Coronavirus (COVID-19) – Laboratory testing, Diagnosis, Guidelines

Novel coronavirus, also called COVID-19, is the newest discovered coronavirus that originated in Wuhan, China. It belongs in the same family of MERS-CoV and SARS-CoV. It is called coronavirus because, on electron microscopy, the shape of the virus looks like a crown.

A series of genetic amplification assays associated with the Center for Disease Control in China was developed to help check dozens of cases of the novel coronavirus.

The World Health Organization shared the virus’ full genome sequence data and information about the development of specific diagnostic procedures for the COVID-19. The primary goal of diagnostic testing is to:

  • Detect the earliest time possible the conventional causes of pneumonia
  • Work with reference laboratories that can conduct detection of coronavirus and directed sequencing
  • Support activities center around disease control.(1, 2, 3, and 4)

microscopic-examination-image-of-novel-coronavirus

Image 1: A microscopic examination/image of novel coronavirus.

Picture Source: elsevier.com

 

Collecting and handling of specimen for testing guidelines by the World Health Organization

Patients under investigation for novel coronavirus are taken sample specimens for appropriate testing. Various tests have to be performed and sufficient sampling of clinical material is recommended. The sample should be handled with care – the same way of handling samples of suspected human influenza. To culture the virus, a heightened biosafety control measure has to be observed.

Sample for testing can be collected through the following ways:

  • Respiratory material – It is collected through the nose and/or mouth swab or sputum if the coughing is productive. In a patient in severe respiratory distress, an endotracheal aspirate or bronchoalveolar lavage is used.
  • Serum – It is done for serological testing and acute and convalescent sample.(3, 4, 5 & 6)

Novel-coronavirus-specimen-should-be-collected-using-strict-collection-measures

Image 2: Novel coronavirus specimen should be collected using strict collection measures as per the guidelines othe f World Health Organization.

Picture Source: encrypted-tbn0.gstatic.com

 

Collecting-a-specimen-on-suspected-novel-coronavirus-patient-should-only-be-done-by-a-healthcare-worker-with-skills-and-experience-handling-dreaded-viruses-case

Image 3: Collecting a specimen on suspected novel coronavirus patient should only be done by a healthcare worker with skills and experience handling dreaded viruses/cases.

Picture Source: 1.bp.blogspot.com

 

What to keep in mind when collecting samples for testing of novel coronavirus?

  • Nasal and oral swab – The sample should be collected using a sacron or polyester flocked swab. It should be immediately sent to the laboratory making sure that the temperature during transport is 4 degrees Celsius. It should be immediately tested on or before it reaches five days post collection. It is a must to place the swab in the same tube to increase the viral load.
  • Bronchoalveolar lavage – The specimen should be placed in a sterile container and the temperature during transport should be 4 degrees Celsius and has to be checked within two days. If it passed two days, the temperature should be less than 70 degrees Celsius.
  • Endotracheal and/or nasopharynheal aspirate/nasal wash – The sample must be placed in a sterile container and transported to the laboratory in a 4-degrees Celsius. It can be stored up to two days at the same temperature. When more than two days, the desired temperature should be less than 70 degrees Celsius.
  • Sputum – The specimen is placed in a sterile container and transported to the laboratory at a temperature of 4 degrees Celsius.
  • Tissue from biopsy/autopsy of the lung – The specimen is placed in a sterile container with water and transported to the laboratory for testing at a temperature of 4 degrees Celsius.
  • Serum – the serum is collected and placed in a serum separator tube and transported to the laboratory at 4-degrees Celsius.
  • Whole blood – The specimen is placed in a collection tube and transported to the laboratory for testing at a 4 degrees Celsius.
  • Urine – the urine is placed in a sterile urine collection container and transported to the laboratory at a 4 degrees Celsius. (5, 6, 7, and 8)

 

Sample collection and transport

  1. All specimen for laboratory testing should be treated as infectious and healthcare personnel should strictly adhere with the infection prevention and control guidelines to minimize the possibility of exposure to pathogens.
  2. There should be a good communication with the laboratory personnel to ensure proper and speedy processing of samples. Make sure you fill up the diagnostic request form with all important details such as the type of specimen, when the specimen was collected, the patient’s name, gender, and birthdate, to name a few. (1, 6, and 9)

Protective clothing gear must be worn at all times when handling patients suspected with the novel coronavirus

Image 4: Protective clothing/gear must be worn at all times when handling patients suspected with the novel coronavirus.

Picture Source: assets.rappler.com

 

Infection prevention and control for suspected novel coronavirus infection 

  • Health workers should strictly perform aerosol-generating procedures and use strict precautions.
  • Protection gear should be worn at all times, especially respirators for a high level of protection. When wearing a respirator, make it a habit to check the seal/fitness. In a more advanced country, a powered air-purifying respirator is used instead of the regular respirator as it gives a higher level of protection.
  • Aside from respirators, eye protectors should be worn such as a face shied or goggles. Wear a clean, long-sleeved waterproof gown and gloves.
  • The procedure should be performed in a well-ventilated room and limit the number of person inside the room.
  • Observe hygienic measures before and after contact with the patient.
  • Observe waste management and decontamination procedures. All materials used should be disposed of appropriately. Disinfect the work area using a chlorine-based solution. (4, 7, 9, and 10)

 

Global laboratory networking

Some countries don’t have the tools and equipment needed to conduct novel coronavirus testing. They need to network with other laboratories around the globe. As such, it is important to pack and ship the specimen properly. The following has to be carefully observed:

  • Make sure you comply with national regulations and international transport regulations.
  • Specimens for novel coronavirus should strictly follow the UN Model regulations.
  • It is important to have a timely and accurate laboratory testing of specimens.

Detecting novel coronavirus infection through nucleic acid amplification test

NAAT Assays

A sequence information from novel coronavirus has been made available and a PCR assay can be done to detect such sequences. However, the process can be a complicated one. The practical way is to contact experienced laboratories that publicize their assays and request access to assay chemistries.

The desirable option is to use a pan-coronavirus assay for amplification and proceed with amplicons sequencing from non-conserved regions for identification and confirmation. The virus is confirmed according to a particular detection of distinct sequences of viral nucleic acid using a reverse-transcriptase polymerase chain reaction

Serological testing

It is done to confirm immunologic response to a pathogen from a particular viral group. A paired serum sample should be collected from a suspected person.

Sequencing in outbreaks

Studying the sequence data provides information about the origin and spread of the virus. Different laboratories are highly encouraged to share their sequence data with the World Health Organization and the scientific community to help in the development and distribution of diagnostic assays in countries where the infection is rampant.

Centers for Disease Control and Prevention (CDC) 2019

Novel Coronavirus (COVID-19) Real-Time Reverse Transcriptase (RT)-PCR Diagnostic Panel – It is a new test kit developed by Center for Disease Control which is useful in testing the specimen of patients suspected for novel coronavirus.

It is used in conjunction with the applied biosystems 7500 Fast DX Real-Time PCR instrument with SDS 1.4 software. The specimen that can be used using this tool is both upper and lower respiratory specimens.

The test kit should be used by CDC qualified laboratories, in the United States, and laboratories certified by the Clinical Laboratory Improvement Amendments to perform high-risk tests. It will be shipped to qualified international laboratories. (3, 7, 9, and 10)

 

CDC Laboratory Test Kit for COVID-19

The Center for Disease Control has developed a test kit that can check the patient’s specimen for SARS coronavirus 2, which is the same virus that causes coronavirus disease 2019.

The test kit is known as center for disease control and prevention 2019-novel coronavirus real-rime reverse transcriptase-PCR diagnostic panel. It should be used with applied biosystems 7500 fast DX real-time PCR instrument with SDS 1.4 software.

The test kit is used to check for specimens of the upper and lower respiratory tract of a person that meets the criteria of CDC for coronavirus disease 2019.

The test kit should only be used by CDC approved laboratories. In the United States, such laboratories should be certified under the Clinical Laboratory Improvement Amendments in performing high complexity tests.

However, it is important to note that the test kit will not be made available in the United States hospitals and related primary care settings. On the flip side, the test kit will be shipped to qualified international laboratories. It will be distributed through the International Reagent Resource.

Novel coronavirus Indian laboratory guidelines by ICMR and NIV

When collecting a sample specimen in a patient suspected with novel coronavirus, strict measures should be applied at all times. The testing should only be done when there is a need to do so – following a case definition by the health authorities, Government of India.

Only experienced laboratory personnel should collect the sample with strict adherence to the biosafety precautions. The lab personnel should wear personal protective equipment while taking samples and once done, the sample should be immediately sent to the designated laboratory for thorough examination. (1, 4, 6, and 8)

 

Who should be submitted for novel coronavirus testing?

  • People exhibiting the symptoms of severe acute respiratory illness like cough, cold, fever, and difficulty of breathing.
  • Anyone who has a history of travel to Wuhan, China 14 days prior to the onset of symptoms.

 

Specimen collection details

  • Nasopharyngeal and oropharyngeal swab – the recommended material to be used is Dacron or polyester flocked swabs. During transport of specimen, the ideal temperature is 4 degrees Celsius. If you have to store the specimen, make sure that the temperature is 70 degree sCelsius, especially if it is more than five days’ post specimen collection. Make sure you place the specimen in the same tube to increase viral load.
  • Bronchoalveolar lavage – the specimen is placed in a sterile container at a temperature of 4 degrees Celsius. If it is way pass 48 hours post specimen collection, you have to store the specimen in less than 70-degree Celsius temperature.
  • Tracheal aspirate/nasopharyngeal aspirate/nasal wash – The specimen is placed in a sterile container at a temperature of 4 degrees Celsius. If it is way pass 48 hours post specimen collection, you have to store the specimen in less than 70-degree Celsius temperature.
  • Sputum – The specimen is placed in a sterile container at a temperature of 4 degrees Celsius. If it is way pass 48 hours post specimen collection, you have to store the specimen in less than 70-degree Celsius temperature.
  • Tissue from biopsy/autopsy of the lungs – The specimen is placed in a sterile container with saline at a temperature of 4 degrees Celsius. If it is way pass 24 hours post specimen collection, you have to store the specimen in less than 70-degree Celsius temperature.
  • Serum (acute and convalescent) – A serum separator tube is used to collect the specimen and transported to the lab immediately. If it needs to be transported and passed five days post specimen collection, the temperature of the specimen should be not more than 70 degrees Celsius. (2, 4, 7, and 10)

Labelling and processing of specimen

  1. Personal protective equipment/PPE has to be worn at all times when handling a patient suspected of novel coronavirus and when collecting and transporting specimens. Personal protective equipment includes face shield/mask/n95 mask, apron, hand gloves, and the likes.
  2. The specimen should be labeled properly. It should contain the patient’s name, age, gender, and specimen details. (3, 6, and 10)

Latest updates on 2019 novel coronavirus

Novel coronavirus, COVID-19, is a global emergency. In China alone, thousands of cases have been reported. The viral infection has not only affected China where the new virus was detected, but also scattered in the neighboring countries in Asia and as far as Europe, Middle East, and Oceania, to name a few.

Other countries with reported cases include Australia, Belgium, Cambodia, France, Hong Kong, Macau, Finland, Germany, Italy, India, Korea, Japan, Macao, Nepal, Malaysia, Philippines, Singapore, Russia, Sri Lanka, Spain, Taiwan, Sweden, Thailand, United Kingdom, United Arab Emirates, United States of America, and Vietnam.

To date, there are over 1,000 deaths caused by novel coronavirus in China. It has surpassed the final death toll of MERS-cOv in 2012.

Next to China, the second highest cases of novel coronavirus is Japan followed by Singapore, Hong Kong, Thailand, South Korea, Taiwan, Malaysia, Australia, Vietnam, Germany, the United States, France, Macao, the United Kingdom, Canada, United Arab Emirates, Philippines, India, Italy, Russia, Spain, Sri Lanka, Cambodia, Finland, Nepal, Sweden, and Belgium.

The first known death linked to novel coronavirus outside China was a 44-year-old man in the Philippines. The second outside mainland China and the first death in Hong Kong was a 39-year-old man – both have history of travel to Wuhan, China, where novel coronavirus originated.

The World Health Organization (WHO) is actively observing all measures to trace, limit, and prevent the spread of novel coronavirus. It closely monitors the event and actively communicates with counterparts in China.

An incident management system has been activated across all levels of World Health Organization – country office, regional, and headquarters. Although the death toll has become increasingly alarming, the number of people who recovered from the said viral infection has increased significantly. (3, 6, 8, and 9)

Countries all across the globe are employing strict measures to contain the virus and prevent its spread through strict quarantine

Image 5: Countries all across the globe are employing strict measures to contain the virus and prevent its spread through strict quarantine.

Picture Source: washingtonpost.com

Live Update on Corona virus death toll number  – Link

Preventing the spread of infection

The Chinese government put Wuhan and other nearby cities on lockdown mode. People are not allowed to go in and out of the area. Major airports across the globe are conducting screenings to check for symptoms of novel virus infection. Countries all across the globe recommend its citizen to avoid non-essential travel to China.

Even the Chinese government is employing all measures to prevent the spread of infection as the number of cases rise by thousands and the death toll has already reach over 1,000. It has banned the sale of wildlife in markets and restaurants.

Official name of novel coronavirus – COVID-19

The World Health Organization has come up with the official name of the disease – COVID-19 or coronavirus disease 2019. WHO makes sure that no reference is made to the city where the viral infection was first detected to prevent stigmatizing.

It also gives a standard format to use for any coronavirus outbreaks that may occur in the future. The World Health Organization referenced the 2015 guidelines ensuring that no animal, individual, group, or geographical location will be associated with a disease.  (11 and 12)

 

References

  1. https://www.cdc.gov/coronavirus/mers/guidelines-clinical-specimens.html
  2. https://www.cdc.gov/coronavirus/2019-ncov/lab/guidelines-clinical-specimens.html
  3. https://asm.org/Articles/2020/February/Next-Steps-for-Novel-Coronavirus-Medical-Laborator
  4. https://www.nejm.org/coronavirus
  5. https://www.who.int/docs/default-source/coronaviruse/situation-reports/20200206-sitrep-17-ncov.pdf
  6. https://www.health.gov.au/news/coronavirus-update-at-a-glance
  7. https://www.channelnewsasia.com/news/singapore/coronavirus-singapore-fully-recovered-patients-list-12416232
  8. https://www.cbsnews.com/live-updates/coronavirus-death-toll-infections-outbreak-evacuations-quarantine-latest-updates-2020-02-10/
  9. https://www.nbcnews.com/news/world/new-coronavirus-updates-number-confirmed-cases-drops-disease-s-epicenter-n1133141
  10. https://www.moh.gov.sg/2019-ncov-wuhan
  11. https://time.com/5782284/who-name-coronavirus-covid-19/
  12. https://www.vox.com/2020/2/14/21135208/coronavirus-wuhan-china-covid-19-name-sars-cov-2

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