Number of sequences in each epidemiological event type by climatic zone (temperate, sub-tropical, or tropical) in Australia.

<p>Number of sequences in each epidemiological event type by climatic zone (temperate, sub-tropical, or tropical) in Australia.</p

Patterns (event types) of inter-seasonal influenza transmission.

<p>The black line represents the theoretical periodicity of influenza in a typical seasonal pattern, horizontal bars represent lengths of transmission events and are colored blue when falling inside the season and red when in the inter-seasonal period.</p

Phylogenetic trees showing a real data example of each event type.

<p>Australian inter-seasonal sequences are shown in red, seasonal sequences are shown in blue, and global sequences are shown in black. Bootstrap support values (>70%) are shown for key nodes. (<b>a</b>) Importation event within influenza A/H1N1pdm. This imported lineage transmitted for at least two months during the 2010/2011 inter-seasonal period within Australia (earliest sample collected on 13 Jan 2011 and latest on 18 March 2011, both from Darwin), and spread to a temperate region (Perth). (<b>b</b>) Herald event within influenza B virus, with virus Sydney/2/2012 isolated on 27 February 2012 and then extending into the following influenza season in both Australia (Sydney and South Australia) and New Zealand. (<b>c</b>) Straggler event within influenza A/H1N1pdm, with viruses transmitting within the 2010 season into the 2010–2011 inter-seasonal period. Although the strongest evidence for this involves A/Victoria/662/2010 isolated on 17 November 2010 (bottom clade), a similar pattern may occur with A/Brisbane/32/2011 sampled on 4 February 2011 although with weak bootstrap support (top clade). (<b>d</b>) Persistent lineage of influenza B virus transmitting within the 2010 season, throughout the 2010/2011 inter-seasonal period, and into the 2011 season (i.e. for a total of 14 months). (<b>e</b>) A two-tailed A/H1N1pdm lineage transmitting from 18 February 2011 (2010/2011 inter-seasonal period) to 01 December 2011 (2011/2012 inter-seasonal period). All trees were rooted using the earliest non-Australian sequence shown to be an outgroup in the expansive phylogenetic trees shown in <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1004991#ppat.1004991.s001" target="_blank">S1 Fig</a>. The date of sampling is shown in the sequence label in the format year-month-day.</p

NNDSS influenza notifications in Australia.

<p>Laboratory-confirmed influenza notifications throughout the seasonal and inter-seasonal period in Australia. The plot shows laboratory-confirmed diagnoses per 100,000 population from 2009–2014, with states and territories displayed separately. Data on laboratory confirmed cases of influenza in Australia was obtained from the Australian National Notifiable Diseases Surveillance Systems (NNDSS) website (<a href="http://www9.health.gov.au/cda/source/cda-index.cfm" target="_blank">http://www9.health.gov.au/cda/source/cda-index.cfm</a>).</p

Cases positive for influenza B viruses

Tab delimited text file providing patient age, country, date of sampling and lineage (Victoria or Yamagata) of 5260 influenza B viruses collected in Australia and New Zealand, 2002–201

BEAST xml file - B/Yamagata

Beast input file (xml) with data and parameters used for Bayesian phylogenetic analysis of the HA dataset of B/Yamagata viruses isolated in Australia and New Zealand

Hemagglutination inhibition titers

Excel file with two sheets proving raw HI titer values for representative influenza B virus antigens of Victoria and Yamagata viruses isolated in Australia and New Zealand during 2002–2013 estimated against representative antisera. Strain names and passage history are provided for each antigen and antisera

Virus accession numbers

Tab delimited text file for 908 newly generated influenza B virus samples isolated from humans in Australia and New Zealand during 2002–2013. For each of these samples, virus sample name, collection data, country and GenBank or GISAID accession numbers of each gene segment are provided

Prevalence percentage

Tab delimited text file providing percentages of viruses that were of type B in Australia (aus) and New Zealand (nz) and the three eastern states of Australia, New South Wales (nsw), Queensland (qld) and Victoria (vic). The percentage of viruses that were of Yamagata and Victoria lineages among all influenza B virus positive samples are provided for Australia (aus_yamagata and aus_victoria) and New Zealand (nz_yamagata and nz_victoria)

Phylodynamic analysis

Beast input file (xml) with data and parameters used to estimate epidemiological parameters (the effective reproductive number, Re) for each epidemic of virus lineages in Australia and New Zealand using the Birth-Death susceptible-infected-removed (BDSIR) model