Case definition and clinical testing guidelines for COVID-19

Guidance for health professionals to identify and test those individuals who may have COVID-19, including clinical criteria, case definitions, testing guidance and notification procedures.

Last updated: 23 May 2022

On 23 May 2022 the Higher Index of Suspicion (HIS) criteria was retired as they no longer reflect New Zealand’s COVID-19 response.

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Clinical criteria for COVID-19

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

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

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.

Case definitions

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)
  • See guidance below on reinfection.

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 (eg, a likely false positive). 

Guidance on testing

The two main purposes for testing are for diagnostic purposes and for surveillance testing.

People should be tested who have symptoms that meet the clinical criteria for COVID-19 (see further detailed advice below on reinfection within 90 days). 

People may also be tested when they are asymptomatic and they are:

  • required to undertake mandatory routine testing at specified intervals (eg, border and MIQ workers),
  • a Household Contact of a confirmed (or probable) case
  • a recent returnee or visitor from international locations

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.

Instructions for specimen collection

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

Notification of cases

Most people will upload their RAT results via My Covid Record. Attending medical practitioners should ensure that supervised RAT results are also uploaded. 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.

Guidance on managing cases and contacts

This guidance for health practitioners provides information for assessing and managing COVID-19 cases and contacts

Guidance on reinfection

Reinfection with COVID-19 within 90 days is uncommon but possible, particularly with a different variant.

This guidance provides clinical advice to healthcare providers about how to manage patients who present with COVID-19 symptoms, or a positive COVID-19 RAT, within 90 days of a prior probable COVID-19 infection.

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