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. 2022 Sep 28;14(10):2135.
doi: 10.3390/v14102135.

An Unusual Resurgence of Human Metapneumovirus in Western Australia Following the Reduction of Non-Pharmaceutical Interventions to Prevent SARS-CoV-2 Transmission

David Anthony Foley  1   2   3 , Chisha T Sikazwe  1   4 , Cara A Minney-Smith  1 , Timo Ernst  4 , Hannah C Moore  2   5 , Mark P Nicol  4 , David W Smith  1   3 , Avram Levy  1   4 , Christopher C Blyth  1   2   3   6
Affiliations

An Unusual Resurgence of Human Metapneumovirus in Western Australia Following the Reduction of Non-Pharmaceutical Interventions to Prevent SARS-CoV-2 Transmission

David Anthony Foley et al. Viruses. .

Abstract

Non-pharmaceutical interventions (NPIs) to reduce SARS-CoV-2 transmission disrupted respiratory virus seasonality. We examined the unusual return of human metapneumovirus (hMPV) in Western Australia following a period of absence in 2020. We analysed hMPV laboratory testing data from 1 January 2017 to 31 December 2021. Whole-genome sequencing of selected hMPV-positive samples was performed using a tiled-amplicon approach. Following an absence in spring 2020, an unusual hMPV surge was observed during the wet summer season in the tropical Northern region in late 2020. Following a six-month delay, an intense winter season occurred in the subtropical/temperate Southern and Metropolitan regions. Compared to 2017-2019, hMPV incidence in 2021 increased by 3-fold, with a greater than 4-fold increase in children aged 1-4 years. There was a collapse in hMPV diversity in 2020, with the emergence of a single subtype. NPIs contributed to an absent 2020 season and a clonal hMPV resurgence. The summer surge and delayed winter season suggest that prevailing temperature and humidity are keys determinant of hMPV transmission. The increased incidence in 2021 was linked to an expanded cohort of hMPV-naïve 1-4-year-old children and waning population immunity. Further intense and unusual respiratory virus seasons are expected as COVID-19 associated NPIs are removed.

Keywords: human metapneumovirus; non-pharmaceutical interventions; seasonality; transmission.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
hMPV tests and detections per week by region between week one, 2019 and week 52, 2021. The average epidemic curve is based on hMPV detections in PathWest Laboratory Medicine between 2013 and 2019, inclusive. The first local case of SARS-CoV-2 was in week eight of 2020. State-wide stay at home order (weeks 14–17 of 2020) was followed by sequential lifting of restrictions (18–26 weeks) with gatherings of 10 allowed at week 18, 20 at 21 weeks and 100 at week 24. Periods of increased NPIs included mask requirements in the Metropolitan and Southern region (weeks 5 and 6, weeks 16 to 19 and 26 to 27) in 2021. hMPV, human metapneumovirus; NPI, non-pharmaceutical intervention; SARS-CoV-2, severe acute respiratory syndrome coronavirus 2).
Figure 2
Figure 2
(A) Total hMPV tests and percentage positivity per year in Western Australia; (B) Total hMPV tests and percentage positivity per year by age groupings; (C) Total hMPV tests and percentage positivity per year by age groupings by region.
Figure 2
Figure 2
(A) Total hMPV tests and percentage positivity per year in Western Australia; (B) Total hMPV tests and percentage positivity per year by age groupings; (C) Total hMPV tests and percentage positivity per year by age groupings by region.
Figure 3
Figure 3
(A) Phylogenetic analysis of hMPV lineage A viruses sampled in Western Australia (WA) between 2017 and 2021. WA hMPV genomes sampled during the period after the instigation of SARS-CoV-2 related non-pharmaceutical interventions are shaded pale orange. WA hMPV genomes sampled before this period are shaded red. Reference sequences download from GenBank are shaded green. The scale represents the number of nucleotide substitutions per site; (B) Maximum clade credibility phylogeny of 153 complete genomes of hMPV, with estimated date and 95% posterior densities given for the node of interest (shaded purple) described in the text.
Figure 3
Figure 3
(A) Phylogenetic analysis of hMPV lineage A viruses sampled in Western Australia (WA) between 2017 and 2021. WA hMPV genomes sampled during the period after the instigation of SARS-CoV-2 related non-pharmaceutical interventions are shaded pale orange. WA hMPV genomes sampled before this period are shaded red. Reference sequences download from GenBank are shaded green. The scale represents the number of nucleotide substitutions per site; (B) Maximum clade credibility phylogeny of 153 complete genomes of hMPV, with estimated date and 95% posterior densities given for the node of interest (shaded purple) described in the text.
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