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(copy)Stanford Medicine COVID-19 test now in use
03.05.2020
The Stanford Clinical Virology Laboratory has deployed an in-house diagnostic test for the virus that causes COVID-19. Rapid identification of infected people could help limit the spread of the virus.
By Krista Conger
The Stanford Health Care Clinical Virology Laboratory has launched a diagnostic test developed for the virus that causes COVID-19.
The test is being used for patients at Stanford Hospital and Lucile Packard Children’s Hospital Stanford suspected of being infected with the respiratory virus SARS-CoV-2, which is spreading globally after being first identified in Wuhan, a city in China, late last year. It is expected to deliver results within 12-24 hours.
As with all currently available tests, it’s not yet clear how long a person needs to be infected before testing positive, or whether they could be identified by the test before displaying symptoms.
Information about the Coronavirus Disease 2019 (COVID-19)
Stanford Health Care is providing the following information in conjunction with the national Centers for Disease Control and Prevention (CDC) to help keep our patients and families informed about the Coronavirus Disease 2019 (COVID-19).
Public health experts have indicated that prompt identification and quarantine of infected people is critical to limiting the spread of the virus, which can be deadly to the elderly or those with other health problems. The global mortality rate of the virus, according to the World Health Organization, is estimated to be around 3.4%. Because many mild cases may remain undiagnosed, the actual mortality rate may be much lower, however.
As of this morning, more than 160 people in the United States have been diagnosed; experts expect the actual number of cases nationwide is much larger. Washington and Northern California are currently most heavily affected, but cases have been diagnosed in several states.
Clinical virologist Benjamin Pinsky, MD, PhD, associate professor of pathology and of infectious diseases at the Stanford School of Medicine, and his team in the clinical virology lab began working on the test in late January. They spent February validating and confirming that the test meets the requirements to be a useful clinical tool.
“The test successfully identified the presence of SARS-CoV-2 in positive samples without cross-reacting with the seasonal coronaviruses or other common respiratory viruses, including influenza,” Pinsky said.
Crown-like spikes
Coronaviruses are a family of viruses named for the crown-like spikes found on their surface. They carry their genetic material in single strands of RNA, rather than DNA. They infect a variety of human and animal hosts, causing mostly upper-respiratory symptoms like those of the common cold.
Until recently, two coronaviruses have been known to have caused severe disease in humans: Middle East Respiratory Syndrome, or MERS, identified in 2012, and Severe Acute Respiratory Syndrome, or SARS, which was identified in humans in 2002. The SARS-CoV-2 that causes the currently circulating COVID-19 disease is the third example.
On Feb. 29, the Food and Drug Administration announced that it was relaxing the restrictions for the use of diagnostic tests for SARS-CoV-2 developed by laboratories in the United States that meet the certification guidelines for high-complexity testing. The new policy allows these laboratories to begin using in-house developed clinical tests for the virus before obtaining the agency’s approval through an emergency use authorization. The FDA noted that “Rapid detection of COVID-19 cases in the United States requires wide availability of diagnostic testing to control the emergence of this rapidly spreading, severe illness.” Laboratories developing their own tests are expected to apply for emergency use authorization from the FDA within 15 days.
Until the announcement, samples from throat and nasal swabs of possibly infected people were sent to public health agencies for testing with an assay developed and distributed by the Centers for Disease Control and Prevention through an emergency use authorization from the FDA.
How test works
The Stanford test uses a technique called reverse-transcriptase polymerase chain reaction, or RT-PCR, to rapidly identify the presence of viral RNA in swabs from the noses of potentially infected people. RT-PCR uses short stretches of DNA called primers that bind tightly and specifically only to matching sequences in SARS-CoV-2 RNA. An enzyme called reverse transcriptase then converts the viral RNA into complementary DNA, and as the reaction continues, an enzyme called polymerase is used to generate billions of DNA copies that can be detected by fluorescently tagged molecules called probes.
Pinsky and his colleagues used primers and probes developed at a laboratory in Germany that has studied the SARS and MERS coronaviruses for many years. They then optimized the use of these diagnostic tools to meet the United States’ testing guidelines.
The Stanford test screens first for the presence of viral RNA encoding a protein called an envelope protein, which is found in the membrane that surrounds the virus and plays an important role in the viral life cycle, including budding from an infected host cells. It then confirms the positive result by testing for a gene encoding a second protein called RNA-dependent RNA polymerase.
The test used by the CDC screens for yet a third gene encoding a protein that forms the viral nucleocapsid that forms a kind of shell around the viral genetic material. The availability of a variety of tests targeting different viral-specific RNA sequences will provide an important way to cross-confirm laboratory results.
Coronavirus Disease 2019 Basics
A novel coronavirus is a new coronavirus that has not been previously identified. The virus causing coronavirus disease 2019 (COVID-19), is not the same as the coronaviruses that commonly circulate among humans and cause mild illness, like the common cold.
A diagnosis with coronavirus 229E, NL63, OC43, or HKU1 is not the same as a COVID-19 diagnosis. Patients with COVID-19 will be evaluated and cared for differently than patients with common coronavirus diagnosis.
On February 11, 2020 the World Health Organization announced an official name for the disease that is causing the 2019 novel coronavirus outbreak, first identified in Wuhan China. The new name of this disease is coronavirus disease 2019, abbreviated as COVID-19. In COVID-19, ‘CO’ stands for ‘corona,’ ‘VI’ for ‘virus,’ and ‘D’ for disease. Formerly, this disease was referred to as “2019 novel coronavirus” or “2019-nCoV.”
There are many types of human coronaviruses including some that commonly cause mild upper-respiratory tract illnesses. COVID-19 is a new disease, caused be a novel (or new) coronavirus that has not previously been seen in humans. The name of this disease was selected following the World Health Organization (WHO) best practice external icon for naming of new human infectious diseases.
On February 11, 2020, the International Committee on Taxonomy of Viruses, charged with naming new viruses, named the novel coronavirus, first identified in Wuhan, China, severe acute respiratory syndrome coronavirus 2, shortened to SARS-CoV-2.
As the name indicates, the virus is related to the SARS-associated coronavirus (SARS-CoV) that caused an outbreak of severe acute respiratory syndrome (SARS) in 2002-2003, however it is not the same virus.
No. Coronaviruses are a large family of viruses. Some coronaviruses cause cold-like illnesses in people. Others cause illness in certain types of animals, such as cattle, camels and bats. Rarely, animal coronaviruses can spread to people. This happened with SARS-CoV and MERS-CoV. The virus that causes COVID-19 likely also originated in an animal and spread to humans. The coronavirus most similar to the virus causing COVID-19 is SARS-CoV. There are ongoing investigations to learn more. The situation is changing, and information will be updated as it becomes available.
How It Spreads
Coronaviruses are a large family of viruses. Some cause illness in people, and others, such as canine and feline coronaviruses, only infect animals. Rarely, animal coronaviruses that infect animals have emerged to infect people and can spread between people. This is suspected to have occurred for the virus that causes COVID-19. Middle East Respiratory Syndrome (MERS) and Severe Acute Respiratory Syndrome (SARS) are two other examples of coronaviruses that originated from animals and then spread to people. More information about the source and spread of COVID-19 is available on the Situation Summary: Source and Spread of the Virus.
This virus was first detected in Wuhan City, Hubei Province, China. The first infections were linked to a live animal market, but the virus is now spreading from person-to-person. It’s important to note that person-to-person spread can happen on a continuum. Some viruses are highly contagious (like measles), while other viruses are less so.
The virus that causes COVID-19 seems to be spreading easily and sustainably in the community (“community spread”) in some affected geographic areas. Community spread means people have been infected with the virus in an area, including some who are not sure how or where they became infected.
Learn what is known about the spread of newly emerged coronaviruses.
The virus that causes COVID-19 is spreading from person-to-person. Someone who is actively sick with COVID-19 can spread the illness to others. That is why CDC recommends that these patients be isolated either in the hospital or at home (depending on how sick they are) until they are better and no longer pose a risk of infecting others.
How long someone is actively sick can vary so the decision on when to release someone from isolation is made on a case-by-case basis in consultation with doctors, infection prevention and control experts, and public health officials and involves considering specifics of each situation including disease severity, illness signs and symptoms, and results of laboratory testing for that patient.
Current CDC guidance for when it is OK to release someone from isolation is made on a case-by-case basis and includes meeting all of the following requirements:
- The patient is free from fever without the use of fever-reducing medications.
- The patient is no longer showing symptoms, including cough.
- The patient has tested negative on at least two consecutive respiratory specimens collected at least 24 hours apart.
Someone who has been released from isolation is not considered to pose a risk of infection to others.
Quarantine means separating a person or group of people who have been exposed to a contagious disease but have not developed illness (symptoms) from others who have not been exposed, in order to prevent the possible spread of that disease. Quarantine is usually established for the incubation period of the communicable disease, which is the span of time during which people have developed illness after exposure. For COVID-19, the period of quarantine is 14 days from the last date of exposure, because 14 days is the longest incubation period seen for similar coronaviruses. Someone who has been released from COVID-19 quarantine is not considered a risk for spreading the virus to others because they have not developed illness during the incubation period.
It is not yet known whether weather and temperature impact the spread of COVID-19. Some other viruses, like the common cold and flu, spread more during cold weather months but that does not mean it is impossible to become sick with these viruses during other months. At this time, it is not known whether the spread of COVID-19 will decrease when weather becomes warmer. There is much more to learn about the transmissibility, severity, and other features associated with COVID-19 and investigations are ongoing.
Community spread means people have been infected with the virus in an area, including some who are not sure how or where they became infected.
How to Protect Yourself
This is a rapidly evolving situation and the risk assessment may change daily. The latest updates are available on CDC’s Coronavirus Disease 2019 (COVID-19) website.
Yes. There have been cases of COVID-19 in the U.S. related to travel and person-to-person spread. U.S. case counts are updated regularly on Mondays, Wednesday, and Fridays. See the current U.S. case count of COVID-19.
There is currently no vaccine to prevent coronavirus disease 2019 (COVID-19). The best way to prevent illness is to avoid being exposed to this virus. However, as a reminder, CDC always recommends everyday preventive actions to help prevent the spread of respiratory diseases, including:
- Avoid close contact with people who are sick.
- Avoid touching your eyes, nose, and mouth.
- Stay home when you are sick.
- Cover your cough or sneeze with a tissue, then throw the tissue in the trash.
- Clean and disinfect frequently touched objects and surfaces using a regular household cleaning spray or wipe.
- Follow CDC’s recommendations for using a facemask.
- CDC does not recommend that people who are well wear a facemask to protect themselves from respiratory diseases, including COVID-19.
- Facemasks should be used by people who show symptoms of COVID-19 to help prevent the spread of the disease to others. The use of facemasks is also crucial for health workers and people who are taking care of someone in close settings (at home or in a health care facility).
- Wash your hands often with soap and water for at least 20 seconds, especially after going to the bathroom; before eating; and after blowing your nose, coughing, or sneezing.
- If soap and water are not readily available, use an alcohol-based hand sanitizer with at least 60% alcohol. Always wash hands with soap and water if hands are visibly dirty.
For information about handwashing, see CDC’s Handwashing website
For information specific to healthcare, see CDC’s Hand Hygiene in Healthcare Settings
These are everyday habits that can help prevent the spread of several viruses. CDC does have specific guidance for travelers.
There is information for people who have had close contact with a person confirmed to have, or being evaluated for, COVID-19 available online.
CDC does not recommend that people who are well wear a facemask to protect themselves from respiratory illnesses, including COVID-19. You should only wear a mask if a healthcare professional recommends it. A facemask should be used by people who have COVID-19 and are showing symptoms. This is to protect others from the risk of getting infected. The use of facemasks also is crucial for health workers and other people who are taking care of someone infected with COVID-19 in close settings (at home or in a health care facility).
There is still a lot that is unknown about the newly emerged COVID-19 and how it spreads. In general, because of poor survivability of these coronaviruses on surfaces, there is likely very low risk of spread from products or packaging that are shipped over a period of days or weeks at ambient temperatures. Coronaviruses are generally thought to be spread most often by respiratory droplets. Currently there is no evidence to support transmission of COVID-19 associated with imported goods and there have not been any cases of COVID-19 in the United States associated with imported goods. Information will be provided on the Coronavirus Disease 2019 (COVID-19) website as it becomes available.
Symptoms & Testing
Current symptoms reported for patients with COVID-19 have included mild to severe respiratory illness with fever, cough, and difficulty breathing. Read about COVID-19 Symptoms.
Call your healthcare professional if you feel sick with fever, cough, or difficulty breathing, and have been in close contact with a person known to have COVID-19, or if you live in or have recently traveled from an area with ongoing spread of COVID-19.
Your healthcare professional will work with your state’s public health department and CDC to determine if you need to be tested for COVID-19.
State and local health departments who have identified a person under investigation (PUI) should immediately notify CDC’s Emergency Operations Center (EOC) to report the PUI and determine whether testing for COVID-19 at CDC is indicated. The EOC will assist local/state health departments to collect, store, and ship specimens appropriately to CDC, including during afterhours or on weekends/holidays.
For more information on specimen collection see CDC Information for Laboratories.
Using the CDC-developed diagnostic test, a negative result means that the virus that causes COVID-19 was not found in the person’s sample. In the early stages of infection, it is possible the virus will not be detected.
For COVID-19, a negative test result for a sample collected while a person has symptoms likely means that the COVID-19 virus is not causing their current illness.
COVID-19 and Stanford Health Care
As soon as the CDC sent an alert about the outbreak, Stanford Health Care’s Emerging Infectious Diseases subcommittee was activated. The subcommittee, along with the Stanford Health Care Infection Prevention & Control Department, relies on information from the CDC, World Health Organization, State and local County Public Health Departments to maintain the most current information and recommendations. They also provide guidelines for screening of patients and procedures for healthcare workers to follow should a patient require isolation, and to ensure patient and healthcare worker safety.
With standard protocols in place at all times and working closely with our local and national government health agencies to update protocols as necessary, Stanford Health Care is well-prepared to care for patients with symptoms of COVID-19.
Stanford Health Care has well-established measures in place to prevent transmission of all communicable diseases, including flu and other respiratory illnesses. There are respiratory etiquette stations for persons visiting with cough, and hand sanitizer is available. Our staff is trained to screen patients for cough, fever, and recent travel when they arrive.
If you are ill, please call ahead to your healthcare provider’s office prior to arriving.
Our hospitals and clinical locations have taken additional measures to ensure safety for all patients, visitors and staff during the COVID-19 outbreak. If you have specific questions or concerns, please do not hesitate to ask your health care provider prior to your visit.
The CDC website has additional FAQs on the topics of Travel, Pregnant Women and COVID-19, and COVID-19 and animals.
This page was adapted from CDC.gov, last accessed March 2, 2020: https://www.cdc.gov/coronavirus/2019-ncov/faq.html#