1. Introduction
Several coronaviruses can infect humans, the globally endemic human coronaviruses HCoV-229E, HCoV-NL63, HCoV-HKU1 and HCoV-OC43 that tend to cause mild respiratory disease, and the zoonotic Middle East respiratory syndrome coronavirus (MERS-CoV) and severe acute
respiratory syndrome coronavirus (SARS-CoV) that have a higher case fatality rate. In December 2019, a cluster of patients with a novel coronavirus was identified in Wuhan, China (1). Initially tentatively named 2019 novel coronavirus (2019-nCoV), the virus has now been named SARS-CoV-2 by the International Committee of Taxonomy of Viruses (ICTV) (2). This virus can cause the disease named coronavirus disease 2019 (COVID-19). WHO refers to the virus as COVID-19 virus in its current documentation. The purpose of this document is to provide interim guidance to laboratories and
stakeholders involved in COVID-19 virus laboratory testing of patients.
Existing WHO documents have been consulted for drafting this interim guidance, including the interim guidance on laboratory testing for MERS (3-9). Information on human infection with the COVID-19 virus is evolving and WHO continues to monitor developments and revise recommendations as necessary.

2. Laboratory testing guiding principles for patients who meet the suspect case definition

The decision to test should be based on clinical and
epidemiological factors and linked to an assessment of the likelihood of infection. PCR testing of asymptomatic or mildly symptomatic contacts can be considered in the assessment of individuals who have had contact with a COVID-19 case. Screening protocols should be adapted to the local situation.
The case definitions are being regularly reviewed and updated as new information becomes available.

Rapid collection and testing of appropriate specimens from patients meeting the suspect case definition for COVID-19 is a priority for clinical management and outbreak control and should be guided by a laboratory expert. Suspect cases should
be screened for the virus with nucleic acid amplification tests (NAAT), such as RT-PCR.

3. Specimen collection and shipment
Safety procedures during specimen collection Ensure that adequate SOPs are in use and that staff are trained for appropriate specimen collection, storage, packaging and transport. All specimens collected for laboratory investigations should be regarded as potentially infectious.

Specimens to be collected
At minimum, respiratory material should be collected:
– upper respiratory specimens:
nasopharyngeal and oropharyngeal swab or wash in ambulatory patients
– and/or lower respiratory specimens:
sputum (if produced) and/or endotracheal
aspirate or bronchoalveolar lavage in
patients with more severe respiratory
disease. (Note high risk of aerosolization;
adhere strictly to infection prevention and
control procedures).
Additional clinical specimens may be collected as
COVID-19 virus has been detected in blood and
stool, as had the coronaviruses responsible for SARS
and MERS (14,16,19-21). The duration and
frequency of shedding of COVID-19 virus in stool
and potentially in urine is unknown. In case of
patients who are deceased, consider autopsy
material including lung tissue. In surviving patients,
paired serum (acute and convalescent) can be useful
to retrospectively define cases as serological assays
become available.

Packaging and shipment of clinical specimens
Specimens for virus detection should reach the
laboratory as soon as possible after collection.
Correct handling of specimens during transportation
is essential. Specimens which can be delivered
promptly to the laboratory can be stored and shipped
at 2-8°C. When there is likely to be a delay in
specimens reaching the laboratory, the use of viral
transport medium is strongly recommended.
Specimens may be frozen to – 20°C or ideally -70°C
and shipped on dry ice if further delays are expected. It is important to avoid repeated freezing and thawing of specimens.

4. Laboratory testing for COVID-19 virus

Laboratories undertaking testing for COVID-19
virus should adhere strictly to appropriate biosafety
practices.
Nucleic acid amplification tests (NAAT) forCOVID-19 virus
Routine confirmation of cases of COVID-19 is
based on detection of unique sequences of virus
RNA by NAAT such as real-time reversetranscription polymerase chain reaction (rRT-PCR)
with confirmation by nucleic acid sequencing when
necessary. The viral genes targeted so far include the
N, E, S and RdRP genes. Examples of protocols used
may be found here. RNA extraction should be done
in a biosafety cabinet in a BSL-2 or equivalent
facility. Heat treatment of samples prior to RNA
extraction is not recommended.
Laboratory confirmation of cases by NAAT in areas with no known COVID-19 virus circulation
To consider a case as laboratory-confirmed by
NAAT in an area with no COVID-19 virus
circulation, one of the following conditions need to
be met:
– A positive NAAT result for at least two
different targets on the COVID-19 virus
genome, of which at least one target is
preferably specific for COVID-19 virus
using a validated assay (as at present no
other SARS-like coronaviruses are
circulating in the human population it can
be debated whether it has to be COVID-19
or SARS-like coronavirus specific); OR
– One positive NAAT result for the presence
of betacoronavirus, and COVID-19 virus
further identified by sequencing partial or whole genome of the virus as long as the sequence target is larger or different from the amplicon probed in the NAAT assay used. 

5.Reporting of cases and test results
Laboratories should follow national reporting
requirements. In general, all test results, positive or
negative, should be immediately reported to national
authorities. States Parties to the IHR are reminded of
their obligations to share with WHO relevant public
health information for events for which they notified
WHO, using the decision instrument in Annex 1 of
the IHR (2005).

Acknowledgements
The following people contributed to the drafting of
the evolving versions of this guidance document:
Katrin Leitmeyer, European Center for Disease
Control, Maria Zambon, Public Health England, UK;
Christian Drosten, Charité – Universitätsmedizin
Berlin, Germany; Marion Koopmans, Erasmus MC,
Rotterdam, The Netherlands; Leo Poon, Hong Kong
University, China, Hong Kong SAR; George Gao,
Chinese CDC, China.

References

1.Severe acute respiratory syndrome-related
coronavirus: The species and its viruses – a
statement of the Coronavirus Study Group.
Alexander E. Gorbalenya, Susan C. Baker,
Ralph S. Baric, Raoul J. de Groot,
Christian Drosten, Anastasia A. Gulyaeva,
Bart L. Haagmans, Chris Lauber.

2. Laboratory testing for Middle East
Respiratory Syndrome coronavirus, interim
guidance (revised), January 2019,
WHO/MERS/LAB/15.1/Rev1/2019, World
Health Organization, 2018.

3. Protocol to investigate non-seasonal
influenza and other emerging acute
respiratory diseases. Geneva: World Health
Organization; 2018

4. Managing epidemics, key facts about major
deadly diseases. Geneva: World Health
Organization; 2018.

5. Guidance to minimize risks for facilities
collecting, handling or storing materials
potentially infectious for polioviruses (PIM
Guidance). Geneva: World Health
Organization;2018

April 30, 2021

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