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WHO COVID 19 Laboratory 2020.4 Eng PDF
WHO COVID 19 Laboratory 2020.4 Eng PDF
Interim guidance
2 March 2020
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Laboratory testing for coronavirus disease 2019 (COVID-19) in suspected human cases
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Laboratory testing for coronavirus disease 2019 (COVID-19) in suspected human cases
Infectious Substances 2019-2020”(22) and “WHO whole genome of the virus as long as the
interim guidance for laboratory biosafety related to sequence target is larger or different from
2019-nCoV”(18). the amplicon probed in the NAAT assay
used.
Ensure good communication with the laboratory
and provide needed information When there are discordant results, the patient should
Alerting the laboratory before sending specimens be resampled and, if appropriate, sequencing of the
encourages proper and timely processing of samples virus from the original specimen or of an amplicon
and timely reporting. Specimens should be correctly generated from an appropriate NAAT assay,
labelled and accompanied by a diagnostic request different from the NAAT assay initially used, should
form (template provided in Annex I). be obtained to provide a reliable test result.
Laboratories are urged to seek confirmation of any
surprising results in an international reference
laboratory.
4. Laboratory testing for COVID-19 virus
Laboratory confirmed case by NAAT in areas
Laboratories undertaking testing for COVID-19 with established COVID-19 virus circulation
virus should adhere strictly to appropriate biosafety In areas where COVID-19 virus is widely spread a
practices. simpler algorithm might be adopted in which for
example screening by rRT-PCR of a single
Nucleic acid amplification tests (NAAT) for discriminatory target is considered sufficient.
COVID-19 virus
Routine confirmation of cases of COVID-19 is One or more negative results do not rule out the
based on detection of unique sequences of virus possibility of COVID-19 virus infection. A number
RNA by NAAT such as real-time reverse- of factors could lead to a negative result in an
transcription polymerase chain reaction (rRT-PCR) infected individual, including:
with confirmation by nucleic acid sequencing when
necessary. The viral genes targeted so far include the - poor quality of the specimen, containing
N, E, S and RdRP genes. Examples of protocols used little patient material (as a control, consider
may be found here. RNA extraction should be done determining whether there is adequate
in a biosafety cabinet in a BSL-2 or equivalent human DNA in the sample by including a
facility. Heat treatment of samples prior to RNA human target in the PCR testing)
extraction is not recommended. - the specimen was collected late or very
early in the infection
Laboratory confirmation of cases by NAAT in - the specimen was not handled and shipped
areas with no known COVID-19 virus circulation appropriately
To consider a case as laboratory-confirmed by - technical reasons inherent in the test, e.g.
NAAT in an area with no COVID-19 virus virus mutation or PCR inhibition.
circulation, one of the following conditions need to
be met: If a negative result is obtained from a patient with a
high index of suspicion for COVID-19 virus
- A positive NAAT result for at least two infection, particularly when only upper respiratory
different targets on the COVID-19 virus tract specimens were collected, additional
genome, of which at least one target is specimens, including from the lower respiratory
preferably specific for COVID-19 virus tract if possible, should be collected and tested.
using a validated assay (as at present no
other SARS-like coronaviruses are Each NAAT run should include both external and
circulating in the human population it can internal controls, and laboratories are encouraged to
be debated whether it has to be COVID-19 participate in external quality assessment schemes
or SARS-like coronavirus specific); OR when they become available. It is also recommended
- One positive NAAT result for the presence to laboratories who order their own primers and
of betacoronavirus, and COVID-19 virus probes to perform entry testing/validation on
further identified by sequencing partial or functionality and potential contaminants.
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Laboratory testing for coronavirus disease 2019 (COVID-19) in suspected human cases
For laboratories testing for COVID-19 virus in 6. Reporting of cases and test results
countries where COVID-19 was not previously
circulating, WHO advises the confirmation of Laboratories should follow national reporting
testing results for: requirements. In general, all test results, positive or
- the first 5 positive specimens, negative, should be immediately reported to national
- the first 10 negative specimens (collected authorities. States Parties to the IHR are reminded of
from patients that fit the case definition) their obligations to share with WHO relevant public
health information for events for which they notified
by referring them to one of the WHO reference WHO, using the decision instrument in Annex 1 of
laboratories providing confirmatory testing for the IHR (2005) (28).
COVID-19. For national COVID-19 laboratories
that require support with specimen shipment to one
of the reference laboratories for testing confirmation,
a WHO shipment fund is available. Please refer to
7. Research toward improved detection
the WHO website for the most updated list of
reference laboratories and shipment instructions. of COVID-19 virus
Serological testing Many aspects of the virus and disease are still not
Serological surveys can aid investigation of an understood. A better understanding will be needed
ongoing outbreak and retrospective assessment of to provide improved guidance. For example:
the attack rate or extent of an outbreak. In cases
where NAAT assays are negative and there is a Viral dynamics: optimal timing and type of clinical
strong epidemiological link to COVID-19 infection, material to sample for molecular testing
paired serum samples (in the acute and convalescent
phase) could support diagnosis once validated - Dynamic of immunological response
serology tests are available. Serum samples can be - Disease severity in various populations, e.g.
stored for these purposes. by age.
Cross reactivity to other coronaviruses can be - The relationship between viral
challenging (24) but commercial and non- concentration and disease severity
commercial serological tests are currently under - The duration of shedding, and relation to
development. Some studies with COVID-19 clinical picture (e.g. clinical recovery
serological data on clinical samples have been occurs with viral clearing, or shedding
published (25,26). persists despite clinical improvement)
Viral sequencing - Development and validation of useful
In addition to providing confirmation of the serological assays
presence of the virus, regular sequencing of a - Comparative studies of available molecular
percentage of specimens from clinical cases can be and serological assays
useful to monitor for viral genome mutations that - Optimal percentage of positive cases that
might affect the performance of medical requires sequencing to monitor mutations
countermeasures, including diagnostic tests. Virus that might affect the performance of
whole genome sequencing can also inform molecular tests.
molecular epidemiology studies. Many public- WHO encourages the sharing of data to better
access databases for deposition of genetic sequence understand and thus manage the COVID-19
data are available, including GISAID, which is outbreak, and to develop countermeasures.
intended to protect the rights of the submitting party
(27).
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Laboratory testing for coronavirus disease 2019 (COVID-19) in suspected human cases
- nasopharyngeal and
- oropharyngeal swabs
- nasopharyngeal
wash/nasopharyngeal
aspirate
Patient Serology Serum for serological Paired samples are necessary for confirmation with
testing once validated and the initial sample collected in the first week of illness
available and the second ideally collected 2-4 weeks later
(optimal timing for convalescent sample needs to be
established).
Contact NAAT Nasopharyngeal and Within incubation period of last documented contact.
oropharyngeal swabs
(in health-care centre associated
outbreaks or other settings Serology Serum for serological Baseline serum taken as early as possible within
where contacts have symptoms, testing once validated and incubation period of contact and convalescent serum
or where asymptomatic contacts available taken 2-4 weeks after last contact (optimal timing for
have had high-intensity contact convalescent sample needs to be established).
with a COVID-19 case.
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Laboratory testing for coronavirus disease 2019 (COVID-19) in suspected human cases
Table 2. Specimen collection and storage (adapted from ref 6 and ref 29,30)
Specimen type Collection materials Storage temperature Recommended temperature for shipment
until testing in-country according to expected shipment time
laboratory
* For transport of samples for viral detection, use viral transport medium (VTM) containing antifungal and antibiotic supplements.
Avoid repeated freezing and thawing of specimens. If VTM is not available sterile saline may be used in place of VTM (in such
case, duration of sample storage at 2-8 °C may be different from what is indicated above).
Aside from specific collection materials indicated in the table also assure other materials and equipment are available: e.g. transport
containers and specimen collection bags and packaging, coolers and cold packs or dry ice, sterile blood-drawing equipment (e.g.
needles, syringes and tubes), labels and permanent markers, PPE, materials for decontamination of surfaces etc.
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Laboratory testing for coronavirus disease 2019 (COVID-19) in suspected human cases
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Laboratory testing for coronavirus disease 2019 (COVID-19) in suspected human cases
Annex I
COVID-19 virus LABORATORY TEST REQUEST FORM 1
Submitter information
Has the patient had contact with a confirmed case? ☐ Yes ☐ No ☐ Unknown ☐ Other exposure:
Additional
Comments
1
Form in accordance with ISO 15189:2012 requirements
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https://www.who.int/publications-detail/global-surveillance-for-human-infection-with-novel-coronavirus-(2019-ncov)
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