Table 2.

pol population diversity and divergence,between plasma (week 30) and tissues at necropsy (week 30/31)

Tissue	Untreated				Treated
	6760		8232		8272		8030
	APD (%)	Panmixiaa (19 sequences)	APD (%)	Panmixiaa (17 sequences)	APD (%)	Panmixiaa (7 sequences)	APD (%)	Panmixiaa (12 sequences)
Challenge virus	0.23	<10 −6*	0.23	<10 −6*	0.23	0.59	0.23	0.04
Plasma week 1	0.28	10 −4*	0.36	<10 −6*	0.3	0.4	0.19	0.08
Plasma week 30	0.5	NA	0.19	NA	0.17	NA	0.35	NA
PBMC	0.85	0.13	0.41	0.07	0.39	0.28	0.26	0.63
Duodenum	0.3	0.002	0.09	0.06	0.32	0.05	0.14	–
Jejunum	0.43	0.07	0.4	0.48	0.41	0.37	0.37	0.3
Ileum	0.59	0.08	0.17	0.53	1.19	–	–	–
Lung	0.82	0.27	0.25	0.06	0.85	0.39	–	–
Thymus	0.46	0.001	–	–	–	–	–	–
Bone marrow	0.47	0.35	0.23	0.24	0.65	0.23	0.33	0.85
Spleen	0.61	0.0004*	0.21	0.72	0.28	0.33	0.19	0.521
Axillary LN	0.5	0.008	0.23	0.002	0.55	0.22	–	–
Mesenteric LN	0.49	0.45	0.39	0.00090*	0.64	0.02	0.24	0.64
Mean APD	0.55		0.26		0.59		0.26

– Too few sequences to analyze (<7 sequences)

* p value (10⁻³ was used as the criterion for significance due to the numbers of multiple comparisons. Significant differences indicated by bold)

^aProbability of panmixia of sequences in each tissue compared to an equal number of randomly selected unique sequences in the plasma