Genetic diversity among pandemic 2009 influenza viruses isolated from a transmission chain

Table 4 Locations and details of genome nucleotide positions containing variation

Case	Gene	nt	Dom base (freq)	Alt base (freq)	Total Cov	Var %	Log LH (AA)	Log LH (AB)	Log LH (BB)	S or NS.	Amino Acid
C	PA	184	A(116)	C(11)	127	9	−48	−38	−501	NS	I62L
D	PA	1800	T(114)	C(18)	131	14	−77	−39	−524	S	S600
D	HA	844	A(103)	G(33)	136	24	−142	−41	−478	NS	I282V
D	PB1	437	C(106)	T(22)	126	18	−98	−38	−450	NS	T146I
D	PB1	796	C(103)	A(20)	123	16	−86	−37	−430	NS	L266I
D	PB1	1791	C(96)	A(35)	131	27	−149	−39	−407	NS	N597K
D	NA	458	G(128)	A(10)	138	7	−48	−42	−552	NS	S153N
D	NA	823	T(134)	C(4)	138	97	−624	−41	−17	NS	H275Y

Footnotes: ‘ nt’ refers to nucleotide position. ‘Dom’ refers to dominant nucleotide. ‘Alt’ refers to alternative nucleotide. ‘Cov’ refers to sequence coverage. ‘Freq’ refers to frequency. ‘Var’ refers to level (%) of variant. ‘Log LH’ refers to log likelihood, where AA represents no variation from the reference, BB represents 100% variation from the reference and AB represents some variation from the reference. ‘S’ and ‘NS’ indicates synonymous and non-synonymous amino acid substitutions. The bold text highlights the variation associated with the NA H275Y, oseltamivir-resistance conferring substitution.

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