The innate immune system is activated first, releasing interferons and cytokines to contain the virus, followed by activation of the adaptive immune system, where T cells and B cells work to identify and eliminate the infection and build lasting immunity. Identification is very important, so these B cells are taking measurements and compositional analysis to warn the body and other immune cells, through the production of antibodies. Once the antibodies are produced they begin tagging the viruses so that the T cells can attack and neutralize the viral infection. This allows the most acute infections are cleared this way, leaving behind immune memory to protect against reinfection.

Our Immune System is responsible for building up mucus membranes, elevating temperature, and triggering other processes that we feel as symptoms. We can still take medications that lower fever and symptoms, but that doesn't mean we should ignore the potential underlying causes. We know that more than just pathogens/microbes are triggering our immune system, things like aersolized chemicals (global emissions), weather changes, pollen, pesticide usage, and other environmental conditions can trigger the immune system. 

"The microbiome is the collection of all microbes, such as bacteria, fungi, viruses, and their genes, that naturally live on our bodies and inside us. Although microbes are so small that they require a microscope to see them, they contribute in big ways to human health and wellness. They protect us against pathogens, help our immune system develop, and enable us to digest food to produce energy.

Because the microbiome is a key interface between the body and the environment, these microbes can affect health in many ways and can even affect how we respond to certain environmental substances. Some microbes alter environmental substances in ways that make them more toxic, while others act as a buffer and make environmental substances less harmful."

National Institute of Environmental Health Sciences

"The critical role of the microbiome is not surprising when considering that there are as many microbes as there are human cells in the body. The human microbiome is diverse, and each body site – for example, the gut, skin, and oral and nasal cavities – has a different community of microbes.

A person’s core microbiome is formed in the first years of life but can change over time in response to different factors including diet, medications, and environmental exposures.

Differences in the microbiome may lead to different health effects from environmental exposures and may also help determine individual susceptibility to certain illnesses. Environmental exposures can also disrupt a person’s microbiome in ways that could increase the likelihood of developing conditions such as diabetes, obesity, cardiovascular and neurological diseases, allergies, and inflammatory bowel disease. For example, specific changes in the gut microbiome have been linked to liver health. NIEHS-funded researchers and collaborators developed a rapid, low-cost tool that uses stool samples to detect microbial changes that can accurately diagnose liver fibrosis and cirrhosis."

National Institute of Environmental Health Sciences

Herd immunity, or community immunity, occurs when a large enough portion of a population becomes immune to a disease—either through vaccination or previous infection—making it difficult for the disease to spread from person to person. This helps protect individuals who are not immune, such as newborns, the elderly, or those with weakened immune systems. There are lots of disabled and/or chronically ill people in our communities that rely on us to get vaccines and wear appropriate PPE (Masking, Eye protection, Washing of Hands, and other Communal Hygiene). 

 Positive Impacts of Herd Immunity:

• Protects vulnerable people who cannot be vaccinated (e.g., due to medical conditions)

• Slows or stops outbreaks, even if not everyone is vaccinated

• Reduces strain on healthcare systems by lowering the number of serious cases

• Can lead to disease elimination or eradication, as seen with smallpox

• Promotes a Healthy Microbiome

• People can spread Antibodies from person-to-person through their microbiome

 Potential Negative Impacts or Misunderstandings:

• Relying too much on natural infection to build herd immunity can lead to high death rates, especially in pandemics (e.g., COVID-19)

• Vaccine refusal in certain groups can create immunity gaps, causing outbreaks of diseases that were previously under control (like measles)

• Herd immunity thresholds vary by disease—highly contagious diseases like measles require 90–95% immunity, making it harder to achieve

• Mutating viruses (like influenza or COVID-19 variants) may reduce the effectiveness of herd immunity over time

Mutation is a natural process for survival. By becoming more effective in moving from host to host and reproducing faster, a virus can extend its life. Other natural reasons for mutation include becoming more effective in adhering to host surfaces, such as the spike protein of COVID-19. Mutation also helps viruses to evade immune responses and vaccines. Sometimes viruses mutate as they make copies of themselves. Sometimes reproduction causes errors, and a gene reproduces incorrectly. Sometimes these errors have no impact at all. Often, however, these errors, or mutations, can be beneficial. If the changes are heritable, they’re passed down to future generations. All organisms mutate. Mutations are the basis for evolution and natural selection. Virus mutation is one of the most compelling arguments for viruses to be classed as living organisms. As with any mutation, some changes will provide a benefit that leads to more efficient reproduction. Others may be dead ends or even harmful, limiting an organism’s ability to thrive. 

• Mutation. Mutations are errors in the replication of the virus’s genetic code. Mutations can be beneficial to the virus, deleterious to the virus, or neutral.

• Variants. Viruses with these mutations are called variants. The Delta and Omicron variants are examples of coronavirus mutations that cause different symptoms from the original infection.

• Strains. Variants that have different physical properties are called strains. These strains may have different behaviors or mechanisms for infection or reproduction.  

Tulane University

Mutations impact on disease control:

Mutations lead to more Variants, and Variants lead to more Re-Infections of people who had antibodies for a virus without this variant mutation. This allows the virus to re-infect a population for long periods of time, keeping it alive and spreadable for much longer. 

Vaccine (defined):

A vaccine trains your immune system to recognize and destroy harmful viruses or bacteria by exposing it to a safe version of the germ (or a part of it), so if you encounter the real thing later, your body can fight it off quickly and effectively. 

A vaccine is a biological preparation that stimulates the body's immune system to recognize and fight specific diseases, without causing the disease itself.

Step By Step: How do Vaccines Work and What Makes them Effective?

Vaccine introduction

• A vaccine is injected (or sometimes taken orally or nasally) into your body.

• It contains antigens—these are harmless versions or parts of a disease-causing organism (such as a protein from a virus or a weakened/killed form of the virus or bacteria).

Immune System Recognition

• Your immune system detects the antigens as foreign invaders.

• It does not know this is a harmless version, so it begins a defensive response.

Anti-body Production 

• Special white blood cells called B cells produce antibodies that match the shape of the antigens.

• These antibodies neutralize the antigens and mark them for destruction.

Memory-(Immune) Cell Formation

• At the same time, your immune system creates memory cells (both B and T cells).

• These memory cells "remember" the shape of the antigen for future protection.

Long-Term Immunity

• If you're later exposed to the real virus or bacteria:

  • Your immune system recognizes it immediately.

  • It rapidly produces the right antibodies and launches a defense before you get sick—or greatly reduces the severity of the illness.

Effectiveness:

• Strong immune response: Vaccines must trigger a good immune memory without causing disease.

• High coverage: The more people vaccinated, the better the community protection (herd immunity).

• Stability and storage: Vaccines must remain potent during manufacturing, storage, and transport.

• Booster doses: Some vaccines require multiple doses to build or maintain immunity.

• Variant targeting: Effective vaccines are updated to protect against evolving viruses (e.g., flu or COVID-19 variants).

• Viral Mutation: Viruses mutate to their environment, allowing for multiple 'versions' of a virus to be spread, with different effects on the body. While some vaccines cover all types of a virus, mutations occur over periods of time, occuring faster the more bodies/space it infects and transmits between. 

The history of inoculation and vaccines spans centuries, originating long before the development of modern medical science. The earliest recorded practice of inoculation, known as variolation, began in China and India as early as the 10th century. Practitioners would expose healthy individuals to material (often puss) taken from smallpox sores in hopes of inducing a mild infection that would confer immunity. This method spread to the Ottoman Empire and eventually reached Europe in the early 18th century, notably introduced to Britain by Lady Mary Wortley Montagu. However, the true breakthrough came in 1796 when Edward Jenner, an English physician, discovered that milkmaids who had contracted cowpox (a much milder disease) seemed immune to smallpox.

  Jenner inoculated a young boy with cowpox and later exposed him to smallpox, and the boy did not contract the virus. Jenner’s method, safer than variolation, laid the foundation for the development of vaccines. The term “vaccine,” is derived from “vacca,” the Latin word for cow, in honor of Jenner’s work. Throughout the 19th and 20th centuries, scientists like Louis Pasteur and Jonas Salk expanded on Jenner’s principles to develop vaccines for rabies, polio, and other infectious diseases. Pasteur, in particular, introduced the concept of using weakened or attenuated pathogens to stimulate immunity. Mass immunization campaigns in the 20th century, such as the global effort to eradicate smallpox, demonstrated the immense public health power of vaccines. Today, vaccines remain one of the most effective tools in preventing disease and improving global health.