Molecular epidemiology and evolution of norovirus in Australia and New Zealand, 2018 to 2020.

Abstract

Background: Norovirus causes an estimated 699 million cases of gastroenteritis and 219,000 deaths each year. Historically, novel strains with a genogroup II genotype 4 (GII.4) capsid have emerged every 3-5 years to cause gastroenteritis pandemics. Contrary to historical trends, viruses with aGII.4 Sydney 2012 capsid have extended the timeframe of capsid circulation, well beyond the usual 3-5 years, through genetic recombination to obtain new non-structural regions, for example, a GII.P16 ORF1.

Objectives and methods: The molecular evolution in the GII.4 capsid of strains in New South Wales (NSW), Australia and New Zealand (NZ) before and into the COVID-19 pandemic (2018-20) was investigated by sequencing noroviruses from clinical specimens and wastewater.

Results: A continued high prevalence of GII.4 Sydney 2012 [P16] was observed (NSW: 23.0%; NZ: 24.2%), albeit co-dominant with GII.2 [P16] (NSW: 20.2%; NZ: 29.4%). Unlike the historical trends, the GII.4 Sydney 2012 capsid has been in circulation for eight years. Circulating norovirus in the community was disrupted by COVID-19 control measures; lockdowns reduced viral concentration in wastewater by >90% (1.4 × 10⁵ genome copies (gc)/L) from May to September 2020 compared to equivalent timeframes in 2018 (1.6 × 10⁶gc/L) and 2019 (1.9 × 10⁶gc/L). The relaxation of lockdown measures in late-2020 coincided with a strong resurgence of GII.2[P16] prevalence both clinically and in wastewater in NSW and Melbourne, accompanied by a decline in the diversity of circulating noroviruses. Conclusion: In summary, COVID-19 disrupted the strain diversity and levels of norovirus in Australia and New Zealand.