Omicron Subvariant JN.1: New Strain Emerging in Aotearoa New Zealand Amidst the Ongoing Pandemic

In 2024, if you contracted Covid-19 in Aotearoa New Zealand, chances are you were infected with the Omicron subvariant JN.1. This subvariant garnered attention just before Christmas and swiftly became predominant, accounting for 98 percent of sequenced cases by March.

However, the reign of JN.1 is now waning as it gives way to a new subset of variants known as “FLiRT” or “FLip,” characterized by distinctive mutations.

The Covid family tree is intricate, with JN.1 akin to a robust branch, now proliferating with diverse offshoots. SARS-CoV-2 has exhibited a propensity for significant evolutionary leaps, evident in the emergence of Omicron as the dominant strain in early 2022, replacing Delta. Omicron subvariants, propelled by favorable spike protein mutations, have since circulated, with JN.1 supplanting other lineages both domestically and internationally.

According to Environmental Science and Research (ESR), JN.1 or its derivatives accounted for nearly all sequenced cases, with FLiRT mutations emerging as a new concern. FLiRT lineages exhibit a growth advantage over JN.1, albeit not yet substantial enough to trigger a variant-driven wave. Notable FLiRT variants, including JN.1.16, KP.2, and KP.3, have begun to surface in surveillance data.

While FLiRT variants contribute to the uptick in Covid cases, their impact remains modest compared to previous waves. Nevertheless, the colder weather may facilitate transmission, potentially resulting in a wave akin to the summer surge but smaller than those witnessed in 2022 and 2023.

Epidemiologists emphasize that despite new nomenclature, the fundamental nature of the virus remains unchanged. The primary concern lies in its ability to evade immunity, leading to increased transmissibility at a population level. Vaccine-induced immunity remains crucial in mitigating the virus’s impact, especially amidst the approaching winter season, coinciding with a rise in respiratory illnesses.

Looking ahead, Covid waves will subside as immunity levels rise, driven by prior exposure or vaccination. However, Covid’s persistent burden on healthcare systems, the risk of hospital-acquired infections, and the specter of long Covid underscore the need for continued vigilance and preventive measures.

As the pandemic evolves, access to free Covid rapid antigen tests (RATs) remains available until at least June 30, 2024, ensuring ongoing surveillance and containment efforts.