Frequency of influenza H3N2 intra-subtype reassortment: attributes and implications of reassortant spread

Table 1 Reassortant geographical and temporal distributions and time of the most recent common ancestor (TMRCA)

Reassortant lineage	Genomes (N)^a	Sampling year	TMRCA (95% HPD^b)	Lineage persistence^c (CI)	Existence since TMRCA^d(CI)	Sampling lag^g	Global	High Local	Low Local
I (Baby Blue)	4	2012	2011.8 (2011.5-2011.9)	0.5 (0-1)*	0.7 (0.1-1.5)	0.2			N America
II (Dark Blue)^e	20	2013-2014	2012.5 (2012.2-2012.8)	0.7 (0.53-0.87)	1.7 (1.23-2.17)	1		M East^e
III (Light Blue)	103	2010-2013	2009.7 (2009.6-2009.8)	3 (2.64-3.36)	3.8 (3.34-4.26)	0.8	Yes
IV (BlueD)	25	2011	2010.3	0.5 (0-1)*	1.2 (0.7-1.7)	0.7		Asia
V (GreenD)	11	2012	2011.5 (2011.2-2011.7)	0.5 (0-1)*	1 (0.3-1.8)	0.5			N America
VI (GreenL)	5	2012	2011.3 (2011-2011.7)	0.47 (0.27-0.67)	1.2 (0.6-1.7)	0.7		Australia
VII (Green)	85	2010-2011	2009.2 (2009-2009.3)	1 (0.5-1.5)	2.3 (1.7-3)	1.3		SC America
VIII (Dark Green)	8	2010	2009.7 (2009.4-2009.8)	0.5 (0-1)*	0.8 (0.2-1.6)	0.3			SC America
IX (Salmon)	13	2010	2009.3 (2009-2009.5)	0.5 (0-1)*	1.2 (0.5-2)	0.7			SC America
X (Red)	351	2010-2012	2008.8 (2008.3-2009.1)	2 (1.54-2.46)	3.7 (2.94-4.66)	1.7	Yes
XI (Maroon)	46	2012-2013	2011.1 (2010.9-2011.3)	1 (0.5-1.5)	2.4 (1.7-3.1)	1.4		N America
XII (Dark Red)	14	2011-2013	2010.9 (2010.6-2011.4)	2 (1.57-2.43)	2.6 (1.67-3.33)	0.6	Yes
XIII (Orange)	15	2010-2011	2009.1 (2009-2009.2)	1 (0.5-1.5)	2.4 (1.8-3)	1.4		Asia
XIV (Purple)	40	2009	2007.8 (2007.4-2008.1)	0.5 (0-1)*	1.7 (0.9-2.6)	1.2		N America
XV (Lavender)	5	2009	2008.6 (2008.3-2008.9)	0.5 (0-1)*	0.9 (0.1-1.7)	0.4			N America
XVI (Pink)	3	2009	2008.9 (2008.7-2009)	0.5 (0-1)*	0.6 (0-1.3)	0.1			N America
Yellow (single unique)^f	53 + 4	2008-2013
Total	805

^aThe 7 recurring reassortant vaccine genomes (see Methods) were not counted
^b HPD highest posterior density intervals
^cRefers to the period of time when the lineage was observed in the human population
^dRefers to the total lifespan of the reassortant variant in question
^eAlthough assigned High Local by the criteria, it cannot with certainty be regarded as such due to low regional and temporal sampling
^f4 genomes were identical to 4 of the unique reassortants
^gSampling lag is defined in the “Between-lineage and vaccine clade reassortment despite limited reassortant lifespan” subsection of Results
*All genomes were sampled in the same year with no exact dates. Thus, the persistence was given a value of 0.5, given the sampling uncertainty of 6 months

ISSN: 1741-7007