Patients with abortive polio infections recover completely. In those who develop only aseptic meningitis, the symptoms can be expected to persist for two to ten days, followed by complete recovery. In cases of spinal polio, if the affected nerve cells are completely destroyed, paralysis will be permanent; cells that are not destroyed, but lose function temporarily, may recover within four to six weeks after onset. Half the patients with spinal polio recover fully; one-quarter recover with mild disability, and the remaining quarter are left with severe disability. The degree of both acute paralysis and residual paralysis is likely to be proportional to the degree of viremia, and inversely proportional to the degree of immunity. Spinal polio is rarely fatal.

Without respiratory support, consequences of poliomyelitis with respiratory involvement include suffocation or pneumonia from aspiration of secretions. Overall, 5 to 10 percent of patients with paralytic polio die due to the paralysis of muscles used for breathing. The case fatality rate (CFR) varies by age: 2 to 5 percent of children and up to 15 to 30 percent of adults die. Bulbar polio often causes death if respiratory support is not provided; with support, its CFR ranges from 25 to 75 percent, depending on the age of the patient. When intermittent positive pressure ventilation is available, the fatalities can be reduced to 15 percent.

In 1950, William Hammon at the University of Pittsburgh purified the gamma globulin component of the blood plasma of polio survivors. Hammon proposed the gamma globulin, which contained antibodies to poliovirus, could be used to halt poliovirus infection, prevent disease, and reduce the severity of disease in other patients who had contracted polio. The results of a large clinical trial were promising; the gamma globulin was shown to be about 80 percent effective in preventing the development of paralytic poliomyelitis. It was also shown to reduce the severity of the disease in patients who developed polio. Due to the limited supply of blood plasma gamma globulin was later deemed impractical for widespread use and the medical community focused on the development of a polio vaccine.

At the October 23 meeting of the Child Neurology Society, it was a matter of debate whether acute flaccid myelitis would be likely to return the next year. Enteroviruses D68 and A71 tend to cause neurological symptoms more often than other enteroviruses, but have been infrequent causes of colds. It is possible that enteroviruses have been causing acute flaccid myelitis at a very low rate for many years, misdiagnosed as transverse myelitis, and enterovirus 68 simply happened to become more prevalent in the 2014 season.

The CDC had confirmed 538 cases of enterovirus 68 infection in 43 states. The CDC has determined and submitted to GenBank complete or nearly-complete genomic sequences for three known strains of the virus, which are "genetically related to strains of EV-D68 that were detected in previous years in the United States, Europe, and Asia."

While rates of paralytic symptoms appear to be correlated with the number of respiratory infections, in initial anecdotal reports the cases are not clustered within a family or school, suggesting that the paralysis "per se" is not directly contagious, but arises as a very rare complication of the common respiratory infection.

The CDC MMWR report advised, "To prevent infections in general, persons should stay home if they are ill, wash their hands often with soap and water, avoid close contact (such as touching and shaking hands) with those who are ill, and clean and disinfect frequently touched surfaces."

Unlike polio, acute flaccid myelitis can not currently be prevented with a vaccine.

The number of new cases a year of acute encephalitis in Western countries is 7.4 cases per 100,000 population per year. In tropical countries, the incidence is 6.34 per 100,000 per year. The incidence of Encephalitis has not changed much over time, with an incidence of encephalitis in the US of 250,000 from 2005 to 2015. Approximately seven per 100,000 patients were hospitalized for encephalitis in the US during this time. In 2015, encephalitis was estimated to have affected 4.3 million people and resulted in 150,000 deaths worldwide. Herpes simplex encephalitis has an incidence of 2–4 per million population per year.

Identification of poor prognostic factors include thrombocytopenia, cerebral edema, status epilepticus, and thrombocytopenia. In contrast, a normal encephalogram at the early stages of diagnosis is associated with high rates of survival.

While the general prognosis is favorable, current studies indicate that West Nile Fever can often be more severe than previously recognized, with studies of various recent outbreaks indicating that it may take as long as 60–90 days to recover. People with milder WNF are just as likely as those with more severe manifestations of neuroinvasive disease to experience multiple long term (>1+ years) somatic complaints such as tremor, and dysfunction in motor skills and executive functions. People with milder illness are just as likely as people with more severe illness to experience adverse outcomes. Recovery is marked by a long convalescence with fatigue. One study found that neuroinvasive WNV infection was associated with an increased risk for subsequent kidney disease.

Meningitis is a very common in children. Newborns can develop herpes virus infections through contact with infected secretions in the birth canal. Other viral infections are acquired by breathing air contaminated with virus-containing droplets exhaled by an infected person. Arbovirus infections are acquired from bites by infected insects (called epidemic encephalitis). Viral central nervous system infections in newborns and infants usually begin with fever. The inability of infants to communicate directly makes it difficult to understand their symptoms. Newborns may have no other symptoms and may initially not otherwise appear ill. Infants older than a month or so typically become irritable and fussy and refuse to eat. Vomiting is common. Sometimes the soft spot on top of a newborn's head (fontanelle) bulges, indicating an increase in pressure on the brain. Because irritation of the meninges is worsened by movement, an infant with meningitis may cry more, rather than calm down, when picked up and rocked. Some infants develop a strange, high-pitched cry. Infants with encephalitis often have seizures or other abnormal movements. Infants with severe encephalitis may become lethargic and comatose and then die. To make the diagnosis of meningitis or the diagnosis of encephalitis, doctors do a spinal tap (lumbar puncture) to obtain cerebrospinal fluid (CSF) for laboratory analysis in children.

The virus is most often spread by person to person contact with the stool or saliva of the infected person. Two types of vaccines have been developed to prevent the occurrence and spread of the poliomyelitis virus. The first is an inactivated, or killed, form of the virus and the second is an attenuated, or weakened, form of the virus. The development of vaccines has successfully eliminated the disease from the United States. There are continued vaccination efforts in the U.S. to maintain this success rate as this disease still occurs in some areas of the world.

Risk factors independently associated with developing a clinical infection with WNV include a suppressed immune system and a patient history of organ transplantation. For neuroinvasive disease the additional risk factors include older age (>50+), male sex, hypertension, and diabetes mellitus.

A genetic factor also appears to increase susceptibility to West Nile disease. A mutation of the gene "CCR5" gives some protection against HIV but leads to more serious complications of WNV infection. Carriers of two mutated copies of "CCR5" made up 4.0 to 4.5% of a sample of West Nile disease sufferers, while the incidence of the gene in the general population is only 1.0%.

Many viral infections of the central nervous system occur in seasonal peaks or as epidemics, whereas others, such as herpes simplex encephalitis, are sporadic. In endemic areas it is mostly a disease of children, but as the disease spreads to new regions, or nonimmune travelers visit endemic regions, nonimmune adults are also affected.

Polioencephalitis is a viral infection of the brain, causing inflammation within the grey matter of the brain stem. The virus has an affinity for neuronal cell bodies and has been found to affect mostly the midbrain, pons, medulla and cerebellum of most infected patients. The infection can reach up through the thalamus and hypothalamus and possibly reach the cerebral hemispheres. The infection is caused by the poliomyelitis virus which is a single-stranded RNA virus surrounded by a non-enveloped capsid. Humans are the only known natural hosts of this virus. The disease has been eliminated from the U.S. since the mid-twentieth century, but is still found in certain areas of the world such as Africa.

Myelitis occurs due to various reasons such as infections. Direct infection by viruses, bacteria, mold, or parasites such as human immunodeficiency virus (HIV), human T-lymphotropic virus types I and II (HTLV-I/II), syphilis, lyme disease, and tuberculosis can cause myelitis but it can also be caused due to non-infectious or inflammatory pathway. Myelitis often follows after the infections or after vaccination. These phenomena can be explained by a theory of autoimmune attack which states that the autoimmune bodies attack its spinal cord in response to immune reaction.

The theory of autoimmune attack claims that a person with neuroimmunologic disorders have genetic predisposition to auto-immune disorder, and the environmental factors would trigger the disease. The specific genetics in myelitis is not completely understood. It is believed that the immune system response could be to viral, bacterial, fungal, or parasitic infection; however, it is not known why the immune system attacks itself. Especially, for immune system to cause inflammatory response anywhere in the central nervous system, the cells from immune system must pass through the blood brain barrier. In the case of myelitis, not only is the immune system dysfunctional, but the dysfunction also crosses this protective blood brain barrier to affect the spinal cord.

In 2012, the World Health Organization estimated that vaccination prevents 2.5 million deaths each year. If there is 100% immunization, and 100% efficacy of the vaccines, one out of seven deaths among young children could be prevented, mostly in developing countries, making this an important global health issue. Four diseases were responsible for 98% of vaccine-preventable deaths: measles, "Haemophilus influenzae" serotype b, pertussis, and neonatal tetanus.

The Immunization Surveillance, Assessment and Monitoring program of the WHO monitors and assesses the safety and effectiveness of programs and vaccines at reducing illness and deaths from diseases that could be prevented by vaccines.

Vaccine-preventable deaths are usually caused by a failure to obtain the vaccine in a timely manner. This may be due to financial constraints or to lack of access to the vaccine. A vaccine that is generally recommended may be medically inappropriate for a small number of people due to severe allergies or a damaged immune system. In addition, a vaccine against a given disease may not be recommended for general use in a given country, or may be recommended only to certain populations, such as young children or older adults. Every country makes its own vaccination recommendations, based on the diseases that are common in its area and its healthcare priorities. If a vaccine-preventable disease is uncommon in a country, then residents of that country are unlikely to receive a vaccine against it. For example, residents of Canada and the United States do not routinely receive vaccines against yellow fever, which leaves them vulnerable to infection if travelling to areas where risk of yellow fever is highest (endemic or transitional regions).

Encephalomyelitis is inflammation of the brain and spinal cord. Various types of encephalomyelitis include:

- "Acute disseminated encephalomyelitis" or "postinfectious encephalomyelitis", a demyelinating disease of the brain and spinal cord, possibly triggered by viral infection.

- "Encephalomyelitis disseminata", a synonym for multiple sclerosis.

- "AntiMOG associated encephalomyelitis", one of the underlying conditions for the phenotype neuromyelitis optica and in general all the spectrum of MOG autoantibody-associated demyelinating diseases.

- "Equine encephalomyelitis", also called "equine encephalitis", a potentially fatal mosquito-borne viral disease that infects horses and humans.

- "Myalgic encephalomyelitis", a disease involving presumed inflammation of the central nervous system with symptoms of muscle pain and fatigue; the term has sometimes been used interchangeably with "chronic fatigue syndrome", though there is still controversy over the distinction.

- "Experimental autoimmune encephalomyelitis" (EAE), an animal model of brain inflammation.

- Progressive encephalomyelitis with rigidity and myoclonus (PERM) – A kind of stiff person syndrome.

- AIDS related encephalomyelitis, caused by opportunistic Human T-lymphotropic virus type III (HTLV-III) infection.

The WHO lists 25 diseases for which vaccines are available:

1. Measles

2. Rubella

3. Cholera

4. Meningococcal disease

5. Influenza

6. Diphtheria

7. Mumps

8. Tetanus

9. Hepatitis A

10. Pertussis

11. Tuberculosis

12. Hepatitis B

13. Pneumoccocal disease

14. Typhoid fever

15. Hepatitis E

16. Poliomyelitis

17. Tick-borne encephalitis

18. Haemophilus influenzae type b

19. Rabies

20. Varicella and herpes zoster (shingles)

21. Human papilloma-virus

22. Rotavirus gastroenteritis

23. Yellow fever

24. Japanese encephalitis

25. Malaria

26. Dengue fever

Given that some conditions as MS show cortical damage together with the WM damage, there has been interest if this can appear as a secondary damage of the WM. It seems that some researchers claim so.

Guillain–Barré syndrome can lead to death as a result of a number of complications: severe infections, blood clots, and cardiac arrest likely due to autonomic neuropathy. Despite optimum care this occurs in about 5% of cases.

There is a variation in the rate and extent of recovery. The prognosis of Guillain–Barré syndrome is determined mainly by age (those over 40 may have a poorer outcome), and by the severity of symptoms after two weeks. Furthermore, those who experienced diarrhea before the onset of disease have a worse prognosis. On the nerve conduction study, the presence of conduction block predicts poorer outcome at 6 months. In those who have received intravenous immunoglobulins, a smaller increase in IgG in the blood two weeks after administration is associated with poorer mobility outcomes at six months than those whose IgG level increased substantially. If the disease continues to progress beyond four weeks, or there are multiple fluctuations in the severity (more than two in eight weeks), the diagnosis may be chronic inflammatory demyelinating polyneuropathy, which is treated differently.

In research studies, the outcome from an episode of Guillain–Barré syndrome is recorded on a scale from 0 to 6, where 0 denotes completely healthy, 1 very minor symptoms but able to run, 2 able to walk but not to run, 3 requiring a stick or other support, 4 confined to bed or chair, 5 requiring long-term respiratory support, 6 death.

The health-related quality of life (HRQL) after an attack of Guillain–Barré syndrome can be significantly impaired. About a fifth are unable to walk unaided after six months, and many experience chronic pain, fatigue and difficulty with work, education, hobbies and social activities. HRQL improves significantly in the first year.

According to a review by Brainard, et al., Ebola virus was identified in almost 3 out of 4 seminal fluid samples ( 18 survivors) almost 4 months after initial infection, with the last positive samples being more than 6 months (203 days) after infection had occurred. Another aspect of survivors of the Ebola virus, is that it could become sexually transmitted, as the virus is present in semen nine months after the individuals are declared free of Ebola. A 2017 study found the virus in the semen of some men after more than two years following the recovery from the acute infection.

In Western countries, the number of new episodes per year has been estimated to be between 0.89 and 1.89 cases per 100,000 people. Children and young adults are less likely to be affected than the elderly: the risk increases by 20% for every decade of life. Men are more likely to develop Guillain–Barré syndrome than women; the relative risk for men is 1.78 compared to women.

The distribution of subtypes varies between countries. In Europe and the United States, 60–80% of people with Guillain–Barré syndrome have the demyelinating subtype (AIDP), and AMAN affects only a small number (6–7%). In Asia and Central and South America, that proportion is significantly higher (30–65%). This may be related to the exposure to different kinds of infection, but also the genetic characteristics of that population. Miller Fisher variant is thought to be more common in Southeast Asia.

Demyelination is produced by injection of brain extracts, CNS proteins (such as myelin basic protein), or peptides from such protein emulsified in an adjuvant such as complete Freund's adjuvant. The presence of the adjuvant allows the generation of inflammatory responses to the protein/peptides. In many protocols, mice are coinjected with pertussis toxin to break down the blood-brain barrier and allow immune cells access to the CNS tissue. This immunisation leads to multiple small disseminated lesions of demyelination (as well as micro-necroses) in the brain and spinal cord and the onset of clinical symptoms.

Although sharing some features, mostly demyelination, this model, first introduced in 1930s, differs from human MS in several ways. EAE either kills animals or leaves them with permanent disabilities; animals with EAE also suffer severe nerve inflammation, and the time course of EAE is entirely different from MS, being the main antigen (MBP) in charge.

Although there is some progress that may potentially help Ebola survivors, adequate funding and further research is required to help provide more answers about post-Ebola syndrome. Studies from previous outbreaks reveal that the virus is able to survive for months after recovery in some parts of the body such as the eyes and testes, where the immune system cannot reach. It is not known if the neurologic symptoms seen in survivors are a direct result of the virus or, instead, triggered by the immune system’s response to the infection. It is known that Ebola can trigger a massive cytokine storm that can cause bleeding throughout the body, including the brain, which may explain various neurological symptoms that have been reported.

Post-polio syndrome occurs in approximately 25 to 50 percent of people who survive a poliomyelitis infection. On average, it occurs 30–35 years afterwards; however, delays of between 8–71 years have been recorded. The disease occurs sooner in persons with more severe initial infection. Other factors that increase the risk of postpolio syndrome include increasing length of time since acute poliovirus infection, presence of permanent residual impairment after recovery from the acute illness, and being female.

Post-polio syndrome is documented to occur in cases of nonparalytic polio (NPP). One review states late-onset weakness and fatigue occurs in 14 to 42 percent of NPP patients.

Infectious diseases causing ILI include malaria, acute HIV/AIDS infection, herpes, hepatitis C, Lyme disease, rabies, myocarditis, Q fever, dengue fever, poliomyelitis, pneumonia, measles, and many others.

Pharmaceutical drugs that may cause ILI include many biologics such as interferons and monoclonal antibodies. Chemotherapeutic agents also commonly cause flu-like symptoms. Other drugs associated with a flu-like syndrome include bisphosphonates, caspofungin, and levamisole. A flu-like syndrome can also be caused by an influenza vaccine or other vaccines, and by opioid withdrawal in addicts.