended that everyone six months or older should get it, unless you have a medical condition that does not allow you to get the vaccine (ie: if you are immunocompromised or you have an egg allergy).


It is new every year because of how much the flu viruses mutate. We don't often see the exact same flu viruses, espcially with influenza A. The WHO and others spend all year monitoring the flu all over the world. They track which strains are present, where, and for how long. They predict where and how far the strains will spread and they develop the vaccines based on that data. Which means that, yes, sometimes the viruses included in the vaccine are not the ones that people will encounter. But most of the time, that is not the case. The flu vaccine in the US usually covers four different flu strains. It used to be three until recently and there have been the odd year where the number will be different.

The flu shot is the best way to prevent the flu.

There is not a cure for the flu. Generally, care focuses on trying to relieve the symptoms and on hydration until your body can fight it off.

According to the WHO, there are neuraminidase inhibitos (like oseltamivir) available that help, but that many strains resistant to some other antiviral treatments.

And I want to talk briefly about the myths of the flu vaccine.

• You CANNOT get the flu from the flu shot. The flu shot contains inactivated virus, they cannot cause an infection. Some people may feel a little feverish for a day after a flu shot. This is not the flu. This is your immune system reacting to the vaccine. It is actually a good thing, it means that your body is creating a strong immune reaction and studies generally show that a robust immune response gives you better protective immunity in the future. (Side note, this is why many vaccines use adjuvants. An adjuvant is something added to a vaccine like a protein that causes your body to give a better response. When you body responds to the adjuvant, it will respond to the vaccine better, too. It's like a way of making your immune system pay more attention to what is in the vaccine.)
• You can still catch the flu if it is not one of the strains in the vaccine.
• A bad cold is not the same as the flu.
• Vaccines do not cause autism.

I hope that about covers it. Please reach out if you have questions! Thanks!

Sources: 
Medical Microbiology 6th Edition by Patrick R. Murray, Ken S. Rosenthal, and Michael A. Pfaller
World Health Organization (WHO): Influenza
Centers for Disease Control (CDC): Influenza 
The Great Influenza by John M. Barry

Disease Post: Anthrax

Something a little different: our first bacteria!

Background:

Anthrax is a disease caused by a bacteria called Bacillus anthracis.

What is bacteria? A bacterium is a single-celled organism. The cells are a little like ours, but a bit more primitive. They are called "prokaryotes" which means "primitive nucleus." (Our cells are "eukaryotes," meaning "true nucleus.") This means that they do not have a nucleus that holds the DNA like our cells do.

Bacteria come in all different sizes and shapes. Bacillus anthracis is in the shape of a rod and is large (relatively speaking). It is Gram-positive, which refers to the way bacteria are stained before looking at them under a microscope. Gram-positive means that they stain with crystal violet dye because they have a cell wall made of peptidoglycan. I won't go into too much detail about peptidoglycan, but it is made of sugars and amino acids and is important in how the bacteria functions and how the immune system interacts with the bacteria.

Anthrax bacillus. Credit: the Wellcome Collection. The bottom two images show the long, rod-shaped bacteria the best.

Another important thing is that this bacteria forms endospores. Endospores (or just "spores") are dormant bacterial cells that cannot reproduce and are very resistant to anything that would kill a normal bacterium. This means that anthrax can survive in bad conditions and in the environment for a long time (usually a few months to a few years, but some can survive for decades). Once a spore enters a host, it can enter the active phase and start reproducing again. Once they are exposed to the environment again, they can sporulate and wait in the dormant state until they can infect another host.

Anthrax bacteria can contain up to three genes in their DNA that codes for different toxins. It is the toxins that cause symptoms. There are particular ways that these genes can be present and they can be transferred between the bacteria, but I don't want to go into too much detail about that. Just know that there are important toxins that can make an anthrax infection worse if the bacteria have any of those genes.

How is it spread?

There are a few types of infection that anthrax can cause: cutaneous (skin), gastrointestinal (in the digestive tract), inhalational (infected through the lungs), and, rarely, meningitis (infecting the nervous system).

Anthrax is mostly a disease of animals and is naturally present in soil all over most of the world. Human to human transmission is very, very rare. We see it in domestic livestock like cattle and in wild animals. Humans are usually infected through the skin or the lungs, often from animals that have the disease or animal products that are contaminated with anthrax.

Symptoms:

Let's break it down into the different types of infection.

Cutaneous: It takes about 1-7 days (incubation period) until a small papule forms on the skin at the infection site. It may become larger. They are usually painless. They can rupture easily and become ulcers and the base will become black, which is characteristic of cutaneous anthrax infection. As long as there are no complications and treatment is received, the lesions will heal just fine. This form is very rarely fatal and is one of the more common forms humans get.

Meat handler: skin lesion of anthrax. Credit: Royal Veterinary College and the Wellcome Collection

Gastrointestinal: This is often how animals are infected, by ingesting the bacteria, and it is an uncommon infection in humans. The incubation period is abut 1-5 days. There will be a fever and localized symptoms like nausea, vomiting, diarrhea, and/or abdominal pain. From here, it can spread to the blood stream (sepsis) and may cause secondary meningitis if it gets into the central nervous system. The gastrointestinal form can be treated, but is about 40% lethal without treatment.

Inhalational: This is the other infection type that humans get (relatively speaking, inhalational anthrax cases are actually quite rare). It is this form that makes anthrax so scary. Inhalational antrax infection is extremely dangerous and is nearly always fatal without treatment. And treatment needs to happen very quickly and aggressively. This type is about 92% fatal, even with treatment. Usually in this form, spores are inhaled and enter the lungs. They incubate for about 1-6 days. The first symptoms are flu-like (fever, tiredness, aches, headaches). As the disease progresses, there is a high fever, decreased lung function, respiratory distress, chest pain, and more. This form can also cause secondary sepsis and/or meningitis as the bacteria spread. While all forms of human cases of anthrax are rare, this one is the reason it is an agent for bioterrorism.

Meningitis: This form is rare and is mostly associated with gastrointestinal or inhalational infections. This happens when the bacteria infect the central nervous system via the blood stream.

Prevention and Treatment:

There is an anthrax vaccine, but it is not normally available to the public. People who usually have access are laboratory and military personnel and other people who may come in contact with infected animals. The vaccine can also be used after a person has been exposed, much like the rabies vaccine.

There are vaccines available for animals like livestock. Vaccinating these animals significantly reduces human exposure.

There are various antibiotics that can be used to treat the different types of infections. Doxycycline and Ciprofloxacin are commonly used, according to the CDC, but there are others. The treatment with antibiotics is very long and intensive to make sure that the bacteria and any spores are treated.

Sources:
Medical Microbiology 6th Edition by Patrick R. Murray, Ken S. Rosenthal, and Michael A. Pfaller
Centers for Disease Control: Anthrax
WHO: Anthrax

Disease Post: Rabies

Welcome to the Rabies post!

Background:

Rabies is caused by a virus from the rhabdovirus family and is bullet-shaped. The virus has an envelope (a double layer of lipids like those that form our cell membranes). Rabies' genetic material is single-stranded RNA.

Transmisson electron microscopy picture of a rhabdovirus. Image from the Wellcome Collection.

Brief review: in humans, our genetic material is double-stranded DNA (deoxyribonucleic acid) that is kept in the nucleus of our cells. Kind of like the control center. When we need to make a protein, the DNA strands unwind and we have cellular proteins that make a copy of the DNA which is called RNA. Human RNA (ribonucleic acid) is always single-stranded. This strand of RNA then exits the nucleus and into the cytoplasm of the cell where other proteins translate the RNA instructions into a protein.

Since rabies contains single-stranded RNA, it can enter the cytoplasm of our cells and use our cell's machinery to make more viruses.

Rabies is a disease that is present all around the world (except in Antarctica) and has been around for thousands of years (at least). It is thought to have evolved with dogs and wolves as those are usually the most easily affected and infected animals. Most cases in humans occur in Asia and Africa, but it is regularly seen in Europe, Australia, and the Americas, too. In places where dog vaccination is common (like the US), fewer dogs are problems and bats become more likely to spread the disease. There are also vaccination programs in wild animals like foxes and raccoons via food baits, which is great, but there aren't any programs that can easily vaccinate bats, to my knowledge.

How is it spread?

Rabies is often found in wild animals like raccoons, foxes, coyotes, and bats. Domestic animals, like dogs and cats can become infected. And of course, humans. To my knowledge, rabies only infects mammals.

Rabies is spread through the saliva of an infected mammal and enters the new host through broken skin. Infections are usually caused by a bite, but can be transmitted by a scratch.

The virus enters the wound and moves into the local nerve cells or neurons. Once it is in the neurons, it can hide really well from your immune system (obviously your immune system should not normally attack your nervous system because it is so important for all of your normal functions). From the local nerves it makes its way from nerve to nerve to reach the central nervous system (your spinal cord and brain). After that, the virus travels down to the salivary glands where they can shed into the saliva and try to spread further! (Side note: viruses when they multiply are said to be "shed" or released, usually in very large numbers. This is how they enter the environment and spread to other hosts.)

One lucky thing about this virus is that it moves pretty slowly, depending on how far away it is from the central nervous system when it enters the body. For example, if you are bitten on your calf, you will have a lot more time before the virus reaches your brain than someone who is bitten on the neck. Viral load, or how many viruses enter the wound, also plays a role in how quickly it moves. If only a few viruses enter a wound, it will take longer to get to the brain. It's slow movement is important for treatment, which we will discuss later.

Symptoms:

According to the WHO, "incubation period for rabies is typically 2–3 months but may vary from 1 week to 1 year, dependent upon factors such as the location of virus entry and viral load."

Rabid dog. Image from the Wellcome Collection.

Early symptoms are pretty standard: fever, weakness, headache, and body aches. Oftentimes, people will feel tingling, prickling, and/or burning sensations as the virus spreads through the nerve cells. Hydrophobia (fear of water) and sometimes photophobia (fear of light or sensitivity to light) are later symptoms.

There are two forms of the disease: paralytic rabies and furious rabies. Furious rabies is the rabies most of us are familiar with. Furious rabies is a faster moving manifestation of the disease. It is characterized by hyperactivity, excitability, hydrophobia, agitation, confusion, and insomnia.

What is super interesting to me is the hydrophobia. The people who experience this (and not all rabies-infected people/animals do) have pain when they try to swallow. This is a viral strategy (so to speak, they aren't alive) to help spread it. The virus is present in saliva and the virus wants to get out, not be swallowed. Being swallowed defeats the virus' purpose. The virus affects an animal's ability to swallow in order to spread. Much like a cold virus will cause a person to sneeze so that virus can be spread in the air to new hosts.

In paralytic rabies, the disease is slower and not as exciting, so to speak. As the virus spreads, the person becomes paralyzed starting at the site of infection and slowly spreading until the person is completely paralyzed and falls into a coma.

No matter which form you get, the ultimate outcome is almost always death. According to the CDC, "less than 20 cases of human survival from clinical rabies have been documented" and only a few of the survivors had not had any preventative treatment (like the rabies vaccine) or treatment after they were exposed. This shows just how deadly this virus is. It has been noted throughout much of history that if a victim reaches the hydrophobia stage of disease, the outcome will be death.

Prevention and Treatment:

For those of you with dogs, you probably know that rabies vaccines are routine. Generally, they receive the vaccine as puppies and then have a booster every three years, though some areas require a booster every year. Dogs are often vaccinated against rabies, which is good because most cases of human rabies are from domestic dogs. Humans who work closely with animals, like veterinary doctors and staff, or laboratory staff that work with animals may receive the vaccine as prevention. Vaccination against rabies is not standard in humans, though.

If you get bitten or scratched by an animal that can carry rabies, what do you do? Seek care as soon as you can, especially if you do not know the animal or their health state. Cleaning the wound very well can help a person's chances. Normally, people who may have been infected receive the rabies vaccine because the virus moves slowly enough for your body to react to the vaccine and then to react to the actual virus to clear it. Your body just needs a little help from that vaccine. If someone is further along or more at-risk, they may receive rabies immunoglobulin. Immunoglobulin are antibodies specific to a disease, rabies in this case. Antibodies are produced by your immune system to help target and inactivate viruses (or bacteria, and so on). The immunoglobulin is produced in a laboratory and given to people to help their immune system combat the disease until that person's own immune system can catch up and start making its own antibodies.

Miscellaneous Information: 

If you are interested in rabies, I highly recommend the book Rabid: A Cultural History of the World's Most Diabolical Virus by Bill Wasik and Monica Murphy. My favorite parts were about how the rabies virus may have helped inspire the stories of werewolves and vampires. Both horror figures are strongly associated with wolves/dogs. Vampires are also associated with bats. Both involve biting to spread the conditions. Werewolves are often associated with rage and being unpredictable and uncontrollable. And then vampires don't do well (or can't exist at all) in sunlight--photophobia. Many classic vampires also can't cross water--hydrophobia.

The book also goes into the history of the disease, old time treatments (like drinking something containing "the hair of the dog that bit you," which is a common phrase even now) and how it has caused people throughout time to create laws to prevent the spread of rabies.

That is about it for rabies! Please let me know if you have any questions or if I have any information incorrect! Thanks for reading!

And a very special thank you to my friend, Veronica! She edited this post and helped me find things that needed more information or clarification. So thank you for your help!

Sources:
Virology: Principles and Applications by John Carter and Venetia Saunders
World Health Organization
Centers for Disease Control and Prevention
Rabid: A Cultural History of the World's Most Diabolical Virus by Bill Wasik and Monica Murphy
Medical Microbiology 6th Edition by Patrick R. Murray, Ken S. Rosenthal, and Michael A. Pfaller
WebMD Pet Vaccines: Schedules for Cats and Dogs

Disease Post: Smallpox

Greetings and welcome to my first (hopefully of many) science posts.

If you read my last post, I was inspired by the second half of the vaccine episode of the podcast This Podcast Will Kill You (which is an awesome podcast and everyone should listen to it). In the second part of the vaccine episodes, they discussed that people not believing science and scientific research is because scientists don't make information accessible and easy to understand. I agree and think this is a huge shortcoming in the field of science. To that end, I would like to contribute to the scientific knowledge that is available out there.

Let me start with a little introduction and background:

I have my Bachelor's degree in Biology with a minor in Chemistry. I did a decent amount of focus on molecular biology at this time. I have my Master's in Microbiology and infectious diseases are certainly my passion. Currently I am taking steps (slow baby steps, but steps) towards medical school and on to be a doctor who specializes in infectious diseases (fingers crossed). Because that would be the most amazing thing ever. I have a pretty good science background. I have worked in a lab for several years and have background as a tutor. I am hoping that these things will enable me to take on this blog project.

However, my background is almost entirely in Biology and Microbiology. I can get by Chemistry alright, but that is about the extent of what I know. So as much as I wish I could educate on topics like global warming, I can't and don't plan to try unless I get help from someone who knows the field. So that means that I will end up focusing on diseases (at least to start). I do have an older post about vaccination here: Why You Should Vaccinate, and I may do more like that in the future. Right now this is a bit of a pet project and we will see how it goes.

And now for:
Disease Post One: Smallpox!

A tiny bit of background information: what is a virus? The Merriam-Webster dictionary says a virus is
     any of a large group of submicroscopic infective 
     agents that are usually regarded as nonliving 
     extremely complex molecules, that typically 
     contain a protein coat surrounding an RNA or DNA 
     core of genetic material but no semipermeable 
     membrane, that are capable of growth and 
     multiplication only in living cells, and that 
     causes very important diseases in humans, 
     animals, and plants

Basically, this means that there are several different kinds and families and types of viruses. They might have DNA or RNA genetic material which may be single- or double-stranded (which will affect how they use the host cell to make more copies). Some have an envelope around them that is basically the same as our cell's membranes. Some do not have a membrane. These will affect how a virus enters and exits a host cell and provide some level of protection/preservation when the virus is not inside a host. It is up for debate whether viruses are actually alive or not. That's not something we are going to get into here. Viruses are mostly considered non-living because of one important feature: they need another living cell in order to multiply their numbers and spread. 

Viruses are the source of many different diseases, some are lethal and others are minor. Some can even cause cancer. I'm going to underline this next point: viruses cannot be treated with antibiotics! Antibiotics treat bacterial infections, not viral. There are anti-viral medications out there for serious infections, but viruses can be harder to treat because they like to hide in our cells.

Smallpox is a disease caused by a virus, namely Variola major. (There is a less common and less lethal virus that causes smallpox called Variola minor.) The variola viruses are double-stranded DNA viruses so their genetic material is like ours! They are very large viruses because they have to carry a bunch of machinery around due to the fact that they replicate their DNA in the cytoplasm of human cells. Since we, as humans, replicate out DNA in the nucleus of our cells, the virus can't hijack our own machinery to aid them. Therefore, they carry their tools with them!

Smallpox was common around the world for thousands of years. It was officially eradicated in 1980. Smallpox virus only has one host: humans. Which made it a good target for eradication because it cannot be hiding somewhere in the environment or in an animal host, waiting to re-establish itself in the human population. Once the vaccination programs spread, the virus had no where to go, and now its gone! The only smallpox left in the world are in a couple of laboratories (both in the US and in Russia because it is a great pick for bioterrorism and biowarfare--maybe an idea for a future post as I actually took a course on that very thing during my Master's).

While smallpox seems less relevant today, it is a historically important disease that killed loads of people. According to the CDC (Center for Disease Control): "On average, 3 out of every 10 people who got it died. Those who survived were usually left with scars." It is also where vaccines started. I won't get too into all of the history here, but in the late 1700's Edward Jenner used a live vaccinia virus (which causes cowpox, a virus/disease related to smallpox) to inoculate or infect a patient. The reason for this was that he noticed that milkmaids often didn't get smallpox if they had contracted the much milder cowpox. His methods worked (luckily since he used human subjects in the days before scientific ethics was a thing). And the word "vaccine" comes from "vacca," which is latin for "cow!"

Edward Jenner vaccinating a child. Image from Wellcome Collection.

How is it spread? 

Smallpox initially infects the respiratory system and so it is usually transmitted in the air from one person to another. It can also be spread through touch because the scabs and sores contain live virus, but that is less common. Namely, it happened when the infected person sneezed or coughed virus into the air.

Once smallpox is in the body, it incubates (develops, multiplies) for several days, the CDC estimates between 7 and 19 days. During this time, there may not be any symptoms present and the person probably won't know he or she is sick.

Symptoms: 

• First symptoms are pretty common for diseases: fever and body aches. Some patients may experience vomiting. The CDC states that this stage is not usually contagious, but it can be.
• Next the patient will start to develop a rash in the mouth and tongue. This is when patients are most contagious! That is part of why this disease is dangerous and easy to spread: people around you don't know you have smallpox!
• Following this stage, the sores in the mouth will begin to fade to be replaced by the signature skin sores. 
• The sores become pustules (bumps filled with fluid) form that have a characteristic dent in the middle. 
• The pustules will start to scab over and the scabs eventually fall off. This happens after about 3 weeks of obvious disease (from the mouth sores). And remember, the pustules and scabs are also contagious. Once the scabs are all gone, the person is not contagious anymore.

This highlights another reason this disease is important: if you got smallpox (and almost everyone did before vaccines), you were sick and contagious for about a month. If you survived. Remember the mortality rate was about 33%. Meaning that about a third of the people who were infected would die of the disease.

If the virus moved to the eye, the patient could become blind.

According to the WHO, "Between 65–80% of survivors are marked with deep pitted scars (pockmarks), most prominent on the face."

One upside: if you survived, you had life-long immunity! This means you cannot get smallpox twice!

Smallpox rash and pustules. Image from Wellcome Collection.

Prevention and Treatment:
These are not super important now that smallpox is eradicated, but there are still stocks of smallpox vaccine out there. Military personnel are the most common people vaccinated these days, and not even all of them receive the vaccine. I believe it is available to medical professionals in some places, but many never receive it. The main reason for this is that the vaccine is still a live virus (a weaker vaccinia virus that was developed in labs for the vaccine for many generations) and can cause people nearby to become infected by the vaccine strain. When a person gets the vaccine, they are supposed to avoid human contact for a while until the vaccine site heals. (I know the old vaccines gave a pox mark/pock mark and pustule, so you would have to wait for the scab to fall off, just like with smallpox. I'm unsure if the current vaccines are the same, but I know they are still contagious.)


As for treatment, there are a couple options, just in case! None of these antivirals (medication used to treat viruses) have been used to treat smallpox because there are no more cases, but they are: tecovirimat (TPOXX), cidofovir and brincidofovir.

That's about it for smallpox! I hope you liked it and learned something. And if I missed anything or got anything wrong, please, please let me know so that I can correct it! Feel free to reach out with questions or if something needs clarification. Thanks!

Sources:
Centers for Disease Control and Prevention
World Health Organization
Medical Microbiology, 6th edition by Patrick R. Murray, Ken S. Rosenthal, and Michael A. Pfaller
Mayo Clinic

Also, thanks so much to my friend, Veronica, for helping me edit this post!