Table 1 Comparison of demographic characteristics of influenza A positive patients sampled by the general UVRI-NIC surveillance programme whose viral swabs were successfully or not sequenced.

From: Phylogenomic analysis uncovers a 9-year variation of Uganda influenza type-A strains from the WHO-recommended vaccines and other Africa strains

Variable	Subgroup	Total [N]	Successfully Sequenced [n%]	Un-sequenced [n%]	P-value
Subtype	H1N1pdm09	588	106 [18.03]	482 [81.97]	< 0.0001*
	H3N2	1190	105 [8.82]	1085 [91.18]
	H1N1	29	0 [0]	29 [100]
Case	ILI	1196	139 [11.62]	1057 [88.38]	0.9809
Case	SARI	611	72 [11.78]	539 [88.22]	0.9809
Gender	Male	951	120 [12.62]	831 [87.38]	0.2149
Gender	Female	856	91 [10.63]	765 [89.37]	0.2149
Age [years]	1 month to < 2	589	66 [11.21]	523 [88.79]	0.5851
	2 to < 5	635	84 [13.23]	551 [86.77]
	5 to < 15	338	39 [11.54]	299 [88.46]
	15 to < 50	222	20 [9.01]	202 [90.99]
	50 to < 65	15	2 [13.33]	13 [86.67]
	≥ 65	7	0 [0]	7 [100]
	No age data	1
Sample origin, by year
2010	Central	81	20 [24.69]	61 [75.31]	0.5986
2010	Northwest	5	2 [40]	3 [60]	0.5986
2011	Central	106	29 [27.36]	77 [72.64]	0.5451
	Eastern	1	0 [0]	1 [100]
	Northwest	9	4 [44.44]	5 [55.56]
	Western	8	1 [12.5]	7 [87.5]
2012	Central	193	14 [7.25]	179 [92.75]	0.5272
	Eastern	18	0 [0]	18 [100]
	Northwest	21	2 [9.52]	19 [90.48]
	Western	10	1 [10]	9 [90]
2013	Central	67	14 [20.9]	53 [79.1]	0.9346
	Eastern	3	1 [33.33]	2 [66.67]
	Northwest	10	2 [20]	8 [80]
	Western	4	1 [25]	3 [75]
2014	Central	218	18 [8.26]	200 [91.74]	0.004*
	Eastern	46	0 [0]	46 [100]
	Northwest	35	1 [2.86]	34 [97.14]
	Western	61	11 [18.03]	50 [81.97]
2015	Central	192	18 [9.38]	174 [90.62]	0.6795
	Eastern	42	6 [14.29]	36 [85.71]
	Northwest	19	2 [10.53]	17 [89.47]
	Western	39	5 [12.82]	34 [87.18]
2016	Central	139	13 [9.25]	126 [90.65]	0.0085*
	Eastern	6	3 [50]	3 [50]
	Northwest	15	0 [0]	15 [100]
	Western	21	0 [0]	21 [100]
2017	Central	271	28 [10.33]	243 [89.67]	0.3299
	Eastern	22	0 [0]	22 [100]
	Northwest	11	0 [0]	11 [100]
	Western	35	4 [11.43]	31 [88.57]
2018	Central	33	11 [33.33]	22 [99.67]	0.0555

Initially, there were 1800 positives for a single influenza A subtype (H1, H1N1pdm09 and H3N2) in the UVRI-NIC dataset. After excluding one duplicated H1N1pdm09 viral sample (ARU0583), there remained 1799 positive A samples. We included 8 successfully sequenced samples that tested and were reported as positive in the laboratory dataset (used for sample randomization) but were reported as negative in the UVRI-NIC dataset. Therefore, the demographic characteristics presented in this table were for 1807 patients recorded in the UVRI-NIC dataset. 234 of the 1807 patient’s viral swabs were sampled for whole genome sequencing, and 215 of the 234 were successfully sequenced. However, four sequenced viruses (ARU0587, EBB2521, KIB0497, and KSW0631) lacked complete demographic data so we present data for only the 211 viruses that were successfully sequenced with complete data.
Percentage number of sequenced or un-sequenced swabs are in [italics]. P-values showing significant differences between compared groups (< 0.05) are indicated in bold with a star (*).

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Table 1 Comparison of demographic characteristics of influenza A positive patients sampled by the general UVRI-NIC surveillance programme whose viral swabs were successfully or not sequenced.

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