Compiled by Dr. Asma Waheed/Dr. Mehnaz Ali Bangash/ Dr. Shahroz Saud Ahmed/Hafsa Ashraf.
Updated March 22nd, 2020
Corona Virus
Case definition
Coronavirus disease 2019 (COVID-19) Literature review Feb 2020.
Coronaviruses are important human and animal pathogens. At the end of 2019, a novel coronavirus was identified as the cause of a cluster of pneumonia cases in Wuhan, a city in the Hubei Province of China. It rapidly spread, resulting in an epidemic throughout China, followed by an increasing number of cases in other countries throughout the world. In February 2020, the World Health Organization designated the disease COVID-19, which stands for coronavirus disease 2019. The virus that causes COVID-19 is designated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2); previously, it was referred to as 2019-nCoV.
-Currently the virus has been labeled as a Pandemic with cases now arising in all continents except Antarctica.
Pneumonia of unknown etiology an illness : ✓Fever (≥38°C)
✓Radiographic evidence of pneumonia
✓ Low or normal white-cell count or low lymphocyte count
✓ No symptomatic improvement after antimicrobial treatment for 3 to 5 days following standard clinical guidelines.
– The New England Journal of Medicine
Mode of Spread:
Respiratory Droplet Infection
Direct contact with infected person, surfaces, clothes and environment WHO
Pathophysiology:
Coronaviruses are a family of enveloped, single-stranded, positive-strand RNA viruses classified within the Nidovirales order. This coronavirus family consists of pathogens of many animal species and of humans, including the recently isolated severe acute respiratory syndrome coronavirus (SARS-CoV).
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1306801/
Coronaviruses are a large family of viruses that are common in people and many different species of animals, including camels, cattle, cats, and bats. Rarely, animal coronaviruses can infect people and then spread between people such as with MERS-CoV, SARS-CoV, and now with this new virus (named SARS-CoV-2).
The SARS-CoV-2 virus is a betacoronavirus, like MERS-CoV and SARS-CoV. All three of these viruses have their origins in bats. The sequences from U.S. patients are similar to the one that China initially posted, suggesting a likely single, recent emergence of this virus from an animal reservoir.
Early on, many of the patients at the epicenter of the outbreak in Wuhan, Hubei Province, China had some link to a large seafood and live animal market, suggesting animal-to-person spread. Later, a growing number of patients reportedly did not have exposure to animal markets, indicating person-to-person spread. Person-to-person spread was subsequently reported outside Hubei and in countries outside China, including in the United States. Some international destinations now have ongoing community spread with the virus that causes COVID-19, as do some parts of the United States. Community spread means some people have been infected and it is not known how or where they became exposed. Learn what is known about the spread of this newly emerged coronaviruses. cdc.gov
Temperature influence:
Assessment of the risks posed by severe acute respiratory syndrome (SARS) coronavirus (SARS-CoV) on surfaces requires data on survival of this virus on environmental surfaces and on how survival is affected by environmental variables, such as air temperature (AT) and relative humidity (RH).
Virus survival in stool and urine
Virus is stable in faeces(and urine) at room temperature for at least 1-2 days.
Virus is more stable (up to 4 days) in stool from diarrhea patients (which has higher pH than normal stool). –WHO
Virus survival in cell-culture supernatant
Only minimal reduction in virus concentration after 21 days at 4°C and -80°C.
Reduction in virus concentration by one log only at stable room temperature for 2 days. This would indicate that the virus is more stable than the known human coronaviruses under these conditions.
Heat at 56°C kills the SARS coronavirus at around 10000 units per 15 min (quick reduction). –WHO
Transmission
Epidemiologic research in Wuhan, China, at the beginning of the outbreak showed an association with a wet seafood market that sold live animals. As the outbreak progressed, person-to-person spread became the principal mode of transmission, which occurs mainly via respiratory droplets. With droplet transmission, virus released in the respiratory secretions when a person with infection coughs, sneezes, or talks can infect another person if it makes direct contact with the mucous membranes; infection can also occur if a person touches an infected surface and then touches his or her eyes, nose, or mouth. Droplets typically do not travel more than six feet (about two meters) and do not linger in the air. However, given the current uncertainty regarding transmission mechanisms, airborne precautions are recommended routinely in some countries and in the setting of certain high-risk procedures in others.
SARS-CoV-2 RNA has also been detected in blood and stool specimens, but according to a joint WHO-China report, fecal-oral transmission did not appear to be a significant factor in the spread of infection.
Transmission of SARS-CoV-2 from asymptomatic individuals (or individuals within the incubation period) has also been reported, the extent to which this occurs is still unknown.
Incubation period
The incubation period for COVID-19 is thought to be within 14 days following exposure, with most cases occurring approximately four to five days after exposure.
Spectrum of illness severity
In a report from the Chinese Center for Disease Control and Prevention that included approximately 44,500 confirmed infections with an estimation of disease severity:
●Mild (no or mild pneumonia) was reported in 81 percent.
●Severe disease (eg, with dyspnea, hypoxia, or >50 percent lung involvement on imaging within 24 to 48 hours) was reported in 14 percent.
●Critical disease (eg, with respiratory failure, shock, or multiorgan dysfunction) was reported in 5 percent.
●The overall case fatality rate was 2.3 percent; no deaths were reported among noncritical cases.
Most fatal cases have occurred in patients with advanced age or underlying medical co-morbidities (including cardiovascular disease, diabetes mellitus, chronic lung disease, hypertension, and cancer).
Impact of age
Individuals of any age can acquire severe infection, although adults of middle age and older are most commonly affected.
In some cohorts of hospitalized patients diagnosed with COVID-19, the median age ranged from 49 to 56 years.
Symptomatic infection in children appears to be uncommon; when it occurs, it is usually mild, although severe cases have been reported.
Asymptomatic infections
Asymptomatic infections have also been described, but their frequency is unknown.
In a COVID-19 outbreak on a cruise ship where nearly all passengers and staff were screened for SARS-CoV-2, approximately 17 percent of the population on board tested positive as of February 20; about half of the 619 confirmed COVID-19 cases were asymptomatic at the time of diagnosis.
Even patients with asymptomatic infection may have objective clinical abnormalities. In another study of 24 patients with asymptomatic infection who all underwent chest computed tomography (CT), 50 percent had typical ground-glass opacities or patchy shadowing, and another 20 percent had atypical imaging abnormalities. Five patients developed low-grade fever, with or without other typical symptoms, a few days after diagnosis.
Clinical manifestations
Initial presentation — Pneumonia appears to be the most frequent serious manifestation of infection, characterized by fever, cough, dyspnea, and bilateral infiltrates on chest imaging. There are no specific clinical features that can reliably distinguish COVID-19 from other viral respiratory infections.
In a study describing 138 patients with COVID-19 pneumonia in Wuhan, the most common clinical features at the onset of illness were:
●Fever in 99%
●Fatigue in 70%
●Dry cough in 59%
●Anorexia in 40%
●Myalgias in 35%
●Dyspnea in 31%
●Sputum production in 27%
However, fever might not be a universal finding. In one study, fever was reported in almost all patients, but approximately 20 percent had a very low grade fever <100.4°F/38°C. In another study of 1099 patients from Wuhan and other areas in China, fever (defined as an axillary temperature over 99.5°F/37.5°C) was present in only 44 percent on admission but was ultimately noted in 89 percent during the hospitalization.
Other, less common symptoms have included headache, sore throat, and rhinorrhea. In addition to respiratory symptoms, gastrointestinal symptoms (eg, nausea and diarrhea) have also been reported in some patients, but these are relatively uncommon.
Course and complications — As above, symptomatic infection can range from mild to critical.
Some patients with initially mild symptoms may progress over the course of a week. In one study of 138 patients hospitalized in Wuhan for pneumonia due to SARS-CoV-2, dyspnea developed after a median of five days since the onset of symptoms, and hospital admission occurred after a median of seven days of symptoms. In another study, the median time to dyspnea was eight days.
Acute respiratory distress syndrome (ARDS) is a major complication in patients with severe disease. In the study of 138 patients described above, ARDS developed in 20 percent after a median of eight days, and mechanical ventilation was implemented in 12.3 percent. In another study of 201 hospitalized patients with COVID-19 in Wuhan, 41 percent developed ARDS; age greater than 65 years, diabetes mellitus, and hypertension were each associated with ARDS.
Other complications have included arrhythmias, acute cardiac injury, and shock. In one study, these were reported in 17, 7, and 9 percent, respectively.
Courtesy of Uptodate.
DIAGNOSTICS FOR COVID – 19
For initial diagnostic testing for COVID-19 CDC recommends :
- Collecting and testing an upper respiratory nasopharyngeal swab (NP).
- Collection of oropharyngeal swabs (OP) is a lower priority and if collected should be combined in the same tube as the NP.
- Collection of sputum should only be done for those patients with productive coughs. Induction of sputum is not recommended.
- Specimens should be collected as soon as possible once a PUI is identified, regardless of the time of symptom onset.
- CDC also recommends testing lower respiratory tract specimens, if available.
- For patients who develop a productive cough, sputum should be collected and tested for SARS-CoV-2. A lower respiratory tract aspirate or bronchoalveolar lavage sample should be collected and tested as a lower respiratory tract specimen.
Respiratory Specimens
- Lower respiratory tract
Bronchoalveolar lavage or tracheal aspirate: Collect 2-3 mL into a sterile, leak-proof, screw-cap sputum collection cup or sterile dry container.
Sputum : Have the patient rinse the mouth with water and then expectorate deep cough sputum directly into a sterile, leak-proof, screw-cap sputum collection cup or sterile dry container.
B. Upper respiratory tract
Nasopharyngeal swab (NP) /oropharyngeal swab (OP): In general CDC is now recommending collecting only the NP swab. If both swabs are used, NP and OP specimens should be combined at collection into a single vial.
Nasopharyngeal swab: Insert a swab into nostril parallel to the palate. Swab should reach depth equal to distance from nostrils to outer opening of the ear. Leave swab in place for several seconds to absorb secretions. Slowly remove swab while rotating it.
Oropharyngeal swab: Swab the posterior pharynx, avoiding the tongue.
Nasopharyngeal wash/aspirate or nasal aspirate: Collect 2-3 mL into a sterile, leak-proof, screw-cap sputum collection cup or sterile dry container.
SEROLOGICAL TEST
CDC is working to develop a new laboratory test to assist with efforts to determine how much of the U.S. population has been exposed to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes COVID-19.
The serology test will look for the presence of antibodies, which are specific proteins made in response to infections. Antibodies can be found in the blood and in other tissues of those who are tested after infection. Initial work to develop a serology test for SARS-CoV-2 is underway at CDC.
