Use of consensus sequences for the design of high density resequencing microarrays: the influenza virus paradigm

BMC Genomics

Table 2 Resequencing microarray output for identification and characterisation of the 12 influenza A viral RNAs

Origin	Tested strain	Identification		Genes	Call rate (%)	Time range	Median
		Typing	Subtyping	Genotyping
Swine			H3N2	PB2	76.2	1981 - 1987	1984
	A/swine/Gent/1/84 (H3N2)	A		H	94.3	1984	1984
				N	92.6	1984	1984
			H1N2	PB2	60.3	1999	1999
	A/swine/Gent/7625/99 (H1N2)	A		H	88.8	2000	2000
				N	81.2	1999	1999
Human			H3N2	PB2	35.5	1972 - 1982	1975
	A/Victoria/3/75 (H3N2)	A		H	89.9	1968 - 1975	1974
				N	84.6	1968 - 2005	1975
			H3N2	PB2	67.9	1988 - 1994	1993
	A/Johannesburg/33/1994 (H3N2)	A		H	80.4	1988 - 1999	1993
				N	80.7	1993 - 2008	2008
			H3N2	PB2	93.4	2000 - 2006	2003
	A/Wyoming/3/2003 (H3N2)	A		H	89.9	2002 - 2003	2003
				N	85.8	2001 - 2008	2006
Equine			H7N7	PB2	60.7	1956	1956
	A/equine/Prague/1/56 (H7N7)	A		H	48.5	1975 - 2008	2004
				N	100	1956 - 1992	1974
			H3Nx	PB2	60.3	1972	1972
	A/equine/Miami/1/63 (H3N8)	A		H	65.6	1963 - 2007	1987
				N	-	-	-
			H3Nx	PB2	64.3	1978-1980	1979
	A/equine/Fontainebleau/1/79 (H3N8)	A		H	57.4	1974 - 2008	1992
				N	-	-	-
			H3Nx	PB2	67.3	1976 - 1994	1989
	A/equine/Grosbois/99 (H3N8)	A		H	69.4	1976 - 2006	1986
				N	-	-	-
Avian			H3N2	PB2	77.3	2005	2005
	Viral strain 221	A		H	84.7	2006	2006
				N	99.4	2004	2004
			H1N1	PB2	93	2006	2006
	Viral strain 223	A		H	66.5	1976	1976
				N	90.7	2006 - 2007	2007
		A	H1N1	PB2	97.4	2006	2006
	Viral strain 224			H	81.8	2003 - 2007	2006
				N	94.9	2001	2001

The call rate is the percentage of bases determined by the resequencing algorithm. Time ranges indicate the oldest isolate with high homology provided by the BLASTN algorithm and the most recent one. The medians were calculated based upon the sequences showing the highest alignment scores.

ISSN: 1471-2164