Chapter last reviewed and updated in January 2024 A description of changes can be found at Updates to the Communicable Disease Control Manual.


Global Epidemiology

Coronavirus disease 2019 (COVID‑19) is caused by the SARS-CoV-2 virus, which infects the respiratory tract and is transmitted human to human primarily through respiratory droplets and aerosols. Documented transmission has also occurred through direct contact and rarely fomites (objects or materials that can carry infection).

In 2019, the first case of “pneumonia with unknown cause” was identified in Wuhan, China. The cause was identified as a novel coronavirus and WHO declared the outbreak a Public Health Emergency of International Concern on 30 January 2020. At the time of writing in July 2023, global case numbers were over 768,000,000 confirmed cases across more than 100 countries.

New Zealand Epidemiology

The first case of COVID-19 was reported in New Zealand on 28 February 2020. Border restrictions were implemented on 16 March 2020 as cases numbers increased and clusters of transmission were identified. On 25 March 2020, New Zealand entered a nationwide lockdown (‘Alert level four’). With rapid contact tracing and the public health COVID-19 protection framework, the spread of SARS-CoV-2 was restricted during 2020 and 2021. Only 19 percent of the introductions of virus in 2020 resulted in ongoing transmission or more than one additional case. Prior to the outbreak of the Delta variant in August 2021, most of the reported cases during 2021 were imported from overseas (over 95 percent from 1 January to 9 August 2021).

From 16 August 2021, the number of cases in New Zealand began to increase sharply due initially to the highly infectious Delta variant. From January 2022, when the more infectious Omicron variant entered the community, case numbers rose sharply but at this stage around 90 percent of the population aged from 12 years had been vaccinated with at least two doses of COVID-19 vaccine. Almost three years after the first case as of late February 2023, there were over 2.2 million cases recorded, over 26,000 hospitalisations, and 711 ICU admissions for COVID-19. There were 1,599 deaths coded with COVID-19 as the underlying cause, and the vast majority (96 percent) were aged over 59 years.

The COVID-19 Mortality Report  (September 2022) found that although COVID-19-attributed mortality was highest in older age groups, based on age-adjusted estimates, the risk of mortality for those aged under 60 years was 3.7 times higher for those Māori and 3.9 times higher for those of Pacific ethnicities than of European and Other ethnicities. Comorbidity in those under the age of 60 years significantly increased the risk of mortality by 78 times and explained 59 percent of the increased risk for Māori and 69 percent for Pacific ethnicities. Vaccination was shown to have a strong protective effect: after adjusting for age, sex, comorbidities and vaccination status (>2 doses), mortality risk was lowered but still 1.7 times higher in Māori and 1.9 times higher for Pacific compared with European/Other ethnicities.

Emergence of new variants is monitored in New Zealand by ESR through whole genome sequencing of specimens taken from hospitalised cases and wastewater sampling. For current details on case demographics see COVID-19: Data and statistics and for the mortality report see COVID-19 Mortality in Aotearoa New Zealand: Inequities in Risk.

The disease

Clinical presentation

The clinical presentation of COVID-19 is similar to other acute respiratory infections (ARI).

Typical presentations of COVID-19 may include one or more of:

  • 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.

In the early stages, it is difficult to distinguish COVID 19 symptoms from other common viral infections.

Many people (estimates vary from 20-60%)  infected with SARS-CoV-2 will remain asymptomatic.


Most people who get COVID-19 recover fully, but some may go on to develop longer term symptoms from the virus. This is known as long COVID, or for recording purposes is described as:

  • Ongoing symptomatic COVID-19: Signs and symptoms of COVID 19 from 4 weeks up to 12 weeks
  • Post-COVID-19 syndrome: Signs and symptoms that develop during or after an infection consistent with COVID 19, continue for more than 12 weeks and are not explained by an alternative diagnosis.

Groups at higher risk of severe disease

Risk factors for severe disease include older age, male, smoking, obesity and chronic medical conditions, including diabetes, cancer, chronic respiratory disease, cardiovascular disease, chronic kidney disease, hypertension, immunocompromise and pregnancy (see below).

Increased incidence is well documented in some ethnic groups but seems primarily related to prevalence of the risk factors listed above. Increasing age is the most important risk factor for severe disease, due to declining immune function and high prevalence of comorbidities. The highest risk group for severe illness and mortality is those aged over 70 years, although Māori and Pacific populations experience age-related risk at a younger age.

Risk of severe disease also increases with:

  • The number, severity and nature of comorbidities
  • Immunosuppression
  • Disability and frailty
  • Māori and Pacific ethnicity
  • Pregnancy

Spread of infection


The natural reservoir of COVID-19 or ancestral strains of SARS-CoV-2 remains unknown. However, it is likely it originated in animals.

Incubation period

The incubation period of ancestral strains of SARS-CoV-2 is typically 5 to 6 days, with a range of 1 to 14 days. Studies have shown shorter incubation periods for both Delta and Omicron variants of concern (VOCs) than ancestral SARS-CoV-2.

Mode of transmission

SARS-CoV-2 is primarily transmitted by exposure to infectious respiratory droplets and particles. Exposure occurs primarily through three routes:

  • Inhalation of respiratory droplets and aerosolised particles.
  • Deposits of respiratory droplets and particles on mucous membranes (mouth, nose, eyes).
  • Touching of mucous membranes with hands directly contaminated with virus-containing respiratory fluids, noting that virus-contaminated surfaces containing respiratory fluids are thought to be a rare source of transmission.

Infectious period 

The infectious period begins 48 hours prior to symptom onset (or positive test if asymptomatic). Cases with mild-to-moderate illness are highly unlikely to be infectious more than 10 days after symptom onset. The infectious period can vary based on individual factors and variants. Cases with  severe disease, or who are significantly immunocompromised may have longer infectious periods.

Priority populations

COVID-19 priority populations

Priority people are defined as those who are inequitably impacted by COVID-19. People in this group are eligible for targeted assessments regarding additional clinical and social support. The COVID-19 pandemic has exacerbated existing inequities for specific groups, including:

  • Māori who experience greater inequity and disadvantage due to COVID-19 resulting in poorer outcomes.
  • Pacific People who have had the highest age-standardised hospitalisation rates for COVID-19, and experienced age-standardised mortality rates 2.4 times greater than European and other population groups.

Higher risk settings

In the context of widespread community transmission, higher-risk settings are generally settings where there is both a:

  • High proportion of people at higher-risk of severe disease (for example, due to age or chronic medical conditions)
  • Higher risk of transmission due to close proximity and difficulty instituting control measures such as physical distancing or environmental controls.

The following settings are considered as higher-risk:

  • Healthcare settings
  • Aged Residential Care (ARC) facilities
  • Disability care facilities
  • Correctional facilities

Higher risk occupations

Health care workers

Patient-facing health care workers caring for patients with COVID-19 without using appropriate infection prevention control (IPC) interventions including personal protective equipment (PPE) are likely to be exposed to higher viral loads, placing them and their household members at greater risk of developing COVID-19 than the general population.

However, the use of a risk assessment to determine the appropriate personal protective equipment and other measures aimed at reducing nosocomial viral transmission have been shown to be effective, such that, when COVID-19 is prevalent in the community, health care workers are more likely to catch SARS-CoV-2 from an infected household member.

Further guidance on IPC practices and PPE in health and disability care settings can be found here.

Routine Prevention


It is recommended that all individuals from age 12 years receive two doses of mRNA-CV (30 µg) given at least 21 days apart, preferably eight weeks apart. Children aged 5–11 years are recommended two doses of paediatric mRNA-CV (10 µg) given at least 8 weeks apart. Children aged 6 months to 4 years with severe immunocompromise or complex/multiple health conditions that increase their risk of severe COVID-19 are recommended three doses of paediatric mRNA-CV (3 µg), with the second dose administered at least 21 days after the dose one followed by dose three at least eight weeks after dose two.

Certain individuals with severe immunosuppression are recommended to receive three primary doses with the third dose given at least eight weeks after dose two (see section ‎5.5.8; this is part of the primary course and not the same as first booster or additional doses).

Bivalent mRNA-CVs were approved for use by Medsafe on 21 December 2022. One vaccine contains mRNA expressing the original spike protein (tozinameran) and mRNA expressing the Omicron BA.4-5 strain spike protein (famtozinameran). It is approved for use as booster doses for individuals who have received at least a primary course against COVID-19. The original/BA.4-5 (tozinameran/famtozinameran) version has been included in the COVID-19 immunisation programme (abbreviation: bivalent mRNA-CV (15/15 µg)). For use as a booster, this replaces the first approved mRNA-CV (30µg) from 1 March 2023.

Booster Dose

Anyone aged 16 years or over who has not yet received a first booster dose since completion of the primary course are recommended to receive a dose of mRNA-CV (15/15 µg), if not contraindicated.

From 1 April 2023, bivalent mRNA-CV (15/15 µg) is available as an additional dose for all adults aged from 30 years and recommended for those aged from 16 years at increased risk of severe COVID-19, regardless of number prior booster doses received.

This includes:

  • People of Māori or Pacific ethnicities aged 30 years and over
  • All other individuals aged 65 years and over
  • Residents aged 16 years or over living in aged care and disability care facilities
  • Severely immunocompromised people who were eligible to receive a third primary dose (see section ‎5.5.8)
  • Individuals aged from 16 years who have certain medical conditions (see Table ‎5.5 in section ‎5.5.8) that increase the risk of severe breakthrough COVID-19 illness.
  • Individuals aged from 16 years who live with disability with significant or complex health needs or multiple comorbidities (see Table ‎5.5 in section ‎5.5.8)
  • Individuals aged from 16 years who are severely obese (BMI ≥40 kg/m2) or severely underweight (BMI <16.5 kg/m2).

Further information on COVID-19 vaccination, including booster doses, can be found in the Immunisation Handbook 2020.

Universal prevention activities

Refer to 'other control measures' for guidance on basic infection prevention and control measures.

Case definition

Case classification

The majority of cases are no longer actively followed up. Therefore, clinical and epidemiological criteria are not included in the case definition. This does not prevent capturing symptomatic contacts without laboratory evidence in an institutional outbreak investigation for the purposes of acute respiratory infection outbreak surveillance where outbreak criteria are elsewhere defined.

  • Confirmed case: A confirmed case has definitive laboratory evidence AND has not been a confirmed or probable case in the previous 28 days.
  • Probable case: A probable case has suggestive laboratory evidence AND has not been a confirmed or probable case in the previous 28 days.
  • 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: A case under investigation who doesn’t meet the definition of a confirmed or probable case.
  • Reinfection:
    • The latest evidence shows that reinfection with COVID-19 can occur within a short period of time. Reinfection will become more likely as new variants spread in the community.
    • When someone tests positive for COVID-19 and it has been 29 or more days since the last infection, it will be categorised as reinfection (same advice and support as for a new infection).

COVID-19 Death

A COVID-19 death is reported when COVID-19 is determined to have been the underlying cause of death or a contributory cause of death. This contribution can range from death not related, for instance someone with COVID-19 who dies in a car accident; to COVID-19 being a contributing cause, for example when someone dies with an existing health condition combined with COVID-19; and to COVID-19 being recorded as the cause of death.

All deaths where someone has died within 28 days of being reported as having a positive test result for COVID-19 are now reported.

Clinical criteria

Not applicable.

Epidemiological criteria

Not applicable.

Laboratory criteria

Definitive laboratory evidence

SARS-CoV-2 detected from a clinical specimen using a validated nucleic amplification acid testing (NAAT) OR by a Rapid Antigen Test in a health care setting.

Suggestive laboratory evidence

SARS-CoV-2 detected through a self-reported rapid antigen test where the quality of result cannot be verified.

Testing Guidance


The current COVID-19 Testing Plan recommends Rapid Antigen Tests (RATs) as the preferred modality for symptomatic testing. PCR testing is only recommended where a result can influence treatment options for priority people and those at higher risk of severe illness from COVID-19. The current COVID-19 Testing Plan provides the framework to support decisions about why, when and who to test for COVID-19 in Aotearoa New Zealand. 

The current COVID-19 guidance documents provide recommendations for specific settings and facilities on testing, along with advice for preventing and managing COVID-19 transmission and outbreaks.

Notification and reporting

Notification procedure

COVID-19 is a notifiable disease under Section 74 of the Health Act 1956, which requires all health practitioners and those in charge of medical laboratories to officially report actual and suspected cases of COVID-19 to the medical officer of health in the local public health service. Self-diagnosed cases detected by RAT are not required to be reported under the Health Act.  

Direct notification to a medical officer of health is not required.

Most people will upload their RAT results via My Health Record. Attending medical practitioners should ensure that supervised RAT results are also uploaded. A GP can notify a positive RAT test via their Patient Management System (PMS), via My Health Record or through the 0800 number. PCR results will be uploaded via Eclair.

See Appendix 5: Escalation pathways for more information

National escalation

There is no expectation that Public Health Services will escalate any COVID-19 related event(s) to the National Public Health Service or Manatū Hauora.


With widespread community transmission of SARS-CoV-2, reporting priorities to central communicable diseases units should include:

  • Laboratory notification of positive SARS-CoV-2 NAAT results
  • Timely self-reporting of positive RAT results
  • Collection of case demographics
  • Notification of clusters and outbreaks in high-risk settings and communities
  • Notification of COVID-19 cases in hospital and intensive care
  • Notification of COVID-19 related deaths

International reporting

There are no international reporting requirements for COVID-19. However, an exception to this would be reporting to the World Health Organization in the following situations:

    • An emerging variant that has evidence of being particularly transmissible or severe
    • A significant increase in community case numbers.

Data management

Cases and contacts

Case records are automatically created in the National Contact Tracing Solution (NCTS) when a positive result is recorded.

Positive results will generate a text message to the case encouraging them to complete the case self-serve form online.

Cases that meet the prioritised criteria (aged 65+ all ethnicities, aged 35+ Māori and Pasifika, all cases under 6 months old) AND who have not completed the case self-serve form within 24 hours OR who are not enrolled with a primary care provider will be automatically sent to a Care in the Community Hub for proactive outreach for antivirals (if eligible).

Contact records are not created in NCTS as contacts are not actively managed by public health services.


Case management

Public health priority

There is an ongoing COVID-19 pandemic globally. New Zealand has implemented control measures to limit the spread of SARS-CoV-2 in the community as described on the -COVID- 19 website.

All individuals with symptoms of COVID-19 are recommended to isolate, test for COVID-19 and seek medical advice if concerned. Rapid antigen testing and nasopharyngeal PCR testing continue to be fundamental components of the public health measures. Up to date information on public health measures is available on the -COVID- 19 website.

Immunisation using COVID-19 vaccines is part of the public health strategy aimed at reducing the risk of severe disease to minimise the burden on the health care system and slowing the rate of transmission during community outbreaks.


Case Investigation

An automated case management system should prioritise cases to allow targeted follow up where appropriate, particularly in high-risk settings.

Where automated case management systems are utilised, jurisdictions should ensure cases are provided with accessible and up to date information on how to manage their illness, access medical care, and understand the recommendations to stay-at-home and restrictions for certain workplaces. Cases should also be provided with advice that their household and social/workplace contacts are at risk of COVID-19 and should be advised to monitor for COVID-19 symptoms and get tested if symptomatic.

In addition to automated case management systems, jurisdictions may also consider a random or targeted selection of case interviews. This can help monitor for changes in disease epidemiology and assist in modelling projections of future COVID-19 case counts.

Source Investigation

Not required.

Exposure Event Investigation

Not required. 

Isolation and restriction

Recommended isolation of COVID-19 cases

Cases are recommended to isolate at home for a minimum of 5 days from the first onset of symptoms or the date of test if asymptomatic (whichever comes first). If symptoms persist after 5 days than the case should stay at home until their symptoms have resolved and they feel well.

Isolation means that:

  • Where able, cases should sleep in a separate room and avoid contact with household members
  • Cases should wear a mask when in the same room as others
  • Cases should maintain physical distance in shared spaces

Cases should be advised to avoid visiting high-risk settings (such as residential aged care facilities, disability care facilities and hospitals), unless seeking treatment (or it is their home) until at least 10 days following their positive test result and they are well.

Health care workers

Due to the vulnerability of patients in healthcare settings, return to work for health care workers with COVID-19 is carefully managed. Healthcare workers should refer to the Healthcare Worker Return to Work Guidance for advice.

Recommendations following completion of self-isolation

In addition to the above, cases may be recommended to take additional precautions for up to 10 days after their onset of symptoms, such as:

  • Avoid contact with people who are at higher risk of severe disease, including immunosuppressed people, older people, and people with a disability with multiple conditions, or wear a mask.
  • Wear a mask when in an indoor setting outside the home
  • Work from home where practical
  • Practise careful hand and respiratory hygiene

COVID-19 antiviral Medicines

The COVID-19 antiviral medicines Nirmatrelvir with ritonavir (Paxlovid) and remdesivir (intravenous treatment) are the treatments available in New Zealand, to reduce the risk of severe illness and hospitalisation from COVID-19 infections for those most at risk as defined by the Pharmac access criteria available here.

The Care in the Community Team at Te Whatu Ora and the Ministry of Health have developed a range of guidance on the use of COVID-19 antivirals which is available on their website.

Health education

The -COVID- 19 website provides accurate and up-to-date public health advice for COVID-19 cases.

Manaaki and wellbeing

If cases are unable to work due to a medical condition, they should talk to their employer about sick leave or other paid leave. Employment NZ has information about leave entitlements.

If a case requires help with urgent costs, or only has unpaid leave, they may be eligible for support from Work and Income. Check or call 0800 559 009.

Contact management


Contacts are not actively managed by public health services and are recommended to self-monitor for symptoms and test as recommended.

The risk of developing COVID-19 increases with the amount of time and intimacy of contact that a susceptible person has with an infectious case. People are identified as close contacts when that risk warrants public health measures to minimise the risk of further transmission.

If a new case is identified in a household:

  • >10 days after the initial case completed their recommended isolation: other household contacts (except those who became cases) do need to test daily for 5 days.
  • ≤10 days of the initial case completing their recommended isolation: other household contacts do not need to test daily for 5 days. If symptoms develop, stay home and test. If test is negative, recommend RATs continue daily until symptoms resolve or up to a maximum of a further 5 days. Stay at home until 24 hours after symptoms resolve.

Close contact – household

  • Normally share a residence with case (either on a permanent or part time, or shared custody basis), and
  • Spent at least one night or day (more than 8 hours) in that residence while case was infectious
  • Includes shared houses and flats, travellers in shared holiday accommodation (e.g., hotel room or campervan)
  • Don’t normally reside with the case but have spent a night together in the same room.

Close contact – other

  • Live in same group accommodation with case[1]
  • Had contact with case during their infectious period

Casual contact

  • Any person with exposure to the case who does not meet the criteria for a Close contact.


[1] e.g. halls of residences, boarding houses, hostels, backpackers, transitional housing or similar


Household Close contacts are recommended to:

  • Test with a RAT each day for five days, from the day that the first case in the household tests positive
  • Wear a mask outside home for duration of testing particularly around people at higher risk of severe disease (e.g., elderly or immunocompromised), on public transport or in crowded indoor places
  • Continue with daily life provided no symptoms and a negative RAT result each day for five days
  • If symptomatic, continue with daily tests up to five days and if all tests negative no need for further tests; stay at home until 24 hours after symptoms resolve
  • Avoid or minimise contact with the case(s) in the household as much as possible whilst they are isolating
  • If final daily test is negative, but newly symptomatic, recommend daily RATs continue until symptoms resolve or up to a maximum of a further 5 days. Stay at home until 24 hours after symptoms resolve
  • If any RAT result is positive, it is recommended to commence at least 5 days self-isolation as a case (from date symptoms developed or date of test if asymptomatic, whichever comes first)
  • If a positive case enters a household partway through the case’s isolation period (e.g., student returning from hostel to home, or shared care situations), the new household contacts should test for 5 days from the date of entry of the case (5 days from exposure)
  • Daily testing does not restart if additional members of the household are identified as cases within the initial case’s isolation period

Other Close contacts are recommended to:

  • Self-monitor for symptoms for 10 days
  • If symptoms develop at any time during the 10 days, stay at home and test with a RAT immediately. If test is negative, recommend RATs continue daily until symptoms resolve or up to a maximum of 5 days. Stay at home until 24 hours after symptoms resolve.


Public health priority

The people at highest risk of developing COVID-19 are household close contacts.

Quarantine and restriction

There is no recommended quarantine or restrictions for Close contacts.

Health education

The -COVID- 19 website provides accurate and up-to-date public health advice for COVID-19 contacts.

Special setting management

Special setting

In the context of widespread community transmission, high-risk settings are generally settings where there is both a:

  • High proportion of people at high-risk of severe disease (for example, due to age or chronic medical conditions)
  • Higher risk of transmission due to close proximity and difficulty instituting control measures such as physical distancing or environmental controls.

In the context of widespread community transmission, jurisdictions routinely define the following settings as high-risk:

  • Healthcare settings
  • Residential aged and disability care facilities
  • Faith based facilities
  • Correctional facilities

There is no expectation that public health services will routinely manage COVID-19 cases in special settings. Where support is specifically requested by a facility, it is at the public health services discretion whether this is provided. 

Further information on testing and management of special settings can be found here

Further information on testing and management of health care settings can be found here


Outbreak definition

COVID-19 is infectious illness that may spread within residential facilities, from staff, visitors and residents, resulting in what we refer to as an outbreak. Outbreaks of infectious illnesses, such as COVID-19, in residential facilities are a risk to the health and wellbeing of residents, staff, and families.

An outbreak of COVID-19 occurs when 2 or more residents test positive to COVID-19 within a 72-hour period.

An outbreak can be declared over 20 days (standard two incubation periods) after the last COVID-19 case tests positive or the date of isolation of the last COVID-19 case in a resident, whichever is longer.

Outbreak control

The ongoing role of PHS in the management of COVID-19 outbreaks is under active review.  PHS are advised to continue with their existing arrangements for management of outbreaks in high risk settings.

Other control measures

Infection prevention control

Basic infection prevention and control measures

  • Hand hygiene – Clean hands either through using an alcohol-based hand sanitiser or, wash and dry thoroughly.
  • Respiratory hygiene – Cover coughs and sneezes, dispose of any used tissues into bin and clean hands.
  • Vaccination – It is recommended that health care workers are fully vaccinated. If unwell –stay home and test.
  • Personal protective equipment (PPE) – Wear a well-fitting face mask appropriate for the task or person, situation (i.e. particulate respirators and medical masks). Healthcare workers may also need to wear additional PPE including eye protection, apron or gown and gloves. Further information is provided below.
  • Ventilation – Ensuring the air in rooms used for living or work is circulating and fresh is important in reducing the amount of virus in the air. Overcrowding and being in close proximity to others can also increases risk of infectious particles circulating. Further information on ventilation for homes and public transport can be found here. Health care workers should undertake a risk assessment regarding the need to wear respiratory protection.
  • Cleaning and disinfection –General regular cleaning products for surfaces or objects can be used as the SARS-CoV-2 virus is susceptible to regular household cleaning products. There should be cleaning schedules and work-based policies for cleaning shared work vehicles and for multiuse patient/client equipment in-between use.
  • Waste – Waste relating to COVID-19 can be treated as normal household waste. Within healthcare facilities, workers should follow recommended policies.


Please find further information on infection prevention and control recommendations for health and disability care workers here, and general information for the public here.