Additional file 1: Figure S1. of A systematic review of reported reassortant viral lineages of influenza A
Creators: name: Pinsent, Amy
name: Fraser, Christophe
name: Ferguson, Neil
name: Riley, Steven
Publisher: name: Figshare
Year: 2016
Subjects: subject: Medicine
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: FOS: Earth and related environmental sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: FOS: Biological sciences
subject: Statistics
subject: FOS: Mathematics
subject: FOS: Mathematics
subject: Science Policy

description: Number of papers published by year on reassortment, analysing all eight influenza A gene segments. * indicates data available for a partial year. Figure S2. Flow diagram showing the criteria for papers being included in the review. The number of papers excluded and included at each stage are indicated on the flow diagram. Figure S3. Inter-subtype reassortant analysis: Odds ratios for reporting inter-subtype reassortants by region, host and year. Crude (red) and adjusted (blue) odds ratios for the rate of reporting novel inter-subtype reassortants by region (a), host (b) and year (c). The dashed line at 1.00 on (a) and (b) represents the baseline level of risk, vertical bars crossing the dashed line indicate no effect at the 5 % level. The vertical lines above and below each point indicate 95 % confidence intervals. Adjusted odds are from the general additive logistic model of region and host as factors and year of isolated as a smooth term (c) [35]. Blue areas of (c) show 95 % confidence interval for smooth term for the contribution to the odds from the year of isolation. The univariate analysis where year was treated as a categorical variable is presented in Additional file 1: Table S1. Blue areas of c show 95 % confidence interval for smooth term for year of isolation. Figure S4. Intra-subtype reassortant analysis: Odds ratios for reporting intra-subtype reassortants by region, host and year. Crude (red) and adjusted (blue) odds ratios for the rate of reporting novel intra-subtype reassortants by region (a), host (b) and year (c). The dashed line at 1.00 on (a) and (b) represents the baseline level of risk, vertical bars crossing the dashed line indicate no effect at the 5 % level. The vertical lines above and below each point indicate 95 % confidence intervals. Adjusted odds are from the general additive logistic model of region and host as factors and year of isolated as a smooth term (c) [35]. Blue areas of (c) show 95 % confidence interval for smooth term for the contribution to the odds from the year of isolation. The univariate analysis where year was treated as a categorical variable is presented in Additional file 1: Table S1. Blue areas of c show 95 % confidence interval for smooth term for year of isolation. Figure S5. Funnel plot of the log odds of reporting reassorted viruses in China and Swine. A funnel plot of the log odds of identifying reassorted viruses in (a) swine hosts and (b) China across all years analysed in this study. Years are indicated on the plot. Group one includes the following years – 1991, 1992, 1993, 1994, 1995. Group two includes years 1996, 1997, 1998, 1999, 2000. Group 3 includes years 2011, 2012, and 2013. Banding of years was performed due to the low number of sequences uploaded to GenBank and reassortants identified in the years prior to 2000. The black dashed line indicates 0.00, the no effect line. The red dashed line indicates the estimated log odds from the adjusted regression model. Note that the data point for China in 2002 is not presented in (b) as the standard error was substantially larger than all other year groups analysed, therefore for visual reasons it has not been plotted. Figure S6. Odds ratios for reporting inter and intra-subtype reassortants for the sensitivity analysis for adding missed FRIs, by region, host and year. Crude (red) and adjusted (blue) odds ratios for the rate of reporting novel inter and intra-subtype reassortants for the sensitivity analysis by region (a), host (b) and year (c). The dashed line at 1.00 on (a) and (b) represents the baseline level of risk, vertical bars crossing the dashed line indicate no effect at the 5 % level. The vertical lines above and below each point indicate 95 % confidence intervals. Adjusted odds are from the general additive logistic model of region and host as factors and year of isolated as a smooth term (c) [35]. Blue areas of (c) show 95 % confidence interval for smooth term for the contribution to the odds from the year of isolation. The univariate analysis where year was treated as a categorical variable is presented in Additional file 4: Table S5. Blue areas of c show 95 % confidence interval for smooth term for year of isolation. (PDF 521 kb)