Deep Learning Technology: Sebastian Arnold, Betty van Aken, Paul Grundmann, Felix A. Gers and Alexander Löser. Learning Contextualized Document Representations for Healthcare Answer Retrieval. The Web Conference 2020 (WWW'20)
Funded by The Federal Ministry for Economic Affairs and Energy; Grant: 01MD19013D, Smart-MD Project, Digital Technologies
Human parainfluenza viruses (HPIVs) are the viruses that cause human parainfluenza. HPIVs are a group of four distinct single-stranded RNA viruses belonging to the Paramyxoviridae family. These viruses are closely associated with both human and veterinary disease. Virions are approximately 150–250 nm in size and contain negative sense RNA with a genome encompassing ~15,000 nucleotides.
The viruses can be detected via cell culture, immunofluorescent microscopy, and PCR. HPIVs remain the second main cause of hospitalisation in children under 5 years of age suffering from a respiratory illness (only respiratory syncytial virus causes more respiratory hospitalisations for this age group).
The incubation period is 5–7 days (with a range of 3–10). Symptoms can include a harsh, dry cough, retching, sneezing, snorting, gagging or vomiting in response to light pressing of the trachea or after excitement or exercise. The presence of a fever varies from case to case.
In the United States it is estimated that there are 5 million children with lower respiratory infections (LRI) each year. Estimates have shown that HPIV-1, HPIV-2 and HPIV-3 have been linked with up to a third of these infections. Upper respiratory infections (URI) are also important in the context of HPIV, however are caused to a lesser extent by the virus. The highest rates of serious HPIV illnesses occur among young children and surveys have shown that about 75% of children aged 5 or older have antibodies to HPIV-1.
For infants and young children it has been estimated that ~25% will develop 'clinically significant disease.'
Repeated infection throughout the life of the host is not uncommon and symptoms of later breakouts include upper respiratory tract illness, such as cold and a sore throat. The incubation period for all four serotypes is 1 to 7 days. In immunosuppressed people, parainfluenza virus infections can cause severe pneumonia which can be fatal.
HPIV-1 and HPIV-2 have been demonstrated to be the principal causative agent behind croup (laryngotracheobronchitis) which is a viral disease of the upper airway and is mainly problematic in children aged 6–48 months of age. Biennial epidemics starting in Autumn are associated with both HPIV-1 and 2 however, HPIV-2 can also have yearly outbreaks. Additionally, HPIV-1 tends to cause biennial outbreaks of croup in the fall. In the United States, large peaks have presently been occurring during odd-numbered years.
HPIV-3 has been closely associated with bronchiolitis and pneumonia and principally targets those aged <1 year.
HPIV-4 remains infrequently detected. However, it is now believed to be more common than previously thought, but is less likely to cause severe disease. By the age of 10, the majority of children are sero-positive for HPIV-4 infection which may be indicative of a large proportion of asymptomatic or mild infections.
Important epidemiological factors that are associated with a higher risk of infection and mortality are those who are immuno-compromised and may be taken ill with more extreme forms of LRI. Associations between HPIVs and neurologic disease are known, for example hospitalisation with certain HPIVs has a strong association with febrile seizures. HPIV-4B has the strongest association (up to 62%) followed by hPIV-3 and 1.
HPIVs have also been linked with rare cases of virally caused meningitis and Guillain–Barré syndrome.
HPIVs are spread person to person by contact with infected secretions through respiratory droplets or contaminated surfaces or objects. Infection can occur when infectious material contacts mucous membranes of the eyes, mouth, or nose, and possibly through the inhalation of droplets generated by a sneeze or cough. HPIVs can remain infectious in airborne droplets for over an hour.
Overall, HPIVs remain best known for its effects on the respiratory system and this appears to be where the majority of the focus has been upon.
Although kennel cough is considered to be a multifactorial infection, there are two main forms. The first is more mild and is caused by B. bronchiseptica and canine parainfluenza virus infections, without complications from canine distemper virus (CDV) or canine adenovirus (CAV). This form occurs most regularly in autumn, and can be distinguished by symptoms such as a retching cough and vomiting. The second form has a more complex combination of causative organisms including CDV and CAV. It typically occurs in dogs that have not been vaccinated and it is not seasonal. Symptoms are more severe than the first form, and may include rhinitis, conjunctivitis, and fever in addition to a hacking cough.
A dog that survives distemper will continue to have both nonlife-threatening and life-threatening signs throughout its lifespan. The most prevalent nonlife-threatening symptom is hard pad disease. This occurs when a dog experiences the thickening of the skin on the pads of its paws as well as on the end of its nose. Another lasting symptom commonly is enamel hypoplasia. Puppies, especially, will have damage to the enamel of teeth that are not completely formed or those that have not yet grown through the gums. This is a result of the virus's killing the cells responsible for manufacturing the tooth enamel. These affected teeth tend to erode quickly.
Life-threatening signs usually include those due to the degeneration of the nervous system. Dogs that have been infected with distemper tend to suffer a progressive deterioration of mental abilities and motor skills. With time, the dog can acquire more severe seizures, paralysis, reduction in sight and incoordination. These dogs are usually humanely euthanized because of the immense pain and suffering they face.
In dogs, signs of distemper vary widely from no signs, to mild respiratory signs indistinguishable from kennel cough, to severe pneumonia with vomiting, bloody diarrhea and death.
Commonly observed signs are a runny nose, vomiting and diarrhea, dehydration, excessive salivation, coughing and/or labored breathing, loss of appetite, and weight loss. If neurological signs develop, incontinence may ensue. Central nervous system signs include a localized involuntary twitching of muscles or groups of muscles, seizures with salivation and jaw movements commonly described as "chewing gum fits", or more appropriately as "distemper myoclonus". As the condition progresses, the seizures worsen and advance to grand mal convulsions followed by death of the animal. The animal may also show signs of sensitivity to light, incoordination, circling, increased sensitivity to sensory stimuli such as pain or touch, and deterioration of motor capabilities. Less commonly, they may lead to blindness and paralysis. The length of the systemic disease may be as short as 10 days, or the start of neurological signs may not come until several weeks or months later. Those few that survive usually have a small tic or twitch of varying levels of severity. With time, this tic will usually diminish somewhat in its severity.
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the virus strain that causes coronavirus disease 2019 (COVID-19), a respiratory illness. It is colloquially known as the coronavirus, and was previously referred to by its provisional name 2019 novel coronavirus (2019-nCoV). SARS-CoV-2 is a positive-sense single-stranded RNA virus. It is contagious in humans, and the World Health Organization (WHO) has designated the ongoing pandemic of COVID-19 a Public Health Emergency of International Concern. Because the strain was first discovered in Wuhan, China, it is sometimes referred to as "Wuhan virus" or "Wuhan coronavirus". Since the WHO discourages the use of names based on locations such as MERS, and to avoid confusion with the disease SARS, it sometimes refers to SARS-CoV-2 as "the COVID-19 virus" in public health communications. The general public frequently calls both SARS-CoV-2 and the disease it causes "coronavirus", but scientists typically use more precise terminology.
Taxonomically, SARS-CoV-2 is a strain of Severe acute respiratory syndrome-related coronavirus (SARSr-CoV). It is believed to have zoonotic origins and has close genetic similarity to bat coronaviruses, suggesting it emerged from a bat-borne virus. An intermediate animal reservoir such as a pangolin is also thought to be involved in its introduction to humans. The virus shows little genetic diversity, indicating that the spillover event introducing SARS-CoV-2 to humans is likely to have occurred in late 2019.
Epidemiological studies estimate each infection results in 1.4 to 3.9 new ones when no members of the community are immune and no preventive measures taken. The virus is primarily spread between people through close contact and via respiratory droplets produced from coughs or sneezes. It mainly enters human cells by binding to the receptor angiotensin converting enzyme 2 (ACE2).
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.
Symptoms of viral pneumonia include fever, non-productive cough, runny nose, and systemic symptoms (e.g. myalgia, headache). Different viruses cause different symptoms.
The causes of influenza-like illness range from benign self-limited illnesses such as gastroenteritis, rhinoviral disease, and influenza, to severe, sometimes life-threatening, diseases such as meningitis, sepsis, and leukemia.
Viral pneumonia is a pneumonia caused by a virus.
Viruses are one of the two major causes of pneumonia, the other being bacteria; less common causes are fungi and parasites. Viruses are the most common cause of pneumonia in children, while in adults bacteria are a more common cause.
Paravaccinia virus presents itself with blisters, nodules, or lesions about 4 mm in diameter, typically in the area that has made contact with livestock that is infected with bovine papular stomatitis. Lesions may begin forming as late as three weeks after contact has been made with an infected animal. In rare cases, lesions may be seen systemic. General signs of infection are also common, such as fever and fatigue.
Infected livestock may present with blisters or lesions on their udders or snout. Often, however, infected livestock show little to no symptoms.
Approximately 33% of people with influenza are asymptomatic.
Symptoms of influenza can start quite suddenly one to two days after infection. Usually the first symptoms are chills or a chilly sensation, but fever is also common early in the infection, with body temperatures ranging from 38 to 39 °C (approximately 100 to 103 °F). Many people are so ill that they are confined to bed for several days, with aches and pains throughout their bodies, which are worse in their backs and legs. Symptoms of influenza may include:
- Fever and extreme coldness (chills shivering, shaking (rigor))
- Nasal congestion
- Runny nose
- Body aches, especially joints and throat
- Irritated, watering eyes
- Reddened eyes, skin (especially face), mouth, throat and nose
- Petechial rash
- In children, gastrointestinal symptoms such as diarrhea and abdominal pain, (may be severe in children with influenza B)
It can be difficult to distinguish between the common cold and influenza in the early stages of these infections. Influenza is a mixture of symptoms of common cold and pneumonia, body ache, headache, and fatigue. Diarrhea is not normally a symptom of influenza in adults, although it has been seen in some human cases of the H5N1 "bird flu" and can be a symptom in children. The symptoms most reliably seen in influenza are shown in the adjacent table.
Since antiviral drugs are effective in treating influenza if given early (see treatment section, below), it can be important to identify cases early. Of the symptoms listed above, the combinations of fever with cough, sore throat and/or nasal congestion can improve diagnostic accuracy. Two decision analysis studies suggest that "during local outbreaks" of influenza, the prevalence will be over 70%, and thus patients with any of these combinations of symptoms may be treated with neuraminidase inhibitors without testing. Even in the absence of a local outbreak, treatment may be justified in the elderly during the influenza season as long as the prevalence is over 15%.
The available laboratory tests for influenza continue to improve. The United States Centers for Disease Control and Prevention (CDC) maintains an up-to-date summary of available laboratory tests. According to the CDC, rapid diagnostic tests have a sensitivity of 50–75% and specificity of 90–95% when compared with viral culture. These tests may be especially useful during the influenza season (prevalence=25%) but in the absence of a local outbreak, or peri-influenza season (prevalence=10%).
Occasionally, influenza can cause severe illness including primary viral pneumonia or secondary bacterial pneumonia. The obvious symptom is trouble breathing. In addition, if a child (or presumably an adult) seems to be getting better and then relapses with a high fever, that is a danger sign since this relapse can be bacterial pneumonia.
Croup is characterized by a "barking" cough, stridor, hoarseness, and difficulty breathing which usually worsens at night. The "barking" cough is often described as resembling the call of a seal or sea lion. The stridor is worsened by agitation or crying, and if it can be heard at rest, it may indicate critical narrowing of the airways. As croup worsens, stridor may decrease considerably.
Other symptoms include fever, coryza (symptoms typical of the common cold), and indrawing of the chest wall–known as Hoover's sign. Drooling or a very sick appearance indicate other medical conditions, such as epiglottitis.
Paravaccinia virus is a viral infection of the Parapoxvirus genus of viruses. Human can contract the virus from contact with livestock infected with Bovine papular stomatitis and is common with ranchers, milkers, and veterinarians. Infection will present with fever, fatigue, and lesion on the skin.
The typical symptoms of a cold include a cough, a runny nose, nasal congestion and a sore throat, sometimes accompanied by muscle ache, fatigue, headache, and loss of appetite. A sore throat is present in about 40% of cases and a cough in about 50%, while muscle ache occurs in about half. In adults, a fever is generally not present but it is common in infants and young children. The cough is usually mild compared to that accompanying influenza. While a cough and a fever indicate a higher likelihood of influenza in adults, a great deal of similarity exists between these two conditions. A number of the viruses that cause the common cold may also result in asymptomatic infections.
The color of the sputum or nasal secretion may vary from clear to yellow to green and does not indicate the class of agent causing the infection.
In swine, an influenza infection produces fever, lethargy, sneezing, coughing, difficulty breathing and decreased appetite. In some cases the infection can cause abortion. Although mortality is usually low (around 1–4%), the virus can produce weight loss and poor growth, causing economic loss to farmers. Infected pigs can lose up to 12 pounds of body weight over a three- to four-week period. Swine have receptors to which both avian and mammalian influenza viruses are able to bind to, which leads to the virus being able to evolve and mutate into different forms. Influenza A is responsible for infecting swine, and was first identified in the summer of 1918. Pigs have often been seen as "mixing vessels", which help to change and evolve strains of disease that are then passed on to other mammals, such as humans.
Direct transmission of a swine flu virus from pigs to humans is occasionally possible (zoonotic swine flu). In all, 50 cases are known to have occurred since the first report in medical literature in 1958, which have resulted in a total of six deaths. Of these six people, one was pregnant, one had leukemia, one had Hodgkin's lymphoma and two were known to be previously healthy. Despite these apparently low numbers of infections, the true rate of infection may be higher, since most cases only cause a very mild disease, and will probably never be reported or diagnosed.
According to the Centers for Disease Control and Prevention (CDC), in humans the symptoms of the 2009 "swine flu" H1N1 virus are similar to those of influenza and of influenza-like illness in general. Symptoms include fever; cough, sore throat, watery eyes, body aches, shortness of breath, headache, weight loss, chills, sneezing, runny nose, coughing, dizziness, abdominal pain, lack of appetite and fatigue. The 2009 outbreak has shown an increased percentage of patients reporting diarrhea and vomiting as well. The 2009 H1N1 virus is not zoonotic swine flu, as it is not transmitted from pigs to humans, but from person to person through airborne droplets.
Because these symptoms are not specific to swine flu, a differential diagnosis of "probable" swine flu requires not only symptoms, but also a high likelihood of swine flu due to the person's recent and past medical history. For example, during the 2009 swine flu outbreak in the United States, the CDC advised physicians to "consider swine influenza infection in the differential diagnosis of patients with acute febrile respiratory illness who have either been in contact with persons with confirmed swine flu, or who were in one of the five U.S. states that have reported swine flu cases or in Mexico during the seven days preceding their illness onset." A diagnosis of "confirmed" swine flu requires laboratory testing of a respiratory sample (a simple nose and throat swab).
The most common cause of death is respiratory failure. Other causes of death are pneumonia (leading to sepsis), high fever (leading to neurological problems), dehydration (from excessive vomiting and diarrhea), electrolyte imbalance and kidney failure. Fatalities are more likely in young children and the elderly.
Croup, also known as laryngotracheobronchitis, is a type of respiratory infection that is usually caused by a virus. The infection leads to swelling inside the trachea, which interferes with normal breathing and produces the classic symptoms of "barking" cough, stridor, and a hoarse voice. Fever and runny nose may also be present. These symptoms may be mild, moderate, or severe. Often it starts or is worse at night. It normally lasts one to two days.
Croup can be caused by a number of viruses including parainfluenza and influenza virus. Rarely is it due to a bacterial infection. Croup is typically diagnosed based on signs and symptoms after potentially more severe causes, such as epiglottitis or an airway foreign body, have been ruled out. Further investigations—such as blood tests, X-rays, and cultures—are usually not needed.
Many cases of croup are preventable by immunization for influenza and diphtheria. Croup is usually treated with a single dose of steroids by mouth. In more severe cases inhaled epinephrine may also be used. Hospitalization is required in one to five percent of cases.
Croup is a relatively common condition that affects about 15% of children at some point. It most commonly occurs between 6 months and 5 years of age but may rarely be seen in children as old as fifteen. It is slightly more common in males than females. It occurs most often in autumn. Before vaccination, croup was frequently caused by diphtheria and was often fatal. This cause is now very rare in the Western world due to the success of the diphtheria vaccine.
A cold usually begins with fatigue, a feeling of being chilled, sneezing, and a headache, followed in a couple of days by a runny nose and cough. Symptoms may begin within sixteen hours of exposure and typically peak two to four days after onset. They usually resolve in seven to ten days, but some can last for up to three weeks. The average duration of cough is eighteen days and in some cases people develop a post-viral cough which can linger after the infection is gone. In children, the cough lasts for more than ten days in 35–40% of cases and continues for more than 25 days in 10%.
Roseola typically affects children between six months and two years of age, and begins with a sudden high fever (39–40 °C; 102.2-104 °F). In rare cases, this can cause cause febrile convulsions (also known as febrile seizures or "fever fits") due to the sudden rise in body temperature, but in many cases the child appears normal. After a few days the fever subsides, and just as the child appears to be recovering, a red rash appears. This usually begins on the trunk and then spreads to the arms, legs, and neck. The rash is not itchy and may last 1 to 2 days. In contrast, a child suffering from measles would usually appear sicker, with symptoms of conjunctivitis, cold-like symptoms, and a cough, and their rash would affect the face and last for several days. Liver dysfunction can occur in rare cases.
A small percentage of children acquire HHV-6 with few sign or symptoms of the disease. Exanthema subitum occurs in approximately 30% of children during primary HHV-6 infection. Others may show symptoms significant enough that other more serious infections, such as meningitis or measles should be ruled out. In case of febrile seizures, medical advice can be sought for reassurance. However, febrile seizures are not harmful, do not require treatment, and have no long term negative effects unless they last longer than five minutes.
In rare cases, HHV-6 can become active in an adult previously infected during childhood and can show signs of mononucleosis.
Roseola is an infectious disease caused by certain types of virus. Most infections occur before the age of three. Symptoms vary from absent to the classic presentation of a fever of rapid onset followed by a rash. The fever generally lasts for three to five days. The rash is generally pink and lasts for less than three days. Complications may include febrile seizures, with serious complications being rare.
It is caused by either "human herpesvirus 6" (HHV-6) or "human herpesvirus 7" (HHV-7). Spread is usually through the saliva of those who are otherwise healthy. However, it may also spread from the mother to baby during pregnancy. Diagnosis is typically based on symptoms but can be confirmed with blood tests. Low numbers of white blood cells may also be present.
Treatment includes sufficient fluids and medications to treat the fever. Nearly all people are infected at some point in time. Males and females are affected equally often. The disease was first described in 1910 while the causal virus was determined in 1988. The disease may reactivate in those with a weakened immune system and may result in significant health problems.
Human-to-human transmission of SARS-CoV-2 has been confirmed during the 2019–20 coronavirus pandemic. Transmission occurs primarily via respiratory droplets from coughs and sneezes within a range of about 1.8 metres (6 ft). Indirect contact via contaminated surfaces is another possible cause of infection. Preliminary research indicates that the virus may remain viable on plastic and steel for up to three days, but does not survive on cardboard for more than one day or on copper for more than four hours; the virus is inactivated by soap, which destabilises its lipid bilayer. Viral RNA has also been found in stool samples from infected individuals.
The degree to which the virus is infectious during the incubation period is uncertain, but research has indicated that the pharynx reaches peak viral load approximately four days after infection. On 1 February 2020, the World Health Organization (WHO) indicated that "transmission from asymptomatic cases is likely not a major driver of transmission". However, an epidemiological model of the beginning of the outbreak in China suggested that "pre-symptomatic shedding may be typical among documented infections" and that subclinical infections may have been the source of a majority of infections.
There is some evidence of human-to-animal transmission of SARS-CoV-2, including examples in felids. Some institutions have advised those infected with SARS-CoV-2 to restrict contact with animals.
Influenza, commonly known as "the flu", is an infectious disease caused by an influenza virus. Symptoms can be mild to severe. The most common symptoms include: a high fever, runny nose, sore throat, muscle pains, headache, coughing, and feeling tired. These symptoms typically begin two days after exposure to the virus and most last less than a week. The cough, however, may last for more than two weeks. In children, there may be nausea and vomiting, but these are not common in adults. Nausea and vomiting occur more commonly in the unrelated infection gastroenteritis, which is sometimes inaccurately referred to as "stomach flu" or "24-hour flu". Complications of influenza may include viral pneumonia, secondary bacterial pneumonia, sinus infections, and worsening of previous health problems such as asthma or heart failure.
Three types of influenza viruses affect people, called Type A, Type B, and Type C. Usually, the virus is spread through the air from coughs or sneezes. This is believed to occur mostly over relatively short distances. It can also be spread by touching surfaces contaminated by the virus and then touching the mouth or eyes. A person may be infectious to others both before and during the time they are showing symptoms. The infection may be confirmed by testing the throat, sputum, or nose for the virus. A number of rapid tests are available; however, people may still have the infection if the results are negative. A type of polymerase chain reaction that detects the virus's RNA is more accurate.
Frequent hand washing reduces the risk of viral spread. Wearing a surgical mask is also useful. Yearly vaccinations against influenza are recommended by the World Health Organization for those at high risk. The vaccine is usually effective against three or four types of influenza. It is usually well tolerated. A vaccine made for one year may not be useful in the following year, since the virus evolves rapidly. Antiviral drugs such as the neuraminidase inhibitor oseltamivir, among others, have been used to treat influenza. Their benefits in those who are otherwise healthy do not appear to be greater than their risks. No benefit has been found in those with other health problems.
Influenza spreads around the world in a yearly outbreak, resulting in about three to five million cases of severe illness and about 250,000 to 500,000 deaths. In the Northern and Southern parts of the world, outbreaks occur mainly in winter while in areas around the equator outbreaks may occur at any time of the year. Death occurs mostly in the young, the old and those with other health problems. Larger outbreaks known as pandemics are less frequent. In the 20th century, three influenza pandemics occurred: Spanish influenza in 1918 (~50 million deaths), Asian influenza in 1957 (two million deaths), and Hong Kong influenza in 1968 (one million deaths). The World Health Organization declared an outbreak of a new type of influenza A/H1N1 to be a pandemic in June 2009. Influenza may also affect other animals, including pigs, horses and birds.
Avian influenza—known informally as avian flu or bird flu is a variety of influenza caused by viruses adapted to birds. The type with the greatest risk is highly pathogenic avian influenza (HPAI). Bird flu is similar to swine flu, dog flu, horse flu and human flu as an illness caused by strains of influenza viruses that have adapted to a specific host. Out of the three types of influenza viruses (A, B, and C), influenza A virus is a zoonotic infection with a natural reservoir almost entirely in birds. Avian influenza, for most purposes, refers to the influenza A virus.
Though influenza A is adapted to birds, it can also stably adapt and sustain person-to person transmission. Recent influenza research into the genes of the Spanish flu virus shows it to have genes adapted from both human and avian strains. Pigs can also be infected with human, avian, and swine influenza viruses, allow for mixtures of genes (reassortment) to create a new virus, which can cause an antigenic shift to a new influenza A virus subtype which most people have little to no immune protection.
Avian influenza strains are divided into two types based on their pathogenicity: high pathogenicity (HP) or low pathogenicity (LP). The most well-known HPAI strain, H5N1, appeared in China in 1996, and also has low pathogenic strains found in North America. Companion birds in captivity are unlikely to contract the virus and there has been no report of a companion bird with avian influenza since 2003. Pigeons do not contract or spread the virus.
Between early 2013 to early 2017, 916 lab-confirmed human cases of H7N9 were reported to the World Health Organization (WHO). On 9 January 2017, the National Health and Family Planning Commission of China reported to WHO 106 cases of H7N9 which occurred from late November through late December, including 35 deaths, 2 potential cases of human-to-human transmission, and 80 of these 106 persons stating that they have visited live poultry markets. The cases are reported from Jiangsu (52), Zhejiang (21), Anhui (14), Guangdong (14), Shanghai (2), Fujian (2) and Hunan (1). Similar sudden increases in the number of human cases of H7N9 have occurred in previous years during December and January.