Real-time genomics to track SARS-CoV-2 help contain transmission in New Zealand

By Angela Betsaida B. Laguipo, BSNAug 16 2021Reviewed by Benedette Cuffari, M.Sc.

For much of the current pandemic, New Zealand successfully mitigated the impacts of the coronavirus disease (COVID-19), which is a disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Between January 3, 2020 and August 16, 2021, New Zealand reported a total of 2,926 COVID-19 cases and 26 deaths.

Between May 2020 and April 30, 2021, New Zealand maintained the elimination of SARS-CoV-2. During this time, 13 community outbreaks were reported in New Zealand, which consisted of a total of 225 recorded community cases.

Study: Real-Time Genomics for Tracking Severe Acute Respiratory Syndrome Coronavirus 2 Border Incursions after Virus Elimination, New Zealand. Image Credit: kovop58 / Shutterstock.com

A recent study published by the U.S. Centers for Disease Control and Prevention (CDC)’s Emerging Infections Diseases discusses how New Zealand rapidly employed real-time genomics to contain new COVID-19 cases. These efforts were essential in helping scientists establish links between cases and determine when concurrent outbreaks had different origins.

Public health response to community outbreaks

New Zealand has been one of the most successful countries in tackling the global health crisis of COVID-19. During outbreaks, New Zealand employed an elimination strategy that largely relied on a strictly controlled border.

To this end, all individuals entering the country were required to isolate for 14 days at a manage isolation and quarantine (MIQ) facility. Any individual at a MIQ facility was also subjected to a reverse-transcriptase polymerase chain reaction (RT-PCR) tests to detect the presence of SARS-CoV-2 at days 0, 3, and 12 of their stay.

Real-time genomic sequencing has been an essential component of New Zealand’s COVID-19 response, as it not only filled in the gaps of epidemiologic data but also allowed for outbreaks of different origins to be quickly identified.

About the study

Viral genomic sequencing of every infected individual has played a pivotal role in tracking and delineating all community outbreaks in New Zealand. It complements all other measures, including border controls, contact tracing, and the alert level system.

Individuals in MIQ facilities undergo weekly sequencing, while community patients are sequenced more frequently. The results of complete genomes are available within 12 hours after the first positive test.

In the current study, researchers constructed a multiple sequence alignment containing 225 genomes from New Zealand community outbreaks and 663 from other countries around the world. For each outbreak in the country, the team sampled 50 global sequences from the same pangolin lineage. These sequences were then used to reconstruct a phylogenetic tree for all border incursions identified in New Zealand, with international viral genomes incorporated into the tree for reference.

Study findings

In the current study, the authors discuss the genomic data acquired from each of the community outbreaks that were reported in New Zealand since June 1, 2020. In Aukland, for example, a total of 4 COVID-19 cases were reported at a cold storage facility on August 11, 2020, which ended a 102-day COVID-19-free period. Upon the identification of these cases, restrictions were immediately implemented in Aukland and the city was sent into an alert level 3 lockdown.

The genomic analysis of the viral isolates obtained from these individuals demonstrated that all viruses were closely related, thus indicating a single origin. This observation allowed public health officials to confidently declare this single outbreak as controlled, despite the lack of epidemiologic links between these infected individuals.

Several different SARS-CoV-2 lineages were also found to have been imported into New Zealand over the course of the pandemic. Overall, four outbreaks of locally acquired infection in 2021 were caused by SARS-CoV-2 variants of concern (VoCs) B.1.1.7 (Alpha) and B.1.351 (Beta).

These observations, therefore, indicate that these strains of SARS-CoV-2 arrived at the border. In fact, a total of 83 of the 142 genomes identified from overseas returnees between January 1, 2021, and April 30, 2021, were from these two lineages.

Conclusion

The current study found that real-time genomic surveillance is vital for confirming or disproving links between COVID-19 cases, especially when epidemiologic data are lacking. This can help health officials to identify new outbreaks and mitigate community transmission.