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)
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Initial symptoms are flu-like and may include fever, myalgia, lethargy symptoms, cough, sore throat, and other nonspecific symptoms. The only symptom common to all patients appears to be a fever above . SARS may eventually lead to shortness of breath and/or pneumonia; either direct viral pneumonia or first bacterial pneumonia.
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).
SARS may be "suspected" in a patient who has:
- Any of the symptoms, including a fever of or higher, and
- Either a history of:
1. Contact (sexual or casual) with someone with a diagnosis of SARS within the last 10 days OR
2. Travel to any of the regions identified by the World Health Organization (WHO) as areas with recent local transmission of SARS (affected regions as of 10 May 2003 were parts of China, Hong Kong, Singapore and the town of Geraldton, Ontario, Canada).
For a case to be considered "probable," a chest X-ray must be positive for atypical pneumonia or respiratory distress syndrome.
The World Health Organization (WHO) has added the category of "laboratory confirmed SARS" for patients who would otherwise be considered ""probable"" but who have not yet had a positive chest X-ray changes, but have tested positive for SARS based on one of the approved tests (ELISA, immunofluorescence or PCR).
When it comes to the chest X-ray the appearance of SARS is not always uniform but generally appears as an abnormality with patchy infiltrates.
Early reports compared the virus to severe acute respiratory syndrome (SARS), and it has been referred to as Saudi Arabia's SARS-like virus. The first person, in June 2012, had a "seven-day history of fever, cough, expectoration, and shortness of breath." One review of 47 laboratory confirmed cases in Saudi Arabia gave the most common presenting symptoms as fever in 98%, cough in 83%, shortness of breath in 72% and myalgia in 32% of people. There were also frequent gastrointestinal symptoms with diarrhea in 26%, vomiting in 21%, abdominal pain in 17% of people. 72% of people required mechanical ventilation. There were also 3.3 males for every female. One study of a hospital-based outbreak of MERS had an estimated incubation period of 5.5 days (95% confidence interval 1.9 to 14.7 days). MERS can range from asymptomatic disease to severe pneumonia leading to acute respiratory distress syndrome (ARDS). Kidney failure, disseminated intravascular coagulation (DIC), and pericarditis have also been reported.
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.
Coronavirus disease 2019 (COVID-19) is an infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The disease was first identified in December 2019 in Wuhan, the capital of China's Hubei province, and has since spread globally, resulting in the ongoing 2019–20 coronavirus pandemic. Common symptoms include fever, cough, and shortness of breath. Other symptoms may include fatigue, muscle pain, diarrhea, sore throat, loss of smell, and abdominal pain. The time from exposure to onset of symptoms is typically around five days but may range from two to fourteen days. While the majority of cases result in mild symptoms, some progress to viral pneumonia and multi-organ failure. As of 17 April 2020, more than 2.23 million cases have been reported across 210 countries and territories, resulting in more than 153,000 deaths. More than 567,000 people have recovered.
The virus is primarily spread between people during close contact, often via small droplets produced by coughing, sneezing, or talking. While these droplets are produced when breathing out, they usually fall to the ground or onto surfaces rather than being infectious over long distances. People may also become infected by touching a contaminated surface and then touching their eyes, nose, or mouth. The virus can survive on surfaces up to 72 hours. It is most contagious during the first three days after the onset of symptoms, although spread may be possible before symptoms appear and in later stages of the disease.
The standard method of diagnosis is by real-time reverse transcription polymerase chain reaction (rRT-PCR) from a nasopharyngeal swab. Chest CT imaging may also be helpful for diagnosis in individuals where there is a high suspicion of infection based on symptoms and risk factors; however, it is not recommended for routine screening.
Recommended measures to prevent infection include frequent hand washing, maintaining physical distance from others (especially from those with symptoms), covering coughs and sneezes with a tissue or inner elbow, and keeping unwashed hands away from the face. The use of masks is recommended for those who suspect they have the virus and their caregivers. Recommendations for mask use by the general public vary, with some authorities recommending against their use, some recommending their use, and others requiring their use. Currently, there is no vaccine or specific antiviral treatment for COVID-19. Management involves treatment of symptoms, supportive care, isolation, and experimental measures.
The World Health Organization (WHO) declared the 2019–20 coronavirus outbreak a Public Health Emergency of International Concern (PHEIC) on 30 January 2020 and a pandemic on 11 March 2020. Local transmission of the disease has been recorded in most countries across all six WHO regions.
Those infected with the virus may be asymptomatic or develop flu-like symptoms such as fever, cough, fatigue, and shortness of breath. Emergency symptoms include difficulty breathing, persistent chest pain or pressure, confusion, difficulty waking, and bluish face or lips; immediate medical attention is advised if these symptoms are present. Less commonly, upper respiratory symptoms such as sneezing, runny nose or sore throat may be seen. Gastrointestinal symptoms such as nausea, vomiting and diarrhoea have been observed in varying percentages. Some cases in China initially presented only with chest tightness and palpitations. In some, the disease may progress to pneumonia, multi-organ failure, and death. In those who develop severe symptoms, time from symptom onset to needing mechanical ventilation is typically eight days.
Loss of smell was identified as a common early symptom of COVID-19 in March 2020, although not as common as initially reported.
As is common with infections, there is a delay between the moment when a person is infected with the virus and the time when they develop symptoms. This is called the incubation period. The incubation period for COVID-19 is typically five to six days but may range from two to 14 days. 97.5% of people who develop symptoms will do so within 11.5 days of infection.
Reports indicate that not all who are infected develop symptoms. The role of these asymptomatic carriers in transmission is not yet fully known; however, preliminary evidence suggests that they may contribute to the spread of the disease. The proportion of infected people who do not display symptoms is currently unknown and being studied, with the Korea Centers for Disease Control and Prevention (KCDC) reporting that 20% of all confirmed cases remained asymptomatic during their hospital stay. China's National Health Commission began including asymptomatic cases in its daily cases on 1 April; of the 166 infections on that day, 130 (78%) were asymptomatic at the time of testing.
Middle East respiratory syndrome (MERS), also known as camel flu, is a viral respiratory infection caused by the MERS-coronavirus (MERS-CoV). Symptoms may range from mild to severe. They include fever, cough, diarrhea, and shortness of breath. Disease is typically more severe in those with other health problems.
MERS-CoV is a betacoronavirus derived from bats. Camels have been shown to have antibodies to MERS-CoV but the exact source of infection in camels has not been identified. Camels are believed to be involved in its spread to humans but it is unclear how. Spread between humans typically requires close contact with an infected person. Its spread is uncommon outside of hospitals. Thus, its risk to the global population is currently deemed to be fairly low.
As of 2016 there is no specific vaccine or treatment for the disease. However, a number of antiviral medications are currently being studied. The World Health Organization recommends that those who come in contact with camels wash their hands frequently and do not touch sick camels. They also recommend that camel products be appropriately cooked. Among those who are infected treatments that help with the symptoms may be given.
Just under 2000 cases have been reported as of April 4, 2017. About 36% of those who are diagnosed with the disease die from it. The overall risk of death may be lower as those with mild symptoms may be undiagnosed. The first identified case occurred in 2012 in Saudi Arabia and most cases have occurred in the Arabian Peninsula. A strain of MERS-CoV known as HCoV-EMC/2012 found in the first infected person in London in 2012 was found to have a 100% match to Egyptian tomb bats. A large outbreak occurred in the Republic of Korea in 2015.
The most common form of the disease is the head and eye form. Typical symptoms of this form include fever, depression, discharge from the eyes and nose, lesions of the buccal cavity and muzzle, swelling of the lymph nodes, opacity of the corneas leading to blindness, inappetance and diarrhea. Some animals have neurologic signs, such as ataxia, nystagmus, and head pressing. Peracute, alimentary and cutaneous clinical disease patterns have also been described. Death usually occurs within ten days. The mortality rate in symptomatic animals is 90 to 100 percent. Treatment is supportive only.
Symptoms of viral pneumonia include fever, non-productive cough, runny nose, and systemic symptoms (e.g. myalgia, headache). Different viruses cause different symptoms.
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.
Bovine malignant catarrhal fever (BMCF) is a fatal lymphoproliferative disease caused by a group of ruminant gamma herpes viruses including Alcelaphine gammaherpesvirus 1 (AlHV-1) and Ovine gammaherpesvirus 2 (OvHV-2) These viruses cause unapparent infection in their reservoir hosts (sheep with OvHV-2 and wildebeest with AlHV-1), but are usually fatal in cattle and other ungulates such as deer, antelope, and buffalo.
BMCF is an important disease where reservoir and susceptible animals mix. There is a particular problem with Bali cattle in Indonesia, bison in the US and in pastoralist herds in Eastern and Southern Africa.
Disease outbreaks in cattle are usually sporadic although infection of up to 40% of a herd has been reported. The reasons for this are unknown. Some species appear to be particularly susceptible, for example Pére Davids deer, Bali cattle and bison, with many deer dying within 48 hours of the appearance of the first symptoms and bison within three days. In contrast, post infection cattle will usually survive a week or more.
Porcine circoviral disease (PCVD) and Porcine circovirus associated disease (PCVAD), is a disease seen in domestic pigs. This disease causes illness in piglets, with clinical signs including progressive loss of body condition, visibly enlarged lymph nodes, difficulty in breathing, and sometimes diarrhea, pale skin, and jaundice. PCVD is very damaging to the pig-producing industry and has been reported worldwide. PCVD is caused by porcine circovirus type 2 (PCV-2).
The North American industry endorses "PCVAD" and European use "PCVD" to describe this disease.
An emerging infectious disease (EID) is an infectious disease whose incidence has increased in the past 20 years and could increase in the near future. Emerging infections account for at least 12% of all human pathogens. EIDs are caused by newly identified species or strains (e.g. Severe acute respiratory syndrome, HIV/AIDS) that may have evolved from a known infection (e.g. influenza) or spread to a new population (e.g. West Nile fever) or to an area undergoing ecologic transformation (e.g. Lyme disease), or be "reemerging" infections, like drug resistant tuberculosis. Nosocomial (hospital-acquired) infections, such as methicillin-resistant Staphylococcus aureus are emerging in hospitals, and extremely problematic in that they are resistant to many antibiotics. Of growing concern are adverse synergistic interactions between emerging diseases and other infectious and non-infectious conditions leading to the development of novel syndemics. Many emerging diseases are zoonotic - an animal reservoir incubates the organism, with only occasional transmission into human populations.
On post-mortem examination (necropsy), the most obvious gross lesion is subcutaneous oedema in the submandibular and pectoral (brisket) regions. Petechial haemorrhages are found subcutaneously and in the thoracic cavity. In addition, congestion and various degrees of consolidation of the lung may occur. Animals that die within 24–36 hours, have only few petechial haemorrhages on the heart and generalised congestion of the lung, while in animals that die after 72 hours, petechial and ecchymotic haemorrhages were more evident and lung consolidation are more extensive.
The mode of transmission of BoDV-1/2 is unclear but probably occurs through intranasal exposure to contaminated saliva or nasal secretions. Following infection, individuals may develop Borna disease, or may remain subclinical, possibly acting as a carrier of the virus.
Both PMWS and porcine dermatitis and nephropathy syndrome (PDNS) are associated to PCV-2. Many pigs affected by the circovirus also seem to develop secondary bacterial infections, like Glässer disease ("Haemophilus parasuis"), pulmonary pasteurellosis, colibacilosis, salmonellosis and others. Postmortem lesions occur in multiple organs, especially in lymphoid tissues and lung, giving rise to the term "multisystemic". Lesions may also affect the skin, kidney, reproductive tissue, brain, or blood vessels.
Wasting pigs is the most common sign of PMWS infection, increasing the mortality rate significantly.
Borna disease is an infectious neurological syndrome of warm-blooded animals, caused by Borna disease viruses 1 and 2 (BoDV-1/2), both of which are members of the species "Mammalian 1 bornavirus". BoDV-1 an 2 cause abnormal behaviour and fatality. Borna disease viruses 1 and 2 are neurotropic viruses and members of the "Bornaviridae" family within the "Mononegavirales" order.
Although Borna disease viruses 1 and 2 are mainly seen as the causative agent of Borna disease in horses and other animals, they are also controversially discussed as human infectious agents and therefore as potential zoonotic agents. The role of BoDV-1 and -2 in human illness is controversial and it is yet to be established whether BoDV-1 or -2 cause any overt disease in humans. However, correlative evidence exists linking BoDV-1/2 infection with neuropsychiatric disorders such as bipolar disorder.
Usually the atypical causes also involve atypical symptoms:
- No response to common antibiotics such as sulfonamide and beta-lactams like penicillin.
- No signs and symptoms of lobar consolidation, meaning that the infection is restricted to small areas, rather than involving a whole lobe. As the disease progresses, however, the look can tend to lobar pneumonia.
- Absence of leukocytosis.
- Extrapulmonary symptoms, related to the causing organism.
- Moderate amount of sputum, or no sputum at all (i.e. non-productive).
- Lack of alveolar exudate.
- Despite general symptoms and problems with the upper respiratory tract (such as high fever, headache, a dry irritating cough followed later by a productive cough with radiographs showing consolidation), there are in general few physical signs. The patient looks better than the symptoms suggest.
A wide variety of clinical signs have been described for HS in cattle and buffaloes. The incubation periods (the time between exposure and observable disease) for buffalo calves 4–10 months of age varies according to the route of infection. The incubation period is 12–14 hours, approximately 30 hours and 46–80 hours for subcutaneous infection, oral infection and natural exposure, respectively.
There is variability in the duration of the clinical course of the disease. In the case of experimental subcutaneous infection, the clinical course lasted only a few hours, while it persisted for 2–5 days following oral infection and in buffaloes and cattle that had been exposed to naturally-infected animals. It has also been recorded from field observations that the clinical courses of per-acute and acute cases were 4–12 hours and 2–3 days, respectively.
Generally, progression of the disease in buffaloes and cattle is divided into three phases. Phase one is characterised by fever, with a rectal temperature of , loss of appetite and depression. Phase two is typified by increased respiration rate (40–50/minute), laboured breathing, clear nasal discharge (turns opaque and mucopurulent as the disease progresses), salivation and submandibular oedema spreading to the pectoral (brisket) region and even to the forelegs. Finally, in phase three, there is typically recumbency, continued acute respiratory distress and terminal septicaemia. The three phases overlap when the disease course is short. In general, buffaloes have a more acute onset of disease than cattle, with a shorter duration.
Vaccination helps prevent bronchopneumonia, mostly against influenza viruses, adenoviruses, measles, rubella, streptococcus pneumoniae, haemophilus influenzae, diphtheria, bacillus anthracis, chickenpox, and bordetella pertussis.
Lower respiratory tract infection (LRTI), while often used as a synonym for pneumonia, can also be applied to other types of infection including lung abscess and acute bronchitis. Symptoms include shortness of breath, weakness, fever, coughing and fatigue.
There are a number of symptoms that are characteristic of lower respiratory tract infections. The two most common are bronchitis and edema. Influenza affects both the upper and lower respiratory tracts.
Antibiotics are the first line treatment for pneumonia; however, they are not effective or indicated for parasitic or viral infections. Acute bronchitis typically resolves on its own with time.
In 2015 there were about 291 million cases. These resulted in 2.74 million deaths down from 3.4 million deaths in 1990. This was 4.8% of all deaths in 2013.
Bronchitis describes the swelling or inflammation of the bronchial tubes. Additionally, bronchitis is described as either acute or chronic depending on its presentation and is also further described by the causative agent. Acute bronchitis can be defined as acute bacterial or viral infection of the larger airways in healthy patients with no history of recurrent disease. It affects over 40 adults per 1000 each year and consists of transient inflammation of the major bronchi and trachea. Most often it is caused by viral infection and hence antibiotic therapy is not indicated in immunocompetent individuals. Viral bronchitis can sometimes be treated using antiviral medications depending on the virus causing the infection, and medications such as anti-inflammatory drugs and expectorants can help mitigate the symptoms. Treatment of acute bronchitis with antibiotics is common but controversial as their use has only moderate benefit weighted against potential side effects (nausea and vomiting), increased resistance, and cost of treatment in a self-limiting condition. Beta2 agonists are sometimes used to relieve the cough associated with acute bronchitis. In a recent systematic review it was found there was no evidence to support their use.
Chest radiographs (X-ray photographs) often show a pulmonary infection before physical signs of atypical pneumonia are observable at all.
This is occult pneumonia. In general, occult pneumonia is rather often present in patients with pneumonia and can also be caused by "Streptococcus pneumoniae", as the decrease of occult pneumonia after vaccination of children with a pneumococcal vaccine suggests.
Infiltration commonly begins in the perihilar region (where the bronchus begins) and spreads in a wedge- or fan-shaped fashion toward the periphery of the lung field. The process most often involves the lower lobe, but may affect any lobe or combination of lobes.
People with infectious pneumonia often have a productive cough, fever accompanied by shaking chills, shortness of breath, sharp or stabbing chest pain during deep breaths, and an increased rate of breathing. In the elderly, confusion may be the most prominent sign.
The typical signs and symptoms in children under five are fever, cough, and fast or difficult breathing. Fever is not very specific, as it occurs in many other common illnesses, may be absent in those with severe disease, malnutrition or in the elderly. In addition, a cough is frequently absent in children less than 2 months old. More severe signs and symptoms in children may include blue-tinged skin, unwillingness to drink, convulsions, ongoing vomiting, extremes of temperature, or a decreased level of consciousness.
Bacterial and viral cases of pneumonia usually present with similar symptoms. Some causes are associated with classic, but non-specific, clinical characteristics. Pneumonia caused by "Legionella" may occur with abdominal pain, diarrhea, or confusion, while pneumonia caused by "Streptococcus pneumoniae" is associated with rusty colored sputum, and pneumonia caused by "Klebsiella" may have bloody sputum often described as "currant jelly". Bloody sputum (known as hemoptysis) may also occur with tuberculosis, Gram-negative pneumonia, and lung abscesses as well as more commonly with acute bronchitis. "Mycoplasma" pneumonia may occur in association with swelling of the lymph nodes in the neck, joint pain, or a middle ear infection. Viral pneumonia presents more commonly with wheezing than does bacterial pneumonia. Pneumonia was historically divided into "typical" and "atypical" based on the belief that the presentation predicted the underlying cause. However, evidence has not supported this distinction, thus it is no longer emphasized.
Over 100 microorganisms can cause CAP, with most cases caused by "Streptococcus pneumoniae". Certain groups of people are more susceptible to CAP-causing pathogens; for example, infants, adults with chronic conditions (such as chronic obstructive pulmonary disease), senior citizens, alcoholics and others with compromised immune systems are more likely to develop CAP from "Haemophilus influenzae" or "Pneumocystis carinii". A definitive cause is identified in only half the cases.