Case definition and clinical testing guidelines for COVID-19

Case definition and clinical testing guidelines for health practitioners

Last updated: 11 March 2022

Summary of changes:

  • 9 March – Updated to reflect change in isolation times for the Omicron response
  • 7 March - Updated to reflect Phase 3 guidelines for the Omicron response
  • 24 February – Updated definitions of case classification
  • 27 January – Updated actions for contacts in primary care and community

This page provides guidance to support health professionals to identify and test those individuals who may have a higher risk of having COVID-19. It includes clinical criteria of COVID-19, the Higher Index of Suspicion (HIS) criteria, case definitions and notification procedures.

For more information on testing refer to the Testing Guidance for the Health Sector. This includes detailed advice for the health sector who to test, and why and when to test them. It is updated based on the latest knowledge about the virus and its symptoms, and on current conditions and response settings in New Zealand.

On this page:

Guidelines for testing

People should be tested who have symptoms that meet the clinical criteria for COVID-19 (detailed below). 

Where people meet both the clinical criteria for COVID-19 and the HIS criteria as well, extra steps (self-isolation and notification) are needed.

People may also be tested when they are asymptomatic and:

  • they are required to undertake mandatory routine testing at specified intervals (e.g., border and MIQ workers),
  • they are a Household Contact of a confirmed (or probable) case.

For definitions and guidance on management of contacts see Contact tracing.

Types of testing

Instructions for specimen collection

Guidance on how to take nasopharyngeal, and oropharyngeal + anterior nasal specimens for COVID-19.

Clinical criteria for COVID-19

Common symptoms of COVID-19 are similar to colds or influenza. A person may have one or more of the following symptoms

Common symptoms:

  • new or worsening cough
  • sneezing and runny nose 
  • fever
  • loss of smell or altered sense of taste
  • sore throat
  • shortness of breath.

Less common symptoms of COVID-19 may include diarrhoea, headache, muscle aches, nausea, vomiting, malaise, chest pain, abdominal pain, joint pain, or confusion/irritability. These almost always occur with one or more of the common symptoms.

Symptoms tend to arise around two to five days after a person has been infected but can take longer to show. The virus can be passed to others before they know they have it-from up to two days before symptoms develop,

Other conditions that require urgent assessment and management should always be considered as possible diagnoses alongside COVID-19.

Higher Index of Suspicion (HIS) criteria

People who meet the HIS criteria are those who have, in the 14 days prior to symptom onset:  

  • travelled internationally (excluding travel by air from a country/area with which New Zealand has quarantine-free travel (QFT)*),
  • had direct contact with a person who has travelled internationally in the preceding 14 days (excluding travel by air from a QFT country/area), eg, Customs and Immigration staff, staff at quarantine/isolation facilities,
  • exited an MIQ facility (excluding recovered COVID-19 cases),
  • worked on an international aircraft or shipping vessel (excluding aircraft from a QFT country/area), 
  • cleaned at an international airport or maritime port in areas/conveniences visited by international arrivals (excluding areas/conveniences for travellers by air from a QFT country/area), 
  • worked in cold storage areas of facilities that receive imported chilled and frozen goods directly from an international airport or maritime port, or 
  • travelled from an area with an evolving COVID-19 community outbreak (including in New Zealand and in any country/area with which New Zealand has QFT), or 
  • any other criteria requested by the local Medical Officer of Health. 

*a list of QFT countries/areas can be found on the Unite Against COVID-19 website. QFT only refers to travel by air at this point. 

People meeting the HIS criteria who also meet the clinical criteria for COVID-19 (a HIS person) should be tested for COVID-19 and self-isolate while awaiting test results to reduce the risk to others. Notification of the HIS person needs to be made to local Medical Officer of Health.

Table 1: Testing in primary care and community

Presentation

Action

Symptomatic

High index of suspicion

Typical symptoms

or

Less typical symptoms with no other likely diagnosis

  • Test

Household Contact

Typical symptoms

or

Less typical symptoms with no other likely diagnosis

  • Self-isolate from the day that the first Positive Case receives their positive test result, until they complete their 7 days of self-isolation and are released.
  • Test on day 3 and day 7 of your isolation period. Or if symptoms develop.

Not higher index of suspicion or contact

Typical symptoms

  • Test as per most recent advice.

Asymptomatic

Surveillance testing: Border worker including managed isolation or quarantine facilities

  • Test as per Border Order3
  • No need to isolate following a surveillance test unless they also meet any other testing criteria.

Surveillance testing: New Zealand-based air crew

  • Test as per requirements

Household Contact

  • Monitor for symptoms
  • Self -isolate from the day that the first person in your household receives their positive test result until they complete their 7 days of self-isolation and are released.

Other Close Contacts

  • Monitor for symptoms
  1. More information is available under Self-isolation guidance.
  2. More information is available under Staying at home
  3. More information on Border Orders is available at Epidemic notice and Orders.
  4. More information on requirements for international airline crew is available at Aviation sector.
Table 2: Testing in hospital including emergency departments

Presentation

Action

Symptomatic

Higher index of suspicion or a contact

Typical symptoms

  • Test1
  • Isolate while test result is pending and until clearance

Less typical symptoms with no other likely diagnosis

Not higher index of suspicion or a contact

Typical symptoms

  • Test1
  • Manage as per local infection prevention and control protocols
  1. Testing can be omitted if on clinical assessment there is another clear cause, not a transmissible respiratory infection.

Case classification

Confirmed case

A case that has laboratory definitive evidence. Laboratory definitive evidence requires at least one of the following:

  • detection of SARS-CoV-2 from a clinical specimen using a validated NAAT (PCR). Very weak positive results will only be labelled a confirmed case when the result is confirmed on a second sample.
  • detection of coronavirus from a clinical specimen using pan-coronavirus NAAT (PCR) and confirmation as SARS-CoV-2 by sequencing
  • significant rise in IgG antibody level to SARS-CoV-2 between paired sera.
  • detection of SARS-CoV-2 from a clinical specimen using a validated laboratory multi-target NAAT (PCR) OR a validated single target point of care NAAT (PCR) test.

Probable case

  • A close contact of a confirmed case that has a high exposure history, meets the clinical criteria and for whom testing cannot be performed, or
  • A close contact of a confirmed case that has a high exposure history, meets the clinical criteria, and has a negative PCR result but it has been more than 7 days since symptom onset before their first negative PCR test was taken.
  • An individual with a positive result from a clinical specimen using a certified Rapid Antigen Test (RAT), either supervised or self-tested who
    • Has symptoms consistent with COVID-19 OR 
    • Is a close contact of a confirmed or positive case OR
    • Is asymptomatic (in phase 3 only)

Historical case 

A confirmed case that is deemed to have recovered (no longer considered infectious) at the time of testing or a person with a positive NAAT(PCR) result with a high CT value, which is followed by a negative rapid antigen test (RAT).

Under investigation case

A case that has been notified where information is not yet available to classify it as confirmed, probable or not a case. 

Not a case

  • An ‘under investigation’ case who: 

  • has a negative test and has been assessed as not a case; 
  • a person where SARS-CoV-2 has been detected, where the detection is determined to be due to a previous COVID-19 infection which has already been recorded either in New Zealand or overseas within the previous 28 days from release.   
  • a person who has detection of SARS-CoV-2 from a clinical specimen but, following further investigations such as serology, repeat testing, history, and symptoms, they are deemed to not be a case (e.g., a likely false positive). 

Notification of cases

Attending medical practitioners should ensure that RAT results are uploaded via My Covid Record. A GP can notify of a positive RAT test via their Patient Management System (PMS), via My Covid Record or through the 0800 number. PCR results will be uploaded via Eclair. They should notify the local Medical Officer of Health of any confirmed cases, people they believe may be probable cases AND anyone who meets both the clinical and HIS criteria (notification should include the symptoms meeting the clinical criteria and how the HIS person meets the HIS criteria).

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