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Wellington SCL Newsletter
16th March 2020

(Please forward on to your clinical staff) 

Update for Primary Care: Testing for suspected COVID-19

Over the weekend, several important changes have occurred with respect to the COVID-19 outbreak and the response in New Zealand.

From 1:00am Monday 16th  March, all people entering New Zealand will be required to self-isolate for 14 days. The only exceptions to this are passengers arriving from Pacific Islands (except French Polynesia).

This enforced quarantine will aid in case identification and preventing secondary generations of transmission.

The Ministry of Health COVID-19 suspected case definition has been broadened. The key changes are that the countries or areas of interest has been widened to all overseas countries or territories except for Pacific Islands (except French Polynesia).
  Clinical criteria   Epidemiological criteria
1 Fever (≥38oC) OR any acute respiratory infection with at least one of the following symptoms: shortness of breath, cough or sore throat with or without fever.   AND Travel to or from (excluding airport transit) countries or areas of concern within 14 days before onset of illness
2 Fever (≥38oC) OR any acute respiratory illness with at least one of the following symptoms: shortness of breath, cough or sore throat with or without fever   AND Close contact1 or casual contact4 with a suspect, probable or confirmed case of SARS-CoV-2 infection in the 14 days before onset of illness
Healthcare workers3 with moderate or severe community-acquired pneumonia   AND Regardless of any international travel

Due to the changing global and domestic situation, clinical judgment is recommended if the patient does not quite meet the case definition regarding testing.

Further information, including a complete description of countries or areas of concern, and of definitions of close and casual contact can be found at:

This week is it expected that several community based assessment and testing centres will be established across the region. This will assist in easing the pressure in some primary care practices. There still may be times when patients with suspected COVID-19 infection come to primary care practices, so procedures must be in place to ensure safety of staff and other patients while providing appropriate care for suspected cases.

WSCL is presently developing capability to test for COVID-19 on site at the Wellington laboratory. Presently testing is performed at ESR, Wallaceville and has a 24 hour turnaround time weekdays and up to 48 hour turnaround time on weekends. Bringing in the test on site will reduce the time to result and increase the national capacity for testing.

It is essential that we are testing responsibly at this time to ensure that there are enough swabs and other materials available to run COVID-19 tests in suspected cases. While there are sufficient stocks in the country for quite some time, it is important to ensure the resources we are efficiently used as there is a great worldwide demand for testing resources at this time.

Consequently we have altered our testing recommendations:
  • WSCL collection rooms CANNOT perform nasopharyngeal swabs for COVID-19. This is due to the risk to other patients and staff if symptomatic cases are sent for testing. Please do not advise patients to come to collection rooms.
  • There is NO patient self-request testing available.
  • Requests for COVID testing no longer require approval from a clinical microbiologist or Medical Officer of Health. However, all patients being tested must continue to be notified to the Regional Public Health by phone/fax/email.
  • A named doctor must be responsible for the COVID-19 test request and result.
  • The clinician must provide instruction for the case to remain in isolation until the results are known as well as any quarantine required of their close contacts.
  1. Useful resources for suspect, probable or confirmed cases who do not need to be hospitalised:
  2. Close contact of a suspected case:
  3. Close contact of a confirmed case:
  4. Welfare support factsheet useful for all:
  • If COVID-19 test is negative, the referring clinician is to contact the case to let him or her know the result, to discuss clinical progress and the need for a repeat swab (e.g. if patient high-risk or deteriorating), and to reinforce any remaining need to self-isolate.
    1. People meeting high-risk epidemiological criteria should be advised to re-contact if worsening symptoms, since a repeat swab may be indicated.
    2.  Symptomatic people should continue to avoid contact with others until 48 hours symptom-free AND until the requirement for self-quarantine for 14 days has been completed (whichever is later), irrespective of a negative COVID-19 test result
  • If COVID-19 test is positive, Regional Public Health will inform the case and commence contact tracing.  The referring clinician must review the patient’s clinical progress.
  • For patients with severe symptoms suggestive of pneumonia or with tachypnoea or hypoxia – do NOT take any samples but refer to hospital for testing and assessment. For patients with mild to moderate symptoms who do not require admission to hospital on severity criteria – please see testing procedure below.
  • Staff taking sample should wear appropriate PPE and should perform hand hygiene appropriately:
    • Eye protection (visor/goggles)
    • Surgical mask
    • Gloves
    • Apron or long sleep impermeable gown
    • A useful video guide for donning and doffing PPE is available at:
  • Specimens required:
    • 1 x red viral swab in viral transport media for COVID-19 testing -> first swept over oropharynx and then with same swab sample the nasopharynx; if patient is not cooperative, a nasopharyngeal swab is acceptable
    • 1 x red viral swab in viral transport media for testing of other respiratory viruses -> nasopharyngeal only. This is helpful as we head into winter and respiratory viruses become more common.
  • Sputum sample if possible, for coronavirus testing (most patients do not produce sputum, but when they do this is a very good sample)
  • Clinical details MUST be recorded on the request form. This is required by ESR. Patient identification information, physicians name and contact information, date and time of sample collection, specimen type and tests requested, clinical symptoms/date of onset/travel or contact history
  • Place all samples into a clear plastic sample bag and seal. Place this first bag inside another sample bag and seal (i.e. double bagged) – place request form into the sleeve of the outer bag
  • Perform hand hygiene
  • Specimen should be transported to WSCL on next available courier. 
  • Weekend transportation will require a taxi to be organised by the referrer.
  • Stores ordering - for large practices we will distribute x1 box (50 swabs per box). For medium to small practices between 10-20 swabs, depending on size.  This is to ensure adequate supplies are maintained.  
In order to help us facilitate the expected high demand for COVID-19 testing we will need to rationalise other molecular and microbiology tests.
The reagents and staff required are a finite resource.
  • HSV/VZV or Enterovirus testing of skin lesions will not be routinely available and should primarily be diagnosed using clinical criteria.
  • Faecal PCR should not be requested unless diarrhoea present for >7 days. Exceptions are hospitalised patients, bloody diarrhoea or if part of an outbreak. STI screen in asymptomatic patients with no risk factors and age>30yrs.
  • Viral loads for CMV, EBV, HBV, HCV, HIV should only be performed in line with agreed local and international guidelines
It would be helpful to review need for testing for other microbiology samples to enable more staff to work on COVID-19 testing:
  • Toenail/skin scraping for superficial fungal infections
  • Mouth swabs
  • Superficial ear swabs for otitis externa unless complex situation such as malignant otitis externa or mastoid osteomyelitis
  • Throat swabs in patients without risk factors for rheumatic fever – risk factors must be clearly stated on the request form
  • Vaginal swabs unless post-partum or post-operative
  • Skin swabs from chronic wounds without evidence of surrounding cellulitis (if sending please ensure wound is cleaned with saline first)
  • Community urine samples with insufficient clinical details
  • Community sputum samples without clinical evidence of pneumonia (excludes cystic fibrosis and suspected TB)
Please note that samples from sterile sites (blood, CSF, tissue) will always be processed. Clinical details are essential in all microbiological specimens and will help laboratory doctors to prioritise important samples.
Further information on COVID-19 pertaining to primary care, PPE, self-isolation, travel advisories, information for clinicians and for general public is available on the Ministry of Health website:

We thank you all for your ongoing work to contain the COVID-19 outbreak.

Dr Michelle Balm
Clinical Microbiologist – Wellington Southern Community Laboratories
Infectious Diseases physician – Capital & Coast District Health Board

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